hse-homeworks / example / modeller_cox3.md @ 491b9a4d
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| 1 | 491b9a4d | HSE Student | |
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| 2 | |||
| 3 | ```python |
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| 4 | import sys |
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| 5 | sys.path.append('/usr/lib/modeller9.12/modlib/')
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| 6 | sys.path.append('/usr/lib/modeller9.12/lib/x86_64-intel8/python2.5/')
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| 7 | import modeller |
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| 8 | import _modeller |
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| 9 | import modeller.automodel |
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| 10 | #impo modeller.automodel import * |
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| 11 | ``` |
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| 12 | |||
| 13 | |||
| 14 | ```python |
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| 15 | env=modeller.environ() |
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| 16 | env.io.hetatm=False #True |
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| 17 | |||
| 18 | ``` |
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| 19 | |||
| 20 | |||
| 21 | ```python |
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| 22 | cd /home/domain/anur/work/cox3 |
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| 23 | ``` |
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| 24 | |||
| 25 | /home/domain/anur/work/cox3 |
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| 26 | |||
| 27 | |||
| 28 | |||
| 29 | ```python |
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| 30 | alignm=modeller.alignment(env) |
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| 31 | alignm.append(file='COX3.fasta', align_codes='all',alignment_format='FASTA') |
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| 32 | mdl1 = modeller.model(env, file='1v55.pdb', model_segment=('FIRST:'+'C', 'LAST:'+'C'))
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| 33 | mdl2 = modeller.model(env, file='1v55.pdb', model_segment=('FIRST:'+'P', 'LAST:'+'P'))
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| 34 | alignm.append_model(mdl1, atom_files='1v55.pdb', align_codes='1v55_C') |
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| 35 | alignm.append_model(mdl2, atom_files='1v55.pdb', align_codes='1v55_P') |
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| 36 | |||
| 37 | ``` |
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| 38 | |||
| 39 | |||
| 40 | ```python |
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| 41 | alignm.salign() |
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| 42 | s= alignm[0] |
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| 43 | for i in range(len(alignm)): |
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| 44 | print "%s identical to wt in %4.1f perc" %(alignm[i].code,s.get_sequence_identity(alignm[i])) |
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| 45 | aln.write(file='all_in_one.ali', alignment_format='PIR') |
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| 46 | ``` |
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| 47 | |||
| 48 | |||
| 49 | SALIGN_____> adding the next group to the alignment; iteration 1 |
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| 50 | |||
| 51 | SALIGN_____> adding the next group to the alignment; iteration 2 |
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| 52 | |||
| 53 | SALIGN_____> adding the next group to the alignment; iteration 3 |
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| 54 | |||
| 55 | SALIGN_____> adding the next group to the alignment; iteration 4 |
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| 56 | |||
| 57 | SALIGN_____> adding the next group to the alignment; iteration 5 |
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| 58 | |||
| 59 | SALIGN_____> adding the next group to the alignment; iteration 6 |
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| 60 | |||
| 61 | SALIGN_____> adding the next group to the alignment; iteration 7 |
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| 62 | |||
| 63 | SALIGN_____> adding the next group to the alignment; iteration 8 |
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| 64 | |||
| 65 | SALIGN_____> adding the next group to the alignment; iteration 9 |
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| 66 | |||
| 67 | SALIGN_____> adding the next group to the alignment; iteration 10 |
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| 68 | |||
| 69 | SALIGN_____> adding the next group to the alignment; iteration 11 |
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| 70 | 9913 identical to wt in 100.0 perc |
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| 71 | 9606_V identical to wt in 87.7 perc |
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| 72 | 9606_A identical to wt in 87.4 perc |
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| 73 | 9606_I identical to wt in 87.4 perc |
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| 74 | 9606_F identical to wt in 87.4 perc |
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| 75 | 9606_S identical to wt in 87.4 perc |
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| 76 | 9606_L identical to wt in 87.4 perc |
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| 77 | 9606_M identical to wt in 87.4 perc |
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| 78 | 9606_E identical to wt in 87.4 perc |
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| 79 | 9606_T identical to wt in 87.4 perc |
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| 80 | 1v55_C identical to wt in 100.0 perc |
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| 81 | 1v55_P identical to wt in 100.0 perc |
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| 82 | |||
| 83 | |||
| 84 | |||
| 85 | ```python |
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| 86 | for s in aln[:-2]: |
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| 87 | print s.code |
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| 88 | a = modeller.automodel.automodel(env, alnfile='all_in_one.ali', knowns= ('1v55_C','1v55_P'), sequence = s.code )
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| 89 | a.name='mod'+s.code |
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| 90 | a.starting_model = 1 |
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| 91 | a.ending_model = 1 |
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| 92 | a.make() |
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| 93 | |||
| 94 | ``` |
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| 95 | |||
| 96 | 9913 |
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| 97 | automodel__W> Topology and/or parameter libraries already in memory. These will |
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| 98 | be used instead of the automodel defaults. If this is not what you |
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| 99 | want, clear them before creating the automodel object with |
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| 100 | env.libs.topology.clear() and env.libs.parameters.clear() |
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| 101 | |||
| 102 | |||
| 103 | check_ali___> Checking pairwise structural superpositions. |
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| 104 | |||
| 105 | Equivalent CA pairs with distance difference larger than 6.0 angstroms: |
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| 106 | |||
| 107 | ALN_POS TMPL1 TMPL2 RID1 RID2 NAM1 NAM2 DIST |
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| 108 | ---------------------------------------------------- |
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| 109 | END OF TABLE |
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| 110 | |||
| 111 | check_ali___> Checking the sequence-structure alignment. |
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| 112 | |||
| 113 | Implied target CA(i)-CA(i+1) distances longer than 8.0 angstroms: |
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| 114 | |||
| 115 | ALN_POS TMPL RID1 RID2 NAM1 NAM2 DIST |
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| 116 | ---------------------------------------------- |
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| 117 | END OF TABLE |
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| 118 | |||
| 119 | getf_______W> RTF restraint not found in the atoms list: |
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| 120 | residue type, indices: 16 261 |
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| 121 | atom names : C +N |
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| 122 | atom indices : 2123 0 |
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| 123 | |||
| 124 | getf_______W> RTF restraint not found in the atoms list: |
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| 125 | residue type, indices: 16 261 |
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| 126 | atom names : C CA +N O |
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| 127 | atom indices : 2123 2120 0 2124 |
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| 128 | mdtrsr__446W> A potential that relies on one protein is used, yet you have at |
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| 129 | least one known structure available. MDT, not library, potential is used. |
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| 130 | 0 atoms in HETATM/BLK residues constrained |
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| 131 | to protein atoms within 2.30 angstroms |
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| 132 | and protein CA atoms within 10.00 angstroms |
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| 133 | 0 atoms in residues without defined topology |
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| 134 | constrained to be rigid bodies |
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| 135 | condens_443_> Restraints marked for deletion were removed. |
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| 136 | Total number of restraints before, now: 26595 24757 |
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| 137 | iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
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| 138 | iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
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| 139 | iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
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| 140 | iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
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| 141 | iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
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| 142 | iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
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| 143 | iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
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| 144 | iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
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| 145 | iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
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| 146 | iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
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| 147 | |||
| 148 | |||
| 149 | >> ENERGY; Differences between the model's features and restraints: |
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| 150 | Number of all residues in MODEL : 261 |
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| 151 | Number of all, selected real atoms : 2125 2125 |
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| 152 | Number of all, selected pseudo atoms : 0 0 |
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| 153 | Number of all static, selected restraints : 24757 24757 |
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| 154 | COVALENT_CYS : F |
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| 155 | NONBONDED_SEL_ATOMS : 1 |
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| 156 | Number of non-bonded pairs (excluding 1-2,1-3,1-4): 4695 |
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| 157 | Dynamic pairs routine : 2, NATM x NATM cell sorting |
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| 158 | Atomic shift for contacts update (UPDATE_DYNAMIC) : 0.390 |
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| 159 | LENNARD_JONES_SWITCH : 6.500 7.500 |
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| 160 | COULOMB_JONES_SWITCH : 6.500 7.500 |
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| 161 | RESIDUE_SPAN_RANGE : 0 99999 |
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| 162 | NLOGN_USE : 15 |
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| 163 | CONTACT_SHELL : 4.000 |
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| 164 | DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER : T T F F F |
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| 165 | SPHERE_STDV : 0.050 |
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| 166 | RADII_FACTOR : 0.820 |
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| 167 | Current energy : 7158.1758 |
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| 168 | |||
| 169 | |||
| 170 | |||
| 171 | |||
| 172 | |||
| 173 | Summary of the restraint violations: |
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| 174 | |||
| 175 | NUM ... number of restraints. |
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| 176 | NUMVI ... number of restraints with RVIOL > VIOL_REPORT_CUT[i]. |
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| 177 | RVIOL ... relative difference from the best value. |
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| 178 | NUMVP ... number of restraints with -Ln(pdf) > VIOL_REPORT_CUT2[i]. |
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| 179 | RMS_1 ... RMS(feature, minimally_violated_basis_restraint, NUMB). |
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| 180 | RMS_2 ... RMS(feature, best_value, NUMB). |
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| 181 | MOL.PDF ... scaled contribution to -Ln(Molecular pdf). |
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| 182 | |||
| 183 | # RESTRAINT_GROUP NUM NUMVI NUMVP RMS_1 RMS_2 MOL.PDF S_i |
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| 184 | ------------------------------------------------------------------------------------------------------ |
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| 185 | 1 Bond length potential : 2212 0 0 0.004 0.004 11.948 1.000 |
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| 186 | 2 Bond angle potential : 3027 0 2 1.873 1.873 208.11 1.000 |
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| 187 | 3 Stereochemical cosine torsion poten: 1709 0 19 38.273 38.273 369.73 1.000 |
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| 188 | 4 Stereochemical improper torsion pot: 1048 0 1 1.125 1.125 25.935 1.000 |
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| 189 | 5 Soft-sphere overlap restraints : 4695 0 0 0.001 0.001 0.43761 1.000 |
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| 190 | 6 Lennard-Jones 6-12 potential : 0 0 0 0.000 0.000 0.0000 1.000 |
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| 191 | 7 Coulomb point-point electrostatic p: 0 0 0 0.000 0.000 0.0000 1.000 |
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| 192 | 8 H-bonding potential : 0 0 0 0.000 0.000 0.0000 1.000 |
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| 193 | 9 Distance restraints 1 (CA-CA) : 4433 0 2 0.120 0.120 586.51 1.000 |
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| 194 | 10 Distance restraints 2 (N-O) : 4608 0 0 0.133 0.133 869.96 1.000 |
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| 195 | 11 Mainchain Phi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
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| 196 | 12 Mainchain Psi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
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| 197 | 13 Mainchain Omega dihedral restraints: 260 0 2 3.409 3.409 34.801 1.000 |
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| 198 | 14 Sidechain Chi_1 dihedral restraints: 226 0 1 46.061 46.061 13.243 1.000 |
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| 199 | 15 Sidechain Chi_2 dihedral restraints: 165 0 2 63.301 63.301 33.559 1.000 |
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| 200 | 16 Sidechain Chi_3 dihedral restraints: 46 0 0 69.837 69.837 26.999 1.000 |
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| 201 | 17 Sidechain Chi_4 dihedral restraints: 8 0 0 125.128 125.128 7.1805 1.000 |
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| 202 | 18 Disulfide distance restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
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| 203 | 19 Disulfide angle restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
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| 204 | 20 Disulfide dihedral angle restraints: 0 0 0 0.000 0.000 0.0000 1.000 |
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| 205 | 21 Lower bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
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| 206 | 22 Upper bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
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| 207 | 23 Distance restraints 3 (SDCH-MNCH) : 4161 0 0 0.334 0.334 2942.5 1.000 |
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| 208 | 24 Sidechain Chi_5 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000 |
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| 209 | 25 Phi/Psi pair of dihedral restraints: 259 3 9 15.024 19.220 -172.15 1.000 |
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| 210 | 26 Distance restraints 4 (SDCH-SDCH) : 2595 0 12 0.772 0.772 2199.4 1.000 |
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| 211 | 27 Distance restraints 5 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000 |
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| 212 | 28 NMR distance restraints 6 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000 |
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| 213 | 29 NMR distance restraints 7 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000 |
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| 214 | 30 Minimal distance restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
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| 215 | 31 Non-bonded restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
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| 216 | 32 Atomic accessibility restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
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| 217 | 33 Atomic density restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
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| 218 | 34 Absolute position restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
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| 219 | 35 Dihedral angle difference restraint: 0 0 0 0.000 0.000 0.0000 1.000 |
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| 220 | 36 GBSA implicit solvent potential : 0 0 0 0.000 0.000 0.0000 1.000 |
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| 221 | 37 EM density fitting potential : 0 0 0 0.000 0.000 0.0000 1.000 |
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| 222 | 38 SAXS restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
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| 223 | 39 Symmetry restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
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| 224 | |||
| 225 | |||
| 226 | |||
| 227 | # Heavy relative violation of each residue is written to: 9913.V99990001 |
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| 228 | # The profile is NOT normalized by the number of restraints. |
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| 229 | # The profiles are smoothed over a window of residues: 1 |
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| 230 | # The sum of all numbers in the file: 18744.2441 |
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| 231 | |||
| 232 | |||
| 233 | |||
| 234 | List of the violated restraints: |
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| 235 | A restraint is violated when the relative difference |
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| 236 | from the best value (RVIOL) is larger than CUTOFF. |
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| 237 | |||
| 238 | ICSR ... index of a restraint in the current set. |
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| 239 | RESNO ... residue numbers of the first two atoms. |
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| 240 | ATM ... IUPAC atom names of the first two atoms. |
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| 241 | FEAT ... the value of the feature in the model. |
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| 242 | restr ... the mean of the basis restraint with the smallest |
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| 243 | difference from the model (local minimum). |
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| 244 | viol ... difference from the local minimum. |
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| 245 | rviol ... relative difference from the local minimum. |
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| 246 | RESTR ... the best value (global minimum). |
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| 247 | VIOL ... difference from the best value. |
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| 248 | RVIOL ... relative difference from the best value. |
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| 249 | |||
| 250 | |||
| 251 | ------------------------------------------------------------------------------------------------- |
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| 252 | |||
| 253 | Feature 25 : Phi/Psi pair of dihedral restraints |
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| 254 | List of the RVIOL violations larger than : 6.5000 |
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| 255 | |||
| 256 | # ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL |
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| 257 | 1 7997 1M 2T C N 7 9 -90.07 -78.10 21.48 0.71 -63.20 152.65 21.37 |
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| 258 | 1 2T 2T N CA 9 10 167.63 149.80 -42.10 |
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| 259 | 2 8123 127L 128E C N 1023 1025 -85.08 -63.60 83.66 12.37 -69.30 97.63 6.89 |
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| 260 | 2 128E 128E N CA 1025 1026 -121.16 -40.30 142.50 |
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| 261 | 3 8227 231H 232H C N 1849 1851 -111.37 -63.20 75.39 8.23 -63.20 75.39 8.23 |
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| 262 | 3 232H 232H N CA 1851 1852 15.69 -42.30 -42.30 |
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| 263 | |||
| 264 | |||
| 265 | report______> Distribution of short non-bonded contacts: |
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| 266 | |||
| 267 | |||
| 268 | DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 |
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| 269 | DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50 |
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| 270 | FREQUENCY: 0 0 0 0 0 7 11 61 168 215 199 279 378 411 383 |
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| 271 | |||
| 272 | |||
| 273 | << end of ENERGY. |
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| 274 | |||
| 275 | >> Summary of successfully produced models: |
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| 276 | Filename molpdf |
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| 277 | ---------------------------------------- |
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| 278 | 9913.B99990001.pdb 7158.17578 |
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| 279 | |||
| 280 | 9606_V |
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| 281 | automodel__W> Topology and/or parameter libraries already in memory. These will |
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| 282 | be used instead of the automodel defaults. If this is not what you |
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| 283 | want, clear them before creating the automodel object with |
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| 284 | env.libs.topology.clear() and env.libs.parameters.clear() |
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| 285 | |||
| 286 | |||
| 287 | check_ali___> Checking pairwise structural superpositions. |
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| 288 | |||
| 289 | Equivalent CA pairs with distance difference larger than 6.0 angstroms: |
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| 290 | |||
| 291 | ALN_POS TMPL1 TMPL2 RID1 RID2 NAM1 NAM2 DIST |
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| 292 | ---------------------------------------------------- |
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| 293 | END OF TABLE |
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| 294 | |||
| 295 | check_ali___> Checking the sequence-structure alignment. |
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| 296 | |||
| 297 | Implied target CA(i)-CA(i+1) distances longer than 8.0 angstroms: |
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| 298 | |||
| 299 | ALN_POS TMPL RID1 RID2 NAM1 NAM2 DIST |
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| 300 | ---------------------------------------------- |
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| 301 | END OF TABLE |
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| 302 | |||
| 303 | getf_______W> RTF restraint not found in the atoms list: |
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| 304 | residue type, indices: 16 261 |
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| 305 | atom names : C +N |
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| 306 | atom indices : 2125 0 |
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| 307 | |||
| 308 | getf_______W> RTF restraint not found in the atoms list: |
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| 309 | residue type, indices: 16 261 |
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| 310 | atom names : C CA +N O |
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| 311 | atom indices : 2125 2122 0 2126 |
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| 312 | mdtrsr__446W> A potential that relies on one protein is used, yet you have at |
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| 313 | least one known structure available. MDT, not library, potential is used. |
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| 314 | 0 atoms in HETATM/BLK residues constrained |
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| 315 | to protein atoms within 2.30 angstroms |
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| 316 | and protein CA atoms within 10.00 angstroms |
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| 317 | 0 atoms in residues without defined topology |
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| 318 | constrained to be rigid bodies |
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| 319 | condens_443_> Restraints marked for deletion were removed. |
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| 320 | Total number of restraints before, now: 26187 24337 |
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| 321 | iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
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| 322 | iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
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| 323 | iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
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| 324 | iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
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| 325 | |||
| 326 | |||
| 327 | >> ENERGY; Differences between the model's features and restraints: |
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| 328 | Number of all residues in MODEL : 261 |
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| 329 | Number of all, selected real atoms : 2127 2127 |
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| 330 | Number of all, selected pseudo atoms : 0 0 |
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| 331 | Number of all static, selected restraints : 24337 24337 |
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| 332 | COVALENT_CYS : F |
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| 333 | NONBONDED_SEL_ATOMS : 1 |
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| 334 | Number of non-bonded pairs (excluding 1-2,1-3,1-4): 4811 |
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| 335 | Dynamic pairs routine : 2, NATM x NATM cell sorting |
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| 336 | Atomic shift for contacts update (UPDATE_DYNAMIC) : 0.390 |
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| 337 | LENNARD_JONES_SWITCH : 6.500 7.500 |
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| 338 | COULOMB_JONES_SWITCH : 6.500 7.500 |
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| 339 | RESIDUE_SPAN_RANGE : 0 99999 |
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| 340 | NLOGN_USE : 15 |
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| 341 | CONTACT_SHELL : 4.000 |
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| 342 | DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER : T T F F F |
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| 343 | SPHERE_STDV : 0.050 |
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| 344 | RADII_FACTOR : 0.820 |
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| 345 | Current energy : 6565.6021 |
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| 346 | |||
| 347 | |||
| 348 | |||
| 349 | |||
| 350 | |||
| 351 | Summary of the restraint violations: |
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| 352 | |||
| 353 | NUM ... number of restraints. |
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| 354 | NUMVI ... number of restraints with RVIOL > VIOL_REPORT_CUT[i]. |
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| 355 | RVIOL ... relative difference from the best value. |
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| 356 | NUMVP ... number of restraints with -Ln(pdf) > VIOL_REPORT_CUT2[i]. |
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| 357 | RMS_1 ... RMS(feature, minimally_violated_basis_restraint, NUMB). |
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| 358 | RMS_2 ... RMS(feature, best_value, NUMB). |
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| 359 | MOL.PDF ... scaled contribution to -Ln(Molecular pdf). |
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| 360 | |||
| 361 | # RESTRAINT_GROUP NUM NUMVI NUMVP RMS_1 RMS_2 MOL.PDF S_i |
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| 362 | ------------------------------------------------------------------------------------------------------ |
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| 363 | 1 Bond length potential : 2214 0 0 0.004 0.004 10.728 1.000 |
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| 364 | 2 Bond angle potential : 3030 0 2 1.780 1.780 190.34 1.000 |
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| 365 | 3 Stereochemical cosine torsion poten: 1707 0 16 38.781 38.781 372.96 1.000 |
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| 366 | 4 Stereochemical improper torsion pot: 1045 0 0 1.058 1.058 23.385 1.000 |
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| 367 | 5 Soft-sphere overlap restraints : 4811 0 0 0.001 0.001 1.0434 1.000 |
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| 368 | 6 Lennard-Jones 6-12 potential : 0 0 0 0.000 0.000 0.0000 1.000 |
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| 369 | 7 Coulomb point-point electrostatic p: 0 0 0 0.000 0.000 0.0000 1.000 |
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| 370 | 8 H-bonding potential : 0 0 0 0.000 0.000 0.0000 1.000 |
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| 371 | 9 Distance restraints 1 (CA-CA) : 4433 0 0 0.094 0.094 588.07 1.000 |
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| 372 | 10 Distance restraints 2 (N-O) : 4608 0 0 0.117 0.117 689.60 1.000 |
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| 373 | 11 Mainchain Phi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
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| 374 | 12 Mainchain Psi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
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| 375 | 13 Mainchain Omega dihedral restraints: 260 0 1 3.209 3.209 30.726 1.000 |
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| 376 | 14 Sidechain Chi_1 dihedral restraints: 227 0 1 54.523 54.523 23.232 1.000 |
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| 377 | 15 Sidechain Chi_2 dihedral restraints: 168 0 1 61.214 61.214 40.466 1.000 |
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| 378 | 16 Sidechain Chi_3 dihedral restraints: 48 0 0 58.055 58.055 24.592 1.000 |
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| 379 | 17 Sidechain Chi_4 dihedral restraints: 8 0 0 120.815 120.815 4.9296 1.000 |
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| 380 | 18 Disulfide distance restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
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| 381 | 19 Disulfide angle restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
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| 382 | 20 Disulfide dihedral angle restraints: 0 0 0 0.000 0.000 0.0000 1.000 |
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| 383 | 21 Lower bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
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| 384 | 22 Upper bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
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| 385 | 23 Distance restraints 3 (SDCH-MNCH) : 3900 0 0 0.332 0.332 2735.1 1.000 |
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| 386 | 24 Sidechain Chi_5 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 387 | 25 Phi/Psi pair of dihedral restraints: 259 3 10 14.794 19.369 -174.12 1.000 |
||
| 388 | 26 Distance restraints 4 (SDCH-SDCH) : 2430 0 11 0.714 0.714 2004.5 1.000 |
||
| 389 | 27 Distance restraints 5 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 390 | 28 NMR distance restraints 6 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 391 | 29 NMR distance restraints 7 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 392 | 30 Minimal distance restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 393 | 31 Non-bonded restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 394 | 32 Atomic accessibility restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 395 | 33 Atomic density restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 396 | 34 Absolute position restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 397 | 35 Dihedral angle difference restraint: 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 398 | 36 GBSA implicit solvent potential : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 399 | 37 EM density fitting potential : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 400 | 38 SAXS restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 401 | 39 Symmetry restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 402 | |||
| 403 | |||
| 404 | |||
| 405 | # Heavy relative violation of each residue is written to: 9606_V.V99990001 |
||
| 406 | # The profile is NOT normalized by the number of restraints. |
||
| 407 | # The profiles are smoothed over a window of residues: 1 |
||
| 408 | # The sum of all numbers in the file: 18410.9668 |
||
| 409 | |||
| 410 | |||
| 411 | |||
| 412 | List of the violated restraints: |
||
| 413 | A restraint is violated when the relative difference |
||
| 414 | from the best value (RVIOL) is larger than CUTOFF. |
||
| 415 | |||
| 416 | ICSR ... index of a restraint in the current set. |
||
| 417 | RESNO ... residue numbers of the first two atoms. |
||
| 418 | ATM ... IUPAC atom names of the first two atoms. |
||
| 419 | FEAT ... the value of the feature in the model. |
||
| 420 | restr ... the mean of the basis restraint with the smallest |
||
| 421 | difference from the model (local minimum). |
||
| 422 | viol ... difference from the local minimum. |
||
| 423 | rviol ... relative difference from the local minimum. |
||
| 424 | RESTR ... the best value (global minimum). |
||
| 425 | VIOL ... difference from the best value. |
||
| 426 | RVIOL ... relative difference from the best value. |
||
| 427 | |||
| 428 | |||
| 429 | ------------------------------------------------------------------------------------------------- |
||
| 430 | |||
| 431 | Feature 25 : Phi/Psi pair of dihedral restraints |
||
| 432 | List of the RVIOL violations larger than : 6.5000 |
||
| 433 | |||
| 434 | # ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL |
||
| 435 | 1 7997 1M 2T C N 7 9 -73.89 -78.10 5.52 0.36 -63.20 164.87 21.85 |
||
| 436 | 1 2T 2T N CA 9 10 153.38 149.80 -42.10 |
||
| 437 | 2 8123 127L 128E C N 1026 1028 -86.32 -63.60 82.64 12.30 -69.30 99.21 6.96 |
||
| 438 | 2 128E 128E N CA 1028 1029 -119.76 -40.30 142.50 |
||
| 439 | 3 8227 231H 232H C N 1851 1853 -113.42 -63.20 79.87 8.68 -63.20 79.87 8.68 |
||
| 440 | 3 232H 232H N CA 1853 1854 19.80 -42.30 -42.30 |
||
| 441 | |||
| 442 | |||
| 443 | report______> Distribution of short non-bonded contacts: |
||
| 444 | |||
| 445 | |||
| 446 | DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 |
||
| 447 | DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50 |
||
| 448 | FREQUENCY: 0 0 0 0 0 9 17 72 217 228 179 284 367 429 353 |
||
| 449 | |||
| 450 | |||
| 451 | << end of ENERGY. |
||
| 452 | |||
| 453 | >> Summary of successfully produced models: |
||
| 454 | Filename molpdf |
||
| 455 | ---------------------------------------- |
||
| 456 | 9606_V.B99990001.pdb 6565.60205 |
||
| 457 | |||
| 458 | 9606_A |
||
| 459 | automodel__W> Topology and/or parameter libraries already in memory. These will |
||
| 460 | be used instead of the automodel defaults. If this is not what you |
||
| 461 | want, clear them before creating the automodel object with |
||
| 462 | env.libs.topology.clear() and env.libs.parameters.clear() |
||
| 463 | |||
| 464 | |||
| 465 | check_ali___> Checking pairwise structural superpositions. |
||
| 466 | |||
| 467 | Equivalent CA pairs with distance difference larger than 6.0 angstroms: |
||
| 468 | |||
| 469 | ALN_POS TMPL1 TMPL2 RID1 RID2 NAM1 NAM2 DIST |
||
| 470 | ---------------------------------------------------- |
||
| 471 | END OF TABLE |
||
| 472 | |||
| 473 | check_ali___> Checking the sequence-structure alignment. |
||
| 474 | |||
| 475 | Implied target CA(i)-CA(i+1) distances longer than 8.0 angstroms: |
||
| 476 | |||
| 477 | ALN_POS TMPL RID1 RID2 NAM1 NAM2 DIST |
||
| 478 | ---------------------------------------------- |
||
| 479 | END OF TABLE |
||
| 480 | |||
| 481 | getf_______W> RTF restraint not found in the atoms list: |
||
| 482 | residue type, indices: 16 261 |
||
| 483 | atom names : C +N |
||
| 484 | atom indices : 2123 0 |
||
| 485 | |||
| 486 | getf_______W> RTF restraint not found in the atoms list: |
||
| 487 | residue type, indices: 16 261 |
||
| 488 | atom names : C CA +N O |
||
| 489 | atom indices : 2123 2120 0 2124 |
||
| 490 | mdtrsr__446W> A potential that relies on one protein is used, yet you have at |
||
| 491 | least one known structure available. MDT, not library, potential is used. |
||
| 492 | 0 atoms in HETATM/BLK residues constrained |
||
| 493 | to protein atoms within 2.30 angstroms |
||
| 494 | and protein CA atoms within 10.00 angstroms |
||
| 495 | 0 atoms in residues without defined topology |
||
| 496 | constrained to be rigid bodies |
||
| 497 | condens_443_> Restraints marked for deletion were removed. |
||
| 498 | Total number of restraints before, now: 26163 24314 |
||
| 499 | iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
||
| 500 | iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
||
| 501 | iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
||
| 502 | iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
||
| 503 | iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
||
| 504 | iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
||
| 505 | iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
||
| 506 | iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
||
| 507 | iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
||
| 508 | iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
||
| 509 | iupac_m_484W> Dihedral still outside +-90: 90.0977 |
||
| 510 | iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
||
| 511 | |||
| 512 | |||
| 513 | >> ENERGY; Differences between the model's features and restraints: |
||
| 514 | Number of all residues in MODEL : 261 |
||
| 515 | Number of all, selected real atoms : 2125 2125 |
||
| 516 | Number of all, selected pseudo atoms : 0 0 |
||
| 517 | Number of all static, selected restraints : 24314 24314 |
||
| 518 | COVALENT_CYS : F |
||
| 519 | NONBONDED_SEL_ATOMS : 1 |
||
| 520 | Number of non-bonded pairs (excluding 1-2,1-3,1-4): 4761 |
||
| 521 | Dynamic pairs routine : 2, NATM x NATM cell sorting |
||
| 522 | Atomic shift for contacts update (UPDATE_DYNAMIC) : 0.390 |
||
| 523 | LENNARD_JONES_SWITCH : 6.500 7.500 |
||
| 524 | COULOMB_JONES_SWITCH : 6.500 7.500 |
||
| 525 | RESIDUE_SPAN_RANGE : 0 99999 |
||
| 526 | NLOGN_USE : 15 |
||
| 527 | CONTACT_SHELL : 4.000 |
||
| 528 | DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER : T T F F F |
||
| 529 | SPHERE_STDV : 0.050 |
||
| 530 | RADII_FACTOR : 0.820 |
||
| 531 | Current energy : 6569.2383 |
||
| 532 | |||
| 533 | |||
| 534 | |||
| 535 | |||
| 536 | |||
| 537 | Summary of the restraint violations: |
||
| 538 | |||
| 539 | NUM ... number of restraints. |
||
| 540 | NUMVI ... number of restraints with RVIOL > VIOL_REPORT_CUT[i]. |
||
| 541 | RVIOL ... relative difference from the best value. |
||
| 542 | NUMVP ... number of restraints with -Ln(pdf) > VIOL_REPORT_CUT2[i]. |
||
| 543 | RMS_1 ... RMS(feature, minimally_violated_basis_restraint, NUMB). |
||
| 544 | RMS_2 ... RMS(feature, best_value, NUMB). |
||
| 545 | MOL.PDF ... scaled contribution to -Ln(Molecular pdf). |
||
| 546 | |||
| 547 | # RESTRAINT_GROUP NUM NUMVI NUMVP RMS_1 RMS_2 MOL.PDF S_i |
||
| 548 | ------------------------------------------------------------------------------------------------------ |
||
| 549 | 1 Bond length potential : 2212 0 0 0.004 0.004 11.764 1.000 |
||
| 550 | 2 Bond angle potential : 3027 0 3 1.803 1.803 193.50 1.000 |
||
| 551 | 3 Stereochemical cosine torsion poten: 1704 0 17 38.650 38.650 371.69 1.000 |
||
| 552 | 4 Stereochemical improper torsion pot: 1044 0 0 1.071 1.071 24.081 1.000 |
||
| 553 | 5 Soft-sphere overlap restraints : 4761 0 0 0.001 0.001 0.95893 1.000 |
||
| 554 | 6 Lennard-Jones 6-12 potential : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 555 | 7 Coulomb point-point electrostatic p: 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 556 | 8 H-bonding potential : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 557 | 9 Distance restraints 1 (CA-CA) : 4433 0 0 0.094 0.094 588.59 1.000 |
||
| 558 | 10 Distance restraints 2 (N-O) : 4608 0 0 0.118 0.118 687.22 1.000 |
||
| 559 | 11 Mainchain Phi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 560 | 12 Mainchain Psi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 561 | 13 Mainchain Omega dihedral restraints: 260 0 1 3.305 3.305 32.628 1.000 |
||
| 562 | 14 Sidechain Chi_1 dihedral restraints: 226 0 0 51.035 51.035 11.649 1.000 |
||
| 563 | 15 Sidechain Chi_2 dihedral restraints: 168 0 1 60.161 60.161 31.284 1.000 |
||
| 564 | 16 Sidechain Chi_3 dihedral restraints: 48 0 0 48.215 48.215 25.921 1.000 |
||
| 565 | 17 Sidechain Chi_4 dihedral restraints: 8 0 0 71.145 71.145 6.3579 1.000 |
||
| 566 | 18 Disulfide distance restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 567 | 19 Disulfide angle restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 568 | 20 Disulfide dihedral angle restraints: 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 569 | 21 Lower bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 570 | 22 Upper bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 571 | 23 Distance restraints 3 (SDCH-MNCH) : 3891 0 0 0.350 0.350 2733.9 1.000 |
||
| 572 | 24 Sidechain Chi_5 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 573 | 25 Phi/Psi pair of dihedral restraints: 259 3 8 14.878 19.641 -174.12 1.000 |
||
| 574 | 26 Distance restraints 4 (SDCH-SDCH) : 2426 0 7 0.754 0.754 2023.8 1.000 |
||
| 575 | 27 Distance restraints 5 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 576 | 28 NMR distance restraints 6 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 577 | 29 NMR distance restraints 7 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 578 | 30 Minimal distance restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 579 | 31 Non-bonded restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 580 | 32 Atomic accessibility restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 581 | 33 Atomic density restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 582 | 34 Absolute position restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 583 | 35 Dihedral angle difference restraint: 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 584 | 36 GBSA implicit solvent potential : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 585 | 37 EM density fitting potential : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 586 | 38 SAXS restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 587 | 39 Symmetry restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 588 | |||
| 589 | |||
| 590 | |||
| 591 | # Heavy relative violation of each residue is written to: 9606_A.V99990001 |
||
| 592 | # The profile is NOT normalized by the number of restraints. |
||
| 593 | # The profiles are smoothed over a window of residues: 1 |
||
| 594 | # The sum of all numbers in the file: 17983.2812 |
||
| 595 | |||
| 596 | |||
| 597 | |||
| 598 | List of the violated restraints: |
||
| 599 | A restraint is violated when the relative difference |
||
| 600 | from the best value (RVIOL) is larger than CUTOFF. |
||
| 601 | |||
| 602 | ICSR ... index of a restraint in the current set. |
||
| 603 | RESNO ... residue numbers of the first two atoms. |
||
| 604 | ATM ... IUPAC atom names of the first two atoms. |
||
| 605 | FEAT ... the value of the feature in the model. |
||
| 606 | restr ... the mean of the basis restraint with the smallest |
||
| 607 | difference from the model (local minimum). |
||
| 608 | viol ... difference from the local minimum. |
||
| 609 | rviol ... relative difference from the local minimum. |
||
| 610 | RESTR ... the best value (global minimum). |
||
| 611 | VIOL ... difference from the best value. |
||
| 612 | RVIOL ... relative difference from the best value. |
||
| 613 | |||
| 614 | |||
| 615 | ------------------------------------------------------------------------------------------------- |
||
| 616 | |||
| 617 | Feature 25 : Phi/Psi pair of dihedral restraints |
||
| 618 | List of the RVIOL violations larger than : 6.5000 |
||
| 619 | |||
| 620 | # ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL |
||
| 621 | 1 7988 1M 2T C N 7 9 -133.19 -124.80 17.39 0.55 -63.20 173.88 26.89 |
||
| 622 | 1 2T 2T N CA 9 10 158.73 143.50 -42.10 |
||
| 623 | 2 8114 127L 128E C N 1024 1026 -86.72 -63.60 84.50 12.57 -69.30 97.50 6.82 |
||
| 624 | 2 128E 128E N CA 1026 1027 -121.57 -40.30 142.50 |
||
| 625 | 3 8218 231H 232H C N 1849 1851 -114.73 -63.20 81.73 8.89 -63.20 81.73 8.89 |
||
| 626 | 3 232H 232H N CA 1851 1852 21.13 -42.30 -42.30 |
||
| 627 | |||
| 628 | |||
| 629 | report______> Distribution of short non-bonded contacts: |
||
| 630 | |||
| 631 | |||
| 632 | DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 |
||
| 633 | DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50 |
||
| 634 | FREQUENCY: 0 0 0 0 0 8 13 55 183 249 221 279 367 400 354 |
||
| 635 | |||
| 636 | |||
| 637 | << end of ENERGY. |
||
| 638 | |||
| 639 | >> Summary of successfully produced models: |
||
| 640 | Filename molpdf |
||
| 641 | ---------------------------------------- |
||
| 642 | 9606_A.B99990001.pdb 6569.23828 |
||
| 643 | |||
| 644 | 9606_I |
||
| 645 | automodel__W> Topology and/or parameter libraries already in memory. These will |
||
| 646 | be used instead of the automodel defaults. If this is not what you |
||
| 647 | want, clear them before creating the automodel object with |
||
| 648 | env.libs.topology.clear() and env.libs.parameters.clear() |
||
| 649 | |||
| 650 | |||
| 651 | check_ali___> Checking pairwise structural superpositions. |
||
| 652 | |||
| 653 | Equivalent CA pairs with distance difference larger than 6.0 angstroms: |
||
| 654 | |||
| 655 | ALN_POS TMPL1 TMPL2 RID1 RID2 NAM1 NAM2 DIST |
||
| 656 | ---------------------------------------------------- |
||
| 657 | END OF TABLE |
||
| 658 | |||
| 659 | check_ali___> Checking the sequence-structure alignment. |
||
| 660 | |||
| 661 | Implied target CA(i)-CA(i+1) distances longer than 8.0 angstroms: |
||
| 662 | |||
| 663 | ALN_POS TMPL RID1 RID2 NAM1 NAM2 DIST |
||
| 664 | ---------------------------------------------- |
||
| 665 | END OF TABLE |
||
| 666 | |||
| 667 | getf_______W> RTF restraint not found in the atoms list: |
||
| 668 | residue type, indices: 16 261 |
||
| 669 | atom names : C +N |
||
| 670 | atom indices : 2126 0 |
||
| 671 | |||
| 672 | getf_______W> RTF restraint not found in the atoms list: |
||
| 673 | residue type, indices: 16 261 |
||
| 674 | atom names : C CA +N O |
||
| 675 | atom indices : 2126 2123 0 2127 |
||
| 676 | mdtrsr__446W> A potential that relies on one protein is used, yet you have at |
||
| 677 | least one known structure available. MDT, not library, potential is used. |
||
| 678 | 0 atoms in HETATM/BLK residues constrained |
||
| 679 | to protein atoms within 2.30 angstroms |
||
| 680 | and protein CA atoms within 10.00 angstroms |
||
| 681 | 0 atoms in residues without defined topology |
||
| 682 | constrained to be rigid bodies |
||
| 683 | condens_443_> Restraints marked for deletion were removed. |
||
| 684 | Total number of restraints before, now: 26179 24328 |
||
| 685 | iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
||
| 686 | iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
||
| 687 | iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
||
| 688 | iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
||
| 689 | iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
||
| 690 | |||
| 691 | |||
| 692 | >> ENERGY; Differences between the model's features and restraints: |
||
| 693 | Number of all residues in MODEL : 261 |
||
| 694 | Number of all, selected real atoms : 2128 2128 |
||
| 695 | Number of all, selected pseudo atoms : 0 0 |
||
| 696 | Number of all static, selected restraints : 24328 24328 |
||
| 697 | COVALENT_CYS : F |
||
| 698 | NONBONDED_SEL_ATOMS : 1 |
||
| 699 | Number of non-bonded pairs (excluding 1-2,1-3,1-4): 4871 |
||
| 700 | Dynamic pairs routine : 2, NATM x NATM cell sorting |
||
| 701 | Atomic shift for contacts update (UPDATE_DYNAMIC) : 0.390 |
||
| 702 | LENNARD_JONES_SWITCH : 6.500 7.500 |
||
| 703 | COULOMB_JONES_SWITCH : 6.500 7.500 |
||
| 704 | RESIDUE_SPAN_RANGE : 0 99999 |
||
| 705 | NLOGN_USE : 15 |
||
| 706 | CONTACT_SHELL : 4.000 |
||
| 707 | DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER : T T F F F |
||
| 708 | SPHERE_STDV : 0.050 |
||
| 709 | RADII_FACTOR : 0.820 |
||
| 710 | Current energy : 6929.7739 |
||
| 711 | |||
| 712 | |||
| 713 | |||
| 714 | |||
| 715 | |||
| 716 | Summary of the restraint violations: |
||
| 717 | |||
| 718 | NUM ... number of restraints. |
||
| 719 | NUMVI ... number of restraints with RVIOL > VIOL_REPORT_CUT[i]. |
||
| 720 | RVIOL ... relative difference from the best value. |
||
| 721 | NUMVP ... number of restraints with -Ln(pdf) > VIOL_REPORT_CUT2[i]. |
||
| 722 | RMS_1 ... RMS(feature, minimally_violated_basis_restraint, NUMB). |
||
| 723 | RMS_2 ... RMS(feature, best_value, NUMB). |
||
| 724 | MOL.PDF ... scaled contribution to -Ln(Molecular pdf). |
||
| 725 | |||
| 726 | # RESTRAINT_GROUP NUM NUMVI NUMVP RMS_1 RMS_2 MOL.PDF S_i |
||
| 727 | ------------------------------------------------------------------------------------------------------ |
||
| 728 | 1 Bond length potential : 2215 0 1 0.006 0.006 18.748 1.000 |
||
| 729 | 2 Bond angle potential : 3031 7 9 3.444 3.444 511.68 1.000 |
||
| 730 | 3 Stereochemical cosine torsion poten: 1708 0 16 38.513 38.513 368.84 1.000 |
||
| 731 | 4 Stereochemical improper torsion pot: 1045 0 0 1.028 1.028 21.971 1.000 |
||
| 732 | 5 Soft-sphere overlap restraints : 4871 1 1 0.004 0.004 11.126 1.000 |
||
| 733 | 6 Lennard-Jones 6-12 potential : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 734 | 7 Coulomb point-point electrostatic p: 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 735 | 8 H-bonding potential : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 736 | 9 Distance restraints 1 (CA-CA) : 4433 0 0 0.095 0.095 588.96 1.000 |
||
| 737 | 10 Distance restraints 2 (N-O) : 4608 0 0 0.119 0.119 684.27 1.000 |
||
| 738 | 11 Mainchain Phi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 739 | 12 Mainchain Psi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 740 | 13 Mainchain Omega dihedral restraints: 260 0 1 3.259 3.259 31.709 1.000 |
||
| 741 | 14 Sidechain Chi_1 dihedral restraints: 227 0 0 53.884 53.884 19.977 1.000 |
||
| 742 | 15 Sidechain Chi_2 dihedral restraints: 169 0 2 65.492 65.492 43.653 1.000 |
||
| 743 | 16 Sidechain Chi_3 dihedral restraints: 48 0 0 64.926 64.926 28.202 1.000 |
||
| 744 | 17 Sidechain Chi_4 dihedral restraints: 8 0 0 80.914 80.914 5.9267 1.000 |
||
| 745 | 18 Disulfide distance restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 746 | 19 Disulfide angle restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 747 | 20 Disulfide dihedral angle restraints: 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 748 | 21 Lower bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 749 | 22 Upper bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 750 | 23 Distance restraints 3 (SDCH-MNCH) : 3891 0 0 0.340 0.340 2729.0 1.000 |
||
| 751 | 24 Sidechain Chi_5 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 752 | 25 Phi/Psi pair of dihedral restraints: 259 3 9 15.002 18.434 -174.51 1.000 |
||
| 753 | 26 Distance restraints 4 (SDCH-SDCH) : 2426 0 14 0.785 0.785 2040.2 1.000 |
||
| 754 | 27 Distance restraints 5 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 755 | 28 NMR distance restraints 6 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 756 | 29 NMR distance restraints 7 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 757 | 30 Minimal distance restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 758 | 31 Non-bonded restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 759 | 32 Atomic accessibility restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 760 | 33 Atomic density restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 761 | 34 Absolute position restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 762 | 35 Dihedral angle difference restraint: 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 763 | 36 GBSA implicit solvent potential : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 764 | 37 EM density fitting potential : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 765 | 38 SAXS restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 766 | 39 Symmetry restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 767 | |||
| 768 | |||
| 769 | |||
| 770 | # Heavy relative violation of each residue is written to: 9606_I.V99990001 |
||
| 771 | # The profile is NOT normalized by the number of restraints. |
||
| 772 | # The profiles are smoothed over a window of residues: 1 |
||
| 773 | # The sum of all numbers in the file: 18748.8809 |
||
| 774 | |||
| 775 | |||
| 776 | |||
| 777 | List of the violated restraints: |
||
| 778 | A restraint is violated when the relative difference |
||
| 779 | from the best value (RVIOL) is larger than CUTOFF. |
||
| 780 | |||
| 781 | ICSR ... index of a restraint in the current set. |
||
| 782 | RESNO ... residue numbers of the first two atoms. |
||
| 783 | ATM ... IUPAC atom names of the first two atoms. |
||
| 784 | FEAT ... the value of the feature in the model. |
||
| 785 | restr ... the mean of the basis restraint with the smallest |
||
| 786 | difference from the model (local minimum). |
||
| 787 | viol ... difference from the local minimum. |
||
| 788 | rviol ... relative difference from the local minimum. |
||
| 789 | RESTR ... the best value (global minimum). |
||
| 790 | VIOL ... difference from the best value. |
||
| 791 | RVIOL ... relative difference from the best value. |
||
| 792 | |||
| 793 | |||
| 794 | ------------------------------------------------------------------------------------------------- |
||
| 795 | |||
| 796 | Feature 2 : Bond angle potential |
||
| 797 | List of the RVIOL violations larger than : 4.5000 |
||
| 798 | |||
| 799 | # ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL |
||
| 800 | 1 5103 251F 251F CB CG 2028 2029 152.26 122.30 29.96 6.51 122.30 29.96 6.51 |
||
| 801 | |||
| 802 | ------------------------------------------------------------------------------------------------- |
||
| 803 | |||
| 804 | Feature 25 : Phi/Psi pair of dihedral restraints |
||
| 805 | List of the RVIOL violations larger than : 6.5000 |
||
| 806 | |||
| 807 | # ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL |
||
| 808 | 1 8000 1M 2T C N 7 9 -78.13 -78.10 12.53 0.53 -63.20 156.29 21.03 |
||
| 809 | 1 2T 2T N CA 9 10 162.32 149.80 -42.10 |
||
| 810 | 2 8126 127L 128E C N 1027 1029 -80.62 -63.60 87.36 12.61 -69.30 92.21 6.63 |
||
| 811 | 2 128E 128E N CA 1029 1030 -125.99 -40.30 142.50 |
||
| 812 | 3 8230 231H 232H C N 1852 1854 -114.01 -63.20 79.74 8.70 -63.20 79.74 8.70 |
||
| 813 | 3 232H 232H N CA 1854 1855 19.15 -42.30 -42.30 |
||
| 814 | |||
| 815 | |||
| 816 | report______> Distribution of short non-bonded contacts: |
||
| 817 | |||
| 818 | |||
| 819 | DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 |
||
| 820 | DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50 |
||
| 821 | FREQUENCY: 0 0 0 0 0 10 16 74 185 265 204 297 367 415 381 |
||
| 822 | |||
| 823 | |||
| 824 | << end of ENERGY. |
||
| 825 | |||
| 826 | >> Summary of successfully produced models: |
||
| 827 | Filename molpdf |
||
| 828 | ---------------------------------------- |
||
| 829 | 9606_I.B99990001.pdb 6929.77393 |
||
| 830 | |||
| 831 | 9606_F |
||
| 832 | automodel__W> Topology and/or parameter libraries already in memory. These will |
||
| 833 | be used instead of the automodel defaults. If this is not what you |
||
| 834 | want, clear them before creating the automodel object with |
||
| 835 | env.libs.topology.clear() and env.libs.parameters.clear() |
||
| 836 | |||
| 837 | |||
| 838 | check_ali___> Checking pairwise structural superpositions. |
||
| 839 | |||
| 840 | Equivalent CA pairs with distance difference larger than 6.0 angstroms: |
||
| 841 | |||
| 842 | ALN_POS TMPL1 TMPL2 RID1 RID2 NAM1 NAM2 DIST |
||
| 843 | ---------------------------------------------------- |
||
| 844 | END OF TABLE |
||
| 845 | |||
| 846 | check_ali___> Checking the sequence-structure alignment. |
||
| 847 | |||
| 848 | Implied target CA(i)-CA(i+1) distances longer than 8.0 angstroms: |
||
| 849 | |||
| 850 | ALN_POS TMPL RID1 RID2 NAM1 NAM2 DIST |
||
| 851 | ---------------------------------------------- |
||
| 852 | END OF TABLE |
||
| 853 | |||
| 854 | getf_______W> RTF restraint not found in the atoms list: |
||
| 855 | residue type, indices: 16 261 |
||
| 856 | atom names : C +N |
||
| 857 | atom indices : 2129 0 |
||
| 858 | |||
| 859 | getf_______W> RTF restraint not found in the atoms list: |
||
| 860 | residue type, indices: 16 261 |
||
| 861 | atom names : C CA +N O |
||
| 862 | atom indices : 2129 2126 0 2130 |
||
| 863 | mdtrsr__446W> A potential that relies on one protein is used, yet you have at |
||
| 864 | least one known structure available. MDT, not library, potential is used. |
||
| 865 | 0 atoms in HETATM/BLK residues constrained |
||
| 866 | to protein atoms within 2.30 angstroms |
||
| 867 | and protein CA atoms within 10.00 angstroms |
||
| 868 | 0 atoms in residues without defined topology |
||
| 869 | constrained to be rigid bodies |
||
| 870 | condens_443_> Restraints marked for deletion were removed. |
||
| 871 | Total number of restraints before, now: 26199 24348 |
||
| 872 | iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
||
| 873 | iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
||
| 874 | iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
||
| 875 | iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
||
| 876 | iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
||
| 877 | iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
||
| 878 | |||
| 879 | |||
| 880 | >> ENERGY; Differences between the model's features and restraints: |
||
| 881 | Number of all residues in MODEL : 261 |
||
| 882 | Number of all, selected real atoms : 2131 2131 |
||
| 883 | Number of all, selected pseudo atoms : 0 0 |
||
| 884 | Number of all static, selected restraints : 24348 24348 |
||
| 885 | COVALENT_CYS : F |
||
| 886 | NONBONDED_SEL_ATOMS : 1 |
||
| 887 | Number of non-bonded pairs (excluding 1-2,1-3,1-4): 4778 |
||
| 888 | Dynamic pairs routine : 2, NATM x NATM cell sorting |
||
| 889 | Atomic shift for contacts update (UPDATE_DYNAMIC) : 0.390 |
||
| 890 | LENNARD_JONES_SWITCH : 6.500 7.500 |
||
| 891 | COULOMB_JONES_SWITCH : 6.500 7.500 |
||
| 892 | RESIDUE_SPAN_RANGE : 0 99999 |
||
| 893 | NLOGN_USE : 15 |
||
| 894 | CONTACT_SHELL : 4.000 |
||
| 895 | DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER : T T F F F |
||
| 896 | SPHERE_STDV : 0.050 |
||
| 897 | RADII_FACTOR : 0.820 |
||
| 898 | Current energy : 6458.9883 |
||
| 899 | |||
| 900 | |||
| 901 | |||
| 902 | |||
| 903 | |||
| 904 | Summary of the restraint violations: |
||
| 905 | |||
| 906 | NUM ... number of restraints. |
||
| 907 | NUMVI ... number of restraints with RVIOL > VIOL_REPORT_CUT[i]. |
||
| 908 | RVIOL ... relative difference from the best value. |
||
| 909 | NUMVP ... number of restraints with -Ln(pdf) > VIOL_REPORT_CUT2[i]. |
||
| 910 | RMS_1 ... RMS(feature, minimally_violated_basis_restraint, NUMB). |
||
| 911 | RMS_2 ... RMS(feature, best_value, NUMB). |
||
| 912 | MOL.PDF ... scaled contribution to -Ln(Molecular pdf). |
||
| 913 | |||
| 914 | # RESTRAINT_GROUP NUM NUMVI NUMVP RMS_1 RMS_2 MOL.PDF S_i |
||
| 915 | ------------------------------------------------------------------------------------------------------ |
||
| 916 | 1 Bond length potential : 2219 0 0 0.004 0.004 10.494 1.000 |
||
| 917 | 2 Bond angle potential : 3036 0 2 1.731 1.731 180.53 1.000 |
||
| 918 | 3 Stereochemical cosine torsion poten: 1714 0 15 38.612 38.612 367.11 1.000 |
||
| 919 | 4 Stereochemical improper torsion pot: 1050 0 0 0.952 0.952 19.641 1.000 |
||
| 920 | 5 Soft-sphere overlap restraints : 4778 0 0 0.001 0.001 0.58739 1.000 |
||
| 921 | 6 Lennard-Jones 6-12 potential : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 922 | 7 Coulomb point-point electrostatic p: 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 923 | 8 H-bonding potential : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 924 | 9 Distance restraints 1 (CA-CA) : 4433 0 0 0.088 0.088 582.88 1.000 |
||
| 925 | 10 Distance restraints 2 (N-O) : 4608 0 0 0.116 0.116 683.82 1.000 |
||
| 926 | 11 Mainchain Phi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 927 | 12 Mainchain Psi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 928 | 13 Mainchain Omega dihedral restraints: 260 0 1 3.247 3.247 31.478 1.000 |
||
| 929 | 14 Sidechain Chi_1 dihedral restraints: 227 0 0 51.888 51.888 7.6842 1.000 |
||
| 930 | 15 Sidechain Chi_2 dihedral restraints: 169 0 1 64.007 64.007 31.177 1.000 |
||
| 931 | 16 Sidechain Chi_3 dihedral restraints: 48 0 0 65.360 65.360 28.065 1.000 |
||
| 932 | 17 Sidechain Chi_4 dihedral restraints: 8 0 0 76.540 76.540 4.6040 1.000 |
||
| 933 | 18 Disulfide distance restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 934 | 19 Disulfide angle restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 935 | 20 Disulfide dihedral angle restraints: 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 936 | 21 Lower bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 937 | 22 Upper bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 938 | 23 Distance restraints 3 (SDCH-MNCH) : 3891 0 0 0.294 0.294 2710.2 1.000 |
||
| 939 | 24 Sidechain Chi_5 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 940 | 25 Phi/Psi pair of dihedral restraints: 259 3 9 14.765 19.037 -178.33 1.000 |
||
| 941 | 26 Distance restraints 4 (SDCH-SDCH) : 2426 0 5 0.669 0.669 1979.0 1.000 |
||
| 942 | 27 Distance restraints 5 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 943 | 28 NMR distance restraints 6 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 944 | 29 NMR distance restraints 7 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 945 | 30 Minimal distance restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 946 | 31 Non-bonded restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 947 | 32 Atomic accessibility restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 948 | 33 Atomic density restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 949 | 34 Absolute position restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 950 | 35 Dihedral angle difference restraint: 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 951 | 36 GBSA implicit solvent potential : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 952 | 37 EM density fitting potential : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 953 | 38 SAXS restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 954 | 39 Symmetry restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 955 | |||
| 956 | |||
| 957 | |||
| 958 | # Heavy relative violation of each residue is written to: 9606_F.V99990001 |
||
| 959 | # The profile is NOT normalized by the number of restraints. |
||
| 960 | # The profiles are smoothed over a window of residues: 1 |
||
| 961 | # The sum of all numbers in the file: 17361.5898 |
||
| 962 | |||
| 963 | |||
| 964 | |||
| 965 | List of the violated restraints: |
||
| 966 | A restraint is violated when the relative difference |
||
| 967 | from the best value (RVIOL) is larger than CUTOFF. |
||
| 968 | |||
| 969 | ICSR ... index of a restraint in the current set. |
||
| 970 | RESNO ... residue numbers of the first two atoms. |
||
| 971 | ATM ... IUPAC atom names of the first two atoms. |
||
| 972 | FEAT ... the value of the feature in the model. |
||
| 973 | restr ... the mean of the basis restraint with the smallest |
||
| 974 | difference from the model (local minimum). |
||
| 975 | viol ... difference from the local minimum. |
||
| 976 | rviol ... relative difference from the local minimum. |
||
| 977 | RESTR ... the best value (global minimum). |
||
| 978 | VIOL ... difference from the best value. |
||
| 979 | RVIOL ... relative difference from the best value. |
||
| 980 | |||
| 981 | |||
| 982 | ------------------------------------------------------------------------------------------------- |
||
| 983 | |||
| 984 | Feature 25 : Phi/Psi pair of dihedral restraints |
||
| 985 | List of the RVIOL violations larger than : 6.5000 |
||
| 986 | |||
| 987 | # ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL |
||
| 988 | 1 8020 1M 2T C N 7 9 -76.22 -78.10 9.41 0.47 -63.20 159.41 21.31 |
||
| 989 | 1 2T 2T N CA 9 10 159.02 149.80 -42.10 |
||
| 990 | 2 8146 127L 128E C N 1030 1032 -86.22 -63.60 82.68 12.30 -69.30 99.13 6.96 |
||
| 991 | 2 128E 128E N CA 1032 1033 -119.82 -40.30 142.50 |
||
| 992 | 3 8250 231H 232H C N 1855 1857 -112.98 -63.20 78.73 8.57 -63.20 78.73 8.57 |
||
| 993 | 3 232H 232H N CA 1857 1858 18.69 -42.30 -42.30 |
||
| 994 | |||
| 995 | |||
| 996 | report______> Distribution of short non-bonded contacts: |
||
| 997 | |||
| 998 | |||
| 999 | DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 |
||
| 1000 | DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50 |
||
| 1001 | FREQUENCY: 0 0 0 0 0 5 20 66 185 232 194 296 363 405 376 |
||
| 1002 | |||
| 1003 | |||
| 1004 | << end of ENERGY. |
||
| 1005 | |||
| 1006 | >> Summary of successfully produced models: |
||
| 1007 | Filename molpdf |
||
| 1008 | ---------------------------------------- |
||
| 1009 | 9606_F.B99990001.pdb 6458.98828 |
||
| 1010 | |||
| 1011 | 9606_S |
||
| 1012 | automodel__W> Topology and/or parameter libraries already in memory. These will |
||
| 1013 | be used instead of the automodel defaults. If this is not what you |
||
| 1014 | want, clear them before creating the automodel object with |
||
| 1015 | env.libs.topology.clear() and env.libs.parameters.clear() |
||
| 1016 | |||
| 1017 | |||
| 1018 | check_ali___> Checking pairwise structural superpositions. |
||
| 1019 | |||
| 1020 | Equivalent CA pairs with distance difference larger than 6.0 angstroms: |
||
| 1021 | |||
| 1022 | ALN_POS TMPL1 TMPL2 RID1 RID2 NAM1 NAM2 DIST |
||
| 1023 | ---------------------------------------------------- |
||
| 1024 | END OF TABLE |
||
| 1025 | |||
| 1026 | check_ali___> Checking the sequence-structure alignment. |
||
| 1027 | |||
| 1028 | Implied target CA(i)-CA(i+1) distances longer than 8.0 angstroms: |
||
| 1029 | |||
| 1030 | ALN_POS TMPL RID1 RID2 NAM1 NAM2 DIST |
||
| 1031 | ---------------------------------------------- |
||
| 1032 | END OF TABLE |
||
| 1033 | |||
| 1034 | getf_______W> RTF restraint not found in the atoms list: |
||
| 1035 | residue type, indices: 16 261 |
||
| 1036 | atom names : C +N |
||
| 1037 | atom indices : 2124 0 |
||
| 1038 | |||
| 1039 | getf_______W> RTF restraint not found in the atoms list: |
||
| 1040 | residue type, indices: 16 261 |
||
| 1041 | atom names : C CA +N O |
||
| 1042 | atom indices : 2124 2121 0 2125 |
||
| 1043 | mdtrsr__446W> A potential that relies on one protein is used, yet you have at |
||
| 1044 | least one known structure available. MDT, not library, potential is used. |
||
| 1045 | 0 atoms in HETATM/BLK residues constrained |
||
| 1046 | to protein atoms within 2.30 angstroms |
||
| 1047 | and protein CA atoms within 10.00 angstroms |
||
| 1048 | 0 atoms in residues without defined topology |
||
| 1049 | constrained to be rigid bodies |
||
| 1050 | condens_443_> Restraints marked for deletion were removed. |
||
| 1051 | Total number of restraints before, now: 26168 24318 |
||
| 1052 | iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
||
| 1053 | iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
||
| 1054 | iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
||
| 1055 | iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
||
| 1056 | iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
||
| 1057 | |||
| 1058 | |||
| 1059 | >> ENERGY; Differences between the model's features and restraints: |
||
| 1060 | Number of all residues in MODEL : 261 |
||
| 1061 | Number of all, selected real atoms : 2126 2126 |
||
| 1062 | Number of all, selected pseudo atoms : 0 0 |
||
| 1063 | Number of all static, selected restraints : 24318 24318 |
||
| 1064 | COVALENT_CYS : F |
||
| 1065 | NONBONDED_SEL_ATOMS : 1 |
||
| 1066 | Number of non-bonded pairs (excluding 1-2,1-3,1-4): 4781 |
||
| 1067 | Dynamic pairs routine : 2, NATM x NATM cell sorting |
||
| 1068 | Atomic shift for contacts update (UPDATE_DYNAMIC) : 0.390 |
||
| 1069 | LENNARD_JONES_SWITCH : 6.500 7.500 |
||
| 1070 | COULOMB_JONES_SWITCH : 6.500 7.500 |
||
| 1071 | RESIDUE_SPAN_RANGE : 0 99999 |
||
| 1072 | NLOGN_USE : 15 |
||
| 1073 | CONTACT_SHELL : 4.000 |
||
| 1074 | DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER : T T F F F |
||
| 1075 | SPHERE_STDV : 0.050 |
||
| 1076 | RADII_FACTOR : 0.820 |
||
| 1077 | Current energy : 6496.0596 |
||
| 1078 | |||
| 1079 | |||
| 1080 | |||
| 1081 | |||
| 1082 | |||
| 1083 | Summary of the restraint violations: |
||
| 1084 | |||
| 1085 | NUM ... number of restraints. |
||
| 1086 | NUMVI ... number of restraints with RVIOL > VIOL_REPORT_CUT[i]. |
||
| 1087 | RVIOL ... relative difference from the best value. |
||
| 1088 | NUMVP ... number of restraints with -Ln(pdf) > VIOL_REPORT_CUT2[i]. |
||
| 1089 | RMS_1 ... RMS(feature, minimally_violated_basis_restraint, NUMB). |
||
| 1090 | RMS_2 ... RMS(feature, best_value, NUMB). |
||
| 1091 | MOL.PDF ... scaled contribution to -Ln(Molecular pdf). |
||
| 1092 | |||
| 1093 | # RESTRAINT_GROUP NUM NUMVI NUMVP RMS_1 RMS_2 MOL.PDF S_i |
||
| 1094 | ------------------------------------------------------------------------------------------------------ |
||
| 1095 | 1 Bond length potential : 2213 0 0 0.004 0.004 10.469 1.000 |
||
| 1096 | 2 Bond angle potential : 3028 0 3 1.765 1.765 185.98 1.000 |
||
| 1097 | 3 Stereochemical cosine torsion poten: 1705 0 16 38.623 38.623 370.38 1.000 |
||
| 1098 | 4 Stereochemical improper torsion pot: 1044 0 0 0.990 0.990 20.826 1.000 |
||
| 1099 | 5 Soft-sphere overlap restraints : 4781 0 0 0.001 0.001 0.59371 1.000 |
||
| 1100 | 6 Lennard-Jones 6-12 potential : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 1101 | 7 Coulomb point-point electrostatic p: 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 1102 | 8 H-bonding potential : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 1103 | 9 Distance restraints 1 (CA-CA) : 4433 0 1 0.095 0.095 587.31 1.000 |
||
| 1104 | 10 Distance restraints 2 (N-O) : 4608 0 0 0.117 0.117 682.60 1.000 |
||
| 1105 | 11 Mainchain Phi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 1106 | 12 Mainchain Psi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 1107 | 13 Mainchain Omega dihedral restraints: 260 0 1 3.238 3.238 31.315 1.000 |
||
| 1108 | 14 Sidechain Chi_1 dihedral restraints: 227 0 0 46.690 46.690 2.9465 1.000 |
||
| 1109 | 15 Sidechain Chi_2 dihedral restraints: 168 0 2 61.521 61.521 38.612 1.000 |
||
| 1110 | 16 Sidechain Chi_3 dihedral restraints: 48 0 0 52.863 52.863 26.667 1.000 |
||
| 1111 | 17 Sidechain Chi_4 dihedral restraints: 8 0 0 99.049 99.049 5.3430 1.000 |
||
| 1112 | 18 Disulfide distance restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 1113 | 19 Disulfide angle restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 1114 | 20 Disulfide dihedral angle restraints: 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 1115 | 21 Lower bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 1116 | 22 Upper bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 1117 | 23 Distance restraints 3 (SDCH-MNCH) : 3891 0 0 0.308 0.308 2711.7 1.000 |
||
| 1118 | 24 Sidechain Chi_5 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 1119 | 25 Phi/Psi pair of dihedral restraints: 259 2 10 15.336 16.194 -173.24 1.000 |
||
| 1120 | 26 Distance restraints 4 (SDCH-SDCH) : 2426 0 8 0.704 0.704 1994.5 1.000 |
||
| 1121 | 27 Distance restraints 5 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 1122 | 28 NMR distance restraints 6 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 1123 | 29 NMR distance restraints 7 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 1124 | 30 Minimal distance restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 1125 | 31 Non-bonded restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 1126 | 32 Atomic accessibility restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 1127 | 33 Atomic density restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 1128 | 34 Absolute position restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 1129 | 35 Dihedral angle difference restraint: 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 1130 | 36 GBSA implicit solvent potential : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 1131 | 37 EM density fitting potential : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 1132 | 38 SAXS restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 1133 | 39 Symmetry restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 1134 | |||
| 1135 | |||
| 1136 | |||
| 1137 | # Heavy relative violation of each residue is written to: 9606_S.V99990001 |
||
| 1138 | # The profile is NOT normalized by the number of restraints. |
||
| 1139 | # The profiles are smoothed over a window of residues: 1 |
||
| 1140 | # The sum of all numbers in the file: 16972.8242 |
||
| 1141 | |||
| 1142 | |||
| 1143 | |||
| 1144 | List of the violated restraints: |
||
| 1145 | A restraint is violated when the relative difference |
||
| 1146 | from the best value (RVIOL) is larger than CUTOFF. |
||
| 1147 | |||
| 1148 | ICSR ... index of a restraint in the current set. |
||
| 1149 | RESNO ... residue numbers of the first two atoms. |
||
| 1150 | ATM ... IUPAC atom names of the first two atoms. |
||
| 1151 | FEAT ... the value of the feature in the model. |
||
| 1152 | restr ... the mean of the basis restraint with the smallest |
||
| 1153 | difference from the model (local minimum). |
||
| 1154 | viol ... difference from the local minimum. |
||
| 1155 | rviol ... relative difference from the local minimum. |
||
| 1156 | RESTR ... the best value (global minimum). |
||
| 1157 | VIOL ... difference from the best value. |
||
| 1158 | RVIOL ... relative difference from the best value. |
||
| 1159 | |||
| 1160 | |||
| 1161 | ------------------------------------------------------------------------------------------------- |
||
| 1162 | |||
| 1163 | Feature 25 : Phi/Psi pair of dihedral restraints |
||
| 1164 | List of the RVIOL violations larger than : 6.5000 |
||
| 1165 | |||
| 1166 | # ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL |
||
| 1167 | 1 8117 127L 128E C N 1025 1027 -86.68 -63.60 83.76 12.47 -69.30 98.23 6.87 |
||
| 1168 | 1 128E 128E N CA 1027 1028 -120.82 -40.30 142.50 |
||
| 1169 | 2 8221 231H 232H C N 1850 1852 -114.13 -63.20 81.80 8.88 -63.20 81.80 8.88 |
||
| 1170 | 2 232H 232H N CA 1852 1853 21.72 -42.30 -42.30 |
||
| 1171 | |||
| 1172 | |||
| 1173 | report______> Distribution of short non-bonded contacts: |
||
| 1174 | |||
| 1175 | |||
| 1176 | DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 |
||
| 1177 | DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50 |
||
| 1178 | FREQUENCY: 0 0 0 0 0 9 17 61 175 237 197 299 355 418 379 |
||
| 1179 | |||
| 1180 | |||
| 1181 | << end of ENERGY. |
||
| 1182 | |||
| 1183 | >> Summary of successfully produced models: |
||
| 1184 | Filename molpdf |
||
| 1185 | ---------------------------------------- |
||
| 1186 | 9606_S.B99990001.pdb 6496.05957 |
||
| 1187 | |||
| 1188 | 9606_L |
||
| 1189 | automodel__W> Topology and/or parameter libraries already in memory. These will |
||
| 1190 | be used instead of the automodel defaults. If this is not what you |
||
| 1191 | want, clear them before creating the automodel object with |
||
| 1192 | env.libs.topology.clear() and env.libs.parameters.clear() |
||
| 1193 | |||
| 1194 | |||
| 1195 | check_ali___> Checking pairwise structural superpositions. |
||
| 1196 | |||
| 1197 | Equivalent CA pairs with distance difference larger than 6.0 angstroms: |
||
| 1198 | |||
| 1199 | ALN_POS TMPL1 TMPL2 RID1 RID2 NAM1 NAM2 DIST |
||
| 1200 | ---------------------------------------------------- |
||
| 1201 | END OF TABLE |
||
| 1202 | |||
| 1203 | check_ali___> Checking the sequence-structure alignment. |
||
| 1204 | |||
| 1205 | Implied target CA(i)-CA(i+1) distances longer than 8.0 angstroms: |
||
| 1206 | |||
| 1207 | ALN_POS TMPL RID1 RID2 NAM1 NAM2 DIST |
||
| 1208 | ---------------------------------------------- |
||
| 1209 | END OF TABLE |
||
| 1210 | |||
| 1211 | getf_______W> RTF restraint not found in the atoms list: |
||
| 1212 | residue type, indices: 16 261 |
||
| 1213 | atom names : C +N |
||
| 1214 | atom indices : 2126 0 |
||
| 1215 | |||
| 1216 | getf_______W> RTF restraint not found in the atoms list: |
||
| 1217 | residue type, indices: 16 261 |
||
| 1218 | atom names : C CA +N O |
||
| 1219 | atom indices : 2126 2123 0 2127 |
||
| 1220 | mdtrsr__446W> A potential that relies on one protein is used, yet you have at |
||
| 1221 | least one known structure available. MDT, not library, potential is used. |
||
| 1222 | 0 atoms in HETATM/BLK residues constrained |
||
| 1223 | to protein atoms within 2.30 angstroms |
||
| 1224 | and protein CA atoms within 10.00 angstroms |
||
| 1225 | 0 atoms in residues without defined topology |
||
| 1226 | constrained to be rigid bodies |
||
| 1227 | condens_443_> Restraints marked for deletion were removed. |
||
| 1228 | Total number of restraints before, now: 26177 24326 |
||
| 1229 | iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
||
| 1230 | iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
||
| 1231 | iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
||
| 1232 | iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
||
| 1233 | iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
||
| 1234 | iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
||
| 1235 | iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
||
| 1236 | iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
||
| 1237 | iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
||
| 1238 | iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
||
| 1239 | |||
| 1240 | |||
| 1241 | >> ENERGY; Differences between the model's features and restraints: |
||
| 1242 | Number of all residues in MODEL : 261 |
||
| 1243 | Number of all, selected real atoms : 2128 2128 |
||
| 1244 | Number of all, selected pseudo atoms : 0 0 |
||
| 1245 | Number of all static, selected restraints : 24326 24326 |
||
| 1246 | COVALENT_CYS : F |
||
| 1247 | NONBONDED_SEL_ATOMS : 1 |
||
| 1248 | Number of non-bonded pairs (excluding 1-2,1-3,1-4): 4822 |
||
| 1249 | Dynamic pairs routine : 2, NATM x NATM cell sorting |
||
| 1250 | Atomic shift for contacts update (UPDATE_DYNAMIC) : 0.390 |
||
| 1251 | LENNARD_JONES_SWITCH : 6.500 7.500 |
||
| 1252 | COULOMB_JONES_SWITCH : 6.500 7.500 |
||
| 1253 | RESIDUE_SPAN_RANGE : 0 99999 |
||
| 1254 | NLOGN_USE : 15 |
||
| 1255 | CONTACT_SHELL : 4.000 |
||
| 1256 | DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER : T T F F F |
||
| 1257 | SPHERE_STDV : 0.050 |
||
| 1258 | RADII_FACTOR : 0.820 |
||
| 1259 | Current energy : 6708.4106 |
||
| 1260 | |||
| 1261 | |||
| 1262 | |||
| 1263 | |||
| 1264 | |||
| 1265 | Summary of the restraint violations: |
||
| 1266 | |||
| 1267 | NUM ... number of restraints. |
||
| 1268 | NUMVI ... number of restraints with RVIOL > VIOL_REPORT_CUT[i]. |
||
| 1269 | RVIOL ... relative difference from the best value. |
||
| 1270 | NUMVP ... number of restraints with -Ln(pdf) > VIOL_REPORT_CUT2[i]. |
||
| 1271 | RMS_1 ... RMS(feature, minimally_violated_basis_restraint, NUMB). |
||
| 1272 | RMS_2 ... RMS(feature, best_value, NUMB). |
||
| 1273 | MOL.PDF ... scaled contribution to -Ln(Molecular pdf). |
||
| 1274 | |||
| 1275 | # RESTRAINT_GROUP NUM NUMVI NUMVP RMS_1 RMS_2 MOL.PDF S_i |
||
| 1276 | ------------------------------------------------------------------------------------------------------ |
||
| 1277 | 1 Bond length potential : 2215 0 0 0.005 0.005 12.566 1.000 |
||
| 1278 | 2 Bond angle potential : 3031 0 3 1.867 1.867 206.95 1.000 |
||
| 1279 | 3 Stereochemical cosine torsion poten: 1706 0 18 39.086 39.086 379.94 1.000 |
||
| 1280 | 4 Stereochemical improper torsion pot: 1045 0 0 1.093 1.093 24.881 1.000 |
||
| 1281 | 5 Soft-sphere overlap restraints : 4822 0 0 0.001 0.001 0.90441 1.000 |
||
| 1282 | 6 Lennard-Jones 6-12 potential : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 1283 | 7 Coulomb point-point electrostatic p: 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 1284 | 8 H-bonding potential : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 1285 | 9 Distance restraints 1 (CA-CA) : 4433 0 2 0.124 0.124 621.07 1.000 |
||
| 1286 | 10 Distance restraints 2 (N-O) : 4608 0 4 0.143 0.143 723.61 1.000 |
||
| 1287 | 11 Mainchain Phi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 1288 | 12 Mainchain Psi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 1289 | 13 Mainchain Omega dihedral restraints: 260 0 1 3.542 3.542 37.629 1.000 |
||
| 1290 | 14 Sidechain Chi_1 dihedral restraints: 227 0 0 50.898 50.898 15.005 1.000 |
||
| 1291 | 15 Sidechain Chi_2 dihedral restraints: 169 0 1 62.237 62.237 40.949 1.000 |
||
| 1292 | 16 Sidechain Chi_3 dihedral restraints: 48 0 0 67.335 67.335 29.038 1.000 |
||
| 1293 | 17 Sidechain Chi_4 dihedral restraints: 8 0 0 76.220 76.220 6.3086 1.000 |
||
| 1294 | 18 Disulfide distance restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 1295 | 19 Disulfide angle restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 1296 | 20 Disulfide dihedral angle restraints: 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 1297 | 21 Lower bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 1298 | 22 Upper bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 1299 | 23 Distance restraints 3 (SDCH-MNCH) : 3891 0 0 0.335 0.335 2726.8 1.000 |
||
| 1300 | 24 Sidechain Chi_5 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 1301 | 25 Phi/Psi pair of dihedral restraints: 259 7 14 19.300 28.110 -152.14 1.000 |
||
| 1302 | 26 Distance restraints 4 (SDCH-SDCH) : 2426 0 14 0.775 0.775 2034.9 1.000 |
||
| 1303 | 27 Distance restraints 5 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 1304 | 28 NMR distance restraints 6 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 1305 | 29 NMR distance restraints 7 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 1306 | 30 Minimal distance restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 1307 | 31 Non-bonded restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 1308 | 32 Atomic accessibility restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 1309 | 33 Atomic density restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 1310 | 34 Absolute position restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 1311 | 35 Dihedral angle difference restraint: 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 1312 | 36 GBSA implicit solvent potential : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 1313 | 37 EM density fitting potential : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 1314 | 38 SAXS restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 1315 | 39 Symmetry restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 1316 | |||
| 1317 | |||
| 1318 | |||
| 1319 | # Heavy relative violation of each residue is written to: 9606_L.V99990001 |
||
| 1320 | # The profile is NOT normalized by the number of restraints. |
||
| 1321 | # The profiles are smoothed over a window of residues: 1 |
||
| 1322 | # The sum of all numbers in the file: 19367.4160 |
||
| 1323 | |||
| 1324 | |||
| 1325 | |||
| 1326 | List of the violated restraints: |
||
| 1327 | A restraint is violated when the relative difference |
||
| 1328 | from the best value (RVIOL) is larger than CUTOFF. |
||
| 1329 | |||
| 1330 | ICSR ... index of a restraint in the current set. |
||
| 1331 | RESNO ... residue numbers of the first two atoms. |
||
| 1332 | ATM ... IUPAC atom names of the first two atoms. |
||
| 1333 | FEAT ... the value of the feature in the model. |
||
| 1334 | restr ... the mean of the basis restraint with the smallest |
||
| 1335 | difference from the model (local minimum). |
||
| 1336 | viol ... difference from the local minimum. |
||
| 1337 | rviol ... relative difference from the local minimum. |
||
| 1338 | RESTR ... the best value (global minimum). |
||
| 1339 | VIOL ... difference from the best value. |
||
| 1340 | RVIOL ... relative difference from the best value. |
||
| 1341 | |||
| 1342 | |||
| 1343 | ------------------------------------------------------------------------------------------------- |
||
| 1344 | |||
| 1345 | Feature 25 : Phi/Psi pair of dihedral restraints |
||
| 1346 | List of the RVIOL violations larger than : 6.5000 |
||
| 1347 | |||
| 1348 | # ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL |
||
| 1349 | 1 7998 1M 2T C N 7 9 -80.00 -78.10 7.10 0.25 -63.20 162.13 21.91 |
||
| 1350 | 1 2T 2T N CA 9 10 156.64 149.80 -42.10 |
||
| 1351 | 2 8007 10M 11V C N 84 86 -63.70 -62.40 2.01 0.23 -73.50 -179.80 15.52 |
||
| 1352 | 2 11V 11V N CA 86 87 -40.87 -42.40 139.20 |
||
| 1353 | 3 8008 11V 12K C N 91 93 84.34 -70.20 154.84 11.07 -70.20 154.84 11.07 |
||
| 1354 | 3 12K 12K N CA 93 94 130.79 140.40 140.40 |
||
| 1355 | 4 8119 122T 123P C N 989 991 -57.88 -58.70 24.55 1.96 -64.50 157.91 12.14 |
||
| 1356 | 4 123P 123P N CA 991 992 -55.03 -30.50 147.20 |
||
| 1357 | 5 8120 123P 124L C N 996 998 126.04 -108.50 125.73 5.89 -70.70 163.26 14.87 |
||
| 1358 | 5 124L 124L N CA 998 999 140.81 132.50 141.60 |
||
| 1359 | 6 8124 127L 128E C N 1027 1029 -87.12 -63.60 81.35 12.18 -69.30 100.90 7.06 |
||
| 1360 | 6 128E 128E N CA 1029 1030 -118.18 -40.30 142.50 |
||
| 1361 | 7 8228 231H 232H C N 1852 1854 -113.64 -63.20 79.29 8.64 -63.20 79.29 8.64 |
||
| 1362 | 7 232H 232H N CA 1854 1855 18.87 -42.30 -42.30 |
||
| 1363 | |||
| 1364 | |||
| 1365 | report______> Distribution of short non-bonded contacts: |
||
| 1366 | |||
| 1367 | |||
| 1368 | DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 |
||
| 1369 | DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50 |
||
| 1370 | FREQUENCY: 0 0 0 0 0 8 15 81 183 233 198 284 381 403 371 |
||
| 1371 | |||
| 1372 | |||
| 1373 | << end of ENERGY. |
||
| 1374 | |||
| 1375 | >> Summary of successfully produced models: |
||
| 1376 | Filename molpdf |
||
| 1377 | ---------------------------------------- |
||
| 1378 | 9606_L.B99990001.pdb 6708.41064 |
||
| 1379 | |||
| 1380 | 9606_M |
||
| 1381 | automodel__W> Topology and/or parameter libraries already in memory. These will |
||
| 1382 | be used instead of the automodel defaults. If this is not what you |
||
| 1383 | want, clear them before creating the automodel object with |
||
| 1384 | env.libs.topology.clear() and env.libs.parameters.clear() |
||
| 1385 | |||
| 1386 | |||
| 1387 | check_ali___> Checking pairwise structural superpositions. |
||
| 1388 | |||
| 1389 | Equivalent CA pairs with distance difference larger than 6.0 angstroms: |
||
| 1390 | |||
| 1391 | ALN_POS TMPL1 TMPL2 RID1 RID2 NAM1 NAM2 DIST |
||
| 1392 | ---------------------------------------------------- |
||
| 1393 | END OF TABLE |
||
| 1394 | |||
| 1395 | check_ali___> Checking the sequence-structure alignment. |
||
| 1396 | |||
| 1397 | Implied target CA(i)-CA(i+1) distances longer than 8.0 angstroms: |
||
| 1398 | |||
| 1399 | ALN_POS TMPL RID1 RID2 NAM1 NAM2 DIST |
||
| 1400 | ---------------------------------------------- |
||
| 1401 | END OF TABLE |
||
| 1402 | |||
| 1403 | getf_______W> RTF restraint not found in the atoms list: |
||
| 1404 | residue type, indices: 16 261 |
||
| 1405 | atom names : C +N |
||
| 1406 | atom indices : 2126 0 |
||
| 1407 | |||
| 1408 | getf_______W> RTF restraint not found in the atoms list: |
||
| 1409 | residue type, indices: 16 261 |
||
| 1410 | atom names : C CA +N O |
||
| 1411 | atom indices : 2126 2123 0 2127 |
||
| 1412 | mdtrsr__446W> A potential that relies on one protein is used, yet you have at |
||
| 1413 | least one known structure available. MDT, not library, potential is used. |
||
| 1414 | 0 atoms in HETATM/BLK residues constrained |
||
| 1415 | to protein atoms within 2.30 angstroms |
||
| 1416 | and protein CA atoms within 10.00 angstroms |
||
| 1417 | 0 atoms in residues without defined topology |
||
| 1418 | constrained to be rigid bodies |
||
| 1419 | condens_443_> Restraints marked for deletion were removed. |
||
| 1420 | Total number of restraints before, now: 26177 24324 |
||
| 1421 | iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
||
| 1422 | iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
||
| 1423 | iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
||
| 1424 | iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
||
| 1425 | iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
||
| 1426 | iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
||
| 1427 | |||
| 1428 | |||
| 1429 | >> ENERGY; Differences between the model's features and restraints: |
||
| 1430 | Number of all residues in MODEL : 261 |
||
| 1431 | Number of all, selected real atoms : 2128 2128 |
||
| 1432 | Number of all, selected pseudo atoms : 0 0 |
||
| 1433 | Number of all static, selected restraints : 24324 24324 |
||
| 1434 | COVALENT_CYS : F |
||
| 1435 | NONBONDED_SEL_ATOMS : 1 |
||
| 1436 | Number of non-bonded pairs (excluding 1-2,1-3,1-4): 4830 |
||
| 1437 | Dynamic pairs routine : 2, NATM x NATM cell sorting |
||
| 1438 | Atomic shift for contacts update (UPDATE_DYNAMIC) : 0.390 |
||
| 1439 | LENNARD_JONES_SWITCH : 6.500 7.500 |
||
| 1440 | COULOMB_JONES_SWITCH : 6.500 7.500 |
||
| 1441 | RESIDUE_SPAN_RANGE : 0 99999 |
||
| 1442 | NLOGN_USE : 15 |
||
| 1443 | CONTACT_SHELL : 4.000 |
||
| 1444 | DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER : T T F F F |
||
| 1445 | SPHERE_STDV : 0.050 |
||
| 1446 | RADII_FACTOR : 0.820 |
||
| 1447 | Current energy : 6481.8320 |
||
| 1448 | |||
| 1449 | |||
| 1450 | |||
| 1451 | |||
| 1452 | |||
| 1453 | Summary of the restraint violations: |
||
| 1454 | |||
| 1455 | NUM ... number of restraints. |
||
| 1456 | NUMVI ... number of restraints with RVIOL > VIOL_REPORT_CUT[i]. |
||
| 1457 | RVIOL ... relative difference from the best value. |
||
| 1458 | NUMVP ... number of restraints with -Ln(pdf) > VIOL_REPORT_CUT2[i]. |
||
| 1459 | RMS_1 ... RMS(feature, minimally_violated_basis_restraint, NUMB). |
||
| 1460 | RMS_2 ... RMS(feature, best_value, NUMB). |
||
| 1461 | MOL.PDF ... scaled contribution to -Ln(Molecular pdf). |
||
| 1462 | |||
| 1463 | # RESTRAINT_GROUP NUM NUMVI NUMVP RMS_1 RMS_2 MOL.PDF S_i |
||
| 1464 | ------------------------------------------------------------------------------------------------------ |
||
| 1465 | 1 Bond length potential : 2215 0 0 0.004 0.004 10.731 1.000 |
||
| 1466 | 2 Bond angle potential : 3030 0 3 1.777 1.777 188.35 1.000 |
||
| 1467 | 3 Stereochemical cosine torsion poten: 1705 0 16 38.765 38.765 371.22 1.000 |
||
| 1468 | 4 Stereochemical improper torsion pot: 1044 0 0 1.009 1.009 21.571 1.000 |
||
| 1469 | 5 Soft-sphere overlap restraints : 4830 0 0 0.001 0.001 0.79378 1.000 |
||
| 1470 | 6 Lennard-Jones 6-12 potential : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 1471 | 7 Coulomb point-point electrostatic p: 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 1472 | 8 H-bonding potential : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 1473 | 9 Distance restraints 1 (CA-CA) : 4433 0 0 0.088 0.088 582.13 1.000 |
||
| 1474 | 10 Distance restraints 2 (N-O) : 4608 0 0 0.118 0.118 684.87 1.000 |
||
| 1475 | 11 Mainchain Phi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 1476 | 12 Mainchain Psi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 1477 | 13 Mainchain Omega dihedral restraints: 260 0 1 3.280 3.280 32.136 1.000 |
||
| 1478 | 14 Sidechain Chi_1 dihedral restraints: 227 0 1 51.328 51.328 10.403 1.000 |
||
| 1479 | 15 Sidechain Chi_2 dihedral restraints: 169 0 1 60.299 60.299 30.779 1.000 |
||
| 1480 | 16 Sidechain Chi_3 dihedral restraints: 49 0 0 66.051 66.051 29.338 1.000 |
||
| 1481 | 17 Sidechain Chi_4 dihedral restraints: 8 0 0 86.862 86.862 5.4540 1.000 |
||
| 1482 | 18 Disulfide distance restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 1483 | 19 Disulfide angle restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 1484 | 20 Disulfide dihedral angle restraints: 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 1485 | 21 Lower bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 1486 | 22 Upper bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 1487 | 23 Distance restraints 3 (SDCH-MNCH) : 3891 0 0 0.318 0.318 2721.0 1.000 |
||
| 1488 | 24 Sidechain Chi_5 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 1489 | 25 Phi/Psi pair of dihedral restraints: 259 3 8 14.925 19.469 -174.50 1.000 |
||
| 1490 | 26 Distance restraints 4 (SDCH-SDCH) : 2426 0 8 0.647 0.647 1967.6 1.000 |
||
| 1491 | 27 Distance restraints 5 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 1492 | 28 NMR distance restraints 6 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 1493 | 29 NMR distance restraints 7 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 1494 | 30 Minimal distance restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 1495 | 31 Non-bonded restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 1496 | 32 Atomic accessibility restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 1497 | 33 Atomic density restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 1498 | 34 Absolute position restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 1499 | 35 Dihedral angle difference restraint: 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 1500 | 36 GBSA implicit solvent potential : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 1501 | 37 EM density fitting potential : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 1502 | 38 SAXS restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 1503 | 39 Symmetry restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 1504 | |||
| 1505 | |||
| 1506 | |||
| 1507 | # Heavy relative violation of each residue is written to: 9606_M.V99990001 |
||
| 1508 | # The profile is NOT normalized by the number of restraints. |
||
| 1509 | # The profiles are smoothed over a window of residues: 1 |
||
| 1510 | # The sum of all numbers in the file: 17671.6875 |
||
| 1511 | |||
| 1512 | |||
| 1513 | |||
| 1514 | List of the violated restraints: |
||
| 1515 | A restraint is violated when the relative difference |
||
| 1516 | from the best value (RVIOL) is larger than CUTOFF. |
||
| 1517 | |||
| 1518 | ICSR ... index of a restraint in the current set. |
||
| 1519 | RESNO ... residue numbers of the first two atoms. |
||
| 1520 | ATM ... IUPAC atom names of the first two atoms. |
||
| 1521 | FEAT ... the value of the feature in the model. |
||
| 1522 | restr ... the mean of the basis restraint with the smallest |
||
| 1523 | difference from the model (local minimum). |
||
| 1524 | viol ... difference from the local minimum. |
||
| 1525 | rviol ... relative difference from the local minimum. |
||
| 1526 | RESTR ... the best value (global minimum). |
||
| 1527 | VIOL ... difference from the best value. |
||
| 1528 | RVIOL ... relative difference from the best value. |
||
| 1529 | |||
| 1530 | |||
| 1531 | ------------------------------------------------------------------------------------------------- |
||
| 1532 | |||
| 1533 | Feature 25 : Phi/Psi pair of dihedral restraints |
||
| 1534 | List of the RVIOL violations larger than : 6.5000 |
||
| 1535 | |||
| 1536 | # ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL |
||
| 1537 | 1 7995 1M 2T C N 7 9 -118.91 -124.80 11.30 0.35 -63.20 -175.43 20.51 |
||
| 1538 | 1 2T 2T N CA 9 10 133.86 143.50 -42.10 |
||
| 1539 | 2 8121 127L 128E C N 1027 1029 -84.52 -63.60 86.20 12.68 -69.30 94.80 6.69 |
||
| 1540 | 2 128E 128E N CA 1029 1030 -123.93 -40.30 142.50 |
||
| 1541 | 3 8225 231H 232H C N 1852 1854 -113.35 -63.20 79.68 8.67 -63.20 79.68 8.67 |
||
| 1542 | 3 232H 232H N CA 1854 1855 19.62 -42.30 -42.30 |
||
| 1543 | |||
| 1544 | |||
| 1545 | report______> Distribution of short non-bonded contacts: |
||
| 1546 | |||
| 1547 | |||
| 1548 | DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 |
||
| 1549 | DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50 |
||
| 1550 | FREQUENCY: 0 0 0 0 0 12 19 68 185 260 187 275 353 408 393 |
||
| 1551 | |||
| 1552 | |||
| 1553 | << end of ENERGY. |
||
| 1554 | |||
| 1555 | >> Summary of successfully produced models: |
||
| 1556 | Filename molpdf |
||
| 1557 | ---------------------------------------- |
||
| 1558 | 9606_M.B99990001.pdb 6481.83203 |
||
| 1559 | |||
| 1560 | 9606_E |
||
| 1561 | automodel__W> Topology and/or parameter libraries already in memory. These will |
||
| 1562 | be used instead of the automodel defaults. If this is not what you |
||
| 1563 | want, clear them before creating the automodel object with |
||
| 1564 | env.libs.topology.clear() and env.libs.parameters.clear() |
||
| 1565 | |||
| 1566 | |||
| 1567 | check_ali___> Checking pairwise structural superpositions. |
||
| 1568 | |||
| 1569 | Equivalent CA pairs with distance difference larger than 6.0 angstroms: |
||
| 1570 | |||
| 1571 | ALN_POS TMPL1 TMPL2 RID1 RID2 NAM1 NAM2 DIST |
||
| 1572 | ---------------------------------------------------- |
||
| 1573 | END OF TABLE |
||
| 1574 | |||
| 1575 | check_ali___> Checking the sequence-structure alignment. |
||
| 1576 | |||
| 1577 | Implied target CA(i)-CA(i+1) distances longer than 8.0 angstroms: |
||
| 1578 | |||
| 1579 | ALN_POS TMPL RID1 RID2 NAM1 NAM2 DIST |
||
| 1580 | ---------------------------------------------- |
||
| 1581 | END OF TABLE |
||
| 1582 | |||
| 1583 | getf_______W> RTF restraint not found in the atoms list: |
||
| 1584 | residue type, indices: 16 261 |
||
| 1585 | atom names : C +N |
||
| 1586 | atom indices : 2127 0 |
||
| 1587 | |||
| 1588 | getf_______W> RTF restraint not found in the atoms list: |
||
| 1589 | residue type, indices: 16 261 |
||
| 1590 | atom names : C CA +N O |
||
| 1591 | atom indices : 2127 2124 0 2128 |
||
| 1592 | mdtrsr__446W> A potential that relies on one protein is used, yet you have at |
||
| 1593 | least one known structure available. MDT, not library, potential is used. |
||
| 1594 | 0 atoms in HETATM/BLK residues constrained |
||
| 1595 | to protein atoms within 2.30 angstroms |
||
| 1596 | and protein CA atoms within 10.00 angstroms |
||
| 1597 | 0 atoms in residues without defined topology |
||
| 1598 | constrained to be rigid bodies |
||
| 1599 | condens_443_> Restraints marked for deletion were removed. |
||
| 1600 | Total number of restraints before, now: 26181 24329 |
||
| 1601 | iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
||
| 1602 | iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
||
| 1603 | iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
||
| 1604 | iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
||
| 1605 | |||
| 1606 | |||
| 1607 | >> ENERGY; Differences between the model's features and restraints: |
||
| 1608 | Number of all residues in MODEL : 261 |
||
| 1609 | Number of all, selected real atoms : 2129 2129 |
||
| 1610 | Number of all, selected pseudo atoms : 0 0 |
||
| 1611 | Number of all static, selected restraints : 24329 24329 |
||
| 1612 | COVALENT_CYS : F |
||
| 1613 | NONBONDED_SEL_ATOMS : 1 |
||
| 1614 | Number of non-bonded pairs (excluding 1-2,1-3,1-4): 4776 |
||
| 1615 | Dynamic pairs routine : 2, NATM x NATM cell sorting |
||
| 1616 | Atomic shift for contacts update (UPDATE_DYNAMIC) : 0.390 |
||
| 1617 | LENNARD_JONES_SWITCH : 6.500 7.500 |
||
| 1618 | COULOMB_JONES_SWITCH : 6.500 7.500 |
||
| 1619 | RESIDUE_SPAN_RANGE : 0 99999 |
||
| 1620 | NLOGN_USE : 15 |
||
| 1621 | CONTACT_SHELL : 4.000 |
||
| 1622 | DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER : T T F F F |
||
| 1623 | SPHERE_STDV : 0.050 |
||
| 1624 | RADII_FACTOR : 0.820 |
||
| 1625 | Current energy : 6525.7900 |
||
| 1626 | |||
| 1627 | |||
| 1628 | |||
| 1629 | |||
| 1630 | |||
| 1631 | Summary of the restraint violations: |
||
| 1632 | |||
| 1633 | NUM ... number of restraints. |
||
| 1634 | NUMVI ... number of restraints with RVIOL > VIOL_REPORT_CUT[i]. |
||
| 1635 | RVIOL ... relative difference from the best value. |
||
| 1636 | NUMVP ... number of restraints with -Ln(pdf) > VIOL_REPORT_CUT2[i]. |
||
| 1637 | RMS_1 ... RMS(feature, minimally_violated_basis_restraint, NUMB). |
||
| 1638 | RMS_2 ... RMS(feature, best_value, NUMB). |
||
| 1639 | MOL.PDF ... scaled contribution to -Ln(Molecular pdf). |
||
| 1640 | |||
| 1641 | # RESTRAINT_GROUP NUM NUMVI NUMVP RMS_1 RMS_2 MOL.PDF S_i |
||
| 1642 | ------------------------------------------------------------------------------------------------------ |
||
| 1643 | 1 Bond length potential : 2216 0 0 0.004 0.004 11.308 1.000 |
||
| 1644 | 2 Bond angle potential : 3032 0 3 1.798 1.798 194.33 1.000 |
||
| 1645 | 3 Stereochemical cosine torsion poten: 1706 0 18 38.780 38.780 372.87 1.000 |
||
| 1646 | 4 Stereochemical improper torsion pot: 1045 0 0 1.055 1.055 23.452 1.000 |
||
| 1647 | 5 Soft-sphere overlap restraints : 4776 0 0 0.001 0.001 0.93099 1.000 |
||
| 1648 | 6 Lennard-Jones 6-12 potential : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 1649 | 7 Coulomb point-point electrostatic p: 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 1650 | 8 H-bonding potential : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 1651 | 9 Distance restraints 1 (CA-CA) : 4433 0 0 0.105 0.105 597.93 1.000 |
||
| 1652 | 10 Distance restraints 2 (N-O) : 4608 0 0 0.126 0.126 694.13 1.000 |
||
| 1653 | 11 Mainchain Phi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 1654 | 12 Mainchain Psi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 1655 | 13 Mainchain Omega dihedral restraints: 260 0 1 3.414 3.414 34.899 1.000 |
||
| 1656 | 14 Sidechain Chi_1 dihedral restraints: 227 0 0 48.551 48.551 12.009 1.000 |
||
| 1657 | 15 Sidechain Chi_2 dihedral restraints: 169 0 1 55.942 55.942 31.060 1.000 |
||
| 1658 | 16 Sidechain Chi_3 dihedral restraints: 49 0 0 58.473 58.473 27.663 1.000 |
||
| 1659 | 17 Sidechain Chi_4 dihedral restraints: 8 0 0 104.502 104.502 4.9916 1.000 |
||
| 1660 | 18 Disulfide distance restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 1661 | 19 Disulfide angle restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 1662 | 20 Disulfide dihedral angle restraints: 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 1663 | 21 Lower bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 1664 | 22 Upper bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 1665 | 23 Distance restraints 3 (SDCH-MNCH) : 3891 0 0 0.307 0.307 2713.5 1.000 |
||
| 1666 | 24 Sidechain Chi_5 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 1667 | 25 Phi/Psi pair of dihedral restraints: 259 5 10 17.664 24.563 -164.98 1.000 |
||
| 1668 | 26 Distance restraints 4 (SDCH-SDCH) : 2426 0 4 0.652 0.652 1971.7 1.000 |
||
| 1669 | 27 Distance restraints 5 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 1670 | 28 NMR distance restraints 6 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 1671 | 29 NMR distance restraints 7 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 1672 | 30 Minimal distance restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 1673 | 31 Non-bonded restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 1674 | 32 Atomic accessibility restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 1675 | 33 Atomic density restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 1676 | 34 Absolute position restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 1677 | 35 Dihedral angle difference restraint: 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 1678 | 36 GBSA implicit solvent potential : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 1679 | 37 EM density fitting potential : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 1680 | 38 SAXS restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 1681 | 39 Symmetry restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 1682 | |||
| 1683 | |||
| 1684 | |||
| 1685 | # Heavy relative violation of each residue is written to: 9606_E.V99990001 |
||
| 1686 | # The profile is NOT normalized by the number of restraints. |
||
| 1687 | # The profiles are smoothed over a window of residues: 1 |
||
| 1688 | # The sum of all numbers in the file: 17560.6973 |
||
| 1689 | |||
| 1690 | |||
| 1691 | |||
| 1692 | List of the violated restraints: |
||
| 1693 | A restraint is violated when the relative difference |
||
| 1694 | from the best value (RVIOL) is larger than CUTOFF. |
||
| 1695 | |||
| 1696 | ICSR ... index of a restraint in the current set. |
||
| 1697 | RESNO ... residue numbers of the first two atoms. |
||
| 1698 | ATM ... IUPAC atom names of the first two atoms. |
||
| 1699 | FEAT ... the value of the feature in the model. |
||
| 1700 | restr ... the mean of the basis restraint with the smallest |
||
| 1701 | difference from the model (local minimum). |
||
| 1702 | viol ... difference from the local minimum. |
||
| 1703 | rviol ... relative difference from the local minimum. |
||
| 1704 | RESTR ... the best value (global minimum). |
||
| 1705 | VIOL ... difference from the best value. |
||
| 1706 | RVIOL ... relative difference from the best value. |
||
| 1707 | |||
| 1708 | |||
| 1709 | ------------------------------------------------------------------------------------------------- |
||
| 1710 | |||
| 1711 | Feature 25 : Phi/Psi pair of dihedral restraints |
||
| 1712 | List of the RVIOL violations larger than : 6.5000 |
||
| 1713 | |||
| 1714 | # ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL |
||
| 1715 | 1 8000 1M 2T C N 7 9 -75.07 -78.10 15.73 0.58 -63.20 176.86 21.92 |
||
| 1716 | 1 2T 2T N CA 9 10 134.36 149.80 -42.10 |
||
| 1717 | 2 8009 10M 11V C N 84 86 -64.17 -62.40 1.80 0.30 -73.50 178.32 15.36 |
||
| 1718 | 2 11V 11V N CA 86 87 -42.72 -42.40 139.20 |
||
| 1719 | 3 8010 11V 12K C N 91 93 90.81 -118.00 151.52 5.89 -70.20 161.40 11.51 |
||
| 1720 | 3 12K 12K N CA 93 94 129.07 139.10 140.40 |
||
| 1721 | 4 8126 127L 128E C N 1028 1030 -85.27 -63.60 84.15 12.45 -69.30 97.21 6.85 |
||
| 1722 | 4 128E 128E N CA 1030 1031 -121.61 -40.30 142.50 |
||
| 1723 | 5 8230 231H 232H C N 1853 1855 -113.24 -63.20 78.26 8.54 -63.20 78.26 8.54 |
||
| 1724 | 5 232H 232H N CA 1855 1856 17.86 -42.30 -42.30 |
||
| 1725 | |||
| 1726 | |||
| 1727 | report______> Distribution of short non-bonded contacts: |
||
| 1728 | |||
| 1729 | |||
| 1730 | DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 |
||
| 1731 | DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50 |
||
| 1732 | FREQUENCY: 0 0 0 0 0 11 16 63 193 239 209 270 378 398 347 |
||
| 1733 | |||
| 1734 | |||
| 1735 | << end of ENERGY. |
||
| 1736 | |||
| 1737 | >> Summary of successfully produced models: |
||
| 1738 | Filename molpdf |
||
| 1739 | ---------------------------------------- |
||
| 1740 | 9606_E.B99990001.pdb 6525.79004 |
||
| 1741 | |||
| 1742 | 9606_T |
||
| 1743 | automodel__W> Topology and/or parameter libraries already in memory. These will |
||
| 1744 | be used instead of the automodel defaults. If this is not what you |
||
| 1745 | want, clear them before creating the automodel object with |
||
| 1746 | env.libs.topology.clear() and env.libs.parameters.clear() |
||
| 1747 | |||
| 1748 | |||
| 1749 | check_ali___> Checking pairwise structural superpositions. |
||
| 1750 | |||
| 1751 | Equivalent CA pairs with distance difference larger than 6.0 angstroms: |
||
| 1752 | |||
| 1753 | ALN_POS TMPL1 TMPL2 RID1 RID2 NAM1 NAM2 DIST |
||
| 1754 | ---------------------------------------------------- |
||
| 1755 | END OF TABLE |
||
| 1756 | |||
| 1757 | check_ali___> Checking the sequence-structure alignment. |
||
| 1758 | |||
| 1759 | Implied target CA(i)-CA(i+1) distances longer than 8.0 angstroms: |
||
| 1760 | |||
| 1761 | ALN_POS TMPL RID1 RID2 NAM1 NAM2 DIST |
||
| 1762 | ---------------------------------------------- |
||
| 1763 | END OF TABLE |
||
| 1764 | |||
| 1765 | getf_______W> RTF restraint not found in the atoms list: |
||
| 1766 | residue type, indices: 16 261 |
||
| 1767 | atom names : C +N |
||
| 1768 | atom indices : 2125 0 |
||
| 1769 | |||
| 1770 | getf_______W> RTF restraint not found in the atoms list: |
||
| 1771 | residue type, indices: 16 261 |
||
| 1772 | atom names : C CA +N O |
||
| 1773 | atom indices : 2125 2122 0 2126 |
||
| 1774 | mdtrsr__446W> A potential that relies on one protein is used, yet you have at |
||
| 1775 | least one known structure available. MDT, not library, potential is used. |
||
| 1776 | 0 atoms in HETATM/BLK residues constrained |
||
| 1777 | to protein atoms within 2.30 angstroms |
||
| 1778 | and protein CA atoms within 10.00 angstroms |
||
| 1779 | 0 atoms in residues without defined topology |
||
| 1780 | constrained to be rigid bodies |
||
| 1781 | condens_443_> Restraints marked for deletion were removed. |
||
| 1782 | Total number of restraints before, now: 26174 24324 |
||
| 1783 | iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
||
| 1784 | iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
||
| 1785 | iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
||
| 1786 | iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
||
| 1787 | iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
||
| 1788 | |||
| 1789 | |||
| 1790 | >> ENERGY; Differences between the model's features and restraints: |
||
| 1791 | Number of all residues in MODEL : 261 |
||
| 1792 | Number of all, selected real atoms : 2127 2127 |
||
| 1793 | Number of all, selected pseudo atoms : 0 0 |
||
| 1794 | Number of all static, selected restraints : 24324 24324 |
||
| 1795 | COVALENT_CYS : F |
||
| 1796 | NONBONDED_SEL_ATOMS : 1 |
||
| 1797 | Number of non-bonded pairs (excluding 1-2,1-3,1-4): 4799 |
||
| 1798 | Dynamic pairs routine : 2, NATM x NATM cell sorting |
||
| 1799 | Atomic shift for contacts update (UPDATE_DYNAMIC) : 0.390 |
||
| 1800 | LENNARD_JONES_SWITCH : 6.500 7.500 |
||
| 1801 | COULOMB_JONES_SWITCH : 6.500 7.500 |
||
| 1802 | RESIDUE_SPAN_RANGE : 0 99999 |
||
| 1803 | NLOGN_USE : 15 |
||
| 1804 | CONTACT_SHELL : 4.000 |
||
| 1805 | DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER : T T F F F |
||
| 1806 | SPHERE_STDV : 0.050 |
||
| 1807 | RADII_FACTOR : 0.820 |
||
| 1808 | Current energy : 6491.0776 |
||
| 1809 | |||
| 1810 | |||
| 1811 | |||
| 1812 | |||
| 1813 | |||
| 1814 | Summary of the restraint violations: |
||
| 1815 | |||
| 1816 | NUM ... number of restraints. |
||
| 1817 | NUMVI ... number of restraints with RVIOL > VIOL_REPORT_CUT[i]. |
||
| 1818 | RVIOL ... relative difference from the best value. |
||
| 1819 | NUMVP ... number of restraints with -Ln(pdf) > VIOL_REPORT_CUT2[i]. |
||
| 1820 | RMS_1 ... RMS(feature, minimally_violated_basis_restraint, NUMB). |
||
| 1821 | RMS_2 ... RMS(feature, best_value, NUMB). |
||
| 1822 | MOL.PDF ... scaled contribution to -Ln(Molecular pdf). |
||
| 1823 | |||
| 1824 | # RESTRAINT_GROUP NUM NUMVI NUMVP RMS_1 RMS_2 MOL.PDF S_i |
||
| 1825 | ------------------------------------------------------------------------------------------------------ |
||
| 1826 | 1 Bond length potential : 2214 0 0 0.004 0.004 10.739 1.000 |
||
| 1827 | 2 Bond angle potential : 3030 0 3 1.772 1.772 188.93 1.000 |
||
| 1828 | 3 Stereochemical cosine torsion poten: 1707 0 16 38.673 38.673 373.66 1.000 |
||
| 1829 | 4 Stereochemical improper torsion pot: 1045 0 0 1.005 1.005 21.394 1.000 |
||
| 1830 | 5 Soft-sphere overlap restraints : 4799 0 0 0.001 0.001 0.85217 1.000 |
||
| 1831 | 6 Lennard-Jones 6-12 potential : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 1832 | 7 Coulomb point-point electrostatic p: 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 1833 | 8 H-bonding potential : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 1834 | 9 Distance restraints 1 (CA-CA) : 4433 0 0 0.093 0.093 587.81 1.000 |
||
| 1835 | 10 Distance restraints 2 (N-O) : 4608 0 0 0.123 0.123 692.58 1.000 |
||
| 1836 | 11 Mainchain Phi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 1837 | 12 Mainchain Psi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 1838 | 13 Mainchain Omega dihedral restraints: 260 0 2 3.344 3.344 33.443 1.000 |
||
| 1839 | 14 Sidechain Chi_1 dihedral restraints: 227 0 1 45.689 45.689 2.8490 1.000 |
||
| 1840 | 15 Sidechain Chi_2 dihedral restraints: 168 0 1 61.520 61.520 35.658 1.000 |
||
| 1841 | 16 Sidechain Chi_3 dihedral restraints: 48 0 0 67.905 67.905 29.969 1.000 |
||
| 1842 | 17 Sidechain Chi_4 dihedral restraints: 8 0 0 99.536 99.536 6.2528 1.000 |
||
| 1843 | 18 Disulfide distance restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 1844 | 19 Disulfide angle restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 1845 | 20 Disulfide dihedral angle restraints: 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 1846 | 21 Lower bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 1847 | 22 Upper bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 1848 | 23 Distance restraints 3 (SDCH-MNCH) : 3891 0 0 0.295 0.295 2711.0 1.000 |
||
| 1849 | 24 Sidechain Chi_5 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 1850 | 25 Phi/Psi pair of dihedral restraints: 259 5 10 17.714 23.571 -167.37 1.000 |
||
| 1851 | 26 Distance restraints 4 (SDCH-SDCH) : 2426 0 8 0.636 0.636 1963.3 1.000 |
||
| 1852 | 27 Distance restraints 5 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 1853 | 28 NMR distance restraints 6 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 1854 | 29 NMR distance restraints 7 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 1855 | 30 Minimal distance restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 1856 | 31 Non-bonded restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 1857 | 32 Atomic accessibility restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 1858 | 33 Atomic density restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 1859 | 34 Absolute position restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 1860 | 35 Dihedral angle difference restraint: 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 1861 | 36 GBSA implicit solvent potential : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 1862 | 37 EM density fitting potential : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 1863 | 38 SAXS restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 1864 | 39 Symmetry restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 1865 | |||
| 1866 | |||
| 1867 | |||
| 1868 | # Heavy relative violation of each residue is written to: 9606_T.V99990001 |
||
| 1869 | # The profile is NOT normalized by the number of restraints. |
||
| 1870 | # The profiles are smoothed over a window of residues: 1 |
||
| 1871 | # The sum of all numbers in the file: 17342.1797 |
||
| 1872 | |||
| 1873 | |||
| 1874 | |||
| 1875 | List of the violated restraints: |
||
| 1876 | A restraint is violated when the relative difference |
||
| 1877 | from the best value (RVIOL) is larger than CUTOFF. |
||
| 1878 | |||
| 1879 | ICSR ... index of a restraint in the current set. |
||
| 1880 | RESNO ... residue numbers of the first two atoms. |
||
| 1881 | ATM ... IUPAC atom names of the first two atoms. |
||
| 1882 | FEAT ... the value of the feature in the model. |
||
| 1883 | restr ... the mean of the basis restraint with the smallest |
||
| 1884 | difference from the model (local minimum). |
||
| 1885 | viol ... difference from the local minimum. |
||
| 1886 | rviol ... relative difference from the local minimum. |
||
| 1887 | RESTR ... the best value (global minimum). |
||
| 1888 | VIOL ... difference from the best value. |
||
| 1889 | RVIOL ... relative difference from the best value. |
||
| 1890 | |||
| 1891 | |||
| 1892 | ------------------------------------------------------------------------------------------------- |
||
| 1893 | |||
| 1894 | Feature 25 : Phi/Psi pair of dihedral restraints |
||
| 1895 | List of the RVIOL violations larger than : 6.5000 |
||
| 1896 | |||
| 1897 | # ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL |
||
| 1898 | 1 7997 1M 2T C N 7 9 -87.71 -78.10 36.56 1.29 -63.20 135.07 18.96 |
||
| 1899 | 1 2T 2T N CA 9 10 -174.93 149.80 -42.10 |
||
| 1900 | 2 8006 10M 11V C N 84 86 -63.39 -62.40 1.21 0.15 -73.50 179.37 15.46 |
||
| 1901 | 2 11V 11V N CA 86 87 -41.72 -42.40 139.20 |
||
| 1902 | 3 8007 11V 12K C N 91 93 93.97 -118.00 148.04 5.62 -70.20 164.20 11.91 |
||
| 1903 | 3 12K 12K N CA 93 94 137.03 139.10 140.40 |
||
| 1904 | 4 8123 127L 128E C N 1026 1028 -80.18 -63.60 88.05 12.67 -69.30 91.37 6.59 |
||
| 1905 | 4 128E 128E N CA 1028 1029 -126.78 -40.30 142.50 |
||
| 1906 | 5 8227 231H 232H C N 1851 1853 -114.00 -63.20 79.02 8.64 -63.20 79.02 8.64 |
||
| 1907 | 5 232H 232H N CA 1853 1854 18.23 -42.30 -42.30 |
||
| 1908 | |||
| 1909 | |||
| 1910 | report______> Distribution of short non-bonded contacts: |
||
| 1911 | |||
| 1912 | |||
| 1913 | DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 |
||
| 1914 | DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50 |
||
| 1915 | FREQUENCY: 0 0 0 0 0 7 18 66 184 242 213 284 362 395 365 |
||
| 1916 | |||
| 1917 | |||
| 1918 | << end of ENERGY. |
||
| 1919 | |||
| 1920 | >> Summary of successfully produced models: |
||
| 1921 | Filename molpdf |
||
| 1922 | ---------------------------------------- |
||
| 1923 | 9606_T.B99990001.pdb 6491.07764 |
||
| 1924 | |||
| 1925 | |||
| 1926 | |||
| 1927 | |||
| 1928 | ```python |
||
| 1929 | text = 'load 1v55.pdb\nsel 2save, byres(n. ca) and not c. C+P\n' |
||
| 1930 | for s in aln[:-2]: |
||
| 1931 | text+='load out/%s.B99990001.pdb,aa\n' % s.code |
||
| 1932 | text+='load out/%s.B99990001.pdb,bb\n' % s.code |
||
| 1933 | text+='super aa, C//\n' |
||
| 1934 | text+='super bb, P//\n' |
||
| 1935 | text+='''alter aa, chain='5'\n''' |
||
| 1936 | text+='''alter bb, chain='6'\n''' |
||
| 1937 | text+='save mod/%s.pdb, 2save or aa or bb\n' %s.code |
||
| 1938 | text+='delete aa or bb\n' |
||
| 1939 | fl=open('make_mods.pml','w')
|
||
| 1940 | print fl.write(text) |
||
| 1941 | fl.close() |
||
| 1942 | ``` |
||
| 1943 | |||
| 1944 | None |
||
| 1945 | |||
| 1946 | |||
| 1947 | |||
| 1948 | ```python |
||
| 1949 | class mymodel(modeller.automodel.automodel): |
||
| 1950 | def special_restraints(self, aln): |
||
| 1951 | rsr = self.restraints |
||
| 1952 | for ids in (('OD1:98:A', 'O6A:131:A'),
|
||
| 1953 | ('N:65:A', 'O7B:132:A'),
|
||
| 1954 | ('OD2:73:A', 'O1C:133:A')):
|
||
| 1955 | atoms = [self.atoms[i] for i in ids] |
||
| 1956 | rsr.add(forms.upper_bound(group=physical.upper_distance, |
||
| 1957 | feature=features.distance(*atoms), mean=3.5, stdev=0.1)) |
||
| 1958 | ``` |
||
| 1959 | |||
| 1960 | |||
| 1961 | ```python |
||
| 1962 | mod = modeller.model(env, file='1v55.pdb') |
||
| 1963 | ``` |
||
| 1964 | |||
| 1965 | |||
| 1966 | ```python |
||
| 1967 | chains=['A','B','C','D','E','F','G','H','I','J','K','L','M'] |
||
| 1968 | accs='''P00395 |
||
| 1969 | P00403 |
||
| 1970 | P00414 |
||
| 1971 | P13073 |
||
| 1972 | Q96KJ9 |
||
| 1973 | P20674 |
||
| 1974 | P10606 |
||
| 1975 | P09669 |
||
| 1976 | P24311 |
||
| 1977 | P15954 |
||
| 1978 | O14548 |
||
| 1979 | O60397 |
||
| 1980 | P10176 |
||
| 1981 | Q7Z4L0 |
||
| 1982 | P12074 |
||
| 1983 | Q02221 |
||
| 1984 | P14854 |
||
| 1985 | Q6YFQ2 |
||
| 1986 | P24310 |
||
| 1987 | P14406'''.split('\n')
|
||
| 1988 | ``` |
||
| 1989 | |||
| 1990 | |||
| 1991 | ```python |
||
| 1992 | mods=[] |
||
| 1993 | result={}
|
||
| 1994 | text='='*60+'\n' |
||
| 1995 | for c in chains: |
||
| 1996 | pdbname='' |
||
| 1997 | m = modeller.model(env, file='1v55.pdb', model_segment=('FIRST:'+c, 'LAST:'+c))
|
||
| 1998 | names=m.name.split('EC 1.9.3.1;')
|
||
| 1999 | for n in names: |
||
| 2000 | c1 = 'CHAIN '+c |
||
| 2001 | if c1 in n: |
||
| 2002 | pdbname= n+'\n' |
||
| 2003 | ident={}
|
||
| 2004 | |||
| 2005 | for ac in accs: |
||
| 2006 | a=modeller.alignment(env) |
||
| 2007 | a.append(file='seq/'+ac+'.fasta', align_codes='all',alignment_format='FASTA') |
||
| 2008 | a.append_model(m, atom_files='1v55.pdb', align_codes='1v55_'+c) |
||
| 2009 | a.salign() |
||
| 2010 | ident[ac]=a[1].get_sequence_identity(a[0]) |
||
| 2011 | |||
| 2012 | |||
| 2013 | top=sorted(ident, key=ident.get , reverse=True)[0] |
||
| 2014 | result[c]=top |
||
| 2015 | |||
| 2016 | |||
| 2017 | |||
| 2018 | ``` |
||
| 2019 | |||
| 2020 | |||
| 2021 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2022 | |||
| 2023 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2024 | |||
| 2025 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2026 | |||
| 2027 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2028 | |||
| 2029 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2030 | |||
| 2031 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2032 | |||
| 2033 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2034 | |||
| 2035 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2036 | |||
| 2037 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2038 | |||
| 2039 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2040 | |||
| 2041 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2042 | |||
| 2043 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2044 | |||
| 2045 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2046 | |||
| 2047 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2048 | |||
| 2049 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2050 | |||
| 2051 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2052 | |||
| 2053 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2054 | |||
| 2055 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2056 | |||
| 2057 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2058 | |||
| 2059 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2060 | |||
| 2061 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2062 | |||
| 2063 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2064 | |||
| 2065 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2066 | |||
| 2067 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2068 | |||
| 2069 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2070 | |||
| 2071 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2072 | |||
| 2073 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2074 | |||
| 2075 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2076 | |||
| 2077 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2078 | |||
| 2079 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2080 | |||
| 2081 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2082 | |||
| 2083 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2084 | |||
| 2085 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2086 | |||
| 2087 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2088 | |||
| 2089 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2090 | |||
| 2091 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2092 | |||
| 2093 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2094 | |||
| 2095 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2096 | |||
| 2097 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2098 | |||
| 2099 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2100 | |||
| 2101 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2102 | |||
| 2103 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2104 | |||
| 2105 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2106 | |||
| 2107 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2108 | |||
| 2109 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2110 | |||
| 2111 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2112 | |||
| 2113 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2114 | |||
| 2115 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2116 | |||
| 2117 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2118 | |||
| 2119 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2120 | |||
| 2121 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2122 | |||
| 2123 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2124 | |||
| 2125 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2126 | |||
| 2127 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2128 | |||
| 2129 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2130 | |||
| 2131 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2132 | |||
| 2133 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2134 | |||
| 2135 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2136 | |||
| 2137 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2138 | |||
| 2139 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2140 | |||
| 2141 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2142 | |||
| 2143 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2144 | |||
| 2145 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2146 | |||
| 2147 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2148 | |||
| 2149 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2150 | |||
| 2151 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2152 | |||
| 2153 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2154 | |||
| 2155 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2156 | |||
| 2157 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2158 | |||
| 2159 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2160 | |||
| 2161 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2162 | |||
| 2163 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2164 | |||
| 2165 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2166 | |||
| 2167 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2168 | |||
| 2169 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2170 | |||
| 2171 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2172 | |||
| 2173 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2174 | |||
| 2175 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2176 | |||
| 2177 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2178 | |||
| 2179 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2180 | |||
| 2181 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2182 | |||
| 2183 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2184 | |||
| 2185 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2186 | |||
| 2187 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2188 | |||
| 2189 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2190 | |||
| 2191 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2192 | |||
| 2193 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2194 | |||
| 2195 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2196 | |||
| 2197 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2198 | |||
| 2199 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2200 | |||
| 2201 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2202 | |||
| 2203 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2204 | |||
| 2205 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2206 | |||
| 2207 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2208 | |||
| 2209 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2210 | |||
| 2211 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2212 | |||
| 2213 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2214 | |||
| 2215 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2216 | |||
| 2217 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2218 | |||
| 2219 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2220 | |||
| 2221 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2222 | |||
| 2223 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2224 | |||
| 2225 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2226 | |||
| 2227 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2228 | |||
| 2229 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2230 | |||
| 2231 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2232 | |||
| 2233 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2234 | |||
| 2235 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2236 | |||
| 2237 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2238 | |||
| 2239 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2240 | |||
| 2241 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2242 | |||
| 2243 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2244 | |||
| 2245 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2246 | |||
| 2247 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2248 | |||
| 2249 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2250 | |||
| 2251 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2252 | |||
| 2253 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2254 | |||
| 2255 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2256 | |||
| 2257 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2258 | |||
| 2259 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2260 | |||
| 2261 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2262 | |||
| 2263 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2264 | |||
| 2265 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2266 | |||
| 2267 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2268 | |||
| 2269 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2270 | |||
| 2271 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2272 | |||
| 2273 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2274 | |||
| 2275 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2276 | |||
| 2277 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2278 | |||
| 2279 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2280 | |||
| 2281 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2282 | |||
| 2283 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2284 | |||
| 2285 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2286 | |||
| 2287 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2288 | |||
| 2289 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2290 | |||
| 2291 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2292 | |||
| 2293 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2294 | |||
| 2295 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2296 | |||
| 2297 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2298 | |||
| 2299 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2300 | |||
| 2301 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2302 | |||
| 2303 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2304 | |||
| 2305 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2306 | |||
| 2307 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2308 | |||
| 2309 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2310 | |||
| 2311 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2312 | |||
| 2313 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2314 | |||
| 2315 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2316 | |||
| 2317 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2318 | |||
| 2319 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2320 | |||
| 2321 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2322 | |||
| 2323 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2324 | |||
| 2325 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2326 | |||
| 2327 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2328 | |||
| 2329 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2330 | |||
| 2331 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2332 | |||
| 2333 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2334 | |||
| 2335 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2336 | |||
| 2337 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2338 | |||
| 2339 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2340 | |||
| 2341 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2342 | |||
| 2343 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2344 | |||
| 2345 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2346 | |||
| 2347 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2348 | |||
| 2349 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2350 | |||
| 2351 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2352 | |||
| 2353 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2354 | |||
| 2355 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2356 | |||
| 2357 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2358 | |||
| 2359 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2360 | |||
| 2361 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2362 | |||
| 2363 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2364 | |||
| 2365 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2366 | |||
| 2367 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2368 | |||
| 2369 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2370 | |||
| 2371 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2372 | |||
| 2373 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2374 | |||
| 2375 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2376 | |||
| 2377 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2378 | |||
| 2379 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2380 | |||
| 2381 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2382 | |||
| 2383 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2384 | |||
| 2385 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2386 | |||
| 2387 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2388 | |||
| 2389 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2390 | |||
| 2391 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2392 | |||
| 2393 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2394 | |||
| 2395 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2396 | |||
| 2397 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2398 | |||
| 2399 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2400 | |||
| 2401 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2402 | |||
| 2403 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2404 | |||
| 2405 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2406 | |||
| 2407 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2408 | |||
| 2409 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2410 | |||
| 2411 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2412 | |||
| 2413 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2414 | |||
| 2415 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2416 | |||
| 2417 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2418 | |||
| 2419 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2420 | |||
| 2421 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2422 | |||
| 2423 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2424 | |||
| 2425 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2426 | |||
| 2427 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2428 | |||
| 2429 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2430 | |||
| 2431 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2432 | |||
| 2433 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2434 | |||
| 2435 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2436 | |||
| 2437 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2438 | |||
| 2439 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2440 | |||
| 2441 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2442 | |||
| 2443 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2444 | |||
| 2445 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2446 | |||
| 2447 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2448 | |||
| 2449 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2450 | |||
| 2451 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2452 | |||
| 2453 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2454 | |||
| 2455 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2456 | |||
| 2457 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2458 | |||
| 2459 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2460 | |||
| 2461 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2462 | |||
| 2463 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2464 | |||
| 2465 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2466 | |||
| 2467 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2468 | |||
| 2469 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2470 | |||
| 2471 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2472 | |||
| 2473 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2474 | |||
| 2475 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2476 | |||
| 2477 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2478 | |||
| 2479 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2480 | |||
| 2481 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2482 | |||
| 2483 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2484 | |||
| 2485 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2486 | |||
| 2487 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2488 | |||
| 2489 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2490 | |||
| 2491 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2492 | |||
| 2493 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2494 | |||
| 2495 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2496 | |||
| 2497 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2498 | |||
| 2499 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2500 | |||
| 2501 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2502 | |||
| 2503 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2504 | |||
| 2505 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2506 | |||
| 2507 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2508 | |||
| 2509 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2510 | |||
| 2511 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2512 | |||
| 2513 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2514 | |||
| 2515 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2516 | |||
| 2517 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2518 | |||
| 2519 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2520 | |||
| 2521 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2522 | |||
| 2523 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2524 | |||
| 2525 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2526 | |||
| 2527 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2528 | |||
| 2529 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2530 | |||
| 2531 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2532 | |||
| 2533 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2534 | |||
| 2535 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2536 | |||
| 2537 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2538 | |||
| 2539 | SALIGN_____> adding the next group to the alignment; iteration 1 |
||
| 2540 | |||
| 2541 | |||
| 2542 | |||
| 2543 | ```python |
||
| 2544 | %%bash |
||
| 2545 | cat seq/uni_ids |
||
| 2546 | cat seq/_how_to |
||
| 2547 | ``` |
||
| 2548 | |||
| 2549 | COX1_HUMAN |
||
| 2550 | COX2_HUMAN |
||
| 2551 | COX3_HUMAN |
||
| 2552 | COX41_HUMAN |
||
| 2553 | COX42_HUMAN |
||
| 2554 | COX5A_HUMAN |
||
| 2555 | COX5B_HUMAN |
||
| 2556 | CX6A1_HUMAN |
||
| 2557 | CX6A2_HUMAN |
||
| 2558 | CX6B1_HUMAN |
||
| 2559 | CX6B2_HUMAN |
||
| 2560 | COX6C_HUMAN |
||
| 2561 | CX7A1_HUMAN |
||
| 2562 | CX7A2_HUMAN |
||
| 2563 | COX7S_HUMAN |
||
| 2564 | COX7B_HUMAN |
||
| 2565 | COX7C_HUMAN |
||
| 2566 | COX7R_HUMAN |
||
| 2567 | COX8A_HUMAN |
||
| 2568 | COX8C_HUMAN |
||
| 2569 | |||
| 2570 | |||
| 2571 | cat uni_ids | parallel --gnu "wget http://www.uniprot.org/uniprot/?query={1}\&sort=score\&columns=id\&format=tab -O {1}.txt"
|
||
| 2572 | cat C*txt | grep -v Ent > uni_acc |
||
| 2573 | cat uni_acc | parallel --gnu "wget http://www.uniprot.org/uniprot/{1}.fasta"
|
||
| 2574 | |||
| 2575 | |||
| 2576 | |||
| 2577 | |||
| 2578 | ```python |
||
| 2579 | from Bio import pairwise2 |
||
| 2580 | from Bio import SeqIO |
||
| 2581 | from Bio.SubsMat import MatrixInfo as matlist |
||
| 2582 | matrix = matlist.blosum62 |
||
| 2583 | gap_open = -10 |
||
| 2584 | gap_extend = -5.50 |
||
| 2585 | ``` |
||
| 2586 | |||
| 2587 | |||
| 2588 | ```python |
||
| 2589 | alighs={}
|
||
| 2590 | struct='' |
||
| 2591 | models='' |
||
| 2592 | for c in chains: |
||
| 2593 | m = modeller.model(env, file='1v55.pdb', model_segment=('FIRST:'+c, 'LAST:'+c))
|
||
| 2594 | mseq=''.join(map(lambda x: x.code, m.residues)) |
||
| 2595 | seq=SeqIO.read('seq/'+result[c]+'.fasta','fasta')
|
||
| 2596 | alns = pairwise2.align.globalds(mseq, seq.seq.tostring() , matrix, gap_open, gap_extend) |
||
| 2597 | a_mseq, a_seq, score, begin, end = alns[0] |
||
| 2598 | #print '>%s-%s %s\n%s\n%s\n' % (c,result[c],score, a_mseq,a_seq) |
||
| 2599 | #print a_mseq+'\n'+a_seq |
||
| 2600 | struct+=a_mseq+'/\n' |
||
| 2601 | models+=a_seq+'/\n' |
||
| 2602 | #break |
||
| 2603 | |||
| 2604 | |||
| 2605 | print '>P1;1v55_P \nstructureX:1v55.pdb: :A: :M:: 1.90: 0.20' |
||
| 2606 | print struct+struct[:-2]+'*' |
||
| 2607 | print '>P1;9913\nsequence:: : : : :::-1.00:-1.00' |
||
| 2608 | print models+models[:-2]+'*' |
||
| 2609 | ``` |
||
| 2610 | |||
| 2611 | >P1;1v55_P |
||
| 2612 | structureX:1v55.pdb: :A: :M:: 1.90: 0.20 |
||
| 2613 | -FINRWLFSTNHKDIGTLYLLFGAWAGMVGTALSLLIRAELGQPGTLLGDDQIYNVVVTAHAFVMIFFMVMPIMIGGFGNWLVPLMIGAPDMAFPRMNNMSFWLLPPSFLLLLASSMVEAGAGTGWTVYPPLAGNLAHAGASVDLTIFSLHLAGVSSILGAINFITTIINMKPPAMSQYQTPLFVWSVMITAVLLLLSLPVLAAGITMLLTDRNLNTTFFDPAGGGDPILYQHLFWFFGHPEVYILILPGFGMISHIVTYYSGKKEPFGYMGMVWAMMSIGFLGFIVWAHHMFTVGMDVDTRAYFTSATMIIAIPTGVKVFSWLATLHGGNIKWSPAMMWALGFIFLFTVGGLTGIVLANSSLDIVLHDTYYVVAHFHYVLSMGAVFAIMGGFVHWFPLFSGYTLNDTWAKIHFAIMFVGVNMTFFPQHFLGLSGMPRRYSDYPDAYTMWNTISSMGSFISLTAVMLMVFIIWEAFASKREVLTVDLTTTNLEWLNGCPPPYHTFEEPTYVNLK/ |
||
| 2614 | -AYPMQLGFQDATSPIMEELLHFHDHTLMIVFLISSLVLYIISLMLTTKLTHTSTMDAQEVETIWTILPAIILILIALPSLRILYMMDEINNPSLTVKTMGHQWYWSYEYTDYEDLSFDSYMIPTSELKPGELRLLEVDNRVVLPMEMTIRMLVSSEDVLHSWAVPSLGLKTDAIPGRLNQTTLMSSRPGLYYGQCSEICGSNHSFMPIVLELVPLKYFEKWSASML/ |
||
| 2615 | --HQTHAYHMVNPSPWPLTGALSALLMTSGLTMWFHFNSMTLLMIGLTTNMLTMYQWWRDVIRESTFQGHHTPAVQKGLRYGMILFIISEVLFFTGFFWAFYHSSLAPTPELGGCWPPTGIHPLNPLEVPLLNTSVLLASGVSITWAHHSLMEGDRKHMLQALFITITLGVYFTLLQASEYYEAPFTISDGVYGSTFFVATGFHGLHVIIGSTFLIVCFFRQLKFHFTSNHHFGFEAAAWYWHFVDVVWLFLYVSIYWWGS/ |
||
| 2616 | -------------------------SVVKSEDYALPSYVDRRDYPLPDVAHVKNLSASQKALKEKEKASWSSLSIDEKVELYRLKFKESFAEMNRSTNEWKTVVGAAMFFIGFTALLLIWEKHYVYGPIPHTFEEEWVAKQTKRMLDMKVAPIQGFSAKWDYDKNEWKK/ |
||
| 2617 | ------------------------------------------H---ETDEEFDARWVTYFNKPDIDAWELRKGMNTLVGYDLVPEPKIIDAALRACRRLNDFASAVRILEVVKDKAGPHKEIYPYVIQELRPTLNELGISTPEELGLDKV/ |
||
| 2618 | -------------------------------ASGGGVPTDEEQATGLEREVMLAARKGQDPYNILAPKATSGTKEDPNLVPSITNKRIVGCICEEDNSTVIWFWLHKGEAQRCPSCGTHYKLVPHQLAH/ |
||
| 2619 | ------------ASAAKGDHGG-GARTWRFLTFGLALPSVALCTLNSWLHSGHRERPAFIPYHHLRIRTKPFSWGDGNHTFFHNPRVNPLPTGYEK-/ |
||
| 2620 | -------KIKNYQTAPFDSRFPNQNQTRNCWQNYLDFHRCEKAMTAKGGDVSVCEWYRRVYKSLCPISWVSTWDDRRAEGTFPGKI/ |
||
| 2621 | TA---LAKPQMRGLLARRLRFHIVGAFMVSLGFATFYKFAVAEKRKKAYADFYRNYDSMKDFEEMRKAGIFQSAK/ |
||
| 2622 | ---------------------FENRVAEKQKLFQEDNGLPVHLKGGATDNILYRVTMTLCLGGTLYSLYCLGWASFPHK/ |
||
| 2623 | -----------------------------APDFHDKYGNAVLASGATFCVAVWVYMATQIGIEWNPSPVGRVTPKEWR--/ |
||
| 2624 | -----------------HYEEGPGKNIPFSVENKWRLLAMMTLFFGSGFAAPFFIVRHQLLKK/ |
||
| 2625 | -----------IT--AK----P-AKTPTSP---K----EQAIGLSVTFLSFLLPAGWVLYHLDNYKK-S/ |
||
| 2626 | -FINRWLFSTNHKDIGTLYLLFGAWAGMVGTALSLLIRAELGQPGTLLGDDQIYNVVVTAHAFVMIFFMVMPIMIGGFGNWLVPLMIGAPDMAFPRMNNMSFWLLPPSFLLLLASSMVEAGAGTGWTVYPPLAGNLAHAGASVDLTIFSLHLAGVSSILGAINFITTIINMKPPAMSQYQTPLFVWSVMITAVLLLLSLPVLAAGITMLLTDRNLNTTFFDPAGGGDPILYQHLFWFFGHPEVYILILPGFGMISHIVTYYSGKKEPFGYMGMVWAMMSIGFLGFIVWAHHMFTVGMDVDTRAYFTSATMIIAIPTGVKVFSWLATLHGGNIKWSPAMMWALGFIFLFTVGGLTGIVLANSSLDIVLHDTYYVVAHFHYVLSMGAVFAIMGGFVHWFPLFSGYTLNDTWAKIHFAIMFVGVNMTFFPQHFLGLSGMPRRYSDYPDAYTMWNTISSMGSFISLTAVMLMVFIIWEAFASKREVLTVDLTTTNLEWLNGCPPPYHTFEEPTYVNLK/ |
||
| 2627 | -AYPMQLGFQDATSPIMEELLHFHDHTLMIVFLISSLVLYIISLMLTTKLTHTSTMDAQEVETIWTILPAIILILIALPSLRILYMMDEINNPSLTVKTMGHQWYWSYEYTDYEDLSFDSYMIPTSELKPGELRLLEVDNRVVLPMEMTIRMLVSSEDVLHSWAVPSLGLKTDAIPGRLNQTTLMSSRPGLYYGQCSEICGSNHSFMPIVLELVPLKYFEKWSASML/ |
||
| 2628 | --HQTHAYHMVNPSPWPLTGALSALLMTSGLTMWFHFNSMTLLMIGLTTNMLTMYQWWRDVIRESTFQGHHTPAVQKGLRYGMILFIISEVLFFTGFFWAFYHSSLAPTPELGGCWPPTGIHPLNPLEVPLLNTSVLLASGVSITWAHHSLMEGDRKHMLQALFITITLGVYFTLLQASEYYEAPFTISDGVYGSTFFVATGFHGLHVIIGSTFLIVCFFRQLKFHFTSNHHFGFEAAAWYWHFVDVVWLFLYVSIYWWGS/ |
||
| 2629 | -------------------------SVVKSEDYALPSYVDRRDYPLPDVAHVKNLSASQKALKEKEKASWSSLSIDEKVELYRLKFKESFAEMNRSTNEWKTVVGAAMFFIGFTALLLIWEKHYVYGPIPHTFEEEWVAKQTKRMLDMKVAPIQGFSAKWDYDKNEWKK/ |
||
| 2630 | ------------------------------------------H---ETDEEFDARWVTYFNKPDIDAWELRKGMNTLVGYDLVPEPKIIDAALRACRRLNDFASAVRILEVVKDKAGPHKEIYPYVIQELRPTLNELGISTPEELGLDKV/ |
||
| 2631 | -------------------------------ASGGGVPTDEEQATGLEREVMLAARKGQDPYNILAPKATSGTKEDPNLVPSITNKRIVGCICEEDNSTVIWFWLHKGEAQRCPSCGTHYKLVPHQLAH/ |
||
| 2632 | ------------ASAAKGDHGG-GARTWRFLTFGLALPSVALCTLNSWLHSGHRERPAFIPYHHLRIRTKPFSWGDGNHTFFHNPRVNPLPTGYEK-/ |
||
| 2633 | -------KIKNYQTAPFDSRFPNQNQTRNCWQNYLDFHRCEKAMTAKGGDVSVCEWYRRVYKSLCPISWVSTWDDRRAEGTFPGKI/ |
||
| 2634 | TA---LAKPQMRGLLARRLRFHIVGAFMVSLGFATFYKFAVAEKRKKAYADFYRNYDSMKDFEEMRKAGIFQSAK/ |
||
| 2635 | ---------------------FENRVAEKQKLFQEDNGLPVHLKGGATDNILYRVTMTLCLGGTLYSLYCLGWASFPHK/ |
||
| 2636 | -----------------------------APDFHDKYGNAVLASGATFCVAVWVYMATQIGIEWNPSPVGRVTPKEWR--/ |
||
| 2637 | -----------------HYEEGPGKNIPFSVENKWRLLAMMTLFFGSGFAAPFFIVRHQLLKK/ |
||
| 2638 | -----------IT--AK----P-AKTPTSP---K----EQAIGLSVTFLSFLLPAGWVLYHLDNYKK-S* |
||
| 2639 | >P1;9913 |
||
| 2640 | sequence:: : : : :::-1.00:-1.00 |
||
| 2641 | MFADRWLFSTNHKDIGTLYLLFGAWAGVLGTALSLLIRAELGQPGNLLGNDHIYNVIVTAHAFVMIFFMVMPIMIGGFGNWLVPLMIGAPDMAFPRMNNMSFWLLPPSLLLLLASAMVEAGAGTGWTVYPPLAGNYSHPGASVDLTIFSLHLAGVSSILGAINFITTIINMKPPAMTQYQTPLFVWSVLITAVLLLLSLPVLAAGITMLLTDRNLNTTFFDPAGGGDPILYQHLFWFFGHPEVYILILPGFGMISHIVTYYSGKKEPFGYMGMVWAMMSIGFLGFIVWAHHMFTVGMDVDTRAYFTSATMIIAIPTGVKVFSWLATLHGSNMKWSAAVLWALGFIFLFTVGGLTGIVLANSSLDIVLHDTYYVVAHFHYVLSMGAVFAIMGGFIHWFPLFSGYTLDQTYAKIHFTIMFIGVNLTFFPQHFLGLSGMPRRYSDYPDAYTTWNILSSVGSFISLTAVMLMIFMIWEAFASKRKVLMVEEPSMNLEWLYGCPPPYHTFEEPVYMK-S/ |
||
| 2642 | MAHAAQVGLQDATSPIMEELITFHDHALMIIFLICFLVLYALFLTLTTKLTNTNISDAQEMETVWTILPAIILVLIALPSLRILYMTDEVNDPSLTIKSIGHQWYWTYEYTDYGGLIFNSYMLPPLFLEPGDLRLLDVDNRVVLPIEAPIRMMITSQDVLHSWAVPTLGLKTDAIPGRLNQTTFTATRPGVYYGQCSEICGANHSFMPIVLELIPLKIFEMGPVFTL/ |
||
| 2643 | MTHQSHAYHMVKPSPWPLTGALSALLMTSGLAMWFHFHSMTLLMLGLLTNTLTMYQWWRDVTRESTYQGHHTPPVQKGLRYGMILFITSEVFFFAGFFWAFYHSSLAPTPQLGGHWPPTGITPLNPLEVPLLNTSVLLASGVSITWAHHSLMENNRNQMIQALLITILLGLYFTLLQASEYFESPFTISDGIYGSTFFVATGFHGLHVIIGSTFLTICFIRQLMFHFTSKHHFGFEAAAWYWHFVDVVWLFLYVSIYWWGS/ |
||
| 2644 | MLATRVFSLVGKRAISTSVCVRAHESVVKSEDFSLPAYMDRRDHPLPEVAHVKHLSASQKALKEKEKASWSSLSMDEKVELYRIKFKESFAEMNRGSNEWKTVVGGAMFFIGFTALVIMWQKHYVYGPLPQSFDKEWVAKQTKRMLDMKVNPIQGLASKWDYEKNEWKK/ |
||
| 2645 | MLGAALRRCAVAATTRADPRGLLHSARTPGPAVAIQSVRCYSHGSQETDEEFDARWVTYFNKPDIDAWELRKGINTLVTYDMVPEPKIIDAALRACRRLNDFASTVRILEVVKDKAGPHKEIYPYVIQELRPTLNELGISTPEELGLDKV/ |
||
| 2646 | MASRLLRGAGTLAAQALRARGPSGAAAMRSMASGGGVPTDEEQATGLEREIMLAAKKGLDPYNVLAPKGASGTREDPNLVPSISNKRIVGCICEEDNTSVVWFWLHKGEAQRCPRCGAHYKLVPQQLAH/ |
||
| 2647 | MALPLRPLTRGLASAAKGGHGGAGARTWRLLTFVLALPSVALCTFNSYLHSGHRPRPEFRPYQHLRIRTKPYPWGDGNHTLFHNSHVNPLPTGYEHP/ |
||
| 2648 | MAEDMETKIKNYKTAPFDSRFPNQNQTRNCWQNYLDFHRCQKAMTAKGGDISVCEWYQRVYQSLCPTSWVTDWDEQRAEGTFPGKI/ |
||
| 2649 | MAPEVLPKPRMRGLLARRLRNHMAVAFVLSLGVAALYKFRVADQRKKAYADFYRNYDVMKDFEEMRKAGIFQSVK/ |
||
| 2650 | MQALRVSQALIRSFSSTARNRFQNRVREKQKLFQEDNDIPLYLKGGIVDNILYRVTMTLCLGGTVYSLYSLGWASFPRN/ |
||
| 2651 | MFPLVKSALNRLQVRSIQQTMARQSHQKRTPDFHDKYGNAVLASGATFCIVTWTYVATQVGIEWNLSPVGRVTPKEWRNQ/ |
||
| 2652 | MLGQSIRRFTTSVVRRSHYEEGPGKNLPFSVENKWSLLAKMCLYFGSAFATPFLVVRHQLLKT/ |
||
| 2653 | MSVLTPLLLRGLTGSARRLPVPRAKIHSLPPEGKLGIMELAVGLTSCFVTFLLPAGWILSHLETYRRPE/ |
||
| 2654 | MFADRWLFSTNHKDIGTLYLLFGAWAGVLGTALSLLIRAELGQPGNLLGNDHIYNVIVTAHAFVMIFFMVMPIMIGGFGNWLVPLMIGAPDMAFPRMNNMSFWLLPPSLLLLLASAMVEAGAGTGWTVYPPLAGNYSHPGASVDLTIFSLHLAGVSSILGAINFITTIINMKPPAMTQYQTPLFVWSVLITAVLLLLSLPVLAAGITMLLTDRNLNTTFFDPAGGGDPILYQHLFWFFGHPEVYILILPGFGMISHIVTYYSGKKEPFGYMGMVWAMMSIGFLGFIVWAHHMFTVGMDVDTRAYFTSATMIIAIPTGVKVFSWLATLHGSNMKWSAAVLWALGFIFLFTVGGLTGIVLANSSLDIVLHDTYYVVAHFHYVLSMGAVFAIMGGFIHWFPLFSGYTLDQTYAKIHFTIMFIGVNLTFFPQHFLGLSGMPRRYSDYPDAYTTWNILSSVGSFISLTAVMLMIFMIWEAFASKRKVLMVEEPSMNLEWLYGCPPPYHTFEEPVYMK-S/ |
||
| 2655 | MAHAAQVGLQDATSPIMEELITFHDHALMIIFLICFLVLYALFLTLTTKLTNTNISDAQEMETVWTILPAIILVLIALPSLRILYMTDEVNDPSLTIKSIGHQWYWTYEYTDYGGLIFNSYMLPPLFLEPGDLRLLDVDNRVVLPIEAPIRMMITSQDVLHSWAVPTLGLKTDAIPGRLNQTTFTATRPGVYYGQCSEICGANHSFMPIVLELIPLKIFEMGPVFTL/ |
||
| 2656 | MTHQSHAYHMVKPSPWPLTGALSALLMTSGLAMWFHFHSMTLLMLGLLTNTLTMYQWWRDVTRESTYQGHHTPPVQKGLRYGMILFITSEVFFFAGFFWAFYHSSLAPTPQLGGHWPPTGITPLNPLEVPLLNTSVLLASGVSITWAHHSLMENNRNQMIQALLITILLGLYFTLLQASEYFESPFTISDGIYGSTFFVATGFHGLHVIIGSTFLTICFIRQLMFHFTSKHHFGFEAAAWYWHFVDVVWLFLYVSIYWWGS/ |
||
| 2657 | MLATRVFSLVGKRAISTSVCVRAHESVVKSEDFSLPAYMDRRDHPLPEVAHVKHLSASQKALKEKEKASWSSLSMDEKVELYRIKFKESFAEMNRGSNEWKTVVGGAMFFIGFTALVIMWQKHYVYGPLPQSFDKEWVAKQTKRMLDMKVNPIQGLASKWDYEKNEWKK/ |
||
| 2658 | MLGAALRRCAVAATTRADPRGLLHSARTPGPAVAIQSVRCYSHGSQETDEEFDARWVTYFNKPDIDAWELRKGINTLVTYDMVPEPKIIDAALRACRRLNDFASTVRILEVVKDKAGPHKEIYPYVIQELRPTLNELGISTPEELGLDKV/ |
||
| 2659 | MASRLLRGAGTLAAQALRARGPSGAAAMRSMASGGGVPTDEEQATGLEREIMLAAKKGLDPYNVLAPKGASGTREDPNLVPSISNKRIVGCICEEDNTSVVWFWLHKGEAQRCPRCGAHYKLVPQQLAH/ |
||
| 2660 | MALPLRPLTRGLASAAKGGHGGAGARTWRLLTFVLALPSVALCTFNSYLHSGHRPRPEFRPYQHLRIRTKPYPWGDGNHTLFHNSHVNPLPTGYEHP/ |
||
| 2661 | MAEDMETKIKNYKTAPFDSRFPNQNQTRNCWQNYLDFHRCQKAMTAKGGDISVCEWYQRVYQSLCPTSWVTDWDEQRAEGTFPGKI/ |
||
| 2662 | MAPEVLPKPRMRGLLARRLRNHMAVAFVLSLGVAALYKFRVADQRKKAYADFYRNYDVMKDFEEMRKAGIFQSVK/ |
||
| 2663 | MQALRVSQALIRSFSSTARNRFQNRVREKQKLFQEDNDIPLYLKGGIVDNILYRVTMTLCLGGTVYSLYSLGWASFPRN/ |
||
| 2664 | MFPLVKSALNRLQVRSIQQTMARQSHQKRTPDFHDKYGNAVLASGATFCIVTWTYVATQVGIEWNLSPVGRVTPKEWRNQ/ |
||
| 2665 | MLGQSIRRFTTSVVRRSHYEEGPGKNLPFSVENKWSLLAKMCLYFGSAFATPFLVVRHQLLKT/ |
||
| 2666 | MSVLTPLLLRGLTGSARRLPVPRAKIHSLPPEGKLGIMELAVGLTSCFVTFLLPAGWILSHLETYRRPE* |
||
| 2667 | |||
| 2668 | |||
| 2669 | |||
| 2670 | ```python |
||
| 2671 | a = modeller.automodel.automodel(env, alnfile='big_one.ali', knowns= ('1v55'), sequence = '9606' )
|
||
| 2672 | a.name='mod9606' |
||
| 2673 | a.starting_model = 1 |
||
| 2674 | a.ending_model = 1 |
||
| 2675 | a.make() |
||
| 2676 | |||
| 2677 | |||
| 2678 | ``` |
||
| 2679 | |||
| 2680 | |||
| 2681 | check_ali___> Checking the sequence-structure alignment. |
||
| 2682 | |||
| 2683 | Implied target CA(i)-CA(i+1) distances longer than 8.0 angstroms: |
||
| 2684 | |||
| 2685 | ALN_POS TMPL RID1 RID2 NAM1 NAM2 DIST |
||
| 2686 | ---------------------------------------------- |
||
| 2687 | END OF TABLE |
||
| 2688 | read_to_681_> topology.submodel read from topology file: 3 |
||
| 2689 | |||
| 2690 | getf_______W> RTF restraint not found in the atoms list: |
||
| 2691 | residue type, indices: 16 513 |
||
| 2692 | atom names : C +N |
||
| 2693 | atom indices : 4027 0 |
||
| 2694 | |||
| 2695 | getf_______W> RTF restraint not found in the atoms list: |
||
| 2696 | residue type, indices: 16 513 |
||
| 2697 | atom names : C CA +N O |
||
| 2698 | atom indices : 4027 4024 0 4028 |
||
| 2699 | |||
| 2700 | getf_______W> RTF restraint not found in the atoms list: |
||
| 2701 | residue type, indices: 10 740 |
||
| 2702 | atom names : C +N |
||
| 2703 | atom indices : 5825 0 |
||
| 2704 | |||
| 2705 | getf_______W> RTF restraint not found in the atoms list: |
||
| 2706 | residue type, indices: 10 740 |
||
| 2707 | atom names : C CA +N O |
||
| 2708 | atom indices : 5825 5820 0 5826 |
||
| 2709 | |||
| 2710 | getf_______W> RTF restraint not found in the atoms list: |
||
| 2711 | residue type, indices: 16 1001 |
||
| 2712 | atom names : C +N |
||
| 2713 | atom indices : 7952 0 |
||
| 2714 | |||
| 2715 | getf_______W> RTF restraint not found in the atoms list: |
||
| 2716 | residue type, indices: 16 1001 |
||
| 2717 | atom names : C CA +N O |
||
| 2718 | atom indices : 7952 7949 0 7953 |
||
| 2719 | |||
| 2720 | getf_______W> RTF restraint not found in the atoms list: |
||
| 2721 | residue type, indices: 9 1170 |
||
| 2722 | atom names : C +N |
||
| 2723 | atom indices : 9330 0 |
||
| 2724 | |||
| 2725 | getf_______W> RTF restraint not found in the atoms list: |
||
| 2726 | residue type, indices: 9 1170 |
||
| 2727 | atom names : C CA +N O |
||
| 2728 | atom indices : 9330 9324 0 9331 |
||
| 2729 | |||
| 2730 | getf_______W> RTF restraint not found in the atoms list: |
||
| 2731 | residue type, indices: 18 1320 |
||
| 2732 | atom names : C +N |
||
| 2733 | atom indices : 10509 0 |
||
| 2734 | |||
| 2735 | getf_______W> RTF restraint not found in the atoms list: |
||
| 2736 | residue type, indices: 18 1320 |
||
| 2737 | atom names : C CA +N O |
||
| 2738 | atom indices : 10509 10505 0 10510 |
||
| 2739 | |||
| 2740 | getf_______W> RTF restraint not found in the atoms list: |
||
| 2741 | residue type, indices: 7 1449 |
||
| 2742 | atom names : C +N |
||
| 2743 | atom indices : 11466 0 |
||
| 2744 | |||
| 2745 | getf_______W> RTF restraint not found in the atoms list: |
||
| 2746 | residue type, indices: 7 1449 |
||
| 2747 | atom names : C CA +N O |
||
| 2748 | atom indices : 11466 11459 0 11467 |
||
| 2749 | |||
| 2750 | getf_______W> RTF restraint not found in the atoms list: |
||
| 2751 | residue type, indices: 13 1546 |
||
| 2752 | atom names : C +N |
||
| 2753 | atom indices : 12234 0 |
||
| 2754 | |||
| 2755 | getf_______W> RTF restraint not found in the atoms list: |
||
| 2756 | residue type, indices: 13 1546 |
||
| 2757 | atom names : C CA +N O |
||
| 2758 | atom indices : 12234 12230 0 12235 |
||
| 2759 | |||
| 2760 | getf_______W> RTF restraint not found in the atoms list: |
||
| 2761 | residue type, indices: 8 1632 |
||
| 2762 | atom names : C +N |
||
| 2763 | atom indices : 12949 0 |
||
| 2764 | |||
| 2765 | getf_______W> RTF restraint not found in the atoms list: |
||
| 2766 | residue type, indices: 8 1632 |
||
| 2767 | atom names : C CA +N O |
||
| 2768 | atom indices : 12949 12944 0 12950 |
||
| 2769 | |||
| 2770 | getf_______W> RTF restraint not found in the atoms list: |
||
| 2771 | residue type, indices: 9 1707 |
||
| 2772 | atom names : C +N |
||
| 2773 | atom indices : 13566 0 |
||
| 2774 | |||
| 2775 | getf_______W> RTF restraint not found in the atoms list: |
||
| 2776 | residue type, indices: 9 1707 |
||
| 2777 | atom names : C CA +N O |
||
| 2778 | atom indices : 13566 13560 0 13567 |
||
| 2779 | |||
| 2780 | getf_______W> RTF restraint not found in the atoms list: |
||
| 2781 | residue type, indices: 12 1786 |
||
| 2782 | atom names : C +N |
||
| 2783 | atom indices : 14208 0 |
||
| 2784 | |||
| 2785 | getf_______W> RTF restraint not found in the atoms list: |
||
| 2786 | residue type, indices: 12 1786 |
||
| 2787 | atom names : C CA +N O |
||
| 2788 | atom indices : 14208 14203 0 14209 |
||
| 2789 | |||
| 2790 | getf_______W> RTF restraint not found in the atoms list: |
||
| 2791 | residue type, indices: 14 1866 |
||
| 2792 | atom names : C +N |
||
| 2793 | atom indices : 14854 0 |
||
| 2794 | |||
| 2795 | getf_______W> RTF restraint not found in the atoms list: |
||
| 2796 | residue type, indices: 14 1866 |
||
| 2797 | atom names : C CA +N O |
||
| 2798 | atom indices : 14854 14848 0 14855 |
||
| 2799 | |||
| 2800 | getf_______W> RTF restraint not found in the atoms list: |
||
| 2801 | residue type, indices: 17 1929 |
||
| 2802 | atom names : C +N |
||
| 2803 | atom indices : 15365 0 |
||
| 2804 | |||
| 2805 | getf_______W> RTF restraint not found in the atoms list: |
||
| 2806 | residue type, indices: 17 1929 |
||
| 2807 | atom names : C CA +N O |
||
| 2808 | atom indices : 15365 15361 0 15366 |
||
| 2809 | |||
| 2810 | getf_______W> RTF restraint not found in the atoms list: |
||
| 2811 | residue type, indices: 4 1998 |
||
| 2812 | atom names : C +N |
||
| 2813 | atom indices : 15898 0 |
||
| 2814 | |||
| 2815 | getf_______W> RTF restraint not found in the atoms list: |
||
| 2816 | residue type, indices: 4 1998 |
||
| 2817 | atom names : C CA +N O |
||
| 2818 | atom indices : 15898 15892 0 15899 |
||
| 2819 | |||
| 2820 | getf_______W> RTF restraint not found in the atoms list: |
||
| 2821 | residue type, indices: 16 2511 |
||
| 2822 | atom names : C +N |
||
| 2823 | atom indices : 19927 0 |
||
| 2824 | |||
| 2825 | getf_______W> RTF restraint not found in the atoms list: |
||
| 2826 | residue type, indices: 16 2511 |
||
| 2827 | atom names : C CA +N O |
||
| 2828 | atom indices : 19927 19924 0 19928 |
||
| 2829 | |||
| 2830 | getf_______W> RTF restraint not found in the atoms list: |
||
| 2831 | residue type, indices: 10 2738 |
||
| 2832 | atom names : C +N |
||
| 2833 | atom indices : 21725 0 |
||
| 2834 | |||
| 2835 | getf_______W> RTF restraint not found in the atoms list: |
||
| 2836 | residue type, indices: 10 2738 |
||
| 2837 | atom names : C CA +N O |
||
| 2838 | atom indices : 21725 21720 0 21726 |
||
| 2839 | |||
| 2840 | getf_______W> RTF restraint not found in the atoms list: |
||
| 2841 | residue type, indices: 16 2999 |
||
| 2842 | atom names : C +N |
||
| 2843 | atom indices : 23852 0 |
||
| 2844 | |||
| 2845 | getf_______W> RTF restraint not found in the atoms list: |
||
| 2846 | residue type, indices: 16 2999 |
||
| 2847 | atom names : C CA +N O |
||
| 2848 | atom indices : 23852 23849 0 23853 |
||
| 2849 | |||
| 2850 | getf_______W> RTF restraint not found in the atoms list: |
||
| 2851 | residue type, indices: 9 3168 |
||
| 2852 | atom names : C +N |
||
| 2853 | atom indices : 25230 0 |
||
| 2854 | |||
| 2855 | getf_______W> RTF restraint not found in the atoms list: |
||
| 2856 | residue type, indices: 9 3168 |
||
| 2857 | atom names : C CA +N O |
||
| 2858 | atom indices : 25230 25224 0 25231 |
||
| 2859 | |||
| 2860 | getf_______W> RTF restraint not found in the atoms list: |
||
| 2861 | residue type, indices: 18 3318 |
||
| 2862 | atom names : C +N |
||
| 2863 | atom indices : 26409 0 |
||
| 2864 | |||
| 2865 | getf_______W> RTF restraint not found in the atoms list: |
||
| 2866 | residue type, indices: 18 3318 |
||
| 2867 | atom names : C CA +N O |
||
| 2868 | atom indices : 26409 26405 0 26410 |
||
| 2869 | |||
| 2870 | getf_______W> RTF restraint not found in the atoms list: |
||
| 2871 | residue type, indices: 7 3447 |
||
| 2872 | atom names : C +N |
||
| 2873 | atom indices : 27366 0 |
||
| 2874 | |||
| 2875 | getf_______W> RTF restraint not found in the atoms list: |
||
| 2876 | residue type, indices: 7 3447 |
||
| 2877 | atom names : C CA +N O |
||
| 2878 | atom indices : 27366 27359 0 27367 |
||
| 2879 | |||
| 2880 | getf_______W> RTF restraint not found in the atoms list: |
||
| 2881 | residue type, indices: 13 3544 |
||
| 2882 | atom names : C +N |
||
| 2883 | atom indices : 28134 0 |
||
| 2884 | |||
| 2885 | getf_______W> RTF restraint not found in the atoms list: |
||
| 2886 | residue type, indices: 13 3544 |
||
| 2887 | atom names : C CA +N O |
||
| 2888 | atom indices : 28134 28130 0 28135 |
||
| 2889 | |||
| 2890 | getf_______W> RTF restraint not found in the atoms list: |
||
| 2891 | residue type, indices: 8 3630 |
||
| 2892 | atom names : C +N |
||
| 2893 | atom indices : 28849 0 |
||
| 2894 | |||
| 2895 | getf_______W> RTF restraint not found in the atoms list: |
||
| 2896 | residue type, indices: 8 3630 |
||
| 2897 | atom names : C CA +N O |
||
| 2898 | atom indices : 28849 28844 0 28850 |
||
| 2899 | |||
| 2900 | getf_______W> RTF restraint not found in the atoms list: |
||
| 2901 | residue type, indices: 9 3705 |
||
| 2902 | atom names : C +N |
||
| 2903 | atom indices : 29466 0 |
||
| 2904 | |||
| 2905 | getf_______W> RTF restraint not found in the atoms list: |
||
| 2906 | residue type, indices: 9 3705 |
||
| 2907 | atom names : C CA +N O |
||
| 2908 | atom indices : 29466 29460 0 29467 |
||
| 2909 | |||
| 2910 | getf_______W> RTF restraint not found in the atoms list: |
||
| 2911 | residue type, indices: 12 3784 |
||
| 2912 | atom names : C +N |
||
| 2913 | atom indices : 30108 0 |
||
| 2914 | |||
| 2915 | getf_______W> RTF restraint not found in the atoms list: |
||
| 2916 | residue type, indices: 12 3784 |
||
| 2917 | atom names : C CA +N O |
||
| 2918 | atom indices : 30108 30103 0 30109 |
||
| 2919 | |||
| 2920 | getf_______W> RTF restraint not found in the atoms list: |
||
| 2921 | residue type, indices: 14 3864 |
||
| 2922 | atom names : C +N |
||
| 2923 | atom indices : 30754 0 |
||
| 2924 | |||
| 2925 | getf_______W> RTF restraint not found in the atoms list: |
||
| 2926 | residue type, indices: 14 3864 |
||
| 2927 | atom names : C CA +N O |
||
| 2928 | atom indices : 30754 30748 0 30755 |
||
| 2929 | |||
| 2930 | getf_______W> RTF restraint not found in the atoms list: |
||
| 2931 | residue type, indices: 17 3927 |
||
| 2932 | atom names : C +N |
||
| 2933 | atom indices : 31265 0 |
||
| 2934 | |||
| 2935 | getf_______W> RTF restraint not found in the atoms list: |
||
| 2936 | residue type, indices: 17 3927 |
||
| 2937 | atom names : C CA +N O |
||
| 2938 | atom indices : 31265 31261 0 31266 |
||
| 2939 | |||
| 2940 | getf_______W> RTF restraint not found in the atoms list: |
||
| 2941 | residue type, indices: 4 3996 |
||
| 2942 | atom names : C +N |
||
| 2943 | atom indices : 31798 0 |
||
| 2944 | |||
| 2945 | getf_______W> RTF restraint not found in the atoms list: |
||
| 2946 | residue type, indices: 4 3996 |
||
| 2947 | atom names : C CA +N O |
||
| 2948 | atom indices : 31798 31792 0 31799 |
||
| 2949 | The following 28 residues contain 6-membered rings with poor geometries |
||
| 2950 | after transfer from templates. Rebuilding rings from internal coordinates: |
||
| 2951 | <Residue 377:A (type PHE)> |
||
| 2952 | <Residue 502:A (type TYR)> |
||
| 2953 | <Residue 536:B (type PHE)> |
||
| 2954 | <Residue 618:B (type TYR)> |
||
| 2955 | <Residue 748:C (type TYR)> |
||
| 2956 | <Residue 775:C (type PHE)> |
||
| 2957 | <Residue 842:C (type TYR)> |
||
| 2958 | <Residue 943:C (type PHE)> |
||
| 2959 | <Residue 965:C (type PHE)> |
||
| 2960 | <Residue 1423:F (type PHE)> |
||
| 2961 | <Residue 1511:G (type TYR)> |
||
| 2962 | <Residue 1531:G (type PHE)> |
||
| 2963 | <Residue 1583:H (type PHE)> |
||
| 2964 | <Residue 1819:K (type PHE)> |
||
| 2965 | <Residue 2375:N (type PHE)> |
||
| 2966 | <Residue 2500:N (type TYR)> |
||
| 2967 | <Residue 2534:O (type PHE)> |
||
| 2968 | <Residue 2616:O (type TYR)> |
||
| 2969 | <Residue 2746:P (type TYR)> |
||
| 2970 | <Residue 2773:P (type PHE)> |
||
| 2971 | <Residue 2836:P (type PHE)> |
||
| 2972 | <Residue 2840:P (type TYR)> |
||
| 2973 | <Residue 2941:P (type PHE)> |
||
| 2974 | <Residue 2963:P (type PHE)> |
||
| 2975 | <Residue 3509:T (type TYR)> |
||
| 2976 | <Residue 3529:T (type PHE)> |
||
| 2977 | <Residue 3581:U (type PHE)> |
||
| 2978 | <Residue 3817:X (type PHE)> |
||
| 2979 | mdtrsr__446W> A potential that relies on one protein is used, yet you have at |
||
| 2980 | least one known structure available. MDT, not library, potential is used. |
||
| 2981 | 0 atoms in HETATM/BLK residues constrained |
||
| 2982 | to protein atoms within 2.30 angstroms |
||
| 2983 | and protein CA atoms within 10.00 angstroms |
||
| 2984 | 0 atoms in residues without defined topology |
||
| 2985 | constrained to be rigid bodies |
||
| 2986 | condens_443_> Restraints marked for deletion were removed. |
||
| 2987 | Total number of restraints before, now: 351583 322941 |
||
| 2988 | iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
||
| 2989 | iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
||
| 2990 | iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
||
| 2991 | iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
||
| 2992 | iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
||
| 2993 | iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
||
| 2994 | iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
||
| 2995 | iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
||
| 2996 | iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
||
| 2997 | iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
||
| 2998 | iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
||
| 2999 | iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
||
| 3000 | iupac_m_484W> Dihedral still outside +-90: -90.3017 |
||
| 3001 | iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
||
| 3002 | iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
||
| 3003 | iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
||
| 3004 | iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
||
| 3005 | iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
||
| 3006 | iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
||
| 3007 | iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
||
| 3008 | iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
||
| 3009 | iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
||
| 3010 | iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
||
| 3011 | iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
||
| 3012 | iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
||
| 3013 | iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
||
| 3014 | iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
||
| 3015 | iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
||
| 3016 | iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
||
| 3017 | iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
||
| 3018 | iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
||
| 3019 | iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
||
| 3020 | iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
||
| 3021 | iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
||
| 3022 | iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
||
| 3023 | iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
||
| 3024 | iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
||
| 3025 | iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
||
| 3026 | iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
||
| 3027 | iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
||
| 3028 | iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
||
| 3029 | iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
||
| 3030 | iupac_m_484W> Dihedral still outside +-90: 90.0671 |
||
| 3031 | iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
||
| 3032 | iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
||
| 3033 | iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
||
| 3034 | iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
||
| 3035 | iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
||
| 3036 | iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
||
| 3037 | iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
||
| 3038 | iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
||
| 3039 | iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
||
| 3040 | iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
||
| 3041 | iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. |
||
| 3042 | |||
| 3043 | |||
| 3044 | >> ENERGY; Differences between the model's features and restraints: |
||
| 3045 | Number of all residues in MODEL : 3996 |
||
| 3046 | Number of all, selected real atoms : 31800 31800 |
||
| 3047 | Number of all, selected pseudo atoms : 0 0 |
||
| 3048 | Number of all static, selected restraints : 322941 322941 |
||
| 3049 | COVALENT_CYS : F |
||
| 3050 | NONBONDED_SEL_ATOMS : 1 |
||
| 3051 | Number of non-bonded pairs (excluding 1-2,1-3,1-4): 79302 |
||
| 3052 | Dynamic pairs routine : 2, NATM x NATM cell sorting |
||
| 3053 | Atomic shift for contacts update (UPDATE_DYNAMIC) : 0.390 |
||
| 3054 | LENNARD_JONES_SWITCH : 6.500 7.500 |
||
| 3055 | COULOMB_JONES_SWITCH : 6.500 7.500 |
||
| 3056 | RESIDUE_SPAN_RANGE : 0 99999 |
||
| 3057 | NLOGN_USE : 15 |
||
| 3058 | CONTACT_SHELL : 4.000 |
||
| 3059 | DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER : T T F F F |
||
| 3060 | SPHERE_STDV : 0.050 |
||
| 3061 | RADII_FACTOR : 0.820 |
||
| 3062 | Current energy : 20600.9121 |
||
| 3063 | |||
| 3064 | |||
| 3065 | |||
| 3066 | |||
| 3067 | |||
| 3068 | Summary of the restraint violations: |
||
| 3069 | |||
| 3070 | NUM ... number of restraints. |
||
| 3071 | NUMVI ... number of restraints with RVIOL > VIOL_REPORT_CUT[i]. |
||
| 3072 | RVIOL ... relative difference from the best value. |
||
| 3073 | NUMVP ... number of restraints with -Ln(pdf) > VIOL_REPORT_CUT2[i]. |
||
| 3074 | RMS_1 ... RMS(feature, minimally_violated_basis_restraint, NUMB). |
||
| 3075 | RMS_2 ... RMS(feature, best_value, NUMB). |
||
| 3076 | MOL.PDF ... scaled contribution to -Ln(Molecular pdf). |
||
| 3077 | |||
| 3078 | # RESTRAINT_GROUP NUM NUMVI NUMVP RMS_1 RMS_2 MOL.PDF S_i |
||
| 3079 | ------------------------------------------------------------------------------------------------------ |
||
| 3080 | 1 Bond length potential : 32732 0 0 0.005 0.005 211.11 1.000 |
||
| 3081 | 2 Bond angle potential : 44520 6 85 2.036 2.036 3523.7 1.000 |
||
| 3082 | 3 Stereochemical cosine torsion poten: 22664 0 540 44.600 44.600 6718.7 1.000 |
||
| 3083 | 4 Stereochemical improper torsion pot: 14014 0 5 1.313 1.313 488.93 1.000 |
||
| 3084 | 5 Soft-sphere overlap restraints : 79302 0 4 0.004 0.004 165.31 1.000 |
||
| 3085 | 6 Lennard-Jones 6-12 potential : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 3086 | 7 Coulomb point-point electrostatic p: 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 3087 | 8 H-bonding potential : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 3088 | 9 Distance restraints 1 (CA-CA) : 85829 0 22 0.234 0.234 1590.4 1.000 |
||
| 3089 | 10 Distance restraints 2 (N-O) : 82391 7 149 0.319 0.319 2980.2 1.000 |
||
| 3090 | 11 Mainchain Phi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 3091 | 12 Mainchain Psi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 3092 | 13 Mainchain Omega dihedral restraints: 3970 10 38 8.050 8.050 781.51 1.000 |
||
| 3093 | 14 Sidechain Chi_1 dihedral restraints: 3402 0 52 82.119 82.119 1156.3 1.000 |
||
| 3094 | 15 Sidechain Chi_2 dihedral restraints: 2578 0 25 82.115 82.115 1012.2 1.000 |
||
| 3095 | 16 Sidechain Chi_3 dihedral restraints: 1030 0 1 76.972 76.972 624.68 1.000 |
||
| 3096 | 17 Sidechain Chi_4 dihedral restraints: 352 0 0 94.889 94.889 238.14 1.000 |
||
| 3097 | 18 Disulfide distance restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 3098 | 19 Disulfide angle restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 3099 | 20 Disulfide dihedral angle restraints: 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 3100 | 21 Lower bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 3101 | 22 Upper bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 3102 | 23 Distance restraints 3 (SDCH-MNCH) : 23111 0 0 0.297 0.297 236.76 1.000 |
||
| 3103 | 24 Sidechain Chi_5 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 3104 | 25 Phi/Psi pair of dihedral restraints: 3944 663 375 26.961 72.073 690.46 1.000 |
||
| 3105 | 26 Distance restraints 4 (SDCH-SDCH) : 2404 0 2 0.912 0.912 182.64 1.000 |
||
| 3106 | 27 Distance restraints 5 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 3107 | 28 NMR distance restraints 6 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 3108 | 29 NMR distance restraints 7 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 3109 | 30 Minimal distance restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 3110 | 31 Non-bonded restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 3111 | 32 Atomic accessibility restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 3112 | 33 Atomic density restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 3113 | 34 Absolute position restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 3114 | 35 Dihedral angle difference restraint: 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 3115 | 36 GBSA implicit solvent potential : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 3116 | 37 EM density fitting potential : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 3117 | 38 SAXS restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 3118 | 39 Symmetry restraints : 0 0 0 0.000 0.000 0.0000 1.000 |
||
| 3119 | |||
| 3120 | |||
| 3121 | |||
| 3122 | # Heavy relative violation of each residue is written to: 9606.V99990001 |
||
| 3123 | # The profile is NOT normalized by the number of restraints. |
||
| 3124 | # The profiles are smoothed over a window of residues: 1 |
||
| 3125 | # The sum of all numbers in the file: 452454.7812 |
||
| 3126 | |||
| 3127 | |||
| 3128 | |||
| 3129 | List of the violated restraints: |
||
| 3130 | A restraint is violated when the relative difference |
||
| 3131 | from the best value (RVIOL) is larger than CUTOFF. |
||
| 3132 | |||
| 3133 | ICSR ... index of a restraint in the current set. |
||
| 3134 | RESNO ... residue numbers of the first two atoms. |
||
| 3135 | ATM ... IUPAC atom names of the first two atoms. |
||
| 3136 | FEAT ... the value of the feature in the model. |
||
| 3137 | restr ... the mean of the basis restraint with the smallest |
||
| 3138 | difference from the model (local minimum). |
||
| 3139 | viol ... difference from the local minimum. |
||
| 3140 | rviol ... relative difference from the local minimum. |
||
| 3141 | RESTR ... the best value (global minimum). |
||
| 3142 | VIOL ... difference from the best value. |
||
| 3143 | RVIOL ... relative difference from the best value. |
||
| 3144 | |||
| 3145 | |||
| 3146 | ------------------------------------------------------------------------------------------------- |
||
| 3147 | |||
| 3148 | Feature 2 : Bond angle potential |
||
| 3149 | List of the RVIOL violations larger than : 4.5000 |
||
| 3150 | |||
| 3151 | # ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL |
||
| 3152 | 1 40535 702P 702P N CA 5526 5527 136.20 108.20 28.00 6.36 108.20 28.00 6.36 |
||
| 3153 | 2 43883 994V 994V N CA 7883 7884 122.88 107.00 15.88 4.57 107.00 15.88 4.57 |
||
| 3154 | 3 442111024A1024A N CA 8120 8121 122.76 107.00 15.76 4.53 107.00 15.76 4.53 |
||
| 3155 | 4 488911455R1455R N CA 1150511506 124.85 107.00 17.85 5.13 107.00 17.85 5.13 |
||
| 3156 | 5 554642042P2042P N CA 1623816239 130.79 108.20 22.59 5.13 108.20 22.59 5.13 |
||
| 3157 | 6 627952700P2700P N CA 2142621427 137.07 108.20 28.87 6.56 108.20 28.87 6.56 |
||
| 3158 | |||
| 3159 | ------------------------------------------------------------------------------------------------- |
||
| 3160 | |||
| 3161 | Feature 10 : Distance restraints 2 (N-O) |
||
| 3162 | List of the RVIOL violations larger than : 4.5000 |
||
| 3163 | |||
| 3164 | # ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL |
||
| 3165 | 1 215163 8F 753P N O 66 5935 7.47 5.01 2.46 4.58 5.01 2.46 4.58 |
||
| 3166 | 2 233054 668T 613I N O 5266 4811 7.01 4.69 2.33 4.64 4.69 2.33 4.64 |
||
| 3167 | 3 233078 669S 613I N O 5273 4811 6.13 3.04 3.09 6.31 3.04 3.09 6.31 |
||
| 3168 | 4 236370 793T 789T N O 6234 6210 5.42 3.00 2.41 4.60 3.00 2.41 4.60 |
||
| 3169 | 5 241249 996I 992L N O 7896 7870 5.88 3.39 2.49 4.79 3.39 2.49 4.79 |
||
| 3170 | 6 2867113273T3307I N O 2604526328 8.29 5.60 2.69 4.57 5.60 2.69 4.57 |
||
| 3171 | 7 2932583671V3666L N O 2917029126 5.54 3.19 2.35 4.90 3.19 2.35 4.90 |
||
| 3172 | |||
| 3173 | ------------------------------------------------------------------------------------------------- |
||
| 3174 | |||
| 3175 | Feature 13 : Mainchain Omega dihedral restraints |
||
| 3176 | List of the RVIOL violations larger than : 4.5000 |
||
| 3177 | |||
| 3178 | # ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL |
||
| 3179 | 1 118371 497G 497G CA C 3892 3893 -2.33 -179.18 176.85 41.10 -179.18 176.85 41.10 |
||
| 3180 | 2 118574 701R 701R CA C 5516 5524 -145.15 -180.00 34.85 6.97 -180.00 34.85 6.97 |
||
| 3181 | 3 118727 855H 855H CA C 6754 6761 0.35 -179.18 179.53 41.73 -179.18 179.53 41.73 |
||
| 3182 | 4 1199022041Q2041Q CA C 1623016236 -147.91 -180.00 32.09 6.42 -180.00 32.09 6.42 |
||
| 3183 | 5 1203562495G2495G CA C 1979219793 -1.32 -179.18 177.86 41.34 -179.18 177.86 41.34 |
||
| 3184 | 6 1205592699R2699R CA C 2141621424 -142.55 -180.00 37.45 7.49 -180.00 37.45 7.49 |
||
| 3185 | 7 1207122853H2853H CA C 2265422661 0.47 -179.18 179.66 41.75 -179.18 179.66 41.75 |
||
| 3186 | 8 1212183362A3362A CA C 2670526707 -156.37 -180.00 23.63 4.72 -180.00 23.63 4.72 |
||
| 3187 | 9 1217763926K3926K CA C 3125231258 -0.22 -179.18 178.97 41.59 -179.18 178.97 41.59 |
||
| 3188 | |||
| 3189 | ------------------------------------------------------------------------------------------------- |
||
| 3190 | |||
| 3191 | Feature 25 : Phi/Psi pair of dihedral restraints |
||
| 3192 | List of the RVIOL violations larger than : 6.5000 |
||
| 3193 | |||
| 3194 | # ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL |
||
| 3195 | 1 113945 15I 16G C N 131 133 -62.60 -62.40 0.61 0.10 82.20 153.28 11.66 |
||
| 3196 | 1 16G 16G N CA 133 134 -41.78 -41.20 8.50 |
||
| 3197 | 2 113956 26A 27G C N 217 219 -63.79 -62.40 2.18 0.40 82.20 154.77 11.79 |
||
| 3198 | 2 27G 27G N CA 219 220 -42.88 -41.20 8.50 |
||
| 3199 | 3 113959 29L 30G C N 236 238 -64.71 -62.40 3.51 0.64 82.20 155.96 11.89 |
||
| 3200 | 3 30G 30G N CA 238 239 -43.84 -41.20 8.50 |
||
| 3201 | 4 113971 41L 42G C N 323 325 -136.24 -167.20 31.11 0.53 82.20 -144.10 16.31 |
||
| 3202 | 4 42G 42G N CA 325 326 171.52 174.60 8.50 |
||
| 3203 | 5 113972 42G 43Q C N 327 329 -64.84 -63.80 9.63 1.36 -121.10 179.48 7.44 |
||
| 3204 | 5 43Q 43Q N CA 329 330 -30.73 -40.30 139.70 |
||
| 3205 | 6 113977 47L 48L C N 363 365 67.29 60.20 13.57 0.50 -63.50 143.58 26.45 |
||
| 3206 | 6 48L 48L N CA 365 366 18.03 29.60 -41.20 |
||
| 3207 | 7 114005 75I 76G C N 588 590 -71.63 -62.40 24.70 4.18 82.20 170.11 13.18 |
||
| 3208 | 7 76G 76G N CA 590 591 -64.11 -41.20 8.50 |
||
| 3209 | 8 114006 76G 77G C N 592 594 -67.91 -62.40 5.53 0.96 82.20 157.95 11.97 |
||
| 3210 | 8 77G 77G N CA 594 595 -40.65 -41.20 8.50 |
||
| 3211 | 9 114008 78F 79G C N 607 609 -64.93 -62.40 2.53 0.46 82.20 155.33 11.80 |
||
| 3212 | 9 79G 79G N CA 609 610 -41.29 -41.20 8.50 |
||
| 3213 | 10 114016 86M 87I C N 671 673 64.04 -63.40 167.38 31.52 -120.60 -172.85 14.60 |
||
| 3214 | 10 87I 87I N CA 673 674 64.91 -43.60 130.30 |
||
| 3215 | 11 114020 90P 91D C N 695 697 -83.35 -70.90 20.57 0.73 -63.30 154.64 20.35 |
||
| 3216 | 11 91D 91D N CA 697 698 166.67 150.30 -40.00 |
||
| 3217 | 12 114047 117M 118V C N 908 910 44.32 -73.50 138.52 11.31 -125.40 -176.89 9.17 |
||
| 3218 | 12 118V 118V N CA 910 911 -147.95 139.20 143.30 |
||
| 3219 | 13 114049 119E 120A C N 924 926 102.89 -134.00 127.12 3.17 -62.50 -143.04 34.18 |
||
| 3220 | 13 120A 120A N CA 926 927 178.68 147.00 -40.90 |
||
| 3221 | 14 114052 122A 123G C N 938 940 -136.76 -62.40 80.52 12.83 82.20 142.28 8.80 |
||
| 3222 | 14 123G 123G N CA 940 941 -10.31 -41.20 8.50 |
||
| 3223 | 15 114053 123G 124T C N 942 944 94.68 55.90 128.34 11.90 -124.80 141.71 7.02 |
||
| 3224 | 15 124T 124T N CA 944 945 161.83 39.50 143.50 |
||
| 3225 | 16 114056 126W 127T C N 967 969 55.89 55.90 7.30 0.51 -63.20 148.61 25.56 |
||
| 3226 | 16 127T 127T N CA 969 970 46.80 39.50 -42.10 |
||
| 3227 | 17 114067 137S 138H C N 1050 1052 -63.79 -63.20 12.37 1.58 -125.60 177.64 7.72 |
||
| 3228 | 17 138H 138H N CA 1052 1053 -54.66 -42.30 138.80 |
||
| 3229 | 18 114083 153A 154G C N 1168 1170 -63.27 -62.40 2.55 0.43 82.20 154.52 11.78 |
||
| 3230 | 18 154G 154G N CA 1170 1171 -43.60 -41.20 8.50 |
||
| 3231 | 19 114099 169I 170N C N 1281 1283 -111.13 -119.90 86.86 3.74 -63.20 103.46 11.14 |
||
| 3232 | 19 170N 170N N CA 1283 1284 50.59 137.00 -41.10 |
||
| 3233 | 20 114144 214N 215L C N 1627 1629 73.53 60.20 15.77 1.14 -63.50 150.56 27.73 |
||
| 3234 | 20 215L 215L N CA 1629 1630 21.18 29.60 -41.20 |
||
| 3235 | 21 114146 216N 217T C N 1643 1645 -142.27 -124.80 81.56 4.01 -63.20 132.19 14.03 |
||
| 3236 | 21 217T 217T N CA 1645 1646 63.83 143.50 -42.10 |
||
| 3237 | 22 114179 249P 250G C N 1916 1918 -64.26 -62.40 4.61 0.63 82.20 153.36 11.58 |
||
| 3238 | 22 250G 250G N CA 1918 1919 -36.98 -41.20 8.50 |
||
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||
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||
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||
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||
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| 3830 | 318 1936L1936L N CA 1541115412 -162.17 132.50 -41.20 |
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| 3838 | 322 1943G1943G N CA 1546515466 -28.25 -41.20 8.50 |
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| 3842 | 324 1945A1945A N CA 1547515476 -49.20 -40.90 145.30 |
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| 3844 | 325 1946R1946R N CA 1548015481 101.82 141.90 -41.10 |
||
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| 3846 | 326 1947R1947R N CA 1549115492 152.58 140.60 -41.10 |
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| 3848 | 327 1949P1949P N CA 1551015511 -40.38 -30.50 147.20 |
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| 3849 | 328 1158561950V1951P C N 1552215524 -70.41 -58.70 12.08 1.36 -64.50 174.83 13.36 |
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| 3850 | 328 1951P1951P N CA 1552415525 -27.53 -30.50 147.20 |
||
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||
| 3852 | 329 1952R1952R N CA 1553115532 134.30 140.60 141.90 |
||
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| 3854 | 330 1961E1961E N CA 1560215603 -173.51 136.80 -40.30 |
||
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||
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| 3858 | 332 1963K1963K N CA 1561515616 29.25 38.60 -40.80 |
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| 3859 | 333 1158691963K1964L C N 1562215624 -142.80 -108.50 55.34 2.55 -63.50 163.39 27.57 |
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||
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||
| 3862 | 334 1965G1965G N CA 1563215633 -47.43 -41.20 8.50 |
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| 3863 | 335 1159011995R1996R C N 1587115873 56.71 57.30 5.77 0.34 -63.00 146.73 26.70 |
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| 3864 | 335 1996R1996R N CA 1587315874 43.73 38.00 -41.10 |
||
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||
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| 3868 | 337 2014G2014G N CA 1603316034 -41.10 -41.20 8.50 |
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| 3966 | 386 2494Y2494Y N CA 1977919780 155.26 39.50 135.40 |
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| 4434 | 620 3810H3810H N CA 3031230313 144.45 138.80 -42.30 |
||
| 4435 | 621 1176943810H3811Q C N 3032030322 -101.66 -121.10 23.79 0.74 -63.80 170.55 23.26 |
||
| 4436 | 621 3811Q3811Q N CA 3032230323 125.99 139.70 -40.30 |
||
| 4437 | 622 1176953811Q3812K C N 3032930331 -103.66 -118.00 50.14 2.20 -62.90 138.02 16.18 |
||
| 4438 | 622 3812K3812K N CA 3033130332 91.06 139.10 -40.80 |
||
| 4439 | 623 1177253841A3842T C N 3056430566 -132.07 -124.80 69.83 3.21 -63.20 135.03 14.27 |
||
| 4440 | 623 3842T3842T N CA 3056630567 74.04 143.50 -42.10 |
||
| 4441 | 624 1177263842T3843Q C N 3057130573 -141.72 -63.80 92.70 12.77 -63.80 92.70 12.77 |
||
| 4442 | 624 3843Q3843Q N CA 3057330574 9.92 -40.30 -40.30 |
||
| 4443 | 625 1177273843Q3844V C N 3058030582 66.79 55.90 15.53 0.92 -125.40 -156.63 11.07 |
||
| 4444 | 625 3844V3844V N CA 3058230583 28.42 39.50 143.30 |
||
| 4445 | 626 1177313847E3848W C N 3060830610 55.34 58.80 26.72 1.17 -63.00 157.35 27.23 |
||
| 4446 | 626 3848W3848W N CA 3061030611 59.50 33.00 -44.20 |
||
| 4447 | 627 1177453861W3862R C N 3072630728 -72.76 -72.10 3.19 0.26 -63.00 -179.86 23.69 |
||
| 4448 | 627 3862R3862R N CA 3072830729 138.77 141.90 -41.10 |
||
| 4449 | 628 1177463862R3863N C N 3073730739 -124.35 -119.90 5.18 0.27 -63.20 -174.19 20.51 |
||
| 4450 | 628 3863N3863N N CA 3073930740 134.36 137.00 -41.10 |
||
| 4451 | 629 1177473865M3866L C N 3076330765 -75.72 -70.70 17.65 1.16 -63.50 160.74 23.04 |
||
| 4452 | 629 3866L3866L N CA 3076530766 158.52 141.60 -41.20 |
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| 4453 | 630 1177493867G3868Q C N 3077530777 -61.37 -73.00 16.98 1.31 -63.80 166.64 24.38 |
||
| 4454 | 630 3868Q3868Q N CA 3077730778 153.07 140.70 -40.30 |
||
| 4455 | 631 1177503868Q3869S C N 3078430786 -65.51 -72.40 7.05 0.46 -64.10 174.13 12.70 |
||
| 4456 | 631 3869S3869S N CA 3078630787 150.88 152.40 -35.00 |
||
| 4457 | 632 1177523870I3871R C N 3079830800 -66.15 -72.10 8.92 0.78 -63.00 170.39 23.23 |
||
| 4458 | 632 3871R3871R N CA 3080030801 148.54 141.90 -41.10 |
||
| 4459 | 633 1177533871R3872R C N 3080930811 -65.94 -72.10 18.62 1.30 -63.00 165.45 22.15 |
||
| 4460 | 633 3872R3872R N CA 3081130812 124.33 141.90 -41.10 |
||
| 4461 | 634 1177543872R3873F C N 3082030822 -163.41 -124.20 47.49 1.23 -63.20 176.75 30.69 |
||
| 4462 | 634 3873F3873F N CA 3082230823 170.11 143.30 -44.30 |
||
| 4463 | 635 1177553873F3874T C N 3083130833 -102.60 -124.80 49.74 1.58 -63.20 146.48 16.50 |
||
| 4464 | 635 3874T3874T N CA 3083330834 98.98 143.50 -42.10 |
||
| 4465 | 636 1177563874T3875T C N 3083830840 -143.57 -124.80 25.72 0.84 -63.20 176.22 27.81 |
||
| 4466 | 636 3875T3875T N CA 3084030841 161.08 143.50 -42.10 |
||
| 4467 | 637 1177573875T3876S C N 3084530847 -122.02 -136.60 33.55 1.33 -64.10 166.38 10.26 |
||
| 4468 | 637 3876S3876S N CA 3084730848 120.97 151.20 -35.00 |
||
| 4469 | 638 1177603878V3879R C N 3086530867 -123.98 -125.20 6.76 0.30 -63.00 -174.64 21.67 |
||
| 4470 | 638 3879R3879R N CA 3086730868 133.95 140.60 -41.10 |
||
| 4471 | 639 1177613879R3880R C N 3087630878 -125.81 -125.20 13.11 0.65 -63.00 179.92 20.90 |
||
| 4472 | 639 3880R3880R N CA 3087830879 127.51 140.60 -41.10 |
||
| 4473 | 640 1177663884E3885E C N 3092430926 86.92 54.60 109.43 10.98 -63.60 -130.88 26.91 |
||
| 4474 | 640 3885E3885E N CA 3092630927 146.95 42.40 -40.30 |
||
| 4475 | 641 1177673885E3886G C N 3093330935 45.20 78.70 35.20 1.45 82.20 167.92 9.96 |
||
| 4476 | 641 3886G3886G N CA 3093530936 -155.30 -166.10 8.50 |
||
| 4477 | 642 1177703888G3889K C N 3094830950 -96.75 -118.00 92.32 4.15 -62.90 96.21 11.15 |
||
| 4478 | 642 3889K3889K N CA 3095030951 49.26 139.10 -40.80 |
||
| 4479 | 643 1178073925L3926K C N 3124931251 -144.35 -118.00 33.82 1.15 56.60 -159.73 25.19 |
||
| 4480 | 643 3926K3926K N CA 3125131252 160.30 139.10 38.60 |
||
| 4481 | 644 1178083928M3929S C N 3127431276 -70.36 -72.40 16.17 1.02 -64.10 156.68 11.73 |
||
| 4482 | 644 3929S3929S N CA 3127631277 168.45 152.40 -35.00 |
||
| 4483 | 645 1178103930V3931L C N 3128731289 -114.86 -108.50 41.09 2.28 -63.50 142.67 17.65 |
||
| 4484 | 645 3931L3931L N CA 3128931290 91.90 132.50 -41.20 |
||
| 4485 | 646 1178113931L3932T C N 3129531297 -143.54 -124.80 19.49 0.88 -63.20 -172.84 29.24 |
||
| 4486 | 646 3932T3932T N CA 3129731298 148.86 143.50 -42.10 |
||
| 4487 | 647 1178133933P3934L C N 3130931311 -149.04 -108.50 40.68 1.90 -63.50 -163.37 24.12 |
||
| 4488 | 647 3934L3934L N CA 3131131312 135.84 132.50 -41.20 |
||
| 4489 | 648 1178143934L3935L C N 3131731319 -155.83 -108.50 51.18 2.27 -63.50 -169.33 32.16 |
||
| 4490 | 648 3935L3935L N CA 3131931320 151.98 132.50 -41.20 |
||
| 4491 | 649 1178153935L3936L C N 3132531327 -126.53 -108.50 18.27 0.84 -63.50 -172.43 23.31 |
||
| 4492 | 649 3936L3936L N CA 3132731328 135.47 132.50 -41.20 |
||
| 4493 | 650 1178163936L3937R C N 3133331335 -69.19 -72.10 10.34 0.73 -63.00 173.18 22.99 |
||
| 4494 | 650 3937R3937R N CA 3133531336 131.98 141.90 -41.10 |
||
| 4495 | 651 1178173937R3938G C N 3134431346 -120.08 -80.20 52.84 3.80 78.70 170.17 6.93 |
||
| 4496 | 651 3938G3938G N CA 3134631347 139.43 174.10 -166.10 |
||
| 4497 | 652 1178193939L3940T C N 3135631358 -79.78 -78.10 20.47 0.93 -63.20 172.30 21.04 |
||
| 4498 | 652 3940T3940T N CA 3135831359 129.40 149.80 -42.10 |
||
| 4499 | 653 1178233943A3944R C N 3137831380 -152.86 -63.00 91.05 15.88 -63.00 91.05 15.88 |
||
| 4500 | 653 3944R3944R N CA 3138031381 -55.79 -41.10 -41.10 |
||
| 4501 | 654 1178253945R3946L C N 3140031402 -70.83 -70.70 39.54 2.99 -63.50 137.85 19.57 |
||
| 4502 | 654 3946L3946L N CA 3140231403 -178.86 141.60 -41.20 |
||
| 4503 | 655 1178263946L3947P C N 3140831410 -72.14 -58.70 24.59 1.47 -64.50 157.30 12.15 |
||
| 4504 | 655 3947P3947P N CA 3141031411 -9.91 -30.50 147.20 |
||
| 4505 | 656 1178273947P3948V C N 3141531417 -62.25 -62.40 3.05 0.40 -125.40 -171.74 10.55 |
||
| 4506 | 656 3948V3948V N CA 3141731418 -39.35 -42.40 143.30 |
||
| 4507 | 657 1178293949P3950R C N 3142931431 43.49 57.30 38.50 1.86 -72.10 134.09 8.88 |
||
| 4508 | 657 3950R3950R N CA 3143131432 73.94 38.00 141.90 |
||
| 4509 | 658 1178363956L3957P C N 3148631488 -67.50 -58.70 17.87 1.05 -64.50 162.17 12.26 |
||
| 4510 | 658 3957P3957P N CA 3148831489 -14.94 -30.50 147.20 |
||
| 4511 | 659 1178393959E3960G C N 3150931511 86.00 82.20 4.98 0.39 -62.40 157.55 29.64 |
||
| 4512 | 659 3960G3960G N CA 3151131512 11.72 8.50 -41.20 |
||
| 4513 | 660 1178413961K3962L C N 3152231524 -108.06 -108.50 38.37 2.07 -63.50 142.48 17.79 |
||
| 4514 | 660 3962L3962L N CA 3152431525 94.13 132.50 -41.20 |
||
| 4515 | 661 1178433963G3964I C N 3153431536 -61.34 -63.40 2.82 0.53 -120.60 -178.10 8.26 |
||
| 4516 | 661 3964I3964I N CA 3153631537 -41.68 -43.60 130.30 |
||
| 4517 | 662 1178443964I3965M C N 3154231544 111.82 -125.60 144.61 4.29 -63.40 -157.12 29.52 |
||
| 4518 | 662 3965M3965M N CA 3154431545 -142.79 140.50 -40.50 |
||
| 4519 | 663 1178733993R3994R C N 3177131773 -57.04 -72.10 19.56 1.27 -63.00 170.63 23.45 |
||
| 4520 | 663 3994R3994R N CA 3177331774 129.42 141.90 -41.10 |
||
| 4521 | |||
| 4522 | |||
| 4523 | report______> Distribution of short non-bonded contacts: |
||
| 4524 | |||
| 4525 | |||
| 4526 | DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 |
||
| 4527 | DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50 |
||
| 4528 | FREQUENCY: 0 0 0 0 10 290 402 2478 3299 4417 3808 4620 5824 6048 5636 |
||
| 4529 | |||
| 4530 | |||
| 4531 | << end of ENERGY. |
||
| 4532 | |||
| 4533 | >> Summary of successfully produced models: |
||
| 4534 | Filename molpdf |
||
| 4535 | ---------------------------------------- |
||
| 4536 | 9606.B99990001.pdb 20600.91211 |
||
| 4537 | |||
| 4538 | |||
| 4539 | |||
| 4540 | |||
| 4541 | ```python |
||
| 4542 | r=m.residues[0] |
||
| 4543 | ``` |
||
| 4544 | |||
| 4545 | |||
| 4546 | ```python |
||
| 4547 | r.code |
||
| 4548 | ``` |
||
| 4549 | |||
| 4550 | |||
| 4551 | |||
| 4552 | |||
| 4553 | 'I' |
||
| 4554 | |||
| 4555 | |||
| 4556 | |||
| 4557 | |||
| 4558 | ```python |
||
| 4559 | |||
| 4560 | ``` |