Starting phenix.real_space_refine on Sat Apr 13 04:19:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5u07_8477/04_2024/5u07_8477.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5u07_8477/04_2024/5u07_8477.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5u07_8477/04_2024/5u07_8477.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5u07_8477/04_2024/5u07_8477.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5u07_8477/04_2024/5u07_8477.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5u07_8477/04_2024/5u07_8477.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 92 5.49 5 S 45 5.16 5 C 17065 2.51 5 N 5076 2.21 5 O 5403 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ARG 32": "NH1" <-> "NH2" Residue "C ARG 45": "NH1" <-> "NH2" Residue "C ARG 98": "NH1" <-> "NH2" Residue "C ARG 137": "NH1" <-> "NH2" Residue "C ARG 200": "NH1" <-> "NH2" Residue "C ARG 322": "NH1" <-> "NH2" Residue "C ARG 332": "NH1" <-> "NH2" Residue "C ARG 336": "NH1" <-> "NH2" Residue "D ARG 172": "NH1" <-> "NH2" Residue "D ARG 289": "NH1" <-> "NH2" Residue "D ARG 292": "NH1" <-> "NH2" Residue "E ARG 45": "NH1" <-> "NH2" Residue "E ARG 135": "NH1" <-> "NH2" Residue "E ARG 155": "NH1" <-> "NH2" Residue "E ARG 172": "NH1" <-> "NH2" Residue "E ARG 292": "NH1" <-> "NH2" Residue "F ARG 45": "NH1" <-> "NH2" Residue "F ARG 135": "NH1" <-> "NH2" Residue "F ARG 155": "NH1" <-> "NH2" Residue "F ARG 172": "NH1" <-> "NH2" Residue "F ARG 292": "NH1" <-> "NH2" Residue "G ARG 45": "NH1" <-> "NH2" Residue "G ARG 135": "NH1" <-> "NH2" Residue "G ARG 155": "NH1" <-> "NH2" Residue "G ARG 172": "NH1" <-> "NH2" Residue "G ARG 292": "NH1" <-> "NH2" Residue "H ARG 45": "NH1" <-> "NH2" Residue "H ARG 135": "NH1" <-> "NH2" Residue "H ARG 155": "NH1" <-> "NH2" Residue "H ARG 172": "NH1" <-> "NH2" Residue "H PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 292": "NH1" <-> "NH2" Residue "I ARG 45": "NH1" <-> "NH2" Residue "I ARG 135": "NH1" <-> "NH2" Residue "I ARG 155": "NH1" <-> "NH2" Residue "I ARG 172": "NH1" <-> "NH2" Residue "I ARG 292": "NH1" <-> "NH2" Residue "J ARG 32": "NH1" <-> "NH2" Residue "N ARG 47": "NH1" <-> "NH2" Residue "N ARG 172": "NH1" <-> "NH2" Residue "N ARG 217": "NH1" <-> "NH2" Residue "N ARG 220": "NH1" <-> "NH2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 27681 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 1471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1471 Classifications: {'peptide': 190} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 8, 'TRANS': 181} Chain breaks: 9 Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'TRP:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 28 Chain: "B" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1285 Classifications: {'peptide': 161} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 7, 'TRANS': 153} Chain breaks: 3 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "C" Number of atoms: 3880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3880 Classifications: {'peptide': 493} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 39, 'TRANS': 453} Chain breaks: 3 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 2, 'HIS:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 37 Chain: "D" Number of atoms: 2017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2017 Classifications: {'peptide': 260} Link IDs: {'PTRANS': 10, 'TRANS': 249} Chain breaks: 1 Chain: "E" Number of atoms: 2828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2828 Classifications: {'peptide': 367} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 15, 'TRANS': 351} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "F" Number of atoms: 2834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2834 Classifications: {'peptide': 367} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 15, 'TRANS': 351} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "G" Number of atoms: 2823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2823 Classifications: {'peptide': 366} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 350} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "H" Number of atoms: 2829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2829 Classifications: {'peptide': 366} Link IDs: {'PTRANS': 15, 'TRANS': 350} Chain: "I" Number of atoms: 2544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 2544 Classifications: {'peptide': 329} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 314} Chain breaks: 2 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "J" Number of atoms: 1319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1319 Classifications: {'peptide': 170} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 9, 'TRANS': 160} Chain breaks: 2 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 25 Chain: "K" Number of atoms: 1267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 1267 Classifications: {'RNA': 59} Modifications used: {'5*END': 1, 'rna2p_pur': 9, 'rna2p_pyr': 12, 'rna3p_pur': 25, 'rna3p_pyr': 13} Link IDs: {'rna2p': 21, 'rna3p': 37} Chain breaks: 1 Chain: "M" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 425 Classifications: {'DNA': 21} Link IDs: {'rna3p': 20} Chain: "N" Number of atoms: 1891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1891 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 20, 'TRANS': 220} Chain breaks: 1 Chain: "O" Number of atoms: 268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 268 Classifications: {'DNA': 13} Link IDs: {'rna3p': 12} Time building chain proxies: 14.70, per 1000 atoms: 0.53 Number of scatterers: 27681 At special positions: 0 Unit cell: (184.5, 148.83, 129.15, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 45 16.00 P 92 15.00 O 5403 8.00 N 5076 7.00 C 17065 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 12.63 Conformation dependent library (CDL) restraints added in 4.5 seconds 6492 Ramachandran restraints generated. 3246 Oldfield, 0 Emsley, 3246 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6210 Finding SS restraints... Secondary structure from input PDB file: 132 helices and 34 sheets defined 46.1% alpha, 18.2% beta 16 base pairs and 41 stacking pairs defined. Time for finding SS restraints: 10.07 Creating SS restraints... Processing helix chain 'A' and resid 22 through 32 Processing helix chain 'A' and resid 138 through 138 No H-bonds generated for 'chain 'A' and resid 138 through 138' Processing helix chain 'A' and resid 142 through 154 Processing helix chain 'A' and resid 198 through 209 Processing helix chain 'A' and resid 213 through 217 removed outlier: 3.705A pdb=" N GLY A 217 " --> pdb=" O LYS A 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 24 removed outlier: 3.713A pdb=" N VAL B 22 " --> pdb=" O SER B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 33 removed outlier: 3.784A pdb=" N ARG B 33 " --> pdb=" O ALA B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 35 No H-bonds generated for 'chain 'B' and resid 34 through 35' Processing helix chain 'B' and resid 41 through 43 No H-bonds generated for 'chain 'B' and resid 41 through 43' Processing helix chain 'B' and resid 44 through 52 removed outlier: 3.801A pdb=" N HIS B 48 " --> pdb=" O MET B 44 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ARG B 49 " --> pdb=" O LEU B 45 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N VAL B 50 " --> pdb=" O ALA B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 55 No H-bonds generated for 'chain 'B' and resid 53 through 55' Processing helix chain 'B' and resid 77 through 90 Processing helix chain 'B' and resid 138 through 149 removed outlier: 3.679A pdb=" N SER B 142 " --> pdb=" O ASN B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 165 removed outlier: 3.757A pdb=" N THR B 157 " --> pdb=" O ASN B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 185 removed outlier: 3.998A pdb=" N HIS B 173 " --> pdb=" O LEU B 169 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARG B 174 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Proline residue: B 177 - end of helix Processing helix chain 'B' and resid 191 through 201 Processing helix chain 'B' and resid 205 through 227 Processing helix chain 'C' and resid 43 through 50 Processing helix chain 'C' and resid 61 through 80 removed outlier: 4.184A pdb=" N ARG C 70 " --> pdb=" O ALA C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 105 Processing helix chain 'C' and resid 108 through 117 removed outlier: 3.676A pdb=" N VAL C 112 " --> pdb=" O ASP C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 139 removed outlier: 3.524A pdb=" N LEU C 138 " --> pdb=" O ASP C 135 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ARG C 139 " --> pdb=" O PRO C 136 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 135 through 139' Processing helix chain 'C' and resid 147 through 152 Processing helix chain 'C' and resid 178 through 191 Processing helix chain 'C' and resid 227 through 236 Processing helix chain 'C' and resid 247 through 251 removed outlier: 3.527A pdb=" N GLN C 251 " --> pdb=" O PHE C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 271 Processing helix chain 'C' and resid 334 through 341 Processing helix chain 'C' and resid 352 through 359 Processing helix chain 'C' and resid 367 through 372 removed outlier: 3.790A pdb=" N SER C 371 " --> pdb=" O GLU C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 410 through 446 Processing helix chain 'C' and resid 464 through 486 removed outlier: 3.991A pdb=" N HIS C 468 " --> pdb=" O PRO C 464 " (cutoff:3.500A) Proline residue: C 479 - end of helix Processing helix chain 'C' and resid 502 through 517 removed outlier: 3.639A pdb=" N LEU C 506 " --> pdb=" O ASN C 502 " (cutoff:3.500A) Processing helix chain 'C' and resid 518 through 520 No H-bonds generated for 'chain 'C' and resid 518 through 520' Processing helix chain 'C' and resid 522 through 534 Processing helix chain 'C' and resid 535 through 538 removed outlier: 3.511A pdb=" N SER C 538 " --> pdb=" O THR C 535 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 535 through 538' Processing helix chain 'D' and resid 39 through 55 Processing helix chain 'D' and resid 165 through 170 Processing helix chain 'D' and resid 239 through 247 Processing helix chain 'D' and resid 248 through 266 Processing helix chain 'D' and resid 296 through 301 Processing helix chain 'D' and resid 310 through 329 Processing helix chain 'D' and resid 346 through 350 Processing helix chain 'D' and resid 355 through 368 removed outlier: 3.575A pdb=" N PHE D 368 " --> pdb=" O VAL D 364 " (cutoff:3.500A) Processing helix chain 'E' and resid 39 through 56 Processing helix chain 'E' and resid 64 through 76 removed outlier: 3.695A pdb=" N GLU E 68 " --> pdb=" O ARG E 64 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 93 Processing helix chain 'E' and resid 121 through 134 removed outlier: 3.937A pdb=" N HIS E 134 " --> pdb=" O ILE E 130 " (cutoff:3.500A) Processing helix chain 'E' and resid 134 through 142 Processing helix chain 'E' and resid 152 through 161 removed outlier: 3.553A pdb=" N ILE E 156 " --> pdb=" O PRO E 152 " (cutoff:3.500A) Processing helix chain 'E' and resid 164 through 171 Processing helix chain 'E' and resid 212 through 219 Processing helix chain 'E' and resid 239 through 247 Processing helix chain 'E' and resid 248 through 266 Processing helix chain 'E' and resid 296 through 301 Processing helix chain 'E' and resid 309 through 329 removed outlier: 4.139A pdb=" N ARG E 313 " --> pdb=" O GLY E 309 " (cutoff:3.500A) Processing helix chain 'E' and resid 346 through 350 removed outlier: 3.553A pdb=" N LEU E 349 " --> pdb=" O LEU E 346 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY E 350 " --> pdb=" O ALA E 347 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 346 through 350' Processing helix chain 'E' and resid 355 through 368 Processing helix chain 'F' and resid 39 through 56 removed outlier: 3.518A pdb=" N TRP F 43 " --> pdb=" O SER F 39 " (cutoff:3.500A) Processing helix chain 'F' and resid 64 through 76 removed outlier: 3.695A pdb=" N GLU F 68 " --> pdb=" O ARG F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 79 through 93 Processing helix chain 'F' and resid 121 through 134 removed outlier: 3.982A pdb=" N HIS F 134 " --> pdb=" O ILE F 130 " (cutoff:3.500A) Processing helix chain 'F' and resid 134 through 142 Processing helix chain 'F' and resid 152 through 161 removed outlier: 3.564A pdb=" N ILE F 156 " --> pdb=" O PRO F 152 " (cutoff:3.500A) Processing helix chain 'F' and resid 164 through 171 Processing helix chain 'F' and resid 212 through 218 removed outlier: 3.500A pdb=" N HIS F 216 " --> pdb=" O LYS F 212 " (cutoff:3.500A) Processing helix chain 'F' and resid 239 through 247 Processing helix chain 'F' and resid 248 through 266 Processing helix chain 'F' and resid 296 through 301 Processing helix chain 'F' and resid 309 through 329 removed outlier: 4.289A pdb=" N ARG F 313 " --> pdb=" O GLY F 309 " (cutoff:3.500A) Processing helix chain 'F' and resid 346 through 350 removed outlier: 3.520A pdb=" N GLY F 350 " --> pdb=" O ALA F 347 " (cutoff:3.500A) Processing helix chain 'F' and resid 355 through 368 Processing helix chain 'G' and resid 39 through 56 Processing helix chain 'G' and resid 64 through 76 removed outlier: 3.733A pdb=" N GLU G 68 " --> pdb=" O ARG G 64 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 93 Processing helix chain 'G' and resid 121 through 134 removed outlier: 3.928A pdb=" N HIS G 134 " --> pdb=" O ILE G 130 " (cutoff:3.500A) Processing helix chain 'G' and resid 134 through 142 Processing helix chain 'G' and resid 152 through 161 Processing helix chain 'G' and resid 164 through 171 Processing helix chain 'G' and resid 212 through 219 removed outlier: 3.524A pdb=" N HIS G 216 " --> pdb=" O LYS G 212 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLY G 217 " --> pdb=" O GLU G 213 " (cutoff:3.500A) Processing helix chain 'G' and resid 239 through 247 Processing helix chain 'G' and resid 248 through 266 Processing helix chain 'G' and resid 296 through 301 Processing helix chain 'G' and resid 309 through 329 removed outlier: 4.268A pdb=" N ARG G 313 " --> pdb=" O GLY G 309 " (cutoff:3.500A) Processing helix chain 'G' and resid 346 through 350 removed outlier: 3.507A pdb=" N LEU G 349 " --> pdb=" O LEU G 346 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY G 350 " --> pdb=" O ALA G 347 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 346 through 350' Processing helix chain 'G' and resid 355 through 367 Processing helix chain 'H' and resid 39 through 56 removed outlier: 3.530A pdb=" N TRP H 43 " --> pdb=" O SER H 39 " (cutoff:3.500A) Processing helix chain 'H' and resid 64 through 76 removed outlier: 3.822A pdb=" N GLU H 68 " --> pdb=" O ARG H 64 " (cutoff:3.500A) Processing helix chain 'H' and resid 79 through 93 Processing helix chain 'H' and resid 121 through 134 removed outlier: 3.881A pdb=" N HIS H 134 " --> pdb=" O ILE H 130 " (cutoff:3.500A) Processing helix chain 'H' and resid 134 through 142 Processing helix chain 'H' and resid 152 through 161 Processing helix chain 'H' and resid 164 through 171 Processing helix chain 'H' and resid 239 through 247 Processing helix chain 'H' and resid 248 through 266 Processing helix chain 'H' and resid 271 through 276 Processing helix chain 'H' and resid 296 through 301 Processing helix chain 'H' and resid 309 through 329 removed outlier: 4.246A pdb=" N ARG H 313 " --> pdb=" O GLY H 309 " (cutoff:3.500A) Processing helix chain 'H' and resid 346 through 350 removed outlier: 3.532A pdb=" N GLY H 350 " --> pdb=" O ALA H 347 " (cutoff:3.500A) Processing helix chain 'H' and resid 355 through 367 Processing helix chain 'I' and resid 39 through 56 removed outlier: 3.545A pdb=" N TRP I 43 " --> pdb=" O SER I 39 " (cutoff:3.500A) Processing helix chain 'I' and resid 64 through 76 removed outlier: 3.667A pdb=" N GLU I 68 " --> pdb=" O ARG I 64 " (cutoff:3.500A) Processing helix chain 'I' and resid 79 through 93 Processing helix chain 'I' and resid 121 through 134 removed outlier: 3.989A pdb=" N HIS I 134 " --> pdb=" O ILE I 130 " (cutoff:3.500A) Processing helix chain 'I' and resid 134 through 142 Processing helix chain 'I' and resid 152 through 161 Processing helix chain 'I' and resid 164 through 171 Processing helix chain 'I' and resid 239 through 247 Processing helix chain 'I' and resid 248 through 266 Processing helix chain 'I' and resid 296 through 301 Processing helix chain 'I' and resid 309 through 329 removed outlier: 4.124A pdb=" N ARG I 313 " --> pdb=" O GLY I 309 " (cutoff:3.500A) Processing helix chain 'I' and resid 346 through 350 removed outlier: 3.575A pdb=" N LEU I 349 " --> pdb=" O LEU I 346 " (cutoff:3.500A) Processing helix chain 'I' and resid 355 through 367 Processing helix chain 'J' and resid 6 through 22 removed outlier: 4.032A pdb=" N VAL J 22 " --> pdb=" O SER J 18 " (cutoff:3.500A) Processing helix chain 'J' and resid 25 through 33 removed outlier: 3.783A pdb=" N ARG J 33 " --> pdb=" O ALA J 29 " (cutoff:3.500A) Processing helix chain 'J' and resid 41 through 43 No H-bonds generated for 'chain 'J' and resid 41 through 43' Processing helix chain 'J' and resid 44 through 52 removed outlier: 3.800A pdb=" N HIS J 48 " --> pdb=" O MET J 44 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ARG J 49 " --> pdb=" O LEU J 45 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N VAL J 50 " --> pdb=" O ALA J 46 " (cutoff:3.500A) Processing helix chain 'J' and resid 53 through 55 No H-bonds generated for 'chain 'J' and resid 53 through 55' Processing helix chain 'J' and resid 75 through 90 Processing helix chain 'J' and resid 138 through 151 removed outlier: 3.679A pdb=" N SER J 142 " --> pdb=" O ASN J 138 " (cutoff:3.500A) Processing helix chain 'J' and resid 153 through 165 removed outlier: 3.756A pdb=" N THR J 157 " --> pdb=" O ASN J 153 " (cutoff:3.500A) Processing helix chain 'J' and resid 168 through 185 removed outlier: 3.999A pdb=" N HIS J 173 " --> pdb=" O LEU J 169 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG J 174 " --> pdb=" O ASP J 170 " (cutoff:3.500A) Proline residue: J 177 - end of helix Processing helix chain 'J' and resid 191 through 201 Processing helix chain 'J' and resid 205 through 227 Processing helix chain 'N' and resid 31 through 44 Processing helix chain 'N' and resid 51 through 55 Processing helix chain 'N' and resid 81 through 85 Processing helix chain 'N' and resid 95 through 99 Processing helix chain 'N' and resid 121 through 131 removed outlier: 3.551A pdb=" N ILE N 125 " --> pdb=" O GLU N 121 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ALA N 131 " --> pdb=" O ASP N 127 " (cutoff:3.500A) Processing helix chain 'N' and resid 157 through 164 removed outlier: 3.814A pdb=" N GLU N 161 " --> pdb=" O ASP N 157 " (cutoff:3.500A) Processing helix chain 'N' and resid 227 through 231 Processing helix chain 'N' and resid 236 through 248 removed outlier: 3.741A pdb=" N ASN N 240 " --> pdb=" O ARG N 236 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 4 Processing sheet with id=AA2, first strand: chain 'A' and resid 40 through 41 Processing sheet with id=AA3, first strand: chain 'A' and resid 157 through 159 Processing sheet with id=AA4, first strand: chain 'A' and resid 112 through 114 Processing sheet with id=AA5, first strand: chain 'A' and resid 170 through 172 Processing sheet with id=AA6, first strand: chain 'C' and resid 40 through 42 Processing sheet with id=AA7, first strand: chain 'C' and resid 176 through 177 removed outlier: 3.583A pdb=" N LEU C 176 " --> pdb=" O VAL C 291 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ASP C 293 " --> pdb=" O HIS C 283 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 219 through 224 Processing sheet with id=AA9, first strand: chain 'C' and resid 315 through 318 removed outlier: 3.561A pdb=" N SER C 318 " --> pdb=" O ARG C 322 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ARG C 322 " --> pdb=" O SER C 318 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 27 through 30 removed outlier: 6.001A pdb=" N THR D 36 " --> pdb=" O THR D 193 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA D 191 " --> pdb=" O VAL D 38 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N TYR D 234 " --> pdb=" O ALA D 189 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N ALA D 191 " --> pdb=" O TYR D 232 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N TYR D 232 " --> pdb=" O ALA D 191 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N THR D 193 " --> pdb=" O THR D 230 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N THR D 230 " --> pdb=" O THR D 193 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 27 through 30 removed outlier: 6.001A pdb=" N THR D 36 " --> pdb=" O THR D 193 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA D 191 " --> pdb=" O VAL D 38 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N TYR D 234 " --> pdb=" O ALA D 189 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N ALA D 191 " --> pdb=" O TYR D 232 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N TYR D 232 " --> pdb=" O ALA D 191 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N THR D 193 " --> pdb=" O THR D 230 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N THR D 230 " --> pdb=" O THR D 193 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N SER D 227 " --> pdb=" O TYR D 14 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N TYR D 14 " --> pdb=" O SER D 227 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASP D 5 " --> pdb=" O ALA D 287 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LEU D 283 " --> pdb=" O ILE D 9 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLY D 336 " --> pdb=" O ILE D 286 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 27 through 30 removed outlier: 6.046A pdb=" N THR E 36 " --> pdb=" O THR E 193 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA E 191 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N PHE E 192 " --> pdb=" O TYR E 232 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 27 through 30 removed outlier: 6.046A pdb=" N THR E 36 " --> pdb=" O THR E 193 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA E 191 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N PHE E 192 " --> pdb=" O TYR E 232 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 59 through 62 Processing sheet with id=AB6, first strand: chain 'E' and resid 200 through 203 Processing sheet with id=AB7, first strand: chain 'F' and resid 27 through 30 removed outlier: 6.084A pdb=" N THR F 36 " --> pdb=" O THR F 193 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 27 through 30 removed outlier: 6.084A pdb=" N THR F 36 " --> pdb=" O THR F 193 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLU F 351 " --> pdb=" O ARG F 335 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 59 through 62 Processing sheet with id=AC1, first strand: chain 'F' and resid 200 through 203 Processing sheet with id=AC2, first strand: chain 'G' and resid 27 through 30 removed outlier: 6.130A pdb=" N THR G 36 " --> pdb=" O THR G 193 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N PHE G 192 " --> pdb=" O TYR G 232 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 27 through 30 removed outlier: 6.130A pdb=" N THR G 36 " --> pdb=" O THR G 193 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N PHE G 192 " --> pdb=" O TYR G 232 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N GLU G 351 " --> pdb=" O ARG G 335 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 59 through 62 Processing sheet with id=AC5, first strand: chain 'G' and resid 200 through 203 Processing sheet with id=AC6, first strand: chain 'H' and resid 27 through 30 removed outlier: 6.157A pdb=" N THR H 36 " --> pdb=" O THR H 193 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 27 through 30 removed outlier: 6.157A pdb=" N THR H 36 " --> pdb=" O THR H 193 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLU H 351 " --> pdb=" O ARG H 335 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 59 through 62 Processing sheet with id=AC9, first strand: chain 'H' and resid 200 through 203 Processing sheet with id=AD1, first strand: chain 'I' and resid 27 through 30 removed outlier: 6.214A pdb=" N THR I 36 " --> pdb=" O THR I 193 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE I 192 " --> pdb=" O TYR I 232 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 27 through 30 removed outlier: 6.214A pdb=" N THR I 36 " --> pdb=" O THR I 193 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE I 192 " --> pdb=" O TYR I 232 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 59 through 62 Processing sheet with id=AD4, first strand: chain 'N' and resid 150 through 152 removed outlier: 6.831A pdb=" N LEU N 5 " --> pdb=" O LEU N 151 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL N 112 " --> pdb=" O ASP N 64 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N THR N 60 " --> pdb=" O ALA N 116 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N ASP N 183 " --> pdb=" O VAL N 63 " (cutoff:3.500A) removed outlier: 8.664A pdb=" N ARG N 65 " --> pdb=" O LEU N 181 " (cutoff:3.500A) removed outlier: 13.434A pdb=" N LEU N 181 " --> pdb=" O ARG N 65 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N ARG N 213 " --> pdb=" O PRO N 204 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N SER N 215 " --> pdb=" O ASP N 202 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU N 200 " --> pdb=" O ARG N 217 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'N' and resid 12 through 13 removed outlier: 6.823A pdb=" N ARG N 24 " --> pdb=" O SER N 106 " (cutoff:3.500A) removed outlier: 9.062A pdb=" N LEU N 108 " --> pdb=" O ARG N 24 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'N' and resid 12 through 13 Processing sheet with id=AD7, first strand: chain 'N' and resid 15 through 16 removed outlier: 4.831A pdb=" N TRP N 15 " --> pdb=" O LEU N 27 " (cutoff:3.500A) 1344 hydrogen bonds defined for protein. 3738 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 41 hydrogen bonds 74 hydrogen bond angles 0 basepair planarities 16 basepair parallelities 41 stacking parallelities Total time for adding SS restraints: 10.57 Time building geometry restraints manager: 13.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6700 1.33 - 1.45: 6239 1.45 - 1.57: 15239 1.57 - 1.69: 181 1.69 - 1.81: 78 Bond restraints: 28437 Sorted by residual: bond pdb=" C SER F 269 " pdb=" N GLY F 270 " ideal model delta sigma weight residual 1.332 1.369 -0.037 5.00e-03 4.00e+04 5.54e+01 bond pdb=" C VAL C 364 " pdb=" N PRO C 365 " ideal model delta sigma weight residual 1.331 1.391 -0.060 1.27e-02 6.20e+03 2.25e+01 bond pdb=" N PRO J 25 " pdb=" CD PRO J 25 " ideal model delta sigma weight residual 1.473 1.530 -0.057 1.40e-02 5.10e+03 1.65e+01 bond pdb=" N PRO C 365 " pdb=" CD PRO C 365 " ideal model delta sigma weight residual 1.473 1.529 -0.056 1.40e-02 5.10e+03 1.58e+01 bond pdb=" N PRO J 56 " pdb=" CD PRO J 56 " ideal model delta sigma weight residual 1.473 1.528 -0.055 1.40e-02 5.10e+03 1.55e+01 ... (remaining 28432 not shown) Histogram of bond angle deviations from ideal: 95.83 - 104.54: 863 104.54 - 113.26: 15738 113.26 - 121.97: 16875 121.97 - 130.68: 5396 130.68 - 139.39: 163 Bond angle restraints: 39035 Sorted by residual: angle pdb=" N GLU A 159 " pdb=" CA GLU A 159 " pdb=" C GLU A 159 " ideal model delta sigma weight residual 108.79 123.20 -14.41 1.53e+00 4.27e-01 8.87e+01 angle pdb=" O3' DG O 11 " pdb=" P DC O 12 " pdb=" O5' DC O 12 " ideal model delta sigma weight residual 104.00 115.93 -11.93 1.50e+00 4.44e-01 6.33e+01 angle pdb=" N ILE A 106 " pdb=" CA ILE A 106 " pdb=" CB ILE A 106 " ideal model delta sigma weight residual 111.45 122.36 -10.91 1.64e+00 3.72e-01 4.43e+01 angle pdb=" N TYR A 104 " pdb=" CA TYR A 104 " pdb=" C TYR A 104 " ideal model delta sigma weight residual 108.99 119.35 -10.36 1.57e+00 4.06e-01 4.35e+01 angle pdb=" N TYR A 104 " pdb=" CA TYR A 104 " pdb=" CB TYR A 104 " ideal model delta sigma weight residual 111.52 100.48 11.04 1.86e+00 2.89e-01 3.52e+01 ... (remaining 39030 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.01: 16468 32.01 - 64.03: 595 64.03 - 96.04: 44 96.04 - 128.05: 2 128.05 - 160.06: 2 Dihedral angle restraints: 17111 sinusoidal: 7521 harmonic: 9590 Sorted by residual: dihedral pdb=" O4' C K 55 " pdb=" C1' C K 55 " pdb=" N1 C K 55 " pdb=" C2 C K 55 " ideal model delta sinusoidal sigma weight residual 200.00 50.12 149.88 1 1.50e+01 4.44e-03 7.96e+01 dihedral pdb=" O4' U K 20 " pdb=" C1' U K 20 " pdb=" N1 U K 20 " pdb=" C2 U K 20 " ideal model delta sinusoidal sigma weight residual 200.00 81.53 118.47 1 1.50e+01 4.44e-03 6.30e+01 dihedral pdb=" O4' C K 9 " pdb=" C1' C K 9 " pdb=" N1 C K 9 " pdb=" C2 C K 9 " ideal model delta sinusoidal sigma weight residual -128.00 -58.65 -69.35 1 1.70e+01 3.46e-03 2.15e+01 ... (remaining 17108 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 3722 0.092 - 0.184: 603 0.184 - 0.276: 84 0.276 - 0.368: 13 0.368 - 0.460: 3 Chirality restraints: 4425 Sorted by residual: chirality pdb=" C1' DA M 39 " pdb=" O4' DA M 39 " pdb=" C2' DA M 39 " pdb=" N9 DA M 39 " both_signs ideal model delta sigma weight residual False 2.42 1.96 0.46 2.00e-01 2.50e+01 5.30e+00 chirality pdb=" CA HIS C 343 " pdb=" N HIS C 343 " pdb=" C HIS C 343 " pdb=" CB HIS C 343 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.77e+00 chirality pdb=" CA GLU A 159 " pdb=" N GLU A 159 " pdb=" C GLU A 159 " pdb=" CB GLU A 159 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.68e+00 ... (remaining 4422 not shown) Planarity restraints: 4775 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DA M 39 " 0.021 2.00e-02 2.50e+03 3.27e-02 2.95e+01 pdb=" N9 DA M 39 " -0.087 2.00e-02 2.50e+03 pdb=" C8 DA M 39 " 0.059 2.00e-02 2.50e+03 pdb=" N7 DA M 39 " -0.009 2.00e-02 2.50e+03 pdb=" C5 DA M 39 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DA M 39 " -0.001 2.00e-02 2.50e+03 pdb=" N6 DA M 39 " -0.007 2.00e-02 2.50e+03 pdb=" N1 DA M 39 " 0.006 2.00e-02 2.50e+03 pdb=" C2 DA M 39 " 0.010 2.00e-02 2.50e+03 pdb=" N3 DA M 39 " 0.008 2.00e-02 2.50e+03 pdb=" C4 DA M 39 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 390 " 0.039 2.00e-02 2.50e+03 3.28e-02 2.68e+01 pdb=" CG TRP C 390 " -0.089 2.00e-02 2.50e+03 pdb=" CD1 TRP C 390 " 0.035 2.00e-02 2.50e+03 pdb=" CD2 TRP C 390 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP C 390 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP C 390 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP C 390 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 390 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 390 " 0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP C 390 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR E 30 " -0.024 2.00e-02 2.50e+03 4.76e-02 2.26e+01 pdb=" C TYR E 30 " 0.082 2.00e-02 2.50e+03 pdb=" O TYR E 30 " -0.031 2.00e-02 2.50e+03 pdb=" N GLY E 31 " -0.028 2.00e-02 2.50e+03 ... (remaining 4772 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 368 2.55 - 3.13: 23686 3.13 - 3.72: 44809 3.72 - 4.31: 60836 4.31 - 4.90: 101326 Nonbonded interactions: 231025 Sorted by model distance: nonbonded pdb=" O VAL J 77 " pdb=" N ALA J 80 " model vdw 1.958 2.520 nonbonded pdb=" N2 DG M 54 " pdb=" O2 DC O 1 " model vdw 2.102 2.496 nonbonded pdb=" OD1 ASN F 164 " pdb=" N VAL F 165 " model vdw 2.159 2.520 nonbonded pdb=" O2' C K 6 " pdb=" O4' C K 7 " model vdw 2.166 2.440 nonbonded pdb=" OD1 ASP N 202 " pdb=" N VAL N 203 " model vdw 2.172 2.520 ... (remaining 231020 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'B' and (resid 5 through 15 or (resid 16 and (name N or name CA or name C \ or name O or name CB )) or resid 17 through 18 or (resid 19 through 24 and (nam \ e N or name CA or name C or name O or name CB )) or resid 25 through 83 or (resi \ d 84 through 86 and (name N or name CA or name C or name O or name CB )) or resi \ d 87 through 166 or (resid 167 and (name N or name CA or name C or name O or nam \ e CB )) or resid 168 through 229)) selection = (chain 'J' and (resid 5 through 35 or resid 41 through 55 or resid 76 through 96 \ or resid 136 through 229)) } ncs_group { reference = (chain 'E' and (resid 2 through 42 or (resid 43 and (name N or name CA or name C \ or name O or name CB )) or resid 44 through 198 or resid 227 through 269 or res \ id 279 through 288 or (resid 289 and (name N or name CA or name C or name O or n \ ame CB )) or resid 290 through 345 or (resid 346 through 348 and (name N or name \ CA or name C or name O or name CB )) or resid 349 through 367)) selection = (chain 'F' and (resid 2 through 42 or (resid 43 and (name N or name CA or name C \ or name O or name CB )) or resid 44 through 140 or (resid 141 through 143 and ( \ name N or name CA or name C or name O or name CB )) or resid 144 through 198 or \ resid 227 through 269 or resid 279 through 288 or (resid 289 and (name N or name \ CA or name C or name O or name CB )) or resid 290 through 367)) selection = (chain 'G' and (resid 2 through 42 or (resid 43 and (name N or name CA or name C \ or name O or name CB )) or resid 44 through 140 or (resid 141 through 143 and ( \ name N or name CA or name C or name O or name CB )) or resid 144 through 198 or \ resid 227 through 269 or resid 279 through 330 or (resid 331 and (name N or name \ CA or name C or name O or name CB )) or resid 332 through 345 or (resid 346 thr \ ough 348 and (name N or name CA or name C or name O or name CB )) or resid 349 t \ hrough 367)) selection = (chain 'H' and (resid 2 through 42 or (resid 43 and (name N or name CA or name C \ or name O or name CB )) or resid 44 through 140 or (resid 141 through 143 and ( \ name N or name CA or name C or name O or name CB )) or resid 144 through 198 or \ resid 227 through 269 or resid 279 through 288 or (resid 289 and (name N or name \ CA or name C or name O or name CB )) or resid 290 through 330 or (resid 331 and \ (name N or name CA or name C or name O or name CB )) or resid 332 through 345 o \ r (resid 346 through 348 and (name N or name CA or name C or name O or name CB ) \ ) or resid 349 through 367)) selection = (chain 'I' and (resid 2 through 140 or (resid 141 through 143 and (name N or nam \ e CA or name C or name O or name CB )) or resid 144 through 288 or (resid 289 an \ d (name N or name CA or name C or name O or name CB )) or resid 290 through 330 \ or (resid 331 and (name N or name CA or name C or name O or name CB )) or resid \ 332 through 345 or (resid 346 through 348 and (name N or name CA or name C or na \ me O or name CB )) or resid 349 through 367)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 5.230 Check model and map are aligned: 0.450 Set scattering table: 0.310 Process input model: 81.700 Find NCS groups from input model: 1.470 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 93.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.098 28437 Z= 0.691 Angle : 1.348 17.885 39035 Z= 0.764 Chirality : 0.072 0.460 4425 Planarity : 0.007 0.110 4775 Dihedral : 14.697 160.064 10901 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 28.98 Ramachandran Plot: Outliers : 1.14 % Allowed : 4.84 % Favored : 94.02 % Rotamer: Outliers : 2.31 % Allowed : 7.74 % Favored : 89.95 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.19 (0.13), residues: 3246 helix: -1.18 (0.12), residues: 1326 sheet: -2.23 (0.21), residues: 455 loop : -1.27 (0.15), residues: 1465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.089 0.006 TRP C 390 HIS 0.020 0.004 HIS J 218 PHE 0.051 0.004 PHE C 276 TYR 0.052 0.005 TYR J 182 ARG 0.041 0.001 ARG A 21 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6492 Ramachandran restraints generated. 3246 Oldfield, 0 Emsley, 3246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6492 Ramachandran restraints generated. 3246 Oldfield, 0 Emsley, 3246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 703 residues out of total 2681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 642 time to evaluate : 2.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 386 ARG cc_start: 0.7449 (mtt180) cc_final: 0.7125 (ttm-80) REVERT: C 387 ASP cc_start: 0.8308 (p0) cc_final: 0.8065 (p0) REVERT: D 33 LYS cc_start: 0.9056 (mttm) cc_final: 0.8644 (mtmt) REVERT: D 319 ASN cc_start: 0.8277 (t0) cc_final: 0.7770 (t0) REVERT: E 92 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8418 (tm) REVERT: E 118 TYR cc_start: 0.8847 (t80) cc_final: 0.8384 (t80) REVERT: E 250 GLN cc_start: 0.7396 (tm-30) cc_final: 0.7060 (tm-30) REVERT: F 222 ASN cc_start: 0.8427 (p0) cc_final: 0.8033 (p0) REVERT: G 241 ARG cc_start: 0.7463 (ttm170) cc_final: 0.7040 (tpp80) REVERT: G 312 LEU cc_start: 0.9034 (tp) cc_final: 0.8760 (tp) REVERT: H 173 MET cc_start: 0.7542 (ttt) cc_final: 0.7199 (ttm) REVERT: H 209 ASP cc_start: 0.9131 (m-30) cc_final: 0.8892 (m-30) REVERT: H 244 GLU cc_start: 0.7968 (pp20) cc_final: 0.7678 (pp20) REVERT: H 312 LEU cc_start: 0.9060 (tp) cc_final: 0.8822 (tp) REVERT: I 10 GLN cc_start: 0.7176 (tt0) cc_final: 0.6948 (tt0) REVERT: I 296 PHE cc_start: 0.8815 (m-10) cc_final: 0.8507 (m-10) REVERT: J 148 PHE cc_start: 0.6850 (t80) cc_final: 0.6648 (t80) REVERT: J 190 ILE cc_start: 0.8138 (OUTLIER) cc_final: 0.7889 (tt) REVERT: J 205 THR cc_start: 0.7697 (p) cc_final: 0.7167 (p) REVERT: J 218 HIS cc_start: 0.7920 (m170) cc_final: 0.7694 (m-70) REVERT: N 164 GLU cc_start: 0.7736 (pm20) cc_final: 0.7499 (pm20) REVERT: N 179 THR cc_start: 0.6893 (m) cc_final: 0.6176 (p) outliers start: 61 outliers final: 15 residues processed: 679 average time/residue: 0.4562 time to fit residues: 464.4758 Evaluate side-chains 337 residues out of total 2681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 320 time to evaluate : 3.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 ARG Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 318 SER Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 347 ASP Chi-restraints excluded: chain C residue 355 LEU Chi-restraints excluded: chain C residue 358 CYS Chi-restraints excluded: chain C residue 416 VAL Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain F residue 52 GLU Chi-restraints excluded: chain F residue 218 SER Chi-restraints excluded: chain H residue 177 LEU Chi-restraints excluded: chain I residue 174 LEU Chi-restraints excluded: chain J residue 181 LEU Chi-restraints excluded: chain J residue 183 LEU Chi-restraints excluded: chain J residue 190 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 282 optimal weight: 0.9990 chunk 253 optimal weight: 0.6980 chunk 140 optimal weight: 3.9990 chunk 86 optimal weight: 0.9990 chunk 171 optimal weight: 0.9980 chunk 135 optimal weight: 0.9980 chunk 262 optimal weight: 5.9990 chunk 101 optimal weight: 2.9990 chunk 159 optimal weight: 6.9990 chunk 195 optimal weight: 7.9990 chunk 304 optimal weight: 3.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 ASN B 9 HIS ** B 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 48 HIS ** B 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 167 GLN ** B 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 169 HIS ** C 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 235 ASN C 283 HIS C 349 ASN ** C 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 18 ASN D 49 HIS D 164 ASN ** D 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 18 ASN E 195 HIS ** E 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 18 ASN F 49 HIS F 134 HIS F 195 HIS G 18 ASN ** G 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 134 HIS H 18 ASN H 49 HIS ** H 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 214 ASN H 216 HIS H 225 GLN H 272 GLN I 16 ASN I 18 ASN ** I 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 285 HIS ** J 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.2687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 28437 Z= 0.242 Angle : 0.744 11.172 39035 Z= 0.388 Chirality : 0.044 0.194 4425 Planarity : 0.005 0.074 4775 Dihedral : 16.152 159.778 4992 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 18.08 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.30 % Favored : 96.49 % Rotamer: Outliers : 4.06 % Allowed : 14.49 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.14), residues: 3246 helix: 0.04 (0.14), residues: 1357 sheet: -1.55 (0.23), residues: 418 loop : -0.94 (0.15), residues: 1471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 390 HIS 0.015 0.001 HIS A 150 PHE 0.022 0.002 PHE C 379 TYR 0.027 0.002 TYR D 14 ARG 0.009 0.001 ARG B 43 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6492 Ramachandran restraints generated. 3246 Oldfield, 0 Emsley, 3246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6492 Ramachandran restraints generated. 3246 Oldfield, 0 Emsley, 3246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 541 residues out of total 2681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 434 time to evaluate : 3.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 121 GLU cc_start: 0.6736 (tp30) cc_final: 0.6341 (tp30) REVERT: C 169 HIS cc_start: 0.7299 (OUTLIER) cc_final: 0.6946 (m170) REVERT: C 386 ARG cc_start: 0.7456 (mtt180) cc_final: 0.7139 (ttp-170) REVERT: C 431 ARG cc_start: 0.8098 (ptt-90) cc_final: 0.7603 (mtm110) REVERT: D 14 TYR cc_start: 0.8749 (t80) cc_final: 0.8533 (t80) REVERT: D 33 LYS cc_start: 0.8882 (mttm) cc_final: 0.8598 (mtmt) REVERT: D 44 LYS cc_start: 0.8702 (tttt) cc_final: 0.8410 (tttp) REVERT: E 92 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8325 (tm) REVERT: E 250 GLN cc_start: 0.6982 (tm-30) cc_final: 0.6679 (tm-30) REVERT: E 317 GLU cc_start: 0.7514 (mm-30) cc_final: 0.7068 (mm-30) REVERT: F 183 ASP cc_start: 0.8095 (p0) cc_final: 0.7610 (p0) REVERT: F 363 MET cc_start: 0.9015 (mmt) cc_final: 0.8599 (mmm) REVERT: G 118 TYR cc_start: 0.8608 (t80) cc_final: 0.8319 (t80) REVERT: G 250 GLN cc_start: 0.7627 (tp40) cc_final: 0.7423 (tp-100) REVERT: G 316 GLN cc_start: 0.8207 (tp40) cc_final: 0.8006 (tp40) REVERT: H 173 MET cc_start: 0.7900 (ttt) cc_final: 0.7373 (ttm) REVERT: I 234 TYR cc_start: 0.7862 (t80) cc_final: 0.7589 (t80) REVERT: N 108 LEU cc_start: 0.8920 (mt) cc_final: 0.8631 (mt) REVERT: N 141 ARG cc_start: 0.9065 (OUTLIER) cc_final: 0.8666 (ppp80) REVERT: N 225 GLU cc_start: 0.7417 (mm-30) cc_final: 0.7090 (mm-30) outliers start: 107 outliers final: 49 residues processed: 505 average time/residue: 0.4111 time to fit residues: 323.4047 Evaluate side-chains 370 residues out of total 2681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 318 time to evaluate : 3.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 ARG Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 169 HIS Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 347 ASP Chi-restraints excluded: chain C residue 355 LEU Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 415 ILE Chi-restraints excluded: chain C residue 420 THR Chi-restraints excluded: chain D residue 50 GLU Chi-restraints excluded: chain D residue 164 ASN Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 227 SER Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain E residue 14 TYR Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 52 GLU Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain E residue 227 SER Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 332 ASP Chi-restraints excluded: chain F residue 27 THR Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 205 THR Chi-restraints excluded: chain G residue 57 ASP Chi-restraints excluded: chain G residue 220 HIS Chi-restraints excluded: chain H residue 39 SER Chi-restraints excluded: chain H residue 177 LEU Chi-restraints excluded: chain I residue 6 ILE Chi-restraints excluded: chain I residue 38 VAL Chi-restraints excluded: chain I residue 159 VAL Chi-restraints excluded: chain I residue 288 VAL Chi-restraints excluded: chain J residue 141 VAL Chi-restraints excluded: chain J residue 181 LEU Chi-restraints excluded: chain N residue 29 TYR Chi-restraints excluded: chain N residue 100 THR Chi-restraints excluded: chain N residue 117 VAL Chi-restraints excluded: chain N residue 125 ILE Chi-restraints excluded: chain N residue 141 ARG Chi-restraints excluded: chain N residue 173 VAL Chi-restraints excluded: chain N residue 203 VAL Chi-restraints excluded: chain N residue 206 SER Chi-restraints excluded: chain N residue 219 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 169 optimal weight: 3.9990 chunk 94 optimal weight: 0.4980 chunk 253 optimal weight: 6.9990 chunk 207 optimal weight: 0.8980 chunk 83 optimal weight: 3.9990 chunk 304 optimal weight: 7.9990 chunk 329 optimal weight: 10.0000 chunk 271 optimal weight: 9.9990 chunk 302 optimal weight: 10.0000 chunk 103 optimal weight: 6.9990 chunk 244 optimal weight: 0.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 167 HIS C 168 HIS C 174 HIS C 381 GLN ** C 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 164 ASN D 272 GLN ** E 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 316 GLN F 18 ASN ** G 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 89 GLN G 272 GLN H 18 ASN H 89 GLN H 316 GLN ** I 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 49 HIS ** J 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.3550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 28437 Z= 0.288 Angle : 0.694 10.542 39035 Z= 0.359 Chirality : 0.043 0.253 4425 Planarity : 0.005 0.047 4775 Dihedral : 15.946 155.725 4974 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 17.32 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.04 % Favored : 95.78 % Rotamer: Outliers : 4.89 % Allowed : 16.20 % Favored : 78.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.14), residues: 3246 helix: 0.51 (0.14), residues: 1360 sheet: -1.29 (0.23), residues: 434 loop : -0.69 (0.16), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP C 390 HIS 0.031 0.001 HIS C 169 PHE 0.023 0.002 PHE N 243 TYR 0.021 0.002 TYR E 234 ARG 0.006 0.001 ARG B 174 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6492 Ramachandran restraints generated. 3246 Oldfield, 0 Emsley, 3246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6492 Ramachandran restraints generated. 3246 Oldfield, 0 Emsley, 3246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 478 residues out of total 2681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 349 time to evaluate : 2.998 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 SER cc_start: 0.3133 (OUTLIER) cc_final: 0.1291 (t) REVERT: A 179 ARG cc_start: -0.2109 (OUTLIER) cc_final: -0.2840 (mpt-90) REVERT: B 20 LEU cc_start: 0.7486 (mm) cc_final: 0.7049 (mt) REVERT: B 43 ARG cc_start: 0.3618 (tpm170) cc_final: 0.3145 (tpm170) REVERT: C 169 HIS cc_start: 0.7231 (OUTLIER) cc_final: 0.6636 (m-70) REVERT: D 14 TYR cc_start: 0.8773 (t80) cc_final: 0.8550 (t80) REVERT: D 30 TYR cc_start: 0.8804 (t80) cc_final: 0.8582 (t80) REVERT: D 33 LYS cc_start: 0.9000 (mttm) cc_final: 0.8639 (mtmt) REVERT: D 44 LYS cc_start: 0.8818 (tttt) cc_final: 0.8551 (tttp) REVERT: E 10 GLN cc_start: 0.7913 (tt0) cc_final: 0.7531 (tt0) REVERT: E 92 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8381 (tm) REVERT: E 250 GLN cc_start: 0.7031 (tm-30) cc_final: 0.6807 (tm-30) REVERT: E 280 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8629 (mt) REVERT: E 317 GLU cc_start: 0.7650 (mm-30) cc_final: 0.7260 (mm-30) REVERT: E 332 ASP cc_start: 0.7768 (OUTLIER) cc_final: 0.7235 (t0) REVERT: H 173 MET cc_start: 0.8224 (ttt) cc_final: 0.7965 (ttt) REVERT: I 119 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8293 (pp) REVERT: I 234 TYR cc_start: 0.8538 (t80) cc_final: 0.8156 (t80) REVERT: N 58 LYS cc_start: 0.8366 (mmtt) cc_final: 0.8066 (mmmt) REVERT: N 141 ARG cc_start: 0.9284 (OUTLIER) cc_final: 0.8465 (ppp80) outliers start: 129 outliers final: 68 residues processed: 450 average time/residue: 0.4094 time to fit residues: 292.9161 Evaluate side-chains 376 residues out of total 2681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 300 time to evaluate : 3.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 179 ARG Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain B residue 93 ARG Chi-restraints excluded: chain B residue 155 ASP Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 169 HIS Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain C residue 347 ASP Chi-restraints excluded: chain C residue 355 LEU Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 415 ILE Chi-restraints excluded: chain C residue 420 THR Chi-restraints excluded: chain C residue 437 CYS Chi-restraints excluded: chain C residue 485 VAL Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 227 SER Chi-restraints excluded: chain E residue 14 TYR Chi-restraints excluded: chain E residue 52 GLU Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 332 ASP Chi-restraints excluded: chain F residue 18 ASN Chi-restraints excluded: chain F residue 41 GLN Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 220 HIS Chi-restraints excluded: chain F residue 222 ASN Chi-restraints excluded: chain F residue 230 THR Chi-restraints excluded: chain G residue 27 THR Chi-restraints excluded: chain G residue 28 VAL Chi-restraints excluded: chain G residue 57 ASP Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 220 HIS Chi-restraints excluded: chain G residue 275 THR Chi-restraints excluded: chain G residue 301 GLU Chi-restraints excluded: chain G residue 341 GLU Chi-restraints excluded: chain G residue 342 ASN Chi-restraints excluded: chain H residue 6 ILE Chi-restraints excluded: chain H residue 18 ASN Chi-restraints excluded: chain H residue 39 SER Chi-restraints excluded: chain H residue 177 LEU Chi-restraints excluded: chain H residue 199 VAL Chi-restraints excluded: chain H residue 230 THR Chi-restraints excluded: chain H residue 341 GLU Chi-restraints excluded: chain I residue 6 ILE Chi-restraints excluded: chain I residue 38 VAL Chi-restraints excluded: chain I residue 113 THR Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain I residue 159 VAL Chi-restraints excluded: chain I residue 288 VAL Chi-restraints excluded: chain I residue 320 ASN Chi-restraints excluded: chain J residue 44 MET Chi-restraints excluded: chain J residue 141 VAL Chi-restraints excluded: chain J residue 156 SER Chi-restraints excluded: chain J residue 181 LEU Chi-restraints excluded: chain J residue 190 ILE Chi-restraints excluded: chain N residue 29 TYR Chi-restraints excluded: chain N residue 101 ILE Chi-restraints excluded: chain N residue 125 ILE Chi-restraints excluded: chain N residue 141 ARG Chi-restraints excluded: chain N residue 173 VAL Chi-restraints excluded: chain N residue 203 VAL Chi-restraints excluded: chain N residue 215 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 301 optimal weight: 0.9990 chunk 229 optimal weight: 1.9990 chunk 158 optimal weight: 7.9990 chunk 33 optimal weight: 4.9990 chunk 145 optimal weight: 0.8980 chunk 204 optimal weight: 4.9990 chunk 305 optimal weight: 7.9990 chunk 323 optimal weight: 6.9990 chunk 159 optimal weight: 10.0000 chunk 289 optimal weight: 6.9990 chunk 87 optimal weight: 5.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 48 HIS ** B 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 169 HIS ** C 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 491 GLN ** C 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 18 ASN ** F 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 18 ASN ** I 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.4177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 28437 Z= 0.324 Angle : 0.680 10.713 39035 Z= 0.350 Chirality : 0.043 0.206 4425 Planarity : 0.005 0.058 4775 Dihedral : 15.977 155.658 4974 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 16.95 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.60 % Favored : 96.24 % Rotamer: Outliers : 5.31 % Allowed : 16.73 % Favored : 77.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.14), residues: 3246 helix: 0.75 (0.14), residues: 1354 sheet: -1.11 (0.23), residues: 444 loop : -0.64 (0.16), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 390 HIS 0.010 0.001 HIS C 169 PHE 0.020 0.002 PHE D 170 TYR 0.031 0.002 TYR E 234 ARG 0.007 0.001 ARG E 241 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6492 Ramachandran restraints generated. 3246 Oldfield, 0 Emsley, 3246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6492 Ramachandran restraints generated. 3246 Oldfield, 0 Emsley, 3246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 2681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 346 time to evaluate : 2.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 20 LEU cc_start: 0.7732 (mm) cc_final: 0.7353 (mt) REVERT: B 183 LEU cc_start: 0.7936 (tp) cc_final: 0.7670 (tt) REVERT: C 519 TYR cc_start: 0.8220 (m-80) cc_final: 0.7931 (m-80) REVERT: D 14 TYR cc_start: 0.8799 (t80) cc_final: 0.8395 (t80) REVERT: D 30 TYR cc_start: 0.8911 (t80) cc_final: 0.8668 (t80) REVERT: D 33 LYS cc_start: 0.8944 (mttm) cc_final: 0.8646 (mtmt) REVERT: D 44 LYS cc_start: 0.8881 (tttt) cc_final: 0.8628 (tttp) REVERT: E 92 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8539 (tm) REVERT: E 332 ASP cc_start: 0.7947 (OUTLIER) cc_final: 0.7502 (t0) REVERT: E 361 ASP cc_start: 0.8097 (p0) cc_final: 0.7709 (p0) REVERT: F 316 GLN cc_start: 0.6882 (tm-30) cc_final: 0.6599 (tm-30) REVERT: G 173 MET cc_start: 0.7953 (ttp) cc_final: 0.7578 (ttp) REVERT: H 173 MET cc_start: 0.8373 (ttt) cc_final: 0.6833 (ttt) REVERT: I 9 ILE cc_start: 0.8605 (OUTLIER) cc_final: 0.8374 (tt) REVERT: I 119 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8381 (pp) REVERT: I 169 LEU cc_start: 0.9123 (OUTLIER) cc_final: 0.8830 (mp) REVERT: I 234 TYR cc_start: 0.8818 (t80) cc_final: 0.8617 (t80) REVERT: I 346 LEU cc_start: 0.7952 (OUTLIER) cc_final: 0.7626 (mt) REVERT: N 141 ARG cc_start: 0.9443 (OUTLIER) cc_final: 0.8908 (ppp80) REVERT: N 202 ASP cc_start: 0.8070 (p0) cc_final: 0.6210 (p0) REVERT: N 225 GLU cc_start: 0.7749 (mm-30) cc_final: 0.7498 (mm-30) outliers start: 140 outliers final: 87 residues processed: 454 average time/residue: 0.4265 time to fit residues: 306.8131 Evaluate side-chains 390 residues out of total 2681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 296 time to evaluate : 3.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain B residue 88 MET Chi-restraints excluded: chain B residue 155 ASP Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain C residue 34 ASP Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain C residue 347 ASP Chi-restraints excluded: chain C residue 355 LEU Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 415 ILE Chi-restraints excluded: chain C residue 420 THR Chi-restraints excluded: chain C residue 437 CYS Chi-restraints excluded: chain C residue 485 VAL Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 50 GLU Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain D residue 269 SER Chi-restraints excluded: chain E residue 14 TYR Chi-restraints excluded: chain E residue 19 ARG Chi-restraints excluded: chain E residue 52 GLU Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain E residue 188 PHE Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 332 ASP Chi-restraints excluded: chain E residue 346 LEU Chi-restraints excluded: chain F residue 6 ILE Chi-restraints excluded: chain F residue 27 THR Chi-restraints excluded: chain F residue 41 GLN Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 220 HIS Chi-restraints excluded: chain F residue 222 ASN Chi-restraints excluded: chain F residue 230 THR Chi-restraints excluded: chain G residue 6 ILE Chi-restraints excluded: chain G residue 27 THR Chi-restraints excluded: chain G residue 57 ASP Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 220 HIS Chi-restraints excluded: chain G residue 266 THR Chi-restraints excluded: chain G residue 301 GLU Chi-restraints excluded: chain G residue 341 GLU Chi-restraints excluded: chain H residue 6 ILE Chi-restraints excluded: chain H residue 39 SER Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 94 VAL Chi-restraints excluded: chain H residue 113 THR Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 177 LEU Chi-restraints excluded: chain H residue 199 VAL Chi-restraints excluded: chain H residue 216 HIS Chi-restraints excluded: chain H residue 230 THR Chi-restraints excluded: chain H residue 341 GLU Chi-restraints excluded: chain I residue 6 ILE Chi-restraints excluded: chain I residue 9 ILE Chi-restraints excluded: chain I residue 27 THR Chi-restraints excluded: chain I residue 113 THR Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain I residue 159 VAL Chi-restraints excluded: chain I residue 169 LEU Chi-restraints excluded: chain I residue 288 VAL Chi-restraints excluded: chain I residue 320 ASN Chi-restraints excluded: chain I residue 346 LEU Chi-restraints excluded: chain J residue 13 LEU Chi-restraints excluded: chain J residue 31 LEU Chi-restraints excluded: chain J residue 44 MET Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 141 VAL Chi-restraints excluded: chain J residue 156 SER Chi-restraints excluded: chain J residue 190 ILE Chi-restraints excluded: chain N residue 29 TYR Chi-restraints excluded: chain N residue 100 THR Chi-restraints excluded: chain N residue 117 VAL Chi-restraints excluded: chain N residue 125 ILE Chi-restraints excluded: chain N residue 141 ARG Chi-restraints excluded: chain N residue 173 VAL Chi-restraints excluded: chain N residue 203 VAL Chi-restraints excluded: chain N residue 215 SER Chi-restraints excluded: chain N residue 219 ILE Chi-restraints excluded: chain N residue 222 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 269 optimal weight: 6.9990 chunk 183 optimal weight: 0.8980 chunk 4 optimal weight: 30.0000 chunk 241 optimal weight: 0.7980 chunk 133 optimal weight: 0.9980 chunk 276 optimal weight: 0.6980 chunk 223 optimal weight: 4.9990 chunk 0 optimal weight: 40.0000 chunk 165 optimal weight: 0.9980 chunk 290 optimal weight: 3.9990 chunk 81 optimal weight: 0.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 48 HIS ** B 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 168 HIS C 235 ASN C 357 ASN ** C 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 164 ASN E 18 ASN E 41 GLN F 18 ASN ** G 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.4484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 28437 Z= 0.192 Angle : 0.635 13.373 39035 Z= 0.319 Chirality : 0.041 0.247 4425 Planarity : 0.004 0.069 4775 Dihedral : 15.846 155.644 4968 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 16.30 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.70 % Favored : 96.15 % Rotamer: Outliers : 4.36 % Allowed : 19.80 % Favored : 75.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.14), residues: 3246 helix: 0.90 (0.14), residues: 1377 sheet: -0.97 (0.23), residues: 433 loop : -0.63 (0.16), residues: 1436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 132 HIS 0.008 0.001 HIS D 220 PHE 0.015 0.001 PHE J 81 TYR 0.031 0.001 TYR E 234 ARG 0.004 0.000 ARG E 241 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6492 Ramachandran restraints generated. 3246 Oldfield, 0 Emsley, 3246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6492 Ramachandran restraints generated. 3246 Oldfield, 0 Emsley, 3246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 2681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 353 time to evaluate : 3.020 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 20 LEU cc_start: 0.7617 (mm) cc_final: 0.7377 (mt) REVERT: B 183 LEU cc_start: 0.7941 (tp) cc_final: 0.7711 (tt) REVERT: C 386 ARG cc_start: 0.7354 (ttp-170) cc_final: 0.6615 (ttm110) REVERT: D 14 TYR cc_start: 0.8702 (t80) cc_final: 0.8335 (t80) REVERT: D 33 LYS cc_start: 0.8941 (mttm) cc_final: 0.8689 (mtmt) REVERT: D 44 LYS cc_start: 0.8821 (tttt) cc_final: 0.8573 (tttp) REVERT: E 92 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8617 (tm) REVERT: E 280 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8405 (mt) REVERT: E 317 GLU cc_start: 0.7674 (mm-30) cc_final: 0.7356 (mm-30) REVERT: E 332 ASP cc_start: 0.7872 (OUTLIER) cc_final: 0.7570 (t0) REVERT: E 361 ASP cc_start: 0.7990 (p0) cc_final: 0.7533 (p0) REVERT: G 173 MET cc_start: 0.7928 (ttp) cc_final: 0.7452 (ttp) REVERT: H 173 MET cc_start: 0.8277 (ttt) cc_final: 0.8075 (ttt) REVERT: H 341 GLU cc_start: 0.7741 (OUTLIER) cc_final: 0.7419 (pm20) REVERT: I 96 LYS cc_start: 0.7588 (mtmm) cc_final: 0.7302 (mtmt) REVERT: I 169 LEU cc_start: 0.9026 (OUTLIER) cc_final: 0.8824 (mp) REVERT: N 141 ARG cc_start: 0.9292 (OUTLIER) cc_final: 0.9000 (tmm-80) outliers start: 115 outliers final: 74 residues processed: 434 average time/residue: 0.3796 time to fit residues: 265.3989 Evaluate side-chains 391 residues out of total 2681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 311 time to evaluate : 3.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain B residue 155 ASP Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain C residue 34 ASP Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 170 ASP Chi-restraints excluded: chain C residue 235 ASN Chi-restraints excluded: chain C residue 276 PHE Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain C residue 347 ASP Chi-restraints excluded: chain C residue 355 LEU Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 420 THR Chi-restraints excluded: chain C residue 485 VAL Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 11 THR Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 50 GLU Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain E residue 6 ILE Chi-restraints excluded: chain E residue 14 TYR Chi-restraints excluded: chain E residue 41 GLN Chi-restraints excluded: chain E residue 52 GLU Chi-restraints excluded: chain E residue 81 ASP Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 188 PHE Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 332 ASP Chi-restraints excluded: chain F residue 14 TYR Chi-restraints excluded: chain F residue 27 THR Chi-restraints excluded: chain F residue 41 GLN Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 222 ASN Chi-restraints excluded: chain G residue 6 ILE Chi-restraints excluded: chain G residue 57 ASP Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 301 GLU Chi-restraints excluded: chain H residue 11 THR Chi-restraints excluded: chain H residue 94 VAL Chi-restraints excluded: chain H residue 165 VAL Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 177 LEU Chi-restraints excluded: chain H residue 181 GLU Chi-restraints excluded: chain H residue 230 THR Chi-restraints excluded: chain H residue 341 GLU Chi-restraints excluded: chain I residue 6 ILE Chi-restraints excluded: chain I residue 113 THR Chi-restraints excluded: chain I residue 154 ASP Chi-restraints excluded: chain I residue 159 VAL Chi-restraints excluded: chain I residue 169 LEU Chi-restraints excluded: chain I residue 288 VAL Chi-restraints excluded: chain I residue 312 LEU Chi-restraints excluded: chain J residue 31 LEU Chi-restraints excluded: chain J residue 44 MET Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 141 VAL Chi-restraints excluded: chain J residue 190 ILE Chi-restraints excluded: chain J residue 212 GLU Chi-restraints excluded: chain N residue 29 TYR Chi-restraints excluded: chain N residue 100 THR Chi-restraints excluded: chain N residue 117 VAL Chi-restraints excluded: chain N residue 125 ILE Chi-restraints excluded: chain N residue 141 ARG Chi-restraints excluded: chain N residue 173 VAL Chi-restraints excluded: chain N residue 203 VAL Chi-restraints excluded: chain N residue 215 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 108 optimal weight: 4.9990 chunk 291 optimal weight: 5.9990 chunk 64 optimal weight: 10.0000 chunk 190 optimal weight: 6.9990 chunk 79 optimal weight: 0.8980 chunk 324 optimal weight: 2.9990 chunk 269 optimal weight: 8.9990 chunk 150 optimal weight: 5.9990 chunk 26 optimal weight: 9.9990 chunk 107 optimal weight: 0.7980 chunk 170 optimal weight: 3.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 48 HIS ** B 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 285 HIS E 18 ASN ** F 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 273 ASN ** H 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 316 GLN ** I 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.4782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 28437 Z= 0.321 Angle : 0.665 12.188 39035 Z= 0.341 Chirality : 0.042 0.264 4425 Planarity : 0.005 0.051 4775 Dihedral : 15.840 156.365 4968 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 16.99 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.91 % Favored : 95.93 % Rotamer: Outliers : 5.16 % Allowed : 19.54 % Favored : 75.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.14), residues: 3246 helix: 1.01 (0.14), residues: 1362 sheet: -0.82 (0.24), residues: 427 loop : -0.65 (0.16), residues: 1457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP C 132 HIS 0.009 0.001 HIS E 134 PHE 0.012 0.002 PHE E 368 TYR 0.023 0.002 TYR F 234 ARG 0.009 0.001 ARG I 37 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6492 Ramachandran restraints generated. 3246 Oldfield, 0 Emsley, 3246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6492 Ramachandran restraints generated. 3246 Oldfield, 0 Emsley, 3246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 2681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 325 time to evaluate : 3.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 20 LEU cc_start: 0.7668 (mm) cc_final: 0.7415 (mt) REVERT: B 183 LEU cc_start: 0.7895 (tp) cc_final: 0.7636 (tt) REVERT: C 292 VAL cc_start: 0.8534 (OUTLIER) cc_final: 0.8325 (t) REVERT: C 349 ASN cc_start: 0.8280 (p0) cc_final: 0.8035 (p0) REVERT: C 386 ARG cc_start: 0.7409 (ttp-170) cc_final: 0.7090 (ttm110) REVERT: D 14 TYR cc_start: 0.8757 (t80) cc_final: 0.8470 (t80) REVERT: D 33 LYS cc_start: 0.8952 (mttm) cc_final: 0.8732 (mtmt) REVERT: D 44 LYS cc_start: 0.8943 (tttt) cc_final: 0.8668 (tttp) REVERT: D 260 LEU cc_start: 0.9362 (OUTLIER) cc_final: 0.9049 (mm) REVERT: E 92 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8648 (tm) REVERT: E 317 GLU cc_start: 0.7767 (mm-30) cc_final: 0.7355 (mm-30) REVERT: E 361 ASP cc_start: 0.8082 (p0) cc_final: 0.7704 (p0) REVERT: F 316 GLN cc_start: 0.6903 (tm-30) cc_final: 0.6592 (tm-30) REVERT: H 7 HIS cc_start: 0.9353 (OUTLIER) cc_final: 0.8085 (m-70) REVERT: H 118 TYR cc_start: 0.8758 (t80) cc_final: 0.8392 (t80) REVERT: I 169 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8725 (mp) outliers start: 136 outliers final: 99 residues processed: 427 average time/residue: 0.3940 time to fit residues: 270.3602 Evaluate side-chains 403 residues out of total 2681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 299 time to evaluate : 3.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain B residue 88 MET Chi-restraints excluded: chain B residue 155 ASP Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 34 ASP Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 170 ASP Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 347 ASP Chi-restraints excluded: chain C residue 355 LEU Chi-restraints excluded: chain C residue 357 ASN Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 415 ILE Chi-restraints excluded: chain C residue 420 THR Chi-restraints excluded: chain C residue 478 GLU Chi-restraints excluded: chain C residue 485 VAL Chi-restraints excluded: chain C residue 497 MET Chi-restraints excluded: chain C residue 506 LEU Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 11 THR Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 50 GLU Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 227 SER Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 269 SER Chi-restraints excluded: chain E residue 6 ILE Chi-restraints excluded: chain E residue 14 TYR Chi-restraints excluded: chain E residue 19 ARG Chi-restraints excluded: chain E residue 39 SER Chi-restraints excluded: chain E residue 41 GLN Chi-restraints excluded: chain E residue 52 GLU Chi-restraints excluded: chain E residue 81 ASP Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 227 SER Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 346 LEU Chi-restraints excluded: chain F residue 6 ILE Chi-restraints excluded: chain F residue 27 THR Chi-restraints excluded: chain F residue 41 GLN Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 210 ILE Chi-restraints excluded: chain F residue 222 ASN Chi-restraints excluded: chain F residue 230 THR Chi-restraints excluded: chain F residue 267 VAL Chi-restraints excluded: chain G residue 6 ILE Chi-restraints excluded: chain G residue 11 THR Chi-restraints excluded: chain G residue 57 ASP Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 248 ASP Chi-restraints excluded: chain G residue 301 GLU Chi-restraints excluded: chain H residue 6 ILE Chi-restraints excluded: chain H residue 7 HIS Chi-restraints excluded: chain H residue 11 THR Chi-restraints excluded: chain H residue 39 SER Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 94 VAL Chi-restraints excluded: chain H residue 113 THR Chi-restraints excluded: chain H residue 165 VAL Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 177 LEU Chi-restraints excluded: chain H residue 216 HIS Chi-restraints excluded: chain H residue 230 THR Chi-restraints excluded: chain H residue 239 LEU Chi-restraints excluded: chain H residue 341 GLU Chi-restraints excluded: chain I residue 6 ILE Chi-restraints excluded: chain I residue 113 THR Chi-restraints excluded: chain I residue 169 LEU Chi-restraints excluded: chain I residue 288 VAL Chi-restraints excluded: chain I residue 312 LEU Chi-restraints excluded: chain I residue 320 ASN Chi-restraints excluded: chain J residue 13 LEU Chi-restraints excluded: chain J residue 31 LEU Chi-restraints excluded: chain J residue 44 MET Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 141 VAL Chi-restraints excluded: chain J residue 156 SER Chi-restraints excluded: chain J residue 190 ILE Chi-restraints excluded: chain J residue 212 GLU Chi-restraints excluded: chain N residue 29 TYR Chi-restraints excluded: chain N residue 69 ARG Chi-restraints excluded: chain N residue 100 THR Chi-restraints excluded: chain N residue 112 VAL Chi-restraints excluded: chain N residue 117 VAL Chi-restraints excluded: chain N residue 125 ILE Chi-restraints excluded: chain N residue 141 ARG Chi-restraints excluded: chain N residue 173 VAL Chi-restraints excluded: chain N residue 203 VAL Chi-restraints excluded: chain N residue 215 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 312 optimal weight: 8.9990 chunk 36 optimal weight: 10.0000 chunk 184 optimal weight: 1.9990 chunk 236 optimal weight: 1.9990 chunk 183 optimal weight: 0.6980 chunk 272 optimal weight: 7.9990 chunk 180 optimal weight: 9.9990 chunk 322 optimal weight: 6.9990 chunk 202 optimal weight: 7.9990 chunk 196 optimal weight: 2.9990 chunk 149 optimal weight: 0.9980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 215 GLN C 235 ASN ** D 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 273 ASN E 41 GLN F 18 ASN ** G 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 216 HIS ** H 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 285 HIS ** I 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 48 HIS ** J 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.5052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 28437 Z= 0.242 Angle : 0.642 13.000 39035 Z= 0.324 Chirality : 0.041 0.276 4425 Planarity : 0.004 0.046 4775 Dihedral : 15.773 156.143 4968 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 16.43 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.97 % Favored : 95.87 % Rotamer: Outliers : 4.67 % Allowed : 19.95 % Favored : 75.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.14), residues: 3246 helix: 1.07 (0.14), residues: 1374 sheet: -0.69 (0.24), residues: 420 loop : -0.70 (0.16), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP C 249 HIS 0.007 0.001 HIS D 220 PHE 0.021 0.001 PHE G 203 TYR 0.022 0.001 TYR F 234 ARG 0.008 0.000 ARG C 531 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6492 Ramachandran restraints generated. 3246 Oldfield, 0 Emsley, 3246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6492 Ramachandran restraints generated. 3246 Oldfield, 0 Emsley, 3246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 2681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 327 time to evaluate : 3.067 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 183 LEU cc_start: 0.7792 (tp) cc_final: 0.7549 (tt) REVERT: C 164 LEU cc_start: 0.8065 (OUTLIER) cc_final: 0.7752 (pp) REVERT: C 312 TYR cc_start: 0.7783 (m-10) cc_final: 0.7452 (m-10) REVERT: C 386 ARG cc_start: 0.7555 (ttp-170) cc_final: 0.7249 (ttm110) REVERT: D 14 TYR cc_start: 0.8672 (t80) cc_final: 0.8454 (t80) REVERT: D 44 LYS cc_start: 0.8916 (tttt) cc_final: 0.8701 (tttp) REVERT: D 260 LEU cc_start: 0.9326 (OUTLIER) cc_final: 0.9005 (mm) REVERT: E 92 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8605 (tm) REVERT: E 109 GLU cc_start: 0.5934 (OUTLIER) cc_final: 0.5475 (pm20) REVERT: E 317 GLU cc_start: 0.7655 (mm-30) cc_final: 0.7278 (mm-30) REVERT: E 361 ASP cc_start: 0.8090 (p0) cc_final: 0.7736 (p0) REVERT: H 118 TYR cc_start: 0.8862 (t80) cc_final: 0.8420 (t80) REVERT: H 155 ARG cc_start: 0.8237 (mtp180) cc_final: 0.7956 (ttp80) REVERT: I 34 GLU cc_start: 0.7330 (pm20) cc_final: 0.7074 (pm20) REVERT: I 96 LYS cc_start: 0.7631 (mtmm) cc_final: 0.7322 (mtmt) REVERT: I 109 GLU cc_start: 0.3237 (OUTLIER) cc_final: 0.2729 (pm20) REVERT: I 169 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8748 (mp) REVERT: J 74 VAL cc_start: 0.7743 (OUTLIER) cc_final: 0.7442 (m) REVERT: N 58 LYS cc_start: 0.8522 (mmmt) cc_final: 0.8263 (mtpp) REVERT: N 141 ARG cc_start: 0.9360 (OUTLIER) cc_final: 0.8861 (ppp80) outliers start: 123 outliers final: 91 residues processed: 417 average time/residue: 0.3974 time to fit residues: 263.3410 Evaluate side-chains 394 residues out of total 2681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 295 time to evaluate : 4.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain B residue 155 ASP Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 34 ASP Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 170 ASP Chi-restraints excluded: chain C residue 347 ASP Chi-restraints excluded: chain C residue 355 LEU Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 420 THR Chi-restraints excluded: chain C residue 478 GLU Chi-restraints excluded: chain C residue 485 VAL Chi-restraints excluded: chain C residue 497 MET Chi-restraints excluded: chain C residue 506 LEU Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 11 THR Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 50 GLU Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 227 SER Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 269 SER Chi-restraints excluded: chain E residue 6 ILE Chi-restraints excluded: chain E residue 14 TYR Chi-restraints excluded: chain E residue 19 ARG Chi-restraints excluded: chain E residue 41 GLN Chi-restraints excluded: chain E residue 52 GLU Chi-restraints excluded: chain E residue 81 ASP Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 109 GLU Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 227 SER Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain F residue 6 ILE Chi-restraints excluded: chain F residue 14 TYR Chi-restraints excluded: chain F residue 18 ASN Chi-restraints excluded: chain F residue 27 THR Chi-restraints excluded: chain F residue 41 GLN Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 220 HIS Chi-restraints excluded: chain F residue 222 ASN Chi-restraints excluded: chain F residue 230 THR Chi-restraints excluded: chain F residue 267 VAL Chi-restraints excluded: chain F residue 275 THR Chi-restraints excluded: chain G residue 6 ILE Chi-restraints excluded: chain G residue 27 THR Chi-restraints excluded: chain G residue 57 ASP Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 248 ASP Chi-restraints excluded: chain G residue 301 GLU Chi-restraints excluded: chain G residue 363 MET Chi-restraints excluded: chain H residue 6 ILE Chi-restraints excluded: chain H residue 11 THR Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 94 VAL Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 177 LEU Chi-restraints excluded: chain H residue 199 VAL Chi-restraints excluded: chain H residue 216 HIS Chi-restraints excluded: chain H residue 230 THR Chi-restraints excluded: chain H residue 341 GLU Chi-restraints excluded: chain I residue 6 ILE Chi-restraints excluded: chain I residue 92 LEU Chi-restraints excluded: chain I residue 109 GLU Chi-restraints excluded: chain I residue 113 THR Chi-restraints excluded: chain I residue 169 LEU Chi-restraints excluded: chain I residue 288 VAL Chi-restraints excluded: chain I residue 312 LEU Chi-restraints excluded: chain J residue 13 LEU Chi-restraints excluded: chain J residue 31 LEU Chi-restraints excluded: chain J residue 44 MET Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 141 VAL Chi-restraints excluded: chain J residue 156 SER Chi-restraints excluded: chain J residue 181 LEU Chi-restraints excluded: chain J residue 190 ILE Chi-restraints excluded: chain J residue 212 GLU Chi-restraints excluded: chain N residue 29 TYR Chi-restraints excluded: chain N residue 69 ARG Chi-restraints excluded: chain N residue 100 THR Chi-restraints excluded: chain N residue 112 VAL Chi-restraints excluded: chain N residue 117 VAL Chi-restraints excluded: chain N residue 125 ILE Chi-restraints excluded: chain N residue 141 ARG Chi-restraints excluded: chain N residue 173 VAL Chi-restraints excluded: chain N residue 203 VAL Chi-restraints excluded: chain N residue 215 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 199 optimal weight: 0.9980 chunk 128 optimal weight: 0.4980 chunk 192 optimal weight: 6.9990 chunk 97 optimal weight: 6.9990 chunk 63 optimal weight: 4.9990 chunk 62 optimal weight: 6.9990 chunk 205 optimal weight: 0.8980 chunk 219 optimal weight: 0.9990 chunk 159 optimal weight: 0.9980 chunk 30 optimal weight: 5.9990 chunk 253 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 235 ASN ** D 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 164 ASN F 18 ASN ** G 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.5198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 28437 Z= 0.197 Angle : 0.637 14.341 39035 Z= 0.320 Chirality : 0.041 0.289 4425 Planarity : 0.004 0.049 4775 Dihedral : 15.762 156.213 4968 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 16.95 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.82 % Favored : 96.06 % Rotamer: Outliers : 4.55 % Allowed : 20.86 % Favored : 74.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.15), residues: 3246 helix: 1.17 (0.14), residues: 1367 sheet: -0.64 (0.24), residues: 424 loop : -0.70 (0.16), residues: 1455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP C 132 HIS 0.006 0.001 HIS D 220 PHE 0.019 0.001 PHE G 203 TYR 0.025 0.001 TYR D 232 ARG 0.011 0.000 ARG F 19 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6492 Ramachandran restraints generated. 3246 Oldfield, 0 Emsley, 3246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6492 Ramachandran restraints generated. 3246 Oldfield, 0 Emsley, 3246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 2681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 328 time to evaluate : 3.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 183 LEU cc_start: 0.7865 (tp) cc_final: 0.7658 (tt) REVERT: C 164 LEU cc_start: 0.8028 (OUTLIER) cc_final: 0.7688 (pp) REVERT: C 349 ASN cc_start: 0.8174 (p0) cc_final: 0.7963 (p0) REVERT: C 386 ARG cc_start: 0.7492 (ttp-170) cc_final: 0.7220 (ttm110) REVERT: D 14 TYR cc_start: 0.8583 (t80) cc_final: 0.8363 (t80) REVERT: D 44 LYS cc_start: 0.8876 (tttt) cc_final: 0.8658 (tttp) REVERT: D 173 MET cc_start: 0.8163 (mmm) cc_final: 0.7961 (mmm) REVERT: D 260 LEU cc_start: 0.9310 (OUTLIER) cc_final: 0.8995 (mm) REVERT: E 109 GLU cc_start: 0.5857 (OUTLIER) cc_final: 0.5496 (pm20) REVERT: E 317 GLU cc_start: 0.7632 (mm-30) cc_final: 0.7275 (mm-30) REVERT: E 361 ASP cc_start: 0.8056 (p0) cc_final: 0.7702 (p0) REVERT: H 7 HIS cc_start: 0.9371 (OUTLIER) cc_final: 0.8140 (m-70) REVERT: H 91 VAL cc_start: 0.8714 (OUTLIER) cc_final: 0.8463 (t) REVERT: H 118 TYR cc_start: 0.8866 (t80) cc_final: 0.8482 (t80) REVERT: H 155 ARG cc_start: 0.8186 (mtp180) cc_final: 0.7890 (ttp80) REVERT: I 34 GLU cc_start: 0.7251 (pm20) cc_final: 0.7011 (pm20) REVERT: I 96 LYS cc_start: 0.7512 (mtmm) cc_final: 0.7211 (mtmt) REVERT: I 109 GLU cc_start: 0.3397 (OUTLIER) cc_final: 0.2965 (pm20) REVERT: I 169 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8702 (mp) REVERT: J 43 ARG cc_start: 0.6928 (mtm180) cc_final: 0.6642 (mtm180) REVERT: J 74 VAL cc_start: 0.7748 (OUTLIER) cc_final: 0.7481 (m) REVERT: N 58 LYS cc_start: 0.8484 (mmmt) cc_final: 0.8189 (mtpp) REVERT: N 141 ARG cc_start: 0.9317 (OUTLIER) cc_final: 0.8610 (ppp80) outliers start: 120 outliers final: 87 residues processed: 418 average time/residue: 0.3869 time to fit residues: 259.0642 Evaluate side-chains 391 residues out of total 2681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 295 time to evaluate : 3.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain B residue 155 ASP Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 34 ASP Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 170 ASP Chi-restraints excluded: chain C residue 347 ASP Chi-restraints excluded: chain C residue 355 LEU Chi-restraints excluded: chain C residue 357 ASN Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 420 THR Chi-restraints excluded: chain C residue 478 GLU Chi-restraints excluded: chain C residue 485 VAL Chi-restraints excluded: chain C residue 497 MET Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 11 THR Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 45 ARG Chi-restraints excluded: chain D residue 50 GLU Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 227 SER Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain E residue 6 ILE Chi-restraints excluded: chain E residue 14 TYR Chi-restraints excluded: chain E residue 19 ARG Chi-restraints excluded: chain E residue 52 GLU Chi-restraints excluded: chain E residue 81 ASP Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 109 GLU Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain E residue 188 PHE Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 346 LEU Chi-restraints excluded: chain F residue 14 TYR Chi-restraints excluded: chain F residue 18 ASN Chi-restraints excluded: chain F residue 27 THR Chi-restraints excluded: chain F residue 41 GLN Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 220 HIS Chi-restraints excluded: chain F residue 230 THR Chi-restraints excluded: chain F residue 267 VAL Chi-restraints excluded: chain G residue 6 ILE Chi-restraints excluded: chain G residue 27 THR Chi-restraints excluded: chain G residue 57 ASP Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 301 GLU Chi-restraints excluded: chain G residue 325 LEU Chi-restraints excluded: chain H residue 6 ILE Chi-restraints excluded: chain H residue 7 HIS Chi-restraints excluded: chain H residue 11 THR Chi-restraints excluded: chain H residue 39 SER Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 94 VAL Chi-restraints excluded: chain H residue 113 THR Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 177 LEU Chi-restraints excluded: chain H residue 199 VAL Chi-restraints excluded: chain H residue 216 HIS Chi-restraints excluded: chain H residue 230 THR Chi-restraints excluded: chain H residue 341 GLU Chi-restraints excluded: chain I residue 6 ILE Chi-restraints excluded: chain I residue 92 LEU Chi-restraints excluded: chain I residue 109 GLU Chi-restraints excluded: chain I residue 113 THR Chi-restraints excluded: chain I residue 169 LEU Chi-restraints excluded: chain I residue 288 VAL Chi-restraints excluded: chain I residue 312 LEU Chi-restraints excluded: chain J residue 13 LEU Chi-restraints excluded: chain J residue 31 LEU Chi-restraints excluded: chain J residue 44 MET Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 141 VAL Chi-restraints excluded: chain J residue 156 SER Chi-restraints excluded: chain J residue 181 LEU Chi-restraints excluded: chain J residue 212 GLU Chi-restraints excluded: chain N residue 29 TYR Chi-restraints excluded: chain N residue 69 ARG Chi-restraints excluded: chain N residue 100 THR Chi-restraints excluded: chain N residue 112 VAL Chi-restraints excluded: chain N residue 117 VAL Chi-restraints excluded: chain N residue 125 ILE Chi-restraints excluded: chain N residue 141 ARG Chi-restraints excluded: chain N residue 173 VAL Chi-restraints excluded: chain N residue 203 VAL Chi-restraints excluded: chain N residue 215 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 293 optimal weight: 8.9990 chunk 309 optimal weight: 10.0000 chunk 282 optimal weight: 5.9990 chunk 300 optimal weight: 3.9990 chunk 181 optimal weight: 0.9980 chunk 131 optimal weight: 20.0000 chunk 236 optimal weight: 5.9990 chunk 92 optimal weight: 0.8980 chunk 271 optimal weight: 10.0000 chunk 284 optimal weight: 10.0000 chunk 299 optimal weight: 1.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 ASN ** B 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 18 ASN ** G 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 273 ASN ** I 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.5381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 28437 Z= 0.327 Angle : 0.680 15.257 39035 Z= 0.346 Chirality : 0.042 0.271 4425 Planarity : 0.005 0.053 4775 Dihedral : 15.781 157.147 4966 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 17.26 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.37 % Favored : 95.50 % Rotamer: Outliers : 4.63 % Allowed : 20.98 % Favored : 74.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.15), residues: 3246 helix: 1.13 (0.14), residues: 1361 sheet: -0.66 (0.24), residues: 426 loop : -0.73 (0.16), residues: 1459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 132 HIS 0.006 0.001 HIS E 134 PHE 0.021 0.002 PHE G 203 TYR 0.024 0.002 TYR H 356 ARG 0.008 0.001 ARG C 531 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6492 Ramachandran restraints generated. 3246 Oldfield, 0 Emsley, 3246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6492 Ramachandran restraints generated. 3246 Oldfield, 0 Emsley, 3246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 2681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 307 time to evaluate : 3.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 349 ASN cc_start: 0.8259 (p0) cc_final: 0.8056 (p0) REVERT: D 260 LEU cc_start: 0.9415 (OUTLIER) cc_final: 0.9014 (mm) REVERT: E 109 GLU cc_start: 0.6010 (OUTLIER) cc_final: 0.5513 (pm20) REVERT: E 118 TYR cc_start: 0.8803 (t80) cc_final: 0.8231 (t80) REVERT: E 317 GLU cc_start: 0.7776 (mm-30) cc_final: 0.7341 (mm-30) REVERT: E 361 ASP cc_start: 0.8165 (p0) cc_final: 0.7860 (p0) REVERT: F 316 GLN cc_start: 0.6926 (tm-30) cc_final: 0.6595 (tm-30) REVERT: G 173 MET cc_start: 0.7967 (ttp) cc_final: 0.7123 (ttp) REVERT: G 305 TYR cc_start: 0.6959 (m-80) cc_final: 0.6362 (m-80) REVERT: H 7 HIS cc_start: 0.9367 (OUTLIER) cc_final: 0.8092 (m-70) REVERT: H 118 TYR cc_start: 0.8869 (t80) cc_final: 0.8462 (t80) REVERT: H 155 ARG cc_start: 0.8301 (mtp180) cc_final: 0.8014 (ttp80) REVERT: I 3 PHE cc_start: 0.8443 (m-80) cc_final: 0.8220 (m-80) REVERT: I 96 LYS cc_start: 0.7574 (mtmm) cc_final: 0.7309 (mtmt) REVERT: I 169 LEU cc_start: 0.8845 (OUTLIER) cc_final: 0.8596 (mp) REVERT: J 43 ARG cc_start: 0.7013 (mtm180) cc_final: 0.6726 (mtm180) REVERT: J 74 VAL cc_start: 0.7940 (OUTLIER) cc_final: 0.7705 (m) REVERT: N 58 LYS cc_start: 0.8552 (mmmt) cc_final: 0.8254 (mtpp) REVERT: N 64 ASP cc_start: 0.8156 (m-30) cc_final: 0.7782 (m-30) outliers start: 122 outliers final: 98 residues processed: 400 average time/residue: 0.3933 time to fit residues: 250.7129 Evaluate side-chains 392 residues out of total 2681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 289 time to evaluate : 2.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 155 ASP Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 34 ASP Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 170 ASP Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 347 ASP Chi-restraints excluded: chain C residue 355 LEU Chi-restraints excluded: chain C residue 357 ASN Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 420 THR Chi-restraints excluded: chain C residue 478 GLU Chi-restraints excluded: chain C residue 485 VAL Chi-restraints excluded: chain C residue 497 MET Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 11 THR Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 45 ARG Chi-restraints excluded: chain D residue 50 GLU Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 227 SER Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 269 SER Chi-restraints excluded: chain E residue 6 ILE Chi-restraints excluded: chain E residue 14 TYR Chi-restraints excluded: chain E residue 19 ARG Chi-restraints excluded: chain E residue 52 GLU Chi-restraints excluded: chain E residue 81 ASP Chi-restraints excluded: chain E residue 109 GLU Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 227 SER Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 346 LEU Chi-restraints excluded: chain F residue 6 ILE Chi-restraints excluded: chain F residue 27 THR Chi-restraints excluded: chain F residue 41 GLN Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 220 HIS Chi-restraints excluded: chain F residue 222 ASN Chi-restraints excluded: chain F residue 230 THR Chi-restraints excluded: chain F residue 267 VAL Chi-restraints excluded: chain G residue 6 ILE Chi-restraints excluded: chain G residue 11 THR Chi-restraints excluded: chain G residue 27 THR Chi-restraints excluded: chain G residue 57 ASP Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 144 LYS Chi-restraints excluded: chain G residue 248 ASP Chi-restraints excluded: chain G residue 275 THR Chi-restraints excluded: chain G residue 301 GLU Chi-restraints excluded: chain G residue 325 LEU Chi-restraints excluded: chain H residue 6 ILE Chi-restraints excluded: chain H residue 7 HIS Chi-restraints excluded: chain H residue 11 THR Chi-restraints excluded: chain H residue 39 SER Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 94 VAL Chi-restraints excluded: chain H residue 113 THR Chi-restraints excluded: chain H residue 165 VAL Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 177 LEU Chi-restraints excluded: chain H residue 199 VAL Chi-restraints excluded: chain H residue 216 HIS Chi-restraints excluded: chain H residue 230 THR Chi-restraints excluded: chain H residue 341 GLU Chi-restraints excluded: chain I residue 6 ILE Chi-restraints excluded: chain I residue 92 LEU Chi-restraints excluded: chain I residue 113 THR Chi-restraints excluded: chain I residue 169 LEU Chi-restraints excluded: chain I residue 288 VAL Chi-restraints excluded: chain I residue 312 LEU Chi-restraints excluded: chain I residue 320 ASN Chi-restraints excluded: chain J residue 13 LEU Chi-restraints excluded: chain J residue 31 LEU Chi-restraints excluded: chain J residue 44 MET Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 141 VAL Chi-restraints excluded: chain J residue 156 SER Chi-restraints excluded: chain J residue 190 ILE Chi-restraints excluded: chain J residue 212 GLU Chi-restraints excluded: chain N residue 29 TYR Chi-restraints excluded: chain N residue 69 ARG Chi-restraints excluded: chain N residue 100 THR Chi-restraints excluded: chain N residue 112 VAL Chi-restraints excluded: chain N residue 117 VAL Chi-restraints excluded: chain N residue 125 ILE Chi-restraints excluded: chain N residue 141 ARG Chi-restraints excluded: chain N residue 173 VAL Chi-restraints excluded: chain N residue 203 VAL Chi-restraints excluded: chain N residue 215 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 197 optimal weight: 2.9990 chunk 318 optimal weight: 1.9990 chunk 194 optimal weight: 2.9990 chunk 150 optimal weight: 0.9990 chunk 221 optimal weight: 0.5980 chunk 333 optimal weight: 0.7980 chunk 307 optimal weight: 30.0000 chunk 265 optimal weight: 1.9990 chunk 27 optimal weight: 8.9990 chunk 205 optimal weight: 2.9990 chunk 162 optimal weight: 2.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 48 HIS B 91 GLN ** B 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 285 HIS ** H 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.5540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 28437 Z= 0.215 Angle : 0.662 14.379 39035 Z= 0.332 Chirality : 0.041 0.263 4425 Planarity : 0.004 0.050 4775 Dihedral : 15.749 158.157 4966 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 16.45 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.88 % Favored : 96.00 % Rotamer: Outliers : 3.64 % Allowed : 21.97 % Favored : 74.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.15), residues: 3246 helix: 1.19 (0.14), residues: 1363 sheet: -0.69 (0.24), residues: 422 loop : -0.75 (0.16), residues: 1461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 132 HIS 0.006 0.001 HIS D 220 PHE 0.019 0.001 PHE G 203 TYR 0.022 0.001 TYR F 234 ARG 0.008 0.000 ARG C 531 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6492 Ramachandran restraints generated. 3246 Oldfield, 0 Emsley, 3246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6492 Ramachandran restraints generated. 3246 Oldfield, 0 Emsley, 3246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 2681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 307 time to evaluate : 2.873 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 180 GLU cc_start: 0.7415 (pm20) cc_final: 0.7194 (pm20) REVERT: C 349 ASN cc_start: 0.7926 (p0) cc_final: 0.7719 (p0) REVERT: D 45 ARG cc_start: 0.8580 (OUTLIER) cc_final: 0.8286 (ptm-80) REVERT: D 216 HIS cc_start: 0.7221 (m170) cc_final: 0.6912 (m90) REVERT: D 260 LEU cc_start: 0.9346 (OUTLIER) cc_final: 0.9009 (mm) REVERT: E 109 GLU cc_start: 0.5842 (OUTLIER) cc_final: 0.5504 (pm20) REVERT: E 317 GLU cc_start: 0.7664 (mm-30) cc_final: 0.7282 (mm-30) REVERT: E 361 ASP cc_start: 0.8060 (p0) cc_final: 0.7728 (p0) REVERT: G 173 MET cc_start: 0.7871 (ttp) cc_final: 0.7164 (ttp) REVERT: G 305 TYR cc_start: 0.6909 (m-80) cc_final: 0.6372 (m-80) REVERT: G 310 TYR cc_start: 0.8508 (m-80) cc_final: 0.8233 (m-10) REVERT: H 7 HIS cc_start: 0.9366 (OUTLIER) cc_final: 0.8120 (m-70) REVERT: H 91 VAL cc_start: 0.8705 (OUTLIER) cc_final: 0.8462 (t) REVERT: H 118 TYR cc_start: 0.8831 (t80) cc_final: 0.8471 (t80) REVERT: H 173 MET cc_start: 0.7225 (ttt) cc_final: 0.6517 (ttm) REVERT: I 34 GLU cc_start: 0.7254 (pm20) cc_final: 0.7032 (pm20) REVERT: I 96 LYS cc_start: 0.7460 (mtmm) cc_final: 0.7229 (mtmt) REVERT: I 169 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8679 (mp) REVERT: J 43 ARG cc_start: 0.7014 (mtm180) cc_final: 0.6700 (mtm180) REVERT: N 58 LYS cc_start: 0.8532 (mmmt) cc_final: 0.8238 (mtpp) REVERT: N 141 ARG cc_start: 0.9348 (OUTLIER) cc_final: 0.8752 (ppp80) outliers start: 96 outliers final: 79 residues processed: 380 average time/residue: 0.4125 time to fit residues: 250.4835 Evaluate side-chains 375 residues out of total 2681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 289 time to evaluate : 3.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain B residue 155 ASP Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain C residue 34 ASP Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 355 LEU Chi-restraints excluded: chain C residue 357 ASN Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 420 THR Chi-restraints excluded: chain C residue 478 GLU Chi-restraints excluded: chain C residue 485 VAL Chi-restraints excluded: chain C residue 497 MET Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 11 THR Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 45 ARG Chi-restraints excluded: chain D residue 50 GLU Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 227 SER Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 269 SER Chi-restraints excluded: chain E residue 6 ILE Chi-restraints excluded: chain E residue 14 TYR Chi-restraints excluded: chain E residue 19 ARG Chi-restraints excluded: chain E residue 52 GLU Chi-restraints excluded: chain E residue 81 ASP Chi-restraints excluded: chain E residue 109 GLU Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 346 LEU Chi-restraints excluded: chain F residue 6 ILE Chi-restraints excluded: chain F residue 27 THR Chi-restraints excluded: chain F residue 41 GLN Chi-restraints excluded: chain F residue 230 THR Chi-restraints excluded: chain G residue 6 ILE Chi-restraints excluded: chain G residue 27 THR Chi-restraints excluded: chain G residue 57 ASP Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 144 LYS Chi-restraints excluded: chain G residue 301 GLU Chi-restraints excluded: chain G residue 325 LEU Chi-restraints excluded: chain G residue 363 MET Chi-restraints excluded: chain H residue 6 ILE Chi-restraints excluded: chain H residue 7 HIS Chi-restraints excluded: chain H residue 11 THR Chi-restraints excluded: chain H residue 39 SER Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 94 VAL Chi-restraints excluded: chain H residue 113 THR Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 177 LEU Chi-restraints excluded: chain H residue 199 VAL Chi-restraints excluded: chain H residue 216 HIS Chi-restraints excluded: chain H residue 230 THR Chi-restraints excluded: chain H residue 341 GLU Chi-restraints excluded: chain I residue 6 ILE Chi-restraints excluded: chain I residue 92 LEU Chi-restraints excluded: chain I residue 113 THR Chi-restraints excluded: chain I residue 169 LEU Chi-restraints excluded: chain I residue 288 VAL Chi-restraints excluded: chain I residue 312 LEU Chi-restraints excluded: chain J residue 13 LEU Chi-restraints excluded: chain J residue 31 LEU Chi-restraints excluded: chain J residue 44 MET Chi-restraints excluded: chain J residue 141 VAL Chi-restraints excluded: chain J residue 156 SER Chi-restraints excluded: chain J residue 212 GLU Chi-restraints excluded: chain N residue 29 TYR Chi-restraints excluded: chain N residue 69 ARG Chi-restraints excluded: chain N residue 100 THR Chi-restraints excluded: chain N residue 112 VAL Chi-restraints excluded: chain N residue 117 VAL Chi-restraints excluded: chain N residue 125 ILE Chi-restraints excluded: chain N residue 141 ARG Chi-restraints excluded: chain N residue 203 VAL Chi-restraints excluded: chain N residue 215 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 211 optimal weight: 2.9990 chunk 283 optimal weight: 2.9990 chunk 81 optimal weight: 0.9980 chunk 245 optimal weight: 0.6980 chunk 39 optimal weight: 0.9980 chunk 73 optimal weight: 7.9990 chunk 266 optimal weight: 0.0870 chunk 111 optimal weight: 5.9990 chunk 273 optimal weight: 0.9980 chunk 33 optimal weight: 4.9990 chunk 49 optimal weight: 10.0000 overall best weight: 0.7558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 48 HIS ** D 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 195 HIS ** F 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 236 ASN G 7 HIS ** G 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 236 ASN ** I 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.128122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.093735 restraints weight = 54977.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.094233 restraints weight = 39093.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.094568 restraints weight = 30060.473| |-----------------------------------------------------------------------------| r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.5674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 28437 Z= 0.190 Angle : 0.655 17.856 39035 Z= 0.329 Chirality : 0.041 0.292 4425 Planarity : 0.004 0.063 4775 Dihedral : 15.690 158.195 4964 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 16.23 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.85 % Favored : 96.00 % Rotamer: Outliers : 3.45 % Allowed : 22.76 % Favored : 73.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.15), residues: 3246 helix: 1.16 (0.14), residues: 1376 sheet: -0.71 (0.24), residues: 423 loop : -0.72 (0.16), residues: 1447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 213 HIS 0.008 0.001 HIS C 532 PHE 0.032 0.001 PHE D 203 TYR 0.024 0.001 TYR F 234 ARG 0.009 0.000 ARG C 531 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5773.28 seconds wall clock time: 106 minutes 34.08 seconds (6394.08 seconds total)