Starting phenix.real_space_refine (version: dev) on Sun May 15 22:06:09 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zpo_11342/05_2022/6zpo_11342_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zpo_11342/05_2022/6zpo_11342.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zpo_11342/05_2022/6zpo_11342.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zpo_11342/05_2022/6zpo_11342.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zpo_11342/05_2022/6zpo_11342_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zpo_11342/05_2022/6zpo_11342_trim_updated.pdb" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.020 sd= 1.116 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "C TYR 446": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Q PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "d PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "d ARG 155": not complete - not flipped Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib" Total number of atoms: 80353 Number of models: 1 Model: "" Number of chains: 42 Chain: "8" Number of atoms: 696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 696 Classifications: {'peptide': 41} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 37} Chain: "A" Number of atoms: 7838 Number of conformers: 1 Conformer: "" Number of residues, atoms: 508, 7838 Classifications: {'peptide': 508} Link IDs: {'PTRANS': 16, 'CIS': 1, 'TRANS': 489, 'PCIS': 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 7392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 477, 7392 Classifications: {'peptide': 477} Link IDs: {'PTRANS': 16, 'CIS': 1, 'TRANS': 458, 'PCIS': 1} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 7698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 498, 7698 Classifications: {'peptide': 498} Link IDs: {'PTRANS': 16, 'CIS': 1, 'TRANS': 479, 'PCIS': 1} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 7163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 7163 Classifications: {'peptide': 469} Link IDs: {'PTRANS': 22, 'CIS': 1, 'TRANS': 444, 'PCIS': 1} Chain: "E" Number of atoms: 7132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 7132 Classifications: {'peptide': 467} Link IDs: {'PTRANS': 22, 'CIS': 1, 'TRANS': 442, 'PCIS': 1} Chain: "F" Number of atoms: 7131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 7131 Classifications: {'peptide': 467} Link IDs: {'PTRANS': 22, 'CIS': 1, 'TRANS': 442, 'PCIS': 1} Chain: "G" Number of atoms: 4300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 4300 Classifications: {'peptide': 272} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 266} Chain: "H" Number of atoms: 1957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1957 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 4, 'TRANS': 127} Chain: "I" Number of atoms: 764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 764 Classifications: {'peptide': 47} Modifications used: {'NH3': 1} Link IDs: {'TRANS': 46} Chain: "J" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 731 Classifications: {'peptide': 47} Link IDs: {'TRANS': 46} Chain: "K" Number of atoms: 1060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1060 Classifications: {'peptide': 74} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 72} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "L" Number of atoms: 1060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1060 Classifications: {'peptide': 74} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 72} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "M" Number of atoms: 1077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1077 Classifications: {'peptide': 75} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 73} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "N" Number of atoms: 1077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1077 Classifications: {'peptide': 75} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 73} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "O" Number of atoms: 1077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1077 Classifications: {'peptide': 75} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 73} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "P" Number of atoms: 1060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1060 Classifications: {'peptide': 74} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 72} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "Q" Number of atoms: 1077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1077 Classifications: {'peptide': 75} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 73} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "R" Number of atoms: 1077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1077 Classifications: {'peptide': 75} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 73} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "S" Number of atoms: 3004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 3004 Classifications: {'peptide': 188} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 8, 'TRANS': 179} Chain: "a" Number of atoms: 3611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 3611 Classifications: {'peptide': 226} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 12, 'TRANS': 213} Chain: "b" Number of atoms: 3454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 3454 Classifications: {'peptide': 209} Modifications used: {'NH2': 1} Link IDs: {'PTRANS': 7, 'TRANS': 201} Chain: "d" Number of atoms: 2567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 2567 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 10, 'TRANS': 144, 'PCIS': 1} Chain: "e" Number of atoms: 687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 687 Classifications: {'peptide': 41} Link IDs: {'PTRANS': 3, 'TRANS': 37} Chain: "f" Number of atoms: 1410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 1410 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 2, 'TRANS': 80} Chain: "g" Number of atoms: 1291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 1291 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 5, 'TRANS': 73} Chain: "h" Number of atoms: 1009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 1009 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 5, 'TRANS': 56} Chain: "j" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 828 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 2, 'TRANS': 45} Chain: "k" Number of atoms: 596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 596 Classifications: {'peptide': 36} Link IDs: {'TRANS': 35} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "b" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 83 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 17 Chain: "f" Number of atoms: 250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 250 Unusual residues: {'CDL': 2, 'LHG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 48 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "F" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Time building chain proxies: 31.62, per 1000 atoms: 0.39 Number of scatterers: 80353 At special positions: 0 Unit cell: (149.864, 145.672, 247.328, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 154 16.00 P 23 15.00 Mg 5 11.99 O 7522 8.00 N 6727 7.00 C 25517 6.00 H 40405 1.00 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: 55.00 Conformation dependent library (CDL) restraints added in 5.0 seconds 10128 Ramachandran restraints generated. 5064 Oldfield, 0 Emsley, 5064 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9408 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 194 helices and 24 sheets defined 52.9% alpha, 8.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.24 Creating SS restraints... Processing helix chain '8' and resid 2 through 4 No H-bonds generated for 'chain '8' and resid 2 through 4' Processing helix chain '8' and resid 6 through 20 removed outlier: 4.465A pdb=" N LEU 8 10 " --> pdb=" O SER 8 7 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N LEU 8 18 " --> pdb=" O SER 8 15 " (cutoff:3.500A) Processing helix chain '8' and resid 23 through 29 Processing helix chain 'A' and resid 9 through 16 Processing helix chain 'A' and resid 101 through 103 No H-bonds generated for 'chain 'A' and resid 101 through 103' Processing helix chain 'A' and resid 151 through 156 Processing helix chain 'A' and resid 175 through 190 removed outlier: 3.887A pdb=" N GLN A 186 " --> pdb=" O THR A 182 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N LYS A 187 " --> pdb=" O ILE A 183 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N ARG A 188 " --> pdb=" O ILE A 184 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N PHE A 189 " --> pdb=" O ASN A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 222 Processing helix chain 'A' and resid 240 through 260 Proline residue: A 247 - end of helix removed outlier: 3.966A pdb=" N PHE A 257 " --> pdb=" O MET A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 284 removed outlier: 3.531A pdb=" N VAL A 276 " --> pdb=" O SER A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 293 No H-bonds generated for 'chain 'A' and resid 291 through 293' Processing helix chain 'A' and resid 299 through 308 removed outlier: 3.715A pdb=" N LEU A 305 " --> pdb=" O LEU A 301 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N ARG A 308 " --> pdb=" O ARG A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 345 Processing helix chain 'A' and resid 355 through 358 No H-bonds generated for 'chain 'A' and resid 355 through 358' Processing helix chain 'A' and resid 375 through 378 Processing helix chain 'A' and resid 381 through 398 removed outlier: 4.073A pdb=" N THR A 389 " --> pdb=" O GLN A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 405 removed outlier: 3.875A pdb=" N GLN A 405 " --> pdb=" O ALA A 402 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 402 through 405' Processing helix chain 'A' and resid 412 through 428 Processing helix chain 'A' and resid 438 through 449 Processing helix chain 'A' and resid 458 through 475 removed outlier: 4.332A pdb=" N THR A 462 " --> pdb=" O SER A 459 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N GLU A 465 " --> pdb=" O THR A 462 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE A 468 " --> pdb=" O GLU A 465 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLN A 475 " --> pdb=" O VAL A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 486 Processing helix chain 'A' and resid 491 through 506 Processing helix chain 'B' and resid 79 through 81 No H-bonds generated for 'chain 'B' and resid 79 through 81' Processing helix chain 'B' and resid 101 through 103 No H-bonds generated for 'chain 'B' and resid 101 through 103' Processing helix chain 'B' and resid 151 through 156 Processing helix chain 'B' and resid 175 through 190 removed outlier: 4.369A pdb=" N LYS B 187 " --> pdb=" O ILE B 183 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N ARG B 188 " --> pdb=" O ILE B 184 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N PHE B 189 " --> pdb=" O ASN B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 222 Processing helix chain 'B' and resid 240 through 260 Proline residue: B 247 - end of helix removed outlier: 4.103A pdb=" N PHE B 257 " --> pdb=" O MET B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 284 removed outlier: 3.535A pdb=" N ALA B 275 " --> pdb=" O LEU B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 293 No H-bonds generated for 'chain 'B' and resid 291 through 293' Processing helix chain 'B' and resid 298 through 306 removed outlier: 3.860A pdb=" N LEU B 305 " --> pdb=" O LEU B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 345 Processing helix chain 'B' and resid 354 through 359 Processing helix chain 'B' and resid 381 through 400 removed outlier: 3.911A pdb=" N VAL B 386 " --> pdb=" O ALA B 382 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N THR B 389 " --> pdb=" O GLN B 385 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU B 399 " --> pdb=" O ALA B 395 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL B 400 " --> pdb=" O GLN B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 428 Processing helix chain 'B' and resid 438 through 449 Processing helix chain 'B' and resid 458 through 474 removed outlier: 3.741A pdb=" N ILE B 461 " --> pdb=" O PRO B 458 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N THR B 462 " --> pdb=" O SER B 459 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU B 469 " --> pdb=" O ASN B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 486 Processing helix chain 'B' and resid 491 through 506 Processing helix chain 'C' and resid 7 through 17 removed outlier: 3.596A pdb=" N ARG C 15 " --> pdb=" O ILE C 11 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE C 16 " --> pdb=" O LEU C 12 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 103 No H-bonds generated for 'chain 'C' and resid 101 through 103' Processing helix chain 'C' and resid 151 through 155 Processing helix chain 'C' and resid 175 through 191 removed outlier: 3.667A pdb=" N GLN C 186 " --> pdb=" O THR C 182 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N LYS C 187 " --> pdb=" O ILE C 183 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N ARG C 188 " --> pdb=" O ILE C 184 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N PHE C 189 " --> pdb=" O ASN C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 222 Processing helix chain 'C' and resid 240 through 243 No H-bonds generated for 'chain 'C' and resid 240 through 243' Processing helix chain 'C' and resid 246 through 260 removed outlier: 3.855A pdb=" N PHE C 257 " --> pdb=" O MET C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 284 removed outlier: 3.686A pdb=" N VAL C 276 " --> pdb=" O SER C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 293 No H-bonds generated for 'chain 'C' and resid 291 through 293' Processing helix chain 'C' and resid 298 through 308 removed outlier: 3.754A pdb=" N HIS C 302 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LEU C 305 " --> pdb=" O LEU C 301 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ARG C 308 " --> pdb=" O ARG C 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 314 through 316 No H-bonds generated for 'chain 'C' and resid 314 through 316' Processing helix chain 'C' and resid 337 through 345 Processing helix chain 'C' and resid 354 through 358 Processing helix chain 'C' and resid 381 through 399 removed outlier: 3.535A pdb=" N GLY C 388 " --> pdb=" O LYS C 384 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N THR C 389 " --> pdb=" O GLN C 385 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU C 399 " --> pdb=" O ALA C 395 " (cutoff:3.500A) Processing helix chain 'C' and resid 412 through 427 Processing helix chain 'C' and resid 438 through 449 Processing helix chain 'C' and resid 453 through 455 No H-bonds generated for 'chain 'C' and resid 453 through 455' Processing helix chain 'C' and resid 461 through 475 removed outlier: 3.756A pdb=" N SER C 474 " --> pdb=" O SER C 470 " (cutoff:3.500A) Processing helix chain 'C' and resid 477 through 486 Processing helix chain 'C' and resid 491 through 506 removed outlier: 3.594A pdb=" N ALA C 506 " --> pdb=" O THR C 502 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 125 No H-bonds generated for 'chain 'D' and resid 123 through 125' Processing helix chain 'D' and resid 138 through 143 Processing helix chain 'D' and resid 162 through 172 Processing helix chain 'D' and resid 190 through 203 Processing helix chain 'D' and resid 226 through 245 removed outlier: 3.587A pdb=" N ARG D 231 " --> pdb=" O GLY D 227 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ALA D 233 " --> pdb=" O ARG D 229 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N LEU D 234 " --> pdb=" O ALA D 230 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 266 Processing helix chain 'D' and resid 270 through 272 No H-bonds generated for 'chain 'D' and resid 270 through 272' Processing helix chain 'D' and resid 285 through 293 removed outlier: 3.704A pdb=" N MET D 292 " --> pdb=" O ASP D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 313 through 315 No H-bonds generated for 'chain 'D' and resid 313 through 315' Processing helix chain 'D' and resid 320 through 328 removed outlier: 4.347A pdb=" N ALA D 327 " --> pdb=" O ALA D 323 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N HIS D 328 " --> pdb=" O THR D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 337 through 340 No H-bonds generated for 'chain 'D' and resid 337 through 340' Processing helix chain 'D' and resid 365 through 388 removed outlier: 3.890A pdb=" N ASP D 386 " --> pdb=" O LYS D 382 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ILE D 387 " --> pdb=" O SER D 383 " (cutoff:3.500A) Processing helix chain 'D' and resid 393 through 395 No H-bonds generated for 'chain 'D' and resid 393 through 395' Processing helix chain 'D' and resid 400 through 413 Processing helix chain 'D' and resid 422 through 425 No H-bonds generated for 'chain 'D' and resid 422 through 425' Processing helix chain 'D' and resid 434 through 446 Processing helix chain 'D' and resid 454 through 457 Processing helix chain 'D' and resid 463 through 475 Processing helix chain 'E' and resid 88 through 90 No H-bonds generated for 'chain 'E' and resid 88 through 90' Processing helix chain 'E' and resid 138 through 143 Processing helix chain 'E' and resid 162 through 176 Processing helix chain 'E' and resid 190 through 203 Processing helix chain 'E' and resid 226 through 229 No H-bonds generated for 'chain 'E' and resid 226 through 229' Processing helix chain 'E' and resid 232 through 245 removed outlier: 3.758A pdb=" N PHE E 243 " --> pdb=" O VAL E 239 " (cutoff:3.500A) Processing helix chain 'E' and resid 258 through 272 Processing helix chain 'E' and resid 285 through 293 removed outlier: 3.979A pdb=" N MET E 292 " --> pdb=" O ASP E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 313 through 315 No H-bonds generated for 'chain 'E' and resid 313 through 315' Processing helix chain 'E' and resid 320 through 325 Processing helix chain 'E' and resid 337 through 340 No H-bonds generated for 'chain 'E' and resid 337 through 340' Processing helix chain 'E' and resid 360 through 363 No H-bonds generated for 'chain 'E' and resid 360 through 363' Processing helix chain 'E' and resid 365 through 391 removed outlier: 3.927A pdb=" N ASP E 386 " --> pdb=" O LYS E 382 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE E 387 " --> pdb=" O SER E 383 " (cutoff:3.500A) Processing helix chain 'E' and resid 393 through 395 No H-bonds generated for 'chain 'E' and resid 393 through 395' Processing helix chain 'E' and resid 398 through 414 removed outlier: 3.687A pdb=" N LEU E 402 " --> pdb=" O GLU E 398 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N THR E 403 " --> pdb=" O GLU E 399 " (cutoff:3.500A) Processing helix chain 'E' and resid 422 through 425 No H-bonds generated for 'chain 'E' and resid 422 through 425' Processing helix chain 'E' and resid 434 through 446 Processing helix chain 'E' and resid 454 through 457 Processing helix chain 'E' and resid 463 through 474 Processing helix chain 'F' and resid 88 through 90 No H-bonds generated for 'chain 'F' and resid 88 through 90' Processing helix chain 'F' and resid 123 through 125 No H-bonds generated for 'chain 'F' and resid 123 through 125' Processing helix chain 'F' and resid 138 through 143 Processing helix chain 'F' and resid 162 through 175 Processing helix chain 'F' and resid 190 through 203 Processing helix chain 'F' and resid 226 through 230 Processing helix chain 'F' and resid 233 through 245 removed outlier: 3.548A pdb=" N PHE F 243 " --> pdb=" O VAL F 239 " (cutoff:3.500A) Processing helix chain 'F' and resid 258 through 272 removed outlier: 3.983A pdb=" N GLN F 263 " --> pdb=" O ARG F 260 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA F 264 " --> pdb=" O PHE F 261 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N SER F 269 " --> pdb=" O SER F 266 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ALA F 270 " --> pdb=" O GLU F 267 " (cutoff:3.500A) Processing helix chain 'F' and resid 285 through 295 removed outlier: 4.176A pdb=" N ARG F 295 " --> pdb=" O THR F 291 " (cutoff:3.500A) Processing helix chain 'F' and resid 313 through 315 No H-bonds generated for 'chain 'F' and resid 313 through 315' Processing helix chain 'F' and resid 320 through 328 removed outlier: 4.456A pdb=" N ALA F 327 " --> pdb=" O ALA F 323 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N HIS F 328 " --> pdb=" O THR F 324 " (cutoff:3.500A) Processing helix chain 'F' and resid 337 through 341 Processing helix chain 'F' and resid 366 through 390 removed outlier: 4.415A pdb=" N ASP F 386 " --> pdb=" O LYS F 382 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N ILE F 387 " --> pdb=" O SER F 383 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE F 390 " --> pdb=" O ASP F 386 " (cutoff:3.500A) Processing helix chain 'F' and resid 398 through 413 Processing helix chain 'F' and resid 422 through 425 No H-bonds generated for 'chain 'F' and resid 422 through 425' Processing helix chain 'F' and resid 434 through 446 Processing helix chain 'F' and resid 454 through 456 No H-bonds generated for 'chain 'F' and resid 454 through 456' Processing helix chain 'F' and resid 463 through 473 Processing helix chain 'G' and resid 3 through 54 Proline residue: G 40 - end of helix removed outlier: 4.381A pdb=" N LEU G 51 " --> pdb=" O GLY G 47 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N TYR G 52 " --> pdb=" O SER G 48 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLU G 53 " --> pdb=" O LEU G 49 " (cutoff:3.500A) Processing helix chain 'G' and resid 82 through 98 Processing helix chain 'G' and resid 110 through 115 Processing helix chain 'G' and resid 138 through 150 Processing helix chain 'G' and resid 181 through 185 Processing helix chain 'G' and resid 188 through 192 removed outlier: 3.628A pdb=" N ILE G 192 " --> pdb=" O SER G 189 " (cutoff:3.500A) Processing helix chain 'G' and resid 200 through 270 Processing helix chain 'H' and resid 100 through 102 No H-bonds generated for 'chain 'H' and resid 100 through 102' Processing helix chain 'H' and resid 105 through 120 removed outlier: 4.258A pdb=" N LEU H 120 " --> pdb=" O GLN H 116 " (cutoff:3.500A) Processing helix chain 'H' and resid 125 through 145 Processing helix chain 'I' and resid 3 through 6 No H-bonds generated for 'chain 'I' and resid 3 through 6' Processing helix chain 'I' and resid 11 through 25 removed outlier: 4.142A pdb=" N ALA I 25 " --> pdb=" O ALA I 21 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 35 removed outlier: 3.791A pdb=" N ALA I 32 " --> pdb=" O THR I 28 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ASN I 33 " --> pdb=" O GLU I 29 " (cutoff:3.500A) Processing helix chain 'J' and resid 15 through 18 No H-bonds generated for 'chain 'J' and resid 15 through 18' Processing helix chain 'J' and resid 21 through 52 removed outlier: 3.791A pdb=" N TYR J 33 " --> pdb=" O GLU J 29 " (cutoff:3.500A) Processing helix chain 'K' and resid 2 through 12 Processing helix chain 'K' and resid 16 through 38 removed outlier: 4.017A pdb=" N GLY K 20 " --> pdb=" O GLY K 17 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N LEU K 32 " --> pdb=" O PHE K 29 " (cutoff:3.500A) Processing helix chain 'K' and resid 46 through 72 removed outlier: 3.992A pdb=" N LEU K 52 " --> pdb=" O SER K 48 " (cutoff:3.500A) Processing helix chain 'L' and resid 2 through 13 removed outlier: 3.802A pdb=" N PHE L 8 " --> pdb=" O THR L 4 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ILE L 9 " --> pdb=" O ALA L 5 " (cutoff:3.500A) Processing helix chain 'L' and resid 16 through 38 removed outlier: 3.931A pdb=" N GLY L 20 " --> pdb=" O GLY L 17 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N THR L 27 " --> pdb=" O GLY L 24 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ARG L 38 " --> pdb=" O GLY L 35 " (cutoff:3.500A) Processing helix chain 'L' and resid 46 through 72 Processing helix chain 'M' and resid 3 through 38 removed outlier: 5.259A pdb=" N PHE M 8 " --> pdb=" O THR M 4 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ILE M 9 " --> pdb=" O ALA M 5 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N VAL M 16 " --> pdb=" O GLY M 12 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N GLY M 17 " --> pdb=" O ALA M 13 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N VAL M 18 " --> pdb=" O ALA M 14 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N ALA M 19 " --> pdb=" O THR M 15 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N GLY M 20 " --> pdb=" O VAL M 16 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N SER M 21 " --> pdb=" O GLY M 17 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ILE M 33 " --> pdb=" O PHE M 29 " (cutoff:3.500A) Processing helix chain 'M' and resid 46 through 72 removed outlier: 4.287A pdb=" N MET M 60 " --> pdb=" O LEU M 56 " (cutoff:3.500A) Processing helix chain 'N' and resid 2 through 16 removed outlier: 3.667A pdb=" N VAL N 16 " --> pdb=" O GLY N 12 " (cutoff:3.500A) Processing helix chain 'N' and resid 19 through 38 removed outlier: 4.056A pdb=" N GLY N 26 " --> pdb=" O GLY N 22 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ILE N 33 " --> pdb=" O PHE N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 45 through 73 removed outlier: 3.880A pdb=" N MET N 60 " --> pdb=" O LEU N 56 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N CYS N 64 " --> pdb=" O MET N 60 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N VAL N 67 " --> pdb=" O PHE N 63 " (cutoff:3.500A) Processing helix chain 'O' and resid 2 through 38 removed outlier: 4.173A pdb=" N VAL O 16 " --> pdb=" O GLY O 12 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N GLY O 17 " --> pdb=" O ALA O 13 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N VAL O 18 " --> pdb=" O ALA O 14 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N ALA O 19 " --> pdb=" O THR O 15 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N GLY O 20 " --> pdb=" O VAL O 16 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N SER O 21 " --> pdb=" O GLY O 17 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ILE O 33 " --> pdb=" O PHE O 29 " (cutoff:3.500A) Processing helix chain 'O' and resid 45 through 72 removed outlier: 3.978A pdb=" N MET O 60 " --> pdb=" O LEU O 56 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N CYS O 64 " --> pdb=" O MET O 60 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 36 removed outlier: 4.253A pdb=" N VAL P 16 " --> pdb=" O GLY P 12 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N GLY P 17 " --> pdb=" O ALA P 13 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N VAL P 18 " --> pdb=" O ALA P 14 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N ALA P 19 " --> pdb=" O THR P 15 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N GLY P 20 " --> pdb=" O VAL P 16 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N SER P 21 " --> pdb=" O GLY P 17 " (cutoff:3.500A) Processing helix chain 'P' and resid 44 through 73 removed outlier: 4.020A pdb=" N MET P 60 " --> pdb=" O SER P 57 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N PHE P 63 " --> pdb=" O MET P 60 " (cutoff:3.500A) Processing helix chain 'Q' and resid 3 through 38 removed outlier: 5.683A pdb=" N PHE Q 8 " --> pdb=" O THR Q 4 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ILE Q 9 " --> pdb=" O ALA Q 5 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N VAL Q 16 " --> pdb=" O GLY Q 12 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N GLY Q 17 " --> pdb=" O ALA Q 13 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N VAL Q 18 " --> pdb=" O ALA Q 14 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N ALA Q 19 " --> pdb=" O THR Q 15 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N GLY Q 20 " --> pdb=" O VAL Q 16 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N SER Q 21 " --> pdb=" O GLY Q 17 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLY Q 26 " --> pdb=" O GLY Q 22 " (cutoff:3.500A) Processing helix chain 'Q' and resid 46 through 74 removed outlier: 4.345A pdb=" N MET Q 60 " --> pdb=" O LEU Q 56 " (cutoff:3.500A) Processing helix chain 'R' and resid 6 through 38 removed outlier: 4.090A pdb=" N VAL R 16 " --> pdb=" O GLY R 12 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N GLY R 17 " --> pdb=" O ALA R 13 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N VAL R 18 " --> pdb=" O ALA R 14 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N ALA R 19 " --> pdb=" O THR R 15 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N GLY R 20 " --> pdb=" O VAL R 16 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N SER R 21 " --> pdb=" O GLY R 17 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE R 33 " --> pdb=" O PHE R 29 " (cutoff:3.500A) Processing helix chain 'R' and resid 46 through 72 removed outlier: 4.429A pdb=" N MET R 60 " --> pdb=" O LEU R 56 " (cutoff:3.500A) Processing helix chain 'S' and resid 14 through 27 Processing helix chain 'S' and resid 32 through 45 removed outlier: 3.571A pdb=" N GLN S 44 " --> pdb=" O LEU S 40 " (cutoff:3.500A) Processing helix chain 'S' and resid 49 through 55 Processing helix chain 'S' and resid 62 through 76 Processing helix chain 'S' and resid 80 through 91 Processing helix chain 'S' and resid 95 through 112 Proline residue: S 99 - end of helix removed outlier: 3.576A pdb=" N SER S 110 " --> pdb=" O THR S 107 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N VAL S 111 " --> pdb=" O MET S 108 " (cutoff:3.500A) Processing helix chain 'S' and resid 128 through 141 Processing helix chain 'S' and resid 175 through 187 Processing helix chain 'a' and resid 6 through 9 Processing helix chain 'a' and resid 19 through 30 removed outlier: 3.738A pdb=" N PHE a 26 " --> pdb=" O ILE a 23 " (cutoff:3.500A) Proline residue: a 27 - end of helix Processing helix chain 'a' and resid 41 through 60 removed outlier: 4.136A pdb=" N GLN a 46 " --> pdb=" O PHE a 42 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N SER a 59 " --> pdb=" O LYS a 55 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N ILE a 60 " --> pdb=" O GLN a 56 " (cutoff:3.500A) Processing helix chain 'a' and resid 63 through 86 removed outlier: 4.270A pdb=" N TRP a 68 " --> pdb=" O LYS a 64 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N THR a 69 " --> pdb=" O GLY a 65 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N LEU a 70 " --> pdb=" O GLN a 66 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N MET a 71 " --> pdb=" O THR a 67 " (cutoff:3.500A) Processing helix chain 'a' and resid 98 through 119 Proline residue: a 107 - end of helix Processing helix chain 'a' and resid 122 through 126 Processing helix chain 'a' and resid 135 through 149 Proline residue: a 139 - end of helix removed outlier: 4.343A pdb=" N ILE a 143 " --> pdb=" O MET a 140 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N THR a 146 " --> pdb=" O ILE a 143 " (cutoff:3.500A) Processing helix chain 'a' and resid 152 through 183 removed outlier: 3.699A pdb=" N ILE a 164 " --> pdb=" O LEU a 160 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N MET a 182 " --> pdb=" O THR a 178 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N SER a 183 " --> pdb=" O LEU a 179 " (cutoff:3.500A) Processing helix chain 'a' and resid 186 through 225 removed outlier: 3.777A pdb=" N MET a 208 " --> pdb=" O PHE a 204 " (cutoff:3.500A) Processing helix chain 'b' and resid 19 through 29 removed outlier: 3.813A pdb=" N TYR b 26 " --> pdb=" O GLN b 23 " (cutoff:3.500A) Proline residue: b 27 - end of helix Processing helix chain 'b' and resid 33 through 47 Processing helix chain 'b' and resid 55 through 186 removed outlier: 3.630A pdb=" N TYR b 69 " --> pdb=" O GLY b 65 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N ALA b 76 " --> pdb=" O LYS b 72 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N SER b 77 " --> pdb=" O LYS b 73 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL b 96 " --> pdb=" O GLN b 92 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LYS b 120 " --> pdb=" O ALA b 116 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N HIS b 122 " --> pdb=" O VAL b 118 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N TYR b 123 " --> pdb=" O GLN b 119 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N LEU b 124 " --> pdb=" O LYS b 120 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N PHE b 125 " --> pdb=" O ARG b 121 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N HIS b 158 " --> pdb=" O ARG b 154 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N SER b 186 " --> pdb=" O VAL b 182 " (cutoff:3.500A) Processing helix chain 'b' and resid 190 through 208 Processing helix chain 'd' and resid 12 through 18 removed outlier: 3.633A pdb=" N GLU d 17 " --> pdb=" O VAL d 13 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ILE d 18 " --> pdb=" O ALA d 14 " (cutoff:3.500A) Processing helix chain 'd' and resid 21 through 43 removed outlier: 3.584A pdb=" N LYS d 24 " --> pdb=" O ARG d 21 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N ALA d 25 " --> pdb=" O ASN d 22 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N ASN d 28 " --> pdb=" O ALA d 25 " (cutoff:3.500A) Processing helix chain 'd' and resid 53 through 59 Processing helix chain 'd' and resid 63 through 75 Processing helix chain 'd' and resid 84 through 100 removed outlier: 4.656A pdb=" N GLN d 88 " --> pdb=" O TYR d 85 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N SER d 99 " --> pdb=" O ASP d 96 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N CYS d 100 " --> pdb=" O VAL d 97 " (cutoff:3.500A) Processing helix chain 'd' and resid 102 through 122 Processing helix chain 'd' and resid 127 through 129 No H-bonds generated for 'chain 'd' and resid 127 through 129' Processing helix chain 'd' and resid 132 through 138 Processing helix chain 'e' and resid 8 through 41 Proline residue: e 34 - end of helix Processing helix chain 'f' and resid 11 through 13 No H-bonds generated for 'chain 'f' and resid 11 through 13' Processing helix chain 'f' and resid 16 through 25 Proline residue: f 20 - end of helix removed outlier: 3.746A pdb=" N LEU f 24 " --> pdb=" O PRO f 20 " (cutoff:3.500A) Processing helix chain 'f' and resid 30 through 48 removed outlier: 3.603A pdb=" N ARG f 39 " --> pdb=" O GLY f 35 " (cutoff:3.500A) Processing helix chain 'f' and resid 56 through 73 removed outlier: 4.011A pdb=" N SER f 60 " --> pdb=" O ALA f 57 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N MET f 61 " --> pdb=" O GLY f 58 " (cutoff:3.500A) Processing helix chain 'f' and resid 76 through 78 No H-bonds generated for 'chain 'f' and resid 76 through 78' Processing helix chain 'g' and resid 22 through 36 removed outlier: 4.564A pdb=" N VAL g 35 " --> pdb=" O TYR g 31 " (cutoff:3.500A) Processing helix chain 'g' and resid 42 through 60 Proline residue: g 46 - end of helix Processing helix chain 'g' and resid 64 through 66 No H-bonds generated for 'chain 'g' and resid 64 through 66' Processing helix chain 'g' and resid 69 through 93 removed outlier: 3.518A pdb=" N TRP g 85 " --> pdb=" O GLU g 81 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N PHE g 86 " --> pdb=" O VAL g 82 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N TYR g 87 " --> pdb=" O TRP g 83 " (cutoff:3.500A) Processing helix chain 'h' and resid 9 through 23 Processing helix chain 'h' and resid 32 through 50 removed outlier: 4.013A pdb=" N GLN h 36 " --> pdb=" O GLY h 32 " (cutoff:3.500A) Processing helix chain 'j' and resid 3 through 9 Processing helix chain 'j' and resid 14 through 18 Processing helix chain 'j' and resid 22 through 46 Processing helix chain 'k' and resid 13 through 16 No H-bonds generated for 'chain 'k' and resid 13 through 16' Processing helix chain 'k' and resid 23 through 45 Processing sheet with id= A, first strand: chain 'A' and resid 28 through 30 removed outlier: 6.346A pdb=" N GLY A 72 " --> pdb=" O LEU A 64 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N HIS A 42 " --> pdb=" O VAL A 31 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N VAL A 31 " --> pdb=" O HIS A 42 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 96 through 99 removed outlier: 3.882A pdb=" N ALA A 125 " --> pdb=" O VAL A 99 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 164 through 169 removed outlier: 8.259A pdb=" N GLU A 165 " --> pdb=" O LEU A 321 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N ALA A 323 " --> pdb=" O GLU A 165 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N ILE A 167 " --> pdb=" O ALA A 323 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N GLY A 169 " --> pdb=" O PRO A 325 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N ILE A 327 " --> pdb=" O GLY A 169 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N TYR A 268 " --> pdb=" O LEU A 324 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N TYR A 200 " --> pdb=" O LEU A 265 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N ILE A 267 " --> pdb=" O TYR A 200 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N ILE A 202 " --> pdb=" O ILE A 267 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N ASP A 269 " --> pdb=" O ILE A 202 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N VAL A 204 " --> pdb=" O ASP A 269 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 28 through 30 removed outlier: 6.188A pdb=" N GLY B 72 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N HIS B 42 " --> pdb=" O VAL B 31 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N VAL B 31 " --> pdb=" O HIS B 42 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 96 through 99 removed outlier: 3.974A pdb=" N ALA B 125 " --> pdb=" O VAL B 99 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 167 through 169 Processing sheet with id= G, first strand: chain 'B' and resid 229 through 234 removed outlier: 8.807A pdb=" N ILE B 230 " --> pdb=" O LEU B 199 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N CYS B 201 " --> pdb=" O ILE B 230 " (cutoff:3.500A) removed outlier: 8.305A pdb=" N VAL B 232 " --> pdb=" O CYS B 201 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N TYR B 203 " --> pdb=" O VAL B 232 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N ALA B 234 " --> pdb=" O TYR B 203 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N ALA B 205 " --> pdb=" O ALA B 234 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N HIS B 263 " --> pdb=" O TYR B 200 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N ILE B 202 " --> pdb=" O HIS B 263 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N LEU B 265 " --> pdb=" O ILE B 202 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N VAL B 204 " --> pdb=" O LEU B 265 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N ILE B 267 " --> pdb=" O VAL B 204 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N ILE B 206 " --> pdb=" O ILE B 267 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N ASP B 269 " --> pdb=" O ILE B 206 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N SER B 320 " --> pdb=" O ALA B 264 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N ILE B 266 " --> pdb=" O SER B 320 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N THR B 322 " --> pdb=" O ILE B 266 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N TYR B 268 " --> pdb=" O THR B 322 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'C' and resid 29 through 35 removed outlier: 6.648A pdb=" N ARG C 40 " --> pdb=" O LEU C 32 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N ILE C 34 " --> pdb=" O ILE C 38 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ILE C 38 " --> pdb=" O ILE C 34 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N VAL C 74 " --> pdb=" O SER C 63 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N SER C 63 " --> pdb=" O VAL C 74 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 96 through 99 removed outlier: 4.135A pdb=" N ALA C 125 " --> pdb=" O VAL C 99 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 164 through 169 removed outlier: 8.301A pdb=" N GLU C 165 " --> pdb=" O LEU C 321 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N ALA C 323 " --> pdb=" O GLU C 165 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N ILE C 167 " --> pdb=" O ALA C 323 " (cutoff:3.500A) removed outlier: 8.073A pdb=" N GLY C 169 " --> pdb=" O PRO C 325 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ILE C 327 " --> pdb=" O GLY C 169 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N TYR C 268 " --> pdb=" O LEU C 324 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N TYR C 200 " --> pdb=" O LEU C 265 " (cutoff:3.500A) removed outlier: 8.166A pdb=" N ILE C 267 " --> pdb=" O TYR C 200 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N ILE C 202 " --> pdb=" O ILE C 267 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N ASP C 269 " --> pdb=" O ILE C 202 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N VAL C 204 " --> pdb=" O ASP C 269 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.654A pdb=" N ARG D 59 " --> pdb=" O ALA D 50 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N HIS D 52 " --> pdb=" O THR D 57 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N THR D 57 " --> pdb=" O HIS D 52 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N GLN D 24 " --> pdb=" O ILE D 13 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N ILE D 13 " --> pdb=" O GLN D 24 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 83 through 86 removed outlier: 4.260A pdb=" N GLN D 112 " --> pdb=" O VAL D 86 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 151 through 156 removed outlier: 7.508A pdb=" N ILE D 152 " --> pdb=" O ILE D 304 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N SER D 306 " --> pdb=" O ILE D 152 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N LEU D 154 " --> pdb=" O SER D 306 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N GLN D 308 " --> pdb=" O LEU D 154 " (cutoff:3.500A) removed outlier: 8.100A pdb=" N GLY D 156 " --> pdb=" O GLN D 308 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N ILE D 310 " --> pdb=" O GLY D 156 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N TYR D 180 " --> pdb=" O LEU D 252 " (cutoff:3.500A) removed outlier: 8.759A pdb=" N PHE D 254 " --> pdb=" O TYR D 180 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N VAL D 182 " --> pdb=" O PHE D 254 " (cutoff:3.500A) removed outlier: 8.432A pdb=" N ASP D 256 " --> pdb=" O VAL D 182 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N ALA D 184 " --> pdb=" O ASP D 256 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ALA D 216 " --> pdb=" O PHE D 183 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N GLY D 185 " --> pdb=" O ALA D 216 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N VAL D 218 " --> pdb=" O GLY D 185 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.611A pdb=" N ARG E 59 " --> pdb=" O ALA E 50 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N HIS E 52 " --> pdb=" O THR E 57 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N THR E 57 " --> pdb=" O HIS E 52 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N GLN E 24 " --> pdb=" O ILE E 13 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N ILE E 13 " --> pdb=" O GLN E 24 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'E' and resid 83 through 85 Processing sheet with id= P, first strand: chain 'E' and resid 332 through 334 removed outlier: 6.353A pdb=" N GLY E 153 " --> pdb=" O THR E 333 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ALA E 216 " --> pdb=" O PHE E 183 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N GLY E 185 " --> pdb=" O ALA E 216 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N VAL E 218 " --> pdb=" O GLY E 185 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N GLY E 187 " --> pdb=" O VAL E 218 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N GLY E 220 " --> pdb=" O GLY E 187 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'F' and resid 10 through 12 removed outlier: 4.493A pdb=" N LYS F 74 " --> pdb=" O GLN F 39 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ARG F 59 " --> pdb=" O ALA F 50 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N HIS F 52 " --> pdb=" O THR F 57 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N THR F 57 " --> pdb=" O HIS F 52 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA F 15 " --> pdb=" O ASP F 22 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N GLN F 24 " --> pdb=" O ILE F 13 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N ILE F 13 " --> pdb=" O GLN F 24 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'F' and resid 83 through 85 Processing sheet with id= S, first strand: chain 'F' and resid 331 through 334 removed outlier: 7.616A pdb=" N ILE F 152 " --> pdb=" O ILE F 304 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N SER F 306 " --> pdb=" O ILE F 152 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N LEU F 154 " --> pdb=" O SER F 306 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N GLN F 308 " --> pdb=" O LEU F 154 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N GLY F 156 " --> pdb=" O GLN F 308 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N ILE F 310 " --> pdb=" O GLY F 156 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'G' and resid 170 through 178 removed outlier: 6.428A pdb=" N LYS G 172 " --> pdb=" O PHE G 165 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N PHE G 165 " --> pdb=" O LYS G 172 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N GLU G 174 " --> pdb=" O ASN G 163 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N ASN G 163 " --> pdb=" O GLU G 174 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N LYS G 176 " --> pdb=" O ILE G 161 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N ILE G 161 " --> pdb=" O LYS G 176 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N ILE G 178 " --> pdb=" O SER G 159 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N SER G 159 " --> pdb=" O ILE G 178 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N ASN G 163 " --> pdb=" O VAL G 71 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N GLU G 102 " --> pdb=" O HIS G 66 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N ILE G 68 " --> pdb=" O GLU G 102 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N LYS G 104 " --> pdb=" O ILE G 68 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N GLY G 70 " --> pdb=" O LYS G 104 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ILE G 106 " --> pdb=" O GLY G 70 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N GLY G 107 " --> pdb=" O LEU G 125 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N THR G 127 " --> pdb=" O GLY G 107 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'H' and resid 54 through 56 removed outlier: 6.258A pdb=" N THR H 19 " --> pdb=" O LEU H 92 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N ALA H 94 " --> pdb=" O THR H 19 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N ALA H 21 " --> pdb=" O ALA H 94 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'H' and resid 45 through 47 removed outlier: 3.691A pdb=" N GLN H 35 " --> pdb=" O HIS H 66 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'S' and resid 115 through 117 removed outlier: 7.283A pdb=" N VAL S 147 " --> pdb=" O VAL S 116 " (cutoff:3.500A) No H-bonds generated for sheet with id= W Processing sheet with id= X, first strand: chain 'S' and resid 152 through 154 removed outlier: 7.325A pdb=" N LYS S 153 " --> pdb=" O CYS S 118 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N VAL S 120 " --> pdb=" O LYS S 153 " (cutoff:3.500A) 1991 hydrogen bonds defined for protein. 5409 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 30.82 Time building geometry restraints manager: 57.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 40384 1.03 - 1.23: 177 1.23 - 1.42: 15956 1.42 - 1.62: 24157 1.62 - 1.81: 302 Bond restraints: 80976 Sorted by residual: bond pdb=" C4 ATP C 600 " pdb=" C5 ATP C 600 " ideal model delta sigma weight residual 1.388 1.462 -0.074 1.00e-02 1.00e+04 5.55e+01 bond pdb=" C4 ATP A 600 " pdb=" C5 ATP A 600 " ideal model delta sigma weight residual 1.388 1.462 -0.074 1.00e-02 1.00e+04 5.49e+01 bond pdb=" C4 ATP B 600 " pdb=" C5 ATP B 600 " ideal model delta sigma weight residual 1.388 1.462 -0.074 1.00e-02 1.00e+04 5.42e+01 bond pdb=" CB7 CDL f 102 " pdb=" OB8 CDL f 102 " ideal model delta sigma weight residual 1.334 1.409 -0.075 1.10e-02 8.26e+03 4.60e+01 bond pdb=" CB7 CDL f 101 " pdb=" OB8 CDL f 101 " ideal model delta sigma weight residual 1.334 1.407 -0.073 1.10e-02 8.26e+03 4.37e+01 ... (remaining 80971 not shown) Histogram of bond angle deviations from ideal: 73.69 - 86.22: 7 86.22 - 98.75: 8 98.75 - 111.27: 93028 111.27 - 123.80: 48123 123.80 - 136.33: 5522 Bond angle restraints: 146688 Sorted by residual: angle pdb=" PB ATP A 600 " pdb=" O3B ATP A 600 " pdb=" PG ATP A 600 " ideal model delta sigma weight residual 139.87 116.12 23.75 1.00e+00 1.00e+00 5.64e+02 angle pdb=" PB ATP C 600 " pdb=" O3B ATP C 600 " pdb=" PG ATP C 600 " ideal model delta sigma weight residual 139.87 117.89 21.98 1.00e+00 1.00e+00 4.83e+02 angle pdb=" PA ATP B 600 " pdb=" O3A ATP B 600 " pdb=" PB ATP B 600 " ideal model delta sigma weight residual 136.83 117.95 18.88 1.00e+00 1.00e+00 3.56e+02 angle pdb=" PB ATP B 600 " pdb=" O3B ATP B 600 " pdb=" PG ATP B 600 " ideal model delta sigma weight residual 139.87 121.36 18.51 1.00e+00 1.00e+00 3.43e+02 angle pdb=" PA ATP C 600 " pdb=" O3A ATP C 600 " pdb=" PB ATP C 600 " ideal model delta sigma weight residual 136.83 121.56 15.27 1.00e+00 1.00e+00 2.33e+02 ... (remaining 146683 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.96: 31380 35.96 - 71.91: 616 71.91 - 107.87: 32 107.87 - 143.83: 0 143.83 - 179.78: 2 Dihedral angle restraints: 32030 sinusoidal: 15342 harmonic: 16688 Sorted by residual: dihedral pdb=" CD ARG d 155 " pdb=" NE ARG d 155 " pdb=" CZ ARG d 155 " pdb=" NH1 ARG d 155 " ideal model delta sinusoidal sigma weight residual 0.00 -179.78 179.78 1 1.00e+01 1.00e-02 1.92e+02 dihedral pdb=" C5' ADP E 600 " pdb=" O5' ADP E 600 " pdb=" PA ADP E 600 " pdb=" O2A ADP E 600 " ideal model delta sinusoidal sigma weight residual 300.00 146.22 153.78 1 2.00e+01 2.50e-03 4.55e+01 dihedral pdb=" CA GLN H 132 " pdb=" C GLN H 132 " pdb=" N ILE H 133 " pdb=" CA ILE H 133 " ideal model delta harmonic sigma weight residual 180.00 153.48 26.52 0 5.00e+00 4.00e-02 2.81e+01 ... (remaining 32027 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 5381 0.058 - 0.116: 851 0.116 - 0.173: 118 0.173 - 0.231: 0 0.231 - 0.289: 1 Chirality restraints: 6351 Sorted by residual: chirality pdb=" CA HIS 8 35 " pdb=" N HIS 8 35 " pdb=" C HIS 8 35 " pdb=" CB HIS 8 35 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.09e+00 chirality pdb=" CA PRO a 89 " pdb=" N PRO a 89 " pdb=" C PRO a 89 " pdb=" CB PRO a 89 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 7.43e-01 chirality pdb=" CA ILE b 174 " pdb=" N ILE b 174 " pdb=" C ILE b 174 " pdb=" CB ILE b 174 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 6.93e-01 ... (remaining 6348 not shown) Planarity restraints: 11850 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C7 LHG f 103 " 0.082 2.00e-02 2.50e+03 4.76e-02 2.27e+01 pdb=" C8 LHG f 103 " -0.024 2.00e-02 2.50e+03 pdb=" O7 LHG f 103 " -0.025 2.00e-02 2.50e+03 pdb=" O9 LHG f 103 " -0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C7 LHG f 104 " 0.069 2.00e-02 2.50e+03 3.97e-02 1.58e+01 pdb=" C8 LHG f 104 " -0.020 2.00e-02 2.50e+03 pdb=" O7 LHG f 104 " -0.021 2.00e-02 2.50e+03 pdb=" O9 LHG f 104 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP b 176 " 0.019 2.00e-02 2.50e+03 1.61e-02 1.03e+01 pdb=" CG TRP b 176 " -0.054 2.00e-02 2.50e+03 pdb=" CD1 TRP b 176 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 TRP b 176 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP b 176 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 TRP b 176 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP b 176 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP b 176 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP b 176 " 0.013 2.00e-02 2.50e+03 pdb=" CH2 TRP b 176 " -0.003 2.00e-02 2.50e+03 pdb=" HD1 TRP b 176 " 0.010 2.00e-02 2.50e+03 pdb=" HE1 TRP b 176 " 0.003 2.00e-02 2.50e+03 pdb=" HE3 TRP b 176 " -0.004 2.00e-02 2.50e+03 pdb=" HZ2 TRP b 176 " -0.000 2.00e-02 2.50e+03 pdb=" HZ3 TRP b 176 " 0.003 2.00e-02 2.50e+03 pdb=" HH2 TRP b 176 " 0.000 2.00e-02 2.50e+03 ... (remaining 11847 not shown) Histogram of nonbonded interaction distances: 1.15 - 1.84: 251 1.84 - 2.53: 70516 2.53 - 3.22: 255185 3.22 - 3.91: 324352 3.91 - 4.60: 521442 Nonbonded interactions: 1171746 Sorted by model distance: nonbonded pdb="HD23 LEU f 69 " pdb=" C81 CDL f 102 " model vdw 1.148 2.920 nonbonded pdb="HD21 LEU f 69 " pdb=" C81 CDL f 102 " model vdw 1.378 2.920 nonbonded pdb="HH12 ARG f 43 " pdb=" O5 LHG f 103 " model vdw 1.451 1.850 nonbonded pdb=" CD2 LEU f 69 " pdb=" C81 CDL f 102 " model vdw 1.497 3.400 nonbonded pdb=" O LEU M 42 " pdb=" H GLN M 44 " model vdw 1.526 1.850 ... (remaining 1171741 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 'A' and ((resid 23 and (name N or name CA or name C or name O or name CB \ or name CG1 or name CG2 or name HA or name HB or name HG11 or name HG12 or name \ HG13 or name HG21 or name HG22 or name HG23)) or resid 24 through 401 or (resid \ 411 and (name N or name CA or name C or name O or name CB or name CG or name OD1 \ or name OD2 or name HA or name HB2 or name HB3)) or resid 412 through 508 or re \ sid 600 through 601)) selection = chain 'B' selection = (chain 'C' and ((resid 23 and (name N or name CA or name C or name O or name CB \ or name CG1 or name CG2 or name HA or name HB or name HG11 or name HG12 or name \ HG13 or name HG21 or name HG22 or name HG23)) or resid 24 through 401 or (resid \ 411 and (name N or name CA or name C or name O or name CB or name CG or name OD1 \ or name OD2 or name HA or name HB2 or name HB3)) or resid 412 through 508 or re \ sid 600 through 601)) } ncs_group { reference = (chain 'D' and resid 9 through 475) selection = (chain 'E' and (resid 9 through 162 or (resid 163 and (name N or name CA or name \ C or name O or name CB or name OG1 or name CG2 or name H or name HA or name HB \ or name HG21 or name HG22 or name HG23)) or resid 164 through 475)) selection = (chain 'F' and resid 9 through 475) } ncs_group { reference = chain 'K' selection = chain 'L' selection = (chain 'M' and resid 1 through 74) selection = (chain 'N' and resid 1 through 74) selection = (chain 'O' and resid 1 through 74) selection = chain 'P' selection = (chain 'Q' and resid 1 through 74) selection = (chain 'R' and resid 1 through 74) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians P 23 5.49 5 Mg 5 5.21 5 S 154 5.16 5 C 25517 2.51 5 N 6727 2.21 5 O 7522 1.98 5 H 40405 0.53 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.75 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: 5.240 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: 0.920 Extract box with map and model: 29.320 Check model and map are aligned: 0.910 Convert atoms to be neutral: 0.520 Process input model: 202.890 Find NCS groups from input model: 2.920 Set up NCS constraints: 0.320 Set refine NCS operators: 0.000 Set scattering table: 0.030 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:2.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 245.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 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 : 0.007 0.079 40571 Z= 0.427 Angle : 0.813 23.754 54815 Z= 0.479 Chirality : 0.043 0.289 6351 Planarity : 0.004 0.052 6934 Dihedral : 15.512 179.783 15112 Min Nonbonded Distance : 1.497 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.59 % Cis-general : 0.12 % 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: -0.81 (0.12), residues: 5064 helix: 0.33 (0.10), residues: 2709 sheet: -1.62 (0.21), residues: 608 loop : -1.36 (0.15), residues: 1747 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10128 Ramachandran restraints generated. 5064 Oldfield, 0 Emsley, 5064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10128 Ramachandran restraints generated. 5064 Oldfield, 0 Emsley, 5064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 176 is missing expected H atoms. Skipping. Residue SER 481 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue SER 481 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue SER 481 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Evaluate side-chains 559 residues out of total 4173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 559 time to evaluate : 5.034 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 559 average time/residue: 1.0732 time to fit residues: 979.4271 Evaluate side-chains 459 residues out of total 4173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 459 time to evaluate : 4.906 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.9394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 499 random chunks: chunk 421 optimal weight: 2.9990 chunk 378 optimal weight: 5.9990 chunk 209 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 chunk 255 optimal weight: 1.9990 chunk 202 optimal weight: 0.5980 chunk 391 optimal weight: 3.9990 chunk 151 optimal weight: 1.9990 chunk 237 optimal weight: 2.9990 chunk 291 optimal weight: 0.9990 chunk 453 optimal weight: 0.5980 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 208 GLN C 471 HIS ** D 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 180 GLN ** a 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 56 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.0653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.053 40571 Z= 0.241 Angle : 0.562 9.600 54815 Z= 0.291 Chirality : 0.041 0.298 6351 Planarity : 0.004 0.060 6934 Dihedral : 8.561 178.352 5829 Min Nonbonded Distance : 1.724 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer Outliers : 0.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.59 % Cis-general : 0.12 % 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: -0.54 (0.12), residues: 5064 helix: 0.53 (0.10), residues: 2706 sheet: -1.51 (0.21), residues: 598 loop : -1.19 (0.15), residues: 1760 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10128 Ramachandran restraints generated. 5064 Oldfield, 0 Emsley, 5064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10128 Ramachandran restraints generated. 5064 Oldfield, 0 Emsley, 5064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 176 is missing expected H atoms. Skipping. Residue SER 481 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue SER 481 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue SER 481 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Evaluate side-chains 517 residues out of total 4173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 497 time to evaluate : 5.472 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 outliers start: 20 outliers final: 17 residues processed: 507 average time/residue: 1.0254 time to fit residues: 839.3541 Evaluate side-chains 480 residues out of total 4173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 463 time to evaluate : 4.915 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.7364 time to fit residues: 29.3939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 499 random chunks: chunk 251 optimal weight: 0.0670 chunk 140 optimal weight: 4.9990 chunk 377 optimal weight: 0.9990 chunk 308 optimal weight: 1.9990 chunk 125 optimal weight: 0.7980 chunk 453 optimal weight: 2.9990 chunk 490 optimal weight: 7.9990 chunk 404 optimal weight: 4.9990 chunk 450 optimal weight: 8.9990 chunk 154 optimal weight: 2.9990 chunk 364 optimal weight: 3.9990 overall best weight: 1.3724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 180 GLN ** a 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 48 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.0839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 40571 Z= 0.251 Angle : 0.545 9.363 54815 Z= 0.281 Chirality : 0.040 0.298 6351 Planarity : 0.004 0.061 6934 Dihedral : 8.165 178.631 5829 Min Nonbonded Distance : 1.715 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer Outliers : 0.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.59 % Cis-general : 0.12 % 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: -0.38 (0.12), residues: 5064 helix: 0.67 (0.10), residues: 2710 sheet: -1.49 (0.21), residues: 608 loop : -1.12 (0.15), residues: 1746 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10128 Ramachandran restraints generated. 5064 Oldfield, 0 Emsley, 5064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10128 Ramachandran restraints generated. 5064 Oldfield, 0 Emsley, 5064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 176 is missing expected H atoms. Skipping. Residue SER 481 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue SER 481 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue SER 481 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Evaluate side-chains 512 residues out of total 4173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 495 time to evaluate : 4.898 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 outliers start: 17 outliers final: 12 residues processed: 503 average time/residue: 1.0415 time to fit residues: 851.1910 Evaluate side-chains 477 residues out of total 4173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 465 time to evaluate : 4.852 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 12 outliers final: 1 residues processed: 12 average time/residue: 0.7827 time to fit residues: 23.0442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 499 random chunks: chunk 448 optimal weight: 6.9990 chunk 341 optimal weight: 2.9990 chunk 235 optimal weight: 0.0870 chunk 50 optimal weight: 1.9990 chunk 216 optimal weight: 2.9990 chunk 304 optimal weight: 1.9990 chunk 455 optimal weight: 4.9990 chunk 482 optimal weight: 2.9990 chunk 238 optimal weight: 1.9990 chunk 431 optimal weight: 1.9990 chunk 129 optimal weight: 0.9990 overall best weight: 1.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 503 ASN ** E 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 180 GLN ** a 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 48 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.0989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 40571 Z= 0.254 Angle : 0.539 9.346 54815 Z= 0.277 Chirality : 0.040 0.298 6351 Planarity : 0.004 0.058 6934 Dihedral : 7.876 178.789 5829 Min Nonbonded Distance : 1.687 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer Outliers : 0.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.59 % Cis-general : 0.12 % 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: -0.26 (0.12), residues: 5064 helix: 0.78 (0.10), residues: 2709 sheet: -1.46 (0.21), residues: 613 loop : -1.08 (0.15), residues: 1742 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10128 Ramachandran restraints generated. 5064 Oldfield, 0 Emsley, 5064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10128 Ramachandran restraints generated. 5064 Oldfield, 0 Emsley, 5064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 176 is missing expected H atoms. Skipping. Residue SER 481 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue SER 481 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue SER 481 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Evaluate side-chains 510 residues out of total 4173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 491 time to evaluate : 5.045 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: symmetry clash outliers start: 19 outliers final: 10 residues processed: 507 average time/residue: 1.0274 time to fit residues: 843.6907 Evaluate side-chains 475 residues out of total 4173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 465 time to evaluate : 4.872 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 10 outliers final: 1 residues processed: 10 average time/residue: 0.7422 time to fit residues: 19.3841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 499 random chunks: chunk 401 optimal weight: 3.9990 chunk 273 optimal weight: 0.0770 chunk 7 optimal weight: 1.9990 chunk 359 optimal weight: 1.9990 chunk 199 optimal weight: 0.7980 chunk 411 optimal weight: 0.5980 chunk 333 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 246 optimal weight: 2.9990 chunk 432 optimal weight: 2.9990 chunk 121 optimal weight: 1.9990 overall best weight: 1.0942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 180 GLN a 46 GLN ** a 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 28 ASN ** f 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 48 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.1133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 40571 Z= 0.211 Angle : 0.524 9.300 54815 Z= 0.268 Chirality : 0.040 0.299 6351 Planarity : 0.003 0.053 6934 Dihedral : 7.600 178.839 5829 Min Nonbonded Distance : 1.746 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer Outliers : 0.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.59 % Cis-general : 0.12 % 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 (0.12), residues: 5064 helix: 0.92 (0.10), residues: 2710 sheet: -1.41 (0.21), residues: 615 loop : -0.99 (0.15), residues: 1739 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10128 Ramachandran restraints generated. 5064 Oldfield, 0 Emsley, 5064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10128 Ramachandran restraints generated. 5064 Oldfield, 0 Emsley, 5064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 176 is missing expected H atoms. Skipping. Residue SER 481 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue SER 481 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue SER 481 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Evaluate side-chains 509 residues out of total 4173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 492 time to evaluate : 5.060 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 outliers start: 17 outliers final: 15 residues processed: 503 average time/residue: 1.0343 time to fit residues: 848.6256 Evaluate side-chains 483 residues out of total 4173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 468 time to evaluate : 4.838 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 15 outliers final: 1 residues processed: 15 average time/residue: 0.7349 time to fit residues: 26.1960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 499 random chunks: chunk 162 optimal weight: 2.9990 chunk 434 optimal weight: 0.6980 chunk 95 optimal weight: 4.9990 chunk 283 optimal weight: 0.7980 chunk 119 optimal weight: 3.9990 chunk 482 optimal weight: 2.9990 chunk 400 optimal weight: 2.9990 chunk 223 optimal weight: 0.0980 chunk 40 optimal weight: 0.5980 chunk 159 optimal weight: 0.9980 chunk 253 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 78 ASN C 432 GLN ** E 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 180 GLN ** a 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 48 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.1306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.051 40571 Z= 0.162 Angle : 0.506 9.040 54815 Z= 0.257 Chirality : 0.039 0.303 6351 Planarity : 0.003 0.048 6934 Dihedral : 7.273 179.079 5829 Min Nonbonded Distance : 1.782 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer Outliers : 0.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.59 % Cis-general : 0.12 % 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: 0.15 (0.12), residues: 5064 helix: 1.11 (0.10), residues: 2708 sheet: -1.30 (0.21), residues: 604 loop : -0.87 (0.15), residues: 1752 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10128 Ramachandran restraints generated. 5064 Oldfield, 0 Emsley, 5064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10128 Ramachandran restraints generated. 5064 Oldfield, 0 Emsley, 5064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 176 is missing expected H atoms. Skipping. Residue SER 481 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue SER 481 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue SER 481 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Evaluate side-chains 513 residues out of total 4173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 504 time to evaluate : 5.002 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: symmetry clash outliers start: 9 outliers final: 7 residues processed: 508 average time/residue: 1.0052 time to fit residues: 828.8727 Evaluate side-chains 483 residues out of total 4173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 476 time to evaluate : 4.931 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 7 outliers final: 1 residues processed: 7 average time/residue: 0.7350 time to fit residues: 15.3917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 499 random chunks: chunk 465 optimal weight: 0.1980 chunk 54 optimal weight: 0.7980 chunk 275 optimal weight: 2.9990 chunk 352 optimal weight: 1.9990 chunk 273 optimal weight: 0.8980 chunk 406 optimal weight: 5.9990 chunk 269 optimal weight: 0.7980 chunk 480 optimal weight: 2.9990 chunk 300 optimal weight: 4.9990 chunk 293 optimal weight: 0.0670 chunk 222 optimal weight: 0.9980 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 180 GLN ** a 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 48 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.1457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.052 40571 Z= 0.151 Angle : 0.502 8.784 54815 Z= 0.253 Chirality : 0.039 0.305 6351 Planarity : 0.003 0.048 6934 Dihedral : 7.040 179.306 5829 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer Outliers : 0.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.59 % Cis-general : 0.12 % 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: 0.35 (0.12), residues: 5064 helix: 1.26 (0.10), residues: 2710 sheet: -1.21 (0.21), residues: 590 loop : -0.75 (0.15), residues: 1764 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10128 Ramachandran restraints generated. 5064 Oldfield, 0 Emsley, 5064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10128 Ramachandran restraints generated. 5064 Oldfield, 0 Emsley, 5064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 176 is missing expected H atoms. Skipping. Residue SER 481 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue SER 481 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue SER 481 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Evaluate side-chains 504 residues out of total 4173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 496 time to evaluate : 4.957 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 outliers start: 8 outliers final: 6 residues processed: 500 average time/residue: 1.0408 time to fit residues: 842.4503 Evaluate side-chains 478 residues out of total 4173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 472 time to evaluate : 4.887 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 6 outliers final: 1 residues processed: 6 average time/residue: 0.7135 time to fit residues: 14.0451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 499 random chunks: chunk 297 optimal weight: 2.9990 chunk 192 optimal weight: 2.9990 chunk 287 optimal weight: 1.9990 chunk 144 optimal weight: 0.9980 chunk 94 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 305 optimal weight: 2.9990 chunk 327 optimal weight: 2.9990 chunk 237 optimal weight: 1.9990 chunk 44 optimal weight: 7.9990 chunk 378 optimal weight: 5.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 16 GLN S 180 GLN ** f 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.1377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.067 40571 Z= 0.368 Angle : 0.573 9.664 54815 Z= 0.295 Chirality : 0.042 0.293 6351 Planarity : 0.004 0.052 6934 Dihedral : 7.490 179.540 5829 Min Nonbonded Distance : 1.679 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer Outliers : 0.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.59 % Cis-general : 0.12 % 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 (0.12), residues: 5064 helix: 1.00 (0.10), residues: 2712 sheet: -1.41 (0.21), residues: 622 loop : -0.90 (0.15), residues: 1730 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10128 Ramachandran restraints generated. 5064 Oldfield, 0 Emsley, 5064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10128 Ramachandran restraints generated. 5064 Oldfield, 0 Emsley, 5064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 176 is missing expected H atoms. Skipping. Residue SER 481 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue SER 481 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue SER 481 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Evaluate side-chains 486 residues out of total 4173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 468 time to evaluate : 5.000 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 outliers start: 18 outliers final: 17 residues processed: 476 average time/residue: 1.0574 time to fit residues: 816.0149 Evaluate side-chains 477 residues out of total 4173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 460 time to evaluate : 4.921 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 17 outliers final: 1 residues processed: 17 average time/residue: 0.8494 time to fit residues: 31.2261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 499 random chunks: chunk 437 optimal weight: 0.7980 chunk 460 optimal weight: 5.9990 chunk 420 optimal weight: 0.4980 chunk 448 optimal weight: 3.9990 chunk 269 optimal weight: 0.7980 chunk 195 optimal weight: 2.9990 chunk 351 optimal weight: 0.0970 chunk 137 optimal weight: 2.9990 chunk 405 optimal weight: 0.6980 chunk 423 optimal weight: 0.9980 chunk 446 optimal weight: 6.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 180 GLN ** a 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.1535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.062 40571 Z= 0.160 Angle : 0.515 8.888 54815 Z= 0.259 Chirality : 0.039 0.306 6351 Planarity : 0.003 0.067 6934 Dihedral : 7.053 179.001 5829 Min Nonbonded Distance : 1.752 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer Outliers : 0.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.59 % Cis-general : 0.12 % 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: 0.38 (0.12), residues: 5064 helix: 1.25 (0.10), residues: 2716 sheet: -1.21 (0.21), residues: 599 loop : -0.69 (0.15), residues: 1749 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10128 Ramachandran restraints generated. 5064 Oldfield, 0 Emsley, 5064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10128 Ramachandran restraints generated. 5064 Oldfield, 0 Emsley, 5064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 176 is missing expected H atoms. Skipping. Residue SER 481 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue SER 481 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue SER 481 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Evaluate side-chains 503 residues out of total 4173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 497 time to evaluate : 5.030 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 outliers start: 6 outliers final: 4 residues processed: 501 average time/residue: 1.0216 time to fit residues: 827.4166 Evaluate side-chains 483 residues out of total 4173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 479 time to evaluate : 4.899 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 4 average time/residue: 0.7306 time to fit residues: 11.4130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 499 random chunks: chunk 294 optimal weight: 1.9990 chunk 473 optimal weight: 1.9990 chunk 289 optimal weight: 2.9990 chunk 224 optimal weight: 2.9990 chunk 329 optimal weight: 1.9990 chunk 497 optimal weight: 0.0870 chunk 457 optimal weight: 3.9990 chunk 395 optimal weight: 0.8980 chunk 41 optimal weight: 3.9990 chunk 305 optimal weight: 1.9990 chunk 242 optimal weight: 2.9990 overall best weight: 1.3964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 180 GLN ** a 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.1528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.065 40571 Z= 0.253 Angle : 0.534 9.052 54815 Z= 0.271 Chirality : 0.040 0.300 6351 Planarity : 0.003 0.054 6934 Dihedral : 7.094 179.606 5829 Min Nonbonded Distance : 1.728 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.59 % Cis-general : 0.12 % 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: 0.32 (0.12), residues: 5064 helix: 1.23 (0.10), residues: 2709 sheet: -1.30 (0.21), residues: 622 loop : -0.72 (0.15), residues: 1733 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10128 Ramachandran restraints generated. 5064 Oldfield, 0 Emsley, 5064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10128 Ramachandran restraints generated. 5064 Oldfield, 0 Emsley, 5064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 176 is missing expected H atoms. Skipping. Residue SER 481 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue SER 481 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue SER 481 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Evaluate side-chains 483 residues out of total 4173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 480 time to evaluate : 5.029 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 outliers start: 3 outliers final: 2 residues processed: 481 average time/residue: 1.0293 time to fit residues: 801.4243 Evaluate side-chains 475 residues out of total 4173 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 473 time to evaluate : 4.863 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 2 average time/residue: 0.6822 time to fit residues: 8.5301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 499 random chunks: chunk 314 optimal weight: 1.9990 chunk 421 optimal weight: 0.7980 chunk 121 optimal weight: 1.9990 chunk 365 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 chunk 110 optimal weight: 0.7980 chunk 396 optimal weight: 0.9990 chunk 165 optimal weight: 1.9990 chunk 407 optimal weight: 6.9990 chunk 50 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 180 GLN ** a 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.116161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.099267 restraints weight = 189633.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.098404 restraints weight = 184683.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.099785 restraints weight = 165805.602| |-----------------------------------------------------------------------------| r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3246 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3246 r_free = 0.3246 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3246 r_free = 0.3246 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3246 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.1579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.070 40571 Z= 0.209 Angle : 0.522 9.009 54815 Z= 0.263 Chirality : 0.040 0.302 6351 Planarity : 0.003 0.053 6934 Dihedral : 6.977 179.290 5829 Min Nonbonded Distance : 1.756 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer Outliers : 0.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.59 % Cis-general : 0.12 % 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: 0.41 (0.12), residues: 5064 helix: 1.30 (0.10), residues: 2699 sheet: -1.22 (0.21), residues: 599 loop : -0.70 (0.15), residues: 1766 =============================================================================== Job complete usr+sys time: 14042.30 seconds wall clock time: 244 minutes 32.81 seconds (14672.81 seconds total)