Starting phenix.real_space_refine (version: 1.21rc1) on Fri Oct 13 17:06:02 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wel_8820/10_2023/5wel_8820_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wel_8820/10_2023/5wel_8820.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wel_8820/10_2023/5wel_8820.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wel_8820/10_2023/5wel_8820.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wel_8820/10_2023/5wel_8820_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wel_8820/10_2023/5wel_8820_updated.pdb" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 4 5.49 5 S 144 5.16 5 C 17760 2.51 5 N 4530 2.21 5 O 5188 1.98 5 F 12 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 198": "NH1" <-> "NH2" Residue "A ARG 261": "NH1" <-> "NH2" Residue "A ARG 300": "NH1" <-> "NH2" Residue "A ARG 309": "NH1" <-> "NH2" Residue "A ARG 369": "NH1" <-> "NH2" Residue "A ARG 628": "NH1" <-> "NH2" Residue "A ARG 660": "NH1" <-> "NH2" Residue "A ARG 661": "NH1" <-> "NH2" Residue "A ARG 675": "NH1" <-> "NH2" Residue "A ARG 692": "NH1" <-> "NH2" Residue "A ARG 1005": "NH1" <-> "NH2" Residue "A ARG 1006": "NH1" <-> "NH2" Residue "A ARG 1090": "NH1" <-> "NH2" Residue "B PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 198": "NH1" <-> "NH2" Residue "B ARG 261": "NH1" <-> "NH2" Residue "B ARG 300": "NH1" <-> "NH2" Residue "B ARG 309": "NH1" <-> "NH2" Residue "B ARG 369": "NH1" <-> "NH2" Residue "B ARG 660": "NH1" <-> "NH2" Residue "B ARG 661": "NH1" <-> "NH2" Residue "B ARG 675": "NH1" <-> "NH2" Residue "B ARG 692": "NH1" <-> "NH2" Residue "C PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 198": "NH1" <-> "NH2" Residue "C ARG 261": "NH1" <-> "NH2" Residue "C ARG 300": "NH1" <-> "NH2" Residue "C ARG 309": "NH1" <-> "NH2" Residue "C ARG 369": "NH1" <-> "NH2" Residue "C ARG 628": "NH1" <-> "NH2" Residue "C ARG 660": "NH1" <-> "NH2" Residue "C ARG 661": "NH1" <-> "NH2" Residue "C ARG 675": "NH1" <-> "NH2" Residue "C ARG 692": "NH1" <-> "NH2" Residue "C ARG 1005": "NH1" <-> "NH2" Residue "C ARG 1006": "NH1" <-> "NH2" Residue "C ARG 1090": "NH1" <-> "NH2" Residue "D PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 198": "NH1" <-> "NH2" Residue "D ARG 261": "NH1" <-> "NH2" Residue "D ARG 300": "NH1" <-> "NH2" Residue "D ARG 309": "NH1" <-> "NH2" Residue "D ARG 369": "NH1" <-> "NH2" Residue "D ARG 660": "NH1" <-> "NH2" Residue "D ARG 661": "NH1" <-> "NH2" Residue "D ARG 675": "NH1" <-> "NH2" Residue "D ARG 692": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 27638 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 7555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 962, 7555 Classifications: {'peptide': 962} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 5, 'PTRANS': 21, 'TRANS': 935} Chain breaks: 5 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "B" Number of atoms: 6125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 780, 6125 Classifications: {'peptide': 780} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 4, 'PTRANS': 18, 'TRANS': 757} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "C" Number of atoms: 7555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 962, 7555 Classifications: {'peptide': 962} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 5, 'PTRANS': 21, 'TRANS': 935} Chain breaks: 5 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "D" Number of atoms: 6125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 780, 6125 Classifications: {'peptide': 780} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 4, 'PTRANS': 18, 'TRANS': 757} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 112 Unusual residues: {'AJP': 1, 'ZK1': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ZK1': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 112 Unusual residues: {'AJP': 1, 'ZK1': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ZK1': 1} Classifications: {'undetermined': 1} Time building chain proxies: 14.22, per 1000 atoms: 0.51 Number of scatterers: 27638 At special positions: 0 Unit cell: (120.54, 157.78, 189.14, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 144 16.00 P 4 15.00 F 12 9.00 O 5188 8.00 N 4530 7.00 C 17760 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 63 " - pdb=" SG CYS A 315 " distance=2.03 Simple disulfide: pdb=" SG CYS A 718 " - pdb=" SG CYS A 773 " distance=2.02 Simple disulfide: pdb=" SG CYS A1099 " - pdb=" SG CYS A1110 " distance=2.03 Simple disulfide: pdb=" SG CYS B 63 " - pdb=" SG CYS B 315 " distance=2.03 Simple disulfide: pdb=" SG CYS B 718 " - pdb=" SG CYS B 773 " distance=2.02 Simple disulfide: pdb=" SG CYS C 63 " - pdb=" SG CYS C 315 " distance=2.03 Simple disulfide: pdb=" SG CYS C 718 " - pdb=" SG CYS C 773 " distance=2.02 Simple disulfide: pdb=" SG CYS C1099 " - pdb=" SG CYS C1110 " distance=2.03 Simple disulfide: pdb=" SG CYS D 63 " - pdb=" SG CYS D 315 " distance=2.03 Simple disulfide: pdb=" SG CYS D 718 " - pdb=" SG CYS D 773 " distance=2.02 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 11.46 Conformation dependent library (CDL) restraints added in 4.0 seconds 6904 Ramachandran restraints generated. 3452 Oldfield, 0 Emsley, 3452 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6408 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 122 helices and 34 sheets defined 43.1% alpha, 11.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.54 Creating SS restraints... Processing helix chain 'A' and resid 23 through 35 Processing helix chain 'A' and resid 55 through 68 Processing helix chain 'A' and resid 82 through 92 Processing helix chain 'A' and resid 118 through 128 Processing helix chain 'A' and resid 144 through 155 removed outlier: 3.598A pdb=" N GLU A 155 " --> pdb=" O ASP A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 187 removed outlier: 3.505A pdb=" N GLN A 182 " --> pdb=" O ARG A 178 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LYS A 187 " --> pdb=" O ASP A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 211 Processing helix chain 'A' and resid 253 through 262 removed outlier: 3.528A pdb=" N PHE A 258 " --> pdb=" O LEU A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 302 removed outlier: 3.526A pdb=" N GLN A 290 " --> pdb=" O TYR A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 334 removed outlier: 3.513A pdb=" N ALA A 332 " --> pdb=" O ILE A 329 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU A 333 " --> pdb=" O GLU A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 420 Processing helix chain 'A' and resid 424 through 436 Processing helix chain 'A' and resid 462 through 468 Processing helix chain 'A' and resid 483 through 486 No H-bonds generated for 'chain 'A' and resid 483 through 486' Processing helix chain 'A' and resid 517 through 519 No H-bonds generated for 'chain 'A' and resid 517 through 519' Processing helix chain 'A' and resid 523 through 537 removed outlier: 3.930A pdb=" N VAL A 530 " --> pdb=" O TRP A 526 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TYR A 533 " --> pdb=" O ILE A 529 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE A 534 " --> pdb=" O VAL A 530 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLY A 535 " --> pdb=" O PHE A 531 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N VAL A 536 " --> pdb=" O ALA A 532 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N SER A 537 " --> pdb=" O TYR A 533 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 542 No H-bonds generated for 'chain 'A' and resid 540 through 542' Processing helix chain 'A' and resid 576 through 582 removed outlier: 3.530A pdb=" N LEU A 581 " --> pdb=" O LEU A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 629 removed outlier: 3.803A pdb=" N TRP A 605 " --> pdb=" O VAL A 601 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N TRP A 606 " --> pdb=" O GLY A 602 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU A 610 " --> pdb=" O TRP A 606 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ILE A 611 " --> pdb=" O PHE A 607 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ILE A 612 " --> pdb=" O PHE A 608 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL A 626 " --> pdb=" O ALA A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 641 Processing helix chain 'A' and resid 654 through 661 Processing helix chain 'A' and resid 665 through 675 Processing helix chain 'A' and resid 686 through 696 Processing helix chain 'A' and resid 706 through 714 Processing helix chain 'A' and resid 741 through 756 removed outlier: 4.096A pdb=" N THR A 744 " --> pdb=" O SER A 741 " (cutoff:3.500A) Proline residue: A 745 - end of helix removed outlier: 3.507A pdb=" N VAL A 750 " --> pdb=" O ASN A 747 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N SER A 754 " --> pdb=" O LEU A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 767 Processing helix chain 'A' and resid 777 through 780 Processing helix chain 'A' and resid 790 through 792 No H-bonds generated for 'chain 'A' and resid 790 through 792' Processing helix chain 'A' and resid 796 through 818 removed outlier: 3.599A pdb=" N LEU A 808 " --> pdb=" O GLY A 804 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL A 809 " --> pdb=" O LEU A 805 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU A 811 " --> pdb=" O MET A 807 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N CYS A 815 " --> pdb=" O LEU A 811 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N SER A 818 " --> pdb=" O PHE A 814 " (cutoff:3.500A) Processing helix chain 'A' and resid 1003 through 1028 removed outlier: 3.769A pdb=" N LEU A1028 " --> pdb=" O THR A1024 " (cutoff:3.500A) Processing helix chain 'A' and resid 1119 through 1152 removed outlier: 3.504A pdb=" N VAL A1130 " --> pdb=" O TRP A1126 " (cutoff:3.500A) Processing helix chain 'A' and resid 1160 through 1193 removed outlier: 3.600A pdb=" N VAL A1168 " --> pdb=" O ALA A1164 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N PHE A1169 " --> pdb=" O PHE A1165 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL A1171 " --> pdb=" O ALA A1167 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU A1176 " --> pdb=" O LEU A1172 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N MET A1182 " --> pdb=" O MET A1178 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N THR A1185 " --> pdb=" O HIS A1181 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLN A1186 " --> pdb=" O MET A1182 " (cutoff:3.500A) Processing helix chain 'A' and resid 1209 through 1227 removed outlier: 3.636A pdb=" N GLY A1215 " --> pdb=" O CYS A1211 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N PHE A1217 " --> pdb=" O ALA A1213 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N THR A1218 " --> pdb=" O TRP A1214 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER A1224 " --> pdb=" O CYS A1220 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N THR A1226 " --> pdb=" O ALA A1222 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 35 Processing helix chain 'B' and resid 55 through 68 Processing helix chain 'B' and resid 82 through 92 Processing helix chain 'B' and resid 118 through 128 Processing helix chain 'B' and resid 144 through 155 removed outlier: 3.599A pdb=" N GLU B 155 " --> pdb=" O ASP B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 187 removed outlier: 3.504A pdb=" N GLN B 182 " --> pdb=" O ARG B 178 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LYS B 187 " --> pdb=" O ASP B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 211 Processing helix chain 'B' and resid 253 through 262 removed outlier: 3.528A pdb=" N PHE B 258 " --> pdb=" O LEU B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 302 removed outlier: 3.526A pdb=" N GLN B 290 " --> pdb=" O TYR B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 334 removed outlier: 3.513A pdb=" N ALA B 332 " --> pdb=" O ILE B 329 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU B 333 " --> pdb=" O GLU B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 420 Processing helix chain 'B' and resid 424 through 436 Processing helix chain 'B' and resid 462 through 468 Processing helix chain 'B' and resid 483 through 486 No H-bonds generated for 'chain 'B' and resid 483 through 486' Processing helix chain 'B' and resid 517 through 519 No H-bonds generated for 'chain 'B' and resid 517 through 519' Processing helix chain 'B' and resid 523 through 537 removed outlier: 3.930A pdb=" N VAL B 530 " --> pdb=" O TRP B 526 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TYR B 533 " --> pdb=" O ILE B 529 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE B 534 " --> pdb=" O VAL B 530 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLY B 535 " --> pdb=" O PHE B 531 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N VAL B 536 " --> pdb=" O ALA B 532 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N SER B 537 " --> pdb=" O TYR B 533 " (cutoff:3.500A) Processing helix chain 'B' and resid 540 through 542 No H-bonds generated for 'chain 'B' and resid 540 through 542' Processing helix chain 'B' and resid 576 through 582 removed outlier: 3.530A pdb=" N LEU B 581 " --> pdb=" O LEU B 577 " (cutoff:3.500A) Processing helix chain 'B' and resid 597 through 623 removed outlier: 3.804A pdb=" N TRP B 605 " --> pdb=" O VAL B 601 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N TRP B 606 " --> pdb=" O GLY B 602 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU B 610 " --> pdb=" O TRP B 606 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ILE B 611 " --> pdb=" O PHE B 607 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ILE B 612 " --> pdb=" O PHE B 608 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE B 613 " --> pdb=" O THR B 609 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N SER B 614 " --> pdb=" O LEU B 610 " (cutoff:3.500A) Processing helix chain 'B' and resid 637 through 641 Processing helix chain 'B' and resid 654 through 661 Processing helix chain 'B' and resid 665 through 675 Processing helix chain 'B' and resid 686 through 696 Processing helix chain 'B' and resid 706 through 714 Processing helix chain 'B' and resid 741 through 756 removed outlier: 4.095A pdb=" N THR B 744 " --> pdb=" O SER B 741 " (cutoff:3.500A) Proline residue: B 745 - end of helix removed outlier: 3.506A pdb=" N VAL B 750 " --> pdb=" O ASN B 747 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N SER B 754 " --> pdb=" O LEU B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 767 Processing helix chain 'B' and resid 775 through 779 Processing helix chain 'B' and resid 790 through 816 removed outlier: 3.523A pdb=" N GLY B 794 " --> pdb=" O SER B 790 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N VAL B 795 " --> pdb=" O ASN B 791 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N TYR B 797 " --> pdb=" O ALA B 793 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ILE B 798 " --> pdb=" O GLY B 794 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU B 808 " --> pdb=" O GLY B 804 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL B 809 " --> pdb=" O LEU B 805 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU B 811 " --> pdb=" O MET B 807 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N CYS B 815 " --> pdb=" O LEU B 811 " (cutoff:3.500A) Processing helix chain 'C' and resid 23 through 35 Processing helix chain 'C' and resid 55 through 68 Processing helix chain 'C' and resid 82 through 92 Processing helix chain 'C' and resid 118 through 128 Processing helix chain 'C' and resid 144 through 155 removed outlier: 3.600A pdb=" N GLU C 155 " --> pdb=" O ASP C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 187 removed outlier: 3.505A pdb=" N GLN C 182 " --> pdb=" O ARG C 178 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LYS C 187 " --> pdb=" O ASP C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 211 Processing helix chain 'C' and resid 253 through 262 removed outlier: 3.527A pdb=" N PHE C 258 " --> pdb=" O LEU C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 302 removed outlier: 3.526A pdb=" N GLN C 290 " --> pdb=" O TYR C 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 334 removed outlier: 3.513A pdb=" N ALA C 332 " --> pdb=" O ILE C 329 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU C 333 " --> pdb=" O GLU C 330 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 420 Processing helix chain 'C' and resid 424 through 436 Processing helix chain 'C' and resid 462 through 468 Processing helix chain 'C' and resid 483 through 486 No H-bonds generated for 'chain 'C' and resid 483 through 486' Processing helix chain 'C' and resid 517 through 519 No H-bonds generated for 'chain 'C' and resid 517 through 519' Processing helix chain 'C' and resid 523 through 537 removed outlier: 3.931A pdb=" N VAL C 530 " --> pdb=" O TRP C 526 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TYR C 533 " --> pdb=" O ILE C 529 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE C 534 " --> pdb=" O VAL C 530 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLY C 535 " --> pdb=" O PHE C 531 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N VAL C 536 " --> pdb=" O ALA C 532 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N SER C 537 " --> pdb=" O TYR C 533 " (cutoff:3.500A) Processing helix chain 'C' and resid 540 through 542 No H-bonds generated for 'chain 'C' and resid 540 through 542' Processing helix chain 'C' and resid 576 through 582 removed outlier: 3.530A pdb=" N LEU C 581 " --> pdb=" O LEU C 577 " (cutoff:3.500A) Processing helix chain 'C' and resid 597 through 629 removed outlier: 3.804A pdb=" N TRP C 605 " --> pdb=" O VAL C 601 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N TRP C 606 " --> pdb=" O GLY C 602 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU C 610 " --> pdb=" O TRP C 606 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ILE C 611 " --> pdb=" O PHE C 607 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ILE C 612 " --> pdb=" O PHE C 608 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ILE C 613 " --> pdb=" O THR C 609 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N SER C 614 " --> pdb=" O LEU C 610 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL C 626 " --> pdb=" O ALA C 622 " (cutoff:3.500A) Processing helix chain 'C' and resid 637 through 641 Processing helix chain 'C' and resid 654 through 661 Processing helix chain 'C' and resid 665 through 675 Processing helix chain 'C' and resid 686 through 696 Processing helix chain 'C' and resid 706 through 714 Processing helix chain 'C' and resid 741 through 756 removed outlier: 4.096A pdb=" N THR C 744 " --> pdb=" O SER C 741 " (cutoff:3.500A) Proline residue: C 745 - end of helix removed outlier: 3.507A pdb=" N VAL C 750 " --> pdb=" O ASN C 747 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N SER C 754 " --> pdb=" O LEU C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 767 Processing helix chain 'C' and resid 777 through 780 Processing helix chain 'C' and resid 790 through 792 No H-bonds generated for 'chain 'C' and resid 790 through 792' Processing helix chain 'C' and resid 796 through 816 removed outlier: 3.599A pdb=" N LEU C 808 " --> pdb=" O GLY C 804 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL C 809 " --> pdb=" O LEU C 805 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU C 811 " --> pdb=" O MET C 807 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N CYS C 815 " --> pdb=" O LEU C 811 " (cutoff:3.500A) Processing helix chain 'C' and resid 1003 through 1028 removed outlier: 3.769A pdb=" N LEU C1028 " --> pdb=" O THR C1024 " (cutoff:3.500A) Processing helix chain 'C' and resid 1119 through 1152 removed outlier: 3.504A pdb=" N VAL C1130 " --> pdb=" O TRP C1126 " (cutoff:3.500A) Processing helix chain 'C' and resid 1160 through 1193 removed outlier: 3.600A pdb=" N VAL C1168 " --> pdb=" O ALA C1164 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N PHE C1169 " --> pdb=" O PHE C1165 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL C1171 " --> pdb=" O ALA C1167 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU C1176 " --> pdb=" O LEU C1172 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N MET C1182 " --> pdb=" O MET C1178 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N THR C1185 " --> pdb=" O HIS C1181 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLN C1186 " --> pdb=" O MET C1182 " (cutoff:3.500A) Processing helix chain 'C' and resid 1209 through 1227 removed outlier: 3.637A pdb=" N GLY C1215 " --> pdb=" O CYS C1211 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N PHE C1217 " --> pdb=" O ALA C1213 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N THR C1218 " --> pdb=" O TRP C1214 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER C1224 " --> pdb=" O CYS C1220 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N THR C1226 " --> pdb=" O ALA C1222 " (cutoff:3.500A) Processing helix chain 'D' and resid 23 through 35 Processing helix chain 'D' and resid 55 through 68 Processing helix chain 'D' and resid 82 through 92 Processing helix chain 'D' and resid 118 through 128 Processing helix chain 'D' and resid 144 through 155 removed outlier: 3.600A pdb=" N GLU D 155 " --> pdb=" O ASP D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 187 removed outlier: 3.505A pdb=" N GLN D 182 " --> pdb=" O ARG D 178 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LYS D 187 " --> pdb=" O ASP D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 211 Processing helix chain 'D' and resid 253 through 262 removed outlier: 3.528A pdb=" N PHE D 258 " --> pdb=" O LEU D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 302 removed outlier: 3.526A pdb=" N GLN D 290 " --> pdb=" O TYR D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 334 removed outlier: 3.513A pdb=" N ALA D 332 " --> pdb=" O ILE D 329 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU D 333 " --> pdb=" O GLU D 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 417 through 420 Processing helix chain 'D' and resid 424 through 436 Processing helix chain 'D' and resid 462 through 468 Processing helix chain 'D' and resid 483 through 486 No H-bonds generated for 'chain 'D' and resid 483 through 486' Processing helix chain 'D' and resid 517 through 519 No H-bonds generated for 'chain 'D' and resid 517 through 519' Processing helix chain 'D' and resid 523 through 537 removed outlier: 3.930A pdb=" N VAL D 530 " --> pdb=" O TRP D 526 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TYR D 533 " --> pdb=" O ILE D 529 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE D 534 " --> pdb=" O VAL D 530 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLY D 535 " --> pdb=" O PHE D 531 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N VAL D 536 " --> pdb=" O ALA D 532 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N SER D 537 " --> pdb=" O TYR D 533 " (cutoff:3.500A) Processing helix chain 'D' and resid 540 through 542 No H-bonds generated for 'chain 'D' and resid 540 through 542' Processing helix chain 'D' and resid 576 through 582 removed outlier: 3.529A pdb=" N LEU D 581 " --> pdb=" O LEU D 577 " (cutoff:3.500A) Processing helix chain 'D' and resid 597 through 623 removed outlier: 3.804A pdb=" N TRP D 605 " --> pdb=" O VAL D 601 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N TRP D 606 " --> pdb=" O GLY D 602 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU D 610 " --> pdb=" O TRP D 606 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ILE D 611 " --> pdb=" O PHE D 607 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ILE D 612 " --> pdb=" O PHE D 608 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE D 613 " --> pdb=" O THR D 609 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N SER D 614 " --> pdb=" O LEU D 610 " (cutoff:3.500A) Processing helix chain 'D' and resid 637 through 641 Processing helix chain 'D' and resid 654 through 661 Processing helix chain 'D' and resid 665 through 675 Processing helix chain 'D' and resid 686 through 696 Processing helix chain 'D' and resid 706 through 714 Processing helix chain 'D' and resid 741 through 756 removed outlier: 4.096A pdb=" N THR D 744 " --> pdb=" O SER D 741 " (cutoff:3.500A) Proline residue: D 745 - end of helix removed outlier: 3.508A pdb=" N VAL D 750 " --> pdb=" O ASN D 747 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N SER D 754 " --> pdb=" O LEU D 751 " (cutoff:3.500A) Processing helix chain 'D' and resid 758 through 767 Processing helix chain 'D' and resid 775 through 779 Processing helix chain 'D' and resid 790 through 816 removed outlier: 3.525A pdb=" N GLY D 794 " --> pdb=" O SER D 790 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N VAL D 795 " --> pdb=" O ASN D 791 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N TYR D 797 " --> pdb=" O ALA D 793 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ILE D 798 " --> pdb=" O GLY D 794 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU D 808 " --> pdb=" O GLY D 804 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL D 809 " --> pdb=" O LEU D 805 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU D 811 " --> pdb=" O MET D 807 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N CYS D 815 " --> pdb=" O LEU D 811 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 12 through 19 Processing sheet with id= B, first strand: chain 'A' and resid 72 through 75 removed outlier: 6.842A pdb=" N SER A 95 " --> pdb=" O ILE A 73 " (cutoff:3.500A) removed outlier: 8.291A pdb=" N GLY A 75 " --> pdb=" O SER A 95 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N ILE A 97 " --> pdb=" O GLY A 75 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 159 through 164 removed outlier: 3.607A pdb=" N PHE A 133 " --> pdb=" O GLN A 159 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N ARG A 191 " --> pdb=" O LYS A 132 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N HIS A 219 " --> pdb=" O VAL A 192 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N LEU A 194 " --> pdb=" O HIS A 219 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N ILE A 221 " --> pdb=" O LEU A 194 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N GLU A 241 " --> pdb=" O TYR A 220 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N ILE A 222 " --> pdb=" O GLU A 241 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N SER A 243 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N VAL A 242 " --> pdb=" O LEU A 363 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLY A 372 " --> pdb=" O ILE A 360 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N GLU A 362 " --> pdb=" O LYS A 370 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N LYS A 370 " --> pdb=" O GLU A 362 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 338 through 340 Processing sheet with id= E, first strand: chain 'A' and resid 395 through 399 Processing sheet with id= F, first strand: chain 'A' and resid 489 through 491 Processing sheet with id= G, first strand: chain 'A' and resid 720 through 723 removed outlier: 3.886A pdb=" N ILE A 502 " --> pdb=" O VAL A 723 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N LYS A 505 " --> pdb=" O TYR A 700 " (cutoff:3.500A) removed outlier: 8.937A pdb=" N TYR A 700 " --> pdb=" O LYS A 505 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N ALA A 646 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N LEU A 703 " --> pdb=" O ALA A 646 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N GLY A 648 " --> pdb=" O LEU A 703 " (cutoff:3.500A) removed outlier: 9.116A pdb=" N GLU A 705 " --> pdb=" O GLY A 648 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 1033 through 1036 removed outlier: 3.510A pdb=" N THR A1093 " --> pdb=" O CYS A1033 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 494 through 498 removed outlier: 6.765A pdb=" N TYR A 732 " --> pdb=" O PHE A 495 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N SER A 497 " --> pdb=" O LYS A 730 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LYS A 730 " --> pdb=" O SER A 497 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 12 through 19 Processing sheet with id= K, first strand: chain 'B' and resid 72 through 75 removed outlier: 6.842A pdb=" N SER B 95 " --> pdb=" O ILE B 73 " (cutoff:3.500A) removed outlier: 8.290A pdb=" N GLY B 75 " --> pdb=" O SER B 95 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N ILE B 97 " --> pdb=" O GLY B 75 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 159 through 164 removed outlier: 3.607A pdb=" N PHE B 133 " --> pdb=" O GLN B 159 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N ARG B 191 " --> pdb=" O LYS B 132 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N HIS B 219 " --> pdb=" O VAL B 192 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N LEU B 194 " --> pdb=" O HIS B 219 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N ILE B 221 " --> pdb=" O LEU B 194 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N GLU B 241 " --> pdb=" O TYR B 220 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N ILE B 222 " --> pdb=" O GLU B 241 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N SER B 243 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N VAL B 242 " --> pdb=" O LEU B 363 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLY B 372 " --> pdb=" O ILE B 360 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N GLU B 362 " --> pdb=" O LYS B 370 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N LYS B 370 " --> pdb=" O GLU B 362 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 338 through 340 Processing sheet with id= N, first strand: chain 'B' and resid 395 through 399 Processing sheet with id= O, first strand: chain 'B' and resid 489 through 491 Processing sheet with id= P, first strand: chain 'B' and resid 720 through 723 removed outlier: 3.887A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N LYS B 505 " --> pdb=" O TYR B 700 " (cutoff:3.500A) removed outlier: 8.937A pdb=" N TYR B 700 " --> pdb=" O LYS B 505 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ALA B 646 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N LEU B 703 " --> pdb=" O ALA B 646 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N GLY B 648 " --> pdb=" O LEU B 703 " (cutoff:3.500A) removed outlier: 9.117A pdb=" N GLU B 705 " --> pdb=" O GLY B 648 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'B' and resid 494 through 498 removed outlier: 6.765A pdb=" N TYR B 732 " --> pdb=" O PHE B 495 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N SER B 497 " --> pdb=" O LYS B 730 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LYS B 730 " --> pdb=" O SER B 497 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 12 through 19 Processing sheet with id= S, first strand: chain 'C' and resid 72 through 75 removed outlier: 6.842A pdb=" N SER C 95 " --> pdb=" O ILE C 73 " (cutoff:3.500A) removed outlier: 8.290A pdb=" N GLY C 75 " --> pdb=" O SER C 95 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N ILE C 97 " --> pdb=" O GLY C 75 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'C' and resid 159 through 164 removed outlier: 3.606A pdb=" N PHE C 133 " --> pdb=" O GLN C 159 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N ARG C 191 " --> pdb=" O LYS C 132 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N HIS C 219 " --> pdb=" O VAL C 192 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N LEU C 194 " --> pdb=" O HIS C 219 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N ILE C 221 " --> pdb=" O LEU C 194 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N GLU C 241 " --> pdb=" O TYR C 220 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N ILE C 222 " --> pdb=" O GLU C 241 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N SER C 243 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N VAL C 242 " --> pdb=" O LEU C 363 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLY C 372 " --> pdb=" O ILE C 360 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N GLU C 362 " --> pdb=" O LYS C 370 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N LYS C 370 " --> pdb=" O GLU C 362 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'C' and resid 338 through 340 Processing sheet with id= V, first strand: chain 'C' and resid 395 through 399 Processing sheet with id= W, first strand: chain 'C' and resid 489 through 491 Processing sheet with id= X, first strand: chain 'C' and resid 720 through 723 removed outlier: 3.887A pdb=" N ILE C 502 " --> pdb=" O VAL C 723 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N LYS C 505 " --> pdb=" O TYR C 700 " (cutoff:3.500A) removed outlier: 8.937A pdb=" N TYR C 700 " --> pdb=" O LYS C 505 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N ALA C 646 " --> pdb=" O ALA C 701 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N LEU C 703 " --> pdb=" O ALA C 646 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N GLY C 648 " --> pdb=" O LEU C 703 " (cutoff:3.500A) removed outlier: 9.116A pdb=" N GLU C 705 " --> pdb=" O GLY C 648 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'C' and resid 1033 through 1036 removed outlier: 3.510A pdb=" N THR C1093 " --> pdb=" O CYS C1033 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'C' and resid 494 through 498 removed outlier: 6.765A pdb=" N TYR C 732 " --> pdb=" O PHE C 495 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N SER C 497 " --> pdb=" O LYS C 730 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N LYS C 730 " --> pdb=" O SER C 497 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'D' and resid 12 through 19 Processing sheet with id= AB, first strand: chain 'D' and resid 72 through 75 removed outlier: 6.842A pdb=" N SER D 95 " --> pdb=" O ILE D 73 " (cutoff:3.500A) removed outlier: 8.290A pdb=" N GLY D 75 " --> pdb=" O SER D 95 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N ILE D 97 " --> pdb=" O GLY D 75 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'D' and resid 159 through 164 removed outlier: 3.607A pdb=" N PHE D 133 " --> pdb=" O GLN D 159 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N ARG D 191 " --> pdb=" O LYS D 132 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N HIS D 219 " --> pdb=" O VAL D 192 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N LEU D 194 " --> pdb=" O HIS D 219 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N ILE D 221 " --> pdb=" O LEU D 194 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N GLU D 241 " --> pdb=" O TYR D 220 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N ILE D 222 " --> pdb=" O GLU D 241 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N SER D 243 " --> pdb=" O ILE D 222 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N VAL D 242 " --> pdb=" O LEU D 363 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLY D 372 " --> pdb=" O ILE D 360 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N GLU D 362 " --> pdb=" O LYS D 370 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N LYS D 370 " --> pdb=" O GLU D 362 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'D' and resid 338 through 340 Processing sheet with id= AE, first strand: chain 'D' and resid 395 through 399 Processing sheet with id= AF, first strand: chain 'D' and resid 489 through 491 Processing sheet with id= AG, first strand: chain 'D' and resid 720 through 723 removed outlier: 3.886A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N LYS D 505 " --> pdb=" O TYR D 700 " (cutoff:3.500A) removed outlier: 8.937A pdb=" N TYR D 700 " --> pdb=" O LYS D 505 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ALA D 646 " --> pdb=" O ALA D 701 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N LEU D 703 " --> pdb=" O ALA D 646 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N GLY D 648 " --> pdb=" O LEU D 703 " (cutoff:3.500A) removed outlier: 9.116A pdb=" N GLU D 705 " --> pdb=" O GLY D 648 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'D' and resid 494 through 498 removed outlier: 6.764A pdb=" N TYR D 732 " --> pdb=" O PHE D 495 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N SER D 497 " --> pdb=" O LYS D 730 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LYS D 730 " --> pdb=" O SER D 497 " (cutoff:3.500A) 1053 hydrogen bonds defined for protein. 2955 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: 9.82 Time building geometry restraints manager: 12.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 8660 1.35 - 1.48: 7325 1.48 - 1.61: 12021 1.61 - 1.73: 8 1.73 - 1.86: 234 Bond restraints: 28248 Sorted by residual: bond pdb=" CAT ZK1 D1301 " pdb=" OAA ZK1 D1301 " ideal model delta sigma weight residual 1.214 1.407 -0.193 2.00e-02 2.50e+03 9.29e+01 bond pdb=" CAT ZK1 C1301 " pdb=" OAA ZK1 C1301 " ideal model delta sigma weight residual 1.214 1.407 -0.193 2.00e-02 2.50e+03 9.28e+01 bond pdb=" CAT ZK1 A1301 " pdb=" OAA ZK1 A1301 " ideal model delta sigma weight residual 1.214 1.406 -0.192 2.00e-02 2.50e+03 9.24e+01 bond pdb=" CAT ZK1 B1301 " pdb=" OAA ZK1 B1301 " ideal model delta sigma weight residual 1.214 1.404 -0.190 2.00e-02 2.50e+03 9.01e+01 bond pdb=" CAU ZK1 D1301 " pdb=" OAB ZK1 D1301 " ideal model delta sigma weight residual 1.215 1.403 -0.188 2.00e-02 2.50e+03 8.87e+01 ... (remaining 28243 not shown) Histogram of bond angle deviations from ideal: 95.07 - 103.39: 275 103.39 - 111.71: 13109 111.71 - 120.03: 12210 120.03 - 128.35: 12443 128.35 - 136.67: 217 Bond angle restraints: 38254 Sorted by residual: angle pdb=" CA ILE A 612 " pdb=" C ILE A 612 " pdb=" N ILE A 613 " ideal model delta sigma weight residual 117.69 105.49 12.20 1.27e+00 6.20e-01 9.23e+01 angle pdb=" O ILE C 612 " pdb=" C ILE C 612 " pdb=" N ILE C 613 " ideal model delta sigma weight residual 121.83 112.44 9.39 1.03e+00 9.43e-01 8.31e+01 angle pdb=" O ILE A 612 " pdb=" C ILE A 612 " pdb=" N ILE A 613 " ideal model delta sigma weight residual 121.80 131.60 -9.80 1.13e+00 7.83e-01 7.51e+01 angle pdb=" CA GLU D 634 " pdb=" C GLU D 634 " pdb=" N SER D 635 " ideal model delta sigma weight residual 118.04 106.73 11.31 1.32e+00 5.74e-01 7.34e+01 angle pdb=" CA ILE C 612 " pdb=" C ILE C 612 " pdb=" N ILE C 613 " ideal model delta sigma weight residual 117.28 126.87 -9.59 1.16e+00 7.43e-01 6.83e+01 ... (remaining 38249 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.72: 16309 22.72 - 45.44: 238 45.44 - 68.16: 30 68.16 - 90.88: 9 90.88 - 113.61: 8 Dihedral angle restraints: 16594 sinusoidal: 6570 harmonic: 10024 Sorted by residual: dihedral pdb=" CA GLY A1207 " pdb=" C GLY A1207 " pdb=" N TRP A1208 " pdb=" CA TRP A1208 " ideal model delta harmonic sigma weight residual 180.00 -86.19 -93.81 0 5.00e+00 4.00e-02 3.52e+02 dihedral pdb=" CA GLY C1207 " pdb=" C GLY C1207 " pdb=" N TRP C1208 " pdb=" CA TRP C1208 " ideal model delta harmonic sigma weight residual -180.00 -86.20 -93.80 0 5.00e+00 4.00e-02 3.52e+02 dihedral pdb=" CA GLU A 384 " pdb=" C GLU A 384 " pdb=" N ASP A 385 " pdb=" CA ASP A 385 " ideal model delta harmonic sigma weight residual -180.00 -127.33 -52.67 0 5.00e+00 4.00e-02 1.11e+02 ... (remaining 16591 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.166: 4228 1.166 - 2.333: 0 2.333 - 3.499: 0 3.499 - 4.666: 2 4.666 - 5.832: 66 Chirality restraints: 4296 Sorted by residual: chirality pdb=" C12 AJP C1302 " pdb=" C07 AJP C1302 " pdb=" C11 AJP C1302 " pdb=" C13 AJP C1302 " both_signs ideal model delta sigma weight residual False 3.01 -2.82 5.83 2.00e-01 2.50e+01 8.50e+02 chirality pdb=" C12 AJP A1302 " pdb=" C07 AJP A1302 " pdb=" C11 AJP A1302 " pdb=" C13 AJP A1302 " both_signs ideal model delta sigma weight residual False 3.01 -2.82 5.82 2.00e-01 2.50e+01 8.48e+02 chirality pdb=" C20 AJP C1302 " pdb=" C15 AJP C1302 " pdb=" C19 AJP C1302 " pdb=" C21 AJP C1302 " both_signs ideal model delta sigma weight residual False 2.96 -2.71 5.67 2.00e-01 2.50e+01 8.02e+02 ... (remaining 4293 not shown) Planarity restraints: 4756 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR D 383 " 0.033 2.00e-02 2.50e+03 6.84e-02 4.67e+01 pdb=" C THR D 383 " -0.118 2.00e-02 2.50e+03 pdb=" O THR D 383 " 0.045 2.00e-02 2.50e+03 pdb=" N GLU D 384 " 0.040 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR C 383 " -0.033 2.00e-02 2.50e+03 6.57e-02 4.31e+01 pdb=" C THR C 383 " 0.114 2.00e-02 2.50e+03 pdb=" O THR C 383 " -0.042 2.00e-02 2.50e+03 pdb=" N GLU C 384 " -0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS A 773 " 0.030 2.00e-02 2.50e+03 6.03e-02 3.64e+01 pdb=" C CYS A 773 " -0.104 2.00e-02 2.50e+03 pdb=" O CYS A 773 " 0.039 2.00e-02 2.50e+03 pdb=" N GLY A 774 " 0.035 2.00e-02 2.50e+03 ... (remaining 4753 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 3072 2.74 - 3.28: 27627 3.28 - 3.82: 47084 3.82 - 4.36: 56835 4.36 - 4.90: 91601 Nonbonded interactions: 226219 Sorted by model distance: nonbonded pdb=" O33 AJP C1302 " pdb=" O76 AJP C1302 " model vdw 2.206 2.440 nonbonded pdb=" O33 AJP A1302 " pdb=" O76 AJP A1302 " model vdw 2.206 2.440 nonbonded pdb=" O62 AJP A1302 " pdb=" O75 AJP A1302 " model vdw 2.220 2.440 nonbonded pdb=" O62 AJP C1302 " pdb=" O75 AJP C1302 " model vdw 2.220 2.440 nonbonded pdb=" NE2 GLN C 129 " pdb=" O78 AJP C1302 " model vdw 2.225 2.520 ... (remaining 226214 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' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.810 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: 0.030 Extract box with map and model: 7.260 Check model and map are aligned: 0.370 Set scattering table: 0.220 Process input model: 70.820 Find NCS groups from input model: 1.390 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 84.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6890 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 : 0.006 0.193 28248 Z= 0.420 Angle : 0.981 17.140 38254 Z= 0.549 Chirality : 0.641 5.832 4296 Planarity : 0.007 0.091 4756 Dihedral : 9.593 113.606 10156 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.46 % Favored : 93.40 % Rotamer: Outliers : 0.61 % Allowed : 0.88 % Favored : 98.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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: -4.07 (0.11), residues: 3452 helix: -3.36 (0.07), residues: 1566 sheet: -1.94 (0.25), residues: 380 loop : -1.93 (0.14), residues: 1506 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6904 Ramachandran restraints generated. 3452 Oldfield, 0 Emsley, 3452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6904 Ramachandran restraints generated. 3452 Oldfield, 0 Emsley, 3452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 900 residues out of total 2968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 882 time to evaluate : 3.184 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 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: 2 residues processed: 895 average time/residue: 0.4704 time to fit residues: 632.1698 Evaluate side-chains 420 residues out of total 2968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 418 time to evaluate : 3.195 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2464 time to fit residues: 5.5038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 293 optimal weight: 6.9990 chunk 263 optimal weight: 6.9990 chunk 146 optimal weight: 0.9980 chunk 90 optimal weight: 0.9990 chunk 177 optimal weight: 20.0000 chunk 140 optimal weight: 2.9990 chunk 272 optimal weight: 10.0000 chunk 105 optimal weight: 10.0000 chunk 165 optimal weight: 5.9990 chunk 203 optimal weight: 6.9990 chunk 316 optimal weight: 0.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN A 337 GLN A 412 HIS ** A 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 756 GLN A 791 ASN A1034 GLN A1037 GLN A1181 HIS ** B 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 167 ASN B 219 HIS B 337 GLN ** B 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 35 GLN C 65 GLN C 337 GLN ** C 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 587 GLN ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 756 GLN C 791 ASN C1037 GLN C1092 HIS ** D 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 147 GLN D 167 ASN D 219 HIS D 337 GLN ** D 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 412 HIS D 709 ASN D 756 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7055 moved from start: 0.3898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 28248 Z= 0.254 Angle : 0.968 37.573 38254 Z= 0.415 Chirality : 0.089 2.439 4296 Planarity : 0.005 0.073 4756 Dihedral : 6.560 72.887 3796 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 14.88 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.84 % Favored : 95.05 % Rotamer: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.13 (0.13), residues: 3452 helix: -1.20 (0.11), residues: 1584 sheet: -1.42 (0.27), residues: 386 loop : -1.49 (0.16), residues: 1482 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6904 Ramachandran restraints generated. 3452 Oldfield, 0 Emsley, 3452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6904 Ramachandran restraints generated. 3452 Oldfield, 0 Emsley, 3452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 529 residues out of total 2968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 529 time to evaluate : 3.039 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 revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 529 average time/residue: 0.4054 time to fit residues: 333.5108 Evaluate side-chains 332 residues out of total 2968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 332 time to evaluate : 2.852 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.8157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 175 optimal weight: 9.9990 chunk 98 optimal weight: 9.9990 chunk 263 optimal weight: 9.9990 chunk 215 optimal weight: 10.0000 chunk 87 optimal weight: 5.9990 chunk 316 optimal weight: 1.9990 chunk 342 optimal weight: 0.0870 chunk 281 optimal weight: 0.6980 chunk 313 optimal weight: 10.0000 chunk 107 optimal weight: 1.9990 chunk 253 optimal weight: 20.0000 overall best weight: 2.1564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 GLN A 170 ASN A 219 HIS ** A 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 290 GLN ** A 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1037 GLN B 60 ASN ** B 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 83 ASN ** B 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 65 GLN C 170 ASN D 60 ASN ** D 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7113 moved from start: 0.5017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 28248 Z= 0.220 Angle : 0.881 36.190 38254 Z= 0.379 Chirality : 0.088 2.508 4296 Planarity : 0.005 0.070 4756 Dihedral : 6.149 64.829 3796 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 14.59 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.45 % Favored : 94.50 % Rotamer: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.14), residues: 3452 helix: -0.11 (0.12), residues: 1592 sheet: -1.27 (0.26), residues: 408 loop : -1.39 (0.16), residues: 1452 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6904 Ramachandran restraints generated. 3452 Oldfield, 0 Emsley, 3452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6904 Ramachandran restraints generated. 3452 Oldfield, 0 Emsley, 3452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 2968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 466 time to evaluate : 3.342 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 outliers start: 0 outliers final: 0 residues processed: 466 average time/residue: 0.3893 time to fit residues: 290.9529 Evaluate side-chains 307 residues out of total 2968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 307 time to evaluate : 3.047 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.1810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 312 optimal weight: 0.8980 chunk 238 optimal weight: 0.0070 chunk 164 optimal weight: 0.9990 chunk 35 optimal weight: 10.0000 chunk 151 optimal weight: 0.9990 chunk 212 optimal weight: 6.9990 chunk 317 optimal weight: 7.9990 chunk 336 optimal weight: 8.9990 chunk 165 optimal weight: 5.9990 chunk 301 optimal weight: 0.0370 chunk 90 optimal weight: 6.9990 overall best weight: 0.5880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 GLN A 586 GLN B 60 ASN B 65 GLN B 182 GLN ** B 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 147 GLN C 337 GLN C 412 HIS D 60 ASN D 65 GLN ** D 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7086 moved from start: 0.5394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 28248 Z= 0.153 Angle : 0.836 35.710 38254 Z= 0.352 Chirality : 0.086 2.383 4296 Planarity : 0.004 0.064 4756 Dihedral : 5.846 73.117 3796 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 0.03 % Allowed : 1.93 % Favored : 98.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.85 (0.14), residues: 3452 helix: 0.31 (0.13), residues: 1584 sheet: -1.17 (0.26), residues: 406 loop : -1.28 (0.16), residues: 1462 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6904 Ramachandran restraints generated. 3452 Oldfield, 0 Emsley, 3452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6904 Ramachandran restraints generated. 3452 Oldfield, 0 Emsley, 3452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 2968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 479 time to evaluate : 3.056 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 revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 480 average time/residue: 0.3896 time to fit residues: 297.5574 Evaluate side-chains 323 residues out of total 2968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 323 time to evaluate : 3.221 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.0043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 280 optimal weight: 4.9990 chunk 190 optimal weight: 7.9990 chunk 4 optimal weight: 9.9990 chunk 250 optimal weight: 0.9990 chunk 138 optimal weight: 0.8980 chunk 287 optimal weight: 0.9990 chunk 232 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 171 optimal weight: 5.9990 chunk 301 optimal weight: 0.7980 chunk 84 optimal weight: 10.0000 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 ASN A 246 GLN ** A 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 587 GLN A 619 ASN ** A1189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 60 ASN ** B 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 83 ASN C 147 GLN C 219 HIS ** C 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 337 GLN C 587 GLN ** C1186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 60 ASN ** D 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7110 moved from start: 0.5837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 28248 Z= 0.165 Angle : 0.825 35.408 38254 Z= 0.347 Chirality : 0.085 2.326 4296 Planarity : 0.004 0.063 4756 Dihedral : 5.661 72.946 3796 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.58 (0.15), residues: 3452 helix: 0.55 (0.13), residues: 1586 sheet: -1.15 (0.26), residues: 410 loop : -1.14 (0.17), residues: 1456 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6904 Ramachandran restraints generated. 3452 Oldfield, 0 Emsley, 3452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6904 Ramachandran restraints generated. 3452 Oldfield, 0 Emsley, 3452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 2968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 453 time to evaluate : 3.262 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: 453 average time/residue: 0.3761 time to fit residues: 274.3017 Evaluate side-chains 317 residues out of total 2968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 317 time to evaluate : 3.050 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.2760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 113 optimal weight: 0.5980 chunk 302 optimal weight: 0.0000 chunk 66 optimal weight: 7.9990 chunk 197 optimal weight: 0.9980 chunk 83 optimal weight: 6.9990 chunk 336 optimal weight: 9.9990 chunk 279 optimal weight: 6.9990 chunk 155 optimal weight: 5.9990 chunk 27 optimal weight: 5.9990 chunk 111 optimal weight: 3.9990 chunk 176 optimal weight: 10.0000 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 GLN A 290 GLN ** A1163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 60 ASN ** B 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 65 GLN ** C 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 290 GLN ** C1163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 60 ASN ** D 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7174 moved from start: 0.6362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 28248 Z= 0.220 Angle : 0.857 35.484 38254 Z= 0.368 Chirality : 0.085 2.255 4296 Planarity : 0.004 0.059 4756 Dihedral : 5.691 76.656 3796 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 14.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.15), residues: 3452 helix: 0.59 (0.13), residues: 1584 sheet: -1.28 (0.25), residues: 410 loop : -0.93 (0.17), residues: 1458 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6904 Ramachandran restraints generated. 3452 Oldfield, 0 Emsley, 3452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6904 Ramachandran restraints generated. 3452 Oldfield, 0 Emsley, 3452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 2968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 416 time to evaluate : 3.138 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 outliers start: 0 outliers final: 0 residues processed: 416 average time/residue: 0.3931 time to fit residues: 262.1287 Evaluate side-chains 288 residues out of total 2968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 288 time to evaluate : 3.273 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.5547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/iotbx/cli_parser.py", line 881, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 56.8782 > 50: distance: 40 - 62: 10.822 distance: 44 - 69: 19.225 distance: 48 - 74: 11.330 distance: 52 - 62: 9.428 distance: 53 - 82: 26.608 distance: 63 - 64: 3.062 distance: 63 - 66: 5.981 distance: 64 - 65: 10.453 distance: 64 - 69: 9.670 distance: 65 - 90: 19.303 distance: 66 - 67: 6.090 distance: 66 - 68: 10.670 distance: 69 - 70: 12.813 distance: 70 - 71: 8.027 distance: 70 - 73: 6.305 distance: 71 - 72: 4.887 distance: 71 - 74: 12.359 distance: 72 - 95: 24.347 distance: 74 - 75: 13.671 distance: 75 - 76: 10.186 distance: 75 - 78: 7.135 distance: 77 - 100: 30.771 distance: 78 - 79: 14.719 distance: 79 - 80: 9.164 distance: 79 - 81: 11.869 distance: 82 - 83: 34.691 distance: 83 - 84: 13.913 distance: 83 - 86: 13.379 distance: 84 - 85: 16.010 distance: 84 - 90: 19.399 distance: 86 - 87: 29.646 distance: 87 - 88: 7.208 distance: 87 - 89: 22.466 distance: 90 - 91: 8.249 distance: 91 - 92: 13.209 distance: 91 - 94: 8.460 distance: 92 - 93: 13.988 distance: 92 - 95: 17.806 distance: 95 - 96: 20.998 distance: 96 - 97: 30.640 distance: 96 - 99: 6.594 distance: 97 - 98: 37.071 distance: 97 - 100: 19.440 distance: 100 - 101: 8.175 distance: 101 - 102: 4.599 distance: 101 - 104: 11.449 distance: 102 - 103: 8.001 distance: 102 - 111: 15.899 distance: 104 - 105: 5.170 distance: 105 - 106: 14.813 distance: 105 - 107: 26.962 distance: 106 - 108: 9.701 distance: 107 - 109: 8.998 distance: 108 - 110: 35.498 distance: 109 - 110: 20.330 distance: 111 - 112: 9.140 distance: 112 - 113: 20.532 distance: 112 - 115: 21.594 distance: 113 - 114: 24.549 distance: 113 - 119: 9.407 distance: 115 - 116: 16.408 distance: 116 - 117: 15.876 distance: 116 - 118: 23.800 distance: 120 - 121: 12.886 distance: 120 - 123: 29.369 distance: 121 - 122: 13.368 distance: 121 - 126: 23.312 distance: 123 - 124: 12.765 distance: 123 - 125: 37.279 distance: 126 - 127: 7.756 distance: 127 - 128: 24.530 distance: 127 - 130: 27.370 distance: 128 - 129: 24.151 distance: 128 - 133: 6.865 distance: 130 - 131: 8.530