Starting phenix.real_space_refine on Tue Feb 20 10:57:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7txv_26161/02_2024/7txv_26161_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7txv_26161/02_2024/7txv_26161.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7txv_26161/02_2024/7txv_26161_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7txv_26161/02_2024/7txv_26161_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7txv_26161/02_2024/7txv_26161_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7txv_26161/02_2024/7txv_26161.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7txv_26161/02_2024/7txv_26161.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7txv_26161/02_2024/7txv_26161_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7txv_26161/02_2024/7txv_26161_updated.pdb" } resolution = 2.7 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= 0.005 sd= 0.103 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: 7 Type Number sf(0) Gaussians Zn 4 6.06 5 P 24 5.49 5 Mg 16 5.21 5 S 96 5.16 5 C 17232 2.51 5 N 4904 2.21 5 O 5372 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 27648 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 6650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 870, 6650 Classifications: {'peptide': 870} Link IDs: {'PTRANS': 40, 'TRANS': 829} Chain breaks: 1 Chain: "B" Number of atoms: 6650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 870, 6650 Classifications: {'peptide': 870} Link IDs: {'PTRANS': 40, 'TRANS': 829} Chain breaks: 1 Chain: "C" Number of atoms: 6650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 870, 6650 Classifications: {'peptide': 870} Link IDs: {'PTRANS': 40, 'TRANS': 829} Chain breaks: 1 Chain: "D" Number of atoms: 6650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 870, 6650 Classifications: {'peptide': 870} Link IDs: {'PTRANS': 40, 'TRANS': 829} Chain breaks: 1 Chain: "E" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 61 Classifications: {'peptide': 4} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 3} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'7ID:plan-2': 1, '7ID:plan-3': 1, '7ID:plan-1': 1, '7ID:plan-4': 4} Unresolved non-hydrogen planarities: 18 Chain: "F" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 61 Classifications: {'peptide': 4} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 3} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'7ID:plan-2': 1, '7ID:plan-3': 1, '7ID:plan-1': 1, '7ID:plan-4': 4} Unresolved non-hydrogen planarities: 18 Chain: "G" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 61 Classifications: {'peptide': 4} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 3} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'7ID:plan-2': 1, '7ID:plan-3': 1, '7ID:plan-1': 1, '7ID:plan-4': 4} Unresolved non-hydrogen planarities: 18 Chain: "H" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 61 Classifications: {'peptide': 4} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 3} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'7ID:plan-2': 1, '7ID:plan-3': 1, '7ID:plan-1': 1, '7ID:plan-4': 4} Unresolved non-hydrogen planarities: 18 Chain: "I" Number of atoms: 134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 134 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'7ID:plan-2': 1, '7ID:plan-3': 1, '7ID:plan-1': 1, '7ID:plan-4': 8} Unresolved non-hydrogen planarities: 25 Chain: "J" Number of atoms: 134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 134 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'7ID:plan-2': 1, '7ID:plan-3': 1, '7ID:plan-1': 1, '7ID:plan-4': 8} Unresolved non-hydrogen planarities: 25 Chain: "K" Number of atoms: 134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 134 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'7ID:plan-2': 1, '7ID:plan-3': 1, '7ID:plan-1': 1, '7ID:plan-4': 8} Unresolved non-hydrogen planarities: 25 Chain: "L" Number of atoms: 134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 134 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'7ID:plan-2': 1, '7ID:plan-3': 1, '7ID:plan-1': 1, '7ID:plan-4': 8} Unresolved non-hydrogen planarities: 25 Chain: "A" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 67 Unusual residues: {' MG': 4, ' ZN': 1, 'ATP': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "B" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 67 Unusual residues: {' MG': 4, ' ZN': 1, 'ATP': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "C" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 67 Unusual residues: {' MG': 4, ' ZN': 1, 'ATP': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "D" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 67 Unusual residues: {' MG': 4, ' ZN': 1, 'ATP': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 484 SG CYS A 59 79.190 128.854 41.252 1.00 81.08 S ATOM 7134 SG CYS B 59 69.745 19.817 41.079 1.00 87.56 S ATOM 13784 SG CYS C 59 69.725 128.953 92.285 1.00 84.85 S ATOM 20434 SG CYS D 59 79.040 19.819 92.296 1.00 85.48 S Time building chain proxies: 14.57, per 1000 atoms: 0.53 Number of scatterers: 27648 At special positions: 0 Unit cell: (149.625, 149.625, 134.235, 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) Zn 4 29.99 S 96 16.00 P 24 15.00 Mg 16 11.99 O 5372 8.00 N 4904 7.00 C 17232 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 11.20 Conformation dependent library (CDL) restraints added in 5.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 905 " pdb="ZN ZN A 905 " - pdb=" NE2 HIS A 83 " pdb="ZN ZN A 905 " - pdb=" NE2 HIS A 79 " pdb="ZN ZN A 905 " - pdb=" SG CYS A 59 " pdb=" ZN B 905 " pdb="ZN ZN B 905 " - pdb=" NE2 HIS B 83 " pdb="ZN ZN B 905 " - pdb=" NE2 HIS B 79 " pdb="ZN ZN B 905 " - pdb=" SG CYS B 59 " pdb=" ZN C 905 " pdb="ZN ZN C 905 " - pdb=" NE2 HIS C 83 " pdb="ZN ZN C 905 " - pdb=" NE2 HIS C 79 " pdb="ZN ZN C 905 " - pdb=" SG CYS C 59 " pdb=" ZN D 905 " pdb="ZN ZN D 905 " - pdb=" NE2 HIS D 83 " pdb="ZN ZN D 905 " - pdb=" NE2 HIS D 79 " pdb="ZN ZN D 905 " - pdb=" SG CYS D 59 " 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 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: 128 helices and 24 sheets defined 34.8% alpha, 14.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.06 Creating SS restraints... Processing helix chain 'A' and resid 45 through 50 Processing helix chain 'A' and resid 52 through 56 Processing helix chain 'A' and resid 77 through 92 removed outlier: 4.586A pdb=" N GLN A 82 " --> pdb=" O GLY A 78 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N HIS A 83 " --> pdb=" O HIS A 79 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU A 86 " --> pdb=" O GLN A 82 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N VAL A 92 " --> pdb=" O LEU A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 137 removed outlier: 3.530A pdb=" N VAL A 137 " --> pdb=" O CYS A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 160 removed outlier: 3.795A pdb=" N GLU A 148 " --> pdb=" O LEU A 145 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N LYS A 149 " --> pdb=" O GLU A 146 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLY A 158 " --> pdb=" O ARG A 155 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ASN A 160 " --> pdb=" O LEU A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 176 Processing helix chain 'A' and resid 195 through 197 No H-bonds generated for 'chain 'A' and resid 195 through 197' Processing helix chain 'A' and resid 211 through 218 removed outlier: 3.533A pdb=" N CYS A 218 " --> pdb=" O VAL A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 230 removed outlier: 3.583A pdb=" N ALA A 230 " --> pdb=" O ILE A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 253 removed outlier: 4.308A pdb=" N ASN A 251 " --> pdb=" O GLU A 247 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASP A 252 " --> pdb=" O GLU A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 290 removed outlier: 3.917A pdb=" N GLU A 290 " --> pdb=" O ASP A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 343 Processing helix chain 'A' and resid 364 through 373 removed outlier: 3.727A pdb=" N GLN A 373 " --> pdb=" O VAL A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 397 No H-bonds generated for 'chain 'A' and resid 395 through 397' Processing helix chain 'A' and resid 405 through 407 No H-bonds generated for 'chain 'A' and resid 405 through 407' Processing helix chain 'A' and resid 410 through 423 Processing helix chain 'A' and resid 441 through 444 No H-bonds generated for 'chain 'A' and resid 441 through 444' Processing helix chain 'A' and resid 458 through 461 No H-bonds generated for 'chain 'A' and resid 458 through 461' Processing helix chain 'A' and resid 473 through 479 removed outlier: 3.694A pdb=" N MET A 478 " --> pdb=" O PRO A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 513 removed outlier: 3.523A pdb=" N GLN A 512 " --> pdb=" O HIS A 508 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N THR A 513 " --> pdb=" O ILE A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 547 removed outlier: 3.864A pdb=" N VAL A 545 " --> pdb=" O GLN A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 567 Processing helix chain 'A' and resid 595 through 608 removed outlier: 3.596A pdb=" N LYS A 600 " --> pdb=" O GLU A 596 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL A 604 " --> pdb=" O LYS A 600 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N ILE A 605 " --> pdb=" O VAL A 601 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ALA A 606 " --> pdb=" O LYS A 602 " (cutoff:3.500A) Processing helix chain 'A' and resid 622 through 629 removed outlier: 3.762A pdb=" N ALA A 626 " --> pdb=" O PRO A 622 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N MET A 627 " --> pdb=" O LEU A 623 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ALA A 628 " --> pdb=" O VAL A 624 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N ASP A 629 " --> pdb=" O ALA A 625 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 622 through 629' Processing helix chain 'A' and resid 645 through 653 removed outlier: 3.679A pdb=" N ARG A 653 " --> pdb=" O ALA A 649 " (cutoff:3.500A) Processing helix chain 'A' and resid 679 through 681 No H-bonds generated for 'chain 'A' and resid 679 through 681' Processing helix chain 'A' and resid 691 through 706 Processing helix chain 'A' and resid 711 through 720 Processing helix chain 'A' and resid 750 through 761 removed outlier: 4.070A pdb=" N VAL A 756 " --> pdb=" O GLY A 752 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N PHE A 759 " --> pdb=" O ALA A 755 " (cutoff:3.500A) Processing helix chain 'A' and resid 782 through 790 Processing helix chain 'A' and resid 811 through 824 Processing helix chain 'A' and resid 859 through 869 removed outlier: 3.618A pdb=" N ASP A 864 " --> pdb=" O THR A 860 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N LYS A 867 " --> pdb=" O ILE A 863 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N VAL A 868 " --> pdb=" O ASP A 864 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N ARG A 869 " --> pdb=" O LEU A 865 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 50 Processing helix chain 'B' and resid 52 through 56 Processing helix chain 'B' and resid 77 through 92 removed outlier: 4.586A pdb=" N GLN B 82 " --> pdb=" O GLY B 78 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N HIS B 83 " --> pdb=" O HIS B 79 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU B 86 " --> pdb=" O GLN B 82 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N VAL B 92 " --> pdb=" O LEU B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 137 removed outlier: 3.530A pdb=" N VAL B 137 " --> pdb=" O CYS B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 160 removed outlier: 3.794A pdb=" N GLU B 148 " --> pdb=" O LEU B 145 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N LYS B 149 " --> pdb=" O GLU B 146 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLY B 158 " --> pdb=" O ARG B 155 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASN B 160 " --> pdb=" O LEU B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 176 Processing helix chain 'B' and resid 195 through 197 No H-bonds generated for 'chain 'B' and resid 195 through 197' Processing helix chain 'B' and resid 211 through 218 removed outlier: 3.532A pdb=" N CYS B 218 " --> pdb=" O VAL B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 230 removed outlier: 3.583A pdb=" N ALA B 230 " --> pdb=" O ILE B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 253 removed outlier: 4.309A pdb=" N ASN B 251 " --> pdb=" O GLU B 247 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASP B 252 " --> pdb=" O GLU B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 290 removed outlier: 3.917A pdb=" N GLU B 290 " --> pdb=" O ASP B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 343 Processing helix chain 'B' and resid 364 through 373 removed outlier: 3.727A pdb=" N GLN B 373 " --> pdb=" O VAL B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 397 No H-bonds generated for 'chain 'B' and resid 395 through 397' Processing helix chain 'B' and resid 405 through 407 No H-bonds generated for 'chain 'B' and resid 405 through 407' Processing helix chain 'B' and resid 410 through 423 Processing helix chain 'B' and resid 441 through 444 No H-bonds generated for 'chain 'B' and resid 441 through 444' Processing helix chain 'B' and resid 458 through 461 No H-bonds generated for 'chain 'B' and resid 458 through 461' Processing helix chain 'B' and resid 473 through 479 removed outlier: 3.693A pdb=" N MET B 478 " --> pdb=" O PRO B 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 513 removed outlier: 3.523A pdb=" N GLN B 512 " --> pdb=" O HIS B 508 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N THR B 513 " --> pdb=" O ILE B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 540 through 547 removed outlier: 3.864A pdb=" N VAL B 545 " --> pdb=" O GLN B 541 " (cutoff:3.500A) Processing helix chain 'B' and resid 561 through 567 Processing helix chain 'B' and resid 595 through 608 removed outlier: 3.596A pdb=" N LYS B 600 " --> pdb=" O GLU B 596 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL B 604 " --> pdb=" O LYS B 600 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N ILE B 605 " --> pdb=" O VAL B 601 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ALA B 606 " --> pdb=" O LYS B 602 " (cutoff:3.500A) Processing helix chain 'B' and resid 622 through 629 removed outlier: 3.761A pdb=" N ALA B 626 " --> pdb=" O PRO B 622 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N MET B 627 " --> pdb=" O LEU B 623 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ALA B 628 " --> pdb=" O VAL B 624 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N ASP B 629 " --> pdb=" O ALA B 625 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 622 through 629' Processing helix chain 'B' and resid 645 through 653 removed outlier: 3.680A pdb=" N ARG B 653 " --> pdb=" O ALA B 649 " (cutoff:3.500A) Processing helix chain 'B' and resid 679 through 681 No H-bonds generated for 'chain 'B' and resid 679 through 681' Processing helix chain 'B' and resid 691 through 706 Processing helix chain 'B' and resid 711 through 720 Processing helix chain 'B' and resid 750 through 761 removed outlier: 4.070A pdb=" N VAL B 756 " --> pdb=" O GLY B 752 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N PHE B 759 " --> pdb=" O ALA B 755 " (cutoff:3.500A) Processing helix chain 'B' and resid 782 through 790 Processing helix chain 'B' and resid 811 through 824 Processing helix chain 'B' and resid 859 through 869 removed outlier: 3.618A pdb=" N ASP B 864 " --> pdb=" O THR B 860 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N LYS B 867 " --> pdb=" O ILE B 863 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N VAL B 868 " --> pdb=" O ASP B 864 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N ARG B 869 " --> pdb=" O LEU B 865 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 50 Processing helix chain 'C' and resid 52 through 56 Processing helix chain 'C' and resid 77 through 92 removed outlier: 4.586A pdb=" N GLN C 82 " --> pdb=" O GLY C 78 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N HIS C 83 " --> pdb=" O HIS C 79 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU C 86 " --> pdb=" O GLN C 82 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N VAL C 92 " --> pdb=" O LEU C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 137 removed outlier: 3.529A pdb=" N VAL C 137 " --> pdb=" O CYS C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 160 removed outlier: 3.795A pdb=" N GLU C 148 " --> pdb=" O LEU C 145 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N LYS C 149 " --> pdb=" O GLU C 146 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLY C 158 " --> pdb=" O ARG C 155 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ASN C 160 " --> pdb=" O LEU C 157 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 176 Processing helix chain 'C' and resid 195 through 197 No H-bonds generated for 'chain 'C' and resid 195 through 197' Processing helix chain 'C' and resid 211 through 218 removed outlier: 3.533A pdb=" N CYS C 218 " --> pdb=" O VAL C 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 230 removed outlier: 3.583A pdb=" N ALA C 230 " --> pdb=" O ILE C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 253 removed outlier: 4.308A pdb=" N ASN C 251 " --> pdb=" O GLU C 247 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASP C 252 " --> pdb=" O GLU C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 278 through 290 removed outlier: 3.916A pdb=" N GLU C 290 " --> pdb=" O ASP C 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 336 through 343 Processing helix chain 'C' and resid 364 through 373 removed outlier: 3.727A pdb=" N GLN C 373 " --> pdb=" O VAL C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 395 through 397 No H-bonds generated for 'chain 'C' and resid 395 through 397' Processing helix chain 'C' and resid 405 through 407 No H-bonds generated for 'chain 'C' and resid 405 through 407' Processing helix chain 'C' and resid 410 through 423 Processing helix chain 'C' and resid 441 through 444 No H-bonds generated for 'chain 'C' and resid 441 through 444' Processing helix chain 'C' and resid 458 through 461 No H-bonds generated for 'chain 'C' and resid 458 through 461' Processing helix chain 'C' and resid 473 through 479 removed outlier: 3.693A pdb=" N MET C 478 " --> pdb=" O PRO C 474 " (cutoff:3.500A) Processing helix chain 'C' and resid 499 through 513 removed outlier: 3.523A pdb=" N GLN C 512 " --> pdb=" O HIS C 508 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N THR C 513 " --> pdb=" O ILE C 509 " (cutoff:3.500A) Processing helix chain 'C' and resid 540 through 547 removed outlier: 3.863A pdb=" N VAL C 545 " --> pdb=" O GLN C 541 " (cutoff:3.500A) Processing helix chain 'C' and resid 561 through 567 Processing helix chain 'C' and resid 595 through 608 removed outlier: 3.596A pdb=" N LYS C 600 " --> pdb=" O GLU C 596 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL C 604 " --> pdb=" O LYS C 600 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N ILE C 605 " --> pdb=" O VAL C 601 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ALA C 606 " --> pdb=" O LYS C 602 " (cutoff:3.500A) Processing helix chain 'C' and resid 622 through 629 removed outlier: 3.761A pdb=" N ALA C 626 " --> pdb=" O PRO C 622 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N MET C 627 " --> pdb=" O LEU C 623 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ALA C 628 " --> pdb=" O VAL C 624 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N ASP C 629 " --> pdb=" O ALA C 625 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 622 through 629' Processing helix chain 'C' and resid 645 through 653 removed outlier: 3.679A pdb=" N ARG C 653 " --> pdb=" O ALA C 649 " (cutoff:3.500A) Processing helix chain 'C' and resid 679 through 681 No H-bonds generated for 'chain 'C' and resid 679 through 681' Processing helix chain 'C' and resid 691 through 706 Processing helix chain 'C' and resid 711 through 720 Processing helix chain 'C' and resid 750 through 761 removed outlier: 4.069A pdb=" N VAL C 756 " --> pdb=" O GLY C 752 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N PHE C 759 " --> pdb=" O ALA C 755 " (cutoff:3.500A) Processing helix chain 'C' and resid 782 through 790 Processing helix chain 'C' and resid 811 through 824 Processing helix chain 'C' and resid 859 through 869 removed outlier: 3.617A pdb=" N ASP C 864 " --> pdb=" O THR C 860 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N LYS C 867 " --> pdb=" O ILE C 863 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N VAL C 868 " --> pdb=" O ASP C 864 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N ARG C 869 " --> pdb=" O LEU C 865 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 50 Processing helix chain 'D' and resid 52 through 56 Processing helix chain 'D' and resid 77 through 92 removed outlier: 4.586A pdb=" N GLN D 82 " --> pdb=" O GLY D 78 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N HIS D 83 " --> pdb=" O HIS D 79 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU D 86 " --> pdb=" O GLN D 82 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N VAL D 92 " --> pdb=" O LEU D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 137 removed outlier: 3.529A pdb=" N VAL D 137 " --> pdb=" O CYS D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 160 removed outlier: 3.795A pdb=" N GLU D 148 " --> pdb=" O LEU D 145 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N LYS D 149 " --> pdb=" O GLU D 146 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLY D 158 " --> pdb=" O ARG D 155 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ASN D 160 " --> pdb=" O LEU D 157 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 176 Processing helix chain 'D' and resid 195 through 197 No H-bonds generated for 'chain 'D' and resid 195 through 197' Processing helix chain 'D' and resid 211 through 218 removed outlier: 3.533A pdb=" N CYS D 218 " --> pdb=" O VAL D 214 " (cutoff:3.500A) Processing helix chain 'D' and resid 220 through 230 removed outlier: 3.583A pdb=" N ALA D 230 " --> pdb=" O ILE D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 246 through 253 removed outlier: 4.309A pdb=" N ASN D 251 " --> pdb=" O GLU D 247 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASP D 252 " --> pdb=" O GLU D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 278 through 290 removed outlier: 3.917A pdb=" N GLU D 290 " --> pdb=" O ASP D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 336 through 343 Processing helix chain 'D' and resid 364 through 373 removed outlier: 3.727A pdb=" N GLN D 373 " --> pdb=" O VAL D 369 " (cutoff:3.500A) Processing helix chain 'D' and resid 395 through 397 No H-bonds generated for 'chain 'D' and resid 395 through 397' Processing helix chain 'D' and resid 405 through 407 No H-bonds generated for 'chain 'D' and resid 405 through 407' Processing helix chain 'D' and resid 410 through 423 Processing helix chain 'D' and resid 441 through 444 No H-bonds generated for 'chain 'D' and resid 441 through 444' Processing helix chain 'D' and resid 458 through 461 No H-bonds generated for 'chain 'D' and resid 458 through 461' Processing helix chain 'D' and resid 473 through 479 removed outlier: 3.694A pdb=" N MET D 478 " --> pdb=" O PRO D 474 " (cutoff:3.500A) Processing helix chain 'D' and resid 499 through 513 removed outlier: 3.523A pdb=" N GLN D 512 " --> pdb=" O HIS D 508 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N THR D 513 " --> pdb=" O ILE D 509 " (cutoff:3.500A) Processing helix chain 'D' and resid 540 through 547 removed outlier: 3.864A pdb=" N VAL D 545 " --> pdb=" O GLN D 541 " (cutoff:3.500A) Processing helix chain 'D' and resid 561 through 567 Processing helix chain 'D' and resid 595 through 608 removed outlier: 3.595A pdb=" N LYS D 600 " --> pdb=" O GLU D 596 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL D 604 " --> pdb=" O LYS D 600 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N ILE D 605 " --> pdb=" O VAL D 601 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ALA D 606 " --> pdb=" O LYS D 602 " (cutoff:3.500A) Processing helix chain 'D' and resid 622 through 629 removed outlier: 3.761A pdb=" N ALA D 626 " --> pdb=" O PRO D 622 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N MET D 627 " --> pdb=" O LEU D 623 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ALA D 628 " --> pdb=" O VAL D 624 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N ASP D 629 " --> pdb=" O ALA D 625 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 622 through 629' Processing helix chain 'D' and resid 645 through 653 removed outlier: 3.680A pdb=" N ARG D 653 " --> pdb=" O ALA D 649 " (cutoff:3.500A) Processing helix chain 'D' and resid 679 through 681 No H-bonds generated for 'chain 'D' and resid 679 through 681' Processing helix chain 'D' and resid 691 through 706 Processing helix chain 'D' and resid 711 through 720 Processing helix chain 'D' and resid 750 through 761 removed outlier: 4.070A pdb=" N VAL D 756 " --> pdb=" O GLY D 752 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N PHE D 759 " --> pdb=" O ALA D 755 " (cutoff:3.500A) Processing helix chain 'D' and resid 782 through 790 Processing helix chain 'D' and resid 811 through 824 Processing helix chain 'D' and resid 859 through 869 removed outlier: 3.618A pdb=" N ASP D 864 " --> pdb=" O THR D 860 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N LYS D 867 " --> pdb=" O ILE D 863 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N VAL D 868 " --> pdb=" O ASP D 864 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N ARG D 869 " --> pdb=" O LEU D 865 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 99 through 104 removed outlier: 4.198A pdb=" N VAL A 109 " --> pdb=" O THR A 104 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LYS A 5 " --> pdb=" O ARG A 26 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ASP A 28 " --> pdb=" O ILE A 3 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N ILE A 3 " --> pdb=" O ASP A 28 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 181 through 183 Processing sheet with id= C, first strand: chain 'A' and resid 400 through 403 removed outlier: 6.739A pdb=" N LEU A 311 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N VAL A 320 " --> pdb=" O ARG A 309 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ARG A 309 " --> pdb=" O VAL A 320 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N GLU A 322 " --> pdb=" O ASP A 307 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N ASP A 307 " --> pdb=" O GLU A 322 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N VAL A 433 " --> pdb=" O ILE A 448 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N ILE A 448 " --> pdb=" O VAL A 433 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 327 through 329 Processing sheet with id= E, first strand: chain 'A' and resid 672 through 678 removed outlier: 6.756A pdb=" N LEU A 665 " --> pdb=" O VAL A 676 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N VAL A 635 " --> pdb=" O ILE A 656 " (cutoff:3.500A) removed outlier: 9.010A pdb=" N ALA A 658 " --> pdb=" O VAL A 635 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N TYR A 637 " --> pdb=" O ALA A 658 " (cutoff:3.500A) removed outlier: 8.474A pdb=" N TYR A 660 " --> pdb=" O TYR A 637 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N SER A 639 " --> pdb=" O TYR A 660 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ASN A 618 " --> pdb=" O VAL A 579 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ILE A 527 " --> pdb=" O CYS A 531 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N CYS A 531 " --> pdb=" O ILE A 527 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 733 through 736 removed outlier: 6.541A pdb=" N ARG A 767 " --> pdb=" O LEU A 851 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N VAL A 853 " --> pdb=" O ARG A 767 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N GLY A 769 " --> pdb=" O VAL A 853 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ARG A 795 " --> pdb=" O VAL A 770 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 99 through 104 removed outlier: 4.198A pdb=" N VAL B 109 " --> pdb=" O THR B 104 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS B 5 " --> pdb=" O ARG B 26 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ASP B 28 " --> pdb=" O ILE B 3 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N ILE B 3 " --> pdb=" O ASP B 28 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 181 through 183 Processing sheet with id= I, first strand: chain 'B' and resid 400 through 403 removed outlier: 6.738A pdb=" N LEU B 311 " --> pdb=" O VAL B 318 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N VAL B 320 " --> pdb=" O ARG B 309 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ARG B 309 " --> pdb=" O VAL B 320 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N GLU B 322 " --> pdb=" O ASP B 307 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N ASP B 307 " --> pdb=" O GLU B 322 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N VAL B 433 " --> pdb=" O ILE B 448 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N ILE B 448 " --> pdb=" O VAL B 433 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 327 through 329 Processing sheet with id= K, first strand: chain 'B' and resid 672 through 678 removed outlier: 6.755A pdb=" N LEU B 665 " --> pdb=" O VAL B 676 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N VAL B 635 " --> pdb=" O ILE B 656 " (cutoff:3.500A) removed outlier: 9.010A pdb=" N ALA B 658 " --> pdb=" O VAL B 635 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N TYR B 637 " --> pdb=" O ALA B 658 " (cutoff:3.500A) removed outlier: 8.475A pdb=" N TYR B 660 " --> pdb=" O TYR B 637 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N SER B 639 " --> pdb=" O TYR B 660 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ASN B 618 " --> pdb=" O VAL B 579 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ILE B 527 " --> pdb=" O CYS B 531 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N CYS B 531 " --> pdb=" O ILE B 527 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 733 through 736 removed outlier: 6.542A pdb=" N ARG B 767 " --> pdb=" O LEU B 851 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N VAL B 853 " --> pdb=" O ARG B 767 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N GLY B 769 " --> pdb=" O VAL B 853 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ARG B 795 " --> pdb=" O VAL B 770 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 99 through 104 removed outlier: 4.197A pdb=" N VAL C 109 " --> pdb=" O THR C 104 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LYS C 5 " --> pdb=" O ARG C 26 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ASP C 28 " --> pdb=" O ILE C 3 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N ILE C 3 " --> pdb=" O ASP C 28 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 181 through 183 Processing sheet with id= O, first strand: chain 'C' and resid 400 through 403 removed outlier: 6.738A pdb=" N LEU C 311 " --> pdb=" O VAL C 318 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N VAL C 320 " --> pdb=" O ARG C 309 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ARG C 309 " --> pdb=" O VAL C 320 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N GLU C 322 " --> pdb=" O ASP C 307 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N ASP C 307 " --> pdb=" O GLU C 322 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N VAL C 433 " --> pdb=" O ILE C 448 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N ILE C 448 " --> pdb=" O VAL C 433 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 327 through 329 Processing sheet with id= Q, first strand: chain 'C' and resid 672 through 678 removed outlier: 6.756A pdb=" N LEU C 665 " --> pdb=" O VAL C 676 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N VAL C 635 " --> pdb=" O ILE C 656 " (cutoff:3.500A) removed outlier: 9.010A pdb=" N ALA C 658 " --> pdb=" O VAL C 635 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N TYR C 637 " --> pdb=" O ALA C 658 " (cutoff:3.500A) removed outlier: 8.475A pdb=" N TYR C 660 " --> pdb=" O TYR C 637 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N SER C 639 " --> pdb=" O TYR C 660 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ASN C 618 " --> pdb=" O VAL C 579 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ILE C 527 " --> pdb=" O CYS C 531 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N CYS C 531 " --> pdb=" O ILE C 527 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 733 through 736 removed outlier: 6.541A pdb=" N ARG C 767 " --> pdb=" O LEU C 851 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N VAL C 853 " --> pdb=" O ARG C 767 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N GLY C 769 " --> pdb=" O VAL C 853 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ARG C 795 " --> pdb=" O VAL C 770 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 99 through 104 removed outlier: 4.198A pdb=" N VAL D 109 " --> pdb=" O THR D 104 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LYS D 5 " --> pdb=" O ARG D 26 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ASP D 28 " --> pdb=" O ILE D 3 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N ILE D 3 " --> pdb=" O ASP D 28 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 181 through 183 Processing sheet with id= U, first strand: chain 'D' and resid 400 through 403 removed outlier: 6.738A pdb=" N LEU D 311 " --> pdb=" O VAL D 318 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N VAL D 320 " --> pdb=" O ARG D 309 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ARG D 309 " --> pdb=" O VAL D 320 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N GLU D 322 " --> pdb=" O ASP D 307 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N ASP D 307 " --> pdb=" O GLU D 322 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N VAL D 433 " --> pdb=" O ILE D 448 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N ILE D 448 " --> pdb=" O VAL D 433 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'D' and resid 327 through 329 Processing sheet with id= W, first strand: chain 'D' and resid 672 through 678 removed outlier: 6.755A pdb=" N LEU D 665 " --> pdb=" O VAL D 676 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N VAL D 635 " --> pdb=" O ILE D 656 " (cutoff:3.500A) removed outlier: 9.011A pdb=" N ALA D 658 " --> pdb=" O VAL D 635 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N TYR D 637 " --> pdb=" O ALA D 658 " (cutoff:3.500A) removed outlier: 8.474A pdb=" N TYR D 660 " --> pdb=" O TYR D 637 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N SER D 639 " --> pdb=" O TYR D 660 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ASN D 618 " --> pdb=" O VAL D 579 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ILE D 527 " --> pdb=" O CYS D 531 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N CYS D 531 " --> pdb=" O ILE D 527 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'D' and resid 733 through 736 removed outlier: 6.542A pdb=" N ARG D 767 " --> pdb=" O LEU D 851 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N VAL D 853 " --> pdb=" O ARG D 767 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N GLY D 769 " --> pdb=" O VAL D 853 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ARG D 795 " --> pdb=" O VAL D 770 " (cutoff:3.500A) 936 hydrogen bonds defined for protein. 2544 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: 11.46 Time building geometry restraints manager: 12.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 6029 1.32 - 1.45: 7209 1.45 - 1.58: 14578 1.58 - 1.71: 112 1.71 - 1.84: 160 Bond restraints: 28088 Sorted by residual: bond pdb=" CG GLU B 450 " pdb=" CD GLU B 450 " ideal model delta sigma weight residual 1.516 1.342 0.174 2.50e-02 1.60e+03 4.83e+01 bond pdb=" CG GLU A 450 " pdb=" CD GLU A 450 " ideal model delta sigma weight residual 1.516 1.343 0.173 2.50e-02 1.60e+03 4.80e+01 bond pdb=" CG GLU C 450 " pdb=" CD GLU C 450 " ideal model delta sigma weight residual 1.516 1.343 0.173 2.50e-02 1.60e+03 4.78e+01 bond pdb=" CG GLU D 450 " pdb=" CD GLU D 450 " ideal model delta sigma weight residual 1.516 1.343 0.173 2.50e-02 1.60e+03 4.77e+01 bond pdb=" CZ2 7ID L 1 " pdb=" NH2 7ID L 1 " ideal model delta sigma weight residual 1.451 1.314 0.137 2.00e-02 2.50e+03 4.71e+01 ... (remaining 28083 not shown) Histogram of bond angle deviations from ideal: 94.91 - 103.15: 392 103.15 - 111.38: 10570 111.38 - 119.62: 13945 119.62 - 127.86: 13088 127.86 - 136.10: 181 Bond angle restraints: 38176 Sorted by residual: angle pdb=" PB ATP C 907 " pdb=" O3B ATP C 907 " pdb=" PG ATP C 907 " ideal model delta sigma weight residual 139.87 111.52 28.35 1.00e+00 1.00e+00 8.04e+02 angle pdb=" PB ATP D 907 " pdb=" O3B ATP D 907 " pdb=" PG ATP D 907 " ideal model delta sigma weight residual 139.87 111.55 28.32 1.00e+00 1.00e+00 8.02e+02 angle pdb=" PB ATP A 907 " pdb=" O3B ATP A 907 " pdb=" PG ATP A 907 " ideal model delta sigma weight residual 139.87 111.56 28.31 1.00e+00 1.00e+00 8.02e+02 angle pdb=" PB ATP B 907 " pdb=" O3B ATP B 907 " pdb=" PG ATP B 907 " ideal model delta sigma weight residual 139.87 111.58 28.29 1.00e+00 1.00e+00 8.00e+02 angle pdb=" PB ATP C 906 " pdb=" O3B ATP C 906 " pdb=" PG ATP C 906 " ideal model delta sigma weight residual 139.87 112.55 27.32 1.00e+00 1.00e+00 7.46e+02 ... (remaining 38171 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.35: 16510 32.35 - 64.70: 408 64.70 - 97.05: 122 97.05 - 129.40: 40 129.40 - 161.75: 24 Dihedral angle restraints: 17104 sinusoidal: 7072 harmonic: 10032 Sorted by residual: dihedral pdb=" CA 7ID H 1 " pdb=" C 7ID H 1 " pdb=" N 7ID H 2 " pdb=" CA 7ID H 2 " ideal model delta harmonic sigma weight residual -180.00 -70.64 -109.36 0 5.00e+00 4.00e-02 4.78e+02 dihedral pdb=" CA 7ID F 1 " pdb=" C 7ID F 1 " pdb=" N 7ID F 2 " pdb=" CA 7ID F 2 " ideal model delta harmonic sigma weight residual -180.00 -70.66 -109.34 0 5.00e+00 4.00e-02 4.78e+02 dihedral pdb=" CA 7ID G 1 " pdb=" C 7ID G 1 " pdb=" N 7ID G 2 " pdb=" CA 7ID G 2 " ideal model delta harmonic sigma weight residual -180.00 -70.68 -109.32 0 5.00e+00 4.00e-02 4.78e+02 ... (remaining 17101 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 2968 0.098 - 0.196: 1155 0.196 - 0.294: 219 0.294 - 0.393: 27 0.393 - 0.491: 15 Chirality restraints: 4384 Sorted by residual: chirality pdb=" CA TYR C 256 " pdb=" N TYR C 256 " pdb=" C TYR C 256 " pdb=" CB TYR C 256 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 6.02e+00 chirality pdb=" CA TYR A 256 " pdb=" N TYR A 256 " pdb=" C TYR A 256 " pdb=" CB TYR A 256 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 6.01e+00 chirality pdb=" CA TYR B 256 " pdb=" N TYR B 256 " pdb=" C TYR B 256 " pdb=" CB TYR B 256 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 5.98e+00 ... (remaining 4381 not shown) Planarity restraints: 4988 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB 7ID J 2 " -0.090 2.00e-02 2.50e+03 3.01e-01 1.13e+03 pdb=" CG 7ID J 2 " 0.086 2.00e-02 2.50e+03 pdb=" OD1 7ID J 2 " -0.179 2.00e-02 2.50e+03 pdb=" CA2 7ID J 2 " -0.349 2.00e-02 2.50e+03 pdb=" N2 7ID J 2 " 0.532 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB 7ID G 3 " -0.147 2.00e-02 2.50e+03 3.01e-01 1.13e+03 pdb=" CG 7ID G 3 " 0.093 2.00e-02 2.50e+03 pdb=" OD1 7ID G 3 " -0.128 2.00e-02 2.50e+03 pdb=" CA2 7ID G 3 " -0.351 2.00e-02 2.50e+03 pdb=" N2 7ID G 3 " 0.532 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB 7ID E 3 " -0.147 2.00e-02 2.50e+03 3.01e-01 1.13e+03 pdb=" CG 7ID E 3 " 0.093 2.00e-02 2.50e+03 pdb=" OD1 7ID E 3 " -0.128 2.00e-02 2.50e+03 pdb=" CA2 7ID E 3 " -0.351 2.00e-02 2.50e+03 pdb=" N2 7ID E 3 " 0.532 2.00e-02 2.50e+03 ... (remaining 4985 not shown) Histogram of nonbonded interaction distances: 1.86 - 2.47: 60 2.47 - 3.08: 19186 3.08 - 3.69: 40702 3.69 - 4.29: 64186 4.29 - 4.90: 104170 Nonbonded interactions: 228304 Sorted by model distance: nonbonded pdb=" OE2 GLU A 558 " pdb="MG MG A 904 " model vdw 1.865 2.170 nonbonded pdb=" OE2 GLU D 558 " pdb="MG MG D 904 " model vdw 1.865 2.170 nonbonded pdb=" OE2 GLU B 558 " pdb="MG MG B 904 " model vdw 1.865 2.170 nonbonded pdb=" OE2 GLU C 558 " pdb="MG MG C 904 " model vdw 1.865 2.170 nonbonded pdb="MG MG C 904 " pdb=" O1G ATP C 907 " model vdw 1.930 2.170 ... (remaining 228299 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 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } 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 individual isotropic 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: 4.140 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: 14.600 Check model and map are aligned: 0.470 Set scattering table: 0.300 Process input model: 81.680 Find NCS groups from input model: 1.830 Set up NCS constraints: 0.270 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: 0.000 Load rotamer database and sin/cos tables:16.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 119.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 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 : 0.023 0.174 28088 Z= 1.547 Angle : 1.999 28.351 38176 Z= 1.371 Chirality : 0.105 0.491 4384 Planarity : 0.029 0.301 4988 Dihedral : 17.656 161.747 10696 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.16 % Favored : 95.73 % Rotamer: Outliers : 0.70 % Allowed : 0.84 % Favored : 98.45 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.60 % 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: -0.96 (0.13), residues: 3464 helix: -1.41 (0.13), residues: 1324 sheet: 0.85 (0.23), residues: 440 loop : -0.22 (0.14), residues: 1700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.076 0.011 TRP C 763 HIS 0.011 0.003 HIS A 586 PHE 0.027 0.006 PHE B 43 TYR 0.052 0.008 TYR D 753 ARG 0.009 0.001 ARG D 731 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 387 time to evaluate : 2.979 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: A 677 GLU cc_start: 0.7691 (tp30) cc_final: 0.7422 (tp30) REVERT: A 732 MET cc_start: 0.3816 (mtp) cc_final: 0.3587 (pp-130) REVERT: B 152 GLU cc_start: 0.6468 (mt-10) cc_final: 0.6202 (mm-30) REVERT: B 277 HIS cc_start: 0.6426 (m-70) cc_final: 0.6203 (m170) REVERT: B 306 SER cc_start: 0.8696 (m) cc_final: 0.8487 (t) REVERT: B 388 TYR cc_start: 0.7478 (m-80) cc_final: 0.7164 (m-80) REVERT: B 732 MET cc_start: 0.3367 (mtp) cc_final: 0.3055 (pp-130) REVERT: C 152 GLU cc_start: 0.6495 (mt-10) cc_final: 0.6251 (mm-30) REVERT: C 306 SER cc_start: 0.8670 (m) cc_final: 0.8443 (t) REVERT: C 388 TYR cc_start: 0.7540 (m-80) cc_final: 0.7224 (m-80) REVERT: C 732 MET cc_start: 0.3370 (mtp) cc_final: 0.3080 (pp-130) REVERT: D 152 GLU cc_start: 0.6467 (mt-10) cc_final: 0.6184 (mm-30) REVERT: D 306 SER cc_start: 0.8670 (m) cc_final: 0.8449 (t) REVERT: D 388 TYR cc_start: 0.7544 (m-80) cc_final: 0.7212 (m-80) REVERT: D 732 MET cc_start: 0.3320 (mtp) cc_final: 0.3064 (pp-130) outliers start: 20 outliers final: 9 residues processed: 403 average time/residue: 1.5056 time to fit residues: 698.2316 Evaluate side-chains 257 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 248 time to evaluate : 3.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 PRO Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain B residue 61 PRO Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain C residue 61 PRO Chi-restraints excluded: chain C residue 73 GLU Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain D residue 61 PRO Chi-restraints excluded: chain D residue 80 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 293 optimal weight: 0.8980 chunk 263 optimal weight: 0.9980 chunk 146 optimal weight: 0.9980 chunk 90 optimal weight: 6.9990 chunk 177 optimal weight: 9.9990 chunk 140 optimal weight: 3.9990 chunk 272 optimal weight: 1.9990 chunk 105 optimal weight: 0.7980 chunk 165 optimal weight: 10.0000 chunk 203 optimal weight: 6.9990 chunk 316 optimal weight: 0.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 641 ASN A 707 ASN B 541 GLN B 696 ASN B 707 ASN C 355 ASN C 541 GLN C 696 ASN C 707 ASN D 355 ASN D 541 GLN D 696 ASN D 707 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.2256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 28088 Z= 0.247 Angle : 0.827 16.039 38176 Z= 0.402 Chirality : 0.051 0.373 4384 Planarity : 0.005 0.050 4988 Dihedral : 21.360 160.908 4491 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.04 % Allowed : 6.26 % Favored : 91.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -0.46 (0.14), residues: 3464 helix: -0.29 (0.14), residues: 1300 sheet: 1.08 (0.23), residues: 488 loop : -0.65 (0.14), residues: 1676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 763 HIS 0.006 0.001 HIS D 741 PHE 0.021 0.002 PHE A 43 TYR 0.017 0.002 TYR D 519 ARG 0.004 0.001 ARG D 70 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 282 time to evaluate : 3.113 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 ARG cc_start: 0.7469 (mpp-170) cc_final: 0.7269 (mtp180) REVERT: A 236 ARG cc_start: 0.6532 (ttm-80) cc_final: 0.6227 (ttp-170) REVERT: A 307 ASP cc_start: 0.7966 (t0) cc_final: 0.7765 (t70) REVERT: A 586 HIS cc_start: 0.7844 (m90) cc_final: 0.7561 (m90) REVERT: A 732 MET cc_start: 0.3615 (mtp) cc_final: 0.3195 (pp-130) REVERT: B 18 ARG cc_start: 0.7631 (mpp-170) cc_final: 0.7380 (mtp180) REVERT: B 136 LEU cc_start: 0.5621 (OUTLIER) cc_final: 0.5405 (tt) REVERT: B 155 ARG cc_start: 0.7108 (mtt90) cc_final: 0.6788 (mtt90) REVERT: B 219 ASP cc_start: 0.7845 (t0) cc_final: 0.7631 (t0) REVERT: B 286 ASP cc_start: 0.8216 (m-30) cc_final: 0.8016 (m-30) REVERT: B 306 SER cc_start: 0.8657 (m) cc_final: 0.8452 (t) REVERT: B 459 MET cc_start: 0.8579 (ptm) cc_final: 0.8273 (ptm) REVERT: B 558 GLU cc_start: 0.8854 (OUTLIER) cc_final: 0.7439 (tt0) REVERT: B 661 GLU cc_start: 0.7513 (OUTLIER) cc_final: 0.7026 (pt0) REVERT: B 732 MET cc_start: 0.3370 (mtp) cc_final: 0.2897 (pp-130) REVERT: C 18 ARG cc_start: 0.7662 (mpp-170) cc_final: 0.7374 (mtp180) REVERT: C 151 LEU cc_start: 0.6464 (mm) cc_final: 0.6036 (tp) REVERT: C 155 ARG cc_start: 0.7039 (mtt90) cc_final: 0.6789 (mtt90) REVERT: C 160 ASN cc_start: 0.7630 (t0) cc_final: 0.7236 (m110) REVERT: C 286 ASP cc_start: 0.8237 (m-30) cc_final: 0.8035 (m-30) REVERT: C 306 SER cc_start: 0.8693 (m) cc_final: 0.8463 (t) REVERT: C 459 MET cc_start: 0.8562 (ptm) cc_final: 0.8274 (ptm) REVERT: C 558 GLU cc_start: 0.8860 (OUTLIER) cc_final: 0.7448 (tt0) REVERT: C 661 GLU cc_start: 0.7515 (OUTLIER) cc_final: 0.7024 (pt0) REVERT: C 732 MET cc_start: 0.3382 (mtp) cc_final: 0.2915 (pp-130) REVERT: D 18 ARG cc_start: 0.7664 (mpp-170) cc_final: 0.7417 (mtp180) REVERT: D 151 LEU cc_start: 0.6348 (mm) cc_final: 0.5920 (tp) REVERT: D 155 ARG cc_start: 0.6998 (mtt90) cc_final: 0.6739 (mtt90) REVERT: D 160 ASN cc_start: 0.7597 (t0) cc_final: 0.7211 (m110) REVERT: D 306 SER cc_start: 0.8692 (m) cc_final: 0.8470 (t) REVERT: D 459 MET cc_start: 0.8582 (ptm) cc_final: 0.8290 (ptm) REVERT: D 558 GLU cc_start: 0.8844 (OUTLIER) cc_final: 0.7438 (tt0) REVERT: D 661 GLU cc_start: 0.7506 (OUTLIER) cc_final: 0.6997 (pt0) REVERT: D 732 MET cc_start: 0.3334 (mtp) cc_final: 0.2888 (pp-130) outliers start: 58 outliers final: 17 residues processed: 314 average time/residue: 1.2785 time to fit residues: 473.2602 Evaluate side-chains 274 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 250 time to evaluate : 3.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 156 ASP Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 438 SER Chi-restraints excluded: chain B residue 523 ASP Chi-restraints excluded: chain B residue 558 GLU Chi-restraints excluded: chain B residue 572 ASP Chi-restraints excluded: chain B residue 629 ASP Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 438 SER Chi-restraints excluded: chain C residue 523 ASP Chi-restraints excluded: chain C residue 558 GLU Chi-restraints excluded: chain C residue 572 ASP Chi-restraints excluded: chain C residue 629 ASP Chi-restraints excluded: chain C residue 661 GLU Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 438 SER Chi-restraints excluded: chain D residue 523 ASP Chi-restraints excluded: chain D residue 558 GLU Chi-restraints excluded: chain D residue 572 ASP Chi-restraints excluded: chain D residue 629 ASP Chi-restraints excluded: chain D residue 661 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 175 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 263 optimal weight: 3.9990 chunk 215 optimal weight: 1.9990 chunk 87 optimal weight: 5.9990 chunk 316 optimal weight: 3.9990 chunk 342 optimal weight: 20.0000 chunk 281 optimal weight: 2.9990 chunk 313 optimal weight: 1.9990 chunk 107 optimal weight: 0.5980 chunk 253 optimal weight: 3.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 696 ASN D 512 GLN D 716 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.3203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 28088 Z= 0.362 Angle : 0.780 14.070 38176 Z= 0.393 Chirality : 0.052 0.321 4384 Planarity : 0.005 0.043 4988 Dihedral : 20.288 152.396 4468 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 3.06 % Allowed : 7.95 % Favored : 88.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.14), residues: 3464 helix: -0.25 (0.14), residues: 1316 sheet: 0.47 (0.24), residues: 432 loop : -0.99 (0.14), residues: 1716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 414 HIS 0.007 0.002 HIS A 57 PHE 0.029 0.003 PHE C 692 TYR 0.022 0.002 TYR D 116 ARG 0.007 0.001 ARG B 469 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 253 time to evaluate : 2.964 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 558 GLU cc_start: 0.8893 (OUTLIER) cc_final: 0.7281 (tt0) REVERT: A 732 MET cc_start: 0.4612 (mtp) cc_final: 0.3839 (pmt) REVERT: B 5 LYS cc_start: 0.8321 (OUTLIER) cc_final: 0.8102 (ttpp) REVERT: B 64 GLN cc_start: 0.7668 (tm-30) cc_final: 0.6980 (tm-30) REVERT: B 155 ARG cc_start: 0.7024 (mtt90) cc_final: 0.6823 (mtt90) REVERT: B 160 ASN cc_start: 0.7770 (t0) cc_final: 0.7378 (m-40) REVERT: B 526 TYR cc_start: 0.8572 (m-80) cc_final: 0.8325 (m-80) REVERT: B 558 GLU cc_start: 0.8880 (OUTLIER) cc_final: 0.7529 (tt0) REVERT: B 732 MET cc_start: 0.4005 (mtp) cc_final: 0.3013 (pmm) REVERT: C 5 LYS cc_start: 0.8362 (OUTLIER) cc_final: 0.8152 (ttpp) REVERT: C 64 GLN cc_start: 0.7673 (tm-30) cc_final: 0.7000 (tm-30) REVERT: C 155 ARG cc_start: 0.7066 (mtt90) cc_final: 0.6807 (mtt90) REVERT: C 526 TYR cc_start: 0.8564 (m-80) cc_final: 0.8324 (m-80) REVERT: C 558 GLU cc_start: 0.8877 (OUTLIER) cc_final: 0.7512 (tt0) REVERT: C 732 MET cc_start: 0.4128 (mtp) cc_final: 0.3209 (pmm) REVERT: D 64 GLN cc_start: 0.7656 (tm-30) cc_final: 0.6978 (tm-30) REVERT: D 155 ARG cc_start: 0.7011 (mtt90) cc_final: 0.6744 (mtt90) REVERT: D 526 TYR cc_start: 0.8570 (m-80) cc_final: 0.8358 (m-80) REVERT: D 558 GLU cc_start: 0.8878 (OUTLIER) cc_final: 0.7529 (tt0) REVERT: D 677 GLU cc_start: 0.7817 (tp30) cc_final: 0.7614 (tp30) REVERT: D 732 MET cc_start: 0.4063 (mtp) cc_final: 0.3157 (pmm) outliers start: 87 outliers final: 37 residues processed: 312 average time/residue: 1.3259 time to fit residues: 486.8819 Evaluate side-chains 278 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 235 time to evaluate : 3.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LYS Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 156 ASP Chi-restraints excluded: chain A residue 478 MET Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 558 GLU Chi-restraints excluded: chain A residue 632 LYS Chi-restraints excluded: chain B residue 5 LYS Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 438 SER Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 523 ASP Chi-restraints excluded: chain B residue 558 GLU Chi-restraints excluded: chain B residue 572 ASP Chi-restraints excluded: chain B residue 629 ASP Chi-restraints excluded: chain B residue 711 VAL Chi-restraints excluded: chain B residue 722 THR Chi-restraints excluded: chain C residue 5 LYS Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 156 ASP Chi-restraints excluded: chain C residue 438 SER Chi-restraints excluded: chain C residue 522 THR Chi-restraints excluded: chain C residue 523 ASP Chi-restraints excluded: chain C residue 558 GLU Chi-restraints excluded: chain C residue 572 ASP Chi-restraints excluded: chain C residue 629 ASP Chi-restraints excluded: chain C residue 711 VAL Chi-restraints excluded: chain C residue 722 THR Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 156 ASP Chi-restraints excluded: chain D residue 438 SER Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain D residue 523 ASP Chi-restraints excluded: chain D residue 558 GLU Chi-restraints excluded: chain D residue 572 ASP Chi-restraints excluded: chain D residue 629 ASP Chi-restraints excluded: chain D residue 711 VAL Chi-restraints excluded: chain D residue 722 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 312 optimal weight: 2.9990 chunk 238 optimal weight: 1.9990 chunk 164 optimal weight: 40.0000 chunk 35 optimal weight: 2.9990 chunk 151 optimal weight: 4.9990 chunk 212 optimal weight: 6.9990 chunk 317 optimal weight: 2.9990 chunk 336 optimal weight: 7.9990 chunk 165 optimal weight: 20.0000 chunk 301 optimal weight: 3.9990 chunk 90 optimal weight: 9.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 512 GLN B 541 GLN B 716 GLN C 512 GLN C 541 GLN C 716 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.3621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 28088 Z= 0.464 Angle : 0.805 13.430 38176 Z= 0.412 Chirality : 0.054 0.310 4384 Planarity : 0.006 0.048 4988 Dihedral : 19.565 142.197 4468 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.39 % Favored : 95.50 % Rotamer: Outliers : 2.53 % Allowed : 9.32 % Favored : 88.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.13), residues: 3464 helix: -0.51 (0.14), residues: 1312 sheet: 0.27 (0.24), residues: 432 loop : -1.23 (0.14), residues: 1720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 181 HIS 0.005 0.002 HIS A 57 PHE 0.028 0.003 PHE A 692 TYR 0.024 0.003 TYR D 116 ARG 0.007 0.001 ARG A 469 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 257 time to evaluate : 3.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 221 GLU cc_start: 0.7600 (mp0) cc_final: 0.7159 (mp0) REVERT: A 558 GLU cc_start: 0.8870 (OUTLIER) cc_final: 0.7474 (tt0) REVERT: A 722 THR cc_start: 0.8337 (OUTLIER) cc_final: 0.8091 (t) REVERT: B 18 ARG cc_start: 0.7609 (OUTLIER) cc_final: 0.7406 (mpp-170) REVERT: B 64 GLN cc_start: 0.7672 (tm-30) cc_final: 0.6974 (tm-30) REVERT: B 155 ARG cc_start: 0.6922 (mtt90) cc_final: 0.6690 (mtt90) REVERT: B 160 ASN cc_start: 0.7738 (t0) cc_final: 0.7405 (m-40) REVERT: B 173 GLU cc_start: 0.7942 (OUTLIER) cc_final: 0.6717 (tm-30) REVERT: B 558 GLU cc_start: 0.8833 (OUTLIER) cc_final: 0.7677 (tt0) REVERT: B 722 THR cc_start: 0.8372 (OUTLIER) cc_final: 0.8011 (t) REVERT: B 732 MET cc_start: 0.4782 (mtp) cc_final: 0.3930 (pmt) REVERT: C 18 ARG cc_start: 0.7602 (OUTLIER) cc_final: 0.7401 (mpp-170) REVERT: C 64 GLN cc_start: 0.7670 (tm-30) cc_final: 0.6999 (tm-30) REVERT: C 155 ARG cc_start: 0.7026 (mtt90) cc_final: 0.6801 (mtt90) REVERT: C 173 GLU cc_start: 0.7952 (OUTLIER) cc_final: 0.6716 (tm-30) REVERT: C 558 GLU cc_start: 0.8831 (OUTLIER) cc_final: 0.7524 (tt0) REVERT: C 722 THR cc_start: 0.8357 (OUTLIER) cc_final: 0.8004 (t) REVERT: C 732 MET cc_start: 0.4792 (mtp) cc_final: 0.3934 (pmt) REVERT: C 737 LEU cc_start: 0.0770 (OUTLIER) cc_final: 0.0410 (tp) REVERT: D 18 ARG cc_start: 0.7618 (OUTLIER) cc_final: 0.7410 (mpp-170) REVERT: D 64 GLN cc_start: 0.7688 (tm-30) cc_final: 0.6984 (tm-30) REVERT: D 155 ARG cc_start: 0.6972 (mtt90) cc_final: 0.6737 (mtt90) REVERT: D 173 GLU cc_start: 0.7942 (OUTLIER) cc_final: 0.6710 (tm-30) REVERT: D 541 GLN cc_start: 0.7952 (OUTLIER) cc_final: 0.7739 (mt0) REVERT: D 558 GLU cc_start: 0.8823 (OUTLIER) cc_final: 0.7526 (tt0) REVERT: D 722 THR cc_start: 0.8349 (OUTLIER) cc_final: 0.8004 (t) REVERT: D 732 MET cc_start: 0.4734 (mtp) cc_final: 0.3908 (pmt) outliers start: 72 outliers final: 38 residues processed: 305 average time/residue: 1.3122 time to fit residues: 471.7979 Evaluate side-chains 297 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 243 time to evaluate : 3.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LYS Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 156 ASP Chi-restraints excluded: chain A residue 478 MET Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 558 GLU Chi-restraints excluded: chain A residue 632 LYS Chi-restraints excluded: chain A residue 711 VAL Chi-restraints excluded: chain A residue 722 THR Chi-restraints excluded: chain B residue 18 ARG Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 173 GLU Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 438 SER Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 523 ASP Chi-restraints excluded: chain B residue 558 GLU Chi-restraints excluded: chain B residue 572 ASP Chi-restraints excluded: chain B residue 629 ASP Chi-restraints excluded: chain B residue 711 VAL Chi-restraints excluded: chain B residue 722 THR Chi-restraints excluded: chain C residue 18 ARG Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 156 ASP Chi-restraints excluded: chain C residue 173 GLU Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 438 SER Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 522 THR Chi-restraints excluded: chain C residue 523 ASP Chi-restraints excluded: chain C residue 558 GLU Chi-restraints excluded: chain C residue 572 ASP Chi-restraints excluded: chain C residue 629 ASP Chi-restraints excluded: chain C residue 711 VAL Chi-restraints excluded: chain C residue 722 THR Chi-restraints excluded: chain C residue 737 LEU Chi-restraints excluded: chain D residue 18 ARG Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 156 ASP Chi-restraints excluded: chain D residue 173 GLU Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 438 SER Chi-restraints excluded: chain D residue 471 VAL Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain D residue 523 ASP Chi-restraints excluded: chain D residue 541 GLN Chi-restraints excluded: chain D residue 558 GLU Chi-restraints excluded: chain D residue 572 ASP Chi-restraints excluded: chain D residue 629 ASP Chi-restraints excluded: chain D residue 711 VAL Chi-restraints excluded: chain D residue 722 THR Chi-restraints excluded: chain D residue 737 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 280 optimal weight: 0.6980 chunk 190 optimal weight: 1.9990 chunk 4 optimal weight: 9.9990 chunk 250 optimal weight: 6.9990 chunk 138 optimal weight: 0.7980 chunk 287 optimal weight: 9.9990 chunk 232 optimal weight: 6.9990 chunk 0 optimal weight: 5.9990 chunk 171 optimal weight: 20.0000 chunk 301 optimal weight: 4.9990 chunk 84 optimal weight: 20.0000 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 38 ASN B 251 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.3873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 28088 Z= 0.439 Angle : 0.765 13.087 38176 Z= 0.392 Chirality : 0.053 0.295 4384 Planarity : 0.005 0.047 4988 Dihedral : 19.053 136.063 4468 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.62 % Favored : 95.27 % Rotamer: Outliers : 3.06 % Allowed : 9.42 % Favored : 87.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.13), residues: 3464 helix: -0.54 (0.14), residues: 1308 sheet: -0.01 (0.23), residues: 484 loop : -1.27 (0.14), residues: 1672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 181 HIS 0.004 0.001 HIS B 57 PHE 0.026 0.003 PHE C 692 TYR 0.020 0.003 TYR D 116 ARG 0.005 0.001 ARG B 511 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 248 time to evaluate : 3.388 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: A 221 GLU cc_start: 0.7585 (mp0) cc_final: 0.7144 (mp0) REVERT: A 558 GLU cc_start: 0.8889 (OUTLIER) cc_final: 0.7478 (tt0) REVERT: B 64 GLN cc_start: 0.7673 (tm-30) cc_final: 0.6989 (tm-30) REVERT: B 160 ASN cc_start: 0.7703 (t0) cc_final: 0.7415 (m-40) REVERT: B 173 GLU cc_start: 0.7973 (OUTLIER) cc_final: 0.6702 (tm-30) REVERT: B 558 GLU cc_start: 0.8862 (OUTLIER) cc_final: 0.7647 (tt0) REVERT: B 722 THR cc_start: 0.8292 (OUTLIER) cc_final: 0.7993 (t) REVERT: B 732 MET cc_start: 0.5124 (mtp) cc_final: 0.4269 (pmt) REVERT: C 64 GLN cc_start: 0.7682 (tm-30) cc_final: 0.7033 (tm-30) REVERT: C 155 ARG cc_start: 0.7075 (mtt90) cc_final: 0.6846 (mtt90) REVERT: C 173 GLU cc_start: 0.7979 (OUTLIER) cc_final: 0.6703 (tm-30) REVERT: C 301 ARG cc_start: 0.7117 (OUTLIER) cc_final: 0.6804 (ttt90) REVERT: C 558 GLU cc_start: 0.8862 (OUTLIER) cc_final: 0.7482 (tt0) REVERT: C 722 THR cc_start: 0.8279 (OUTLIER) cc_final: 0.7983 (t) REVERT: D 155 ARG cc_start: 0.7022 (mtt90) cc_final: 0.6788 (mtt90) REVERT: D 173 GLU cc_start: 0.7971 (OUTLIER) cc_final: 0.6696 (tm-30) REVERT: D 301 ARG cc_start: 0.7092 (OUTLIER) cc_final: 0.6782 (ttt90) REVERT: D 541 GLN cc_start: 0.7944 (OUTLIER) cc_final: 0.7716 (mt0) REVERT: D 558 GLU cc_start: 0.8849 (OUTLIER) cc_final: 0.7608 (tt0) REVERT: D 722 THR cc_start: 0.8277 (OUTLIER) cc_final: 0.7980 (t) REVERT: D 732 MET cc_start: 0.5191 (mtp) cc_final: 0.4324 (pmt) REVERT: D 737 LEU cc_start: 0.0758 (OUTLIER) cc_final: 0.0096 (tp) outliers start: 87 outliers final: 49 residues processed: 299 average time/residue: 1.3773 time to fit residues: 481.6360 Evaluate side-chains 303 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 240 time to evaluate : 2.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LYS Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 156 ASP Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 236 ARG Chi-restraints excluded: chain A residue 478 MET Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 558 GLU Chi-restraints excluded: chain A residue 632 LYS Chi-restraints excluded: chain A residue 711 VAL Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 173 GLU Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 438 SER Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 523 ASP Chi-restraints excluded: chain B residue 558 GLU Chi-restraints excluded: chain B residue 572 ASP Chi-restraints excluded: chain B residue 629 ASP Chi-restraints excluded: chain B residue 630 LYS Chi-restraints excluded: chain B residue 711 VAL Chi-restraints excluded: chain B residue 722 THR Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 156 ASP Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 173 GLU Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 301 ARG Chi-restraints excluded: chain C residue 438 SER Chi-restraints excluded: chain C residue 522 THR Chi-restraints excluded: chain C residue 523 ASP Chi-restraints excluded: chain C residue 558 GLU Chi-restraints excluded: chain C residue 572 ASP Chi-restraints excluded: chain C residue 629 ASP Chi-restraints excluded: chain C residue 630 LYS Chi-restraints excluded: chain C residue 711 VAL Chi-restraints excluded: chain C residue 722 THR Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 156 ASP Chi-restraints excluded: chain D residue 161 SER Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 173 GLU Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 301 ARG Chi-restraints excluded: chain D residue 438 SER Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain D residue 523 ASP Chi-restraints excluded: chain D residue 541 GLN Chi-restraints excluded: chain D residue 558 GLU Chi-restraints excluded: chain D residue 572 ASP Chi-restraints excluded: chain D residue 629 ASP Chi-restraints excluded: chain D residue 630 LYS Chi-restraints excluded: chain D residue 711 VAL Chi-restraints excluded: chain D residue 722 THR Chi-restraints excluded: chain D residue 737 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 113 optimal weight: 9.9990 chunk 302 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 197 optimal weight: 0.0010 chunk 83 optimal weight: 0.1980 chunk 336 optimal weight: 0.9990 chunk 279 optimal weight: 0.6980 chunk 155 optimal weight: 0.9980 chunk 27 optimal weight: 6.9990 chunk 111 optimal weight: 0.4980 chunk 176 optimal weight: 2.9990 overall best weight: 0.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 586 HIS C 251 ASN C 586 HIS C 740 HIS D 251 ASN D 740 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.4054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.078 28088 Z= 0.151 Angle : 0.587 11.882 38176 Z= 0.295 Chirality : 0.046 0.228 4384 Planarity : 0.004 0.051 4988 Dihedral : 18.106 132.366 4468 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.39 % Favored : 95.50 % Rotamer: Outliers : 1.83 % Allowed : 10.86 % Favored : 87.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.14), residues: 3464 helix: -0.08 (0.15), residues: 1312 sheet: 0.26 (0.21), residues: 592 loop : -1.18 (0.15), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 278 HIS 0.006 0.001 HIS D 586 PHE 0.009 0.001 PHE D 638 TYR 0.013 0.001 TYR C 519 ARG 0.003 0.000 ARG B 155 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 260 time to evaluate : 3.035 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 558 GLU cc_start: 0.8782 (OUTLIER) cc_final: 0.7334 (tt0) REVERT: A 737 LEU cc_start: 0.1811 (OUTLIER) cc_final: 0.1390 (pt) REVERT: B 90 GLU cc_start: 0.6152 (tp30) cc_final: 0.5795 (mm-30) REVERT: B 160 ASN cc_start: 0.7672 (t0) cc_final: 0.7413 (m-40) REVERT: B 732 MET cc_start: 0.5014 (mtp) cc_final: 0.4030 (pmt) REVERT: C 155 ARG cc_start: 0.7035 (mtt90) cc_final: 0.6808 (mtt90) REVERT: C 732 MET cc_start: 0.4465 (mtm) cc_final: 0.3771 (pp-130) REVERT: C 737 LEU cc_start: 0.0703 (OUTLIER) cc_final: 0.0419 (tp) REVERT: D 155 ARG cc_start: 0.6989 (mtt90) cc_final: 0.6757 (mtt90) REVERT: D 732 MET cc_start: 0.4971 (mtp) cc_final: 0.4118 (pmt) REVERT: D 737 LEU cc_start: 0.0583 (OUTLIER) cc_final: 0.0322 (tp) outliers start: 52 outliers final: 26 residues processed: 293 average time/residue: 1.4175 time to fit residues: 483.2895 Evaluate side-chains 262 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 232 time to evaluate : 2.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 156 ASP Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 558 GLU Chi-restraints excluded: chain A residue 561 ARG Chi-restraints excluded: chain A residue 572 ASP Chi-restraints excluded: chain A residue 711 VAL Chi-restraints excluded: chain A residue 737 LEU Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 438 SER Chi-restraints excluded: chain B residue 523 ASP Chi-restraints excluded: chain B residue 629 ASP Chi-restraints excluded: chain B residue 630 LYS Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 156 ASP Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 438 SER Chi-restraints excluded: chain C residue 523 ASP Chi-restraints excluded: chain C residue 629 ASP Chi-restraints excluded: chain C residue 630 LYS Chi-restraints excluded: chain C residue 737 LEU Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 156 ASP Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 438 SER Chi-restraints excluded: chain D residue 523 ASP Chi-restraints excluded: chain D residue 629 ASP Chi-restraints excluded: chain D residue 630 LYS Chi-restraints excluded: chain D residue 737 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 324 optimal weight: 0.0870 chunk 37 optimal weight: 6.9990 chunk 191 optimal weight: 2.9990 chunk 245 optimal weight: 4.9990 chunk 190 optimal weight: 1.9990 chunk 283 optimal weight: 0.9980 chunk 188 optimal weight: 0.0470 chunk 335 optimal weight: 7.9990 chunk 209 optimal weight: 6.9990 chunk 204 optimal weight: 5.9990 chunk 154 optimal weight: 0.0030 overall best weight: 0.6268 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 355 ASN B 586 HIS C 586 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.4142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 28088 Z= 0.153 Angle : 0.565 8.201 38176 Z= 0.286 Chirality : 0.045 0.184 4384 Planarity : 0.004 0.051 4988 Dihedral : 17.679 132.561 4468 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.01 % Favored : 95.87 % Rotamer: Outliers : 1.55 % Allowed : 11.85 % Favored : 86.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.14), residues: 3464 helix: 0.02 (0.15), residues: 1340 sheet: 0.36 (0.21), residues: 592 loop : -1.11 (0.15), residues: 1532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 181 HIS 0.005 0.001 HIS D 586 PHE 0.011 0.001 PHE A 692 TYR 0.015 0.001 TYR D 519 ARG 0.002 0.000 ARG D 390 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 244 time to evaluate : 3.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 558 GLU cc_start: 0.8800 (OUTLIER) cc_final: 0.7407 (tt0) REVERT: A 737 LEU cc_start: 0.1598 (OUTLIER) cc_final: 0.1274 (pt) REVERT: B 90 GLU cc_start: 0.6175 (tp30) cc_final: 0.5760 (mm-30) REVERT: B 160 ASN cc_start: 0.7661 (t0) cc_final: 0.7442 (m-40) REVERT: B 173 GLU cc_start: 0.7867 (OUTLIER) cc_final: 0.6570 (tm-30) REVERT: B 732 MET cc_start: 0.5030 (mtp) cc_final: 0.3693 (pp-130) REVERT: C 64 GLN cc_start: 0.7677 (tm-30) cc_final: 0.7079 (tm-30) REVERT: C 155 ARG cc_start: 0.7013 (mtt90) cc_final: 0.6811 (mtt90) REVERT: C 173 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.6572 (tm-30) REVERT: C 355 ASN cc_start: 0.7508 (t0) cc_final: 0.7251 (t0) REVERT: C 732 MET cc_start: 0.4455 (mtm) cc_final: 0.3721 (pp-130) REVERT: C 737 LEU cc_start: 0.0690 (OUTLIER) cc_final: 0.0331 (tp) REVERT: D 155 ARG cc_start: 0.6952 (mtt90) cc_final: 0.6732 (mtt90) REVERT: D 173 GLU cc_start: 0.7868 (OUTLIER) cc_final: 0.6565 (tm-30) REVERT: D 355 ASN cc_start: 0.7497 (t0) cc_final: 0.7240 (t0) REVERT: D 732 MET cc_start: 0.5033 (mtp) cc_final: 0.3736 (pp-130) REVERT: D 737 LEU cc_start: 0.0469 (OUTLIER) cc_final: 0.0109 (tp) outliers start: 44 outliers final: 23 residues processed: 276 average time/residue: 1.3734 time to fit residues: 444.1170 Evaluate side-chains 262 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 232 time to evaluate : 2.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 156 ASP Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 558 GLU Chi-restraints excluded: chain A residue 561 ARG Chi-restraints excluded: chain A residue 711 VAL Chi-restraints excluded: chain A residue 737 LEU Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 173 GLU Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 438 SER Chi-restraints excluded: chain B residue 523 ASP Chi-restraints excluded: chain B residue 629 ASP Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 156 ASP Chi-restraints excluded: chain C residue 173 GLU Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 438 SER Chi-restraints excluded: chain C residue 523 ASP Chi-restraints excluded: chain C residue 629 ASP Chi-restraints excluded: chain C residue 630 LYS Chi-restraints excluded: chain C residue 737 LEU Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 156 ASP Chi-restraints excluded: chain D residue 173 GLU Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 438 SER Chi-restraints excluded: chain D residue 523 ASP Chi-restraints excluded: chain D residue 629 ASP Chi-restraints excluded: chain D residue 737 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 207 optimal weight: 6.9990 chunk 133 optimal weight: 1.9990 chunk 200 optimal weight: 10.0000 chunk 101 optimal weight: 8.9990 chunk 65 optimal weight: 0.9980 chunk 64 optimal weight: 0.8980 chunk 213 optimal weight: 9.9990 chunk 228 optimal weight: 0.4980 chunk 165 optimal weight: 20.0000 chunk 31 optimal weight: 1.9990 chunk 263 optimal weight: 0.6980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 355 ASN B 586 HIS C 586 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.4193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 28088 Z= 0.191 Angle : 0.578 8.416 38176 Z= 0.294 Chirality : 0.046 0.180 4384 Planarity : 0.004 0.050 4988 Dihedral : 17.573 132.654 4468 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.16 % Favored : 95.73 % Rotamer: Outliers : 1.72 % Allowed : 11.81 % Favored : 86.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.14), residues: 3464 helix: 0.12 (0.15), residues: 1308 sheet: 0.36 (0.21), residues: 592 loop : -1.19 (0.15), residues: 1564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 181 HIS 0.005 0.001 HIS D 586 PHE 0.015 0.002 PHE A 692 TYR 0.017 0.001 TYR D 519 ARG 0.003 0.000 ARG C 134 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 238 time to evaluate : 2.838 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 355 ASN cc_start: 0.7642 (t0) cc_final: 0.7357 (t0) REVERT: A 558 GLU cc_start: 0.8816 (OUTLIER) cc_final: 0.7414 (tt0) REVERT: A 732 MET cc_start: 0.4838 (ptp) cc_final: 0.4190 (pp-130) REVERT: A 737 LEU cc_start: 0.1613 (OUTLIER) cc_final: 0.1333 (pt) REVERT: B 90 GLU cc_start: 0.6187 (tp30) cc_final: 0.5771 (mm-30) REVERT: B 160 ASN cc_start: 0.7713 (t0) cc_final: 0.7488 (m-40) REVERT: B 173 GLU cc_start: 0.7918 (OUTLIER) cc_final: 0.6612 (tm-30) REVERT: B 732 MET cc_start: 0.5058 (mtp) cc_final: 0.4109 (pmt) REVERT: C 64 GLN cc_start: 0.7718 (tm-30) cc_final: 0.7120 (tm-30) REVERT: C 155 ARG cc_start: 0.7038 (mtt90) cc_final: 0.6826 (mtt90) REVERT: C 173 GLU cc_start: 0.7927 (OUTLIER) cc_final: 0.6613 (tm-30) REVERT: C 355 ASN cc_start: 0.7503 (t0) cc_final: 0.7230 (t0) REVERT: C 732 MET cc_start: 0.4455 (mtm) cc_final: 0.3553 (pp-130) REVERT: C 737 LEU cc_start: 0.0661 (OUTLIER) cc_final: 0.0358 (tp) REVERT: D 1 MET cc_start: 0.8294 (mmm) cc_final: 0.7653 (mtt) REVERT: D 155 ARG cc_start: 0.6991 (mtt90) cc_final: 0.6774 (mtt90) REVERT: D 173 GLU cc_start: 0.7918 (OUTLIER) cc_final: 0.6607 (tm-30) REVERT: D 355 ASN cc_start: 0.7461 (t0) cc_final: 0.7203 (t0) REVERT: D 732 MET cc_start: 0.5041 (mtp) cc_final: 0.3719 (pp-130) REVERT: D 737 LEU cc_start: 0.0424 (OUTLIER) cc_final: 0.0158 (tp) outliers start: 49 outliers final: 30 residues processed: 267 average time/residue: 1.3065 time to fit residues: 409.4868 Evaluate side-chains 269 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 232 time to evaluate : 2.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 156 ASP Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 558 GLU Chi-restraints excluded: chain A residue 711 VAL Chi-restraints excluded: chain A residue 737 LEU Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 173 GLU Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 438 SER Chi-restraints excluded: chain B residue 523 ASP Chi-restraints excluded: chain B residue 629 ASP Chi-restraints excluded: chain B residue 630 LYS Chi-restraints excluded: chain B residue 711 VAL Chi-restraints excluded: chain B residue 722 THR Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 156 ASP Chi-restraints excluded: chain C residue 173 GLU Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 438 SER Chi-restraints excluded: chain C residue 523 ASP Chi-restraints excluded: chain C residue 629 ASP Chi-restraints excluded: chain C residue 630 LYS Chi-restraints excluded: chain C residue 711 VAL Chi-restraints excluded: chain C residue 722 THR Chi-restraints excluded: chain C residue 737 LEU Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 156 ASP Chi-restraints excluded: chain D residue 173 GLU Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 438 SER Chi-restraints excluded: chain D residue 523 ASP Chi-restraints excluded: chain D residue 629 ASP Chi-restraints excluded: chain D residue 630 LYS Chi-restraints excluded: chain D residue 711 VAL Chi-restraints excluded: chain D residue 722 THR Chi-restraints excluded: chain D residue 737 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 305 optimal weight: 0.6980 chunk 321 optimal weight: 0.8980 chunk 293 optimal weight: 6.9990 chunk 312 optimal weight: 0.9990 chunk 188 optimal weight: 0.0970 chunk 136 optimal weight: 5.9990 chunk 245 optimal weight: 3.9990 chunk 95 optimal weight: 0.7980 chunk 282 optimal weight: 1.9990 chunk 295 optimal weight: 6.9990 chunk 311 optimal weight: 0.6980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 355 ASN B 586 HIS C 160 ASN C 586 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.4311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 28088 Z= 0.148 Angle : 0.545 9.863 38176 Z= 0.276 Chirality : 0.045 0.159 4384 Planarity : 0.004 0.052 4988 Dihedral : 17.247 132.982 4468 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.81 % Favored : 96.07 % Rotamer: Outliers : 1.79 % Allowed : 11.67 % Favored : 86.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.14), residues: 3464 helix: 0.22 (0.15), residues: 1308 sheet: 0.42 (0.22), residues: 592 loop : -1.19 (0.15), residues: 1564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 181 HIS 0.006 0.001 HIS A 586 PHE 0.010 0.001 PHE D 692 TYR 0.014 0.001 TYR B 519 ARG 0.003 0.000 ARG B 155 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 251 time to evaluate : 3.013 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 ARG cc_start: 0.7104 (ttm110) cc_final: 0.6864 (mtt90) REVERT: A 236 ARG cc_start: 0.6921 (ttp-170) cc_final: 0.6591 (ptm160) REVERT: A 355 ASN cc_start: 0.7541 (t0) cc_final: 0.7330 (t0) REVERT: A 558 GLU cc_start: 0.8786 (OUTLIER) cc_final: 0.7415 (tt0) REVERT: A 732 MET cc_start: 0.5092 (ptp) cc_final: 0.4254 (pp-130) REVERT: A 737 LEU cc_start: 0.1695 (OUTLIER) cc_final: 0.1467 (pt) REVERT: B 90 GLU cc_start: 0.6150 (tp30) cc_final: 0.5764 (mm-30) REVERT: B 236 ARG cc_start: 0.7059 (ttp-170) cc_final: 0.6835 (ttt180) REVERT: B 732 MET cc_start: 0.5027 (mtp) cc_final: 0.3619 (pp-130) REVERT: C 134 ARG cc_start: 0.6608 (tpm170) cc_final: 0.6385 (tpm170) REVERT: C 355 ASN cc_start: 0.7419 (t0) cc_final: 0.7181 (t0) REVERT: C 732 MET cc_start: 0.4317 (mtm) cc_final: 0.3626 (pp-130) REVERT: D 134 ARG cc_start: 0.6572 (tpm170) cc_final: 0.6351 (tpm170) REVERT: D 155 ARG cc_start: 0.6929 (mtt90) cc_final: 0.6721 (mtt90) REVERT: D 355 ASN cc_start: 0.7406 (t0) cc_final: 0.7174 (t0) REVERT: D 732 MET cc_start: 0.5033 (mtp) cc_final: 0.3773 (pp-130) outliers start: 51 outliers final: 32 residues processed: 287 average time/residue: 1.3675 time to fit residues: 459.1869 Evaluate side-chains 275 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 241 time to evaluate : 2.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 156 ASP Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 558 GLU Chi-restraints excluded: chain A residue 711 VAL Chi-restraints excluded: chain A residue 737 LEU Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 438 SER Chi-restraints excluded: chain B residue 449 VAL Chi-restraints excluded: chain B residue 523 ASP Chi-restraints excluded: chain B residue 629 ASP Chi-restraints excluded: chain B residue 630 LYS Chi-restraints excluded: chain B residue 711 VAL Chi-restraints excluded: chain B residue 722 THR Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 156 ASP Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 438 SER Chi-restraints excluded: chain C residue 523 ASP Chi-restraints excluded: chain C residue 629 ASP Chi-restraints excluded: chain C residue 630 LYS Chi-restraints excluded: chain C residue 711 VAL Chi-restraints excluded: chain C residue 722 THR Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 156 ASP Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 438 SER Chi-restraints excluded: chain D residue 449 VAL Chi-restraints excluded: chain D residue 523 ASP Chi-restraints excluded: chain D residue 629 ASP Chi-restraints excluded: chain D residue 630 LYS Chi-restraints excluded: chain D residue 711 VAL Chi-restraints excluded: chain D residue 722 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 205 optimal weight: 0.9990 chunk 330 optimal weight: 0.6980 chunk 201 optimal weight: 2.9990 chunk 156 optimal weight: 0.6980 chunk 229 optimal weight: 0.8980 chunk 346 optimal weight: 0.9990 chunk 319 optimal weight: 3.9990 chunk 276 optimal weight: 5.9990 chunk 28 optimal weight: 10.0000 chunk 213 optimal weight: 8.9990 chunk 169 optimal weight: 10.0000 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 586 HIS C 586 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.4362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 28088 Z= 0.176 Angle : 0.573 11.814 38176 Z= 0.290 Chirality : 0.045 0.169 4384 Planarity : 0.004 0.050 4988 Dihedral : 17.185 132.661 4468 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.90 % Favored : 95.99 % Rotamer: Outliers : 1.41 % Allowed : 12.27 % Favored : 86.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.14), residues: 3464 helix: 0.19 (0.15), residues: 1304 sheet: 0.39 (0.22), residues: 592 loop : -1.22 (0.15), residues: 1568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 181 HIS 0.007 0.001 HIS A 586 PHE 0.014 0.002 PHE A 692 TYR 0.022 0.001 TYR A 256 ARG 0.004 0.000 ARG C 155 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 239 time to evaluate : 3.037 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 ARG cc_start: 0.7105 (ttm110) cc_final: 0.6869 (mtt90) REVERT: A 236 ARG cc_start: 0.6946 (ttp-170) cc_final: 0.6579 (ptm160) REVERT: A 355 ASN cc_start: 0.7525 (t0) cc_final: 0.7298 (t0) REVERT: A 558 GLU cc_start: 0.8806 (OUTLIER) cc_final: 0.7442 (tt0) REVERT: A 732 MET cc_start: 0.5147 (ptp) cc_final: 0.4275 (pp-130) REVERT: A 737 LEU cc_start: 0.1704 (OUTLIER) cc_final: 0.1490 (pt) REVERT: B 90 GLU cc_start: 0.6137 (tp30) cc_final: 0.5723 (mm-30) REVERT: B 134 ARG cc_start: 0.6587 (tpm170) cc_final: 0.6353 (tpm170) REVERT: B 732 MET cc_start: 0.5041 (mtp) cc_final: 0.3636 (pp-130) REVERT: C 355 ASN cc_start: 0.7475 (t0) cc_final: 0.7210 (t0) REVERT: C 732 MET cc_start: 0.4345 (mtm) cc_final: 0.3521 (pp-130) REVERT: D 134 ARG cc_start: 0.6569 (tpm170) cc_final: 0.6267 (tpm170) REVERT: D 155 ARG cc_start: 0.6916 (mtt90) cc_final: 0.6709 (mtt90) REVERT: D 221 GLU cc_start: 0.7429 (mp0) cc_final: 0.7219 (mp0) REVERT: D 355 ASN cc_start: 0.7463 (t0) cc_final: 0.7198 (t0) REVERT: D 732 MET cc_start: 0.5061 (mtp) cc_final: 0.3770 (pp-130) outliers start: 40 outliers final: 30 residues processed: 271 average time/residue: 1.3790 time to fit residues: 442.9895 Evaluate side-chains 268 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 236 time to evaluate : 3.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 156 ASP Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 558 GLU Chi-restraints excluded: chain A residue 711 VAL Chi-restraints excluded: chain A residue 737 LEU Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 438 SER Chi-restraints excluded: chain B residue 449 VAL Chi-restraints excluded: chain B residue 523 ASP Chi-restraints excluded: chain B residue 629 ASP Chi-restraints excluded: chain B residue 630 LYS Chi-restraints excluded: chain B residue 711 VAL Chi-restraints excluded: chain B residue 722 THR Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 156 ASP Chi-restraints excluded: chain C residue 438 SER Chi-restraints excluded: chain C residue 449 VAL Chi-restraints excluded: chain C residue 523 ASP Chi-restraints excluded: chain C residue 629 ASP Chi-restraints excluded: chain C residue 630 LYS Chi-restraints excluded: chain C residue 711 VAL Chi-restraints excluded: chain C residue 722 THR Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 156 ASP Chi-restraints excluded: chain D residue 438 SER Chi-restraints excluded: chain D residue 449 VAL Chi-restraints excluded: chain D residue 523 ASP Chi-restraints excluded: chain D residue 629 ASP Chi-restraints excluded: chain D residue 630 LYS Chi-restraints excluded: chain D residue 711 VAL Chi-restraints excluded: chain D residue 722 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 219 optimal weight: 0.0070 chunk 294 optimal weight: 6.9990 chunk 84 optimal weight: 20.0000 chunk 254 optimal weight: 4.9990 chunk 40 optimal weight: 0.9980 chunk 76 optimal weight: 8.9990 chunk 276 optimal weight: 5.9990 chunk 115 optimal weight: 5.9990 chunk 283 optimal weight: 2.9990 chunk 35 optimal weight: 0.0980 chunk 50 optimal weight: 0.9980 overall best weight: 1.0200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.212138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.130922 restraints weight = 27988.502| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 2.07 r_work: 0.3215 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.4416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 28088 Z= 0.192 Angle : 0.577 11.767 38176 Z= 0.293 Chirality : 0.046 0.168 4384 Planarity : 0.004 0.051 4988 Dihedral : 17.175 132.489 4468 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.01 % Favored : 95.87 % Rotamer: Outliers : 1.41 % Allowed : 12.34 % Favored : 86.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.14), residues: 3464 helix: 0.15 (0.15), residues: 1304 sheet: 0.38 (0.22), residues: 592 loop : -1.23 (0.15), residues: 1568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 181 HIS 0.007 0.001 HIS A 586 PHE 0.016 0.002 PHE A 692 TYR 0.017 0.001 TYR A 519 ARG 0.004 0.000 ARG C 155 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9391.22 seconds wall clock time: 167 minutes 56.11 seconds (10076.11 seconds total)