Starting phenix.real_space_refine (version: dev) on Fri Mar 17 14:30:26 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7evn_31330/03_2023/7evn_31330.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7evn_31330/03_2023/7evn_31330.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7evn_31330/03_2023/7evn_31330.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7evn_31330/03_2023/7evn_31330.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7evn_31330/03_2023/7evn_31330.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7evn_31330/03_2023/7evn_31330.pdb" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "B TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 81": "OD1" <-> "OD2" Residue "C GLU 491": "OE1" <-> "OE2" Residue "C ARG 495": "NH1" <-> "NH2" Residue "C ASP 546": "OD1" <-> "OD2" Residue "C GLU 548": "OE1" <-> "OE2" Residue "C TYR 561": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 584": "OD1" <-> "OD2" Residue "C GLU 585": "OE1" <-> "OE2" Residue "C ARG 590": "NH1" <-> "NH2" Residue "C GLU 592": "OE1" <-> "OE2" Residue "C GLU 595": "OE1" <-> "OE2" Residue "C ASP 616": "OD1" <-> "OD2" Residue "C ASP 621": "OD1" <-> "OD2" Residue "C GLU 622": "OE1" <-> "OE2" Residue "C TYR 623": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 684": "NH1" <-> "NH2" Residue "C GLU 691": "OE1" <-> "OE2" Residue "C PHE 724": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 725": "OD1" <-> "OD2" Residue "C ARG 736": "NH1" <-> "NH2" Residue "C GLU 760": "OE1" <-> "OE2" Residue "C TYR 761": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 765": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 782": "OE1" <-> "OE2" Residue "C ASP 799": "OD1" <-> "OD2" Residue "C GLU 802": "OE1" <-> "OE2" Residue "C TYR 830": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 831": "NH1" <-> "NH2" Residue "C ASP 859": "OD1" <-> "OD2" Residue "C GLU 870": "OE1" <-> "OE2" Residue "C GLU 873": "OE1" <-> "OE2" Residue "C TYR 898": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 902": "OE1" <-> "OE2" Residue "C GLU 906": "OE1" <-> "OE2" Residue "C ASP 907": "OD1" <-> "OD2" Residue "C ARG 939": "NH1" <-> "NH2" Residue "C ARG 948": "NH1" <-> "NH2" Residue "C GLU 967": "OE1" <-> "OE2" Residue "C TYR 981": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 984": "OE1" <-> "OE2" Residue "C GLU 985": "OE1" <-> "OE2" Residue "C ARG 1027": "NH1" <-> "NH2" Residue "C ASP 1037": "OD1" <-> "OD2" Residue "C ARG 1045": "NH1" <-> "NH2" Residue "C GLU 1054": "OE1" <-> "OE2" Residue "C ARG 1057": "NH1" <-> "NH2" Residue "C PHE 1060": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 1075": "NH1" <-> "NH2" Residue "C PHE 1081": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1092": "OD1" <-> "OD2" Residue "C GLU 1121": "OE1" <-> "OE2" Residue "C GLU 1135": "OE1" <-> "OE2" Residue "C PHE 1153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1160": "OE1" <-> "OE2" Residue "C GLU 1174": "OE1" <-> "OE2" Residue "C ARG 1180": "NH1" <-> "NH2" Residue "C ASP 1206": "OD1" <-> "OD2" Residue "C TYR 1214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1235": "OE1" <-> "OE2" Residue "C ARG 1245": "NH1" <-> "NH2" Residue "C TYR 1249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 21": "NH1" <-> "NH2" Residue "D TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 57": "NH1" <-> "NH2" Residue "D GLU 79": "OE1" <-> "OE2" Residue "D ASP 97": "OD1" <-> "OD2" Residue "A PHE 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 57": "OE1" <-> "OE2" Residue "A PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 136": "OE1" <-> "OE2" Residue "A TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 159": "OE1" <-> "OE2" Residue "A TYR 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 243": "OD1" <-> "OD2" Residue "A PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 266": "OD1" <-> "OD2" Residue "A ARG 274": "NH1" <-> "NH2" Residue "A ARG 275": "NH1" <-> "NH2" Residue "A GLU 282": "OE1" <-> "OE2" Residue "A GLU 316": "OE1" <-> "OE2" Residue "A ASP 318": "OD1" <-> "OD2" Residue "A ARG 326": "NH1" <-> "NH2" Residue "A TYR 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 331": "OD1" <-> "OD2" Residue "A GLU 352": "OE1" <-> "OE2" Residue "A TYR 359": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 366": "OD1" <-> "OD2" Residue "A ASP 367": "OD1" <-> "OD2" Residue "A GLU 369": "OE1" <-> "OE2" Residue "A GLU 380": "OE1" <-> "OE2" Residue "A ASP 383": "OD1" <-> "OD2" Residue "A ASP 399": "OD1" <-> "OD2" Residue "A PHE 409": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 418": "OE1" <-> "OE2" Residue "A TYR 424": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 429": "NH1" <-> "NH2" Residue "A GLU 443": "OE1" <-> "OE2" Residue "A GLU 451": "OE1" <-> "OE2" Residue "A ARG 464": "NH1" <-> "NH2" Residue "A ASP 468": "OD1" <-> "OD2" Residue "A PHE 478": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 489": "OE1" <-> "OE2" Residue "A GLU 493": "OE1" <-> "OE2" Residue "A ASP 522": "OD1" <-> "OD2" Residue "A ARG 528": "NH1" <-> "NH2" Residue "A ASP 530": "OD1" <-> "OD2" Residue "A GLU 535": "OE1" <-> "OE2" Residue "A GLU 562": "OE1" <-> "OE2" Residue "A GLU 567": "OE1" <-> "OE2" Residue "A ASP 569": "OD1" <-> "OD2" Residue "A GLU 582": "OE1" <-> "OE2" Residue "A ASP 586": "OD1" <-> "OD2" Residue "A GLU 638": "OE1" <-> "OE2" Residue "A GLU 644": "OE1" <-> "OE2" Residue "A TYR 664": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 680": "OD1" <-> "OD2" Residue "A ARG 690": "NH1" <-> "NH2" Residue "A GLU 710": "OE1" <-> "OE2" Residue "A ARG 718": "NH1" <-> "NH2" Residue "A TYR 725": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 737": "OE1" <-> "OE2" Residue "A GLU 740": "OE1" <-> "OE2" Residue "A PHE 741": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 748": "OE1" <-> "OE2" Residue "A GLU 768": "OE1" <-> "OE2" Residue "A PHE 788": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 815": "NH1" <-> "NH2" Residue "A GLU 821": "OE1" <-> "OE2" Residue "A GLU 825": "OE1" <-> "OE2" Residue "A GLU 829": "OE1" <-> "OE2" Residue "A GLU 845": "OE1" <-> "OE2" Residue "A GLU 849": "OE1" <-> "OE2" Residue "A PHE 852": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 883": "OE1" <-> "OE2" Residue "A ARG 895": "NH1" <-> "NH2" Residue "A GLU 901": "OE1" <-> "OE2" Residue "A ASP 902": "OD1" <-> "OD2" Residue "A TYR 928": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 938": "OE1" <-> "OE2" Residue "A TYR 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1013": "NH1" <-> "NH2" Residue "A GLU 1018": "OE1" <-> "OE2" Residue "A ASP 1026": "OD1" <-> "OD2" Residue "A PHE 1050": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1136": "OE1" <-> "OE2" Residue "A ASP 1159": "OD1" <-> "OD2" Residue "A TYR 1166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1186": "OE1" <-> "OE2" Residue "A GLU 1196": "OE1" <-> "OE2" Residue "A GLU 1209": "OE1" <-> "OE2" Residue "A ASP 1210": "OD1" <-> "OD2" Residue "A PHE 1217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 70": "OD1" <-> "OD2" Residue "E ASP 78": "OD1" <-> "OD2" Residue "E PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 133": "NH1" <-> "NH2" Residue "E TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/chem_data/mon_lib" Total number of atoms: 19668 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 646 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "C" Number of atoms: 6487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 815, 6487 Classifications: {'peptide': 815} Link IDs: {'PCIS': 1, 'PTRANS': 33, 'TRANS': 780} Chain: "D" Number of atoms: 700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 700 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 3, 'TRANS': 89} Chain: "A" Number of atoms: 9227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1177, 9227 Classifications: {'peptide': 1177} Link IDs: {'PCIS': 2, 'PTRANS': 58, 'TRANS': 1116} Chain breaks: 5 Chain: "E" Number of atoms: 2605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 2605 Classifications: {'peptide': 486} Incomplete info: {'truncation_to_alanine': 366} Link IDs: {'CIS': 3, 'PTRANS': 21, 'TRANS': 461} Chain breaks: 5 Unresolved chain link angles: 20 Unresolved non-hydrogen bonds: 1340 Unresolved non-hydrogen angles: 1709 Unresolved non-hydrogen dihedrals: 1114 Unresolved non-hydrogen chiralities: 119 Planarities with less than four sites: {'GLN:plan1': 21, 'ARG:plan': 27, 'TYR:plan': 8, 'ASN:plan1': 17, 'TRP:plan': 5, 'HIS:plan': 14, 'PHE:plan': 18, 'GLU:plan': 26, 'ASP:plan': 26} Unresolved non-hydrogen planarities: 731 Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 7319 SG CYS D 30 58.922 85.880 76.427 1.00 19.46 S ATOM 7340 SG CYS D 33 56.017 84.874 74.168 1.00 21.93 S ATOM 7635 SG CYS D 72 58.670 82.608 74.913 1.00 18.16 S ATOM 7659 SG CYS D 75 59.864 85.440 72.822 1.00 17.46 S ATOM 7268 SG CYS D 23 53.801 93.245 88.762 1.00 29.17 S ATOM 7292 SG CYS D 26 53.348 92.295 85.340 1.00 33.37 S ATOM 7539 SG CYS D 58 56.697 94.038 86.219 1.00 27.69 S ATOM 7560 SG CYS D 61 53.726 96.297 86.896 1.00 29.63 S ATOM 7181 SG CYS D 11 66.385 101.049 77.365 1.00 21.15 S ATOM 7444 SG CYS D 46 69.231 100.497 80.129 1.00 21.46 S ATOM 7467 SG CYS D 49 65.623 101.088 81.190 1.00 27.61 S ATOM 7738 SG CYS D 85 66.306 97.609 79.305 1.00 20.01 S Time building chain proxies: 11.80, per 1000 atoms: 0.60 Number of scatterers: 19668 At special positions: 0 Unit cell: (144.571, 150.006, 142.397, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 3 29.99 S 105 16.00 O 3715 8.00 N 3431 7.00 C 12414 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: 8.41 Conformation dependent library (CDL) restraints added in 3.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D 201 " pdb="ZN ZN D 201 " - pdb=" SG CYS D 72 " pdb="ZN ZN D 201 " - pdb=" SG CYS D 75 " pdb="ZN ZN D 201 " - pdb=" SG CYS D 33 " pdb="ZN ZN D 201 " - pdb=" SG CYS D 30 " pdb=" ZN D 202 " pdb="ZN ZN D 202 " - pdb=" SG CYS D 61 " pdb="ZN ZN D 202 " - pdb=" SG CYS D 23 " pdb="ZN ZN D 202 " - pdb=" SG CYS D 58 " pdb="ZN ZN D 202 " - pdb=" SG CYS D 26 " pdb=" ZN D 203 " pdb="ZN ZN D 203 " - pdb=" SG CYS D 11 " pdb="ZN ZN D 203 " - pdb=" SG CYS D 46 " pdb="ZN ZN D 203 " - pdb=" SG CYS D 85 " pdb="ZN ZN D 203 " - pdb=" SG CYS D 49 " Number of angles added : 18 5238 Ramachandran restraints generated. 2619 Oldfield, 0 Emsley, 2619 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4960 Finding SS restraints... Secondary structure from input PDB file: 103 helices and 30 sheets defined 43.9% alpha, 18.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.44 Creating SS restraints... Processing helix chain 'B' and resid 6 through 16 Processing helix chain 'B' and resid 27 through 46 Processing helix chain 'B' and resid 46 through 57 removed outlier: 3.532A pdb=" N LEU B 50 " --> pdb=" O HIS B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 71 Processing helix chain 'C' and resid 491 through 498 removed outlier: 4.121A pdb=" N ARG C 495 " --> pdb=" O GLU C 491 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N LYS C 496 " --> pdb=" O GLN C 492 " (cutoff:3.500A) Processing helix chain 'C' and resid 499 through 506 Processing helix chain 'C' and resid 508 through 527 removed outlier: 5.545A pdb=" N ARG C 524 " --> pdb=" O THR C 520 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N GLU C 525 " --> pdb=" O ASP C 521 " (cutoff:3.500A) Processing helix chain 'C' and resid 527 through 540 removed outlier: 3.541A pdb=" N LEU C 531 " --> pdb=" O GLY C 527 " (cutoff:3.500A) Proline residue: C 537 - end of helix Processing helix chain 'C' and resid 545 through 563 removed outlier: 3.606A pdb=" N LYS C 562 " --> pdb=" O ARG C 558 " (cutoff:3.500A) Processing helix chain 'C' and resid 567 through 569 No H-bonds generated for 'chain 'C' and resid 567 through 569' Processing helix chain 'C' and resid 570 through 579 Processing helix chain 'C' and resid 586 through 604 removed outlier: 3.787A pdb=" N ARG C 590 " --> pdb=" O ASP C 586 " (cutoff:3.500A) Processing helix chain 'C' and resid 605 through 614 Processing helix chain 'C' and resid 615 through 618 removed outlier: 4.005A pdb=" N ASP C 618 " --> pdb=" O PRO C 615 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 615 through 618' Processing helix chain 'C' and resid 621 through 640 Processing helix chain 'C' and resid 640 through 652 removed outlier: 3.932A pdb=" N LEU C 644 " --> pdb=" O GLY C 640 " (cutoff:3.500A) Proline residue: C 646 - end of helix Processing helix chain 'C' and resid 657 through 676 Processing helix chain 'C' and resid 677 through 681 removed outlier: 3.568A pdb=" N LEU C 680 " --> pdb=" O CYS C 677 " (cutoff:3.500A) Proline residue: C 681 - end of helix No H-bonds generated for 'chain 'C' and resid 677 through 681' Processing helix chain 'C' and resid 682 through 691 Processing helix chain 'C' and resid 692 through 696 removed outlier: 3.808A pdb=" N VAL C 695 " --> pdb=" O HIS C 692 " (cutoff:3.500A) Processing helix chain 'C' and resid 698 through 717 Processing helix chain 'C' and resid 727 through 738 removed outlier: 3.573A pdb=" N TRP C 732 " --> pdb=" O LEU C 728 " (cutoff:3.500A) Processing helix chain 'C' and resid 740 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 778 Processing helix chain 'C' and resid 781 through 796 removed outlier: 3.591A pdb=" N LYS C 790 " --> pdb=" O LYS C 786 " (cutoff:3.500A) Processing helix chain 'C' and resid 802 through 810 Processing helix chain 'C' and resid 810 through 819 removed outlier: 4.048A pdb=" N TRP C 819 " --> pdb=" O PHE C 815 " (cutoff:3.500A) Processing helix chain 'C' and resid 820 through 826 removed outlier: 3.548A pdb=" N ASP C 826 " --> pdb=" O ARG C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 827 through 845 removed outlier: 3.649A pdb=" N LYS C 843 " --> pdb=" O GLU C 839 " (cutoff:3.500A) Processing helix chain 'C' and resid 845 through 854 removed outlier: 3.897A pdb=" N ILE C 849 " --> pdb=" O GLY C 845 " (cutoff:3.500A) Processing helix chain 'C' and resid 855 through 858 removed outlier: 3.702A pdb=" N LYS C 858 " --> pdb=" O ASP C 855 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 855 through 858' Processing helix chain 'C' and resid 861 through 879 Processing helix chain 'C' and resid 888 through 902 Processing helix chain 'C' and resid 907 through 922 removed outlier: 4.299A pdb=" N LEU C 911 " --> pdb=" O ASP C 907 " (cutoff:3.500A) Processing helix chain 'C' and resid 923 through 925 No H-bonds generated for 'chain 'C' and resid 923 through 925' Processing helix chain 'C' and resid 928 through 942 removed outlier: 4.100A pdb=" N ASN C 942 " --> pdb=" O TRP C 938 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 5.202A pdb=" N VAL C 960 " --> pdb=" O SER C 956 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N VAL C 961 " --> pdb=" O ARG C 957 " (cutoff:3.500A) Processing helix chain 'C' and resid 968 through 981 Processing helix chain 'C' and resid 986 through 1004 removed outlier: 3.561A pdb=" N VAL C1003 " --> pdb=" O ALA C 999 " (cutoff:3.500A) Processing helix chain 'C' and resid 1012 through 1021 Proline residue: C1018 - end of helix Processing helix chain 'C' and resid 1022 through 1026 Processing helix chain 'C' and resid 1028 through 1046 Processing helix chain 'C' and resid 1047 through 1050 Processing helix chain 'C' and resid 1051 through 1063 Processing helix chain 'C' and resid 1064 through 1068 removed outlier: 3.788A pdb=" N LYS C1067 " --> pdb=" O GLU C1064 " (cutoff:3.500A) Processing helix chain 'C' and resid 1070 through 1089 Processing helix chain 'C' and resid 1090 through 1104 removed outlier: 3.696A pdb=" N ALA C1095 " --> pdb=" O HIS C1091 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR C1096 " --> pdb=" O ASP C1092 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N LYS C1102 " --> pdb=" O LEU C1098 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N VAL C1103 " --> pdb=" O ASN C1099 " (cutoff:3.500A) Processing helix chain 'C' and resid 1105 through 1123 removed outlier: 4.671A pdb=" N CYS C1111 " --> pdb=" O GLN C1107 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR C1112 " --> pdb=" O ASN C1108 " (cutoff:3.500A) Processing helix chain 'C' and resid 1124 through 1127 Processing helix chain 'C' and resid 1128 through 1137 removed outlier: 3.555A pdb=" N TYR C1136 " --> pdb=" O LEU C1132 " (cutoff:3.500A) Processing helix chain 'C' and resid 1143 through 1159 Processing helix chain 'C' and resid 1160 through 1164 removed outlier: 3.506A pdb=" N LYS C1163 " --> pdb=" O GLU C1160 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ASP C1164 " --> pdb=" O MET C1161 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1160 through 1164' Processing helix chain 'C' and resid 1165 through 1178 removed outlier: 3.714A pdb=" N VAL C1169 " --> pdb=" O TYR C1165 " (cutoff:3.500A) Proline residue: C1171 - end of helix Processing helix chain 'C' and resid 1181 through 1199 removed outlier: 3.588A pdb=" N ARG C1185 " --> pdb=" O ASP C1181 " (cutoff:3.500A) Processing helix chain 'C' and resid 1204 through 1216 removed outlier: 3.774A pdb=" N TYR C1214 " --> pdb=" O HIS C1210 " (cutoff:3.500A) Processing helix chain 'C' and resid 1217 through 1220 removed outlier: 4.190A pdb=" N PHE C1220 " --> pdb=" O PRO C1217 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1217 through 1220' Processing helix chain 'C' and resid 1223 through 1242 Processing helix chain 'C' and resid 1242 through 1251 removed outlier: 3.726A pdb=" N MET C1246 " --> pdb=" O GLY C1242 " (cutoff:3.500A) Processing helix chain 'C' and resid 1258 through 1275 Processing helix chain 'C' and resid 1277 through 1283 removed outlier: 3.558A pdb=" N ILE C1281 " --> pdb=" O ASP C1278 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA C1282 " --> pdb=" O ALA C1279 " (cutoff:3.500A) Processing helix chain 'C' and resid 1298 through 1302 Processing helix chain 'D' and resid 51 through 55 Processing helix chain 'D' and resid 73 through 78 Processing helix chain 'D' and resid 79 through 83 removed outlier: 4.061A pdb=" N ASP D 83 " --> pdb=" O LYS D 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 432 Processing helix chain 'A' and resid 808 through 825 Processing helix chain 'A' and resid 838 through 845 removed outlier: 3.518A pdb=" N GLU A 845 " --> pdb=" O ALA A 841 " (cutoff:3.500A) Processing helix chain 'A' and resid 848 through 853 Processing helix chain 'A' and resid 1134 through 1152 removed outlier: 4.056A pdb=" N SER A1150 " --> pdb=" O MET A1146 " (cutoff:3.500A) Processing helix chain 'A' and resid 1159 through 1165 Processing helix chain 'A' and resid 1176 through 1180 Processing helix chain 'A' and resid 1181 through 1185 Processing helix chain 'A' and resid 1186 through 1197 Processing helix chain 'A' and resid 1200 through 1216 removed outlier: 3.812A pdb=" N TYR A1215 " --> pdb=" O ILE A1211 " (cutoff:3.500A) Processing helix chain 'E' and resid 70 through 77 Processing helix chain 'E' and resid 115 through 132 removed outlier: 4.244A pdb=" N GLU E 122 " --> pdb=" O ALA E 118 " (cutoff:3.500A) Processing helix chain 'E' and resid 148 through 153 Processing helix chain 'E' and resid 155 through 167 Processing helix chain 'E' and resid 221 through 226 Processing helix chain 'E' and resid 228 through 239 Processing helix chain 'E' and resid 254 through 259 removed outlier: 3.636A pdb=" N PHE E 258 " --> pdb=" O SER E 254 " (cutoff:3.500A) Processing helix chain 'E' and resid 261 through 271 Processing helix chain 'E' and resid 277 through 289 Proline residue: E 285 - end of helix Processing helix chain 'E' and resid 302 through 317 Proline residue: E 310 - end of helix Processing helix chain 'E' and resid 335 through 351 Processing helix chain 'E' and resid 352 through 354 No H-bonds generated for 'chain 'E' and resid 352 through 354' Processing helix chain 'E' and resid 365 through 376 removed outlier: 3.554A pdb=" N GLY E 376 " --> pdb=" O ALA E 372 " (cutoff:3.500A) Processing helix chain 'E' and resid 383 through 393 Processing helix chain 'E' and resid 408 through 415 Processing helix chain 'E' and resid 417 through 428 Processing helix chain 'E' and resid 442 through 453 Processing helix chain 'E' and resid 463 through 465 No H-bonds generated for 'chain 'E' and resid 463 through 465' Processing helix chain 'E' and resid 480 through 482 No H-bonds generated for 'chain 'E' and resid 480 through 482' Processing helix chain 'E' and resid 483 through 497 removed outlier: 3.546A pdb=" N ARG E 491 " --> pdb=" O TRP E 487 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N VAL E 493 " --> pdb=" O THR E 489 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N GLU E 494 " --> pdb=" O ARG E 490 " (cutoff:3.500A) Processing helix chain 'E' and resid 507 through 521 Processing helix chain 'E' and resid 533 through 546 Processing helix chain 'E' and resid 557 through 559 No H-bonds generated for 'chain 'E' and resid 557 through 559' Processing helix chain 'E' and resid 578 through 587 Processing helix chain 'E' and resid 603 through 605 No H-bonds generated for 'chain 'E' and resid 603 through 605' Processing helix chain 'E' and resid 606 through 620 Processing helix chain 'E' and resid 625 through 633 Processing helix chain 'E' and resid 635 through 640 Processing sheet with id=AA1, first strand: chain 'D' and resid 8 through 10 Processing sheet with id=AA2, first strand: chain 'D' and resid 18 through 19 removed outlier: 4.101A pdb=" N ALA D 18 " --> pdb=" O ILE D 45 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 21 through 22 Processing sheet with id=AA4, first strand: chain 'D' and resid 39 through 42 removed outlier: 6.056A pdb=" N TYR D 71 " --> pdb=" O CYS D 40 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1101 through 1108 removed outlier: 3.905A pdb=" N SER A1103 " --> pdb=" O THR A1120 " (cutoff:3.500A) removed outlier: 8.661A pdb=" N GLU A1115 " --> pdb=" O PRO A1131 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ILE A1126 " --> pdb=" O LEU A 8 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 16 through 20 removed outlier: 3.673A pdb=" N PHE A 16 " --> pdb=" O SER A 33 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N LEU A 38 " --> pdb=" O THR A 55 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N THR A 55 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N LEU A 40 " --> pdb=" O LEU A 53 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 62 through 68 removed outlier: 3.726A pdb=" N VAL A 88 " --> pdb=" O VAL A 80 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N SER A 82 " --> pdb=" O ARG A 86 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N ARG A 86 " --> pdb=" O SER A 82 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ILE A 87 " --> pdb=" O GLN A 104 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N GLN A 104 " --> pdb=" O ILE A 87 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ILE A 89 " --> pdb=" O ILE A 102 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 120 through 123 Processing sheet with id=AA9, first strand: chain 'A' and resid 120 through 123 Processing sheet with id=AB1, first strand: chain 'A' and resid 165 through 173 removed outlier: 5.640A pdb=" N VAL A 167 " --> pdb=" O MET A 187 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N MET A 187 " --> pdb=" O VAL A 167 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N HIS A 169 " --> pdb=" O LEU A 185 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N MET A 181 " --> pdb=" O VAL A 173 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N LEU A 208 " --> pdb=" O SER A 225 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N SER A 225 " --> pdb=" O LEU A 208 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N PHE A 210 " --> pdb=" O LYS A 223 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N HIS A 219 " --> pdb=" O ASP A 214 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 232 through 237 removed outlier: 4.394A pdb=" N PHE A 234 " --> pdb=" O CYS A 251 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N TYR A 255 " --> pdb=" O SER A 252 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 273 through 274 removed outlier: 6.320A pdb=" N ARG A 273 " --> pdb=" O PHE A 387 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 287 through 294 removed outlier: 6.940A pdb=" N GLN A 304 " --> pdb=" O VAL A 288 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N SER A 290 " --> pdb=" O LEU A 302 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N LEU A 302 " --> pdb=" O SER A 290 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N THR A 292 " --> pdb=" O PHE A 300 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N PHE A 300 " --> pdb=" O THR A 292 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N PHE A 299 " --> pdb=" O LEU A 315 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N LEU A 315 " --> pdb=" O PHE A 299 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N ASP A 309 " --> pdb=" O THR A 305 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N ILE A 310 " --> pdb=" O TYR A 329 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N TYR A 329 " --> pdb=" O ILE A 310 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N LYS A 312 " --> pdb=" O LEU A 327 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N LEU A 327 " --> pdb=" O LYS A 312 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N THR A 314 " --> pdb=" O ILE A 325 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N ILE A 325 " --> pdb=" O THR A 314 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N GLU A 316 " --> pdb=" O THR A 323 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 336 through 342 removed outlier: 7.127A pdb=" N ALA A 350 " --> pdb=" O ALA A 337 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N MET A 339 " --> pdb=" O PHE A 348 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N PHE A 348 " --> pdb=" O MET A 339 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N VAL A 341 " --> pdb=" O PHE A 346 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N PHE A 346 " --> pdb=" O VAL A 341 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N HIS A 356 " --> pdb=" O GLU A 400 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N GLU A 400 " --> pdb=" O HIS A 356 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N LEU A 358 " --> pdb=" O VAL A 398 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 409 through 413 removed outlier: 3.629A pdb=" N PHE A 409 " --> pdb=" O ALA A 426 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER A 434 " --> pdb=" O CYS A 427 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 448 through 450 Processing sheet with id=AB8, first strand: chain 'A' and resid 458 through 459 removed outlier: 3.584A pdb=" N ALA A 458 " --> pdb=" O SER A 477 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 507 through 510 removed outlier: 4.102A pdb=" N HIS A 526 " --> pdb=" O ASN A 534 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ASN A 534 " --> pdb=" O HIS A 526 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 544 through 549 removed outlier: 3.647A pdb=" N VAL A 545 " --> pdb=" O ALA A 557 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N ALA A 557 " --> pdb=" O VAL A 545 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N CYS A 547 " --> pdb=" O VAL A 555 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N VAL A 555 " --> pdb=" O CYS A 547 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE A 556 " --> pdb=" O VAL A 564 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 587 through 592 removed outlier: 3.627A pdb=" N CYS A 589 " --> pdb=" O GLY A 608 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N THR A 613 " --> pdb=" O LEU A 609 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N SER A 629 " --> pdb=" O ILE A 616 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N SER A 618 " --> pdb=" O PRO A 627 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 637 through 643 removed outlier: 6.994A pdb=" N GLY A 668 " --> pdb=" O GLU A 638 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N LEU A 640 " --> pdb=" O ASN A 666 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ASN A 666 " --> pdb=" O LEU A 640 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N ILE A 642 " --> pdb=" O TYR A 664 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N TYR A 664 " --> pdb=" O ILE A 642 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 703 through 706 Processing sheet with id=AC5, first strand: chain 'A' and resid 720 through 724 Processing sheet with id=AC6, first strand: chain 'A' and resid 785 through 790 removed outlier: 7.147A pdb=" N ILE A 800 " --> pdb=" O ARG A 786 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N PHE A 788 " --> pdb=" O ILE A 798 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ILE A 798 " --> pdb=" O PHE A 788 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASP A 878 " --> pdb=" O VAL A 868 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 886 through 894 removed outlier: 6.492A pdb=" N GLY A 908 " --> pdb=" O PHE A 889 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N VAL A 891 " --> pdb=" O LEU A 906 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N LEU A 906 " --> pdb=" O VAL A 891 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N VAL A 893 " --> pdb=" O TYR A 904 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N TYR A 904 " --> pdb=" O VAL A 893 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLY A 922 " --> pdb=" O LYS A 911 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N GLY A 923 " --> pdb=" O PRO A 944 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N VAL A 925 " --> pdb=" O LYS A 942 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N LYS A 942 " --> pdb=" O VAL A 925 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N THR A 927 " --> pdb=" O LEU A 940 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 953 through 955 removed outlier: 6.829A pdb=" N LEU A 967 " --> pdb=" O GLU A 982 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N GLU A 982 " --> pdb=" O LEU A 967 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N VAL A 969 " --> pdb=" O LYS A 980 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 990 through 996 removed outlier: 3.830A pdb=" N GLY A 992 " --> pdb=" O SER A1003 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N TRP A1011 " --> pdb=" O PHE A1024 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 1033 through 1040 removed outlier: 3.863A pdb=" N THR A1035 " --> pdb=" O ALA A1047 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N THR A1043 " --> pdb=" O LEU A1039 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N ASN A1052 " --> pdb=" O ASP A1048 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ILE A1053 " --> pdb=" O ASN A1094 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ASN A1094 " --> pdb=" O ILE A1053 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N VAL A1055 " --> pdb=" O ILE A1092 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 241 through 244 removed outlier: 6.343A pdb=" N ILE E 294 " --> pdb=" O VAL E 459 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N GLN E 461 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N ILE E 296 " --> pdb=" O GLN E 461 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ALA E 329 " --> pdb=" O VAL E 380 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N CYS E 382 " --> pdb=" O ALA E 329 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ILE E 331 " --> pdb=" O CYS E 382 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 472 through 477 removed outlier: 6.487A pdb=" N THR E 472 " --> pdb=" O ALA E 598 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N THR E 600 " --> pdb=" O THR E 472 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ILE E 474 " --> pdb=" O THR E 600 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N LEU E 602 " --> pdb=" O ILE E 474 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N GLU E 476 " --> pdb=" O LEU E 602 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N SER E 500 " --> pdb=" O ILE E 567 " (cutoff:3.500A) 980 hydrogen bonds defined for protein. 2808 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.41 Time building geometry restraints manager: 9.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4677 1.33 - 1.45: 3802 1.45 - 1.57: 11363 1.57 - 1.69: 0 1.69 - 1.81: 163 Bond restraints: 20005 Sorted by residual: bond pdb=" C HIS A 804 " pdb=" O HIS A 804 " ideal model delta sigma weight residual 1.234 1.318 -0.083 1.27e-02 6.20e+03 4.29e+01 bond pdb=" N GLU E 80 " pdb=" CA GLU E 80 " ideal model delta sigma weight residual 1.455 1.504 -0.049 1.25e-02 6.40e+03 1.52e+01 bond pdb=" N ILE E 151 " pdb=" CA ILE E 151 " ideal model delta sigma weight residual 1.460 1.495 -0.035 1.21e-02 6.83e+03 8.36e+00 bond pdb=" N GLU E 153 " pdb=" CA GLU E 153 " ideal model delta sigma weight residual 1.455 1.491 -0.035 1.23e-02 6.61e+03 8.25e+00 bond pdb=" N ASP E 155 " pdb=" CA ASP E 155 " ideal model delta sigma weight residual 1.453 1.490 -0.037 1.31e-02 5.83e+03 8.19e+00 ... (remaining 20000 not shown) Histogram of bond angle deviations from ideal: 99.02 - 106.07: 432 106.07 - 113.12: 10780 113.12 - 120.17: 7366 120.17 - 127.22: 8415 127.22 - 134.27: 172 Bond angle restraints: 27165 Sorted by residual: angle pdb=" C GLN E 275 " pdb=" N PRO E 276 " pdb=" CA PRO E 276 " ideal model delta sigma weight residual 119.85 111.73 8.12 1.01e+00 9.80e-01 6.47e+01 angle pdb=" CA SER E 271 " pdb=" C SER E 271 " pdb=" N GLU E 272 " ideal model delta sigma weight residual 115.30 124.13 -8.83 1.33e+00 5.65e-01 4.41e+01 angle pdb=" N ASP C 565 " pdb=" CA ASP C 565 " pdb=" C ASP C 565 " ideal model delta sigma weight residual 113.61 104.74 8.87 1.50e+00 4.44e-01 3.50e+01 angle pdb=" O ASP C 564 " pdb=" C ASP C 564 " pdb=" N ASP C 565 " ideal model delta sigma weight residual 122.30 114.49 7.81 1.35e+00 5.49e-01 3.35e+01 angle pdb=" N LYS A 137 " pdb=" CA LYS A 137 " pdb=" CB LYS A 137 " ideal model delta sigma weight residual 114.17 107.91 6.26 1.14e+00 7.69e-01 3.01e+01 ... (remaining 27160 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 10565 17.98 - 35.97: 1072 35.97 - 53.95: 341 53.95 - 71.94: 81 71.94 - 89.92: 30 Dihedral angle restraints: 12089 sinusoidal: 4410 harmonic: 7679 Sorted by residual: dihedral pdb=" CA THR A 490 " pdb=" C THR A 490 " pdb=" N VAL A 491 " pdb=" CA VAL A 491 " ideal model delta harmonic sigma weight residual -180.00 -150.44 -29.56 0 5.00e+00 4.00e-02 3.49e+01 dihedral pdb=" CA TYR E 273 " pdb=" C TYR E 273 " pdb=" N THR E 274 " pdb=" CA THR E 274 " ideal model delta harmonic sigma weight residual 180.00 154.13 25.87 0 5.00e+00 4.00e-02 2.68e+01 dihedral pdb=" CA LYS C 943 " pdb=" C LYS C 943 " pdb=" N SER C 944 " pdb=" CA SER C 944 " ideal model delta harmonic sigma weight residual 180.00 154.33 25.67 0 5.00e+00 4.00e-02 2.64e+01 ... (remaining 12086 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 2645 0.073 - 0.147: 465 0.147 - 0.220: 26 0.220 - 0.293: 1 0.293 - 0.366: 1 Chirality restraints: 3138 Sorted by residual: chirality pdb=" CA HIS A 804 " pdb=" N HIS A 804 " pdb=" C HIS A 804 " pdb=" CB HIS A 804 " both_signs ideal model delta sigma weight residual False 2.51 2.88 -0.37 2.00e-01 2.50e+01 3.36e+00 chirality pdb=" CA ILE E 147 " pdb=" N ILE E 147 " pdb=" C ILE E 147 " pdb=" CB ILE E 147 " both_signs ideal model delta sigma weight residual False 2.43 2.69 -0.26 2.00e-01 2.50e+01 1.67e+00 chirality pdb=" CA MET E 131 " pdb=" N MET E 131 " pdb=" C MET E 131 " pdb=" CB MET E 131 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.16e+00 ... (remaining 3135 not shown) Planarity restraints: 3565 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP C 564 " -0.024 2.00e-02 2.50e+03 4.54e-02 2.06e+01 pdb=" C ASP C 564 " 0.079 2.00e-02 2.50e+03 pdb=" O ASP C 564 " -0.028 2.00e-02 2.50e+03 pdb=" N ASP C 565 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA C 945 " -0.013 2.00e-02 2.50e+03 2.49e-02 6.18e+00 pdb=" C ALA C 945 " 0.043 2.00e-02 2.50e+03 pdb=" O ALA C 945 " -0.016 2.00e-02 2.50e+03 pdb=" N LYS C 946 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU C 680 " -0.034 5.00e-02 4.00e+02 5.16e-02 4.27e+00 pdb=" N PRO C 681 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO C 681 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO C 681 " -0.029 5.00e-02 4.00e+02 ... (remaining 3562 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 858 2.71 - 3.26: 18649 3.26 - 3.81: 31065 3.81 - 4.35: 38964 4.35 - 4.90: 65300 Nonbonded interactions: 154836 Sorted by model distance: nonbonded pdb=" O LYS A 343 " pdb=" OG1 THR A 344 " model vdw 2.168 2.440 nonbonded pdb=" N ASP E 149 " pdb=" OD1 ASP E 149 " model vdw 2.203 2.520 nonbonded pdb=" O ALA C 762 " pdb=" OG1 THR C 766 " model vdw 2.205 2.440 nonbonded pdb=" O GLY E 300 " pdb=" N GLY E 302 " model vdw 2.206 2.520 nonbonded pdb=" O ALA A 200 " pdb=" OG1 THR A 204 " model vdw 2.219 2.440 ... (remaining 154831 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 3 6.06 5 S 105 5.16 5 C 12414 2.51 5 N 3431 2.21 5 O 3715 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 1.520 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: 0.000 Extract box with map and model: 4.510 Check model and map are aligned: 0.280 Process input model: 59.670 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Set scattering table: 0.160 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 81.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.083 20005 Z= 0.416 Angle : 0.858 11.270 27165 Z= 0.542 Chirality : 0.052 0.366 3138 Planarity : 0.005 0.052 3565 Dihedral : 17.469 89.923 7129 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.70 % Favored : 95.15 % Rotamer Outliers : 6.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.09 (0.15), residues: 2619 helix: -0.74 (0.14), residues: 1023 sheet: -0.76 (0.21), residues: 548 loop : -2.32 (0.16), residues: 1048 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5238 Ramachandran restraints generated. 2619 Oldfield, 0 Emsley, 2619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5238 Ramachandran restraints generated. 2619 Oldfield, 0 Emsley, 2619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 2287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 246 time to evaluate : 1.760 Fit side-chains outliers start: 134 outliers final: 74 residues processed: 366 average time/residue: 0.9418 time to fit residues: 385.8653 Evaluate side-chains 275 residues out of total 2287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 201 time to evaluate : 1.594 Switching outliers to nearest non-outliers outliers start: 74 outliers final: 68 residues processed: 6 average time/residue: 0.5972 time to fit residues: 6.4310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 221 optimal weight: 30.0000 chunk 198 optimal weight: 1.9990 chunk 110 optimal weight: 3.9990 chunk 67 optimal weight: 5.9990 chunk 133 optimal weight: 0.0040 chunk 106 optimal weight: 1.9990 chunk 205 optimal weight: 4.9990 chunk 79 optimal weight: 0.7980 chunk 124 optimal weight: 5.9990 chunk 152 optimal weight: 7.9990 chunk 237 optimal weight: 0.0970 overall best weight: 0.9794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: