Starting phenix.real_space_refine on Sun Aug 11 09:14:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ed7_28031/08_2024/8ed7_28031.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ed7_28031/08_2024/8ed7_28031.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ed7_28031/08_2024/8ed7_28031.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ed7_28031/08_2024/8ed7_28031.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ed7_28031/08_2024/8ed7_28031.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ed7_28031/08_2024/8ed7_28031.cif" } resolution = 3.7 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= 0.000 sd= 0.003 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: 4 Type Number sf(0) Gaussians S 226 5.16 5 C 20456 2.51 5 N 5325 2.21 5 O 5511 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 31518 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 7736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 954, 7736 Classifications: {'peptide': 954} Link IDs: {'PTRANS': 33, 'TRANS': 920} Chain breaks: 6 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 85 Classifications: {'peptide': 17} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'TRANS': 16} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'UNK:plan-1': 17} Unresolved non-hydrogen planarities: 17 Chain: "B" Number of atoms: 7760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 957, 7760 Classifications: {'peptide': 957} Link IDs: {'PTRANS': 33, 'TRANS': 923} Chain breaks: 6 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 85 Classifications: {'peptide': 17} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'TRANS': 16} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'UNK:plan-1': 17} Unresolved non-hydrogen planarities: 17 Chain: "C" Number of atoms: 7760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 957, 7760 Classifications: {'peptide': 957} Link IDs: {'PTRANS': 33, 'TRANS': 923} Chain breaks: 6 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 85 Classifications: {'peptide': 17} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'TRANS': 16} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'UNK:plan-1': 17} Unresolved non-hydrogen planarities: 17 Chain: "D" Number of atoms: 7766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 958, 7766 Classifications: {'peptide': 958} Link IDs: {'PTRANS': 33, 'TRANS': 924} Chain breaks: 6 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 85 Classifications: {'peptide': 17} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'TRANS': 16} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'UNK:plan-1': 17} Unresolved non-hydrogen planarities: 17 Chain: "A" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 78 Unusual residues: {'9Z9': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 39 Unusual residues: {'9Z9': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 39 Unusual residues: {'9Z9': 1} Classifications: {'undetermined': 1} Time building chain proxies: 16.54, per 1000 atoms: 0.52 Number of scatterers: 31518 At special positions: 0 Unit cell: (140.175, 140.175, 152.19, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 226 16.00 O 5511 8.00 N 5325 7.00 C 20456 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 12.10 Conformation dependent library (CDL) restraints added in 5.5 seconds 7540 Ramachandran restraints generated. 3770 Oldfield, 0 Emsley, 3770 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7340 Finding SS restraints... Secondary structure from input PDB file: 193 helices and 8 sheets defined 67.3% alpha, 4.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.72 Creating SS restraints... Processing helix chain 'A' and resid 165 through 176 Processing helix chain 'A' and resid 201 through 215 Processing helix chain 'A' and resid 228 through 244 removed outlier: 3.716A pdb=" N LYS A 243 " --> pdb=" O ASP A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 283 removed outlier: 4.188A pdb=" N LYS A 283 " --> pdb=" O PRO A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 322 Processing helix chain 'A' and resid 342 through 355 removed outlier: 4.096A pdb=" N ILE A 346 " --> pdb=" O GLY A 342 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N SER A 347 " --> pdb=" O PRO A 343 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASP A 355 " --> pdb=" O GLU A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 368 No H-bonds generated for 'chain 'A' and resid 366 through 368' Processing helix chain 'A' and resid 369 through 379 removed outlier: 3.663A pdb=" N ILE A 373 " --> pdb=" O ARG A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 402 removed outlier: 3.594A pdb=" N THR A 402 " --> pdb=" O ILE A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 423 Processing helix chain 'A' and resid 439 through 453 removed outlier: 3.539A pdb=" N LEU A 448 " --> pdb=" O ILE A 444 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASN A 453 " --> pdb=" O LEU A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 467 Processing helix chain 'A' and resid 468 through 475 removed outlier: 3.915A pdb=" N ALA A 472 " --> pdb=" O ARG A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 486 through 498 removed outlier: 3.511A pdb=" N VAL A 497 " --> pdb=" O LEU A 493 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU A 498 " --> pdb=" O ASP A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 509 Processing helix chain 'A' and resid 513 through 518 Processing helix chain 'A' and resid 519 through 528 Processing helix chain 'A' and resid 536 through 545 Processing helix chain 'A' and resid 556 through 569 removed outlier: 3.899A pdb=" N GLY A 569 " --> pdb=" O GLU A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 577 Processing helix chain 'A' and resid 578 through 587 Processing helix chain 'A' and resid 636 through 648 removed outlier: 3.941A pdb=" N GLU A 640 " --> pdb=" O PHE A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 659 removed outlier: 4.012A pdb=" N GLN A 659 " --> pdb=" O LEU A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 685 Processing helix chain 'A' and resid 690 through 717 removed outlier: 4.655A pdb=" N ASN A 696 " --> pdb=" O SER A 692 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N HIS A 697 " --> pdb=" O GLN A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 717 through 725 Processing helix chain 'A' and resid 729 through 733 removed outlier: 3.561A pdb=" N TRP A 732 " --> pdb=" O LEU A 729 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N SER A 733 " --> pdb=" O LYS A 730 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 729 through 733' Processing helix chain 'A' and resid 736 through 744 Processing helix chain 'A' and resid 746 through 751 removed outlier: 3.729A pdb=" N ILE A 750 " --> pdb=" O HIS A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 752 through 764 Processing helix chain 'A' and resid 774 through 783 Processing helix chain 'A' and resid 783 through 788 removed outlier: 3.518A pdb=" N ILE A 787 " --> pdb=" O LEU A 783 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N LEU A 788 " --> pdb=" O PRO A 784 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 783 through 788' Processing helix chain 'A' and resid 862 through 869 removed outlier: 3.579A pdb=" N ASN A 869 " --> pdb=" O TYR A 865 " (cutoff:3.500A) Processing helix chain 'A' and resid 870 through 895 Processing helix chain 'A' and resid 902 through 925 Processing helix chain 'A' and resid 930 through 939 removed outlier: 3.689A pdb=" N VAL A 935 " --> pdb=" O LEU A 931 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LYS A 936 " --> pdb=" O LEU A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 941 through 962 removed outlier: 3.536A pdb=" N VAL A 945 " --> pdb=" O GLU A 941 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU A 962 " --> pdb=" O MET A 958 " (cutoff:3.500A) Processing helix chain 'A' and resid 964 through 985 removed outlier: 4.204A pdb=" N ILE A 980 " --> pdb=" O CYS A 976 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N TYR A 981 " --> pdb=" O VAL A 977 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N TRP A 982 " --> pdb=" O ASN A 978 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 991 removed outlier: 3.877A pdb=" N ILE A 989 " --> pdb=" O ARG A 985 " (cutoff:3.500A) Processing helix chain 'A' and resid 995 through 1033 removed outlier: 3.915A pdb=" N TYR A 999 " --> pdb=" O TYR A 995 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL A1000 " --> pdb=" O LEU A 996 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N ILE A1008 " --> pdb=" O GLY A1004 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N ASP A1009 " --> pdb=" O LYS A1005 " (cutoff:3.500A) Processing helix chain 'A' and resid 1041 through 1046 removed outlier: 3.848A pdb=" N ILE A1046 " --> pdb=" O LEU A1042 " (cutoff:3.500A) Processing helix chain 'A' and resid 1047 through 1053 Processing helix chain 'A' and resid 1089 through 1103 removed outlier: 4.099A pdb=" N ALA A1093 " --> pdb=" O TRP A1089 " (cutoff:3.500A) Processing helix chain 'A' and resid 1106 through 1117 Processing helix chain 'A' and resid 1118 through 1142 removed outlier: 4.598A pdb=" N TYR A1134 " --> pdb=" O LYS A1130 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N GLN A1135 " --> pdb=" O PHE A1131 " (cutoff:3.500A) Processing helix chain 'A' and resid 1147 through 1150 Processing helix chain 'A' and resid 1151 through 1163 removed outlier: 3.679A pdb=" N MET A1158 " --> pdb=" O SER A1154 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N ILE A1159 " --> pdb=" O HIS A1155 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N PHE A1160 " --> pdb=" O MET A1156 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N HIS A1162 " --> pdb=" O MET A1158 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N VAL A1163 " --> pdb=" O ILE A1159 " (cutoff:3.500A) Processing helix chain 'A' and resid 1186 through 1214 removed outlier: 3.515A pdb=" N LEU A1190 " --> pdb=" O THR A1186 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N SER A1214 " --> pdb=" O ASP A1210 " (cutoff:3.500A) Processing helix chain 'A' and resid 1215 through 1240 removed outlier: 3.600A pdb=" N ARG A1240 " --> pdb=" O GLU A1236 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 176 Processing helix chain 'B' and resid 201 through 215 Processing helix chain 'B' and resid 228 through 244 removed outlier: 3.535A pdb=" N LYS B 243 " --> pdb=" O ASP B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 322 Processing helix chain 'B' and resid 342 through 355 removed outlier: 3.990A pdb=" N ILE B 346 " --> pdb=" O GLY B 342 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N SER B 347 " --> pdb=" O PRO B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 379 removed outlier: 3.654A pdb=" N ILE B 373 " --> pdb=" O ARG B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 397 through 402 removed outlier: 3.816A pdb=" N THR B 402 " --> pdb=" O ILE B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 423 removed outlier: 4.077A pdb=" N LEU B 417 " --> pdb=" O LEU B 413 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 453 removed outlier: 3.521A pdb=" N LEU B 445 " --> pdb=" O ASP B 441 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU B 448 " --> pdb=" O ILE B 444 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ASN B 453 " --> pdb=" O LEU B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 467 Processing helix chain 'B' and resid 468 through 475 removed outlier: 3.913A pdb=" N ALA B 472 " --> pdb=" O ARG B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 486 through 498 removed outlier: 3.521A pdb=" N VAL B 497 " --> pdb=" O LEU B 493 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU B 498 " --> pdb=" O ASP B 494 " (cutoff:3.500A) Processing helix chain 'B' and resid 500 through 509 Processing helix chain 'B' and resid 513 through 518 Processing helix chain 'B' and resid 519 through 528 Processing helix chain 'B' and resid 536 through 545 Processing helix chain 'B' and resid 556 through 569 removed outlier: 3.908A pdb=" N GLY B 569 " --> pdb=" O GLU B 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 578 through 587 Processing helix chain 'B' and resid 636 through 648 removed outlier: 3.940A pdb=" N GLU B 640 " --> pdb=" O PHE B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 650 through 659 removed outlier: 4.012A pdb=" N GLN B 659 " --> pdb=" O LEU B 655 " (cutoff:3.500A) Processing helix chain 'B' and resid 663 through 685 Processing helix chain 'B' and resid 690 through 717 removed outlier: 4.654A pdb=" N ASN B 696 " --> pdb=" O SER B 692 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N HIS B 697 " --> pdb=" O GLN B 693 " (cutoff:3.500A) Processing helix chain 'B' and resid 717 through 725 Processing helix chain 'B' and resid 729 through 733 removed outlier: 3.564A pdb=" N TRP B 732 " --> pdb=" O LEU B 729 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N SER B 733 " --> pdb=" O LYS B 730 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 729 through 733' Processing helix chain 'B' and resid 736 through 744 Processing helix chain 'B' and resid 746 through 751 removed outlier: 3.742A pdb=" N ILE B 750 " --> pdb=" O HIS B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 752 through 764 Processing helix chain 'B' and resid 774 through 783 Processing helix chain 'B' and resid 783 through 788 removed outlier: 4.042A pdb=" N LEU B 788 " --> pdb=" O PRO B 784 " (cutoff:3.500A) Processing helix chain 'B' and resid 862 through 869 removed outlier: 3.590A pdb=" N ASN B 869 " --> pdb=" O TYR B 865 " (cutoff:3.500A) Processing helix chain 'B' and resid 870 through 895 Processing helix chain 'B' and resid 902 through 925 Processing helix chain 'B' and resid 930 through 939 removed outlier: 3.508A pdb=" N LYS B 934 " --> pdb=" O LYS B 930 " (cutoff:3.500A) Processing helix chain 'B' and resid 941 through 962 removed outlier: 3.528A pdb=" N VAL B 945 " --> pdb=" O GLU B 941 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU B 962 " --> pdb=" O MET B 958 " (cutoff:3.500A) Processing helix chain 'B' and resid 964 through 985 removed outlier: 4.255A pdb=" N ILE B 980 " --> pdb=" O CYS B 976 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N TYR B 981 " --> pdb=" O VAL B 977 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N TRP B 982 " --> pdb=" O ASN B 978 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 991 removed outlier: 3.877A pdb=" N ILE B 989 " --> pdb=" O ARG B 985 " (cutoff:3.500A) Processing helix chain 'B' and resid 995 through 1033 removed outlier: 3.859A pdb=" N TYR B 999 " --> pdb=" O TYR B 995 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N ILE B1008 " --> pdb=" O GLY B1004 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ASP B1009 " --> pdb=" O LYS B1005 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE B1013 " --> pdb=" O ASP B1009 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ILE B1016 " --> pdb=" O TYR B1012 " (cutoff:3.500A) Processing helix chain 'B' and resid 1041 through 1046 removed outlier: 3.739A pdb=" N ILE B1046 " --> pdb=" O LEU B1042 " (cutoff:3.500A) Processing helix chain 'B' and resid 1047 through 1053 Processing helix chain 'B' and resid 1089 through 1103 removed outlier: 4.107A pdb=" N ALA B1093 " --> pdb=" O TRP B1089 " (cutoff:3.500A) Processing helix chain 'B' and resid 1104 through 1117 removed outlier: 3.520A pdb=" N ASN B1108 " --> pdb=" O ILE B1104 " (cutoff:3.500A) Processing helix chain 'B' and resid 1118 through 1143 removed outlier: 4.585A pdb=" N TYR B1134 " --> pdb=" O LYS B1130 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N GLN B1135 " --> pdb=" O PHE B1131 " (cutoff:3.500A) Processing helix chain 'B' and resid 1147 through 1150 Processing helix chain 'B' and resid 1151 through 1156 Processing helix chain 'B' and resid 1156 through 1163 removed outlier: 3.853A pdb=" N PHE B1160 " --> pdb=" O MET B1156 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N VAL B1163 " --> pdb=" O ILE B1159 " (cutoff:3.500A) Processing helix chain 'B' and resid 1186 through 1214 Processing helix chain 'B' and resid 1215 through 1240 removed outlier: 3.596A pdb=" N ARG B1240 " --> pdb=" O GLU B1236 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 176 Processing helix chain 'C' and resid 201 through 215 Processing helix chain 'C' and resid 228 through 242 removed outlier: 4.195A pdb=" N SER C 242 " --> pdb=" O LYS C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 322 Processing helix chain 'C' and resid 342 through 355 removed outlier: 4.289A pdb=" N ILE C 346 " --> pdb=" O GLY C 342 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N SER C 347 " --> pdb=" O PRO C 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 368 removed outlier: 3.715A pdb=" N GLY C 368 " --> pdb=" O ASP C 365 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 365 through 368' Processing helix chain 'C' and resid 369 through 379 removed outlier: 3.679A pdb=" N ILE C 373 " --> pdb=" O ARG C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 397 through 402 Processing helix chain 'C' and resid 407 through 411 removed outlier: 3.565A pdb=" N ALA C 410 " --> pdb=" O ARG C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 423 removed outlier: 3.962A pdb=" N LYS C 423 " --> pdb=" O GLU C 419 " (cutoff:3.500A) Processing helix chain 'C' and resid 439 through 453 removed outlier: 3.532A pdb=" N LEU C 448 " --> pdb=" O ILE C 444 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ASN C 453 " --> pdb=" O LEU C 449 " (cutoff:3.500A) Processing helix chain 'C' and resid 455 through 467 Processing helix chain 'C' and resid 468 through 475 removed outlier: 3.900A pdb=" N ALA C 472 " --> pdb=" O ARG C 468 " (cutoff:3.500A) Processing helix chain 'C' and resid 486 through 498 removed outlier: 3.521A pdb=" N VAL C 497 " --> pdb=" O LEU C 493 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU C 498 " --> pdb=" O ASP C 494 " (cutoff:3.500A) Processing helix chain 'C' and resid 500 through 509 Processing helix chain 'C' and resid 513 through 518 Processing helix chain 'C' and resid 519 through 528 Processing helix chain 'C' and resid 536 through 545 Processing helix chain 'C' and resid 556 through 569 removed outlier: 3.908A pdb=" N GLY C 569 " --> pdb=" O GLU C 565 " (cutoff:3.500A) Processing helix chain 'C' and resid 574 through 577 Processing helix chain 'C' and resid 578 through 587 Processing helix chain 'C' and resid 636 through 648 removed outlier: 3.939A pdb=" N GLU C 640 " --> pdb=" O PHE C 636 " (cutoff:3.500A) Processing helix chain 'C' and resid 650 through 659 removed outlier: 4.005A pdb=" N GLN C 659 " --> pdb=" O LEU C 655 " (cutoff:3.500A) Processing helix chain 'C' and resid 663 through 685 Processing helix chain 'C' and resid 690 through 717 removed outlier: 3.631A pdb=" N LEU C 695 " --> pdb=" O ILE C 691 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N ASN C 696 " --> pdb=" O SER C 692 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N HIS C 697 " --> pdb=" O GLN C 693 " (cutoff:3.500A) Processing helix chain 'C' and resid 717 through 725 Processing helix chain 'C' and resid 729 through 733 removed outlier: 3.561A pdb=" N TRP C 732 " --> pdb=" O LEU C 729 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N SER C 733 " --> pdb=" O LYS C 730 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 729 through 733' Processing helix chain 'C' and resid 736 through 744 Processing helix chain 'C' and resid 746 through 751 removed outlier: 3.746A pdb=" N ILE C 750 " --> pdb=" O HIS C 746 " (cutoff:3.500A) Processing helix chain 'C' and resid 752 through 764 Processing helix chain 'C' and resid 774 through 783 Processing helix chain 'C' and resid 783 through 788 removed outlier: 4.176A pdb=" N LEU C 788 " --> pdb=" O PRO C 784 " (cutoff:3.500A) Processing helix chain 'C' and resid 862 through 869 removed outlier: 3.583A pdb=" N ASN C 869 " --> pdb=" O TYR C 865 " (cutoff:3.500A) Processing helix chain 'C' and resid 870 through 895 Processing helix chain 'C' and resid 902 through 925 Processing helix chain 'C' and resid 930 through 939 Processing helix chain 'C' and resid 941 through 962 removed outlier: 3.564A pdb=" N VAL C 945 " --> pdb=" O GLU C 941 " (cutoff:3.500A) Processing helix chain 'C' and resid 964 through 985 removed outlier: 4.275A pdb=" N ILE C 980 " --> pdb=" O CYS C 976 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N TYR C 981 " --> pdb=" O VAL C 977 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N TRP C 982 " --> pdb=" O ASN C 978 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 991 removed outlier: 3.772A pdb=" N ILE C 989 " --> pdb=" O ARG C 985 " (cutoff:3.500A) Processing helix chain 'C' and resid 995 through 1006 removed outlier: 3.845A pdb=" N TYR C 999 " --> pdb=" O TYR C 995 " (cutoff:3.500A) Processing helix chain 'C' and resid 1006 through 1033 removed outlier: 4.140A pdb=" N ILE C1016 " --> pdb=" O TYR C1012 " (cutoff:3.500A) Processing helix chain 'C' and resid 1041 through 1046 removed outlier: 3.847A pdb=" N ILE C1046 " --> pdb=" O LEU C1042 " (cutoff:3.500A) Processing helix chain 'C' and resid 1047 through 1053 Processing helix chain 'C' and resid 1059 through 1063 removed outlier: 3.676A pdb=" N ILE C1063 " --> pdb=" O ALA C1060 " (cutoff:3.500A) Processing helix chain 'C' and resid 1089 through 1103 removed outlier: 4.129A pdb=" N ALA C1093 " --> pdb=" O TRP C1089 " (cutoff:3.500A) Processing helix chain 'C' and resid 1106 through 1117 Processing helix chain 'C' and resid 1118 through 1143 removed outlier: 4.597A pdb=" N TYR C1134 " --> pdb=" O LYS C1130 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N GLN C1135 " --> pdb=" O PHE C1131 " (cutoff:3.500A) Processing helix chain 'C' and resid 1147 through 1150 Processing helix chain 'C' and resid 1151 through 1163 removed outlier: 3.687A pdb=" N MET C1158 " --> pdb=" O SER C1154 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N ILE C1159 " --> pdb=" O HIS C1155 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N PHE C1160 " --> pdb=" O MET C1156 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N HIS C1162 " --> pdb=" O MET C1158 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N VAL C1163 " --> pdb=" O ILE C1159 " (cutoff:3.500A) Processing helix chain 'C' and resid 1186 through 1214 removed outlier: 3.529A pdb=" N LEU C1190 " --> pdb=" O THR C1186 " (cutoff:3.500A) Processing helix chain 'C' and resid 1215 through 1240 removed outlier: 3.579A pdb=" N ARG C1240 " --> pdb=" O GLU C1236 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 176 Processing helix chain 'D' and resid 201 through 215 Processing helix chain 'D' and resid 228 through 244 Processing helix chain 'D' and resid 308 through 321 Processing helix chain 'D' and resid 342 through 355 removed outlier: 4.002A pdb=" N ILE D 346 " --> pdb=" O GLY D 342 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N SER D 347 " --> pdb=" O PRO D 343 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 368 Processing helix chain 'D' and resid 369 through 379 removed outlier: 3.668A pdb=" N ILE D 373 " --> pdb=" O ARG D 369 " (cutoff:3.500A) Processing helix chain 'D' and resid 413 through 423 removed outlier: 4.729A pdb=" N GLU D 419 " --> pdb=" O ILE D 415 " (cutoff:3.500A) Processing helix chain 'D' and resid 439 through 453 removed outlier: 3.556A pdb=" N LEU D 448 " --> pdb=" O ILE D 444 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ASN D 453 " --> pdb=" O LEU D 449 " (cutoff:3.500A) Processing helix chain 'D' and resid 455 through 467 Processing helix chain 'D' and resid 468 through 475 removed outlier: 3.909A pdb=" N ALA D 472 " --> pdb=" O ARG D 468 " (cutoff:3.500A) Processing helix chain 'D' and resid 486 through 498 removed outlier: 3.519A pdb=" N VAL D 497 " --> pdb=" O LEU D 493 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU D 498 " --> pdb=" O ASP D 494 " (cutoff:3.500A) Processing helix chain 'D' and resid 500 through 509 Processing helix chain 'D' and resid 513 through 518 Processing helix chain 'D' and resid 519 through 528 Processing helix chain 'D' and resid 536 through 545 Processing helix chain 'D' and resid 556 through 569 removed outlier: 3.906A pdb=" N GLY D 569 " --> pdb=" O GLU D 565 " (cutoff:3.500A) Processing helix chain 'D' and resid 578 through 587 Processing helix chain 'D' and resid 636 through 648 removed outlier: 3.937A pdb=" N GLU D 640 " --> pdb=" O PHE D 636 " (cutoff:3.500A) Processing helix chain 'D' and resid 650 through 659 removed outlier: 4.007A pdb=" N GLN D 659 " --> pdb=" O LEU D 655 " (cutoff:3.500A) Processing helix chain 'D' and resid 663 through 685 Processing helix chain 'D' and resid 690 through 717 removed outlier: 4.846A pdb=" N ASN D 696 " --> pdb=" O SER D 692 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N HIS D 697 " --> pdb=" O GLN D 693 " (cutoff:3.500A) Processing helix chain 'D' and resid 717 through 725 Processing helix chain 'D' and resid 729 through 733 removed outlier: 3.531A pdb=" N TRP D 732 " --> pdb=" O LEU D 729 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N SER D 733 " --> pdb=" O LYS D 730 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 729 through 733' Processing helix chain 'D' and resid 736 through 744 Processing helix chain 'D' and resid 746 through 751 removed outlier: 3.712A pdb=" N ILE D 750 " --> pdb=" O HIS D 746 " (cutoff:3.500A) Processing helix chain 'D' and resid 752 through 764 Processing helix chain 'D' and resid 774 through 783 Processing helix chain 'D' and resid 784 through 790 removed outlier: 3.803A pdb=" N LEU D 788 " --> pdb=" O PRO D 785 " (cutoff:3.500A) Processing helix chain 'D' and resid 862 through 869 removed outlier: 3.622A pdb=" N ASN D 869 " --> pdb=" O TYR D 865 " (cutoff:3.500A) Processing helix chain 'D' and resid 870 through 895 Processing helix chain 'D' and resid 902 through 925 Processing helix chain 'D' and resid 930 through 939 removed outlier: 3.721A pdb=" N VAL D 935 " --> pdb=" O LEU D 931 " (cutoff:3.500A) Processing helix chain 'D' and resid 941 through 962 Processing helix chain 'D' and resid 964 through 985 removed outlier: 4.257A pdb=" N ILE D 980 " --> pdb=" O CYS D 976 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N TYR D 981 " --> pdb=" O VAL D 977 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N TRP D 982 " --> pdb=" O ASN D 978 " (cutoff:3.500A) Processing helix chain 'D' and resid 985 through 991 removed outlier: 3.885A pdb=" N ILE D 989 " --> pdb=" O ARG D 985 " (cutoff:3.500A) Processing helix chain 'D' and resid 995 through 1033 removed outlier: 3.906A pdb=" N TYR D 999 " --> pdb=" O TYR D 995 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL D1000 " --> pdb=" O LEU D 996 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ILE D1008 " --> pdb=" O GLY D1004 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N ASP D1009 " --> pdb=" O LYS D1005 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ILE D1016 " --> pdb=" O TYR D1012 " (cutoff:3.500A) Processing helix chain 'D' and resid 1047 through 1053 Processing helix chain 'D' and resid 1059 through 1063 removed outlier: 3.672A pdb=" N ILE D1063 " --> pdb=" O ALA D1060 " (cutoff:3.500A) Processing helix chain 'D' and resid 1089 through 1103 removed outlier: 4.130A pdb=" N ALA D1093 " --> pdb=" O TRP D1089 " (cutoff:3.500A) Processing helix chain 'D' and resid 1106 through 1117 Processing helix chain 'D' and resid 1118 through 1143 removed outlier: 4.593A pdb=" N TYR D1134 " --> pdb=" O LYS D1130 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N GLN D1135 " --> pdb=" O PHE D1131 " (cutoff:3.500A) Processing helix chain 'D' and resid 1147 through 1150 Processing helix chain 'D' and resid 1151 through 1158 Processing helix chain 'D' and resid 1186 through 1214 Processing helix chain 'D' and resid 1215 through 1240 removed outlier: 3.598A pdb=" N ARG D1240 " --> pdb=" O GLU D1236 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 133 through 134 Processing sheet with id=AA2, first strand: chain 'A' and resid 271 through 275 removed outlier: 3.564A pdb=" N GLU A 145 " --> pdb=" O ARG A 272 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL A 158 " --> pdb=" O PHE A 294 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N THR A 250 " --> pdb=" O HIS A 293 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N ILE A 295 " --> pdb=" O THR A 250 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N GLY A 252 " --> pdb=" O ILE A 295 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N ALA A 297 " --> pdb=" O GLY A 252 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ALA A 254 " --> pdb=" O ALA A 297 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ILE A 186 " --> pdb=" O PHE A 221 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N LEU A 185 " --> pdb=" O VAL A 335 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N LEU A 337 " --> pdb=" O LEU A 185 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N SER A 187 " --> pdb=" O LEU A 337 " (cutoff:3.500A) removed outlier: 8.719A pdb=" N VAL A 362 " --> pdb=" O VAL A 334 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ALA A 336 " --> pdb=" O VAL A 362 " (cutoff:3.500A) removed outlier: 8.233A pdb=" N CYS A 364 " --> pdb=" O ALA A 336 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N ILE A 338 " --> pdb=" O CYS A 364 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N VAL A 361 " --> pdb=" O THR A 428 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N PHE A 430 " --> pdb=" O VAL A 361 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N VAL A 363 " --> pdb=" O PHE A 430 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 133 through 134 Processing sheet with id=AA4, first strand: chain 'B' and resid 271 through 275 removed outlier: 3.549A pdb=" N GLU B 145 " --> pdb=" O ARG B 272 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL B 158 " --> pdb=" O PHE B 294 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N THR B 250 " --> pdb=" O HIS B 293 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N ILE B 295 " --> pdb=" O THR B 250 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N GLY B 252 " --> pdb=" O ILE B 295 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N ALA B 297 " --> pdb=" O GLY B 252 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ALA B 254 " --> pdb=" O ALA B 297 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ILE B 186 " --> pdb=" O PHE B 221 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N LEU B 185 " --> pdb=" O VAL B 335 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N LEU B 337 " --> pdb=" O LEU B 185 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N SER B 187 " --> pdb=" O LEU B 337 " (cutoff:3.500A) removed outlier: 8.746A pdb=" N VAL B 362 " --> pdb=" O VAL B 334 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ALA B 336 " --> pdb=" O VAL B 362 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 133 through 134 Processing sheet with id=AA6, first strand: chain 'C' and resid 271 through 275 removed outlier: 3.558A pdb=" N GLU C 145 " --> pdb=" O ARG C 272 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL C 158 " --> pdb=" O PHE C 294 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ILE C 186 " --> pdb=" O PHE C 221 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N LEU C 185 " --> pdb=" O VAL C 335 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N LEU C 337 " --> pdb=" O LEU C 185 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N SER C 187 " --> pdb=" O LEU C 337 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 133 through 134 Processing sheet with id=AA8, first strand: chain 'D' and resid 271 through 275 removed outlier: 3.542A pdb=" N GLU D 145 " --> pdb=" O ARG D 272 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL D 158 " --> pdb=" O PHE D 294 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N THR D 250 " --> pdb=" O HIS D 293 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N ILE D 295 " --> pdb=" O THR D 250 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N GLY D 252 " --> pdb=" O ILE D 295 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N ALA D 297 " --> pdb=" O GLY D 252 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ALA D 254 " --> pdb=" O ALA D 297 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ILE D 186 " --> pdb=" O PHE D 221 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N LEU D 185 " --> pdb=" O VAL D 335 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N LEU D 337 " --> pdb=" O LEU D 185 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N SER D 187 " --> pdb=" O LEU D 337 " (cutoff:3.500A) 1735 hydrogen bonds defined for protein. 5130 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: 11.57 Time building geometry restraints manager: 13.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 9954 1.34 - 1.46: 6682 1.46 - 1.58: 15200 1.58 - 1.69: 0 1.69 - 1.81: 402 Bond restraints: 32238 Sorted by residual: bond pdb=" CA THR D 408 " pdb=" CB THR D 408 " ideal model delta sigma weight residual 1.530 1.548 -0.018 1.69e-02 3.50e+03 1.17e+00 bond pdb=" C PRO D1148 " pdb=" N PRO D1149 " ideal model delta sigma weight residual 1.335 1.347 -0.013 1.19e-02 7.06e+03 1.13e+00 bond pdb=" C GLN D 198 " pdb=" N PRO D 199 " ideal model delta sigma weight residual 1.332 1.344 -0.013 1.26e-02 6.30e+03 9.85e-01 bond pdb=" C TYR A1012 " pdb=" O TYR A1012 " ideal model delta sigma weight residual 1.236 1.247 -0.011 1.15e-02 7.56e+03 8.62e-01 bond pdb=" C PRO C1148 " pdb=" N PRO C1149 " ideal model delta sigma weight residual 1.335 1.346 -0.012 1.28e-02 6.10e+03 8.42e-01 ... (remaining 32233 not shown) Histogram of bond angle deviations from ideal: 99.63 - 106.54: 936 106.54 - 113.44: 17847 113.44 - 120.35: 12348 120.35 - 127.26: 12091 127.26 - 134.17: 381 Bond angle restraints: 43603 Sorted by residual: angle pdb=" C VAL A 688 " pdb=" N ASP A 689 " pdb=" CA ASP A 689 " ideal model delta sigma weight residual 121.54 128.49 -6.95 1.91e+00 2.74e-01 1.32e+01 angle pdb=" C VAL B 688 " pdb=" N ASP B 689 " pdb=" CA ASP B 689 " ideal model delta sigma weight residual 121.54 127.83 -6.29 1.91e+00 2.74e-01 1.09e+01 angle pdb=" N PRO B1148 " pdb=" CA PRO B1148 " pdb=" C PRO B1148 " ideal model delta sigma weight residual 110.70 114.68 -3.98 1.22e+00 6.72e-01 1.06e+01 angle pdb=" N PRO A1148 " pdb=" CA PRO A1148 " pdb=" C PRO A1148 " ideal model delta sigma weight residual 110.70 114.51 -3.81 1.22e+00 6.72e-01 9.74e+00 angle pdb=" N PRO C1148 " pdb=" CA PRO C1148 " pdb=" C PRO C1148 " ideal model delta sigma weight residual 110.70 114.46 -3.76 1.22e+00 6.72e-01 9.49e+00 ... (remaining 43598 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.42: 17708 15.42 - 30.83: 1360 30.83 - 46.25: 366 46.25 - 61.66: 99 61.66 - 77.08: 4 Dihedral angle restraints: 19537 sinusoidal: 8187 harmonic: 11350 Sorted by residual: dihedral pdb=" CA THR D 356 " pdb=" C THR D 356 " pdb=" N PRO D 357 " pdb=" CA PRO D 357 " ideal model delta harmonic sigma weight residual 180.00 158.22 21.78 0 5.00e+00 4.00e-02 1.90e+01 dihedral pdb=" CA THR C 356 " pdb=" C THR C 356 " pdb=" N PRO C 357 " pdb=" CA PRO C 357 " ideal model delta harmonic sigma weight residual 180.00 158.75 21.25 0 5.00e+00 4.00e-02 1.81e+01 dihedral pdb=" CA THR A 356 " pdb=" C THR A 356 " pdb=" N PRO A 357 " pdb=" CA PRO A 357 " ideal model delta harmonic sigma weight residual 180.00 159.20 20.80 0 5.00e+00 4.00e-02 1.73e+01 ... (remaining 19534 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 2991 0.032 - 0.065: 1440 0.065 - 0.097: 314 0.097 - 0.129: 142 0.129 - 0.162: 10 Chirality restraints: 4897 Sorted by residual: chirality pdb=" C08 9Z9 A1402 " pdb=" C07 9Z9 A1402 " pdb=" C09 9Z9 A1402 " pdb=" C11 9Z9 A1402 " both_signs ideal model delta sigma weight residual False 2.45 2.62 -0.16 2.00e-01 2.50e+01 6.53e-01 chirality pdb=" C08 9Z9 B1401 " pdb=" C07 9Z9 B1401 " pdb=" C09 9Z9 B1401 " pdb=" C11 9Z9 B1401 " both_signs ideal model delta sigma weight residual False 2.45 2.61 -0.16 2.00e-01 2.50e+01 6.32e-01 chirality pdb=" C08 9Z9 A1401 " pdb=" C07 9Z9 A1401 " pdb=" C09 9Z9 A1401 " pdb=" C11 9Z9 A1401 " both_signs ideal model delta sigma weight residual False 2.45 2.61 -0.16 2.00e-01 2.50e+01 6.21e-01 ... (remaining 4894 not shown) Planarity restraints: 5416 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 784 " -0.038 5.00e-02 4.00e+02 5.74e-02 5.27e+00 pdb=" N PRO A 785 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO A 785 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 785 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C 784 " 0.038 5.00e-02 4.00e+02 5.70e-02 5.19e+00 pdb=" N PRO C 785 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO C 785 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 785 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO D 784 " -0.038 5.00e-02 4.00e+02 5.69e-02 5.18e+00 pdb=" N PRO D 785 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO D 785 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO D 785 " -0.032 5.00e-02 4.00e+02 ... (remaining 5413 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 5472 2.76 - 3.30: 31041 3.30 - 3.83: 50871 3.83 - 4.37: 57058 4.37 - 4.90: 101161 Nonbonded interactions: 245603 Sorted by model distance: nonbonded pdb=" O HIS A 240 " pdb=" OG SER A 244 " model vdw 2.230 3.040 nonbonded pdb=" O GLU C 922 " pdb=" OG SER C 926 " model vdw 2.248 3.040 nonbonded pdb=" O ILE C 399 " pdb=" OG1 THR C 402 " model vdw 2.276 3.040 nonbonded pdb=" OD1 ASP D 947 " pdb=" OH TYR D 981 " model vdw 2.286 3.040 nonbonded pdb=" OD1 ASP A 947 " pdb=" OH TYR A 981 " model vdw 2.291 3.040 ... (remaining 245598 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 129 through 1059 or resid 1085 through 1243)) selection = (chain 'B' and (resid 129 through 1059 or resid 1085 through 1243)) selection = (chain 'C' and (resid 129 through 1059 or resid 1085 through 1243)) selection = (chain 'D' and (resid 129 through 1059 or resid 1085 through 1243)) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.390 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: 0.020 Extract box with map and model: 1.170 Check model and map are aligned: 0.230 Set scattering table: 0.280 Process input model: 80.730 Find NCS groups from input model: 1.960 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 88.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 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 : 0.004 0.035 32238 Z= 0.227 Angle : 0.541 8.860 43603 Z= 0.288 Chirality : 0.040 0.162 4897 Planarity : 0.004 0.057 5416 Dihedral : 12.282 77.077 12197 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 2.92 % Allowed : 8.26 % Favored : 88.82 % 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: 0.57 (0.14), residues: 3770 helix: 1.26 (0.11), residues: 2343 sheet: 0.03 (0.37), residues: 222 loop : -1.29 (0.17), residues: 1205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 763 HIS 0.003 0.001 HIS C 240 PHE 0.011 0.001 PHE B 792 TYR 0.010 0.001 TYR A1048 ARG 0.004 0.000 ARG A 327 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7540 Ramachandran restraints generated. 3770 Oldfield, 0 Emsley, 3770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7540 Ramachandran restraints generated. 3770 Oldfield, 0 Emsley, 3770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 582 residues out of total 3391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 483 time to evaluate : 3.695 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 266 ILE cc_start: 0.5895 (OUTLIER) cc_final: 0.5352 (mm) REVERT: A 479 TYR cc_start: 0.5170 (OUTLIER) cc_final: 0.3868 (m-80) REVERT: A 665 MET cc_start: 0.7824 (mtm) cc_final: 0.7423 (mtm) REVERT: A 669 LEU cc_start: 0.9241 (OUTLIER) cc_final: 0.8812 (mm) REVERT: A 772 ASN cc_start: 0.8448 (t0) cc_final: 0.8221 (p0) REVERT: A 778 ILE cc_start: 0.9286 (pt) cc_final: 0.9009 (mt) REVERT: A 924 LEU cc_start: 0.8889 (pp) cc_final: 0.8653 (mt) REVERT: A 925 MET cc_start: 0.7778 (ppp) cc_final: 0.7475 (ppp) REVERT: A 932 LEU cc_start: 0.9255 (tt) cc_final: 0.8951 (mm) REVERT: A 1010 MET cc_start: 0.7232 (tmm) cc_final: 0.6821 (tmm) REVERT: A 1022 MET cc_start: 0.7398 (mtm) cc_final: 0.7154 (mtp) REVERT: A 1049 MET cc_start: 0.6665 (mpp) cc_final: 0.6369 (mpp) REVERT: A 1051 TYR cc_start: 0.8073 (t80) cc_final: 0.6875 (t80) REVERT: A 1055 TYR cc_start: 0.7025 (m-10) cc_final: 0.6342 (m-10) REVERT: A 1103 ASN cc_start: 0.7606 (m-40) cc_final: 0.7147 (m110) REVERT: A 1230 MET cc_start: 0.8487 (ttm) cc_final: 0.8008 (ttm) REVERT: B 409 GLN cc_start: 0.6454 (tp40) cc_final: 0.6074 (mm-40) REVERT: B 412 HIS cc_start: 0.3239 (OUTLIER) cc_final: 0.1783 (m-70) REVERT: B 665 MET cc_start: 0.7784 (mtm) cc_final: 0.7394 (mtm) REVERT: B 669 LEU cc_start: 0.9229 (OUTLIER) cc_final: 0.8772 (mm) REVERT: B 764 MET cc_start: 0.8991 (mmt) cc_final: 0.8725 (mmt) REVERT: B 925 MET cc_start: 0.7509 (ppp) cc_final: 0.7242 (ppp) REVERT: B 948 LEU cc_start: 0.8711 (mt) cc_final: 0.8488 (mt) REVERT: B 958 MET cc_start: 0.6122 (mmm) cc_final: 0.5921 (tmm) REVERT: B 1022 MET cc_start: 0.7154 (mtp) cc_final: 0.6653 (mtm) REVERT: B 1053 MET cc_start: 0.7942 (mtt) cc_final: 0.7618 (mtt) REVERT: B 1095 MET cc_start: 0.7501 (tpp) cc_final: 0.7239 (tpp) REVERT: B 1100 LEU cc_start: 0.9134 (tp) cc_final: 0.8924 (tt) REVERT: B 1230 MET cc_start: 0.8456 (ttm) cc_final: 0.7911 (ttm) REVERT: C 266 ILE cc_start: 0.5838 (OUTLIER) cc_final: 0.5289 (mm) REVERT: C 633 HIS cc_start: 0.6296 (m90) cc_final: 0.6058 (m90) REVERT: C 665 MET cc_start: 0.7745 (mtm) cc_final: 0.7367 (mtm) REVERT: C 669 LEU cc_start: 0.9228 (OUTLIER) cc_final: 0.8764 (mm) REVERT: C 726 THR cc_start: 0.9215 (OUTLIER) cc_final: 0.9011 (m) REVERT: C 769 MET cc_start: 0.7922 (ttm) cc_final: 0.7677 (ttp) REVERT: C 772 ASN cc_start: 0.8778 (t0) cc_final: 0.8491 (p0) REVERT: C 778 ILE cc_start: 0.9143 (pt) cc_final: 0.8870 (mt) REVERT: C 958 MET cc_start: 0.6526 (mmm) cc_final: 0.6258 (tmm) REVERT: C 1053 MET cc_start: 0.7945 (mtt) cc_final: 0.7624 (mtt) REVERT: C 1058 VAL cc_start: 0.8256 (OUTLIER) cc_final: 0.7902 (p) REVERT: C 1095 MET cc_start: 0.7382 (tpp) cc_final: 0.7102 (tpp) REVERT: C 1230 MET cc_start: 0.8402 (ttm) cc_final: 0.7939 (ttp) REVERT: D 240 HIS cc_start: 0.7572 (t-90) cc_final: 0.7318 (t70) REVERT: D 266 ILE cc_start: 0.5843 (OUTLIER) cc_final: 0.5302 (mm) REVERT: D 411 GLN cc_start: 0.5565 (OUTLIER) cc_final: 0.5302 (tp-100) REVERT: D 665 MET cc_start: 0.7745 (mtm) cc_final: 0.7363 (mtm) REVERT: D 669 LEU cc_start: 0.9216 (OUTLIER) cc_final: 0.8779 (mm) REVERT: D 764 MET cc_start: 0.9091 (mmt) cc_final: 0.8711 (mmt) REVERT: D 778 ILE cc_start: 0.9177 (pt) cc_final: 0.8874 (mt) REVERT: D 924 LEU cc_start: 0.8752 (pp) cc_final: 0.8383 (mp) REVERT: D 930 LYS cc_start: 0.8474 (OUTLIER) cc_final: 0.8269 (tptt) REVERT: D 958 MET cc_start: 0.6797 (mmm) cc_final: 0.6595 (mmm) REVERT: D 1010 MET cc_start: 0.7222 (tmm) cc_final: 0.6867 (tmm) REVERT: D 1022 MET cc_start: 0.7308 (mtm) cc_final: 0.7082 (mtp) REVERT: D 1051 TYR cc_start: 0.8055 (t80) cc_final: 0.7831 (t80) REVERT: D 1053 MET cc_start: 0.7875 (mtt) cc_final: 0.7644 (mtt) REVERT: D 1055 TYR cc_start: 0.7236 (m-80) cc_final: 0.7032 (m-10) REVERT: D 1058 VAL cc_start: 0.8327 (OUTLIER) cc_final: 0.7916 (p) REVERT: D 1095 MET cc_start: 0.7637 (tpp) cc_final: 0.7288 (tpp) REVERT: D 1099 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8597 (mp) REVERT: D 1103 ASN cc_start: 0.7419 (m-40) cc_final: 0.7111 (m110) outliers start: 99 outliers final: 45 residues processed: 560 average time/residue: 0.4287 time to fit residues: 384.5451 Evaluate side-chains 431 residues out of total 3391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 371 time to evaluate : 3.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 376 PHE Chi-restraints excluded: chain A residue 479 TYR Chi-restraints excluded: chain A residue 502 ASP Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 690 ASP Chi-restraints excluded: chain A residue 794 ASN Chi-restraints excluded: chain A residue 956 VAL Chi-restraints excluded: chain A residue 983 TYR Chi-restraints excluded: chain A residue 1009 ASP Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain A residue 1155 HIS Chi-restraints excluded: chain A residue 1186 THR Chi-restraints excluded: chain B residue 240 HIS Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 327 ARG Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain B residue 502 ASP Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 690 ASP Chi-restraints excluded: chain B residue 956 VAL Chi-restraints excluded: chain B residue 983 TYR Chi-restraints excluded: chain B residue 1150 LEU Chi-restraints excluded: chain B residue 1155 HIS Chi-restraints excluded: chain C residue 266 ILE Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 376 PHE Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 440 ILE Chi-restraints excluded: chain C residue 502 ASP Chi-restraints excluded: chain C residue 549 LEU Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain C residue 688 VAL Chi-restraints excluded: chain C residue 726 THR Chi-restraints excluded: chain C residue 775 LEU Chi-restraints excluded: chain C residue 794 ASN Chi-restraints excluded: chain C residue 956 VAL Chi-restraints excluded: chain C residue 983 TYR Chi-restraints excluded: chain C residue 1009 ASP Chi-restraints excluded: chain C residue 1014 VAL Chi-restraints excluded: chain C residue 1058 VAL Chi-restraints excluded: chain C residue 1155 HIS Chi-restraints excluded: chain C residue 1186 THR Chi-restraints excluded: chain D residue 266 ILE Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 376 PHE Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 411 GLN Chi-restraints excluded: chain D residue 414 PHE Chi-restraints excluded: chain D residue 502 ASP Chi-restraints excluded: chain D residue 669 LEU Chi-restraints excluded: chain D residue 775 LEU Chi-restraints excluded: chain D residue 794 ASN Chi-restraints excluded: chain D residue 930 LYS Chi-restraints excluded: chain D residue 956 VAL Chi-restraints excluded: chain D residue 983 TYR Chi-restraints excluded: chain D residue 1014 VAL Chi-restraints excluded: chain D residue 1058 VAL Chi-restraints excluded: chain D residue 1099 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 324 optimal weight: 0.9990 chunk 291 optimal weight: 5.9990 chunk 161 optimal weight: 1.9990 chunk 99 optimal weight: 5.9990 chunk 196 optimal weight: 3.9990 chunk 155 optimal weight: 0.9980 chunk 300 optimal weight: 1.9990 chunk 116 optimal weight: 4.9990 chunk 183 optimal weight: 2.9990 chunk 224 optimal weight: 0.6980 chunk 348 optimal weight: 4.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 ASN A 275 GLN A 279 ASN A 575 ASN A 772 ASN A 933 GLN A 940 GLN A 965 GLN A1115 ASN A1161 GLN B 275 GLN B 279 ASN ** B 933 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 965 GLN B1115 ASN B1161 GLN C 275 GLN C 279 ASN C 531 HIS C 575 ASN C 772 ASN C 965 GLN ** C1062 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1115 ASN C1161 GLN D 275 GLN D 279 ASN D 965 GLN D1062 GLN D1115 ASN ** D1155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1161 GLN D1199 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.1257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 32238 Z= 0.250 Angle : 0.583 10.189 43603 Z= 0.292 Chirality : 0.040 0.193 4897 Planarity : 0.004 0.053 5416 Dihedral : 7.579 59.812 4688 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.89 % Allowed : 12.39 % Favored : 84.72 % 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: 1.08 (0.14), residues: 3770 helix: 1.70 (0.11), residues: 2402 sheet: 0.30 (0.37), residues: 219 loop : -1.35 (0.17), residues: 1149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 763 HIS 0.004 0.001 HIS A 151 PHE 0.020 0.001 PHE C1047 TYR 0.011 0.001 TYR C 714 ARG 0.005 0.000 ARG A1211 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7540 Ramachandran restraints generated. 3770 Oldfield, 0 Emsley, 3770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7540 Ramachandran restraints generated. 3770 Oldfield, 0 Emsley, 3770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 3391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 383 time to evaluate : 3.758 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 479 TYR cc_start: 0.5408 (OUTLIER) cc_final: 0.4057 (m-80) REVERT: A 665 MET cc_start: 0.7692 (mtm) cc_final: 0.7346 (mtm) REVERT: A 669 LEU cc_start: 0.9256 (OUTLIER) cc_final: 0.8866 (mm) REVERT: A 778 ILE cc_start: 0.9263 (pt) cc_final: 0.9056 (mt) REVERT: A 788 LEU cc_start: 0.7676 (OUTLIER) cc_final: 0.7324 (pp) REVERT: A 925 MET cc_start: 0.7677 (ppp) cc_final: 0.7286 (ppp) REVERT: A 1051 TYR cc_start: 0.8115 (t80) cc_final: 0.6830 (t80) REVERT: A 1055 TYR cc_start: 0.7066 (m-10) cc_final: 0.6310 (m-10) REVERT: A 1103 ASN cc_start: 0.7534 (m-40) cc_final: 0.7157 (m110) REVERT: A 1230 MET cc_start: 0.8540 (ttm) cc_final: 0.8155 (ttm) REVERT: B 266 ILE cc_start: 0.6166 (OUTLIER) cc_final: 0.5622 (mm) REVERT: B 412 HIS cc_start: 0.2964 (OUTLIER) cc_final: 0.1767 (m-70) REVERT: B 665 MET cc_start: 0.7667 (mtm) cc_final: 0.7316 (mtm) REVERT: B 669 LEU cc_start: 0.9252 (OUTLIER) cc_final: 0.8836 (mm) REVERT: B 764 MET cc_start: 0.8990 (mmt) cc_final: 0.8728 (mmt) REVERT: B 925 MET cc_start: 0.7474 (ppp) cc_final: 0.7167 (ppp) REVERT: B 948 LEU cc_start: 0.8701 (mt) cc_final: 0.8461 (mt) REVERT: B 1049 MET cc_start: 0.6768 (mpp) cc_final: 0.6552 (mpp) REVERT: B 1053 MET cc_start: 0.7909 (mtt) cc_final: 0.7582 (mtt) REVERT: B 1095 MET cc_start: 0.7498 (tpp) cc_final: 0.7115 (tpp) REVERT: B 1230 MET cc_start: 0.8492 (ttm) cc_final: 0.8145 (ttm) REVERT: C 479 TYR cc_start: 0.5056 (OUTLIER) cc_final: 0.3461 (m-80) REVERT: C 665 MET cc_start: 0.7627 (mtm) cc_final: 0.7283 (mtm) REVERT: C 669 LEU cc_start: 0.9261 (OUTLIER) cc_final: 0.8836 (mm) REVERT: C 1053 MET cc_start: 0.7947 (mtt) cc_final: 0.7586 (mtt) REVERT: C 1095 MET cc_start: 0.7561 (tpp) cc_final: 0.7241 (tpp) REVERT: C 1230 MET cc_start: 0.8454 (ttm) cc_final: 0.7886 (ttm) REVERT: D 633 HIS cc_start: 0.5973 (m90) cc_final: 0.5688 (m90) REVERT: D 665 MET cc_start: 0.7631 (mtm) cc_final: 0.7289 (mtm) REVERT: D 669 LEU cc_start: 0.9241 (OUTLIER) cc_final: 0.8837 (mm) REVERT: D 764 MET cc_start: 0.9031 (mmt) cc_final: 0.8675 (mmt) REVERT: D 778 ILE cc_start: 0.9212 (pt) cc_final: 0.8965 (mt) REVERT: D 788 LEU cc_start: 0.7771 (OUTLIER) cc_final: 0.7384 (pp) REVERT: D 1010 MET cc_start: 0.7079 (tmm) cc_final: 0.6832 (tmm) REVERT: D 1051 TYR cc_start: 0.8121 (t80) cc_final: 0.7849 (t80) REVERT: D 1058 VAL cc_start: 0.8129 (OUTLIER) cc_final: 0.7811 (p) REVERT: D 1095 MET cc_start: 0.7740 (tpp) cc_final: 0.7271 (tpp) REVERT: D 1099 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8500 (mp) REVERT: D 1103 ASN cc_start: 0.7315 (m-40) cc_final: 0.7051 (m110) outliers start: 98 outliers final: 39 residues processed: 452 average time/residue: 0.3914 time to fit residues: 292.0361 Evaluate side-chains 407 residues out of total 3391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 356 time to evaluate : 3.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 479 TYR Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 690 ASP Chi-restraints excluded: chain A residue 775 LEU Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 794 ASN Chi-restraints excluded: chain A residue 956 VAL Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain A residue 1059 PHE Chi-restraints excluded: chain A residue 1115 ASN Chi-restraints excluded: chain A residue 1150 LEU Chi-restraints excluded: chain B residue 240 HIS Chi-restraints excluded: chain B residue 266 ILE Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 690 ASP Chi-restraints excluded: chain B residue 794 ASN Chi-restraints excluded: chain B residue 956 VAL Chi-restraints excluded: chain B residue 983 TYR Chi-restraints excluded: chain B residue 1021 LEU Chi-restraints excluded: chain B residue 1150 LEU Chi-restraints excluded: chain B residue 1155 HIS Chi-restraints excluded: chain C residue 399 ILE Chi-restraints excluded: chain C residue 432 MET Chi-restraints excluded: chain C residue 440 ILE Chi-restraints excluded: chain C residue 479 TYR Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain C residue 688 VAL Chi-restraints excluded: chain C residue 775 LEU Chi-restraints excluded: chain C residue 794 ASN Chi-restraints excluded: chain C residue 956 VAL Chi-restraints excluded: chain C residue 983 TYR Chi-restraints excluded: chain C residue 1014 VAL Chi-restraints excluded: chain C residue 1021 LEU Chi-restraints excluded: chain C residue 1115 ASN Chi-restraints excluded: chain D residue 152 SER Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 414 PHE Chi-restraints excluded: chain D residue 669 LEU Chi-restraints excluded: chain D residue 775 LEU Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 794 ASN Chi-restraints excluded: chain D residue 931 LEU Chi-restraints excluded: chain D residue 956 VAL Chi-restraints excluded: chain D residue 983 TYR Chi-restraints excluded: chain D residue 1014 VAL Chi-restraints excluded: chain D residue 1021 LEU Chi-restraints excluded: chain D residue 1058 VAL Chi-restraints excluded: chain D residue 1062 GLN Chi-restraints excluded: chain D residue 1099 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 193 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 290 optimal weight: 7.9990 chunk 237 optimal weight: 1.9990 chunk 96 optimal weight: 7.9990 chunk 349 optimal weight: 3.9990 chunk 377 optimal weight: 4.9990 chunk 311 optimal weight: 6.9990 chunk 346 optimal weight: 6.9990 chunk 119 optimal weight: 5.9990 chunk 280 optimal weight: 10.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 510 ASN A 772 ASN B 510 ASN B 575 ASN B1115 ASN C 510 ASN ** C1062 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1115 ASN C1126 ASN D 510 ASN D 575 ASN ** D1062 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.1791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.052 32238 Z= 0.561 Angle : 0.750 7.524 43603 Z= 0.384 Chirality : 0.047 0.200 4897 Planarity : 0.005 0.057 5416 Dihedral : 7.705 80.198 4637 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 3.83 % Allowed : 14.51 % Favored : 81.66 % 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: 0.59 (0.14), residues: 3770 helix: 1.32 (0.11), residues: 2407 sheet: -0.12 (0.35), residues: 224 loop : -1.49 (0.17), residues: 1139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 763 HIS 0.009 0.001 HIS D 240 PHE 0.026 0.002 PHE A 376 TYR 0.014 0.002 TYR A 981 ARG 0.007 0.001 ARG A1143 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7540 Ramachandran restraints generated. 3770 Oldfield, 0 Emsley, 3770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7540 Ramachandran restraints generated. 3770 Oldfield, 0 Emsley, 3770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 505 residues out of total 3391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 375 time to evaluate : 3.974 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 352 TYR cc_start: 0.7730 (OUTLIER) cc_final: 0.7398 (m-10) REVERT: A 376 PHE cc_start: 0.6871 (t80) cc_final: 0.6605 (t80) REVERT: A 479 TYR cc_start: 0.5100 (OUTLIER) cc_final: 0.3994 (m-80) REVERT: A 665 MET cc_start: 0.7901 (mtm) cc_final: 0.7527 (mtm) REVERT: A 669 LEU cc_start: 0.9258 (OUTLIER) cc_final: 0.8705 (mm) REVERT: A 788 LEU cc_start: 0.7813 (OUTLIER) cc_final: 0.7445 (pp) REVERT: A 1051 TYR cc_start: 0.8183 (t80) cc_final: 0.6923 (t80) REVERT: A 1055 TYR cc_start: 0.7034 (m-10) cc_final: 0.6116 (m-10) REVERT: B 412 HIS cc_start: 0.3494 (OUTLIER) cc_final: 0.2691 (m-70) REVERT: B 665 MET cc_start: 0.7867 (mtm) cc_final: 0.7491 (mtm) REVERT: B 669 LEU cc_start: 0.9255 (OUTLIER) cc_final: 0.8679 (mm) REVERT: B 925 MET cc_start: 0.7627 (ppp) cc_final: 0.7320 (ppp) REVERT: B 948 LEU cc_start: 0.8760 (mt) cc_final: 0.8489 (mt) REVERT: B 1051 TYR cc_start: 0.8186 (t80) cc_final: 0.7051 (t80) REVERT: B 1053 MET cc_start: 0.7987 (mtt) cc_final: 0.7686 (mtt) REVERT: B 1055 TYR cc_start: 0.7002 (m-10) cc_final: 0.6500 (m-10) REVERT: B 1095 MET cc_start: 0.7708 (tpp) cc_final: 0.7398 (tpp) REVERT: B 1155 HIS cc_start: 0.5884 (OUTLIER) cc_final: 0.5569 (t-170) REVERT: B 1230 MET cc_start: 0.8676 (ttm) cc_final: 0.8449 (ttm) REVERT: C 376 PHE cc_start: 0.6797 (t80) cc_final: 0.6432 (t80) REVERT: C 400 GLN cc_start: 0.5352 (mp10) cc_final: 0.4863 (mp10) REVERT: C 432 MET cc_start: 0.6241 (OUTLIER) cc_final: 0.5922 (mtt) REVERT: C 479 TYR cc_start: 0.5224 (OUTLIER) cc_final: 0.3825 (m-80) REVERT: C 665 MET cc_start: 0.7840 (mtm) cc_final: 0.7469 (mtm) REVERT: C 669 LEU cc_start: 0.9268 (OUTLIER) cc_final: 0.8681 (mm) REVERT: C 1053 MET cc_start: 0.8011 (mtt) cc_final: 0.7675 (mtm) REVERT: C 1095 MET cc_start: 0.7730 (tpp) cc_final: 0.7284 (tpp) REVERT: C 1230 MET cc_start: 0.8740 (ttm) cc_final: 0.8386 (ttm) REVERT: D 633 HIS cc_start: 0.6428 (m90) cc_final: 0.6223 (m90) REVERT: D 665 MET cc_start: 0.7854 (mtm) cc_final: 0.7496 (mtm) REVERT: D 669 LEU cc_start: 0.9259 (OUTLIER) cc_final: 0.8699 (mm) REVERT: D 764 MET cc_start: 0.9161 (mmt) cc_final: 0.8932 (mmt) REVERT: D 788 LEU cc_start: 0.7901 (OUTLIER) cc_final: 0.7497 (pp) REVERT: D 1010 MET cc_start: 0.7502 (tmm) cc_final: 0.7120 (tmm) REVERT: D 1051 TYR cc_start: 0.8271 (t80) cc_final: 0.8057 (t80) REVERT: D 1095 MET cc_start: 0.7910 (tpp) cc_final: 0.7707 (tpp) REVERT: D 1099 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8606 (mp) REVERT: D 1103 ASN cc_start: 0.7304 (m-40) cc_final: 0.7041 (m110) REVERT: D 1150 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8299 (mp) outliers start: 130 outliers final: 62 residues processed: 474 average time/residue: 0.3778 time to fit residues: 302.1817 Evaluate side-chains 435 residues out of total 3391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 359 time to evaluate : 3.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 205 PHE Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 352 TYR Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 479 TYR Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 690 ASP Chi-restraints excluded: chain A residue 775 LEU Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 794 ASN Chi-restraints excluded: chain A residue 956 VAL Chi-restraints excluded: chain A residue 983 TYR Chi-restraints excluded: chain A residue 1022 MET Chi-restraints excluded: chain A residue 1059 PHE Chi-restraints excluded: chain A residue 1151 ILE Chi-restraints excluded: chain A residue 1155 HIS Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 235 ASP Chi-restraints excluded: chain B residue 240 HIS Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain B residue 646 VAL Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 690 ASP Chi-restraints excluded: chain B residue 794 ASN Chi-restraints excluded: chain B residue 956 VAL Chi-restraints excluded: chain B residue 983 TYR Chi-restraints excluded: chain B residue 1021 LEU Chi-restraints excluded: chain B residue 1115 ASN Chi-restraints excluded: chain B residue 1155 HIS Chi-restraints excluded: chain B residue 1178 ASP Chi-restraints excluded: chain B residue 1242 HIS Chi-restraints excluded: chain C residue 152 SER Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 373 ILE Chi-restraints excluded: chain C residue 399 ILE Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 418 MET Chi-restraints excluded: chain C residue 432 MET Chi-restraints excluded: chain C residue 440 ILE Chi-restraints excluded: chain C residue 479 TYR Chi-restraints excluded: chain C residue 646 VAL Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain C residue 688 VAL Chi-restraints excluded: chain C residue 775 LEU Chi-restraints excluded: chain C residue 794 ASN Chi-restraints excluded: chain C residue 956 VAL Chi-restraints excluded: chain C residue 983 TYR Chi-restraints excluded: chain C residue 1021 LEU Chi-restraints excluded: chain C residue 1022 MET Chi-restraints excluded: chain C residue 1115 ASN Chi-restraints excluded: chain C residue 1155 HIS Chi-restraints excluded: chain C residue 1242 HIS Chi-restraints excluded: chain D residue 152 SER Chi-restraints excluded: chain D residue 168 LEU Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 373 ILE Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 414 PHE Chi-restraints excluded: chain D residue 646 VAL Chi-restraints excluded: chain D residue 669 LEU Chi-restraints excluded: chain D residue 775 LEU Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 794 ASN Chi-restraints excluded: chain D residue 956 VAL Chi-restraints excluded: chain D residue 983 TYR Chi-restraints excluded: chain D residue 1014 VAL Chi-restraints excluded: chain D residue 1021 LEU Chi-restraints excluded: chain D residue 1022 MET Chi-restraints excluded: chain D residue 1099 LEU Chi-restraints excluded: chain D residue 1150 LEU Chi-restraints excluded: chain D residue 1242 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 345 optimal weight: 0.9990 chunk 262 optimal weight: 1.9990 chunk 181 optimal weight: 0.6980 chunk 38 optimal weight: 0.6980 chunk 166 optimal weight: 0.9980 chunk 234 optimal weight: 2.9990 chunk 350 optimal weight: 0.9980 chunk 371 optimal weight: 0.6980 chunk 183 optimal weight: 4.9990 chunk 332 optimal weight: 1.9990 chunk 100 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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: