Starting phenix.real_space_refine (version: 1.21rc1) on Wed Apr 26 12:11:35 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qdy_13927/04_2023/7qdy_13927.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qdy_13927/04_2023/7qdy_13927.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qdy_13927/04_2023/7qdy_13927.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qdy_13927/04_2023/7qdy_13927.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qdy_13927/04_2023/7qdy_13927.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qdy_13927/04_2023/7qdy_13927.pdb" } resolution = 3.1 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= 0.002 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: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 107 5.16 5 C 14494 2.51 5 N 3981 2.21 5 O 4336 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 20": "NH1" <-> "NH2" Residue "A GLU 40": "OE1" <-> "OE2" Residue "A GLU 59": "OE1" <-> "OE2" Residue "A GLU 75": "OE1" <-> "OE2" Residue "A ASP 101": "OD1" <-> "OD2" Residue "A ARG 136": "NH1" <-> "NH2" Residue "A TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 175": "OE1" <-> "OE2" Residue "A GLU 176": "OE1" <-> "OE2" Residue "A ASP 178": "OD1" <-> "OD2" Residue "A ASP 182": "OD1" <-> "OD2" Residue "A GLU 281": "OE1" <-> "OE2" Residue "A TYR 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 371": "NH1" <-> "NH2" Residue "A ARG 374": "NH1" <-> "NH2" Residue "A PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 401": "OE1" <-> "OE2" Residue "A ARG 404": "NH1" <-> "NH2" Residue "A GLU 424": "OE1" <-> "OE2" Residue "A ARG 473": "NH1" <-> "NH2" Residue "A ARG 483": "NH1" <-> "NH2" Residue "A TYR 490": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 510": "NH1" <-> "NH2" Residue "A ARG 564": "NH1" <-> "NH2" Residue "A PHE 574": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 665": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 678": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 682": "NH1" <-> "NH2" Residue "A ARG 690": "NH1" <-> "NH2" Residue "A ARG 706": "NH1" <-> "NH2" Residue "A ARG 707": "NH1" <-> "NH2" Residue "A ARG 722": "NH1" <-> "NH2" Residue "A GLU 798": "OE1" <-> "OE2" Residue "A GLU 810": "OE1" <-> "OE2" Residue "A TYR 812": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 816": "OE1" <-> "OE2" Residue "A GLU 817": "OE1" <-> "OE2" Residue "A GLU 851": "OE1" <-> "OE2" Residue "A GLU 942": "OE1" <-> "OE2" Residue "A PHE 944": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 967": "OE1" <-> "OE2" Residue "A GLU 1006": "OE1" <-> "OE2" Residue "A GLU 1007": "OE1" <-> "OE2" Residue "A ARG 1039": "NH1" <-> "NH2" Residue "A ARG 1041": "NH1" <-> "NH2" Residue "A PHE 1042": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1147": "OE1" <-> "OE2" Residue "A GLU 1160": "OE1" <-> "OE2" Residue "A TYR 1174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1193": "OE1" <-> "OE2" Residue "A GLU 1219": "OE1" <-> "OE2" Residue "A PHE 1239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 525": "OD1" <-> "OD2" Residue "B ARG 570": "NH1" <-> "NH2" Residue "B TYR 574": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 592": "NH1" <-> "NH2" Residue "B PHE 598": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 606": "OE1" <-> "OE2" Residue "B ARG 611": "NH1" <-> "NH2" Residue "B GLU 626": "OE1" <-> "OE2" Residue "B GLU 663": "OE1" <-> "OE2" Residue "B GLU 674": "OE1" <-> "OE2" Residue "B TYR 687": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 757": "OE1" <-> "OE2" Residue "B TYR 766": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 781": "OD1" <-> "OD2" Residue "B ARG 918": "NH1" <-> "NH2" Residue "B GLU 948": "OE1" <-> "OE2" Residue "B TYR 972": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1049": "OE1" <-> "OE2" Residue "B PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1076": "NH1" <-> "NH2" Residue "B GLU 1098": "OE1" <-> "OE2" Residue "B TYR 1099": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1192": "OD1" <-> "OD2" Residue "B TYR 1206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1250": "OD1" <-> "OD2" Residue "B GLU 1251": "OE1" <-> "OE2" Residue "B TYR 1300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1314": "OE1" <-> "OE2" Residue "B GLU 1344": "OE1" <-> "OE2" Residue "B ARG 1367": "NH1" <-> "NH2" Residue "B TYR 1423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1424": "NH1" <-> "NH2" Residue "B ARG 1503": "NH1" <-> "NH2" Residue "B ARG 1507": "NH1" <-> "NH2" Residue "B TYR 1514": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1523": "NH1" <-> "NH2" Residue "B ARG 1553": "NH1" <-> "NH2" Residue "B ARG 1560": "NH1" <-> "NH2" Residue "C TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 12": "OE1" <-> "OE2" Residue "C ASP 16": "OD1" <-> "OD2" Residue "C GLU 30": "OE1" <-> "OE2" Residue "C GLU 94": "OE1" <-> "OE2" Residue "C ASP 103": "OD1" <-> "OD2" Residue "C TYR 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 145": "OD1" <-> "OD2" Residue "C PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 159": "OD1" <-> "OD2" Residue "C PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 272": "OD1" <-> "OD2" Residue "C ASP 294": "OD1" <-> "OD2" Residue "C TYR 301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 33": "OE1" <-> "OE2" Residue "D GLU 52": "OE1" <-> "OE2" Residue "D ASP 85": "OD1" <-> "OD2" Residue "D PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 136": "OE1" <-> "OE2" Residue "D TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 145": "OD1" <-> "OD2" Residue "D PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 211": "OD1" <-> "OD2" Residue "D PHE 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 253": "OD1" <-> "OD2" Residue "D ASP 260": "OD1" <-> "OD2" Residue "D PHE 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 272": "OD1" <-> "OD2" Residue "D TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 294": "OD1" <-> "OD2" Residue "D GLU 297": "OE1" <-> "OE2" Residue "D TYR 301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 302": "OD1" <-> "OD2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 22924 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 9065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1169, 9065 Classifications: {'peptide': 1169} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 75, 'TRANS': 1093} Chain breaks: 4 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 99 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 31 Chain: "B" Number of atoms: 9007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1212, 9007 Classifications: {'peptide': 1212} Incomplete info: {'truncation_to_alanine': 134} Link IDs: {'PTRANS': 26, 'TRANS': 1185} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 522 Unresolved non-hydrogen angles: 667 Unresolved non-hydrogen dihedrals: 443 Unresolved non-hydrogen chiralities: 42 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 6, 'TYR:plan': 11, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 14, 'PHE:plan': 6, 'GLU:plan': 13, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 298 Chain: "C" Number of atoms: 2373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2373 Classifications: {'peptide': 305} Link IDs: {'PTRANS': 8, 'TRANS': 296} Chain: "D" Number of atoms: 2373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2373 Classifications: {'peptide': 305} Link IDs: {'PTRANS': 8, 'TRANS': 296} Chain: "E" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 106 Classifications: {'RNA': 6} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 4} Link IDs: {'rna3p': 5} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen chiralities: 1 Unresolved non-hydrogen planarities: 12 Time building chain proxies: 12.23, per 1000 atoms: 0.53 Number of scatterers: 22924 At special positions: 0 Unit cell: (180.454, 131.085, 142.15, 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) S 107 16.00 P 6 15.00 O 4336 8.00 N 3981 7.00 C 14494 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: 9.50 Conformation dependent library (CDL) restraints added in 3.9 seconds 5950 Ramachandran restraints generated. 2975 Oldfield, 0 Emsley, 2975 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5606 Finding SS restraints... Secondary structure from input PDB file: 115 helices and 22 sheets defined 51.9% alpha, 9.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.51 Creating SS restraints... Processing helix chain 'A' and resid 53 through 64 removed outlier: 3.744A pdb=" N SER A 64 " --> pdb=" O GLN A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 73 removed outlier: 3.841A pdb=" N GLY A 73 " --> pdb=" O PRO A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 91 Processing helix chain 'A' and resid 252 through 263 removed outlier: 3.610A pdb=" N SER A 256 " --> pdb=" O ALA A 252 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N VAL A 261 " --> pdb=" O LEU A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 323 Processing helix chain 'A' and resid 334 through 353 removed outlier: 3.895A pdb=" N LYS A 338 " --> pdb=" O THR A 334 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N THR A 339 " --> pdb=" O SER A 335 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N VAL A 340 " --> pdb=" O ALA A 336 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N VAL A 341 " --> pdb=" O GLY A 337 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ILE A 346 " --> pdb=" O ALA A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 377 removed outlier: 4.481A pdb=" N GLN A 368 " --> pdb=" O ALA A 364 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LYS A 369 " --> pdb=" O LEU A 365 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N PHE A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 409 removed outlier: 3.664A pdb=" N LEU A 403 " --> pdb=" O THR A 399 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N TYR A 408 " --> pdb=" O ARG A 404 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N SER A 409 " --> pdb=" O SER A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 415 No H-bonds generated for 'chain 'A' and resid 413 through 415' Processing helix chain 'A' and resid 424 through 428 removed outlier: 3.689A pdb=" N ILE A 428 " --> pdb=" O VAL A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 444 removed outlier: 4.186A pdb=" N TRP A 437 " --> pdb=" O ARG A 433 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLU A 438 " --> pdb=" O GLY A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 471 Processing helix chain 'A' and resid 514 through 529 removed outlier: 3.931A pdb=" N TYR A 518 " --> pdb=" O HIS A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 563 removed outlier: 3.870A pdb=" N GLY A 552 " --> pdb=" O ALA A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 587 removed outlier: 3.799A pdb=" N ALA A 583 " --> pdb=" O CYS A 579 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N THR A 587 " --> pdb=" O ALA A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 593 through 609 Processing helix chain 'A' and resid 613 through 617 removed outlier: 3.543A pdb=" N GLN A 617 " --> pdb=" O SER A 614 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 631 removed outlier: 3.711A pdb=" N ARG A 630 " --> pdb=" O GLU A 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 652 removed outlier: 3.567A pdb=" N ILE A 646 " --> pdb=" O ILE A 642 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 668 Processing helix chain 'A' and resid 693 through 703 removed outlier: 3.579A pdb=" N TYR A 697 " --> pdb=" O LEU A 693 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLN A 699 " --> pdb=" O GLY A 695 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N MET A 700 " --> pdb=" O GLU A 696 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 734 removed outlier: 3.649A pdb=" N ARG A 731 " --> pdb=" O ALA A 727 " (cutoff:3.500A) Processing helix chain 'A' and resid 747 through 756 Processing helix chain 'A' and resid 761 through 768 removed outlier: 4.010A pdb=" N MET A 765 " --> pdb=" O ARG A 761 " (cutoff:3.500A) Processing helix chain 'A' and resid 769 through 771 No H-bonds generated for 'chain 'A' and resid 769 through 771' Processing helix chain 'A' and resid 772 through 777 Processing helix chain 'A' and resid 778 through 794 removed outlier: 4.071A pdb=" N LYS A 791 " --> pdb=" O ALA A 787 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ARG A 792 " --> pdb=" O GLU A 788 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLY A 794 " --> pdb=" O THR A 790 " (cutoff:3.500A) Processing helix chain 'A' and resid 807 through 831 removed outlier: 3.700A pdb=" N LEU A 818 " --> pdb=" O TRP A 814 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N THR A 819 " --> pdb=" O GLY A 815 " (cutoff:3.500A) Processing helix chain 'A' and resid 832 through 839 Processing helix chain 'A' and resid 884 through 888 removed outlier: 3.795A pdb=" N ASP A 887 " --> pdb=" O ASP A 884 " (cutoff:3.500A) Processing helix chain 'A' and resid 921 through 923 No H-bonds generated for 'chain 'A' and resid 921 through 923' Processing helix chain 'A' and resid 936 through 948 removed outlier: 4.452A pdb=" N LYS A 946 " --> pdb=" O GLU A 942 " (cutoff:3.500A) Processing helix chain 'A' and resid 958 through 974 Processing helix chain 'A' and resid 992 through 1010 removed outlier: 3.565A pdb=" N VAL A 996 " --> pdb=" O ASP A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1011 through 1012 No H-bonds generated for 'chain 'A' and resid 1011 through 1012' Processing helix chain 'A' and resid 1013 through 1017 Processing helix chain 'A' and resid 1019 through 1044 removed outlier: 3.843A pdb=" N GLN A1023 " --> pdb=" O ARG A1019 " (cutoff:3.500A) Processing helix chain 'A' and resid 1051 through 1065 Processing helix chain 'A' and resid 1075 through 1083 removed outlier: 3.715A pdb=" N ALA A1083 " --> pdb=" O ARG A1079 " (cutoff:3.500A) Processing helix chain 'A' and resid 1087 through 1097 Processing helix chain 'A' and resid 1104 through 1113 removed outlier: 3.851A pdb=" N ALA A1109 " --> pdb=" O PRO A1105 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ALA A1110 " --> pdb=" O GLU A1106 " (cutoff:3.500A) Processing helix chain 'A' and resid 1114 through 1116 No H-bonds generated for 'chain 'A' and resid 1114 through 1116' Processing helix chain 'A' and resid 1128 through 1151 removed outlier: 3.999A pdb=" N GLU A1136 " --> pdb=" O LYS A1132 " (cutoff:3.500A) Processing helix chain 'A' and resid 1157 through 1163 Processing helix chain 'A' and resid 1169 through 1177 Processing helix chain 'A' and resid 1181 through 1189 removed outlier: 3.808A pdb=" N LEU A1185 " --> pdb=" O PRO A1181 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N SER A1189 " --> pdb=" O LEU A1185 " (cutoff:3.500A) Processing helix chain 'A' and resid 1192 through 1205 removed outlier: 3.851A pdb=" N VAL A1197 " --> pdb=" O GLU A1193 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N CYS A1199 " --> pdb=" O LEU A1195 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU A1205 " --> pdb=" O GLN A1201 " (cutoff:3.500A) Processing helix chain 'A' and resid 1208 through 1218 removed outlier: 3.625A pdb=" N GLY A1212 " --> pdb=" O ARG A1208 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG A1215 " --> pdb=" O ARG A1211 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU A1216 " --> pdb=" O GLY A1212 " (cutoff:3.500A) Processing helix chain 'A' and resid 1219 through 1230 removed outlier: 3.579A pdb=" N ALA A1224 " --> pdb=" O PRO A1220 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N THR A1228 " --> pdb=" O ALA A1224 " (cutoff:3.500A) Processing helix chain 'A' and resid 1236 through 1240 Processing helix chain 'B' and resid 354 through 366 Processing helix chain 'B' and resid 369 through 383 Processing helix chain 'B' and resid 388 through 400 removed outlier: 3.938A pdb=" N LYS B 392 " --> pdb=" O LEU B 388 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N SER B 393 " --> pdb=" O LEU B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 416 Processing helix chain 'B' and resid 421 through 436 Processing helix chain 'B' and resid 438 through 452 removed outlier: 3.555A pdb=" N CYS B 442 " --> pdb=" O GLN B 438 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N PHE B 443 " --> pdb=" O ALA B 439 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA B 446 " --> pdb=" O CYS B 442 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 470 removed outlier: 3.878A pdb=" N LEU B 460 " --> pdb=" O TYR B 456 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N GLY B 461 " --> pdb=" O HIS B 457 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 489 Processing helix chain 'B' and resid 496 through 504 removed outlier: 3.526A pdb=" N GLY B 500 " --> pdb=" O PHE B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 524 Processing helix chain 'B' and resid 529 through 541 Processing helix chain 'B' and resid 546 through 557 removed outlier: 3.607A pdb=" N LYS B 557 " --> pdb=" O THR B 553 " (cutoff:3.500A) Processing helix chain 'B' and resid 563 through 577 removed outlier: 3.812A pdb=" N ARG B 569 " --> pdb=" O TRP B 565 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ALA B 577 " --> pdb=" O TYR B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 579 through 594 Processing helix chain 'B' and resid 597 through 611 removed outlier: 3.592A pdb=" N TRP B 601 " --> pdb=" O ASP B 597 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ARG B 611 " --> pdb=" O ALA B 607 " (cutoff:3.500A) Processing helix chain 'B' and resid 614 through 627 removed outlier: 3.663A pdb=" N LEU B 627 " --> pdb=" O LYS B 623 " (cutoff:3.500A) Processing helix chain 'B' and resid 631 through 645 removed outlier: 4.017A pdb=" N VAL B 635 " --> pdb=" O SER B 631 " (cutoff:3.500A) Processing helix chain 'B' and resid 647 through 662 removed outlier: 3.787A pdb=" N LYS B 661 " --> pdb=" O MET B 657 " (cutoff:3.500A) Processing helix chain 'B' and resid 665 through 686 removed outlier: 3.820A pdb=" N ASP B 686 " --> pdb=" O ALA B 682 " (cutoff:3.500A) Processing helix chain 'B' and resid 688 through 710 removed outlier: 3.731A pdb=" N ALA B 692 " --> pdb=" O LEU B 688 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL B 693 " --> pdb=" O ASP B 689 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N HIS B 709 " --> pdb=" O CYS B 705 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG B 710 " --> pdb=" O ALA B 706 " (cutoff:3.500A) Processing helix chain 'B' and resid 713 through 726 removed outlier: 4.315A pdb=" N TRP B 717 " --> pdb=" O VAL B 713 " (cutoff:3.500A) Processing helix chain 'B' and resid 741 through 745 removed outlier: 3.677A pdb=" N LEU B 744 " --> pdb=" O GLY B 741 " (cutoff:3.500A) Processing helix chain 'B' and resid 754 through 773 removed outlier: 3.827A pdb=" N LEU B 772 " --> pdb=" O ARG B 768 " (cutoff:3.500A) Processing helix chain 'B' and resid 775 through 796 removed outlier: 3.516A pdb=" N TRP B 779 " --> pdb=" O THR B 775 " (cutoff:3.500A) Processing helix chain 'B' and resid 803 through 821 Processing helix chain 'B' and resid 824 through 836 removed outlier: 3.592A pdb=" N TRP B 828 " --> pdb=" O ASN B 824 " (cutoff:3.500A) Processing helix chain 'B' and resid 842 through 857 Processing helix chain 'B' and resid 860 through 874 removed outlier: 3.747A pdb=" N TRP B 864 " --> pdb=" O ASN B 860 " (cutoff:3.500A) Processing helix chain 'B' and resid 876 through 891 Processing helix chain 'B' and resid 894 through 908 removed outlier: 3.891A pdb=" N TRP B 898 " --> pdb=" O TYR B 894 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 924 removed outlier: 3.505A pdb=" N ASN B 924 " --> pdb=" O THR B 920 " (cutoff:3.500A) Processing helix chain 'B' and resid 926 through 943 Processing helix chain 'B' and resid 951 through 959 Processing helix chain 'B' and resid 960 through 976 Processing helix chain 'B' and resid 979 through 993 removed outlier: 4.047A pdb=" N PHE B 983 " --> pdb=" O TYR B 979 " (cutoff:3.500A) Processing helix chain 'B' and resid 995 through 1010 Processing helix chain 'B' and resid 1016 through 1033 removed outlier: 3.505A pdb=" N THR B1033 " --> pdb=" O LEU B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1035 through 1045 Processing helix chain 'B' and resid 1050 through 1065 Processing helix chain 'B' and resid 1066 through 1080 removed outlier: 3.953A pdb=" N ILE B1080 " --> pdb=" O ARG B1076 " (cutoff:3.500A) Processing helix chain 'B' and resid 1084 through 1102 removed outlier: 3.825A pdb=" N GLN B1101 " --> pdb=" O THR B1097 " (cutoff:3.500A) Processing helix chain 'B' and resid 1103 through 1116 Processing helix chain 'B' and resid 1123 through 1135 Processing helix chain 'B' and resid 1137 through 1152 removed outlier: 4.528A pdb=" N SER B1141 " --> pdb=" O ASP B1137 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N HIS B1151 " --> pdb=" O GLU B1147 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE B1152 " --> pdb=" O LEU B1148 " (cutoff:3.500A) Processing helix chain 'B' and resid 1159 through 1172 removed outlier: 3.704A pdb=" N GLN B1172 " --> pdb=" O ILE B1168 " (cutoff:3.500A) Processing helix chain 'B' and resid 1176 through 1189 Processing helix chain 'B' and resid 1192 through 1206 removed outlier: 3.770A pdb=" N TRP B1196 " --> pdb=" O ASP B1192 " (cutoff:3.500A) Processing helix chain 'B' and resid 1210 through 1224 Processing helix chain 'B' and resid 1228 through 1244 Processing helix chain 'B' and resid 1254 through 1266 Processing helix chain 'B' and resid 1269 through 1291 removed outlier: 4.177A pdb=" N TRP B1273 " --> pdb=" O ASP B1269 " (cutoff:3.500A) Processing helix chain 'B' and resid 1299 through 1313 removed outlier: 3.949A pdb=" N ASP B1313 " --> pdb=" O ALA B1309 " (cutoff:3.500A) Processing helix chain 'B' and resid 1317 through 1340 Processing helix chain 'B' and resid 1341 through 1356 removed outlier: 3.646A pdb=" N ASN B1356 " --> pdb=" O ASN B1352 " (cutoff:3.500A) Processing helix chain 'B' and resid 1361 through 1371 Processing helix chain 'B' and resid 1382 through 1396 removed outlier: 3.708A pdb=" N ASN B1396 " --> pdb=" O THR B1392 " (cutoff:3.500A) Processing helix chain 'B' and resid 1399 through 1414 removed outlier: 3.643A pdb=" N TRP B1403 " --> pdb=" O SER B1399 " (cutoff:3.500A) Processing helix chain 'B' and resid 1415 through 1434 Processing helix chain 'B' and resid 1436 through 1456 removed outlier: 3.517A pdb=" N ALA B1456 " --> pdb=" O LYS B1452 " (cutoff:3.500A) Processing helix chain 'B' and resid 1462 through 1478 Processing helix chain 'B' and resid 1480 through 1494 Processing helix chain 'B' and resid 1498 through 1511 removed outlier: 3.799A pdb=" N ARG B1502 " --> pdb=" O ALA B1498 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLN B1511 " --> pdb=" O ARG B1507 " (cutoff:3.500A) Processing helix chain 'B' and resid 1515 through 1533 Processing helix chain 'B' and resid 1535 through 1548 Processing helix chain 'B' and resid 1552 through 1563 removed outlier: 4.139A pdb=" N SER B1563 " --> pdb=" O GLN B1559 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 23 removed outlier: 3.760A pdb=" N ARG A 20 " --> pdb=" O LEU A 33 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 103 through 104 Processing sheet with id=AA3, first strand: chain 'A' and resid 284 through 286 removed outlier: 6.709A pdb=" N ILE A 285 " --> pdb=" O VAL A 477 " (cutoff:3.500A) removed outlier: 8.346A pdb=" N SER A 479 " --> pdb=" O ILE A 285 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 395 through 398 removed outlier: 7.181A pdb=" N ARG A 355 " --> pdb=" O TRP A 419 " (cutoff:3.500A) removed outlier: 8.599A pdb=" N ILE A 421 " --> pdb=" O ARG A 355 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N ILE A 357 " --> pdb=" O ILE A 421 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N GLU A 418 " --> pdb=" O SER A 449 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N ILE A 451 " --> pdb=" O GLU A 418 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N VAL A 420 " --> pdb=" O ILE A 451 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 503 through 507 removed outlier: 6.846A pdb=" N HIS A 489 " --> pdb=" O LEU A 506 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N VAL A 676 " --> pdb=" O ILE A 716 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N VAL A 570 " --> pdb=" O VAL A 677 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N VAL A 569 " --> pdb=" O LEU A 659 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ALA A 661 " --> pdb=" O VAL A 569 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N VAL A 571 " --> pdb=" O ALA A 661 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N GLY A 633 " --> pdb=" O PHE A 660 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 682 through 683 removed outlier: 3.559A pdb=" N ARG A 690 " --> pdb=" O LYS A 683 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 916 through 920 removed outlier: 7.534A pdb=" N THR A 872 " --> pdb=" O LEU A 860 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ARG A 843 " --> pdb=" O ILE A 859 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N LYS A 848 " --> pdb=" O MET A 925 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N MET A 925 " --> pdb=" O LYS A 848 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 737 through 739 Processing sheet with id=AA9, first strand: chain 'C' and resid 6 through 11 removed outlier: 6.958A pdb=" N ILE C 300 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N LYS C 10 " --> pdb=" O ILE C 298 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ILE C 298 " --> pdb=" O LYS C 10 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE C 289 " --> pdb=" O TYR C 301 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 19 through 25 removed outlier: 6.242A pdb=" N LYS C 48 " --> pdb=" O LEU C 56 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N LEU C 56 " --> pdb=" O LYS C 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 67 through 72 removed outlier: 3.625A pdb=" N ALA C 79 " --> pdb=" O TRP C 91 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 112 through 113 removed outlier: 3.714A pdb=" N TYR C 142 " --> pdb=" O ILE C 132 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N GLY C 134 " --> pdb=" O LYS C 140 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N LYS C 140 " --> pdb=" O GLY C 134 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 151 through 156 removed outlier: 3.600A pdb=" N HIS C 184 " --> pdb=" O ILE C 174 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 196 through 198 removed outlier: 3.511A pdb=" N LEU C 205 " --> pdb=" O TYR C 217 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LYS C 215 " --> pdb=" O THR C 207 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N ILE C 214 " --> pdb=" O THR C 227 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N THR C 227 " --> pdb=" O ILE C 214 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N ILE C 216 " --> pdb=" O ALA C 225 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 235 through 240 removed outlier: 6.718A pdb=" N SER C 250 " --> pdb=" O LEU C 236 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N VAL C 238 " --> pdb=" O VAL C 248 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N VAL C 248 " --> pdb=" O VAL C 238 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N PHE C 240 " --> pdb=" O HIS C 246 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N HIS C 246 " --> pdb=" O PHE C 240 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N HIS C 268 " --> pdb=" O VAL C 258 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ASP C 260 " --> pdb=" O CYS C 266 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N CYS C 266 " --> pdb=" O ASP C 260 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 10 through 11 Processing sheet with id=AB8, first strand: chain 'D' and resid 21 through 25 removed outlier: 6.144A pdb=" N LYS D 48 " --> pdb=" O LEU D 56 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N LEU D 56 " --> pdb=" O LYS D 48 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 67 through 72 removed outlier: 3.697A pdb=" N LYS D 100 " --> pdb=" O LEU D 90 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 112 through 113 Processing sheet with id=AC2, first strand: chain 'D' and resid 154 through 156 removed outlier: 3.578A pdb=" N ALA D 164 " --> pdb=" O ALA D 155 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ILE D 172 " --> pdb=" O THR D 185 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N THR D 185 " --> pdb=" O ILE D 172 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N ILE D 174 " --> pdb=" O LEU D 183 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 196 through 197 removed outlier: 3.517A pdb=" N ILE D 214 " --> pdb=" O LEU D 228 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILE D 216 " --> pdb=" O GLY D 226 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N ASP D 218 " --> pdb=" O LEU D 224 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N LEU D 224 " --> pdb=" O ASP D 218 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 235 through 239 removed outlier: 6.814A pdb=" N SER D 250 " --> pdb=" O LEU D 236 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N VAL D 238 " --> pdb=" O VAL D 248 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N VAL D 248 " --> pdb=" O VAL D 238 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL D 256 " --> pdb=" O PHE D 270 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N HIS D 268 " --> pdb=" O VAL D 258 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N ASP D 260 " --> pdb=" O CYS D 266 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N CYS D 266 " --> pdb=" O ASP D 260 " (cutoff:3.500A) 1160 hydrogen bonds defined for protein. 3384 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: 10.17 Time building geometry restraints manager: 10.32 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: 6344 1.33 - 1.45: 3983 1.45 - 1.57: 12878 1.57 - 1.69: 13 1.69 - 1.81: 168 Bond restraints: 23386 Sorted by residual: bond pdb=" CB VAL B 973 " pdb=" CG2 VAL B 973 " ideal model delta sigma weight residual 1.521 1.431 0.090 3.30e-02 9.18e+02 7.48e+00 bond pdb=" CB ILE B 968 " pdb=" CG2 ILE B 968 " ideal model delta sigma weight residual 1.521 1.434 0.087 3.30e-02 9.18e+02 6.94e+00 bond pdb=" CB ILE C 151 " pdb=" CG2 ILE C 151 " ideal model delta sigma weight residual 1.521 1.437 0.084 3.30e-02 9.18e+02 6.50e+00 bond pdb=" CG1 ILE B1182 " pdb=" CD1 ILE B1182 " ideal model delta sigma weight residual 1.513 1.415 0.098 3.90e-02 6.57e+02 6.31e+00 bond pdb=" CB GLU C 141 " pdb=" CG GLU C 141 " ideal model delta sigma weight residual 1.520 1.445 0.075 3.00e-02 1.11e+03 6.28e+00 ... (remaining 23381 not shown) Histogram of bond angle deviations from ideal: 98.44 - 105.59: 482 105.59 - 112.74: 12383 112.74 - 119.89: 8201 119.89 - 127.04: 10387 127.04 - 134.19: 318 Bond angle restraints: 31771 Sorted by residual: angle pdb=" N PRO B 417 " pdb=" CA PRO B 417 " pdb=" CB PRO B 417 " ideal model delta sigma weight residual 102.65 110.47 -7.82 6.80e-01 2.16e+00 1.32e+02 angle pdb=" N PRO A 162 " pdb=" CA PRO A 162 " pdb=" CB PRO A 162 " ideal model delta sigma weight residual 103.25 111.52 -8.27 1.05e+00 9.07e-01 6.21e+01 angle pdb=" N PRO A 206 " pdb=" CA PRO A 206 " pdb=" CB PRO A 206 " ideal model delta sigma weight residual 103.25 111.15 -7.90 1.05e+00 9.07e-01 5.66e+01 angle pdb=" CA PRO B1294 " pdb=" N PRO B1294 " pdb=" CD PRO B1294 " ideal model delta sigma weight residual 112.00 103.04 8.96 1.40e+00 5.10e-01 4.09e+01 angle pdb=" N PRO B 386 " pdb=" CA PRO B 386 " pdb=" CB PRO B 386 " ideal model delta sigma weight residual 102.86 110.23 -7.37 1.23e+00 6.61e-01 3.59e+01 ... (remaining 31766 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 12608 17.94 - 35.87: 1232 35.87 - 53.80: 179 53.80 - 71.74: 37 71.74 - 89.67: 17 Dihedral angle restraints: 14073 sinusoidal: 5395 harmonic: 8678 Sorted by residual: dihedral pdb=" CA LEU A 586 " pdb=" C LEU A 586 " pdb=" N THR A 587 " pdb=" CA THR A 587 " ideal model delta harmonic sigma weight residual 180.00 150.95 29.05 0 5.00e+00 4.00e-02 3.38e+01 dihedral pdb=" CA LYS C 139 " pdb=" C LYS C 139 " pdb=" N LYS C 140 " pdb=" CA LYS C 140 " ideal model delta harmonic sigma weight residual 180.00 153.23 26.77 0 5.00e+00 4.00e-02 2.87e+01 dihedral pdb=" CA ASP D 201 " pdb=" C ASP D 201 " pdb=" N SER D 202 " pdb=" CA SER D 202 " ideal model delta harmonic sigma weight residual -180.00 -153.33 -26.67 0 5.00e+00 4.00e-02 2.84e+01 ... (remaining 14070 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 2855 0.074 - 0.148: 715 0.148 - 0.222: 70 0.222 - 0.296: 5 0.296 - 0.370: 3 Chirality restraints: 3648 Sorted by residual: chirality pdb=" CB ILE B 968 " pdb=" CA ILE B 968 " pdb=" CG1 ILE B 968 " pdb=" CG2 ILE B 968 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.37 2.00e-01 2.50e+01 3.43e+00 chirality pdb=" CB VAL B 973 " pdb=" CA VAL B 973 " pdb=" CG1 VAL B 973 " pdb=" CG2 VAL B 973 " both_signs ideal model delta sigma weight residual False -2.63 -2.28 -0.35 2.00e-01 2.50e+01 3.04e+00 chirality pdb=" CA MET A 671 " pdb=" N MET A 671 " pdb=" C MET A 671 " pdb=" CB MET A 671 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.43e+00 ... (remaining 3645 not shown) Planarity restraints: 4076 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN B1293 " 0.124 5.00e-02 4.00e+02 1.81e-01 5.25e+01 pdb=" N PRO B1294 " -0.313 5.00e-02 4.00e+02 pdb=" CA PRO B1294 " 0.102 5.00e-02 4.00e+02 pdb=" CD PRO B1294 " 0.088 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 766 " 0.031 2.00e-02 2.50e+03 2.89e-02 1.67e+01 pdb=" CG TYR B 766 " -0.070 2.00e-02 2.50e+03 pdb=" CD1 TYR B 766 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR B 766 " 0.024 2.00e-02 2.50e+03 pdb=" CE1 TYR B 766 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR B 766 " -0.008 2.00e-02 2.50e+03 pdb=" CZ TYR B 766 " 0.007 2.00e-02 2.50e+03 pdb=" OH TYR B 766 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 198 " -0.023 2.00e-02 2.50e+03 2.84e-02 1.41e+01 pdb=" CG PHE C 198 " 0.064 2.00e-02 2.50e+03 pdb=" CD1 PHE C 198 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE C 198 " -0.027 2.00e-02 2.50e+03 pdb=" CE1 PHE C 198 " -0.012 2.00e-02 2.50e+03 pdb=" CE2 PHE C 198 " 0.007 2.00e-02 2.50e+03 pdb=" CZ PHE C 198 " 0.000 2.00e-02 2.50e+03 ... (remaining 4073 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 135 2.51 - 3.11: 17244 3.11 - 3.70: 33606 3.70 - 4.30: 46907 4.30 - 4.90: 80156 Nonbonded interactions: 178048 Sorted by model distance: nonbonded pdb=" OG SER C 251 " pdb=" OD1 ASP C 253 " model vdw 1.910 2.440 nonbonded pdb=" OH TYR A 358 " pdb=" OD2 ASP A 423 " model vdw 1.940 2.440 nonbonded pdb=" OE1 GLU A 663 " pdb=" O2' U E 2 " model vdw 2.034 2.440 nonbonded pdb=" NH1 ARG A 576 " pdb=" OP1 U E 2 " model vdw 2.054 2.520 nonbonded pdb=" OG SER C 209 " pdb=" OD1 ASP C 211 " model vdw 2.073 2.440 ... (remaining 178043 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 6.730 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: 28.640 Check model and map are aligned: 0.320 Set scattering table: 0.190 Process input model: 61.720 Find NCS groups from input model: 1.040 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: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 101.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 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 : 0.009 0.107 23386 Z= 0.619 Angle : 1.113 17.045 31771 Z= 0.605 Chirality : 0.062 0.370 3648 Planarity : 0.008 0.181 4076 Dihedral : 14.475 89.674 8467 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.75 % Favored : 94.15 % Rotamer Outliers : 0.00 % 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: -1.41 (0.15), residues: 2975 helix: 0.96 (0.14), residues: 1458 sheet: -1.78 (0.26), residues: 340 loop : -3.25 (0.14), residues: 1177 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5950 Ramachandran restraints generated. 2975 Oldfield, 0 Emsley, 2975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5950 Ramachandran restraints generated. 2975 Oldfield, 0 Emsley, 2975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 2528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 192 time to evaluate : 2.577 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 192 average time/residue: 0.3740 time to fit residues: 111.2901 Evaluate side-chains 158 residues out of total 2528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 158 time to evaluate : 2.584 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.6309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 250 optimal weight: 0.7980 chunk 225 optimal weight: 0.7980 chunk 124 optimal weight: 0.7980 chunk 76 optimal weight: 3.9990 chunk 151 optimal weight: 0.5980 chunk 120 optimal weight: 6.9990 chunk 232 optimal weight: 3.9990 chunk 90 optimal weight: 9.9990 chunk 141 optimal weight: 0.4980 chunk 173 optimal weight: 0.7980 chunk 269 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 580 HIS B 829 ASN B 866 ASN B 926 HIS B1011 GLN ** B1260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 237 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.1130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 23386 Z= 0.224 Angle : 0.680 12.863 31771 Z= 0.353 Chirality : 0.044 0.223 3648 Planarity : 0.005 0.093 4076 Dihedral : 5.842 74.341 3268 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.11 % Favored : 90.86 % Rotamer Outliers : 0.89 % 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: -0.90 (0.15), residues: 2975 helix: 1.28 (0.14), residues: 1468 sheet: -1.40 (0.28), residues: 333 loop : -2.94 (0.15), residues: 1174 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5950 Ramachandran restraints generated. 2975 Oldfield, 0 Emsley, 2975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5950 Ramachandran restraints generated. 2975 Oldfield, 0 Emsley, 2975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 2528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 199 time to evaluate : 3.164 Fit side-chains outliers start: 21 outliers final: 16 residues processed: 207 average time/residue: 0.3568 time to fit residues: 117.1557 Evaluate side-chains 194 residues out of total 2528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 178 time to evaluate : 2.610 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.2143 time to fit residues: 10.2192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 149 optimal weight: 0.0570 chunk 83 optimal weight: 0.0370 chunk 224 optimal weight: 1.9990 chunk 183 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 chunk 270 optimal weight: 0.3980 chunk 291 optimal weight: 1.9990 chunk 240 optimal weight: 3.9990 chunk 267 optimal weight: 4.9990 chunk 92 optimal weight: 6.9990 chunk 216 optimal weight: 7.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 853 HIS B 580 HIS B 829 ASN B 866 ASN B1253 ASN ** B1260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1491 GLN B1529 HIS ** D 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.1518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 23386 Z= 0.253 Angle : 0.656 12.295 31771 Z= 0.341 Chirality : 0.044 0.226 3648 Planarity : 0.005 0.069 4076 Dihedral : 5.689 74.078 3268 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.03 % Favored : 91.93 % Rotamer Outliers : 1.56 % 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: -0.76 (0.15), residues: 2975 helix: 1.35 (0.14), residues: 1463 sheet: -1.11 (0.28), residues: 336 loop : -2.85 (0.16), residues: 1176 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5950 Ramachandran restraints generated. 2975 Oldfield, 0 Emsley, 2975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5950 Ramachandran restraints generated. 2975 Oldfield, 0 Emsley, 2975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 2528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 189 time to evaluate : 2.754 Fit side-chains revert: symmetry clash outliers start: 37 outliers final: 14 residues processed: 222 average time/residue: 0.3776 time to fit residues: 131.1381 Evaluate side-chains 189 residues out of total 2528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 175 time to evaluate : 2.654 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.2120 time to fit residues: 9.8748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 266 optimal weight: 2.9990 chunk 203 optimal weight: 0.6980 chunk 140 optimal weight: 0.6980 chunk 29 optimal weight: 0.7980 chunk 128 optimal weight: 20.0000 chunk 181 optimal weight: 1.9990 chunk 271 optimal weight: 0.6980 chunk 287 optimal weight: 2.9990 chunk 141 optimal weight: 0.3980 chunk 256 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 853 HIS A1032 GLN B 580 HIS B 829 ASN B 866 ASN B 879 GLN B1253 ASN ** B1260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1356 ASN B1359 GLN ** B1411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 119 GLN D 126 HIS D 237 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 23386 Z= 0.196 Angle : 0.595 11.916 31771 Z= 0.310 Chirality : 0.041 0.218 3648 Planarity : 0.004 0.066 4076 Dihedral : 5.447 74.698 3268 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.64 % Favored : 91.33 % Rotamer Outliers : 1.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.16), residues: 2975 helix: 1.52 (0.14), residues: 1470 sheet: -0.83 (0.29), residues: 324 loop : -2.76 (0.16), residues: 1181 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5950 Ramachandran restraints generated. 2975 Oldfield, 0 Emsley, 2975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5950 Ramachandran restraints generated. 2975 Oldfield, 0 Emsley, 2975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 2528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 190 time to evaluate : 2.464 Fit side-chains outliers start: 38 outliers final: 17 residues processed: 218 average time/residue: 0.3685 time to fit residues: 127.8197 Evaluate side-chains 197 residues out of total 2528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 180 time to evaluate : 2.739 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.2184 time to fit residues: 10.7763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 239 optimal weight: 2.9990 chunk 162 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 213 optimal weight: 1.9990 chunk 118 optimal weight: 20.0000 chunk 244 optimal weight: 0.7980 chunk 198 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 chunk 146 optimal weight: 1.9990 chunk 257 optimal weight: 1.9990 chunk 72 optimal weight: 5.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 623 HIS A 853 HIS B 580 HIS B 829 ASN B 866 ASN ** B1411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 237 ASN C 285 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.055 23386 Z= 0.321 Angle : 0.677 13.240 31771 Z= 0.352 Chirality : 0.045 0.233 3648 Planarity : 0.005 0.066 4076 Dihedral : 5.670 72.842 3268 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.94 % Favored : 90.99 % Rotamer Outliers : 1.86 % 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: -0.70 (0.15), residues: 2975 helix: 1.33 (0.14), residues: 1473 sheet: -0.97 (0.27), residues: 345 loop : -2.81 (0.16), residues: 1157 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5950 Ramachandran restraints generated. 2975 Oldfield, 0 Emsley, 2975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5950 Ramachandran restraints generated. 2975 Oldfield, 0 Emsley, 2975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 2528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 182 time to evaluate : 2.617 Fit side-chains outliers start: 44 outliers final: 20 residues processed: 218 average time/residue: 0.4317 time to fit residues: 153.9997 Evaluate side-chains 190 residues out of total 2528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 170 time to evaluate : 2.783 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.2108 time to fit residues: 11.6871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 96 optimal weight: 6.9990 chunk 258 optimal weight: 0.9980 chunk 56 optimal weight: 0.0970 chunk 168 optimal weight: 0.9990 chunk 70 optimal weight: 0.6980 chunk 287 optimal weight: 5.9990 chunk 238 optimal weight: 2.9990 chunk 133 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 chunk 95 optimal weight: 0.9980 chunk 150 optimal weight: 0.9980 overall best weight: 0.7378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 623 HIS A 853 HIS B 580 HIS B 874 ASN ** B1260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1411 GLN ** B1428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 237 ASN C 285 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.2168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 23386 Z= 0.212 Angle : 0.612 14.908 31771 Z= 0.318 Chirality : 0.042 0.204 3648 Planarity : 0.004 0.062 4076 Dihedral : 5.470 73.158 3268 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.01 % Favored : 90.96 % Rotamer Outliers : 1.18 % 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: -0.52 (0.16), residues: 2975 helix: 1.51 (0.14), residues: 1477 sheet: -0.85 (0.28), residues: 336 loop : -2.79 (0.16), residues: 1162 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5950 Ramachandran restraints generated. 2975 Oldfield, 0 Emsley, 2975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5950 Ramachandran restraints generated. 2975 Oldfield, 0 Emsley, 2975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 2528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 185 time to evaluate : 2.569 Fit side-chains outliers start: 28 outliers final: 12 residues processed: 206 average time/residue: 0.3553 time to fit residues: 117.5339 Evaluate side-chains 187 residues out of total 2528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 175 time to evaluate : 2.680 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.2129 time to fit residues: 8.4465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 277 optimal weight: 0.0170 chunk 32 optimal weight: 0.9980 chunk 163 optimal weight: 1.9990 chunk 209 optimal weight: 2.9990 chunk 162 optimal weight: 1.9990 chunk 241 optimal weight: 1.9990 chunk 160 optimal weight: 2.9990 chunk 286 optimal weight: 3.9990 chunk 179 optimal weight: 0.7980 chunk 174 optimal weight: 1.9990 chunk 132 optimal weight: 5.9990 overall best weight: 1.1622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 HIS ** A 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 623 HIS A 853 HIS B 580 HIS ** B1359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 285 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.2260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.065 23386 Z= 0.294 Angle : 0.660 14.427 31771 Z= 0.343 Chirality : 0.044 0.220 3648 Planarity : 0.005 0.063 4076 Dihedral : 5.597 71.691 3268 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.38 % Favored : 90.55 % Rotamer Outliers : 0.97 % 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: -0.62 (0.15), residues: 2975 helix: 1.35 (0.14), residues: 1485 sheet: -0.86 (0.28), residues: 346 loop : -2.78 (0.16), residues: 1144 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5950 Ramachandran restraints generated. 2975 Oldfield, 0 Emsley, 2975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5950 Ramachandran restraints generated. 2975 Oldfield, 0 Emsley, 2975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 2528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 174 time to evaluate : 2.841 Fit side-chains outliers start: 23 outliers final: 9 residues processed: 191 average time/residue: 0.3731 time to fit residues: 113.4733 Evaluate side-chains 174 residues out of total 2528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 165 time to evaluate : 2.846 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.2110 time to fit residues: 7.5758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 177 optimal weight: 0.6980 chunk 114 optimal weight: 0.4980 chunk 170 optimal weight: 0.6980 chunk 86 optimal weight: 8.9990 chunk 56 optimal weight: 1.9990 chunk 55 optimal weight: 5.9990 chunk 181 optimal weight: 0.9990 chunk 195 optimal weight: 3.9990 chunk 141 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 225 optimal weight: 3.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 623 HIS A 853 HIS B 580 HIS ** B1359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 184 HIS C 237 ASN C 285 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 23386 Z= 0.214 Angle : 0.617 13.638 31771 Z= 0.320 Chirality : 0.042 0.229 3648 Planarity : 0.004 0.061 4076 Dihedral : 5.434 72.184 3268 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.01 % Favored : 90.96 % Rotamer Outliers : 0.68 % 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: -0.44 (0.16), residues: 2975 helix: 1.53 (0.14), residues: 1486 sheet: -0.74 (0.28), residues: 338 loop : -2.74 (0.16), residues: 1151 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5950 Ramachandran restraints generated. 2975 Oldfield, 0 Emsley, 2975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5950 Ramachandran restraints generated. 2975 Oldfield, 0 Emsley, 2975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 2528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 170 time to evaluate : 2.669 Fit side-chains outliers start: 16 outliers final: 8 residues processed: 179 average time/residue: 0.3913 time to fit residues: 111.4635 Evaluate side-chains 176 residues out of total 2528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 168 time to evaluate : 2.760 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.2279 time to fit residues: 7.6085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 260 optimal weight: 2.9990 chunk 274 optimal weight: 1.9990 chunk 250 optimal weight: 0.9990 chunk 266 optimal weight: 3.9990 chunk 160 optimal weight: 0.0270 chunk 116 optimal weight: 0.9980 chunk 209 optimal weight: 2.9990 chunk 81 optimal weight: 9.9990 chunk 241 optimal weight: 2.9990 chunk 252 optimal weight: 1.9990 chunk 265 optimal weight: 0.7980 overall best weight: 0.9642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 623 HIS A 853 HIS B 580 HIS ** B1359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1491 GLN B1511 GLN C 237 ASN C 285 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 23386 Z= 0.252 Angle : 0.641 13.892 31771 Z= 0.332 Chirality : 0.043 0.215 3648 Planarity : 0.004 0.058 4076 Dihedral : 5.476 71.746 3268 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.34 % Favored : 90.62 % Rotamer Outliers : 0.59 % 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: -0.49 (0.16), residues: 2975 helix: 1.49 (0.14), residues: 1486 sheet: -0.75 (0.28), residues: 342 loop : -2.78 (0.16), residues: 1147 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5950 Ramachandran restraints generated. 2975 Oldfield, 0 Emsley, 2975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5950 Ramachandran restraints generated. 2975 Oldfield, 0 Emsley, 2975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 2528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 170 time to evaluate : 2.709 Fit side-chains outliers start: 14 outliers final: 4 residues processed: 179 average time/residue: 0.4189 time to fit residues: 119.6762 Evaluate side-chains 169 residues out of total 2528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 165 time to evaluate : 2.794 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2405 time to fit residues: 5.7118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 175 optimal weight: 2.9990 chunk 282 optimal weight: 2.9990 chunk 172 optimal weight: 1.9990 chunk 133 optimal weight: 6.9990 chunk 196 optimal weight: 0.1980 chunk 295 optimal weight: 3.9990 chunk 272 optimal weight: 4.9990 chunk 235 optimal weight: 3.9990 chunk 24 optimal weight: 0.0040 chunk 181 optimal weight: 0.8980 chunk 144 optimal weight: 0.9980 overall best weight: 0.8194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 623 HIS A 853 HIS B 580 HIS ** B1359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 237 ASN C 285 ASN ** D 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.2513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 23386 Z= 0.226 Angle : 0.625 13.482 31771 Z= 0.324 Chirality : 0.043 0.211 3648 Planarity : 0.004 0.057 4076 Dihedral : 5.419 71.995 3268 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.14 % Favored : 90.82 % Rotamer Outliers : 0.38 % 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: -0.40 (0.16), residues: 2975 helix: 1.58 (0.14), residues: 1480 sheet: -0.66 (0.28), residues: 341 loop : -2.75 (0.16), residues: 1154 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5950 Ramachandran restraints generated. 2975 Oldfield, 0 Emsley, 2975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5950 Ramachandran restraints generated. 2975 Oldfield, 0 Emsley, 2975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 2528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 170 time to evaluate : 2.656 Fit side-chains outliers start: 9 outliers final: 4 residues processed: 175 average time/residue: 0.3948 time to fit residues: 110.5883 Evaluate side-chains 172 residues out of total 2528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 168 time to evaluate : 2.669 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2395 time to fit residues: 5.6112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 187 optimal weight: 2.9990 chunk 250 optimal weight: 1.9990 chunk 72 optimal weight: 5.9990 chunk 217 optimal weight: 0.7980 chunk 34 optimal weight: 0.5980 chunk 65 optimal weight: 0.8980 chunk 235 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 242 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 43 optimal weight: 4.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 623 HIS A 853 HIS ** A 936 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 580 HIS ** B1359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1511 GLN C 95 ASN C 237 ASN C 285 ASN ** D 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.163589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.129518 restraints weight = 33396.185| |-----------------------------------------------------------------------------| r_work (start): 0.3622 rms_B_bonded: 3.37 r_work: 0.3096 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.2544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 23386 Z= 0.264 Angle : 0.649 13.852 31771 Z= 0.336 Chirality : 0.044 0.213 3648 Planarity : 0.004 0.056 4076 Dihedral : 5.489 71.299 3268 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.38 % Favored : 90.59 % Rotamer Outliers : 0.51 % 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: -0.48 (0.16), residues: 2975 helix: 1.46 (0.14), residues: 1488 sheet: -0.66 (0.29), residues: 346 loop : -2.76 (0.16), residues: 1141 =============================================================================== Job complete usr+sys time: 4457.40 seconds wall clock time: 82 minutes 39.36 seconds (4959.36 seconds total)