Starting phenix.real_space_refine (version: dev) on Sat Jun 4 03:12:35 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uhf_26513/06_2022/7uhf_26513_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uhf_26513/06_2022/7uhf_26513.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uhf_26513/06_2022/7uhf_26513_ligands.cif 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 { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uhf_26513/06_2022/7uhf_26513_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uhf_26513/06_2022/7uhf_26513_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uhf_26513/06_2022/7uhf_26513.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uhf_26513/06_2022/7uhf_26513.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uhf_26513/06_2022/7uhf_26513_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uhf_26513/06_2022/7uhf_26513_updated.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= 0.006 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 334": "NH1" <-> "NH2" Residue "A ASP 556": "OD1" <-> "OD2" Residue "A GLU 606": "OE1" <-> "OE2" Residue "A PHE 658": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 768": "OE1" <-> "OE2" Residue "A GLU 770": "OE1" <-> "OE2" Residue "A PHE 922": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1157": "OE1" <-> "OE2" Residue "A GLU 1160": "OE1" <-> "OE2" Residue "A PHE 1207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1431": "OE1" <-> "OE2" Residue "A TYR 1433": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1465": "OD1" <-> "OD2" Residue "A PHE 1467": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 42": "OE1" <-> "OE2" Residue "D TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 115": "OE1" <-> "OE2" Residue "D PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 182": "OE1" <-> "OE2" Residue "D ASP 300": "OD1" <-> "OD2" Residue "D GLU 367": "OE1" <-> "OE2" Residue "D TYR 409": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 513": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 654": "OE1" <-> "OE2" Residue "D ASP 665": "OD1" <-> "OD2" Residue "D PHE 679": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 686": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 719": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 733": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 764": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 801": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 986": "OD1" <-> "OD2" Residue "D ASP 1057": "OD1" <-> "OD2" Residue "C GLU 53": "OE1" <-> "OE2" Residue "C GLU 191": "OE1" <-> "OE2" Residue "C GLU 339": "OE1" <-> "OE2" Residue "C TYR 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4617/modules/chem_data/mon_lib" Total number of atoms: 20379 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 9900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1230, 9900 Classifications: {'peptide': 1230} Link IDs: {'PTRANS': 36, 'TRANS': 1193} Chain breaks: 7 Chain: "D" Number of atoms: 7570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 948, 7570 Classifications: {'peptide': 948} Link IDs: {'PTRANS': 38, 'TRANS': 907, 'PCIS': 2} Chain breaks: 5 Chain: "C" Number of atoms: 2575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2575 Classifications: {'peptide': 324} Link IDs: {'PTRANS': 18, 'TRANS': 304, 'PCIS': 1} Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 123 Unusual residues: {'N90': 1, ' CA': 1, 'Y01': 1, 'NAG': 1, '3PE': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' CA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 12.28, per 1000 atoms: 0.60 Number of scatterers: 20379 At special positions: 0 Unit cell: (171.556, 169.328, 183.81, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 2 19.99 S 112 16.00 P 1 15.00 O 3753 8.00 N 3352 7.00 C 13159 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 301 " - pdb=" SG CYS A 326 " distance=2.03 Simple disulfide: pdb=" SG CYS A 317 " - pdb=" SG CYS A 333 " distance=2.03 Simple disulfide: pdb=" SG CYS A1044 " - pdb=" SG CYS A1055 " distance=2.03 Simple disulfide: pdb=" SG CYS A1421 " - pdb=" SG CYS A1435 " distance=2.03 Simple disulfide: pdb=" SG CYS D 303 " - pdb=" SG CYS D1044 " distance=2.03 Simple disulfide: pdb=" SG CYS D 404 " - pdb=" SG CYS D1071 " distance=2.03 Simple disulfide: pdb=" SG CYS D 667 " - pdb=" SG CYS D 697 " distance=2.04 Simple disulfide: pdb=" SG CYS D 904 " - pdb=" SG CYS D 974 " distance=2.03 Simple disulfide: pdb=" SG CYS D 996 " - pdb=" SG CYS D1026 " distance=2.03 Simple disulfide: pdb=" SG CYS D 999 " - pdb=" SG CYS D1024 " distance=2.03 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 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " NAG B 3 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " NAG F 3 " " NAG F 3 " - " NAG F 4 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG B 1 " - " ASN D 184 " " NAG D1201 " - " ASN D 92 " " NAG E 1 " - " ASN D 348 " " NAG F 1 " - " ASN D 468 " " NAG G 1 " - " ASN D 613 " " NAG H 1 " - " ASN D 895 " Time building additional restraints: 8.41 Conformation dependent library (CDL) restraints added in 2.9 seconds 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4736 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 97 helices and 15 sheets defined 47.1% alpha, 8.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.04 Creating SS restraints... Processing helix chain 'A' and resid 127 through 144 Processing helix chain 'A' and resid 156 through 177 removed outlier: 3.802A pdb=" N TYR A 166 " --> pdb=" O GLU A 162 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ALA A 167 " --> pdb=" O LYS A 163 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N PHE A 168 " --> pdb=" O VAL A 164 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N THR A 176 " --> pdb=" O PHE A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 216 removed outlier: 3.518A pdb=" N GLU A 215 " --> pdb=" O SER A 211 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLN A 216 " --> pdb=" O VAL A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 253 removed outlier: 3.833A pdb=" N PHE A 242 " --> pdb=" O LEU A 239 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N VAL A 244 " --> pdb=" O ALA A 241 " (cutoff:3.500A) Proline residue: A 247 - end of helix removed outlier: 3.556A pdb=" N VAL A 251 " --> pdb=" O LEU A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 266 Processing helix chain 'A' and resid 272 through 292 Processing helix chain 'A' and resid 350 through 362 removed outlier: 3.537A pdb=" N THR A 362 " --> pdb=" O PHE A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 376 Processing helix chain 'A' and resid 382 through 391 Processing helix chain 'A' and resid 394 through 418 removed outlier: 3.660A pdb=" N PHE A 409 " --> pdb=" O LEU A 405 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLU A 414 " --> pdb=" O SER A 410 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LYS A 415 " --> pdb=" O LYS A 411 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ALA A 418 " --> pdb=" O GLU A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 444 removed outlier: 3.609A pdb=" N GLN A 429 " --> pdb=" O LEU A 425 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N GLN A 430 " --> pdb=" O ARG A 426 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LEU A 431 " --> pdb=" O GLU A 427 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N GLU A 432 " --> pdb=" O LYS A 428 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLU A 433 " --> pdb=" O GLN A 429 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LYS A 436 " --> pdb=" O GLU A 432 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLY A 437 " --> pdb=" O GLU A 433 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASP A 440 " --> pdb=" O LYS A 436 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N TRP A 441 " --> pdb=" O GLY A 437 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR A 443 " --> pdb=" O LEU A 439 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLN A 444 " --> pdb=" O ASP A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 521 removed outlier: 3.980A pdb=" N VAL A 520 " --> pdb=" O ARG A 517 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N LYS A 521 " --> pdb=" O ALA A 518 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 517 through 521' Processing helix chain 'A' and resid 523 through 541 removed outlier: 3.500A pdb=" N VAL A 531 " --> pdb=" O TRP A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 556 Processing helix chain 'A' and resid 558 through 577 Processing helix chain 'A' and resid 586 through 604 removed outlier: 3.535A pdb=" N THR A 600 " --> pdb=" O CYS A 596 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 633 removed outlier: 3.713A pdb=" N SER A 616 " --> pdb=" O PRO A 612 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU A 623 " --> pdb=" O ARG A 619 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU A 624 " --> pdb=" O CYS A 620 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ARG A 625 " --> pdb=" O VAL A 621 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N ILE A 626 " --> pdb=" O ARG A 622 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N PHE A 627 " --> pdb=" O LEU A 623 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N LYS A 628 " --> pdb=" O LEU A 624 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N VAL A 629 " --> pdb=" O ARG A 625 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N THR A 630 " --> pdb=" O ILE A 626 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N HIS A 632 " --> pdb=" O LYS A 628 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N TRP A 633 " --> pdb=" O VAL A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 649 removed outlier: 5.127A pdb=" N LYS A 648 " --> pdb=" O LEU A 644 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N SER A 649 " --> pdb=" O ASN A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 651 through 672 Processing helix chain 'A' and resid 691 through 703 Processing helix chain 'A' and resid 707 through 718 removed outlier: 3.681A pdb=" N TYR A 718 " --> pdb=" O GLY A 714 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 728 removed outlier: 4.354A pdb=" N MET A 726 " --> pdb=" O SER A 723 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ILE A 727 " --> pdb=" O SER A 724 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N VAL A 728 " --> pdb=" O GLY A 725 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 723 through 728' Processing helix chain 'A' and resid 731 through 747 removed outlier: 3.584A pdb=" N ILE A 742 " --> pdb=" O CYS A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 755 removed outlier: 3.948A pdb=" N ASP A 753 " --> pdb=" O ALA A 749 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ASN A 754 " --> pdb=" O ILE A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 757 through 760 No H-bonds generated for 'chain 'A' and resid 757 through 760' Processing helix chain 'A' and resid 763 through 767 Processing helix chain 'A' and resid 880 through 884 Processing helix chain 'A' and resid 888 through 904 removed outlier: 4.299A pdb=" N ILE A 892 " --> pdb=" O PHE A 888 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N LEU A 893 " --> pdb=" O THR A 889 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N VAL A 894 " --> pdb=" O ASN A 890 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N MET A 897 " --> pdb=" O LEU A 893 " (cutoff:3.500A) Processing helix chain 'A' and resid 914 through 940 removed outlier: 3.891A pdb=" N LEU A 935 " --> pdb=" O THR A 931 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N LEU A 936 " --> pdb=" O VAL A 932 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N MET A 938 " --> pdb=" O ILE A 934 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N THR A 940 " --> pdb=" O LEU A 936 " (cutoff:3.500A) Processing helix chain 'A' and resid 955 through 969 removed outlier: 3.832A pdb=" N VAL A 962 " --> pdb=" O ASP A 959 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL A 963 " --> pdb=" O MET A 960 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLY A 964 " --> pdb=" O LEU A 961 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU A 967 " --> pdb=" O GLY A 964 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL A 968 " --> pdb=" O VAL A 965 " (cutoff:3.500A) Processing helix chain 'A' and resid 980 through 988 removed outlier: 3.532A pdb=" N ARG A 984 " --> pdb=" O VAL A 980 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL A 985 " --> pdb=" O LYS A 981 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N VAL A 988 " --> pdb=" O ARG A 984 " (cutoff:3.500A) Processing helix chain 'A' and resid 994 through 997 No H-bonds generated for 'chain 'A' and resid 994 through 997' Processing helix chain 'A' and resid 999 through 1015 removed outlier: 3.666A pdb=" N HIS A1003 " --> pdb=" O LYS A 999 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ARG A1013 " --> pdb=" O PHE A1009 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N THR A1014 " --> pdb=" O VAL A1010 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N ILE A1015 " --> pdb=" O ALA A1011 " (cutoff:3.500A) Processing helix chain 'A' and resid 1018 through 1036 removed outlier: 3.778A pdb=" N THR A1023 " --> pdb=" O MET A1019 " (cutoff:3.500A) Processing helix chain 'A' and resid 1063 through 1065 No H-bonds generated for 'chain 'A' and resid 1063 through 1065' Processing helix chain 'A' and resid 1087 through 1098 Processing helix chain 'A' and resid 1103 through 1111 Processing helix chain 'A' and resid 1126 through 1143 removed outlier: 4.050A pdb=" N PHE A1141 " --> pdb=" O ILE A1138 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N MET A1143 " --> pdb=" O ALA A1140 " (cutoff:3.500A) Processing helix chain 'A' and resid 1148 through 1151 No H-bonds generated for 'chain 'A' and resid 1148 through 1151' Processing helix chain 'A' and resid 1158 through 1160 No H-bonds generated for 'chain 'A' and resid 1158 through 1160' Processing helix chain 'A' and resid 1170 through 1180 removed outlier: 4.093A pdb=" N GLN A1174 " --> pdb=" O ASN A1171 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N CYS A1175 " --> pdb=" O GLN A1172 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N VAL A1176 " --> pdb=" O ARG A1173 " (cutoff:3.500A) Processing helix chain 'A' and resid 1193 through 1202 removed outlier: 4.263A pdb=" N LYS A1197 " --> pdb=" O PRO A1193 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N PHE A1198 " --> pdb=" O TYR A1194 " (cutoff:3.500A) Processing helix chain 'A' and resid 1205 through 1224 removed outlier: 3.865A pdb=" N VAL A1213 " --> pdb=" O TYR A1209 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU A1217 " --> pdb=" O VAL A1213 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ASN A1218 " --> pdb=" O LEU A1214 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N THR A1219 " --> pdb=" O ILE A1215 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N MET A1224 " --> pdb=" O LEU A1220 " (cutoff:3.500A) Processing helix chain 'A' and resid 1231 through 1259 removed outlier: 3.629A pdb=" N ILE A1257 " --> pdb=" O VAL A1253 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ALA A1258 " --> pdb=" O LEU A1254 " (cutoff:3.500A) Processing helix chain 'A' and resid 1268 through 1282 removed outlier: 3.969A pdb=" N SER A1274 " --> pdb=" O ASN A1270 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU A1275 " --> pdb=" O THR A1271 " (cutoff:3.500A) Processing helix chain 'A' and resid 1316 through 1325 removed outlier: 3.711A pdb=" N PHE A1321 " --> pdb=" O PHE A1317 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ARG A1322 " --> pdb=" O PHE A1318 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N VAL A1323 " --> pdb=" O ARG A1319 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N MET A1324 " --> pdb=" O LEU A1320 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ARG A1325 " --> pdb=" O PHE A1321 " (cutoff:3.500A) Processing helix chain 'A' and resid 1327 through 1330 No H-bonds generated for 'chain 'A' and resid 1327 through 1330' Processing helix chain 'A' and resid 1336 through 1349 removed outlier: 3.568A pdb=" N PHE A1343 " --> pdb=" O LEU A1339 " (cutoff:3.500A) Processing helix chain 'A' and resid 1352 through 1372 removed outlier: 3.558A pdb=" N LEU A1356 " --> pdb=" O TYR A1352 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ILE A1357 " --> pdb=" O VAL A1353 " (cutoff:3.500A) Processing helix chain 'A' and resid 1392 through 1403 Processing helix chain 'A' and resid 1408 through 1414 Processing helix chain 'A' and resid 1438 through 1453 removed outlier: 3.957A pdb=" N ILE A1441 " --> pdb=" O ASN A1438 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE A1445 " --> pdb=" O VAL A1442 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER A1446 " --> pdb=" O TYR A1443 " (cutoff:3.500A) Processing helix chain 'A' and resid 1479 through 1491 Processing helix chain 'A' and resid 1503 through 1510 removed outlier: 4.138A pdb=" N VAL A1506 " --> pdb=" O LEU A1503 " (cutoff:3.500A) Processing helix chain 'A' and resid 1523 through 1533 removed outlier: 4.606A pdb=" N CYS A1528 " --> pdb=" O HIS A1524 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N LYS A1529 " --> pdb=" O ARG A1525 " (cutoff:3.500A) Processing helix chain 'A' and resid 1547 through 1557 removed outlier: 3.522A pdb=" N PHE A1551 " --> pdb=" O ASN A1547 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ALA A1552 " --> pdb=" O ALA A1548 " (cutoff:3.500A) Processing helix chain 'A' and resid 1565 through 1575 Processing helix chain 'A' and resid 1584 through 1587 No H-bonds generated for 'chain 'A' and resid 1584 through 1587' Processing helix chain 'D' and resid 30 through 52 removed outlier: 3.520A pdb=" N TRP D 36 " --> pdb=" O THR D 32 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N MET D 40 " --> pdb=" O TRP D 36 " (cutoff:3.500A) Processing helix chain 'D' and resid 54 through 64 removed outlier: 3.660A pdb=" N TYR D 64 " --> pdb=" O ILE D 60 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 110 removed outlier: 3.583A pdb=" N GLU D 80 " --> pdb=" O ARG D 76 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU D 100 " --> pdb=" O ALA D 96 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N GLU D 103 " --> pdb=" O ARG D 99 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ALA D 104 " --> pdb=" O LEU D 100 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA D 110 " --> pdb=" O LYS D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 199 removed outlier: 3.580A pdb=" N TRP D 185 " --> pdb=" O ASN D 181 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR D 186 " --> pdb=" O GLU D 182 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N SER D 187 " --> pdb=" O LEU D 183 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ALA D 188 " --> pdb=" O ASN D 184 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N LEU D 189 " --> pdb=" O TRP D 185 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ASP D 190 " --> pdb=" O THR D 186 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N GLU D 191 " --> pdb=" O SER D 187 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N VAL D 192 " --> pdb=" O ALA D 188 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N GLU D 199 " --> pdb=" O LYS D 195 " (cutoff:3.500A) Processing helix chain 'D' and resid 238 through 240 No H-bonds generated for 'chain 'D' and resid 238 through 240' Processing helix chain 'D' and resid 242 through 248 removed outlier: 3.945A pdb=" N GLY D 247 " --> pdb=" O TRP D 243 " (cutoff:3.500A) Processing helix chain 'D' and resid 262 through 264 No H-bonds generated for 'chain 'D' and resid 262 through 264' Processing helix chain 'D' and resid 267 through 282 removed outlier: 3.777A pdb=" N GLU D 281 " --> pdb=" O SER D 277 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N THR D 282 " --> pdb=" O GLU D 278 " (cutoff:3.500A) Processing helix chain 'D' and resid 312 through 324 removed outlier: 4.081A pdb=" N ASN D 324 " --> pdb=" O ASP D 320 " (cutoff:3.500A) Processing helix chain 'D' and resid 333 through 344 removed outlier: 3.520A pdb=" N GLN D 343 " --> pdb=" O PHE D 339 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 376 removed outlier: 3.747A pdb=" N LYS D 375 " --> pdb=" O GLU D 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 397 through 405 removed outlier: 3.608A pdb=" N ALA D 403 " --> pdb=" O ILE D 399 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 422 removed outlier: 4.530A pdb=" N ARG D 420 " --> pdb=" O GLY D 417 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ILE D 421 " --> pdb=" O ALA D 418 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASN D 422 " --> pdb=" O ILE D 419 " (cutoff:3.500A) Processing helix chain 'D' and resid 425 through 430 removed outlier: 3.601A pdb=" N LEU D 430 " --> pdb=" O LEU D 427 " (cutoff:3.500A) Processing helix chain 'D' and resid 432 through 441 removed outlier: 3.902A pdb=" N GLY D 438 " --> pdb=" O MET D 434 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ASP D 439 " --> pdb=" O VAL D 435 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N LYS D 440 " --> pdb=" O LEU D 436 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N ALA D 441 " --> pdb=" O ALA D 437 " (cutoff:3.500A) Processing helix chain 'D' and resid 494 through 500 removed outlier: 3.797A pdb=" N LEU D 500 " --> pdb=" O ASP D 496 " (cutoff:3.500A) Processing helix chain 'D' and resid 561 through 564 No H-bonds generated for 'chain 'D' and resid 561 through 564' Processing helix chain 'D' and resid 569 through 579 removed outlier: 3.631A pdb=" N GLU D 573 " --> pdb=" O ASP D 569 " (cutoff:3.500A) Processing helix chain 'D' and resid 638 through 648 removed outlier: 3.507A pdb=" N TYR D 644 " --> pdb=" O THR D 640 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N LEU D 648 " --> pdb=" O TYR D 644 " (cutoff:3.500A) Processing helix chain 'D' and resid 650 through 656 removed outlier: 3.644A pdb=" N PHE D 653 " --> pdb=" O PRO D 650 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N GLU D 654 " --> pdb=" O ASP D 651 " (cutoff:3.500A) Processing helix chain 'D' and resid 679 through 688 removed outlier: 3.511A pdb=" N ASP D 688 " --> pdb=" O ASN D 684 " (cutoff:3.500A) Processing helix chain 'D' and resid 700 through 718 removed outlier: 4.046A pdb=" N VAL D 705 " --> pdb=" O LEU D 701 " (cutoff:3.500A) Processing helix chain 'D' and resid 748 through 750 No H-bonds generated for 'chain 'D' and resid 748 through 750' Processing helix chain 'D' and resid 758 through 760 No H-bonds generated for 'chain 'D' and resid 758 through 760' Processing helix chain 'D' and resid 762 through 769 removed outlier: 3.674A pdb=" N ASP D 769 " --> pdb=" O LYS D 765 " (cutoff:3.500A) Processing helix chain 'D' and resid 818 through 826 removed outlier: 3.608A pdb=" N GLU D 823 " --> pdb=" O ASN D 819 " (cutoff:3.500A) Processing helix chain 'D' and resid 866 through 869 No H-bonds generated for 'chain 'D' and resid 866 through 869' Processing helix chain 'D' and resid 875 through 877 No H-bonds generated for 'chain 'D' and resid 875 through 877' Processing helix chain 'D' and resid 880 through 888 removed outlier: 3.524A pdb=" N HIS D 885 " --> pdb=" O SER D 881 " (cutoff:3.500A) Processing helix chain 'D' and resid 1043 through 1046 No H-bonds generated for 'chain 'D' and resid 1043 through 1046' Processing helix chain 'C' and resid 39 through 54 removed outlier: 3.927A pdb=" N GLU C 53 " --> pdb=" O GLN C 49 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ARG C 54 " --> pdb=" O GLN C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 131 Processing helix chain 'C' and resid 156 through 158 No H-bonds generated for 'chain 'C' and resid 156 through 158' Processing helix chain 'C' and resid 191 through 207 removed outlier: 3.626A pdb=" N MET C 195 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N MET C 196 " --> pdb=" O VAL C 192 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N LEU C 200 " --> pdb=" O MET C 196 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG C 207 " --> pdb=" O PHE C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 263 removed outlier: 3.721A pdb=" N GLN C 251 " --> pdb=" O ILE C 247 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N SER C 252 " --> pdb=" O ALA C 248 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLU C 253 " --> pdb=" O GLU C 249 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE C 254 " --> pdb=" O VAL C 250 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG C 256 " --> pdb=" O SER C 252 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER C 263 " --> pdb=" O GLU C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 307 Processing helix chain 'C' and resid 315 through 326 removed outlier: 3.533A pdb=" N MET C 320 " --> pdb=" O THR C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 332 No H-bonds generated for 'chain 'C' and resid 330 through 332' Processing helix chain 'C' and resid 342 through 360 removed outlier: 3.581A pdb=" N HIS C 348 " --> pdb=" O ASP C 344 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N LEU C 349 " --> pdb=" O ALA C 345 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N TYR C 352 " --> pdb=" O HIS C 348 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 301 through 303 Processing sheet with id= B, first strand: chain 'A' and resid 1058 through 1062 Processing sheet with id= C, first strand: chain 'D' and resid 68 through 72 Processing sheet with id= D, first strand: chain 'D' and resid 122 through 124 Processing sheet with id= E, first strand: chain 'D' and resid 165 through 167 removed outlier: 6.714A pdb=" N VAL D 466 " --> pdb=" O LEU D 485 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N VAL D 487 " --> pdb=" O LEU D 464 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N LEU D 464 " --> pdb=" O VAL D 487 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'D' and resid 298 through 300 removed outlier: 8.400A pdb=" N ALA D 292 " --> pdb=" O MET D 254 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N ILE D 256 " --> pdb=" O ALA D 292 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N PHE D 294 " --> pdb=" O ILE D 256 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N VAL D 258 " --> pdb=" O PHE D 294 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ASN D 355 " --> pdb=" O ASP D 253 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N LEU D 255 " --> pdb=" O ASN D 355 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ILE D 357 " --> pdb=" O LEU D 255 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N LEU D 257 " --> pdb=" O ILE D 357 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N MET D 359 " --> pdb=" O LEU D 257 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N ASP D 259 " --> pdb=" O MET D 359 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N PHE D 361 " --> pdb=" O ASP D 259 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ARG D 383 " --> pdb=" O ILE D 358 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N LEU D 360 " --> pdb=" O ARG D 383 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N PHE D 385 " --> pdb=" O LEU D 360 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N THR D 362 " --> pdb=" O PHE D 385 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N PHE D 387 " --> pdb=" O THR D 362 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 459 through 461 Processing sheet with id= H, first strand: chain 'D' and resid 511 through 515 removed outlier: 3.552A pdb=" N SER D 618 " --> pdb=" O ILE D 515 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N TYR D 617 " --> pdb=" O VAL D 612 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'D' and resid 658 through 661 removed outlier: 4.513A pdb=" N ILE D 740 " --> pdb=" O THR D 736 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N LYS D 815 " --> pdb=" O LYS D 730 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N ARG D 732 " --> pdb=" O GLY D 813 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N GLY D 813 " --> pdb=" O ARG D 732 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N VAL D 734 " --> pdb=" O VAL D 811 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N VAL D 811 " --> pdb=" O VAL D 734 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N MET D 793 " --> pdb=" O THR D 776 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 849 through 854 removed outlier: 3.578A pdb=" N GLY D 992 " --> pdb=" O PHE D1003 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 892 through 899 removed outlier: 3.640A pdb=" N GLN D 980 " --> pdb=" O ASN D 895 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ILE D 975 " --> pdb=" O SER D1038 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 902 through 904 removed outlier: 3.579A pdb=" N SER D 902 " --> pdb=" O CYS D 974 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLN D 972 " --> pdb=" O CYS D 904 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 62 through 66 removed outlier: 3.944A pdb=" N VAL C 64 " --> pdb=" O LEU C 93 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU C 93 " --> pdb=" O VAL C 64 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR C 66 " --> pdb=" O ASP C 91 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 180 through 183 removed outlier: 5.842A pdb=" N ILE C 288 " --> pdb=" O VAL C 181 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N VAL C 183 " --> pdb=" O ILE C 288 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N VAL C 290 " --> pdb=" O VAL C 183 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N VAL C 335 " --> pdb=" O PHE C 291 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'C' and resid 212 through 215 removed outlier: 6.334A pdb=" N LEU C 266 " --> pdb=" O SER C 213 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N THR C 215 " --> pdb=" O LEU C 266 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N VAL C 268 " --> pdb=" O THR C 215 " (cutoff:3.500A) No H-bonds generated for sheet with id= O 755 hydrogen bonds defined for protein. 2052 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: 6.89 Time building geometry restraints manager: 9.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 3809 1.33 - 1.45: 5203 1.45 - 1.57: 11621 1.57 - 1.70: 7 1.70 - 1.82: 176 Bond restraints: 20816 Sorted by residual: bond pdb=" C07 N90 A2201 " pdb=" N14 N90 A2201 " ideal model delta sigma weight residual 1.480 1.288 0.192 2.00e-02 2.50e+03 9.22e+01 bond pdb=" C20 N90 A2201 " pdb=" N17 N90 A2201 " ideal model delta sigma weight residual 1.486 1.336 0.150 2.00e-02 2.50e+03 5.61e+01 bond pdb=" CAK Y01 A2204 " pdb=" CBD Y01 A2204 " ideal model delta sigma weight residual 1.525 1.639 -0.114 2.00e-02 2.50e+03 3.25e+01 bond pdb=" CBD Y01 A2204 " pdb=" CBG Y01 A2204 " ideal model delta sigma weight residual 1.520 1.412 0.108 2.00e-02 2.50e+03 2.94e+01 bond pdb=" C15 N90 A2201 " pdb=" N14 N90 A2201 " ideal model delta sigma weight residual 1.459 1.355 0.104 2.00e-02 2.50e+03 2.68e+01 ... (remaining 20811 not shown) Histogram of bond angle deviations from ideal: 92.69 - 100.95: 36 100.95 - 109.22: 1254 109.22 - 117.49: 13827 117.49 - 125.75: 12797 125.75 - 134.02: 273 Bond angle restraints: 28187 Sorted by residual: angle pdb=" CAD Y01 A2204 " pdb=" CBH Y01 A2204 " pdb=" CAT Y01 A2204 " ideal model delta sigma weight residual 109.59 128.45 -18.86 3.00e+00 1.11e-01 3.95e+01 angle pdb=" N ILE A1012 " pdb=" CA ILE A1012 " pdb=" C ILE A1012 " ideal model delta sigma weight residual 110.62 116.77 -6.15 1.14e+00 7.69e-01 2.91e+01 angle pdb=" CAD Y01 A2204 " pdb=" CBH Y01 A2204 " pdb=" CAZ Y01 A2204 " ideal model delta sigma weight residual 108.53 93.63 14.90 3.00e+00 1.11e-01 2.47e+01 angle pdb=" C SER A 723 " pdb=" CA SER A 723 " pdb=" CB SER A 723 " ideal model delta sigma weight residual 115.79 109.99 5.80 1.19e+00 7.06e-01 2.38e+01 angle pdb=" CAK Y01 A2204 " pdb=" CBD Y01 A2204 " pdb=" CBG Y01 A2204 " ideal model delta sigma weight residual 110.32 96.36 13.96 3.00e+00 1.11e-01 2.16e+01 ... (remaining 28182 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.48: 11389 22.48 - 44.97: 889 44.97 - 67.45: 102 67.45 - 89.93: 37 89.93 - 112.41: 12 Dihedral angle restraints: 12429 sinusoidal: 5112 harmonic: 7317 Sorted by residual: dihedral pdb=" CB CYS D 904 " pdb=" SG CYS D 904 " pdb=" SG CYS D 974 " pdb=" CB CYS D 974 " ideal model delta sinusoidal sigma weight residual 93.00 160.63 -67.63 1 1.00e+01 1.00e-02 5.95e+01 dihedral pdb=" C1 NAG H 1 " pdb=" C2 NAG H 1 " pdb=" C3 NAG H 1 " pdb=" C4 NAG H 1 " ideal model delta sinusoidal sigma weight residual -50.00 57.79 -107.79 1 2.00e+01 2.50e-03 3.13e+01 dihedral pdb=" C2 NAG B 3 " pdb=" C3 NAG B 3 " pdb=" C4 NAG B 3 " pdb=" C5 NAG B 3 " ideal model delta sinusoidal sigma weight residual 50.00 -51.39 101.39 1 2.00e+01 2.50e-03 2.87e+01 ... (remaining 12426 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.127: 3180 0.127 - 0.255: 27 0.255 - 0.382: 2 0.382 - 0.509: 2 0.509 - 0.636: 1 Chirality restraints: 3212 Sorted by residual: chirality pdb=" C1 NAG G 1 " pdb=" ND2 ASN D 613 " pdb=" C2 NAG G 1 " pdb=" O5 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.76 -0.64 2.00e-01 2.50e+01 1.01e+01 chirality pdb=" C1 NAG B 1 " pdb=" ND2 ASN D 184 " pdb=" C2 NAG B 1 " pdb=" O5 NAG B 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.97 -0.43 2.00e-01 2.50e+01 4.58e+00 chirality pdb=" CBG Y01 A2204 " pdb=" CAQ Y01 A2204 " pdb=" CBD Y01 A2204 " pdb=" CBI Y01 A2204 " both_signs ideal model delta sigma weight residual False -2.33 -2.75 0.42 2.00e-01 2.50e+01 4.43e+00 ... (remaining 3209 not shown) Planarity restraints: 3565 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A2202 " 0.214 2.00e-02 2.50e+03 1.79e-01 3.99e+02 pdb=" C7 NAG A2202 " -0.056 2.00e-02 2.50e+03 pdb=" C8 NAG A2202 " 0.152 2.00e-02 2.50e+03 pdb=" N2 NAG A2202 " -0.296 2.00e-02 2.50e+03 pdb=" O7 NAG A2202 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN D 675 " -0.016 2.00e-02 2.50e+03 3.23e-02 1.04e+01 pdb=" C ASN D 675 " 0.056 2.00e-02 2.50e+03 pdb=" O ASN D 675 " -0.021 2.00e-02 2.50e+03 pdb=" N ASN D 676 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN A1428 " -0.038 5.00e-02 4.00e+02 5.78e-02 5.34e+00 pdb=" N PRO A1429 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO A1429 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A1429 " -0.032 5.00e-02 4.00e+02 ... (remaining 3562 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 180 2.62 - 3.19: 17948 3.19 - 3.76: 30270 3.76 - 4.33: 42096 4.33 - 4.90: 68511 Nonbonded interactions: 159005 Sorted by model distance: nonbonded pdb=" O3 NAG A2202 " pdb=" O7 NAG A2202 " model vdw 2.053 2.440 nonbonded pdb=" O TRP A 550 " pdb=" CG2 ILE A 554 " model vdw 2.201 3.460 nonbonded pdb=" OE1 GLN A 359 " pdb=" OH TYR A 712 " model vdw 2.204 2.440 nonbonded pdb=" O4 NAG E 2 " pdb=" O7 NAG E 2 " model vdw 2.225 2.440 nonbonded pdb=" OD1 ASP D 516 " pdb=" CD PRO D 517 " model vdw 2.233 3.440 ... (remaining 159000 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 'E' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 2 9.91 5 P 1 5.49 5 S 112 5.16 5 C 13159 2.51 5 N 3352 2.21 5 O 3753 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.320 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: 0.010 Extract box with map and model: 6.960 Check model and map are aligned: 0.310 Convert atoms to be neutral: 0.180 Process input model: 52.700 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Set scattering table: 0.020 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 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 0.192 20816 Z= 0.265 Angle : 0.688 18.864 28187 Z= 0.375 Chirality : 0.047 0.636 3212 Planarity : 0.005 0.179 3559 Dihedral : 15.944 112.413 7663 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.50 % Favored : 94.38 % Rotamer Outliers : 2.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: -1.07 (0.17), residues: 2472 helix: -0.23 (0.15), residues: 1138 sheet: -0.19 (0.34), residues: 252 loop : -1.27 (0.18), residues: 1082 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 276 time to evaluate : 2.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 51 outliers final: 33 residues processed: 314 average time/residue: 0.2873 time to fit residues: 145.1570 Evaluate side-chains 268 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 235 time to evaluate : 2.381 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 0 residues processed: 33 average time/residue: 0.2087 time to fit residues: 15.5717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 210 optimal weight: 10.0000 chunk 188 optimal weight: 6.9990 chunk 104 optimal weight: 3.9990 chunk 64 optimal weight: 0.0060 chunk 127 optimal weight: 0.5980 chunk 100 optimal weight: 3.9990 chunk 195 optimal weight: 7.9990 chunk 75 optimal weight: 1.9990 chunk 118 optimal weight: 9.9990 chunk 145 optimal weight: 3.9990 chunk 226 optimal weight: 20.0000 overall best weight: 2.1202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 359 GLN A 555 GLN A 754 ASN ** A 765 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1017 ASN A1114 ASN A1218 ASN ** A1457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 111 HIS D 323 ASN D1004 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.1073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.054 20816 Z= 0.285 Angle : 0.604 9.639 28187 Z= 0.314 Chirality : 0.046 0.635 3212 Planarity : 0.004 0.058 3559 Dihedral : 8.572 113.806 2848 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.42 % Favored : 94.54 % Rotamer Outliers : 1.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: -1.00 (0.16), residues: 2472 helix: -0.01 (0.15), residues: 1165 sheet: -0.40 (0.32), residues: 256 loop : -1.40 (0.18), residues: 1051 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 237 time to evaluate : 2.269 Fit side-chains revert: symmetry clash outliers start: 25 outliers final: 15 residues processed: 254 average time/residue: 0.2898 time to fit residues: 119.2483 Evaluate side-chains 241 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 226 time to evaluate : 2.300 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.2115 time to fit residues: 9.0425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 125 optimal weight: 5.9990 chunk 70 optimal weight: 2.9990 chunk 188 optimal weight: 4.9990 chunk 153 optimal weight: 0.1980 chunk 62 optimal weight: 7.9990 chunk 226 optimal weight: 20.0000 chunk 244 optimal weight: 10.0000 chunk 201 optimal weight: 7.9990 chunk 224 optimal weight: 0.8980 chunk 77 optimal weight: 0.6980 chunk 181 optimal weight: 0.8980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 GLN A 359 GLN ** A 754 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 765 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.1265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.059 20816 Z= 0.189 Angle : 0.536 9.982 28187 Z= 0.279 Chirality : 0.043 0.597 3212 Planarity : 0.004 0.056 3559 Dihedral : 8.368 106.747 2848 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.94 % Favored : 95.02 % Rotamer Outliers : 0.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: -0.84 (0.16), residues: 2472 helix: 0.18 (0.15), residues: 1172 sheet: -0.47 (0.31), residues: 266 loop : -1.37 (0.19), residues: 1034 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 235 time to evaluate : 2.267 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 8 residues processed: 249 average time/residue: 0.2902 time to fit residues: 116.4742 Evaluate side-chains 225 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 217 time to evaluate : 2.213 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1877 time to fit residues: 6.3963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 223 optimal weight: 0.4980 chunk 170 optimal weight: 2.9990 chunk 117 optimal weight: 5.9990 chunk 25 optimal weight: 0.8980 chunk 108 optimal weight: 0.8980 chunk 152 optimal weight: 0.9980 chunk 227 optimal weight: 0.1980 chunk 240 optimal weight: 0.9980 chunk 118 optimal weight: 5.9990 chunk 215 optimal weight: 7.9990 chunk 64 optimal weight: 6.9990 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 359 GLN ** A 765 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1156 GLN ** A1457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.1447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.059 20816 Z= 0.154 Angle : 0.519 11.049 28187 Z= 0.270 Chirality : 0.042 0.579 3212 Planarity : 0.004 0.086 3559 Dihedral : 8.238 105.831 2848 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.02 % Favored : 94.94 % Rotamer Outliers : 1.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: -0.74 (0.17), residues: 2472 helix: 0.28 (0.15), residues: 1177 sheet: -0.31 (0.32), residues: 256 loop : -1.39 (0.19), residues: 1039 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 235 time to evaluate : 2.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 10 residues processed: 250 average time/residue: 0.2825 time to fit residues: 115.2481 Evaluate side-chains 227 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 217 time to evaluate : 2.195 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1883 time to fit residues: 6.9036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 200 optimal weight: 0.4980 chunk 136 optimal weight: 4.9990 chunk 3 optimal weight: 0.6980 chunk 179 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 205 optimal weight: 7.9990 chunk 166 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 122 optimal weight: 0.0670 chunk 216 optimal weight: 6.9990 chunk 60 optimal weight: 0.9990 overall best weight: 0.5920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 359 GLN ** A 765 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1114 ASN A1156 GLN A1218 ASN ** A1457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.1556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.059 20816 Z= 0.148 Angle : 0.522 12.875 28187 Z= 0.267 Chirality : 0.042 0.570 3212 Planarity : 0.003 0.053 3559 Dihedral : 8.174 105.776 2848 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.85 % Favored : 95.11 % Rotamer Outliers : 0.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: -0.64 (0.17), residues: 2472 helix: 0.40 (0.15), residues: 1183 sheet: -0.31 (0.31), residues: 257 loop : -1.37 (0.19), residues: 1032 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 220 time to evaluate : 2.438 Fit side-chains revert: symmetry clash outliers start: 18 outliers final: 7 residues processed: 233 average time/residue: 0.2949 time to fit residues: 111.0530 Evaluate side-chains 213 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 206 time to evaluate : 2.307 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1900 time to fit residues: 5.7278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 80 optimal weight: 0.5980 chunk 216 optimal weight: 0.8980 chunk 47 optimal weight: 0.2980 chunk 141 optimal weight: 3.9990 chunk 59 optimal weight: 7.9990 chunk 240 optimal weight: 4.9990 chunk 199 optimal weight: 6.9990 chunk 111 optimal weight: 9.9990 chunk 20 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 126 optimal weight: 0.0060 overall best weight: 0.9598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 341 ASN A 359 GLN ** A 765 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1114 ASN A1457 ASN D1062 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.1669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.075 20816 Z= 0.171 Angle : 0.525 13.241 28187 Z= 0.270 Chirality : 0.042 0.575 3212 Planarity : 0.004 0.100 3559 Dihedral : 8.150 105.508 2848 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.94 % Favored : 95.02 % Rotamer Outliers : 1.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.17), residues: 2472 helix: 0.44 (0.15), residues: 1192 sheet: -0.22 (0.32), residues: 251 loop : -1.36 (0.19), residues: 1029 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 219 time to evaluate : 2.176 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 9 residues processed: 235 average time/residue: 0.2933 time to fit residues: 112.3203 Evaluate side-chains 227 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 218 time to evaluate : 2.229 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1886 time to fit residues: 6.4158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 232 optimal weight: 5.9990 chunk 27 optimal weight: 9.9990 chunk 137 optimal weight: 1.9990 chunk 175 optimal weight: 4.9990 chunk 136 optimal weight: 5.9990 chunk 202 optimal weight: 7.9990 chunk 134 optimal weight: 0.0060 chunk 239 optimal weight: 5.9990 chunk 150 optimal weight: 0.9980 chunk 146 optimal weight: 1.9990 chunk 110 optimal weight: 9.9990 overall best weight: 2.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 GLN A 359 GLN ** A 765 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1114 ASN C 318 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.1794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.105 20816 Z= 0.267 Angle : 0.580 13.472 28187 Z= 0.299 Chirality : 0.045 0.613 3212 Planarity : 0.004 0.059 3559 Dihedral : 8.290 105.390 2848 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.98 % Favored : 94.98 % Rotamer Outliers : 0.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: -0.69 (0.17), residues: 2472 helix: 0.36 (0.15), residues: 1188 sheet: -0.29 (0.31), residues: 251 loop : -1.42 (0.18), residues: 1033 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 227 time to evaluate : 2.333 Fit side-chains revert: symmetry clash outliers start: 20 outliers final: 7 residues processed: 241 average time/residue: 0.2983 time to fit residues: 117.0723 Evaluate side-chains 218 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 211 time to evaluate : 2.336 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2366 time to fit residues: 6.1122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 148 optimal weight: 0.9980 chunk 95 optimal weight: 9.9990 chunk 143 optimal weight: 0.0980 chunk 72 optimal weight: 3.9990 chunk 47 optimal weight: 0.0670 chunk 46 optimal weight: 2.9990 chunk 152 optimal weight: 0.7980 chunk 163 optimal weight: 1.9990 chunk 118 optimal weight: 0.9990 chunk 22 optimal weight: 0.7980 chunk 188 optimal weight: 0.7980 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 638 ASN ** A 765 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1114 ASN D 377 ASN D1062 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.216 20816 Z= 0.183 Angle : 0.551 18.528 28187 Z= 0.289 Chirality : 0.043 0.558 3212 Planarity : 0.004 0.107 3559 Dihedral : 8.113 105.290 2848 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.37 % Favored : 95.59 % Rotamer Outliers : 0.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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 (0.17), residues: 2472 helix: 0.54 (0.15), residues: 1183 sheet: -0.21 (0.32), residues: 251 loop : -1.37 (0.18), residues: 1038 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 225 time to evaluate : 2.259 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 6 residues processed: 237 average time/residue: 0.3014 time to fit residues: 116.0986 Evaluate side-chains 223 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 217 time to evaluate : 2.381 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1790 time to fit residues: 5.2467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 218 optimal weight: 4.9990 chunk 229 optimal weight: 20.0000 chunk 209 optimal weight: 6.9990 chunk 223 optimal weight: 20.0000 chunk 134 optimal weight: 0.0980 chunk 97 optimal weight: 6.9990 chunk 175 optimal weight: 4.9990 chunk 68 optimal weight: 0.9980 chunk 202 optimal weight: 6.9990 chunk 211 optimal weight: 0.9990 chunk 222 optimal weight: 6.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 GLN A 359 GLN ** A 765 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1114 ASN D 314 ASN ** D 863 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.366 20816 Z= 0.398 Angle : 0.690 33.829 28187 Z= 0.355 Chirality : 0.046 0.629 3212 Planarity : 0.004 0.114 3559 Dihedral : 8.357 105.606 2848 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.02 % Favored : 94.94 % Rotamer Outliers : 0.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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 (0.17), residues: 2472 helix: 0.35 (0.15), residues: 1187 sheet: -0.29 (0.31), residues: 252 loop : -1.43 (0.19), residues: 1033 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 228 time to evaluate : 2.425 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 5 residues processed: 238 average time/residue: 0.2972 time to fit residues: 116.1537 Evaluate side-chains 229 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 224 time to evaluate : 2.258 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1950 time to fit residues: 5.0107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 146 optimal weight: 0.8980 chunk 236 optimal weight: 20.0000 chunk 144 optimal weight: 3.9990 chunk 112 optimal weight: 10.0000 chunk 164 optimal weight: 4.9990 chunk 248 optimal weight: 20.0000 chunk 228 optimal weight: 7.9990 chunk 197 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 chunk 152 optimal weight: 0.6980 chunk 121 optimal weight: 3.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 754 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 765 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1114 ASN A1218 ASN ** D 863 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.2125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.087 20816 Z= 0.300 Angle : 0.601 12.802 28187 Z= 0.310 Chirality : 0.046 0.611 3212 Planarity : 0.004 0.113 3559 Dihedral : 8.367 105.487 2848 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.14 % Favored : 94.82 % Rotamer Outliers : 0.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: -0.77 (0.16), residues: 2472 helix: 0.32 (0.15), residues: 1185 sheet: -0.45 (0.31), residues: 266 loop : -1.47 (0.19), residues: 1021 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 223 time to evaluate : 2.415 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 5 residues processed: 227 average time/residue: 0.3107 time to fit residues: 114.6770 Evaluate side-chains 222 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 217 time to evaluate : 2.340 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1808 time to fit residues: 5.1313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 156 optimal weight: 0.9980 chunk 210 optimal weight: 2.9990 chunk 60 optimal weight: 6.9990 chunk 182 optimal weight: 4.9990 chunk 29 optimal weight: 5.9990 chunk 54 optimal weight: 8.9990 chunk 197 optimal weight: 2.9990 chunk 82 optimal weight: 8.9990 chunk 203 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 36 optimal weight: 0.2980 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 GLN ** A 638 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 754 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 765 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 863 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 197 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.207368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.138575 restraints weight = 25847.257| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 3.46 r_work: 0.3438 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.3415 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work: 0.3390 rms_B_bonded: 3.19 restraints_weight: 0.1250 r_work: 0.3362 rms_B_bonded: 3.35 restraints_weight: 0.0625 r_work: 0.3328 rms_B_bonded: 3.61 restraints_weight: 0.0312 r_work: 0.3288 rms_B_bonded: 4.01 restraints_weight: 0.0156 r_work: 0.3237 rms_B_bonded: 4.62 restraints_weight: 0.0078 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.452 20816 Z= 0.341 Angle : 0.629 29.268 28187 Z= 0.334 Chirality : 0.045 0.607 3212 Planarity : 0.004 0.108 3559 Dihedral : 8.345 105.475 2848 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.10 % Favored : 94.86 % Rotamer Outliers : 0.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: -0.71 (0.16), residues: 2472 helix: 0.38 (0.15), residues: 1181 sheet: -0.42 (0.31), residues: 263 loop : -1.45 (0.18), residues: 1028 =============================================================================== Job complete usr+sys time: 3626.02 seconds wall clock time: 66 minutes 58.50 seconds (4018.50 seconds total)