Starting phenix.real_space_refine (version: dev) on Sun Feb 26 06:44:55 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nd9_12280/02_2023/7nd9_12280.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nd9_12280/02_2023/7nd9_12280.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nd9_12280/02_2023/7nd9_12280.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nd9_12280/02_2023/7nd9_12280.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nd9_12280/02_2023/7nd9_12280.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nd9_12280/02_2023/7nd9_12280.pdb" } resolution = 2.8 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= 0.002 sd= 0.028 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "B TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 817": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 27336 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 7625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 993, 7625 Classifications: {'peptide': 993} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 48, 'TRANS': 944} Chain breaks: 8 Unresolved non-hydrogen bonds: 123 Unresolved non-hydrogen angles: 147 Unresolved non-hydrogen dihedrals: 101 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 2, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 86 Chain: "B" Number of atoms: 7993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1043, 7993 Classifications: {'peptide': 1043} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 52, 'TRANS': 990} Chain breaks: 8 Unresolved non-hydrogen bonds: 145 Unresolved non-hydrogen angles: 174 Unresolved non-hydrogen dihedrals: 116 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 10, 'ASN:plan1': 4, 'ARG:plan': 3, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 91 Chain: "C" Number of atoms: 7750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1013, 7750 Classifications: {'peptide': 1013} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PTRANS': 49, 'TRANS': 963} Chain breaks: 7 Unresolved non-hydrogen bonds: 146 Unresolved non-hydrogen angles: 176 Unresolved non-hydrogen dihedrals: 116 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 10, 'ASN:plan1': 4, 'ARG:plan': 1, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 93 Chain: "H" Number of atoms: 1633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1633 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 206} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "L" Number of atoms: 1639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1639 Classifications: {'peptide': 214} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 201} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" 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: "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: 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: "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: "I" 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: "J" 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: "K" 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: "M" 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: "N" 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: "O" 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: "P" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 14.96, per 1000 atoms: 0.55 Number of scatterers: 27336 At special positions: 0 Unit cell: (122.84, 127.82, 258.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 121 16.00 O 5331 8.00 N 4482 7.00 C 17402 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=44, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B 840 " - pdb=" SG CYS B 851 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C 840 " - pdb=" SG CYS C 851 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 101 " - pdb=" SG CYS H 106 " distance=2.03 Simple disulfide: pdb=" SG CYS H 150 " - pdb=" SG CYS H 206 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS L 135 " - pdb=" SG CYS L 195 " distance=2.04 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 D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " BETA1-6 " NAG P 1 " - " FUC P 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG A1301 " - " ASN A 282 " " NAG A1302 " - " ASN A 331 " " NAG A1303 " - " ASN A 343 " " NAG A1304 " - " ASN A 603 " " NAG A1305 " - " ASN A 616 " " NAG A1306 " - " ASN A 657 " " NAG A1307 " - " ASN A 709 " " NAG A1308 " - " ASN A1074 " " NAG A1309 " - " ASN A1098 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 234 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B 331 " " NAG B1305 " - " ASN B 616 " " NAG B1306 " - " ASN B 657 " " NAG B1307 " - " ASN B 709 " " NAG B1308 " - " ASN B 717 " " NAG B1309 " - " ASN B1074 " " NAG B1310 " - " ASN B 343 " " NAG C1301 " - " ASN C 282 " " NAG C1302 " - " ASN C 331 " " NAG C1303 " - " ASN C 616 " " NAG C1304 " - " ASN C 657 " " NAG C1305 " - " ASN C 709 " " NAG C1306 " - " ASN C1074 " " NAG C1307 " - " ASN C1134 " " NAG C1308 " - " ASN C 343 " " NAG D 1 " - " ASN A 234 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN A 801 " " NAG G 1 " - " ASN A1134 " " NAG I 1 " - " ASN B 801 " " NAG J 1 " - " ASN B1098 " " NAG K 1 " - " ASN B1134 " " NAG M 1 " - " ASN C 717 " " NAG N 1 " - " ASN C 801 " " NAG O 1 " - " ASN C1098 " " NAG P 1 " - " ASN H 102 " Time building additional restraints: 11.17 Conformation dependent library (CDL) restraints added in 4.7 seconds 6848 Ramachandran restraints generated. 3424 Oldfield, 0 Emsley, 3424 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6512 Finding SS restraints... Secondary structure from input PDB file: 88 helices and 55 sheets defined 25.6% alpha, 27.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.44 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.705A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 365 through 371 removed outlier: 3.863A pdb=" N SER A 371 " --> pdb=" O VAL A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 389 removed outlier: 3.608A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.128A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 760 through 783 Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 850 through 854 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.732A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 913 through 919 Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.516A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1032 removed outlier: 4.506A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1147 Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.360A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 619 through 624 Processing helix chain 'B' and resid 625 through 629 Processing helix chain 'B' and resid 633 through 637 removed outlier: 3.611A pdb=" N SER B 637 " --> pdb=" O ARG B 634 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 Processing helix chain 'B' and resid 816 through 824 Processing helix chain 'B' and resid 849 through 855 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.660A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.038A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.489A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 4.022A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 349 through 353 Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 383 through 389 removed outlier: 3.605A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.242A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 Processing helix chain 'C' and resid 816 through 825 Processing helix chain 'C' and resid 832 through 837 Processing helix chain 'C' and resid 837 through 842 removed outlier: 4.219A pdb=" N LEU C 841 " --> pdb=" O TYR C 837 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLY C 842 " --> pdb=" O GLY C 838 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 837 through 842' Processing helix chain 'C' and resid 851 through 855 removed outlier: 4.257A pdb=" N PHE C 855 " --> pdb=" O CYS C 851 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 851 through 855' Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.553A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.166A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 966 removed outlier: 3.719A pdb=" N LEU C 966 " --> pdb=" O LEU C 962 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.940A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 4.169A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 31 removed outlier: 3.648A pdb=" N THR H 31 " --> pdb=" O THR H 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 28 through 31' Processing helix chain 'H' and resid 62 through 65 removed outlier: 3.568A pdb=" N GLN H 65 " --> pdb=" O GLN H 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 62 through 65' Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'H' and resid 166 through 168 No H-bonds generated for 'chain 'H' and resid 166 through 168' Processing helix chain 'H' and resid 197 through 200 removed outlier: 3.859A pdb=" N GLY H 200 " --> pdb=" O SER H 197 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 197 through 200' Processing helix chain 'L' and resid 30 through 32 No H-bonds generated for 'chain 'L' and resid 30 through 32' Processing helix chain 'L' and resid 80 through 84 removed outlier: 3.705A pdb=" N PHE L 84 " --> pdb=" O PRO L 81 " (cutoff:3.500A) Processing helix chain 'L' and resid 122 through 127 Processing helix chain 'L' and resid 184 through 189 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.521A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 8.194A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU A 191 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.589A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 83 through 85 Processing sheet with id=AA4, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.493A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 324 through 328 removed outlier: 6.740A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N ASN A 542 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.866A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 391 through 392 Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.102A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 712 through 715 removed outlier: 3.770A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N GLN A1106 " --> pdb=" O GLU A1111 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N GLU A1111 " --> pdb=" O GLN A1106 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 718 through 728 removed outlier: 6.983A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.373A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AB6, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.619A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 28 through 31 removed outlier: 4.143A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 8.207A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.701A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 83 through 85 removed outlier: 5.958A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 132 through 135 removed outlier: 4.081A pdb=" N ASN B 164 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N SER B 162 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 311 through 314 Processing sheet with id=AC3, first strand: chain 'B' and resid 324 through 327 removed outlier: 6.432A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N ASN B 542 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AC5, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC6, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC7, first strand: chain 'B' and resid 565 through 566 removed outlier: 7.152A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.538A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 702 through 704 removed outlier: 3.513A pdb=" N LYS C 790 " --> pdb=" O ASN B 703 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.674A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 718 through 728 removed outlier: 6.919A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.362A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.089A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.774A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 8.260A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 47 through 55 removed outlier: 7.727A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 83 through 85 removed outlier: 4.006A pdb=" N VAL C 126 " --> pdb=" O SER C 172 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 309 through 319 removed outlier: 5.835A pdb=" N LYS C 310 " --> pdb=" O GLY C 601 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N GLY C 601 " --> pdb=" O LYS C 310 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 325 through 328 Processing sheet with id=AE1, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AE2, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.667A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL C 524 " --> pdb=" O PHE C 392 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE4, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE5, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.021A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.294A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 711 through 715 removed outlier: 4.018A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 718 through 728 removed outlier: 6.882A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.298A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 3.791A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AF2, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.749A pdb=" N VAL H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N TRP H 50 " --> pdb=" O VAL H 34 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'H' and resid 10 through 12 Processing sheet with id=AF4, first strand: chain 'H' and resid 130 through 134 removed outlier: 6.134A pdb=" N TYR H 186 " --> pdb=" O ASP H 154 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'H' and resid 130 through 134 removed outlier: 6.134A pdb=" N TYR H 186 " --> pdb=" O ASP H 154 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'H' and resid 161 through 164 removed outlier: 4.750A pdb=" N TYR H 204 " --> pdb=" O VAL H 221 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'L' and resid 4 through 7 removed outlier: 5.561A pdb=" N THR L 70 " --> pdb=" O ALA L 25 " (cutoff:3.500A) removed outlier: 10.044A pdb=" N GLN L 27 " --> pdb=" O SER L 68 " (cutoff:3.500A) removed outlier: 9.927A pdb=" N SER L 68 " --> pdb=" O GLN L 27 " (cutoff:3.500A) removed outlier: 11.780A pdb=" N VAL L 29 " --> pdb=" O SER L 66 " (cutoff:3.500A) removed outlier: 12.228A pdb=" N SER L 66 " --> pdb=" O VAL L 29 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.761A pdb=" N LEU L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N TYR L 50 " --> pdb=" O LEU L 34 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'L' and resid 115 through 119 removed outlier: 6.082A pdb=" N TYR L 174 " --> pdb=" O ASN L 139 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'L' and resid 154 through 155 1184 hydrogen bonds defined for protein. 3180 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: 14.16 Time building geometry restraints manager: 11.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8686 1.34 - 1.46: 6945 1.46 - 1.58: 12160 1.58 - 1.70: 0 1.70 - 1.82: 149 Bond restraints: 27940 Sorted by residual: bond pdb=" CB CYS C 738 " pdb=" SG CYS C 738 " ideal model delta sigma weight residual 1.808 1.764 0.044 3.30e-02 9.18e+02 1.74e+00 bond pdb=" C7 NAG C1308 " pdb=" N2 NAG C1308 " ideal model delta sigma weight residual 1.337 1.351 -0.014 1.10e-02 8.26e+03 1.68e+00 bond pdb=" N LYS B 113 " pdb=" CA LYS B 113 " ideal model delta sigma weight residual 1.458 1.478 -0.020 1.77e-02 3.19e+03 1.27e+00 bond pdb=" C2 NAG C1308 " pdb=" N2 NAG C1308 " ideal model delta sigma weight residual 1.454 1.464 -0.010 1.00e-02 1.00e+04 1.09e+00 bond pdb=" C PRO B 986 " pdb=" N PRO B 987 " ideal model delta sigma weight residual 1.334 1.350 -0.016 1.51e-02 4.39e+03 1.09e+00 ... (remaining 27935 not shown) Histogram of bond angle deviations from ideal: 99.36 - 106.29: 742 106.29 - 113.21: 15374 113.21 - 120.13: 9156 120.13 - 127.06: 12558 127.06 - 133.98: 255 Bond angle restraints: 38085 Sorted by residual: angle pdb=" C2 NAG C1308 " pdb=" N2 NAG C1308 " pdb=" C7 NAG C1308 " ideal model delta sigma weight residual 123.12 129.08 -5.96 1.28e+00 6.08e-01 2.16e+01 angle pdb=" C SER B 112 " pdb=" N LYS B 113 " pdb=" CA LYS B 113 " ideal model delta sigma weight residual 125.66 132.74 -7.08 1.85e+00 2.92e-01 1.46e+01 angle pdb=" N PHE A 562 " pdb=" CA PHE A 562 " pdb=" C PHE A 562 " ideal model delta sigma weight residual 114.16 109.32 4.84 1.48e+00 4.57e-01 1.07e+01 angle pdb=" C GLN B 52 " pdb=" N ASP B 53 " pdb=" CA ASP B 53 " ideal model delta sigma weight residual 122.32 127.80 -5.48 1.76e+00 3.23e-01 9.69e+00 angle pdb=" CA CYS C 760 " pdb=" CB CYS C 760 " pdb=" SG CYS C 760 " ideal model delta sigma weight residual 114.40 120.93 -6.53 2.30e+00 1.89e-01 8.07e+00 ... (remaining 38080 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.63: 15609 17.63 - 35.26: 653 35.26 - 52.89: 145 52.89 - 70.52: 48 70.52 - 88.15: 28 Dihedral angle restraints: 16483 sinusoidal: 6367 harmonic: 10116 Sorted by residual: dihedral pdb=" CB CYS A1032 " pdb=" SG CYS A1032 " pdb=" SG CYS A1043 " pdb=" CB CYS A1043 " ideal model delta sinusoidal sigma weight residual -86.00 -163.93 77.93 1 1.00e+01 1.00e-02 7.59e+01 dihedral pdb=" CB CYS C1032 " pdb=" SG CYS C1032 " pdb=" SG CYS C1043 " pdb=" CB CYS C1043 " ideal model delta sinusoidal sigma weight residual -86.00 -159.22 73.22 1 1.00e+01 1.00e-02 6.83e+01 dihedral pdb=" CB CYS B1032 " pdb=" SG CYS B1032 " pdb=" SG CYS B1043 " pdb=" CB CYS B1043 " ideal model delta sinusoidal sigma weight residual -86.00 -158.52 72.52 1 1.00e+01 1.00e-02 6.72e+01 ... (remaining 16480 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 3148 0.038 - 0.077: 940 0.077 - 0.115: 368 0.115 - 0.154: 76 0.154 - 0.192: 5 Chirality restraints: 4537 Sorted by residual: chirality pdb=" CG LEU A 916 " pdb=" CB LEU A 916 " pdb=" CD1 LEU A 916 " pdb=" CD2 LEU A 916 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 9.25e-01 chirality pdb=" C1 NAG A1303 " pdb=" ND2 ASN A 343 " pdb=" C2 NAG A1303 " pdb=" O5 NAG A1303 " both_signs ideal model delta sigma weight residual False -2.40 -2.21 -0.19 2.00e-01 2.50e+01 9.05e-01 chirality pdb=" CG LEU B 916 " pdb=" CB LEU B 916 " pdb=" CD1 LEU B 916 " pdb=" CD2 LEU B 916 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 6.95e-01 ... (remaining 4534 not shown) Planarity restraints: 4887 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN A 125 " 0.012 2.00e-02 2.50e+03 2.48e-02 6.15e+00 pdb=" C ASN A 125 " -0.043 2.00e-02 2.50e+03 pdb=" O ASN A 125 " 0.016 2.00e-02 2.50e+03 pdb=" N VAL A 126 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN C 122 " 0.012 2.00e-02 2.50e+03 2.48e-02 6.14e+00 pdb=" C ASN C 122 " -0.043 2.00e-02 2.50e+03 pdb=" O ASN C 122 " 0.017 2.00e-02 2.50e+03 pdb=" N ALA C 123 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA C 924 " 0.012 2.00e-02 2.50e+03 2.39e-02 5.73e+00 pdb=" C ALA C 924 " -0.041 2.00e-02 2.50e+03 pdb=" O ALA C 924 " 0.016 2.00e-02 2.50e+03 pdb=" N ASN C 925 " 0.014 2.00e-02 2.50e+03 ... (remaining 4884 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1765 2.74 - 3.28: 26889 3.28 - 3.82: 44914 3.82 - 4.36: 54152 4.36 - 4.90: 94451 Nonbonded interactions: 222171 Sorted by model distance: nonbonded pdb=" OH TYR A 37 " pdb=" O LEU A 54 " model vdw 2.198 2.440 nonbonded pdb=" O ASN B 439 " pdb=" OG SER B 443 " model vdw 2.204 2.440 nonbonded pdb=" OH TYR B 473 " pdb=" O THR H 104 " model vdw 2.238 2.440 nonbonded pdb=" OD2 ASP B 398 " pdb=" OH TYR B 423 " model vdw 2.238 2.440 nonbonded pdb=" OH TYR C 369 " pdb=" OD1 ASN C 388 " model vdw 2.278 2.440 ... (remaining 222166 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 40 or (resid 41 and (name N or name CA or name \ C or name O or name CB )) or resid 42 through 45 or (resid 46 and (name N or nam \ e CA or name C or name O or name CB )) or resid 47 through 87 or (resid 88 and ( \ name N or name CA or name C or name O or name CB )) or resid 89 through 95 or (r \ esid 96 through 97 and (name N or name CA or name C or name O or name CB )) or r \ esid 98 through 109 or (resid 110 and (name N or name CA or name C or name O or \ name CB )) or resid 111 or (resid 112 through 113 and (name N or name CA or name \ C or name O or name CB )) or resid 116 through 124 or (resid 125 and (name N or \ name CA or name C or name O or name CB )) or resid 126 through 131 or (resid 13 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 133 or (resi \ d 134 through 136 and (name N or name CA or name C or name O or name CB )) or re \ sid 166 through 168 or (resid 169 and (name N or name CA or name C or name O or \ name CB )) or resid 170 through 171 or (resid 172 through 188 and (name N or nam \ e CA or name C or name O or name CB )) or resid 189 through 197 or (resid 198 an \ d (name N or name CA or name C or name O or name CB )) or resid 199 through 209 \ or (resid 210 and (name N or name CA or name C or name O or name CB )) or (resid \ 215 and (name N or name CA or name C or name O or name CB )) or resid 216 throu \ gh 217 or (resid 218 and (name N or name CA or name C or name O or name CB )) or \ resid 219 through 263 or resid 265 through 308 or (resid 309 and (name N or nam \ e CA or name C or name O or name CB )) or resid 310 through 323 or (resid 324 an \ d (name N or name CA or name C or name O or name CB )) or resid 325 through 332 \ or (resid 333 and (name N or name CA or name C or name O or name CB )) or resid \ 334 through 457 or (resid 458 and (name N or name CA or name C or name O or name \ CB )) or resid 459 through 528 or (resid 529 and (name N or name CA or name C o \ r name O or name CB )) or resid 530 through 536 or (resid 537 and (name N or nam \ e CA or name C or name O or name CB )) or resid 538 through 582 or (resid 583 an \ d (name N or name CA or name C or name O or name CB )) or resid 584 through 620 \ or resid 641 through 747 or (resid 748 and (name N or name CA or name C or name \ O or name CB )) or resid 749 through 793 or (resid 794 and (name N or name CA or \ name C or name O or name CB )) or resid 795 or (resid 796 and (name N or name C \ A or name C or name O or name CB )) or resid 797 through 867 or (resid 868 and ( \ name N or name CA or name C or name O or name CB )) or resid 869 through 939 or \ (resid 940 and (name N or name CA or name C or name O or name CB )) or resid 941 \ through 984 or (resid 985 and (name N or name CA or name C or name O or name CB \ )) or resid 986 through 987 or (resid 988 through 989 and (name N or name CA or \ name C or name O or name CB )) or resid 990 through 1141 or (resid 1142 and (na \ me N or name CA or name C or name O or name CB )) or resid 1143 through 1144 or \ (resid 1145 through 1146 and (name N or name CA or name C or name O or name CB ) \ ) or resid 1147 or resid 1301 through 1308)) selection = (chain 'B' and (resid 27 through 40 or (resid 41 and (name N or name CA or name \ C or name O or name CB )) or resid 42 through 45 or (resid 46 and (name N or nam \ e CA or name C or name O or name CB )) or resid 47 through 66 or resid 82 throug \ h 87 or (resid 88 and (name N or name CA or name C or name O or name CB )) or re \ sid 89 through 109 or (resid 110 and (name N or name CA or name C or name O or n \ ame CB )) or resid 111 or (resid 112 through 113 and (name N or name CA or name \ C or name O or name CB )) or resid 116 through 128 or (resid 129 and (name N or \ name CA or name C or name O or name CB )) or resid 130 through 134 or (resid 135 \ through 136 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 66 through 168 or (resid 169 and (name N or name CA or name C or name O or name \ CB )) or resid 170 through 171 or (resid 172 and (name N or name CA or name C or \ name O or name CB )) or resid 188 through 190 or (resid 191 and (name N or name \ CA or name C or name O or name CB )) or resid 192 through 195 or (resid 196 and \ (name N or name CA or name C or name O or name CB )) or resid 197 or (resid 198 \ and (name N or name CA or name C or name O or name CB )) or resid 199 through 2 \ 36 or (resid 237 and (name N or name CA or name C or name O or name CB )) or res \ id 238 or (resid 239 and (name N or name CA or name C or name O or name CB )) or \ resid 240 through 241 or (resid 242 through 243 and (name N or name CA or name \ C or name O or name CB )) or resid 265 through 280 or (resid 281 and (name N or \ name CA or name C or name O or name CB )) or resid 282 through 297 or (resid 298 \ and (name N or name CA or name C or name O or name CB )) or resid 299 through 3 \ 88 or (resid 389 and (name N or name CA or name C or name O or name CB )) or res \ id 390 through 457 or (resid 458 and (name N or name CA or name C or name O or n \ ame CB )) or resid 459 through 567 or (resid 568 and (name N or name CA or name \ C or name O or name CB )) or resid 569 through 570 or (resid 571 and (name N or \ name CA or name C or name O or name CB )) or resid 572 through 613 or (resid 614 \ and (name N or name CA or name C or name O or name CB )) or resid 615 through 6 \ 18 or (resid 619 and (name N or name CA or name C or name O or name CB )) or res \ id 620 or resid 641 through 676 or resid 690 through 744 or (resid 745 and (name \ N or name CA or name C or name O or name CB )) or resid 746 through 827 or resi \ d 849 through 867 or (resid 868 and (name N or name CA or name C or name O or na \ me CB )) or resid 869 through 939 or (resid 940 and (name N or name CA or name C \ or name O or name CB )) or resid 941 through 984 or (resid 985 and (name N or n \ ame CA or name C or name O or name CB )) or resid 986 through 987 or (resid 988 \ through 989 and (name N or name CA or name C or name O or name CB )) or resid 99 \ 0 through 1143 or (resid 1144 through 1146 and (name N or name CA or name C or n \ ame O or name CB )) or resid 1147 or resid 1301 through 1308)) selection = (chain 'C' and (resid 27 through 66 or resid 82 through 95 or (resid 96 through \ 97 and (name N or name CA or name C or name O or name CB )) or resid 98 through \ 113 or resid 116 through 134 or (resid 135 through 136 and (name N or name CA or \ name C or name O or name CB )) or resid 166 through 172 or (resid 188 and (name \ N or name CA or name C or name O or name CB )) or resid 189 through 195 or (res \ id 196 and (name N or name CA or name C or name O or name CB )) or resid 197 thr \ ough 209 or (resid 210 and (name N or name CA or name C or name O or name CB )) \ or resid 215 through 217 or (resid 218 and (name N or name CA or name C or name \ O or name CB )) or resid 219 through 236 or (resid 237 and (name N or name CA or \ name C or name O or name CB )) or resid 238 through 297 or (resid 298 and (name \ N or name CA or name C or name O or name CB )) or resid 299 through 308 or (res \ id 309 and (name N or name CA or name C or name O or name CB )) or resid 310 thr \ ough 332 or (resid 333 and (name N or name CA or name C or name O or name CB )) \ or resid 334 through 388 or (resid 389 and (name N or name CA or name C or name \ O or name CB )) or resid 390 through 527 or (resid 528 through 529 and (name N o \ r name CA or name C or name O or name CB )) or resid 530 through 536 or (resid 5 \ 37 and (name N or name CA or name C or name O or name CB )) or resid 538 through \ 553 or (resid 554 and (name N or name CA or name C or name O or name CB )) or r \ esid 555 through 557 or (resid 558 and (name N or name CA or name C or name O or \ name CB )) or resid 559 through 567 or (resid 568 and (name N or name CA or nam \ e C or name O or name CB )) or resid 569 through 570 or (resid 571 and (name N o \ r name CA or name C or name O or name CB )) or resid 572 through 582 or (resid 5 \ 83 and (name N or name CA or name C or name O or name CB )) or resid 584 through \ 613 or (resid 614 and (name N or name CA or name C or name O or name CB )) or r \ esid 615 through 618 or (resid 619 and (name N or name CA or name C or name O or \ name CB )) or resid 620 through 645 or (resid 646 through 647 and (name N or na \ me CA or name C or name O or name CB )) or resid 648 through 795 or (resid 796 a \ nd (name N or name CA or name C or name O or name CB )) or resid 797 through 828 \ or resid 850 through 1141 or (resid 1142 and (name N or name CA or name C or na \ me O or name CB )) or resid 1143 or (resid 1144 through 1146 and (name N or name \ CA or name C or name O or name CB )) or resid 1147 or resid 1301 through 1308)) \ } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' } 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: 4 Type Number sf(0) Gaussians S 121 5.16 5 C 17402 2.51 5 N 4482 2.21 5 O 5331 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: 3.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 15.280 Check model and map are aligned: 0.430 Process input model: 75.860 Find NCS groups from input model: 2.080 Set up NCS constraints: 0.210 Set refine NCS operators: 0.000 Set scattering table: 0.280 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:11.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 108.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 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 : 0.002 0.044 27940 Z= 0.157 Angle : 0.531 7.403 38085 Z= 0.289 Chirality : 0.044 0.192 4537 Planarity : 0.004 0.052 4849 Dihedral : 11.498 88.154 9839 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.91 % Favored : 94.92 % Rotamer Outliers : 0.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.91 % 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 (0.14), residues: 3424 helix: 0.90 (0.21), residues: 714 sheet: -0.26 (0.17), residues: 896 loop : -1.21 (0.14), residues: 1814 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6848 Ramachandran restraints generated. 3424 Oldfield, 0 Emsley, 3424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6848 Ramachandran restraints generated. 3424 Oldfield, 0 Emsley, 3424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 521 residues out of total 3034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 503 time to evaluate : 3.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 7 residues processed: 517 average time/residue: 1.2571 time to fit residues: 772.1982 Evaluate side-chains 285 residues out of total 3034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 278 time to evaluate : 3.322 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 5 residues processed: 4 average time/residue: 0.3436 time to fit residues: 6.8893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 292 optimal weight: 1.9990 chunk 262 optimal weight: 2.9990 chunk 145 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 176 optimal weight: 0.5980 chunk 140 optimal weight: 30.0000 chunk 271 optimal weight: 3.9990 chunk 104 optimal weight: 4.9990 chunk 164 optimal weight: 2.9990 chunk 201 optimal weight: 0.0050 chunk 314 optimal weight: 5.9990 overall best weight: 1.7200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN A 360 ASN A 388 ASN A 394 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 949 GLN B 394 ASN B 755 GLN B 762 GLN B 764 ASN B1119 ASN C 317 ASN C 394 ASN C 493 GLN C 919 ASN C 949 GLN C1048 HIS C1113 GLN H 174 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.062 27940 Z= 0.341 Angle : 0.577 8.723 38085 Z= 0.307 Chirality : 0.046 0.281 4537 Planarity : 0.004 0.046 4849 Dihedral : 4.678 26.132 4012 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.45 % Favored : 96.47 % Rotamer Outliers : 2.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.91 % 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: -0.21 (0.14), residues: 3424 helix: 1.50 (0.20), residues: 703 sheet: 0.02 (0.17), residues: 910 loop : -0.87 (0.14), residues: 1811 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6848 Ramachandran restraints generated. 3424 Oldfield, 0 Emsley, 3424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6848 Ramachandran restraints generated. 3424 Oldfield, 0 Emsley, 3424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 3034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 280 time to evaluate : 3.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 74 outliers final: 29 residues processed: 328 average time/residue: 1.1957 time to fit residues: 472.7096 Evaluate side-chains 272 residues out of total 3034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 243 time to evaluate : 3.281 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 22 residues processed: 8 average time/residue: 0.3333 time to fit residues: 8.7922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 174 optimal weight: 1.9990 chunk 97 optimal weight: 0.7980 chunk 261 optimal weight: 0.5980 chunk 213 optimal weight: 40.0000 chunk 86 optimal weight: 0.6980 chunk 314 optimal weight: 50.0000 chunk 340 optimal weight: 30.0000 chunk 280 optimal weight: 0.9980 chunk 312 optimal weight: 50.0000 chunk 107 optimal weight: 0.8980 chunk 252 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 532 ASN A 804 GLN ** A 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 GLN A 965 GLN B 607 GLN B 755 GLN B 901 GLN B 935 GLN B 978 ASN C 409 GLN C 969 ASN C 978 ASN C1048 HIS C1119 ASN L 138 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 27940 Z= 0.188 Angle : 0.496 7.750 38085 Z= 0.265 Chirality : 0.043 0.202 4537 Planarity : 0.004 0.049 4849 Dihedral : 4.425 25.921 4012 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.92 % Favored : 96.99 % Rotamer Outliers : 2.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.91 % 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: 0.05 (0.14), residues: 3424 helix: 1.80 (0.20), residues: 703 sheet: 0.14 (0.17), residues: 913 loop : -0.72 (0.14), residues: 1808 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6848 Ramachandran restraints generated. 3424 Oldfield, 0 Emsley, 3424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6848 Ramachandran restraints generated. 3424 Oldfield, 0 Emsley, 3424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 3034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 262 time to evaluate : 3.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 77 outliers final: 42 residues processed: 316 average time/residue: 1.1684 time to fit residues: 447.4978 Evaluate side-chains 284 residues out of total 3034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 242 time to evaluate : 3.178 Switching outliers to nearest non-outliers outliers start: 42 outliers final: 32 residues processed: 10 average time/residue: 0.7356 time to fit residues: 14.0704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 310 optimal weight: 50.0000 chunk 236 optimal weight: 7.9990 chunk 163 optimal weight: 2.9990 chunk 34 optimal weight: 9.9990 chunk 150 optimal weight: 0.8980 chunk 211 optimal weight: 8.9990 chunk 315 optimal weight: 50.0000 chunk 334 optimal weight: 10.0000 chunk 165 optimal weight: 0.6980 chunk 299 optimal weight: 0.5980 chunk 90 optimal weight: 2.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN A 394 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 606 ASN A 907 ASN B 755 GLN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN C 978 ASN C1048 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.2378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.052 27940 Z= 0.317 Angle : 0.537 8.223 38085 Z= 0.286 Chirality : 0.045 0.218 4537 Planarity : 0.004 0.052 4849 Dihedral : 4.549 26.268 4012 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.50 % Favored : 96.41 % Rotamer Outliers : 2.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.91 % 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: 0.09 (0.14), residues: 3424 helix: 1.77 (0.20), residues: 691 sheet: 0.25 (0.17), residues: 916 loop : -0.70 (0.14), residues: 1817 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6848 Ramachandran restraints generated. 3424 Oldfield, 0 Emsley, 3424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6848 Ramachandran restraints generated. 3424 Oldfield, 0 Emsley, 3424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 3034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 242 time to evaluate : 3.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 82 outliers final: 50 residues processed: 304 average time/residue: 1.1253 time to fit residues: 418.0959 Evaluate side-chains 276 residues out of total 3034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 226 time to evaluate : 2.931 Switching outliers to nearest non-outliers outliers start: 50 outliers final: 43 residues processed: 7 average time/residue: 0.4390 time to fit residues: 8.7683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 278 optimal weight: 0.0370 chunk 189 optimal weight: 0.9990 chunk 4 optimal weight: 5.9990 chunk 249 optimal weight: 5.9990 chunk 137 optimal weight: 40.0000 chunk 285 optimal weight: 3.9990 chunk 231 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 170 optimal weight: 2.9990 chunk 300 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 overall best weight: 1.4064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN A 394 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 ASN B 755 GLN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN C 955 ASN C 978 ASN C1048 HIS C1119 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.2549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 27940 Z= 0.273 Angle : 0.521 8.754 38085 Z= 0.278 Chirality : 0.044 0.189 4537 Planarity : 0.004 0.050 4849 Dihedral : 4.496 26.529 4012 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.04 % Favored : 96.88 % Rotamer Outliers : 2.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.91 % 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: 0.21 (0.14), residues: 3424 helix: 1.78 (0.20), residues: 693 sheet: 0.39 (0.17), residues: 890 loop : -0.61 (0.14), residues: 1841 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6848 Ramachandran restraints generated. 3424 Oldfield, 0 Emsley, 3424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6848 Ramachandran restraints generated. 3424 Oldfield, 0 Emsley, 3424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 3034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 232 time to evaluate : 3.015 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 77 outliers final: 48 residues processed: 296 average time/residue: 1.1557 time to fit residues: 415.7706 Evaluate side-chains 268 residues out of total 3034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 220 time to evaluate : 3.001 Switching outliers to nearest non-outliers outliers start: 48 outliers final: 44 residues processed: 4 average time/residue: 0.3016 time to fit residues: 6.2158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 112 optimal weight: 0.9990 chunk 301 optimal weight: 0.0010 chunk 66 optimal weight: 1.9990 chunk 196 optimal weight: 0.8980 chunk 82 optimal weight: 3.9990 chunk 334 optimal weight: 0.8980 chunk 277 optimal weight: 0.9990 chunk 154 optimal weight: 0.7980 chunk 27 optimal weight: 5.9990 chunk 110 optimal weight: 5.9990 chunk 175 optimal weight: 0.4980 overall best weight: 0.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 ASN B 755 GLN B 935 GLN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN C1048 HIS ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.2652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 27940 Z= 0.169 Angle : 0.486 8.934 38085 Z= 0.259 Chirality : 0.043 0.199 4537 Planarity : 0.004 0.048 4849 Dihedral : 4.348 26.709 4012 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.77 % Favored : 97.14 % Rotamer Outliers : 2.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.91 % 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: 0.33 (0.14), residues: 3424 helix: 1.94 (0.20), residues: 694 sheet: 0.44 (0.17), residues: 893 loop : -0.55 (0.14), residues: 1837 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6848 Ramachandran restraints generated. 3424 Oldfield, 0 Emsley, 3424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6848 Ramachandran restraints generated. 3424 Oldfield, 0 Emsley, 3424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 3034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 241 time to evaluate : 3.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 71 outliers final: 45 residues processed: 300 average time/residue: 1.1496 time to fit residues: 421.8608 Evaluate side-chains 273 residues out of total 3034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 228 time to evaluate : 3.137 Switching outliers to nearest non-outliers outliers start: 45 outliers final: 40 residues processed: 6 average time/residue: 0.3478 time to fit residues: 7.7723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 322 optimal weight: 50.0000 chunk 37 optimal weight: 50.0000 chunk 190 optimal weight: 1.9990 chunk 244 optimal weight: 6.9990 chunk 189 optimal weight: 0.7980 chunk 281 optimal weight: 0.9990 chunk 186 optimal weight: 3.9990 chunk 333 optimal weight: 9.9990 chunk 208 optimal weight: 7.9990 chunk 203 optimal weight: 30.0000 chunk 153 optimal weight: 0.0050 overall best weight: 1.5600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 755 GLN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 271 GLN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 607 GLN C 644 GLN C 762 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.2790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.054 27940 Z= 0.298 Angle : 0.527 9.343 38085 Z= 0.281 Chirality : 0.045 0.230 4537 Planarity : 0.004 0.049 4849 Dihedral : 4.484 28.339 4012 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.33 % Favored : 96.58 % Rotamer Outliers : 2.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.91 % 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: 0.29 (0.14), residues: 3424 helix: 1.82 (0.20), residues: 691 sheet: 0.48 (0.17), residues: 893 loop : -0.57 (0.14), residues: 1840 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6848 Ramachandran restraints generated. 3424 Oldfield, 0 Emsley, 3424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6848 Ramachandran restraints generated. 3424 Oldfield, 0 Emsley, 3424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 3034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 236 time to evaluate : 3.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 72 outliers final: 49 residues processed: 292 average time/residue: 1.2779 time to fit residues: 461.3688 Evaluate side-chains 272 residues out of total 3034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 223 time to evaluate : 3.210 Switching outliers to nearest non-outliers outliers start: 49 outliers final: 40 residues processed: 9 average time/residue: 0.5238 time to fit residues: 11.8464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 206 optimal weight: 0.8980 chunk 133 optimal weight: 50.0000 chunk 199 optimal weight: 1.9990 chunk 100 optimal weight: 0.5980 chunk 65 optimal weight: 0.8980 chunk 64 optimal weight: 0.6980 chunk 212 optimal weight: 30.0000 chunk 227 optimal weight: 6.9990 chunk 164 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 262 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 755 GLN B 935 GLN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.2869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 27940 Z= 0.188 Angle : 0.504 9.696 38085 Z= 0.267 Chirality : 0.043 0.200 4537 Planarity : 0.004 0.048 4849 Dihedral : 4.403 37.741 4012 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.89 % Favored : 97.02 % Rotamer Outliers : 1.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.35 (0.14), residues: 3424 helix: 1.92 (0.20), residues: 694 sheet: 0.52 (0.17), residues: 882 loop : -0.55 (0.14), residues: 1848 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6848 Ramachandran restraints generated. 3424 Oldfield, 0 Emsley, 3424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6848 Ramachandran restraints generated. 3424 Oldfield, 0 Emsley, 3424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 3034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 231 time to evaluate : 3.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 55 outliers final: 43 residues processed: 277 average time/residue: 1.1640 time to fit residues: 394.0661 Evaluate side-chains 262 residues out of total 3034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 219 time to evaluate : 3.212 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 40 residues processed: 4 average time/residue: 0.3457 time to fit residues: 6.8920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 303 optimal weight: 0.9980 chunk 319 optimal weight: 9.9990 chunk 291 optimal weight: 3.9990 chunk 310 optimal weight: 40.0000 chunk 187 optimal weight: 0.7980 chunk 135 optimal weight: 0.0980 chunk 244 optimal weight: 10.0000 chunk 95 optimal weight: 0.5980 chunk 280 optimal weight: 0.9990 chunk 293 optimal weight: 0.8980 chunk 309 optimal weight: 40.0000 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 755 GLN B 935 GLN C 271 GLN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.2951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 27940 Z= 0.177 Angle : 0.496 10.535 38085 Z= 0.264 Chirality : 0.043 0.168 4537 Planarity : 0.004 0.055 4849 Dihedral : 4.352 34.920 4012 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.95 % Favored : 96.96 % Rotamer Outliers : 1.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.42 (0.14), residues: 3424 helix: 1.92 (0.20), residues: 700 sheet: 0.56 (0.17), residues: 882 loop : -0.49 (0.14), residues: 1842 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6848 Ramachandran restraints generated. 3424 Oldfield, 0 Emsley, 3424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6848 Ramachandran restraints generated. 3424 Oldfield, 0 Emsley, 3424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 3034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 230 time to evaluate : 3.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 56 outliers final: 40 residues processed: 277 average time/residue: 1.1285 time to fit residues: 384.3360 Evaluate side-chains 260 residues out of total 3034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 220 time to evaluate : 3.093 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 38 residues processed: 2 average time/residue: 0.2891 time to fit residues: 5.3772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 204 optimal weight: 5.9990 chunk 328 optimal weight: 7.9990 chunk 200 optimal weight: 1.9990 chunk 155 optimal weight: 0.8980 chunk 228 optimal weight: 4.9990 chunk 344 optimal weight: 10.0000 chunk 317 optimal weight: 10.0000 chunk 274 optimal weight: 6.9990 chunk 28 optimal weight: 3.9990 chunk 212 optimal weight: 9.9990 chunk 168 optimal weight: 3.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 ASN ** B 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 658 ASN B 755 GLN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1135 ASN C 271 GLN C 409 GLN ** C 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 978 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.3207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.083 27940 Z= 0.550 Angle : 0.651 12.711 38085 Z= 0.344 Chirality : 0.050 0.238 4537 Planarity : 0.005 0.053 4849 Dihedral : 4.884 34.768 4012 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.21 % Favored : 95.71 % Rotamer Outliers : 1.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.13 (0.14), residues: 3424 helix: 1.36 (0.20), residues: 697 sheet: 0.45 (0.17), residues: 928 loop : -0.59 (0.14), residues: 1799 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6848 Ramachandran restraints generated. 3424 Oldfield, 0 Emsley, 3424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6848 Ramachandran restraints generated. 3424 Oldfield, 0 Emsley, 3424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 3034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 234 time to evaluate : 3.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 49 outliers final: 40 residues processed: 279 average time/residue: 1.1543 time to fit residues: 394.0347 Evaluate side-chains 262 residues out of total 3034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 222 time to evaluate : 3.268 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 38 residues processed: 2 average time/residue: 0.3426 time to fit residues: 5.9111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 218 optimal weight: 0.4980 chunk 292 optimal weight: 0.6980 chunk 84 optimal weight: 0.3980 chunk 253 optimal weight: 2.9990 chunk 40 optimal weight: 0.6980 chunk 76 optimal weight: 0.9980 chunk 274 optimal weight: 0.9980 chunk 115 optimal weight: 1.9990 chunk 282 optimal weight: 0.6980 chunk 34 optimal weight: 0.7980 chunk 50 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 532 ASN ** B 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 755 GLN B 935 GLN C 271 GLN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1119 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4496 r_free = 0.4496 target = 0.210136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.131972 restraints weight = 34988.887| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 2.84 r_work: 0.3443 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3321 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.3184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 27940 Z= 0.176 Angle : 0.520 11.842 38085 Z= 0.276 Chirality : 0.043 0.184 4537 Planarity : 0.004 0.048 4849 Dihedral : 4.516 33.524 4012 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.89 % Favored : 97.05 % Rotamer Outliers : 1.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.33 (0.14), residues: 3424 helix: 1.68 (0.20), residues: 703 sheet: 0.54 (0.17), residues: 883 loop : -0.49 (0.14), residues: 1838 =============================================================================== Job complete usr+sys time: 8904.82 seconds wall clock time: 160 minutes 55.11 seconds (9655.11 seconds total)