Starting phenix.real_space_refine on Tue Dec 12 09:05:48 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8we6_37472/12_2023/8we6_37472_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8we6_37472/12_2023/8we6_37472.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8we6_37472/12_2023/8we6_37472_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8we6_37472/12_2023/8we6_37472_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8we6_37472/12_2023/8we6_37472_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8we6_37472/12_2023/8we6_37472.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8we6_37472/12_2023/8we6_37472.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8we6_37472/12_2023/8we6_37472_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8we6_37472/12_2023/8we6_37472_updated.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.122 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 2 9.91 5 P 4 5.49 5 S 104 5.16 5 C 13415 2.51 5 N 3412 2.21 5 O 3821 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 213": "OE1" <-> "OE2" Residue "A PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 407": "OE1" <-> "OE2" Residue "A GLU 413": "OE1" <-> "OE2" Residue "A ASP 420": "OD1" <-> "OD2" Residue "A PHE 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 445": "OE1" <-> "OE2" Residue "A PHE 526": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 557": "OD1" <-> "OD2" Residue "A TYR 583": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 588": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 706": "OE1" <-> "OE2" Residue "A GLU 760": "OE1" <-> "OE2" Residue "A GLU 768": "OE1" <-> "OE2" Residue "A PHE 909": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 957": "OD1" <-> "OD2" Residue "A TYR 958": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1191": "OE1" <-> "OE2" Residue "A GLU 1211": "OE1" <-> "OE2" Residue "A TYR 1230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1482": "OE1" <-> "OE2" Residue "A ASP 1533": "OD1" <-> "OD2" Residue "A GLU 1544": "OE1" <-> "OE2" Residue "D GLU 62": "OE1" <-> "OE2" Residue "D ASP 85": "OD1" <-> "OD2" Residue "D ASP 152": "OD1" <-> "OD2" Residue "D GLU 278": "OE1" <-> "OE2" Residue "D TYR 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 367": "OE1" <-> "OE2" Residue "D PHE 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 496": "OD1" <-> "OD2" Residue "D GLU 565": "OE1" <-> "OE2" Residue "D ASP 569": "OD1" <-> "OD2" Residue "D PHE 628": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 679": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 685": "OE1" <-> "OE2" Residue "D PHE 711": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 760": "OE1" <-> "OE2" Residue "D ASP 771": "OD1" <-> "OD2" Residue "D PHE 780": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 799": "OE1" <-> "OE2" Residue "D GLU 823": "OE1" <-> "OE2" Residue "D GLU 877": "OE1" <-> "OE2" Residue "D ASP 879": "OD1" <-> "OD2" Residue "D TYR 898": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 986": "OD1" <-> "OD2" Residue "D PHE 1003": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1019": "OE1" <-> "OE2" Residue "C TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 191": "OE1" <-> "OE2" Residue "C GLU 249": "OE1" <-> "OE2" Residue "C ASP 270": "OD1" <-> "OD2" Residue "C TYR 322": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 323": "OD1" <-> "OD2" Residue "C PHE 333": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 338": "OD1" <-> "OD2" Residue "C ASP 344": "OD1" <-> "OD2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 20758 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 10172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1260, 10172 Classifications: {'peptide': 1260} Link IDs: {'PTRANS': 39, 'TRANS': 1220} Chain breaks: 7 Chain: "D" Number of atoms: 7570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 948, 7570 Classifications: {'peptide': 948} Link IDs: {'PCIS': 2, 'PTRANS': 38, 'TRANS': 907} Chain breaks: 5 Chain: "C" Number of atoms: 2575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2575 Classifications: {'peptide': 324} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 304} Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 230 Unusual residues: {' CA': 1, '3PE': 1, 'CLR': 4, 'NAG': 1, 'PT5': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PT5:plan-6': 1} Unresolved non-hydrogen planarities: 2 Chain: "D" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' CA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 11.41, per 1000 atoms: 0.55 Number of scatterers: 20758 At special positions: 0 Unit cell: (171.556, 174.898, 184.924, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 2 19.99 S 104 16.00 P 4 15.00 O 3821 8.00 N 3412 7.00 C 13415 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 298 " - pdb=" SG CYS A 326 " distance=2.03 Simple disulfide: pdb=" SG CYS A 316 " - pdb=" SG CYS A 332 " distance=2.03 Simple disulfide: pdb=" SG CYS A1078 " - pdb=" SG CYS A1089 " distance=2.03 Simple disulfide: pdb=" SG CYS A1479 " - pdb=" SG CYS A1495 " distance=2.03 Simple disulfide: pdb=" SG CYS D 303 " - pdb=" SG CYS D1044 " distance=2.03 Simple disulfide: pdb=" SG CYS D 404 " - pdb=" SG CYS D1071 " distance=2.04 Simple disulfide: pdb=" SG CYS D 667 " - pdb=" SG CYS D 697 " distance=2.03 Simple disulfide: pdb=" SG CYS D 904 " - pdb=" SG CYS D 974 " distance=2.03 Simple disulfide: pdb=" SG CYS D 996 " - pdb=" SG CYS D1026 " distance=2.03 Simple disulfide: pdb=" SG CYS D 999 " - pdb=" SG CYS D1024 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " NAG B 3 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " NAG F 3 " " NAG F 3 " - " NAG F 4 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG A2307 " - " ASN A1436 " " NAG B 1 " - " ASN D 184 " " NAG D1202 " - " ASN D 92 " " NAG D1203 " - " ASN D 781 " " NAG E 1 " - " ASN D 348 " " NAG F 1 " - " ASN D 468 " " NAG G 1 " - " ASN D 613 " " NAG H 1 " - " ASN D 895 " Time building additional restraints: 8.53 Conformation dependent library (CDL) restraints added in 4.0 seconds 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4796 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 109 helices and 14 sheets defined 46.7% alpha, 7.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.70 Creating SS restraints... Processing helix chain 'A' and resid 124 through 142 removed outlier: 3.736A pdb=" N ILE A 129 " --> pdb=" O PHE A 126 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ILE A 130 " --> pdb=" O GLU A 127 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N THR A 133 " --> pdb=" O ILE A 130 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ALA A 140 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU A 141 " --> pdb=" O CYS A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 150 No H-bonds generated for 'chain 'A' and resid 148 through 150' Processing helix chain 'A' and resid 154 through 181 removed outlier: 3.640A pdb=" N GLU A 160 " --> pdb=" O ASN A 156 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ARG A 161 " --> pdb=" O SER A 157 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N TYR A 164 " --> pdb=" O GLU A 160 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU A 165 " --> pdb=" O ARG A 161 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ALA A 180 " --> pdb=" O LEU A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 216 Processing helix chain 'A' and resid 237 through 242 Processing helix chain 'A' and resid 244 through 250 Processing helix chain 'A' and resid 252 through 262 removed outlier: 3.890A pdb=" N VAL A 256 " --> pdb=" O PRO A 252 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N VAL A 257 " --> pdb=" O SER A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 289 removed outlier: 3.851A pdb=" N HIS A 270 " --> pdb=" O PRO A 267 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ALA A 272 " --> pdb=" O LEU A 269 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N LEU A 273 " --> pdb=" O HIS A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 360 removed outlier: 3.546A pdb=" N PHE A 357 " --> pdb=" O MET A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 375 Processing helix chain 'A' and resid 382 through 392 removed outlier: 3.793A pdb=" N THR A 387 " --> pdb=" O ILE A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 418 removed outlier: 4.591A pdb=" N LYS A 414 " --> pdb=" O LYS A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 434 removed outlier: 3.838A pdb=" N LEU A 430 " --> pdb=" O GLU A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 444 removed outlier: 3.922A pdb=" N THR A 442 " --> pdb=" O LEU A 438 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA A 444 " --> pdb=" O TRP A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 512 No H-bonds generated for 'chain 'A' and resid 510 through 512' Processing helix chain 'A' and resid 514 through 521 Processing helix chain 'A' and resid 528 through 541 Processing helix chain 'A' and resid 552 through 576 removed outlier: 3.672A pdb=" N ASP A 557 " --> pdb=" O THR A 553 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LEU A 564 " --> pdb=" O ASN A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 607 removed outlier: 4.037A pdb=" N ILE A 604 " --> pdb=" O ILE A 600 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LEU A 605 " --> pdb=" O LEU A 601 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL A 606 " --> pdb=" O GLU A 602 " (cutoff:3.500A) Processing helix chain 'A' and resid 617 through 619 No H-bonds generated for 'chain 'A' and resid 617 through 619' Processing helix chain 'A' and resid 621 through 630 removed outlier: 4.390A pdb=" N LEU A 625 " --> pdb=" O VAL A 622 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N PHE A 628 " --> pdb=" O LEU A 625 " (cutoff:3.500A) Processing helix chain 'A' and resid 635 through 646 removed outlier: 3.535A pdb=" N LEU A 640 " --> pdb=" O SER A 636 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL A 641 " --> pdb=" O LEU A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 673 removed outlier: 3.748A pdb=" N SER A 653 " --> pdb=" O ARG A 649 " (cutoff:3.500A) Processing helix chain 'A' and resid 692 through 704 Processing helix chain 'A' and resid 708 through 719 Processing helix chain 'A' and resid 724 through 727 No H-bonds generated for 'chain 'A' and resid 724 through 727' Processing helix chain 'A' and resid 731 through 747 removed outlier: 4.170A pdb=" N TYR A 742 " --> pdb=" O ILE A 738 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ILE A 743 " --> pdb=" O CYS A 739 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 776 removed outlier: 3.938A pdb=" N ASP A 754 " --> pdb=" O ALA A 750 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ASP A 758 " --> pdb=" O ASP A 754 " (cutoff:3.500A) Processing helix chain 'A' and resid 903 through 913 Processing helix chain 'A' and resid 915 through 918 No H-bonds generated for 'chain 'A' and resid 915 through 918' Processing helix chain 'A' and resid 929 through 974 removed outlier: 3.598A pdb=" N LEU A 953 " --> pdb=" O ARG A 929 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLY A 954 " --> pdb=" O ASN A 930 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N TYR A 958 " --> pdb=" O GLY A 954 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N VAL A 959 " --> pdb=" O ASN A 955 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N MET A 972 " --> pdb=" O ILE A 968 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N THR A 973 " --> pdb=" O ILE A 969 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ALA A 974 " --> pdb=" O LEU A 970 " (cutoff:3.500A) Processing helix chain 'A' and resid 990 through 1006 removed outlier: 3.873A pdb=" N VAL A 997 " --> pdb=" O ASP A 993 " (cutoff:3.500A) Processing helix chain 'A' and resid 1014 through 1017 No H-bonds generated for 'chain 'A' and resid 1014 through 1017' Processing helix chain 'A' and resid 1020 through 1023 Processing helix chain 'A' and resid 1025 through 1027 No H-bonds generated for 'chain 'A' and resid 1025 through 1027' Processing helix chain 'A' and resid 1037 through 1050 removed outlier: 4.116A pdb=" N VAL A1042 " --> pdb=" O VAL A1038 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ARG A1047 " --> pdb=" O PHE A1043 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR A1048 " --> pdb=" O VAL A1044 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE A1049 " --> pdb=" O ALA A1045 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLY A1050 " --> pdb=" O ILE A1046 " (cutoff:3.500A) Processing helix chain 'A' and resid 1052 through 1071 removed outlier: 3.569A pdb=" N GLN A1069 " --> pdb=" O CYS A1065 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU A1070 " --> pdb=" O ILE A1066 " (cutoff:3.500A) Processing helix chain 'A' and resid 1086 through 1088 No H-bonds generated for 'chain 'A' and resid 1086 through 1088' Processing helix chain 'A' and resid 1097 through 1099 No H-bonds generated for 'chain 'A' and resid 1097 through 1099' Processing helix chain 'A' and resid 1121 through 1132 removed outlier: 3.944A pdb=" N MET A1125 " --> pdb=" O VAL A1121 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N MET A1126 " --> pdb=" O LEU A1122 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N THR A1130 " --> pdb=" O MET A1126 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL A1131 " --> pdb=" O ALA A1127 " (cutoff:3.500A) Processing helix chain 'A' and resid 1137 through 1144 Processing helix chain 'A' and resid 1160 through 1172 removed outlier: 3.957A pdb=" N ILE A1164 " --> pdb=" O GLU A1161 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE A1172 " --> pdb=" O TYR A1169 " (cutoff:3.500A) Processing helix chain 'A' and resid 1176 through 1194 Processing helix chain 'A' and resid 1206 through 1214 Processing helix chain 'A' and resid 1228 through 1236 removed outlier: 4.559A pdb=" N VAL A1232 " --> pdb=" O HIS A1228 " (cutoff:3.500A) Processing helix chain 'A' and resid 1239 through 1255 removed outlier: 4.007A pdb=" N TYR A1243 " --> pdb=" O THR A1239 " (cutoff:3.500A) Processing helix chain 'A' and resid 1265 through 1300 removed outlier: 4.588A pdb=" N LEU A1277 " --> pdb=" O ILE A1273 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N PHE A1278 " --> pdb=" O LEU A1274 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALA A1292 " --> pdb=" O LEU A1288 " (cutoff:3.500A) Proline residue: A1295 - end of helix removed outlier: 3.674A pdb=" N PHE A1299 " --> pdb=" O PRO A1295 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SER A1300 " --> pdb=" O LYS A1296 " (cutoff:3.500A) Processing helix chain 'A' and resid 1302 through 1321 removed outlier: 3.698A pdb=" N ILE A1310 " --> pdb=" O PHE A1306 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASP A1317 " --> pdb=" O GLY A1313 " (cutoff:3.500A) Processing helix chain 'A' and resid 1377 through 1388 removed outlier: 3.637A pdb=" N VAL A1381 " --> pdb=" O LEU A1378 " (cutoff:3.500A) Processing helix chain 'A' and resid 1394 through 1407 Processing helix chain 'A' and resid 1411 through 1430 removed outlier: 4.324A pdb=" N ILE A1415 " --> pdb=" O VAL A1411 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL A1416 " --> pdb=" O ALA A1412 " (cutoff:3.500A) Processing helix chain 'A' and resid 1450 through 1461 Processing helix chain 'A' and resid 1466 through 1473 Processing helix chain 'A' and resid 1498 through 1524 removed outlier: 3.689A pdb=" N VAL A1501 " --> pdb=" O SER A1498 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE A1504 " --> pdb=" O VAL A1501 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE A1505 " --> pdb=" O PHE A1502 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N SER A1506 " --> pdb=" O TYR A1503 " (cutoff:3.500A) Processing helix chain 'A' and resid 1527 through 1530 No H-bonds generated for 'chain 'A' and resid 1527 through 1530' Processing helix chain 'A' and resid 1539 through 1550 removed outlier: 3.808A pdb=" N LYS A1546 " --> pdb=" O LEU A1542 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ARG A1547 " --> pdb=" O ASP A1543 " (cutoff:3.500A) Processing helix chain 'A' and resid 1562 through 1566 removed outlier: 3.764A pdb=" N VAL A1565 " --> pdb=" O HIS A1562 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N VAL A1566 " --> pdb=" O LEU A1563 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1562 through 1566' Processing helix chain 'A' and resid 1569 through 1571 No H-bonds generated for 'chain 'A' and resid 1569 through 1571' Processing helix chain 'A' and resid 1586 through 1593 removed outlier: 3.521A pdb=" N VAL A1592 " --> pdb=" O CYS A1588 " (cutoff:3.500A) Processing helix chain 'A' and resid 1606 through 1617 Processing helix chain 'A' and resid 1626 through 1634 removed outlier: 3.802A pdb=" N ARG A1634 " --> pdb=" O ASN A1630 " (cutoff:3.500A) Processing helix chain 'A' and resid 1645 through 1647 No H-bonds generated for 'chain 'A' and resid 1645 through 1647' Processing helix chain 'D' and resid 30 through 42 removed outlier: 3.803A pdb=" N MET D 40 " --> pdb=" O TRP D 36 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU D 42 " --> pdb=" O ASP D 38 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 50 Processing helix chain 'D' and resid 54 through 63 removed outlier: 3.681A pdb=" N VAL D 58 " --> pdb=" O VAL D 54 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ASP D 59 " --> pdb=" O ASN D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 65 through 67 No H-bonds generated for 'chain 'D' and resid 65 through 67' Processing helix chain 'D' and resid 75 through 110 removed outlier: 3.531A pdb=" N GLU D 80 " --> pdb=" O ARG D 76 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARG D 93 " --> pdb=" O LEU D 89 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LYS D 106 " --> pdb=" O LEU D 102 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N VAL D 107 " --> pdb=" O GLU D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 187 removed outlier: 3.545A pdb=" N ASN D 181 " --> pdb=" O THR D 177 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ASN D 184 " --> pdb=" O LEU D 180 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N TRP D 185 " --> pdb=" O ASN D 181 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N SER D 187 " --> pdb=" O LEU D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 189 through 199 Processing helix chain 'D' and resid 238 through 240 No H-bonds generated for 'chain 'D' and resid 238 through 240' Processing helix chain 'D' and resid 242 through 248 removed outlier: 3.737A pdb=" N GLY D 247 " --> pdb=" O TRP D 243 " (cutoff:3.500A) Processing helix chain 'D' and resid 262 through 264 No H-bonds generated for 'chain 'D' and resid 262 through 264' Processing helix chain 'D' and resid 267 through 282 removed outlier: 4.145A pdb=" N GLU D 281 " --> pdb=" O SER D 277 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N THR D 282 " --> pdb=" O GLU D 278 " (cutoff:3.500A) Processing helix chain 'D' and resid 312 through 324 removed outlier: 3.844A pdb=" N ASN D 324 " --> pdb=" O ASP D 320 " (cutoff:3.500A) Processing helix chain 'D' and resid 333 through 345 removed outlier: 3.530A pdb=" N LEU D 345 " --> pdb=" O PHE D 341 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 376 Processing helix chain 'D' and resid 397 through 405 removed outlier: 3.743A pdb=" N ALA D 403 " --> pdb=" O ILE D 399 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 422 removed outlier: 4.313A pdb=" N ARG D 420 " --> pdb=" O GLY D 417 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ILE D 421 " --> pdb=" O ALA D 418 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASN D 422 " --> pdb=" O ILE D 419 " (cutoff:3.500A) Processing helix chain 'D' and resid 425 through 430 removed outlier: 3.546A pdb=" N VAL D 429 " --> pdb=" O TYR D 426 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU D 430 " --> pdb=" O LEU D 427 " (cutoff:3.500A) Processing helix chain 'D' and resid 432 through 441 removed outlier: 4.028A pdb=" N GLY D 438 " --> pdb=" O MET D 434 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N ASP D 439 " --> pdb=" O VAL D 435 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N LYS D 440 " --> pdb=" O LEU D 436 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N ALA D 441 " --> pdb=" O ALA D 437 " (cutoff:3.500A) Processing helix chain 'D' and resid 494 through 500 removed outlier: 3.586A pdb=" N LEU D 500 " --> pdb=" O ASP D 496 " (cutoff:3.500A) Processing helix chain 'D' and resid 561 through 564 No H-bonds generated for 'chain 'D' and resid 561 through 564' Processing helix chain 'D' and resid 570 through 579 Processing helix chain 'D' and resid 640 through 648 removed outlier: 3.975A pdb=" N THR D 647 " --> pdb=" O ARG D 643 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N LEU D 648 " --> pdb=" O TYR D 644 " (cutoff:3.500A) Processing helix chain 'D' and resid 650 through 656 removed outlier: 4.900A pdb=" N GLU D 654 " --> pdb=" O ASP D 651 " (cutoff:3.500A) Processing helix chain 'D' and resid 676 through 685 removed outlier: 3.541A pdb=" N GLU D 685 " --> pdb=" O LEU D 681 " (cutoff:3.500A) Processing helix chain 'D' and resid 700 through 718 removed outlier: 3.888A pdb=" N LEU D 715 " --> pdb=" O PHE D 711 " (cutoff:3.500A) Processing helix chain 'D' and resid 747 through 750 removed outlier: 3.546A pdb=" N GLU D 750 " --> pdb=" O GLU D 747 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 747 through 750' Processing helix chain 'D' and resid 758 through 760 No H-bonds generated for 'chain 'D' and resid 758 through 760' Processing helix chain 'D' and resid 762 through 769 removed outlier: 3.521A pdb=" N ASP D 769 " --> pdb=" O LYS D 765 " (cutoff:3.500A) Processing helix chain 'D' and resid 818 through 826 removed outlier: 3.691A pdb=" N GLU D 823 " --> pdb=" O ASN D 819 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ASN D 824 " --> pdb=" O SER D 820 " (cutoff:3.500A) Processing helix chain 'D' and resid 868 through 870 No H-bonds generated for 'chain 'D' and resid 868 through 870' Processing helix chain 'D' and resid 875 through 878 No H-bonds generated for 'chain 'D' and resid 875 through 878' Processing helix chain 'D' and resid 880 through 888 Processing helix chain 'D' and resid 1021 through 1023 No H-bonds generated for 'chain 'D' and resid 1021 through 1023' Processing helix chain 'D' and resid 1043 through 1046 No H-bonds generated for 'chain 'D' and resid 1043 through 1046' Processing helix chain 'C' and resid 39 through 51 removed outlier: 4.126A pdb=" N VAL C 44 " --> pdb=" O ALA C 40 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N SER C 46 " --> pdb=" O ARG C 42 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N GLN C 47 " --> pdb=" O GLU C 43 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N ALA C 48 " --> pdb=" O VAL C 44 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N GLN C 49 " --> pdb=" O GLU C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 127 Processing helix chain 'C' and resid 130 through 132 No H-bonds generated for 'chain 'C' and resid 130 through 132' Processing helix chain 'C' and resid 192 through 198 removed outlier: 3.937A pdb=" N GLN C 197 " --> pdb=" O THR C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 207 removed outlier: 3.655A pdb=" N LEU C 204 " --> pdb=" O LEU C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 250 No H-bonds generated for 'chain 'C' and resid 247 through 250' Processing helix chain 'C' and resid 258 through 263 removed outlier: 4.400A pdb=" N SER C 263 " --> pdb=" O LEU C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 282 No H-bonds generated for 'chain 'C' and resid 280 through 282' Processing helix chain 'C' and resid 299 through 305 Processing helix chain 'C' and resid 311 through 313 No H-bonds generated for 'chain 'C' and resid 311 through 313' Processing helix chain 'C' and resid 316 through 320 Processing helix chain 'C' and resid 323 through 326 No H-bonds generated for 'chain 'C' and resid 323 through 326' Processing helix chain 'C' and resid 342 through 360 removed outlier: 4.342A pdb=" N GLU C 347 " --> pdb=" O GLU C 343 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N HIS C 348 " --> pdb=" O ASP C 344 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N LEU C 349 " --> pdb=" O ALA C 345 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL C 355 " --> pdb=" O GLU C 351 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ARG C 358 " --> pdb=" O GLU C 354 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 296 through 298 removed outlier: 3.573A pdb=" N THR A 297 " --> pdb=" O LYS A 333 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 1076 through 1078 Processing sheet with id= C, first strand: chain 'A' and resid 1092 through 1096 Processing sheet with id= D, first strand: chain 'D' and resid 69 through 72 Processing sheet with id= E, first strand: chain 'D' and resid 122 through 124 Processing sheet with id= F, first strand: chain 'D' and resid 165 through 167 removed outlier: 6.764A pdb=" N VAL D 466 " --> pdb=" O LEU D 485 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N VAL D 487 " --> pdb=" O LEU D 464 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N LEU D 464 " --> pdb=" O VAL D 487 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N GLY D 489 " --> pdb=" O GLY D 462 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N GLY D 462 " --> pdb=" O GLY D 489 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N ASP D 491 " --> pdb=" O ILE D 460 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ILE D 460 " --> pdb=" O ASP D 491 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 410 through 413 removed outlier: 8.223A pdb=" N TYR D 411 " --> pdb=" O VAL D 384 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N THR D 386 " --> pdb=" O TYR D 411 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N ILE D 413 " --> pdb=" O THR D 386 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N SER D 388 " --> pdb=" O ILE D 413 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N LEU D 255 " --> pdb=" O MET D 359 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N PHE D 361 " --> pdb=" O LEU D 255 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N LEU D 257 " --> pdb=" O PHE D 361 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ASN D 290 " --> pdb=" O ILE D 256 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N VAL D 258 " --> pdb=" O ASN D 290 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ALA D 292 " --> pdb=" O VAL D 258 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 511 through 515 Processing sheet with id= I, first strand: chain 'D' and resid 732 through 736 removed outlier: 3.555A pdb=" N GLY D 813 " --> pdb=" O PHE D 733 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N MET D 793 " --> pdb=" O THR D 776 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 848 through 854 removed outlier: 4.367A pdb=" N LEU D1013 " --> pdb=" O LEU D1008 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLU D1019 " --> pdb=" O ILE D1002 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N ILE D1002 " --> pdb=" O GLU D1019 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 892 through 899 removed outlier: 3.740A pdb=" N GLN D 980 " --> pdb=" O ASN D 895 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ILE D 975 " --> pdb=" O SER D1038 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 902 through 904 removed outlier: 3.834A pdb=" N SER D 902 " --> pdb=" O CYS D 974 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 103 through 107 Processing sheet with id= N, first strand: chain 'C' and resid 180 through 183 removed outlier: 5.740A pdb=" N ILE C 288 " --> pdb=" O VAL C 181 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N VAL C 183 " --> pdb=" O ILE C 288 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N VAL C 290 " --> pdb=" O VAL C 183 " (cutoff:3.500A) No H-bonds generated for sheet with id= N 747 hydrogen bonds defined for protein. 1950 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.99 Time building geometry restraints manager: 9.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 3370 1.32 - 1.44: 5651 1.44 - 1.57: 12015 1.57 - 1.69: 8 1.69 - 1.82: 160 Bond restraints: 21204 Sorted by residual: bond pdb=" CA CYS A 621 " pdb=" C CYS A 621 " ideal model delta sigma weight residual 1.522 1.422 0.100 1.36e-02 5.41e+03 5.41e+01 bond pdb=" CA LYS A1478 " pdb=" C LYS A1478 " ideal model delta sigma weight residual 1.524 1.437 0.086 1.33e-02 5.65e+03 4.19e+01 bond pdb=" CA LEU A 625 " pdb=" C LEU A 625 " ideal model delta sigma weight residual 1.523 1.449 0.073 1.41e-02 5.03e+03 2.71e+01 bond pdb=" CA ARG A 623 " pdb=" C ARG A 623 " ideal model delta sigma weight residual 1.522 1.456 0.066 1.31e-02 5.83e+03 2.55e+01 bond pdb=" CA LEU A 619 " pdb=" C LEU A 619 " ideal model delta sigma weight residual 1.526 1.462 0.064 1.28e-02 6.10e+03 2.52e+01 ... (remaining 21199 not shown) Histogram of bond angle deviations from ideal: 99.42 - 106.36: 537 106.36 - 113.29: 11502 113.29 - 120.23: 7870 120.23 - 127.16: 8643 127.16 - 134.10: 183 Bond angle restraints: 28735 Sorted by residual: angle pdb=" C15 PT5 A2308 " pdb=" C16 PT5 A2308 " pdb=" C17 PT5 A2308 " ideal model delta sigma weight residual 152.67 118.10 34.57 3.00e+00 1.11e-01 1.33e+02 angle pdb=" C21 PT5 A2308 " pdb=" C22 PT5 A2308 " pdb=" C23 PT5 A2308 " ideal model delta sigma weight residual 152.70 118.78 33.92 3.00e+00 1.11e-01 1.28e+02 angle pdb=" C18 PT5 A2308 " pdb=" C19 PT5 A2308 " pdb=" C20 PT5 A2308 " ideal model delta sigma weight residual 85.86 118.25 -32.39 3.00e+00 1.11e-01 1.17e+02 angle pdb=" N ARG A 620 " pdb=" CA ARG A 620 " pdb=" C ARG A 620 " ideal model delta sigma weight residual 113.50 102.65 10.85 1.23e+00 6.61e-01 7.79e+01 angle pdb=" N GLU A1490 " pdb=" CA GLU A1490 " pdb=" C GLU A1490 " ideal model delta sigma weight residual 113.15 102.68 10.47 1.19e+00 7.06e-01 7.74e+01 ... (remaining 28730 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.83: 12011 30.83 - 61.67: 989 61.67 - 92.50: 83 92.50 - 123.33: 48 123.33 - 154.17: 4 Dihedral angle restraints: 13135 sinusoidal: 5726 harmonic: 7409 Sorted by residual: dihedral pdb=" CB CYS D 904 " pdb=" SG CYS D 904 " pdb=" SG CYS D 974 " pdb=" CB CYS D 974 " ideal model delta sinusoidal sigma weight residual 93.00 177.01 -84.01 1 1.00e+01 1.00e-02 8.60e+01 dihedral pdb=" CB CYS A1479 " pdb=" SG CYS A1479 " pdb=" SG CYS A1495 " pdb=" CB CYS A1495 " ideal model delta sinusoidal sigma weight residual -86.00 -151.25 65.25 1 1.00e+01 1.00e-02 5.58e+01 dihedral pdb=" CB CYS D 404 " pdb=" SG CYS D 404 " pdb=" SG CYS D1071 " pdb=" CB CYS D1071 " ideal model delta sinusoidal sigma weight residual 93.00 143.85 -50.85 1 1.00e+01 1.00e-02 3.54e+01 ... (remaining 13132 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 2913 0.065 - 0.130: 348 0.130 - 0.195: 26 0.195 - 0.260: 5 0.260 - 0.325: 2 Chirality restraints: 3294 Sorted by residual: chirality pdb=" C1 NAG D1202 " pdb=" ND2 ASN D 92 " pdb=" C2 NAG D1202 " pdb=" O5 NAG D1202 " both_signs ideal model delta sigma weight residual False -2.40 -2.08 -0.32 2.00e-01 2.50e+01 2.64e+00 chirality pdb=" CB ILE C 214 " pdb=" CA ILE C 214 " pdb=" CG1 ILE C 214 " pdb=" CG2 ILE C 214 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.29 2.00e-01 2.50e+01 2.09e+00 chirality pdb=" C1 NAG G 1 " pdb=" ND2 ASN D 613 " pdb=" C2 NAG G 1 " pdb=" O5 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-01 2.50e+01 1.52e+00 ... (remaining 3291 not shown) Planarity restraints: 3610 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 616 " 0.018 2.00e-02 2.50e+03 3.60e-02 1.30e+01 pdb=" C ILE A 616 " -0.062 2.00e-02 2.50e+03 pdb=" O ILE A 616 " 0.023 2.00e-02 2.50e+03 pdb=" N SER A 617 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TRP A 380 " -0.055 5.00e-02 4.00e+02 8.21e-02 1.08e+01 pdb=" N PRO A 381 " 0.142 5.00e-02 4.00e+02 pdb=" CA PRO A 381 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO A 381 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 124 " -0.056 5.00e-02 4.00e+02 8.12e-02 1.05e+01 pdb=" N PRO A 125 " 0.140 5.00e-02 4.00e+02 pdb=" CA PRO A 125 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 125 " -0.046 5.00e-02 4.00e+02 ... (remaining 3607 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 1067 2.72 - 3.26: 21084 3.26 - 3.81: 33240 3.81 - 4.35: 42373 4.35 - 4.90: 69984 Nonbonded interactions: 167748 Sorted by model distance: nonbonded pdb=" OE2 GLU D 115 " pdb=" O3 NAG F 3 " model vdw 2.174 2.440 nonbonded pdb=" O4 NAG E 2 " pdb=" O7 NAG E 2 " model vdw 2.192 2.440 nonbonded pdb=" O GLU D 42 " pdb=" OG1 THR D 46 " model vdw 2.196 2.440 nonbonded pdb=" O VAL A1053 " pdb=" OG1 THR A1057 " model vdw 2.197 2.440 nonbonded pdb=" O ILE A1052 " pdb=" OG1 THR A1056 " model vdw 2.197 2.440 ... (remaining 167743 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators 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: 0.980 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: 5.810 Check model and map are aligned: 0.330 Set scattering table: 0.190 Process input model: 58.030 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 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 : 0.005 0.100 21204 Z= 0.302 Angle : 0.859 34.570 28735 Z= 0.452 Chirality : 0.045 0.325 3294 Planarity : 0.005 0.082 3602 Dihedral : 21.751 154.166 8309 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.52 % Allowed : 8.39 % Favored : 91.09 % Rotamer: Outliers : 6.34 % Allowed : 33.96 % Favored : 59.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.06 % 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: -2.16 (0.16), residues: 2502 helix: -0.70 (0.15), residues: 1113 sheet: -1.40 (0.32), residues: 251 loop : -2.17 (0.17), residues: 1138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 440 HIS 0.003 0.001 HIS D 864 PHE 0.043 0.001 PHE D 780 TYR 0.016 0.001 TYR A1234 ARG 0.006 0.000 ARG D 704 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 2241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 310 time to evaluate : 2.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 142 outliers final: 111 residues processed: 441 average time/residue: 0.9586 time to fit residues: 501.2781 Evaluate side-chains 408 residues out of total 2241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 297 time to evaluate : 2.308 Switching outliers to nearest non-outliers outliers start: 111 outliers final: 104 residues processed: 7 average time/residue: 0.2623 time to fit residues: 6.0218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 212 optimal weight: 20.0000 chunk 191 optimal weight: 0.9980 chunk 105 optimal weight: 0.9990 chunk 65 optimal weight: 6.9990 chunk 128 optimal weight: 0.0980 chunk 102 optimal weight: 3.9990 chunk 197 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 120 optimal weight: 0.0270 chunk 147 optimal weight: 3.9990 chunk 228 optimal weight: 7.9990 overall best weight: 0.6242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 429 GLN ** A 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 639 ASN A 746 ASN A1103 HIS A1428 GLN A1562 HIS D 314 ASN ** D 684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 693 ASN D 803 GLN C 51 GLN C 276 HIS C 327 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.0869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 21204 Z= 0.175 Angle : 0.667 12.702 28735 Z= 0.331 Chirality : 0.044 0.306 3294 Planarity : 0.005 0.079 3602 Dihedral : 15.450 178.256 3409 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.44 % Allowed : 8.15 % Favored : 91.41 % Rotamer: Outliers : 9.64 % Allowed : 29.99 % Favored : 60.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (0.16), residues: 2502 helix: -0.46 (0.15), residues: 1127 sheet: -1.52 (0.31), residues: 264 loop : -2.06 (0.18), residues: 1111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 440 HIS 0.002 0.001 HIS D 306 PHE 0.017 0.001 PHE C 333 TYR 0.016 0.001 TYR D 64 ARG 0.003 0.000 ARG D 114 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 538 residues out of total 2241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 216 poor density : 322 time to evaluate : 2.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 216 outliers final: 123 residues processed: 499 average time/residue: 0.9516 time to fit residues: 562.3775 Evaluate side-chains 425 residues out of total 2241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 302 time to evaluate : 2.379 Switching outliers to nearest non-outliers outliers start: 123 outliers final: 107 residues processed: 17 average time/residue: 0.3431 time to fit residues: 12.2757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 127 optimal weight: 0.7980 chunk 71 optimal weight: 2.9990 chunk 190 optimal weight: 7.9990 chunk 155 optimal weight: 1.9990 chunk 63 optimal weight: 5.9990 chunk 229 optimal weight: 0.0970 chunk 247 optimal weight: 4.9990 chunk 204 optimal weight: 1.9990 chunk 227 optimal weight: 7.9990 chunk 78 optimal weight: 0.0040 chunk 183 optimal weight: 6.9990 overall best weight: 0.9794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 429 GLN A 537 ASN A 746 ASN A1103 HIS A1237 ASN A1562 HIS D 41 GLN D 77 GLN ** D 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 693 ASN D 803 GLN D1010 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.1196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 21204 Z= 0.185 Angle : 0.639 10.860 28735 Z= 0.317 Chirality : 0.044 0.326 3294 Planarity : 0.005 0.079 3602 Dihedral : 13.095 178.315 3409 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.40 % Allowed : 8.15 % Favored : 91.45 % Rotamer: Outliers : 8.70 % Allowed : 29.99 % Favored : 61.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.16), residues: 2502 helix: -0.27 (0.15), residues: 1141 sheet: -1.26 (0.32), residues: 251 loop : -2.08 (0.18), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 104 HIS 0.002 0.001 HIS A 545 PHE 0.016 0.001 PHE C 333 TYR 0.014 0.001 TYR A1234 ARG 0.003 0.000 ARG A 685 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 505 residues out of total 2241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 195 poor density : 310 time to evaluate : 2.201 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 195 outliers final: 114 residues processed: 469 average time/residue: 0.9472 time to fit residues: 528.7895 Evaluate side-chains 411 residues out of total 2241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 297 time to evaluate : 2.278 Switching outliers to nearest non-outliers outliers start: 114 outliers final: 98 residues processed: 18 average time/residue: 0.4424 time to fit residues: 14.2625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 226 optimal weight: 9.9990 chunk 172 optimal weight: 3.9990 chunk 118 optimal weight: 8.9990 chunk 25 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 153 optimal weight: 2.9990 chunk 230 optimal weight: 40.0000 chunk 243 optimal weight: 10.0000 chunk 120 optimal weight: 4.9990 chunk 218 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 429 GLN A 683 GLN A 746 ASN A1103 HIS A1237 ASN A1428 GLN A1562 HIS A1625 ASN D 77 GLN ** D 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 641 GLN ** D 684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 693 ASN D 803 GLN ** D 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 21204 Z= 0.410 Angle : 0.720 11.164 28735 Z= 0.360 Chirality : 0.048 0.373 3294 Planarity : 0.005 0.088 3602 Dihedral : 12.641 177.364 3409 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.44 % Allowed : 8.99 % Favored : 90.57 % Rotamer: Outliers : 9.64 % Allowed : 29.76 % Favored : 60.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.06 % 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: -2.04 (0.16), residues: 2502 helix: -0.56 (0.15), residues: 1163 sheet: -1.39 (0.32), residues: 249 loop : -2.19 (0.18), residues: 1090 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 380 HIS 0.004 0.001 HIS A1148 PHE 0.027 0.002 PHE D 780 TYR 0.018 0.002 TYR D 512 ARG 0.006 0.000 ARG A1207 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 533 residues out of total 2241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 216 poor density : 317 time to evaluate : 2.054 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 216 outliers final: 129 residues processed: 486 average time/residue: 0.9521 time to fit residues: 550.0575 Evaluate side-chains 432 residues out of total 2241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 303 time to evaluate : 2.310 Switching outliers to nearest non-outliers outliers start: 129 outliers final: 111 residues processed: 22 average time/residue: 0.4038 time to fit residues: 16.2940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 202 optimal weight: 3.9990 chunk 138 optimal weight: 0.4980 chunk 3 optimal weight: 0.6980 chunk 181 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 207 optimal weight: 1.9990 chunk 168 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 124 optimal weight: 0.0270 chunk 218 optimal weight: 0.8980 chunk 61 optimal weight: 0.0770 overall best weight: 0.4396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 429 GLN A1051 ASN A1103 HIS A1237 ASN A1428 GLN A1562 HIS D 77 GLN ** D 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 641 GLN ** D 684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 693 ASN D 751 ASN D 803 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.1669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 21204 Z= 0.161 Angle : 0.627 14.288 28735 Z= 0.310 Chirality : 0.043 0.345 3294 Planarity : 0.005 0.083 3602 Dihedral : 11.876 175.648 3409 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.36 % Allowed : 7.39 % Favored : 92.25 % Rotamer: Outliers : 7.81 % Allowed : 31.77 % Favored : 60.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.17), residues: 2502 helix: -0.22 (0.15), residues: 1161 sheet: -1.23 (0.33), residues: 252 loop : -2.04 (0.19), residues: 1089 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1233 HIS 0.004 0.001 HIS D 864 PHE 0.028 0.001 PHE D 780 TYR 0.016 0.001 TYR A1234 ARG 0.006 0.000 ARG D 499 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 2241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 175 poor density : 314 time to evaluate : 2.521 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 175 outliers final: 117 residues processed: 456 average time/residue: 0.9755 time to fit residues: 528.9801 Evaluate side-chains 408 residues out of total 2241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 291 time to evaluate : 2.412 Switching outliers to nearest non-outliers outliers start: 117 outliers final: 105 residues processed: 13 average time/residue: 0.4256 time to fit residues: 11.0275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 81 optimal weight: 0.7980 chunk 219 optimal weight: 7.9990 chunk 48 optimal weight: 0.0570 chunk 143 optimal weight: 3.9990 chunk 60 optimal weight: 5.9990 chunk 243 optimal weight: 0.5980 chunk 202 optimal weight: 6.9990 chunk 112 optimal weight: 0.6980 chunk 20 optimal weight: 3.9990 chunk 80 optimal weight: 0.9980 chunk 128 optimal weight: 4.9990 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 429 GLN A1051 ASN A1103 HIS A1237 ASN A1428 GLN A1562 HIS D 77 GLN ** D 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 641 GLN ** D 684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 693 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.1829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 21204 Z= 0.166 Angle : 0.631 10.869 28735 Z= 0.313 Chirality : 0.043 0.317 3294 Planarity : 0.005 0.074 3602 Dihedral : 11.478 165.737 3409 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.36 % Allowed : 7.51 % Favored : 92.13 % Rotamer: Outliers : 7.18 % Allowed : 32.66 % Favored : 60.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.17), residues: 2502 helix: -0.10 (0.15), residues: 1167 sheet: -1.02 (0.33), residues: 250 loop : -1.94 (0.19), residues: 1085 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 104 HIS 0.003 0.001 HIS D 306 PHE 0.032 0.001 PHE D 780 TYR 0.028 0.001 TYR D 64 ARG 0.008 0.000 ARG D 499 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 2241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 301 time to evaluate : 2.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 161 outliers final: 117 residues processed: 436 average time/residue: 0.9653 time to fit residues: 500.0815 Evaluate side-chains 409 residues out of total 2241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 292 time to evaluate : 2.281 Switching outliers to nearest non-outliers outliers start: 117 outliers final: 105 residues processed: 12 average time/residue: 0.3643 time to fit residues: 9.5862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 235 optimal weight: 0.0980 chunk 27 optimal weight: 3.9990 chunk 138 optimal weight: 0.5980 chunk 178 optimal weight: 5.9990 chunk 137 optimal weight: 6.9990 chunk 205 optimal weight: 10.0000 chunk 136 optimal weight: 2.9990 chunk 242 optimal weight: 7.9990 chunk 152 optimal weight: 0.6980 chunk 148 optimal weight: 0.5980 chunk 112 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 429 GLN A1103 HIS A1562 HIS D 77 GLN ** D 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 568 ASN D 641 GLN ** D 684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 693 ASN ** D 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1010 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 21204 Z= 0.162 Angle : 0.634 11.751 28735 Z= 0.314 Chirality : 0.043 0.304 3294 Planarity : 0.005 0.076 3602 Dihedral : 10.837 132.322 3409 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.31 % Favored : 92.37 % Rotamer: Outliers : 6.69 % Allowed : 33.07 % Favored : 60.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.17), residues: 2502 helix: 0.12 (0.15), residues: 1147 sheet: -0.91 (0.33), residues: 250 loop : -1.85 (0.19), residues: 1105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1233 HIS 0.002 0.001 HIS D 306 PHE 0.037 0.001 PHE D 780 TYR 0.016 0.001 TYR A1234 ARG 0.009 0.000 ARG D 499 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 2241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 304 time to evaluate : 2.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 150 outliers final: 108 residues processed: 434 average time/residue: 0.9164 time to fit residues: 478.0164 Evaluate side-chains 398 residues out of total 2241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 290 time to evaluate : 2.284 Switching outliers to nearest non-outliers outliers start: 108 outliers final: 100 residues processed: 8 average time/residue: 0.4885 time to fit residues: 8.3670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 150 optimal weight: 2.9990 chunk 96 optimal weight: 5.9990 chunk 145 optimal weight: 0.9990 chunk 73 optimal weight: 0.8980 chunk 47 optimal weight: 0.5980 chunk 154 optimal weight: 4.9990 chunk 165 optimal weight: 4.9990 chunk 120 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 chunk 190 optimal weight: 0.9990 chunk 220 optimal weight: 8.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 429 GLN A1103 HIS A1562 HIS D 77 GLN ** D 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 568 ASN D 641 GLN ** D 684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 693 ASN ** D 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 21204 Z= 0.176 Angle : 0.642 13.522 28735 Z= 0.316 Chirality : 0.043 0.300 3294 Planarity : 0.005 0.074 3602 Dihedral : 10.394 112.481 3409 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.55 % Favored : 92.17 % Rotamer: Outliers : 6.34 % Allowed : 33.87 % Favored : 59.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.17), residues: 2502 helix: 0.16 (0.15), residues: 1150 sheet: -0.83 (0.34), residues: 248 loop : -1.83 (0.19), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 380 HIS 0.002 0.001 HIS C 94 PHE 0.041 0.001 PHE D 780 TYR 0.026 0.001 TYR D1068 ARG 0.010 0.000 ARG D 499 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 2241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 301 time to evaluate : 2.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 142 outliers final: 115 residues processed: 424 average time/residue: 0.8931 time to fit residues: 456.5129 Evaluate side-chains 407 residues out of total 2241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 292 time to evaluate : 2.315 Switching outliers to nearest non-outliers outliers start: 115 outliers final: 106 residues processed: 10 average time/residue: 0.3661 time to fit residues: 8.7312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 232 optimal weight: 2.9990 chunk 212 optimal weight: 7.9990 chunk 226 optimal weight: 7.9990 chunk 136 optimal weight: 10.0000 chunk 98 optimal weight: 4.9990 chunk 177 optimal weight: 5.9990 chunk 69 optimal weight: 6.9990 chunk 204 optimal weight: 7.9990 chunk 214 optimal weight: 7.9990 chunk 225 optimal weight: 0.1980 chunk 148 optimal weight: 0.7980 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 429 GLN A 683 GLN A1051 ASN A1103 HIS A1428 GLN A1562 HIS D 77 GLN ** D 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 568 ASN D 641 GLN D 693 ASN ** D 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 21204 Z= 0.390 Angle : 0.739 13.855 28735 Z= 0.367 Chirality : 0.048 0.341 3294 Planarity : 0.005 0.079 3602 Dihedral : 10.719 112.367 3409 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.28 % Allowed : 8.79 % Favored : 90.93 % Rotamer: Outliers : 6.56 % Allowed : 33.69 % Favored : 59.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.16), residues: 2502 helix: -0.24 (0.15), residues: 1171 sheet: -1.11 (0.33), residues: 250 loop : -2.02 (0.18), residues: 1081 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 380 HIS 0.005 0.001 HIS D 864 PHE 0.043 0.002 PHE D 780 TYR 0.047 0.002 TYR D1068 ARG 0.012 0.001 ARG D 197 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 2241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 300 time to evaluate : 2.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 147 outliers final: 113 residues processed: 428 average time/residue: 0.9428 time to fit residues: 484.3029 Evaluate side-chains 406 residues out of total 2241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 293 time to evaluate : 2.387 Switching outliers to nearest non-outliers outliers start: 113 outliers final: 103 residues processed: 11 average time/residue: 0.3711 time to fit residues: 9.2929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 239 optimal weight: 0.5980 chunk 146 optimal weight: 0.5980 chunk 113 optimal weight: 0.0970 chunk 166 optimal weight: 1.9990 chunk 251 optimal weight: 7.9990 chunk 231 optimal weight: 0.6980 chunk 199 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 154 optimal weight: 3.9990 chunk 122 optimal weight: 7.9990 chunk 158 optimal weight: 0.8980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 429 GLN A1051 ASN A1103 HIS A1562 HIS ** D 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 77 GLN ** D 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 568 ASN D 641 GLN D 693 ASN ** D 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.2213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 21204 Z= 0.169 Angle : 0.669 12.458 28735 Z= 0.330 Chirality : 0.044 0.320 3294 Planarity : 0.005 0.078 3602 Dihedral : 10.239 107.968 3409 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.19 % Favored : 92.53 % Rotamer: Outliers : 5.00 % Allowed : 35.21 % Favored : 59.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.17), residues: 2502 helix: 0.11 (0.15), residues: 1149 sheet: -0.90 (0.33), residues: 253 loop : -1.88 (0.19), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A1233 HIS 0.002 0.001 HIS D 306 PHE 0.042 0.001 PHE D 780 TYR 0.023 0.001 TYR D1068 ARG 0.011 0.000 ARG D 499 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 2241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 297 time to evaluate : 2.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 112 outliers final: 102 residues processed: 406 average time/residue: 0.9792 time to fit residues: 474.3810 Evaluate side-chains 394 residues out of total 2241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 292 time to evaluate : 2.495 Switching outliers to nearest non-outliers outliers start: 102 outliers final: 100 residues processed: 3 average time/residue: 0.7985 time to fit residues: 6.3898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 212 optimal weight: 10.0000 chunk 61 optimal weight: 0.5980 chunk 184 optimal weight: 0.4980 chunk 29 optimal weight: 9.9990 chunk 55 optimal weight: 2.9990 chunk 200 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 205 optimal weight: 10.0000 chunk 25 optimal weight: 3.9990 chunk 36 optimal weight: 0.6980 chunk 175 optimal weight: 0.8980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 429 GLN A1051 ASN A1103 HIS A1562 HIS D 41 GLN D 77 GLN ** D 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 641 GLN D 693 ASN ** D 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.192769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.126853 restraints weight = 25531.223| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 2.65 r_work: 0.3252 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.2283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 21204 Z= 0.204 Angle : 0.668 12.731 28735 Z= 0.329 Chirality : 0.044 0.314 3294 Planarity : 0.005 0.074 3602 Dihedral : 10.183 106.429 3409 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.28 % Allowed : 8.03 % Favored : 91.69 % Rotamer: Outliers : 5.18 % Allowed : 35.16 % Favored : 59.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.17), residues: 2502 helix: 0.11 (0.15), residues: 1167 sheet: -0.97 (0.34), residues: 242 loop : -1.89 (0.18), residues: 1093 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1233 HIS 0.003 0.001 HIS D 306 PHE 0.042 0.001 PHE D 780 TYR 0.023 0.001 TYR D 64 ARG 0.011 0.000 ARG D 499 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8896.20 seconds wall clock time: 158 minutes 10.93 seconds (9490.93 seconds total)