Starting phenix.real_space_refine on Sat Jun 21 04:24:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7r13_14229/06_2025/7r13_14229.cif Found real_map, /net/cci-nas-00/data/ceres_data/7r13_14229/06_2025/7r13_14229.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7r13_14229/06_2025/7r13_14229.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7r13_14229/06_2025/7r13_14229.map" model { file = "/net/cci-nas-00/data/ceres_data/7r13_14229/06_2025/7r13_14229.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7r13_14229/06_2025/7r13_14229.cif" } resolution = 3.6 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= 0.004 sd= 0.091 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 105 5.16 5 C 15498 2.51 5 N 3960 2.21 5 O 4740 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 24303 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 7835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1001, 7835 Classifications: {'peptide': 1001} Link IDs: {'PTRANS': 52, 'TRANS': 948} Chain breaks: 8 Chain: "B" Number of atoms: 7835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1001, 7835 Classifications: {'peptide': 1001} Link IDs: {'PTRANS': 52, 'TRANS': 948} Chain breaks: 8 Chain: "C" Number of atoms: 7835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1001, 7835 Classifications: {'peptide': 1001} Link IDs: {'PTRANS': 52, 'TRANS': 948} Chain breaks: 8 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 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: "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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" 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: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "B" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "C" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Time building chain proxies: 15.22, per 1000 atoms: 0.63 Number of scatterers: 24303 At special positions: 0 Unit cell: (136.962, 136.962, 180.442, 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 105 16.00 O 4740 8.00 N 3960 7.00 C 15498 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, 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=2.07 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=2.02 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=2.07 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " 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 617 " - pdb=" SG CYS B 649 " distance=2.02 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 B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 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=2.07 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=2.02 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 C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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 H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " NAG-ASN " NAG A1301 " - " ASN A 122 " " NAG A1302 " - " ASN A 165 " " NAG A1303 " - " ASN A 234 " " NAG A1304 " - " ASN A 331 " " NAG A1305 " - " ASN A 343 " " NAG A1306 " - " ASN A 616 " " NAG A1307 " - " ASN A 657 " " NAG A1308 " - " ASN A 709 " " NAG A1309 " - " ASN A 801 " " NAG A1310 " - " ASN A1074 " " NAG A1311 " - " ASN A 61 " " NAG A1312 " - " ASN A 282 " " NAG A1313 " - " ASN A 603 " " NAG B1301 " - " ASN B 122 " " NAG B1302 " - " ASN B 165 " " NAG B1303 " - " ASN B 234 " " NAG B1304 " - " ASN B 331 " " NAG B1305 " - " ASN B 343 " " NAG B1306 " - " ASN B 616 " " NAG B1307 " - " ASN B 657 " " NAG B1308 " - " ASN B 709 " " NAG B1309 " - " ASN B 801 " " NAG B1310 " - " ASN B1074 " " NAG B1311 " - " ASN B 61 " " NAG B1312 " - " ASN B 282 " " NAG B1313 " - " ASN B 603 " " NAG C1301 " - " ASN C 122 " " NAG C1302 " - " ASN C 165 " " NAG C1303 " - " ASN C 234 " " NAG C1304 " - " ASN C 331 " " NAG C1305 " - " ASN C 343 " " NAG C1306 " - " ASN C 616 " " NAG C1307 " - " ASN C 657 " " NAG C1308 " - " ASN C 709 " " NAG C1309 " - " ASN C 801 " " NAG C1310 " - " ASN C1074 " " NAG C1311 " - " ASN C 61 " " NAG C1312 " - " ASN C 282 " " NAG C1313 " - " ASN C 603 " " NAG D 1 " - " ASN A 717 " " NAG E 1 " - " ASN A1098 " " NAG F 1 " - " ASN A1134 " " NAG G 1 " - " ASN B 717 " " NAG H 1 " - " ASN B1098 " " NAG I 1 " - " ASN B1134 " " NAG J 1 " - " ASN C 717 " " NAG K 1 " - " ASN C1098 " " NAG L 1 " - " ASN C1134 " Time building additional restraints: 5.68 Conformation dependent library (CDL) restraints added in 2.7 seconds 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5628 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 42 sheets defined 24.0% alpha, 24.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.02 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 364 through 368 removed outlier: 3.746A pdb=" N VAL A 367 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 390 removed outlier: 4.246A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.310A 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 439 through 443 removed outlier: 3.881A pdb=" N SER A 443 " --> pdb=" O ASN A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.527A pdb=" N ALA A 771 " --> pdb=" O LEU A 767 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 removed outlier: 3.671A pdb=" N LEU A 821 " --> pdb=" O PHE A 817 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N PHE A 823 " --> pdb=" O GLU A 819 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.671A pdb=" N ILE A 870 " --> pdb=" O THR A 866 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALA A 871 " --> pdb=" O ASP A 867 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 918 removed outlier: 3.508A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 939 removed outlier: 3.536A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.914A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) 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 977 through 982 removed outlier: 3.621A pdb=" N ALA A 982 " --> pdb=" O ASN A 978 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 5.209A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL A1033 " --> pdb=" O MET A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1142 through 1146 removed outlier: 3.898A pdb=" N ASP A1146 " --> pdb=" O PRO A1143 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 364 through 368 removed outlier: 3.747A pdb=" N VAL B 367 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 390 removed outlier: 4.246A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.310A 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 439 through 443 removed outlier: 3.882A pdb=" N SER B 443 " --> pdb=" O ASN B 440 " (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 758 through 783 removed outlier: 3.527A pdb=" N ALA B 771 " --> pdb=" O LEU B 767 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 removed outlier: 3.671A pdb=" N LEU B 821 " --> pdb=" O PHE B 817 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N PHE B 823 " --> pdb=" O GLU B 819 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 removed outlier: 3.671A pdb=" N ILE B 870 " --> pdb=" O THR B 866 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALA B 871 " --> pdb=" O ASP B 867 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.508A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 939 removed outlier: 3.536A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.914A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) 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 977 through 982 removed outlier: 3.622A pdb=" N ALA B 982 " --> pdb=" O ASN B 978 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 5.210A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL B1033 " --> pdb=" O MET B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1142 through 1146 removed outlier: 3.898A pdb=" N ASP B1146 " --> pdb=" O PRO B1143 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 364 through 368 removed outlier: 3.747A pdb=" N VAL C 367 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 390 removed outlier: 4.246A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.311A 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 439 through 443 removed outlier: 3.881A pdb=" N SER C 443 " --> pdb=" O ASN C 440 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.527A pdb=" N ALA C 771 " --> pdb=" O LEU C 767 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 824 removed outlier: 3.672A pdb=" N LEU C 821 " --> pdb=" O PHE C 817 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N PHE C 823 " --> pdb=" O GLU C 819 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 removed outlier: 3.671A pdb=" N ILE C 870 " --> pdb=" O THR C 866 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALA C 871 " --> pdb=" O ASP C 867 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 918 removed outlier: 3.508A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 939 removed outlier: 3.536A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.914A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 977 through 982 removed outlier: 3.622A pdb=" N ALA C 982 " --> pdb=" O ASN C 978 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 5.210A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL C1033 " --> pdb=" O MET C1029 " (cutoff:3.500A) Processing helix chain 'C' and resid 1142 through 1146 removed outlier: 3.898A pdb=" N ASP C1146 " --> pdb=" O PRO C1143 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 3.757A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N THR A 95 " --> pdb=" O ALA A 264 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.739A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.917A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.070A pdb=" N PHE A 43 " --> pdb=" O ARG C 567 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLY C 548 " --> pdb=" O PHE C 541 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL C 539 " --> pdb=" O GLY C 550 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.502A pdb=" N PHE A 55 " --> pdb=" O GLN A 271 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 11.395A pdb=" N VAL A 126 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 9.924A pdb=" N GLU A 169 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 11.611A pdb=" N ILE A 128 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 9.009A pdb=" N THR A 167 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N VAL A 130 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N ASN A 165 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N GLU A 132 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ALA A 163 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 316 removed outlier: 6.985A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 328 removed outlier: 3.593A pdb=" N VAL A 539 " --> pdb=" O GLY A 550 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLY A 548 " --> pdb=" O PHE A 541 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 357 removed outlier: 5.501A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLY A 431 " --> pdb=" O TYR A 380 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N TYR A 380 " --> pdb=" O GLY A 431 " (cutoff:3.500A) 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: 6.267A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.558A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 702 through 704 removed outlier: 3.629A pdb=" N ASN A 703 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LYS B 790 " --> pdb=" O ASN A 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 712 through 713 removed outlier: 3.857A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 718 through 728 removed outlier: 3.518A pdb=" N SER A 721 " --> pdb=" O THR A1066 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB6, first strand: chain 'A' and resid 788 through 790 removed outlier: 5.572A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1122 removed outlier: 3.598A pdb=" N VAL A1133 " --> pdb=" O ALA A1080 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N CYS A1082 " --> pdb=" O VAL A1133 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 27 through 30 removed outlier: 3.757A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TYR B 265 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N THR B 95 " --> pdb=" O ALA B 264 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.739A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.917A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.502A pdb=" N PHE B 55 " --> pdb=" O GLN B 271 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 84 through 85 removed outlier: 11.394A pdb=" N VAL B 126 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 9.924A pdb=" N GLU B 169 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 11.612A pdb=" N ILE B 128 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 9.008A pdb=" N THR B 167 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N VAL B 130 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N ASN B 165 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N GLU B 132 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ALA B 163 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N GLN B 134 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N VAL B 159 " --> pdb=" O CYS B 136 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 311 through 316 removed outlier: 6.985A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 325 through 328 removed outlier: 3.592A pdb=" N VAL B 539 " --> pdb=" O GLY B 550 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY B 548 " --> pdb=" O PHE B 541 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 354 through 357 removed outlier: 5.501A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLY B 431 " --> pdb=" O TYR B 380 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N TYR B 380 " --> pdb=" O GLY B 431 " (cutoff:3.500A) 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 654 through 655 removed outlier: 6.267A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.558A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 702 through 704 removed outlier: 3.613A pdb=" N ASN B 703 " --> pdb=" O ILE C 788 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS C 790 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'B' and resid 712 through 713 removed outlier: 3.857A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 718 through 728 removed outlier: 3.518A pdb=" N SER B 721 " --> pdb=" O THR B1066 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD3, first strand: chain 'B' and resid 1120 through 1122 removed outlier: 3.598A pdb=" N VAL B1133 " --> pdb=" O ALA B1080 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N CYS B1082 " --> pdb=" O VAL B1133 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 27 through 30 removed outlier: 3.757A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N THR C 95 " --> pdb=" O ALA C 264 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.739A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.917A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.502A pdb=" N PHE C 55 " --> pdb=" O GLN C 271 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 84 through 85 removed outlier: 11.395A pdb=" N VAL C 126 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 9.924A pdb=" N GLU C 169 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 11.612A pdb=" N ILE C 128 " --> pdb=" O THR C 167 " (cutoff:3.500A) removed outlier: 9.009A pdb=" N THR C 167 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N VAL C 130 " --> pdb=" O ASN C 165 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N ASN C 165 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N GLU C 132 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ALA C 163 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N VAL C 159 " --> pdb=" O CYS C 136 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 311 through 316 removed outlier: 6.985A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 354 through 357 removed outlier: 5.501A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLY C 431 " --> pdb=" O TYR C 380 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N TYR C 380 " --> pdb=" O GLY C 431 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE1, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE2, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.267A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.559A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 712 through 713 removed outlier: 3.858A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 718 through 728 removed outlier: 3.518A pdb=" N SER C 721 " --> pdb=" O THR C1066 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AE6, first strand: chain 'C' and resid 1120 through 1122 removed outlier: 3.598A pdb=" N VAL C1133 " --> pdb=" O ALA C1080 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N CYS C1082 " --> pdb=" O VAL C1133 " (cutoff:3.500A) 865 hydrogen bonds defined for protein. 2334 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 11.58 Time building geometry restraints manager: 6.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 7710 1.35 - 1.47: 6465 1.47 - 1.60: 10539 1.60 - 1.72: 0 1.72 - 1.85: 129 Bond restraints: 24843 Sorted by residual: bond pdb=" N CYS C 379 " pdb=" CA CYS C 379 " ideal model delta sigma weight residual 1.455 1.490 -0.034 1.23e-02 6.61e+03 7.71e+00 bond pdb=" N CYS A 379 " pdb=" CA CYS A 379 " ideal model delta sigma weight residual 1.455 1.489 -0.034 1.23e-02 6.61e+03 7.58e+00 bond pdb=" N CYS B 379 " pdb=" CA CYS B 379 " ideal model delta sigma weight residual 1.455 1.489 -0.034 1.23e-02 6.61e+03 7.57e+00 bond pdb=" N TYR B 380 " pdb=" CA TYR B 380 " ideal model delta sigma weight residual 1.454 1.489 -0.035 1.29e-02 6.01e+03 7.37e+00 bond pdb=" N TYR C 380 " pdb=" CA TYR C 380 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.29e-02 6.01e+03 6.94e+00 ... (remaining 24838 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.27: 32242 1.27 - 2.54: 1212 2.54 - 3.81: 293 3.81 - 5.08: 52 5.08 - 6.35: 8 Bond angle restraints: 33807 Sorted by residual: angle pdb=" CA ASN C 122 " pdb=" C ASN C 122 " pdb=" O ASN C 122 " ideal model delta sigma weight residual 121.50 117.97 3.53 1.25e+00 6.40e-01 7.97e+00 angle pdb=" CA ASN A 122 " pdb=" C ASN A 122 " pdb=" O ASN A 122 " ideal model delta sigma weight residual 121.50 117.99 3.51 1.25e+00 6.40e-01 7.90e+00 angle pdb=" CA ASN B 122 " pdb=" C ASN B 122 " pdb=" O ASN B 122 " ideal model delta sigma weight residual 121.50 118.01 3.49 1.25e+00 6.40e-01 7.81e+00 angle pdb=" N ARG C1107 " pdb=" CA ARG C1107 " pdb=" C ARG C1107 " ideal model delta sigma weight residual 111.36 114.39 -3.03 1.09e+00 8.42e-01 7.74e+00 angle pdb=" N PRO B 986 " pdb=" CA PRO B 986 " pdb=" C PRO B 986 " ideal model delta sigma weight residual 110.70 114.09 -3.39 1.22e+00 6.72e-01 7.72e+00 ... (remaining 33802 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.01: 14224 17.01 - 34.02: 977 34.02 - 51.03: 234 51.03 - 68.04: 63 68.04 - 85.06: 36 Dihedral angle restraints: 15534 sinusoidal: 6795 harmonic: 8739 Sorted by residual: dihedral pdb=" CB CYS A 538 " pdb=" SG CYS A 538 " pdb=" SG CYS A 590 " pdb=" CB CYS A 590 " ideal model delta sinusoidal sigma weight residual -86.00 -142.34 56.34 1 1.00e+01 1.00e-02 4.28e+01 dihedral pdb=" CB CYS C 538 " pdb=" SG CYS C 538 " pdb=" SG CYS C 590 " pdb=" CB CYS C 590 " ideal model delta sinusoidal sigma weight residual -86.00 -142.33 56.33 1 1.00e+01 1.00e-02 4.28e+01 dihedral pdb=" CB CYS B 538 " pdb=" SG CYS B 538 " pdb=" SG CYS B 590 " pdb=" CB CYS B 590 " ideal model delta sinusoidal sigma weight residual -86.00 -142.32 56.32 1 1.00e+01 1.00e-02 4.28e+01 ... (remaining 15531 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 2769 0.040 - 0.080: 808 0.080 - 0.120: 385 0.120 - 0.160: 35 0.160 - 0.200: 8 Chirality restraints: 4005 Sorted by residual: chirality pdb=" CA CYS C 379 " pdb=" N CYS C 379 " pdb=" C CYS C 379 " pdb=" CB CYS C 379 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.96e-01 chirality pdb=" CA CYS B 379 " pdb=" N CYS B 379 " pdb=" C CYS B 379 " pdb=" CB CYS B 379 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.93e-01 chirality pdb=" CA CYS A 379 " pdb=" N CYS A 379 " pdb=" C CYS A 379 " pdb=" CB CYS A 379 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.75e-01 ... (remaining 4002 not shown) Planarity restraints: 4353 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 906 " -0.013 2.00e-02 2.50e+03 1.21e-02 2.57e+00 pdb=" CG PHE B 906 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 PHE B 906 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE B 906 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE B 906 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 906 " -0.006 2.00e-02 2.50e+03 pdb=" CZ PHE B 906 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 906 " 0.013 2.00e-02 2.50e+03 1.20e-02 2.53e+00 pdb=" CG PHE A 906 " -0.028 2.00e-02 2.50e+03 pdb=" CD1 PHE A 906 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE A 906 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE A 906 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 906 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE A 906 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 906 " -0.013 2.00e-02 2.50e+03 1.20e-02 2.51e+00 pdb=" CG PHE C 906 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 PHE C 906 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE C 906 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE C 906 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE C 906 " -0.005 2.00e-02 2.50e+03 pdb=" CZ PHE C 906 " -0.000 2.00e-02 2.50e+03 ... (remaining 4350 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 3836 2.77 - 3.30: 22121 3.30 - 3.83: 37741 3.83 - 4.37: 42046 4.37 - 4.90: 75058 Nonbonded interactions: 180802 Sorted by model distance: nonbonded pdb=" OG1 THR B 323 " pdb=" OE1 GLU B 324 " model vdw 2.232 3.040 nonbonded pdb=" OG1 THR C 323 " pdb=" OE1 GLU C 324 " model vdw 2.232 3.040 nonbonded pdb=" OG1 THR A 323 " pdb=" OE1 GLU A 324 " model vdw 2.232 3.040 nonbonded pdb=" OD1 ASN A 360 " pdb=" OG1 THR A 523 " model vdw 2.234 3.040 nonbonded pdb=" OG1 THR A 645 " pdb=" O GLY A 648 " model vdw 2.234 3.040 ... (remaining 180797 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.15 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.040 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: 0.020 Extract box with map and model: 1.020 Check model and map are aligned: 0.190 Set scattering table: 0.250 Process input model: 58.170 Find NCS groups from input model: 1.230 Set up NCS constraints: 0.150 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:3.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 24939 Z= 0.189 Angle : 0.605 6.346 34056 Z= 0.313 Chirality : 0.045 0.200 4005 Planarity : 0.003 0.035 4305 Dihedral : 12.844 85.055 9789 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.15), residues: 2949 helix: 1.68 (0.22), residues: 621 sheet: 0.17 (0.19), residues: 684 loop : -1.43 (0.15), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 353 HIS 0.002 0.001 HIS C 66 PHE 0.028 0.001 PHE B 906 TYR 0.015 0.001 TYR C 380 ARG 0.003 0.000 ARG C 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00186 ( 48) link_NAG-ASN : angle 1.44163 ( 144) link_BETA1-4 : bond 0.00300 ( 9) link_BETA1-4 : angle 0.89518 ( 27) hydrogen bonds : bond 0.21293 ( 865) hydrogen bonds : angle 7.53484 ( 2334) SS BOND : bond 0.01041 ( 39) SS BOND : angle 1.27273 ( 78) covalent geometry : bond 0.00386 (24843) covalent geometry : angle 0.59582 (33807) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 2625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 303 time to evaluate : 2.491 Fit side-chains revert: symmetry clash REVERT: A 515 PHE cc_start: 0.8648 (p90) cc_final: 0.8197 (p90) REVERT: C 515 PHE cc_start: 0.8772 (p90) cc_final: 0.8075 (p90) outliers start: 0 outliers final: 0 residues processed: 303 average time/residue: 0.3473 time to fit residues: 167.3221 Evaluate side-chains 211 residues out of total 2625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 211 time to evaluate : 2.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 253 optimal weight: 0.9980 chunk 227 optimal weight: 1.9990 chunk 126 optimal weight: 6.9990 chunk 77 optimal weight: 0.9990 chunk 153 optimal weight: 1.9990 chunk 121 optimal weight: 0.8980 chunk 235 optimal weight: 6.9990 chunk 90 optimal weight: 0.2980 chunk 142 optimal weight: 10.0000 chunk 175 optimal weight: 1.9990 chunk 272 optimal weight: 0.0970 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 474 GLN A 498 GLN A 804 GLN B 81 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 GLN B 498 GLN B 675 GLN B 804 GLN C 81 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 474 GLN C 498 GLN C 804 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.148041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.111043 restraints weight = 37835.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.108627 restraints weight = 45373.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.110371 restraints weight = 40363.482| |-----------------------------------------------------------------------------| r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.0994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 24939 Z= 0.143 Angle : 0.577 7.207 34056 Z= 0.302 Chirality : 0.044 0.164 4005 Planarity : 0.004 0.038 4305 Dihedral : 6.950 54.392 4410 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 0.57 % Allowed : 6.13 % Favored : 93.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.15), residues: 2949 helix: 1.59 (0.22), residues: 630 sheet: 0.23 (0.19), residues: 738 loop : -1.48 (0.15), residues: 1581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 353 HIS 0.004 0.001 HIS C1088 PHE 0.016 0.001 PHE A 377 TYR 0.014 0.001 TYR A 453 ARG 0.004 0.001 ARG A 214 Details of bonding type rmsd link_NAG-ASN : bond 0.00208 ( 48) link_NAG-ASN : angle 1.55755 ( 144) link_BETA1-4 : bond 0.00315 ( 9) link_BETA1-4 : angle 1.10975 ( 27) hydrogen bonds : bond 0.05631 ( 865) hydrogen bonds : angle 5.79047 ( 2334) SS BOND : bond 0.00565 ( 39) SS BOND : angle 1.22613 ( 78) covalent geometry : bond 0.00329 (24843) covalent geometry : angle 0.56577 (33807) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 242 time to evaluate : 2.676 Fit side-chains revert: symmetry clash REVERT: A 781 VAL cc_start: 0.8686 (t) cc_final: 0.8477 (t) REVERT: B 102 ARG cc_start: 0.7478 (mmp-170) cc_final: 0.7243 (mmp-170) REVERT: C 102 ARG cc_start: 0.7498 (mmp-170) cc_final: 0.7283 (mmp-170) REVERT: C 515 PHE cc_start: 0.8744 (p90) cc_final: 0.7954 (p90) outliers start: 15 outliers final: 11 residues processed: 250 average time/residue: 0.3834 time to fit residues: 155.4401 Evaluate side-chains 216 residues out of total 2625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 205 time to evaluate : 2.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 615 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 270 optimal weight: 0.8980 chunk 204 optimal weight: 3.9990 chunk 63 optimal weight: 0.9980 chunk 299 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 264 optimal weight: 3.9990 chunk 243 optimal weight: 0.9980 chunk 218 optimal weight: 0.9990 chunk 35 optimal weight: 3.9990 chunk 144 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.145453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.108465 restraints weight = 37784.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.107110 restraints weight = 44205.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.108603 restraints weight = 43547.614| |-----------------------------------------------------------------------------| r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.1409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 24939 Z= 0.167 Angle : 0.566 6.406 34056 Z= 0.294 Chirality : 0.045 0.204 4005 Planarity : 0.004 0.052 4305 Dihedral : 6.399 54.174 4410 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 1.56 % Allowed : 7.77 % Favored : 90.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.15), residues: 2949 helix: 1.46 (0.22), residues: 648 sheet: 0.26 (0.19), residues: 708 loop : -1.49 (0.15), residues: 1593 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 353 HIS 0.004 0.001 HIS C1088 PHE 0.025 0.001 PHE A 377 TYR 0.016 0.001 TYR B 904 ARG 0.006 0.000 ARG A 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00180 ( 48) link_NAG-ASN : angle 1.61936 ( 144) link_BETA1-4 : bond 0.00244 ( 9) link_BETA1-4 : angle 1.10904 ( 27) hydrogen bonds : bond 0.05505 ( 865) hydrogen bonds : angle 5.38132 ( 2334) SS BOND : bond 0.00562 ( 39) SS BOND : angle 1.18855 ( 78) covalent geometry : bond 0.00397 (24843) covalent geometry : angle 0.55417 (33807) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 234 time to evaluate : 2.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ARG cc_start: 0.7556 (mmp-170) cc_final: 0.7177 (mmp-170) REVERT: A 368 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8624 (mt) REVERT: A 781 VAL cc_start: 0.8778 (t) cc_final: 0.8514 (t) REVERT: A 1029 MET cc_start: 0.9213 (tpp) cc_final: 0.8905 (ttm) REVERT: B 102 ARG cc_start: 0.7410 (mmp-170) cc_final: 0.7060 (mmp-170) REVERT: B 917 TYR cc_start: 0.8772 (m-80) cc_final: 0.7919 (m-80) REVERT: B 1050 MET cc_start: 0.8315 (ptt) cc_final: 0.8022 (ptp) REVERT: C 102 ARG cc_start: 0.7520 (mmp-170) cc_final: 0.7257 (mmp-170) REVERT: C 353 TRP cc_start: 0.8120 (p-90) cc_final: 0.7725 (p-90) REVERT: C 368 LEU cc_start: 0.8773 (mp) cc_final: 0.8563 (mt) REVERT: C 923 ILE cc_start: 0.8807 (OUTLIER) cc_final: 0.8593 (mp) outliers start: 41 outliers final: 33 residues processed: 260 average time/residue: 0.3204 time to fit residues: 136.2966 Evaluate side-chains 235 residues out of total 2625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 200 time to evaluate : 2.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 923 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 245 optimal weight: 0.5980 chunk 47 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 275 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 223 optimal weight: 0.6980 chunk 226 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 234 optimal weight: 4.9990 chunk 157 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 GLN ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.143765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.106507 restraints weight = 37943.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.104361 restraints weight = 43603.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.105824 restraints weight = 41138.270| |-----------------------------------------------------------------------------| r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 24939 Z= 0.200 Angle : 0.594 6.844 34056 Z= 0.306 Chirality : 0.046 0.162 4005 Planarity : 0.004 0.038 4305 Dihedral : 6.158 54.090 4410 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 1.75 % Allowed : 10.21 % Favored : 88.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.15), residues: 2949 helix: 1.25 (0.21), residues: 648 sheet: 0.11 (0.19), residues: 681 loop : -1.47 (0.15), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 353 HIS 0.005 0.001 HIS A1088 PHE 0.024 0.002 PHE B 377 TYR 0.019 0.001 TYR B 904 ARG 0.004 0.001 ARG B 408 Details of bonding type rmsd link_NAG-ASN : bond 0.00197 ( 48) link_NAG-ASN : angle 1.71942 ( 144) link_BETA1-4 : bond 0.00250 ( 9) link_BETA1-4 : angle 1.08208 ( 27) hydrogen bonds : bond 0.05869 ( 865) hydrogen bonds : angle 5.27556 ( 2334) SS BOND : bond 0.00683 ( 39) SS BOND : angle 1.36675 ( 78) covalent geometry : bond 0.00484 (24843) covalent geometry : angle 0.58081 (33807) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 217 time to evaluate : 2.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 368 LEU cc_start: 0.8973 (mp) cc_final: 0.8713 (mt) REVERT: A 1029 MET cc_start: 0.9214 (tpp) cc_final: 0.8960 (ttm) REVERT: B 102 ARG cc_start: 0.7680 (mmp-170) cc_final: 0.7277 (mmp-170) REVERT: C 102 ARG cc_start: 0.7798 (mmp-170) cc_final: 0.7531 (mmp-170) REVERT: C 923 ILE cc_start: 0.8857 (OUTLIER) cc_final: 0.8638 (mp) outliers start: 46 outliers final: 38 residues processed: 251 average time/residue: 0.3647 time to fit residues: 150.8448 Evaluate side-chains 231 residues out of total 2625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 192 time to evaluate : 2.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 923 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 61 optimal weight: 0.9990 chunk 143 optimal weight: 3.9990 chunk 199 optimal weight: 0.0980 chunk 186 optimal weight: 0.7980 chunk 214 optimal weight: 1.9990 chunk 99 optimal weight: 0.0570 chunk 43 optimal weight: 2.9990 chunk 90 optimal weight: 0.9980 chunk 122 optimal weight: 3.9990 chunk 110 optimal weight: 0.0870 chunk 142 optimal weight: 0.7980 overall best weight: 0.3676 ------------------------------------------------------------------------------- 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** C 394 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.146476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.110215 restraints weight = 37816.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.107999 restraints weight = 49391.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.109678 restraints weight = 43344.092| |-----------------------------------------------------------------------------| r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.1937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 24939 Z= 0.105 Angle : 0.523 6.134 34056 Z= 0.269 Chirality : 0.043 0.161 4005 Planarity : 0.003 0.038 4305 Dihedral : 5.872 53.913 4410 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.45 % Allowed : 11.66 % Favored : 86.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.15), residues: 2949 helix: 1.56 (0.22), residues: 636 sheet: 0.24 (0.19), residues: 714 loop : -1.38 (0.15), residues: 1599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 353 HIS 0.004 0.001 HIS C1088 PHE 0.023 0.001 PHE B 855 TYR 0.013 0.001 TYR A 351 ARG 0.003 0.000 ARG A 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00222 ( 48) link_NAG-ASN : angle 1.48465 ( 144) link_BETA1-4 : bond 0.00387 ( 9) link_BETA1-4 : angle 1.04858 ( 27) hydrogen bonds : bond 0.04641 ( 865) hydrogen bonds : angle 5.01827 ( 2334) SS BOND : bond 0.00420 ( 39) SS BOND : angle 1.11353 ( 78) covalent geometry : bond 0.00230 (24843) covalent geometry : angle 0.51194 (33807) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 222 time to evaluate : 3.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 353 TRP cc_start: 0.8044 (p-90) cc_final: 0.7495 (p-90) REVERT: A 781 VAL cc_start: 0.8560 (t) cc_final: 0.8280 (t) REVERT: A 1029 MET cc_start: 0.9155 (tpp) cc_final: 0.8817 (ttm) REVERT: B 88 ASP cc_start: 0.8456 (OUTLIER) cc_final: 0.8135 (m-30) REVERT: B 102 ARG cc_start: 0.7400 (mmp-170) cc_final: 0.6964 (mmp-170) REVERT: B 408 ARG cc_start: 0.8184 (tmm160) cc_final: 0.7899 (tmm160) REVERT: B 409 GLN cc_start: 0.8266 (mt0) cc_final: 0.7931 (mt0) REVERT: B 917 TYR cc_start: 0.8734 (m-80) cc_final: 0.7799 (m-80) REVERT: C 102 ARG cc_start: 0.7548 (mmp-170) cc_final: 0.7262 (mmp-170) REVERT: C 918 GLU cc_start: 0.7675 (mp0) cc_final: 0.7473 (mp0) outliers start: 38 outliers final: 22 residues processed: 248 average time/residue: 0.3863 time to fit residues: 156.3880 Evaluate side-chains 231 residues out of total 2625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 208 time to evaluate : 2.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 88 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 213 optimal weight: 0.9980 chunk 21 optimal weight: 0.5980 chunk 133 optimal weight: 6.9990 chunk 254 optimal weight: 3.9990 chunk 91 optimal weight: 0.8980 chunk 212 optimal weight: 0.7980 chunk 110 optimal weight: 0.8980 chunk 125 optimal weight: 2.9990 chunk 42 optimal weight: 4.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.144774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.108222 restraints weight = 37732.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.106964 restraints weight = 40647.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.108497 restraints weight = 44631.251| |-----------------------------------------------------------------------------| r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 24939 Z= 0.145 Angle : 0.539 6.441 34056 Z= 0.277 Chirality : 0.044 0.164 4005 Planarity : 0.003 0.042 4305 Dihedral : 5.849 53.860 4410 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 1.79 % Allowed : 13.03 % Favored : 85.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.15), residues: 2949 helix: 1.75 (0.22), residues: 609 sheet: 0.23 (0.19), residues: 714 loop : -1.37 (0.15), residues: 1626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 353 HIS 0.004 0.001 HIS A1088 PHE 0.017 0.001 PHE B 377 TYR 0.014 0.001 TYR B 904 ARG 0.004 0.000 ARG A 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00180 ( 48) link_NAG-ASN : angle 1.56149 ( 144) link_BETA1-4 : bond 0.00241 ( 9) link_BETA1-4 : angle 1.01377 ( 27) hydrogen bonds : bond 0.05097 ( 865) hydrogen bonds : angle 5.07526 ( 2334) SS BOND : bond 0.00514 ( 39) SS BOND : angle 1.19661 ( 78) covalent geometry : bond 0.00350 (24843) covalent geometry : angle 0.52778 (33807) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 213 time to evaluate : 2.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 353 TRP cc_start: 0.8013 (p-90) cc_final: 0.7444 (p-90) REVERT: A 408 ARG cc_start: 0.8149 (ttp-170) cc_final: 0.7858 (tmm-80) REVERT: A 781 VAL cc_start: 0.8720 (t) cc_final: 0.8448 (t) REVERT: A 1029 MET cc_start: 0.9228 (tpp) cc_final: 0.8880 (ttm) REVERT: B 102 ARG cc_start: 0.7464 (mmp-170) cc_final: 0.6997 (mmp-170) REVERT: C 102 ARG cc_start: 0.7697 (mmp-170) cc_final: 0.7444 (mmp-170) REVERT: C 228 ASP cc_start: 0.8070 (p0) cc_final: 0.7811 (p0) REVERT: C 408 ARG cc_start: 0.8079 (ttp-170) cc_final: 0.7728 (tmm-80) outliers start: 47 outliers final: 38 residues processed: 251 average time/residue: 0.3603 time to fit residues: 149.8222 Evaluate side-chains 240 residues out of total 2625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 202 time to evaluate : 3.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 278 optimal weight: 0.9980 chunk 156 optimal weight: 1.9990 chunk 184 optimal weight: 0.7980 chunk 216 optimal weight: 0.7980 chunk 238 optimal weight: 3.9990 chunk 218 optimal weight: 4.9990 chunk 132 optimal weight: 4.9990 chunk 51 optimal weight: 0.6980 chunk 197 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 33 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 519 HIS B 519 HIS C 519 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.143779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.107027 restraints weight = 37939.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.106100 restraints weight = 40882.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.107482 restraints weight = 39173.825| |-----------------------------------------------------------------------------| r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.2236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 24939 Z= 0.148 Angle : 0.544 6.171 34056 Z= 0.279 Chirality : 0.044 0.164 4005 Planarity : 0.003 0.038 4305 Dihedral : 5.850 53.923 4410 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.02 % Allowed : 13.75 % Favored : 84.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.15), residues: 2949 helix: 1.70 (0.22), residues: 609 sheet: 0.24 (0.19), residues: 714 loop : -1.36 (0.15), residues: 1626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 353 HIS 0.004 0.001 HIS A1088 PHE 0.023 0.001 PHE B 374 TYR 0.016 0.001 TYR C 351 ARG 0.004 0.000 ARG A 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00178 ( 48) link_NAG-ASN : angle 1.56665 ( 144) link_BETA1-4 : bond 0.00263 ( 9) link_BETA1-4 : angle 1.01398 ( 27) hydrogen bonds : bond 0.05135 ( 865) hydrogen bonds : angle 5.04947 ( 2334) SS BOND : bond 0.00514 ( 39) SS BOND : angle 1.20207 ( 78) covalent geometry : bond 0.00354 (24843) covalent geometry : angle 0.53252 (33807) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 209 time to evaluate : 2.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ARG cc_start: 0.7671 (mmp-170) cc_final: 0.7323 (mmp-170) REVERT: A 353 TRP cc_start: 0.8048 (p-90) cc_final: 0.7546 (p-90) REVERT: A 408 ARG cc_start: 0.8119 (ttp-170) cc_final: 0.7816 (tmm-80) REVERT: A 781 VAL cc_start: 0.8766 (t) cc_final: 0.8440 (t) REVERT: A 1029 MET cc_start: 0.9223 (tpp) cc_final: 0.8759 (ttm) REVERT: B 88 ASP cc_start: 0.8478 (OUTLIER) cc_final: 0.8212 (m-30) REVERT: B 102 ARG cc_start: 0.7470 (mmp-170) cc_final: 0.6997 (mmp-170) REVERT: C 102 ARG cc_start: 0.7618 (mmp-170) cc_final: 0.7318 (mmp-170) REVERT: C 228 ASP cc_start: 0.8184 (p0) cc_final: 0.7894 (p0) outliers start: 53 outliers final: 46 residues processed: 253 average time/residue: 0.3118 time to fit residues: 129.7381 Evaluate side-chains 248 residues out of total 2625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 201 time to evaluate : 2.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 1082 CYS Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 1082 CYS Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 36 optimal weight: 8.9990 chunk 181 optimal weight: 1.9990 chunk 293 optimal weight: 0.5980 chunk 28 optimal weight: 0.1980 chunk 135 optimal weight: 10.0000 chunk 160 optimal weight: 0.6980 chunk 129 optimal weight: 0.8980 chunk 18 optimal weight: 0.5980 chunk 248 optimal weight: 3.9990 chunk 119 optimal weight: 1.9990 chunk 235 optimal weight: 7.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.145392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.109004 restraints weight = 37682.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.107543 restraints weight = 43869.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.108955 restraints weight = 43286.289| |-----------------------------------------------------------------------------| r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.2321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 24939 Z= 0.121 Angle : 0.533 9.633 34056 Z= 0.273 Chirality : 0.043 0.163 4005 Planarity : 0.003 0.039 4305 Dihedral : 5.782 53.914 4410 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.90 % Allowed : 13.87 % Favored : 84.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.15), residues: 2949 helix: 2.05 (0.22), residues: 588 sheet: 0.22 (0.19), residues: 744 loop : -1.37 (0.15), residues: 1617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 353 HIS 0.004 0.001 HIS A1088 PHE 0.014 0.001 PHE C 377 TYR 0.022 0.001 TYR C 904 ARG 0.004 0.000 ARG B1107 Details of bonding type rmsd link_NAG-ASN : bond 0.00184 ( 48) link_NAG-ASN : angle 1.49197 ( 144) link_BETA1-4 : bond 0.00302 ( 9) link_BETA1-4 : angle 0.99729 ( 27) hydrogen bonds : bond 0.04771 ( 865) hydrogen bonds : angle 4.95719 ( 2334) SS BOND : bond 0.00438 ( 39) SS BOND : angle 1.17094 ( 78) covalent geometry : bond 0.00287 (24843) covalent geometry : angle 0.52175 (33807) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 212 time to evaluate : 2.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 PHE cc_start: 0.8557 (m-80) cc_final: 0.8354 (m-10) REVERT: A 102 ARG cc_start: 0.7750 (mmp-170) cc_final: 0.7424 (mmp-170) REVERT: A 353 TRP cc_start: 0.8056 (p-90) cc_final: 0.7577 (p-90) REVERT: A 781 VAL cc_start: 0.8662 (t) cc_final: 0.8341 (t) REVERT: A 1029 MET cc_start: 0.9231 (tpp) cc_final: 0.8734 (ttm) REVERT: A 1041 ASP cc_start: 0.8451 (t0) cc_final: 0.8209 (t0) REVERT: B 88 ASP cc_start: 0.8491 (OUTLIER) cc_final: 0.8158 (m-30) REVERT: B 102 ARG cc_start: 0.7583 (mmp-170) cc_final: 0.7085 (mmp-170) REVERT: C 102 ARG cc_start: 0.7604 (mmp-170) cc_final: 0.7347 (mmp-170) REVERT: C 228 ASP cc_start: 0.8154 (p0) cc_final: 0.7861 (p0) outliers start: 50 outliers final: 45 residues processed: 252 average time/residue: 0.3604 time to fit residues: 150.7740 Evaluate side-chains 251 residues out of total 2625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 205 time to evaluate : 2.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 1082 CYS Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 1082 CYS Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 130 optimal weight: 0.8980 chunk 264 optimal weight: 1.9990 chunk 27 optimal weight: 0.0070 chunk 172 optimal weight: 0.8980 chunk 122 optimal weight: 3.9990 chunk 271 optimal weight: 0.0060 chunk 136 optimal weight: 8.9990 chunk 109 optimal weight: 2.9990 chunk 194 optimal weight: 0.5980 chunk 231 optimal weight: 3.9990 chunk 12 optimal weight: 0.3980 overall best weight: 0.3814 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.145874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.109182 restraints weight = 37999.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.107589 restraints weight = 43210.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.109116 restraints weight = 41920.386| |-----------------------------------------------------------------------------| r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.2395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 24939 Z= 0.104 Angle : 0.517 6.302 34056 Z= 0.265 Chirality : 0.043 0.163 4005 Planarity : 0.003 0.038 4305 Dihedral : 5.695 53.969 4410 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.75 % Allowed : 13.83 % Favored : 84.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.15), residues: 2949 helix: 2.19 (0.22), residues: 588 sheet: 0.26 (0.19), residues: 747 loop : -1.34 (0.15), residues: 1614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP C 353 HIS 0.003 0.001 HIS A1088 PHE 0.018 0.001 PHE B 377 TYR 0.021 0.001 TYR C 904 ARG 0.004 0.000 ARG C 214 Details of bonding type rmsd link_NAG-ASN : bond 0.00201 ( 48) link_NAG-ASN : angle 1.42463 ( 144) link_BETA1-4 : bond 0.00328 ( 9) link_BETA1-4 : angle 0.98333 ( 27) hydrogen bonds : bond 0.04379 ( 865) hydrogen bonds : angle 4.85174 ( 2334) SS BOND : bond 0.00375 ( 39) SS BOND : angle 1.06996 ( 78) covalent geometry : bond 0.00239 (24843) covalent geometry : angle 0.50766 (33807) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 217 time to evaluate : 2.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 PHE cc_start: 0.8564 (m-80) cc_final: 0.8358 (m-10) REVERT: A 102 ARG cc_start: 0.7768 (mmp-170) cc_final: 0.7416 (mmp-170) REVERT: A 228 ASP cc_start: 0.8083 (p0) cc_final: 0.7853 (p0) REVERT: A 239 GLN cc_start: 0.7973 (tt0) cc_final: 0.7738 (tt0) REVERT: A 353 TRP cc_start: 0.8007 (p-90) cc_final: 0.7566 (p-90) REVERT: A 1041 ASP cc_start: 0.8424 (t0) cc_final: 0.8195 (t0) REVERT: B 102 ARG cc_start: 0.7590 (mmp-170) cc_final: 0.7049 (mmp-170) REVERT: C 102 ARG cc_start: 0.7502 (mmp-170) cc_final: 0.7204 (mmp-170) outliers start: 46 outliers final: 41 residues processed: 253 average time/residue: 0.3181 time to fit residues: 132.0808 Evaluate side-chains 247 residues out of total 2625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 206 time to evaluate : 2.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 1082 CYS Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 1082 CYS Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 133 optimal weight: 0.0070 chunk 138 optimal weight: 4.9990 chunk 155 optimal weight: 0.9980 chunk 90 optimal weight: 0.7980 chunk 148 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 278 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 165 optimal weight: 1.9990 chunk 260 optimal weight: 0.8980 chunk 47 optimal weight: 0.9990 overall best weight: 0.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.144370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.107389 restraints weight = 37731.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.105773 restraints weight = 39977.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.107021 restraints weight = 43085.640| |-----------------------------------------------------------------------------| r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.2476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 24939 Z= 0.137 Angle : 0.550 10.362 34056 Z= 0.281 Chirality : 0.044 0.330 4005 Planarity : 0.003 0.038 4305 Dihedral : 5.721 53.878 4410 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 1.79 % Allowed : 13.87 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.15), residues: 2949 helix: 2.16 (0.22), residues: 588 sheet: 0.25 (0.19), residues: 744 loop : -1.34 (0.15), residues: 1617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 353 HIS 0.003 0.001 HIS A1088 PHE 0.024 0.001 PHE B 377 TYR 0.031 0.001 TYR C 904 ARG 0.004 0.000 ARG B 408 Details of bonding type rmsd link_NAG-ASN : bond 0.00169 ( 48) link_NAG-ASN : angle 1.49537 ( 144) link_BETA1-4 : bond 0.00265 ( 9) link_BETA1-4 : angle 0.98003 ( 27) hydrogen bonds : bond 0.04805 ( 865) hydrogen bonds : angle 4.88934 ( 2334) SS BOND : bond 0.00473 ( 39) SS BOND : angle 1.16686 ( 78) covalent geometry : bond 0.00330 (24843) covalent geometry : angle 0.53978 (33807) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 2625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 211 time to evaluate : 3.059 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 PHE cc_start: 0.8577 (m-80) cc_final: 0.8354 (m-10) REVERT: A 102 ARG cc_start: 0.7551 (mmp-170) cc_final: 0.7249 (mmp-170) REVERT: A 239 GLN cc_start: 0.7962 (tt0) cc_final: 0.7744 (tt0) REVERT: A 353 TRP cc_start: 0.8057 (p-90) cc_final: 0.7701 (p-90) REVERT: A 781 VAL cc_start: 0.8646 (t) cc_final: 0.8357 (t) REVERT: A 1029 MET cc_start: 0.9217 (tpp) cc_final: 0.8717 (ttm) REVERT: B 102 ARG cc_start: 0.7624 (mmp-170) cc_final: 0.7071 (mmp-170) REVERT: B 408 ARG cc_start: 0.8291 (tmm160) cc_final: 0.7897 (tmm160) REVERT: C 102 ARG cc_start: 0.7521 (mmp-170) cc_final: 0.7191 (mmp-170) outliers start: 47 outliers final: 44 residues processed: 249 average time/residue: 0.4028 time to fit residues: 165.5134 Evaluate side-chains 251 residues out of total 2625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 207 time to evaluate : 4.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 1082 CYS Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 1082 CYS Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 188 optimal weight: 1.9990 chunk 125 optimal weight: 0.5980 chunk 235 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 chunk 228 optimal weight: 0.8980 chunk 87 optimal weight: 0.9980 chunk 146 optimal weight: 0.0970 chunk 75 optimal weight: 0.9990 chunk 123 optimal weight: 3.9990 chunk 264 optimal weight: 0.3980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.145749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.109622 restraints weight = 37839.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.107364 restraints weight = 46237.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.108996 restraints weight = 43265.983| |-----------------------------------------------------------------------------| r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.2550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 24939 Z= 0.120 Angle : 0.533 6.427 34056 Z= 0.273 Chirality : 0.043 0.306 4005 Planarity : 0.003 0.039 4305 Dihedral : 5.700 53.954 4410 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.94 % Allowed : 13.75 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.15), residues: 2949 helix: 2.16 (0.22), residues: 591 sheet: 0.28 (0.19), residues: 744 loop : -1.29 (0.15), residues: 1614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 353 HIS 0.003 0.001 HIS A1088 PHE 0.021 0.001 PHE B 377 TYR 0.015 0.001 TYR B 351 ARG 0.002 0.000 ARG A 214 Details of bonding type rmsd link_NAG-ASN : bond 0.00180 ( 48) link_NAG-ASN : angle 1.45758 ( 144) link_BETA1-4 : bond 0.00296 ( 9) link_BETA1-4 : angle 0.97375 ( 27) hydrogen bonds : bond 0.04621 ( 865) hydrogen bonds : angle 4.83229 ( 2334) SS BOND : bond 0.00419 ( 39) SS BOND : angle 1.10193 ( 78) covalent geometry : bond 0.00285 (24843) covalent geometry : angle 0.52305 (33807) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8918.69 seconds wall clock time: 163 minutes 46.00 seconds (9826.00 seconds total)