Starting phenix.real_space_refine on Sun Jan 26 13:36:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6x6p_22078/01_2025/6x6p_22078.cif Found real_map, /net/cci-nas-00/data/ceres_data/6x6p_22078/01_2025/6x6p_22078.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6x6p_22078/01_2025/6x6p_22078.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6x6p_22078/01_2025/6x6p_22078.map" model { file = "/net/cci-nas-00/data/ceres_data/6x6p_22078/01_2025/6x6p_22078.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6x6p_22078/01_2025/6x6p_22078.cif" } resolution = 3.22 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= 0.001 sd= 0.020 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 15663 2.51 5 N 4014 2.21 5 O 4833 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 216 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 24615 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 7939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1017, 7939 Classifications: {'peptide': 1017} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 50, 'TRANS': 966} Chain breaks: 8 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 7939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1017, 7939 Classifications: {'peptide': 1017} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 50, 'TRANS': 966} Chain breaks: 8 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 7939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1017, 7939 Classifications: {'peptide': 1017} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 50, 'TRANS': 966} Chain breaks: 8 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "C" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Time building chain proxies: 14.61, per 1000 atoms: 0.59 Number of scatterers: 24615 At special positions: 0 Unit cell: (131.192, 140.714, 174.57, 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 4833 8.00 N 4014 7.00 C 15663 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, 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=2.02 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.02 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.02 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.02 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=2.02 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.02 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.02 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.02 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=2.02 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.02 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.02 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.02 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.02 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=2.02 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.02 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.02 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.02 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=2.02 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.02 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.02 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.02 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.02 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=2.02 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.02 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.02 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.02 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 M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 234 " " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A 331 " " NAG A1305 " - " ASN A 343 " " NAG A1306 " - " ASN A 603 " " NAG A1307 " - " ASN A 616 " " NAG A1308 " - " ASN A 657 " " NAG A1309 " - " ASN A 709 " " NAG A1314 " - " ASN A1074 " " NAG A1319 " - " ASN A 165 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 234 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B 331 " " NAG B1305 " - " ASN B 343 " " NAG B1306 " - " ASN B 603 " " NAG B1307 " - " ASN B 616 " " NAG B1308 " - " ASN B 657 " " NAG B1309 " - " ASN B 709 " " NAG B1314 " - " ASN B1074 " " NAG B1319 " - " ASN B 165 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 234 " " NAG C1303 " - " ASN C 282 " " NAG C1304 " - " ASN C 331 " " NAG C1305 " - " ASN C 343 " " NAG C1306 " - " ASN C 603 " " NAG C1307 " - " ASN C 616 " " NAG C1308 " - " ASN C 657 " " NAG C1309 " - " ASN C 709 " " NAG C1314 " - " ASN C1074 " " NAG C1319 " - " ASN C 165 " " NAG D 1 " - " ASN A 717 " " NAG E 1 " - " ASN A 801 " " NAG F 1 " - " ASN A1098 " " NAG G 1 " - " ASN A1134 " " NAG H 1 " - " ASN B 717 " " NAG I 1 " - " ASN B 801 " " NAG J 1 " - " ASN B1098 " " NAG K 1 " - " ASN B1134 " " NAG L 1 " - " ASN C 717 " " NAG M 1 " - " ASN C 801 " " NAG N 1 " - " ASN C1098 " " NAG O 1 " - " ASN C1134 " Time building additional restraints: 6.80 Conformation dependent library (CDL) restraints added in 3.4 seconds 5994 Ramachandran restraints generated. 2997 Oldfield, 0 Emsley, 2997 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5730 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 54 sheets defined 26.2% alpha, 24.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.26 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 364 through 370 removed outlier: 3.655A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 389 removed outlier: 3.943A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 410 removed outlier: 4.054A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 618 through 625 removed outlier: 4.017A pdb=" N VAL A 622 " --> pdb=" O THR A 618 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.800A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 756 through 759 removed outlier: 3.567A pdb=" N PHE A 759 " --> pdb=" O TYR A 756 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 756 through 759' Processing helix chain 'A' and resid 760 through 783 removed outlier: 3.778A pdb=" N ASN A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.507A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 941 removed outlier: 5.582A pdb=" N LYS A 921 " --> pdb=" O TYR A 917 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N LEU A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 982 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.749A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1125 through 1129 removed outlier: 3.951A pdb=" N VAL A1128 " --> pdb=" O ASN A1125 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL A1129 " --> pdb=" O CYS A1126 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1125 through 1129' Processing helix chain 'A' and resid 1140 through 1145 removed outlier: 4.317A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 364 through 370 removed outlier: 3.655A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 389 removed outlier: 3.943A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 410 removed outlier: 4.055A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 618 through 625 removed outlier: 4.018A pdb=" N VAL B 622 " --> pdb=" O THR B 618 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.800A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 756 through 759 removed outlier: 3.568A pdb=" N PHE B 759 " --> pdb=" O TYR B 756 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 756 through 759' Processing helix chain 'B' and resid 760 through 783 removed outlier: 3.777A pdb=" N ASN B 764 " --> pdb=" O CYS B 760 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.508A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 913 through 941 removed outlier: 5.583A pdb=" N LYS B 921 " --> pdb=" O TYR B 917 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N LEU B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 982 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.749A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1125 through 1129 removed outlier: 3.952A pdb=" N VAL B1128 " --> pdb=" O ASN B1125 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL B1129 " --> pdb=" O CYS B1126 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1125 through 1129' Processing helix chain 'B' and resid 1140 through 1145 removed outlier: 4.317A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 364 through 370 removed outlier: 3.654A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 389 removed outlier: 3.944A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 410 removed outlier: 4.054A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 618 through 625 removed outlier: 4.017A pdb=" N VAL C 622 " --> pdb=" O THR C 618 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 755 removed outlier: 3.799A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 756 through 759 removed outlier: 3.568A pdb=" N PHE C 759 " --> pdb=" O TYR C 756 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 756 through 759' Processing helix chain 'C' and resid 760 through 783 removed outlier: 3.777A pdb=" N ASN C 764 " --> pdb=" O CYS C 760 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.508A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 941 removed outlier: 5.583A pdb=" N LYS C 921 " --> pdb=" O TYR C 917 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N LEU C 922 " --> pdb=" O GLU C 918 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 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 976 through 982 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.749A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1125 through 1129 removed outlier: 3.952A pdb=" N VAL C1128 " --> pdb=" O ASN C1125 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL C1129 " --> pdb=" O CYS C1126 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1125 through 1129' Processing helix chain 'C' and resid 1140 through 1145 removed outlier: 4.318A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.741A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 51 removed outlier: 3.862A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 54 through 55 Processing sheet with id=AA4, first strand: chain 'A' and resid 169 through 171 removed outlier: 5.780A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 171 removed outlier: 5.780A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 133 through 134 removed outlier: 3.638A pdb=" N SER A 162 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.468A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 324 through 328 removed outlier: 6.407A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N ASN A 542 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AB1, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.550A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB3, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB4, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.035A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 702 through 704 removed outlier: 3.596A pdb=" N LYS B 790 " --> pdb=" O ASN A 703 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 715 Processing sheet with id=AB7, first strand: chain 'A' and resid 718 through 728 removed outlier: 6.935A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB9, first strand: chain 'A' and resid 788 through 790 removed outlier: 5.633A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AC2, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.742A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 48 through 51 removed outlier: 3.863A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 54 through 55 Processing sheet with id=AC5, first strand: chain 'B' and resid 169 through 171 removed outlier: 5.780A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 169 through 171 removed outlier: 5.780A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 133 through 134 removed outlier: 3.637A pdb=" N SER B 162 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.467A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 324 through 328 removed outlier: 6.408A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N ASN B 542 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AD2, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.549A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD4, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD5, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.035A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 702 through 704 removed outlier: 3.565A pdb=" N LYS C 790 " --> pdb=" O ASN B 703 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 711 through 715 Processing sheet with id=AD8, first strand: chain 'B' and resid 718 through 728 removed outlier: 6.935A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AE1, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AE2, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.742A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 48 through 51 removed outlier: 3.862A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 54 through 55 Processing sheet with id=AE5, first strand: chain 'C' and resid 169 through 171 removed outlier: 5.780A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 169 through 171 removed outlier: 5.780A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 133 through 134 removed outlier: 3.638A pdb=" N SER C 162 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.467A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 324 through 328 removed outlier: 6.408A pdb=" N GLU C 324 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N ASN C 542 " --> pdb=" O GLU C 324 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AF2, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.549A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AF4, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AF5, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.035A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 711 through 715 Processing sheet with id=AF7, first strand: chain 'C' and resid 718 through 728 removed outlier: 6.935A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AF9, first strand: chain 'C' and resid 1120 through 1122 1007 hydrogen bonds defined for protein. 2733 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: 11.31 Time building geometry restraints manager: 7.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7211 1.33 - 1.45: 5600 1.45 - 1.58: 12209 1.58 - 1.70: 0 1.70 - 1.82: 132 Bond restraints: 25152 Sorted by residual: bond pdb=" C PHE C 559 " pdb=" N LEU C 560 " ideal model delta sigma weight residual 1.331 1.244 0.087 2.83e-02 1.25e+03 9.55e+00 bond pdb=" C PHE A 559 " pdb=" N LEU A 560 " ideal model delta sigma weight residual 1.331 1.244 0.087 2.83e-02 1.25e+03 9.51e+00 bond pdb=" C PHE B 559 " pdb=" N LEU B 560 " ideal model delta sigma weight residual 1.331 1.244 0.087 2.83e-02 1.25e+03 9.42e+00 bond pdb=" CA THR C1105 " pdb=" CB THR C1105 " ideal model delta sigma weight residual 1.535 1.480 0.055 1.93e-02 2.68e+03 7.98e+00 bond pdb=" CA THR A1105 " pdb=" CB THR A1105 " ideal model delta sigma weight residual 1.535 1.480 0.055 1.93e-02 2.68e+03 7.98e+00 ... (remaining 25147 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.05: 33475 3.05 - 6.10: 685 6.10 - 9.16: 58 9.16 - 12.21: 9 12.21 - 15.26: 6 Bond angle restraints: 34233 Sorted by residual: angle pdb=" N ILE C 100 " pdb=" CA ILE C 100 " pdb=" C ILE C 100 " ideal model delta sigma weight residual 112.96 105.96 7.00 1.00e+00 1.00e+00 4.90e+01 angle pdb=" N ILE A 100 " pdb=" CA ILE A 100 " pdb=" C ILE A 100 " ideal model delta sigma weight residual 112.96 105.99 6.97 1.00e+00 1.00e+00 4.86e+01 angle pdb=" N ILE B 100 " pdb=" CA ILE B 100 " pdb=" C ILE B 100 " ideal model delta sigma weight residual 112.96 106.01 6.95 1.00e+00 1.00e+00 4.84e+01 angle pdb=" CG ARG A 355 " pdb=" CD ARG A 355 " pdb=" NE ARG A 355 " ideal model delta sigma weight residual 112.00 96.74 15.26 2.20e+00 2.07e-01 4.81e+01 angle pdb=" CG ARG B 355 " pdb=" CD ARG B 355 " pdb=" NE ARG B 355 " ideal model delta sigma weight residual 112.00 96.77 15.23 2.20e+00 2.07e-01 4.79e+01 ... (remaining 34228 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.07: 13621 18.07 - 36.13: 1561 36.13 - 54.20: 424 54.20 - 72.27: 81 72.27 - 90.33: 24 Dihedral angle restraints: 15711 sinusoidal: 6822 harmonic: 8889 Sorted by residual: dihedral pdb=" CB CYS A1032 " pdb=" SG CYS A1032 " pdb=" SG CYS A1043 " pdb=" CB CYS A1043 " ideal model delta sinusoidal sigma weight residual 93.00 -176.67 -90.33 1 1.00e+01 1.00e-02 9.66e+01 dihedral pdb=" CB CYS C1032 " pdb=" SG CYS C1032 " pdb=" SG CYS C1043 " pdb=" CB CYS C1043 " ideal model delta sinusoidal sigma weight residual 93.00 -176.67 -90.33 1 1.00e+01 1.00e-02 9.65e+01 dihedral pdb=" CB CYS B1032 " pdb=" SG CYS B1032 " pdb=" SG CYS B1043 " pdb=" CB CYS B1043 " ideal model delta sinusoidal sigma weight residual 93.00 -176.67 -90.33 1 1.00e+01 1.00e-02 9.65e+01 ... (remaining 15708 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.136: 3971 0.136 - 0.273: 97 0.273 - 0.409: 0 0.409 - 0.546: 0 0.546 - 0.682: 6 Chirality restraints: 4074 Sorted by residual: chirality pdb=" C1 NAG B1306 " pdb=" ND2 ASN B 603 " pdb=" C2 NAG B1306 " pdb=" O5 NAG B1306 " both_signs ideal model delta sigma weight residual False -2.40 -1.72 -0.68 2.00e-01 2.50e+01 1.16e+01 chirality pdb=" C1 NAG C1306 " pdb=" ND2 ASN C 603 " pdb=" C2 NAG C1306 " pdb=" O5 NAG C1306 " both_signs ideal model delta sigma weight residual False -2.40 -1.72 -0.68 2.00e-01 2.50e+01 1.16e+01 chirality pdb=" C1 NAG A1306 " pdb=" ND2 ASN A 603 " pdb=" C2 NAG A1306 " pdb=" O5 NAG A1306 " both_signs ideal model delta sigma weight residual False -2.40 -1.72 -0.68 2.00e-01 2.50e+01 1.15e+01 ... (remaining 4071 not shown) Planarity restraints: 4395 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 904 " 0.038 2.00e-02 2.50e+03 3.06e-02 1.87e+01 pdb=" CG TYR C 904 " -0.074 2.00e-02 2.50e+03 pdb=" CD1 TYR C 904 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR C 904 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR C 904 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR C 904 " 0.007 2.00e-02 2.50e+03 pdb=" CZ TYR C 904 " 0.013 2.00e-02 2.50e+03 pdb=" OH TYR C 904 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 904 " -0.038 2.00e-02 2.50e+03 3.04e-02 1.85e+01 pdb=" CG TYR B 904 " 0.073 2.00e-02 2.50e+03 pdb=" CD1 TYR B 904 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 TYR B 904 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR B 904 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR B 904 " -0.007 2.00e-02 2.50e+03 pdb=" CZ TYR B 904 " -0.014 2.00e-02 2.50e+03 pdb=" OH TYR B 904 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 904 " 0.038 2.00e-02 2.50e+03 3.02e-02 1.83e+01 pdb=" CG TYR A 904 " -0.073 2.00e-02 2.50e+03 pdb=" CD1 TYR A 904 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR A 904 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR A 904 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR A 904 " 0.007 2.00e-02 2.50e+03 pdb=" CZ TYR A 904 " 0.013 2.00e-02 2.50e+03 pdb=" OH TYR A 904 " 0.001 2.00e-02 2.50e+03 ... (remaining 4392 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 559 2.63 - 3.20: 24479 3.20 - 3.76: 37989 3.76 - 4.33: 52705 4.33 - 4.90: 87457 Nonbonded interactions: 203189 Sorted by model distance: nonbonded pdb=" OH TYR A 369 " pdb=" OG1 THR C 415 " model vdw 2.062 3.040 nonbonded pdb=" O GLY A 496 " pdb=" OH TYR A 505 " model vdw 2.080 3.040 nonbonded pdb=" O GLY C 496 " pdb=" OH TYR C 505 " model vdw 2.080 3.040 nonbonded pdb=" O GLY B 496 " pdb=" OH TYR B 505 " model vdw 2.080 3.040 nonbonded pdb=" OH TYR B 170 " pdb=" OG SER B 172 " model vdw 2.082 3.040 ... (remaining 203184 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: 0.00 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' selection = chain 'M' selection = chain 'N' selection = chain 'O' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.850 Check model and map are aligned: 0.170 Set scattering table: 0.210 Process input model: 58.650 Find NCS groups from input model: 1.210 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:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 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 : 0.012 0.088 25152 Z= 0.787 Angle : 1.072 15.260 34233 Z= 0.574 Chirality : 0.064 0.682 4074 Planarity : 0.006 0.051 4350 Dihedral : 16.192 80.465 9873 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 25.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 3.15 % Allowed : 4.65 % Favored : 92.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.17 (0.14), residues: 2997 helix: -0.45 (0.18), residues: 729 sheet: -1.42 (0.18), residues: 612 loop : -1.93 (0.14), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.005 TRP A 886 HIS 0.011 0.002 HIS B1064 PHE 0.072 0.006 PHE C1052 TYR 0.074 0.004 TYR C 904 ARG 0.025 0.003 ARG C1107 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5994 Ramachandran restraints generated. 2997 Oldfield, 0 Emsley, 2997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5994 Ramachandran restraints generated. 2997 Oldfield, 0 Emsley, 2997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 124 time to evaluate : 2.965 Fit side-chains REVERT: A 117 LEU cc_start: 0.7260 (tt) cc_final: 0.6387 (mp) REVERT: A 265 TYR cc_start: 0.5572 (p90) cc_final: 0.5324 (p90) REVERT: A 421 TYR cc_start: 0.7983 (m-80) cc_final: 0.7507 (m-80) REVERT: A 507 PRO cc_start: 0.5420 (Cg_endo) cc_final: 0.5196 (Cg_endo) REVERT: A 607 GLN cc_start: 0.8282 (OUTLIER) cc_final: 0.8036 (pt0) REVERT: A 1142 GLN cc_start: 0.8425 (OUTLIER) cc_final: 0.8194 (mm-40) REVERT: B 117 LEU cc_start: 0.7398 (tt) cc_final: 0.6530 (mp) REVERT: B 198 ASP cc_start: 0.7958 (OUTLIER) cc_final: 0.7494 (m-30) REVERT: B 473 TYR cc_start: 0.7708 (t80) cc_final: 0.7413 (t80) REVERT: C 117 LEU cc_start: 0.7183 (tt) cc_final: 0.6304 (mp) REVERT: C 198 ASP cc_start: 0.7902 (OUTLIER) cc_final: 0.7462 (m-30) REVERT: C 265 TYR cc_start: 0.5623 (p90) cc_final: 0.4918 (p90) REVERT: C 278 LYS cc_start: 0.7996 (OUTLIER) cc_final: 0.7790 (tmmt) REVERT: C 421 TYR cc_start: 0.8105 (m-80) cc_final: 0.7624 (m-80) REVERT: C 780 GLU cc_start: 0.8259 (tt0) cc_final: 0.7953 (tt0) REVERT: C 902 MET cc_start: 0.8729 (OUTLIER) cc_final: 0.8466 (tpt) outliers start: 84 outliers final: 22 residues processed: 199 average time/residue: 0.3942 time to fit residues: 122.9823 Evaluate side-chains 116 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 88 time to evaluate : 2.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 TYR Chi-restraints excluded: chain A residue 55 PHE Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 607 GLN Chi-restraints excluded: chain A residue 907 ASN Chi-restraints excluded: chain A residue 1142 GLN Chi-restraints excluded: chain B residue 37 TYR Chi-restraints excluded: chain B residue 55 PHE Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 1107 ARG Chi-restraints excluded: chain B residue 1142 GLN Chi-restraints excluded: chain C residue 55 PHE Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 278 LYS Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 1107 ARG Chi-restraints excluded: chain C residue 1142 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 255 optimal weight: 10.0000 chunk 229 optimal weight: 7.9990 chunk 127 optimal weight: 8.9990 chunk 78 optimal weight: 0.6980 chunk 154 optimal weight: 7.9990 chunk 122 optimal weight: 0.9990 chunk 237 optimal weight: 8.9990 chunk 91 optimal weight: 0.6980 chunk 144 optimal weight: 0.7980 chunk 176 optimal weight: 0.7980 chunk 275 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 563 GLN A 755 GLN A 920 GLN ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 GLN A 955 ASN A1005 GLN A1048 HIS B 122 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 755 GLN B 920 GLN ** B 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 935 GLN B 955 ASN B1048 HIS C 122 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 777 ASN C 920 GLN ** C 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 935 GLN C 955 ASN C1048 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.115260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.073646 restraints weight = 49951.953| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 3.19 r_work: 0.3047 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.1447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 25152 Z= 0.247 Angle : 0.724 9.446 34233 Z= 0.376 Chirality : 0.048 0.263 4074 Planarity : 0.005 0.097 4350 Dihedral : 7.814 58.626 4517 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 1.28 % Allowed : 11.75 % Favored : 86.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.15), residues: 2997 helix: 0.92 (0.20), residues: 705 sheet: -1.13 (0.18), residues: 645 loop : -1.54 (0.14), residues: 1647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 436 HIS 0.008 0.001 HIS B1064 PHE 0.028 0.002 PHE B 347 TYR 0.033 0.002 TYR B 505 ARG 0.013 0.001 ARG A 509 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5994 Ramachandran restraints generated. 2997 Oldfield, 0 Emsley, 2997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5994 Ramachandran restraints generated. 2997 Oldfield, 0 Emsley, 2997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 105 time to evaluate : 2.615 Fit side-chains REVERT: A 34 ARG cc_start: 0.7385 (mmp80) cc_final: 0.7117 (mmm160) REVERT: A 117 LEU cc_start: 0.7053 (tt) cc_final: 0.6337 (mp) REVERT: A 195 LYS cc_start: 0.8542 (OUTLIER) cc_final: 0.8330 (mtpt) REVERT: A 265 TYR cc_start: 0.5345 (p90) cc_final: 0.4996 (p90) REVERT: A 421 TYR cc_start: 0.7874 (m-80) cc_final: 0.7305 (m-80) REVERT: A 507 PRO cc_start: 0.5358 (Cg_endo) cc_final: 0.5105 (Cg_endo) REVERT: B 34 ARG cc_start: 0.7515 (mmp80) cc_final: 0.7187 (mmm160) REVERT: B 117 LEU cc_start: 0.7057 (tt) cc_final: 0.6222 (mp) REVERT: B 220 PHE cc_start: 0.6805 (t80) cc_final: 0.6478 (t80) REVERT: B 421 TYR cc_start: 0.7951 (m-80) cc_final: 0.7492 (m-80) REVERT: C 117 LEU cc_start: 0.7046 (tt) cc_final: 0.6126 (mp) REVERT: C 421 TYR cc_start: 0.7880 (m-80) cc_final: 0.7240 (m-80) REVERT: C 780 GLU cc_start: 0.8939 (tt0) cc_final: 0.8599 (tt0) outliers start: 34 outliers final: 23 residues processed: 135 average time/residue: 0.3480 time to fit residues: 78.6703 Evaluate side-chains 117 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 93 time to evaluate : 2.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 1107 ARG Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 661 GLU Chi-restraints excluded: chain C residue 1107 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 293 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 163 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 224 optimal weight: 0.9980 chunk 197 optimal weight: 2.9990 chunk 272 optimal weight: 1.9990 chunk 141 optimal weight: 0.4980 chunk 110 optimal weight: 8.9990 chunk 116 optimal weight: 9.9990 chunk 262 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 317 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 777 ASN A 901 GLN A 907 ASN ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 777 ASN B 901 GLN ** B 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 607 GLN C 901 GLN C 907 ASN ** C 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.114268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.072308 restraints weight = 49798.087| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 3.18 r_work: 0.3017 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.1788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 25152 Z= 0.293 Angle : 0.646 8.347 34233 Z= 0.333 Chirality : 0.046 0.196 4074 Planarity : 0.005 0.060 4350 Dihedral : 6.657 57.931 4476 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 2.33 % Allowed : 13.03 % Favored : 84.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.15), residues: 2997 helix: 1.32 (0.21), residues: 705 sheet: -0.92 (0.19), residues: 600 loop : -1.47 (0.14), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 436 HIS 0.007 0.001 HIS A1048 PHE 0.027 0.002 PHE C 347 TYR 0.027 0.002 TYR B 505 ARG 0.010 0.001 ARG A 403 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5994 Ramachandran restraints generated. 2997 Oldfield, 0 Emsley, 2997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5994 Ramachandran restraints generated. 2997 Oldfield, 0 Emsley, 2997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 110 time to evaluate : 2.867 Fit side-chains REVERT: A 265 TYR cc_start: 0.5349 (p90) cc_final: 0.5063 (p90) REVERT: A 357 ARG cc_start: 0.7526 (OUTLIER) cc_final: 0.6996 (mmm-85) REVERT: A 405 ASP cc_start: 0.7482 (OUTLIER) cc_final: 0.6563 (t0) REVERT: A 421 TYR cc_start: 0.7799 (m-80) cc_final: 0.7262 (m-80) REVERT: A 423 TYR cc_start: 0.6452 (t80) cc_final: 0.6183 (t80) REVERT: A 507 PRO cc_start: 0.5353 (Cg_endo) cc_final: 0.5099 (Cg_endo) REVERT: B 52 GLN cc_start: 0.8499 (tm-30) cc_final: 0.8122 (tm-30) REVERT: B 117 LEU cc_start: 0.7152 (tt) cc_final: 0.6279 (mp) REVERT: B 220 PHE cc_start: 0.6815 (t80) cc_final: 0.6406 (t80) REVERT: B 357 ARG cc_start: 0.7628 (OUTLIER) cc_final: 0.7194 (mmm-85) REVERT: B 405 ASP cc_start: 0.7295 (OUTLIER) cc_final: 0.6350 (t0) REVERT: C 52 GLN cc_start: 0.8581 (tm-30) cc_final: 0.8303 (tm-30) REVERT: C 117 LEU cc_start: 0.7150 (tt) cc_final: 0.6141 (mp) REVERT: C 357 ARG cc_start: 0.7416 (OUTLIER) cc_final: 0.6808 (mmm-85) REVERT: C 405 ASP cc_start: 0.7115 (OUTLIER) cc_final: 0.6195 (t0) REVERT: C 421 TYR cc_start: 0.7870 (m-80) cc_final: 0.7255 (m-80) REVERT: C 780 GLU cc_start: 0.8946 (tt0) cc_final: 0.8630 (tt0) REVERT: C 900 MET cc_start: 0.8669 (mtp) cc_final: 0.8386 (mtp) outliers start: 62 outliers final: 37 residues processed: 166 average time/residue: 0.3853 time to fit residues: 100.9811 Evaluate side-chains 130 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 87 time to evaluate : 2.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 357 ARG Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 405 ASP Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 907 ASN Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 405 ASP Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 1107 ARG Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 220 PHE Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 405 ASP Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 661 GLU Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 1107 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 128 optimal weight: 8.9990 chunk 97 optimal weight: 1.9990 chunk 271 optimal weight: 2.9990 chunk 57 optimal weight: 0.2980 chunk 194 optimal weight: 1.9990 chunk 218 optimal weight: 1.9990 chunk 179 optimal weight: 0.9980 chunk 91 optimal weight: 0.6980 chunk 199 optimal weight: 0.9990 chunk 214 optimal weight: 5.9990 chunk 90 optimal weight: 0.0770 overall best weight: 0.6140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 ASN A 926 GLN A1002 GLN ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN B 317 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN C 394 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN ** C 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.115976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.074052 restraints weight = 50277.376| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 3.22 r_work: 0.3050 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 25152 Z= 0.191 Angle : 0.598 12.424 34233 Z= 0.306 Chirality : 0.045 0.184 4074 Planarity : 0.004 0.056 4350 Dihedral : 6.085 56.632 4468 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.36 % Allowed : 14.68 % Favored : 82.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.15), residues: 2997 helix: 1.49 (0.21), residues: 705 sheet: -0.71 (0.20), residues: 585 loop : -1.32 (0.14), residues: 1707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 436 HIS 0.005 0.001 HIS B1048 PHE 0.019 0.001 PHE B 347 TYR 0.020 0.002 TYR B 505 ARG 0.007 0.001 ARG A 403 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5994 Ramachandran restraints generated. 2997 Oldfield, 0 Emsley, 2997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5994 Ramachandran restraints generated. 2997 Oldfield, 0 Emsley, 2997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 105 time to evaluate : 2.529 Fit side-chains REVERT: A 117 LEU cc_start: 0.7179 (tt) cc_final: 0.6340 (mp) REVERT: A 265 TYR cc_start: 0.5207 (p90) cc_final: 0.4956 (p90) REVERT: A 357 ARG cc_start: 0.7455 (OUTLIER) cc_final: 0.7094 (mmm-85) REVERT: A 376 THR cc_start: 0.7441 (OUTLIER) cc_final: 0.7219 (p) REVERT: A 421 TYR cc_start: 0.7864 (m-80) cc_final: 0.7317 (m-80) REVERT: B 117 LEU cc_start: 0.7121 (tt) cc_final: 0.6288 (mp) REVERT: B 220 PHE cc_start: 0.6969 (t80) cc_final: 0.6515 (t80) REVERT: B 357 ARG cc_start: 0.7589 (OUTLIER) cc_final: 0.7145 (mmm-85) REVERT: C 117 LEU cc_start: 0.7220 (tt) cc_final: 0.6283 (mp) REVERT: C 265 TYR cc_start: 0.6441 (p90) cc_final: 0.5065 (p90) REVERT: C 357 ARG cc_start: 0.7571 (OUTLIER) cc_final: 0.7200 (mmt90) REVERT: C 421 TYR cc_start: 0.7891 (m-80) cc_final: 0.7220 (m-80) REVERT: C 508 TYR cc_start: 0.7342 (OUTLIER) cc_final: 0.6811 (m-80) REVERT: C 780 GLU cc_start: 0.8914 (tt0) cc_final: 0.8615 (tt0) REVERT: C 900 MET cc_start: 0.8606 (mtp) cc_final: 0.8311 (mtp) outliers start: 63 outliers final: 43 residues processed: 159 average time/residue: 0.3333 time to fit residues: 88.5537 Evaluate side-chains 138 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 90 time to evaluate : 2.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 357 ARG Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 1107 ARG Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 220 PHE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 508 TYR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 661 GLU Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 1107 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 199 optimal weight: 1.9990 chunk 299 optimal weight: 0.9990 chunk 289 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 205 optimal weight: 4.9990 chunk 257 optimal weight: 0.8980 chunk 98 optimal weight: 0.9990 chunk 286 optimal weight: 3.9990 chunk 183 optimal weight: 1.9990 chunk 259 optimal weight: 0.0020 overall best weight: 0.9794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: