Starting phenix.real_space_refine on Sun Jan 26 13:18:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tou_26038/01_2025/7tou_26038.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tou_26038/01_2025/7tou_26038.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7tou_26038/01_2025/7tou_26038.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tou_26038/01_2025/7tou_26038.map" model { file = "/net/cci-nas-00/data/ceres_data/7tou_26038/01_2025/7tou_26038.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tou_26038/01_2025/7tou_26038.cif" } resolution = 3.24 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= 0.148 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 15708 2.51 5 N 4038 2.21 5 O 4836 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 24687 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 7924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1014, 7924 Classifications: {'peptide': 1014} Link IDs: {'PTRANS': 48, 'TRANS': 965} Chain breaks: 7 Chain: "B" Number of atoms: 7924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1014, 7924 Classifications: {'peptide': 1014} Link IDs: {'PTRANS': 48, 'TRANS': 965} Chain breaks: 7 Chain: "C" Number of atoms: 7985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1022, 7985 Classifications: {'peptide': 1022} Link IDs: {'PTRANS': 49, 'TRANS': 972} Chain breaks: 6 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: "P" 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: "Q" 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: 15.17, per 1000 atoms: 0.61 Number of scatterers: 24687 At special positions: 0 Unit cell: (132.84, 137.16, 177.12, 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 4836 8.00 N 4038 7.00 C 15708 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=2.02 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=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.05 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.02 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=2.04 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=1.97 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=2.04 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=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.06 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=2.02 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.04 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=2.02 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=2.01 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=2.04 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=2.04 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.06 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=2.04 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.04 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.04 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=2.01 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 P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " 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 A1310 " - " ASN A1074 " " NAG A1311 " - " ASN A 165 " " NAG B1301 " - " ASN B 331 " " NAG B1302 " - " ASN B 343 " " NAG B1303 " - " ASN B 603 " " NAG B1304 " - " ASN B 61 " " NAG B1305 " - " ASN B 657 " " NAG B1306 " - " ASN B 122 " " NAG B1307 " - " ASN B 282 " " NAG B1308 " - " ASN B 165 " " NAG B1309 " - " ASN B 616 " " NAG B1310 " - " ASN B 709 " " NAG B1311 " - " ASN B1074 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 282 " " NAG C1303 " - " ASN C 331 " " NAG C1304 " - " ASN C 603 " " NAG C1305 " - " ASN C1074 " " NAG C1306 " - " ASN C 343 " " NAG C1307 " - " ASN C 616 " " NAG C1308 " - " ASN C 165 " " NAG C1309 " - " ASN C 657 " " NAG C1310 " - " ASN C 709 " " NAG C1311 " - " ASN C 122 " " NAG D 1 " - " ASN A 234 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN A 801 " " NAG G 1 " - " ASN A1098 " " NAG H 1 " - " ASN A1134 " " NAG I 1 " - " ASN B 234 " " NAG J 1 " - " ASN B 801 " " NAG K 1 " - " ASN B1134 " " NAG L 1 " - " ASN B 717 " " NAG M 1 " - " ASN B1098 " " NAG N 1 " - " ASN C 234 " " NAG O 1 " - " ASN C1098 " " NAG P 1 " - " ASN C1134 " " NAG Q 1 " - " ASN C 801 " Time building additional restraints: 6.23 Conformation dependent library (CDL) restraints added in 3.3 seconds 6008 Ramachandran restraints generated. 3004 Oldfield, 0 Emsley, 3004 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5716 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 47 sheets defined 27.2% alpha, 27.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.06 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.572A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 383 through 387 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.243A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 498 through 500 No H-bonds generated for 'chain 'A' and resid 498 through 500' Processing helix chain 'A' and resid 501 through 506 removed outlier: 3.909A pdb=" N TYR A 505 " --> pdb=" O ASN A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 620 Processing helix chain 'A' and resid 634 through 639 removed outlier: 3.707A pdb=" N THR A 638 " --> pdb=" O VAL A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.630A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.540A pdb=" N GLN A 774 " --> pdb=" O ILE A 770 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.711A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.533A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 918 removed outlier: 3.669A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 939 removed outlier: 3.616A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 941 through 944 Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.808A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (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 976 through 984 removed outlier: 3.637A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.531A pdb=" N VAL A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1147 removed outlier: 4.013A pdb=" N ASP A1146 " --> pdb=" O GLN A1142 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 383 through 387 removed outlier: 3.519A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.439A 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 502 through 505 Processing helix chain 'B' and resid 619 through 623 Processing helix chain 'B' and resid 633 through 639 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 753 Processing helix chain 'B' and resid 754 through 757 Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.556A pdb=" N GLN B 774 " --> pdb=" O ILE B 770 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LYS B 776 " --> pdb=" O VAL B 772 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.672A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.910A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.626A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.527A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (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 984 removed outlier: 3.822A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.545A pdb=" N VAL B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1145 removed outlier: 3.557A pdb=" N LEU B1145 " --> pdb=" O GLN B1142 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 383 through 389 removed outlier: 4.250A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 3.759A 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 removed outlier: 3.720A pdb=" N SER C 443 " --> pdb=" O ASN C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 4.027A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.707A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.672A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 918 removed outlier: 3.557A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.687A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (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 removed outlier: 3.599A pdb=" N ASN C 955 " --> pdb=" O VAL C 951 " (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 976 through 984 removed outlier: 3.503A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.172A pdb=" N VAL C 991 " --> pdb=" O VAL C 987 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1146 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.283A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.570A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 7.468A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.719A 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 Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.095A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.414A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 324 through 328 removed outlier: 4.116A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.665A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.474A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 701 through 704 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.581A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 718 through 728 removed outlier: 3.558A pdb=" N ALA A1056 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB7, first strand: chain 'A' and resid 787 through 790 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.575A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 28 through 30 removed outlier: 7.947A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.737A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.624A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.310A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 325 through 328 Processing sheet with id=AC6, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AC7, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.711A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 452 through 453 Processing sheet with id=AC9, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.302A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 702 through 704 Processing sheet with id=AD2, first strand: chain 'B' and resid 711 through 715 Processing sheet with id=AD3, first strand: chain 'B' and resid 718 through 728 removed outlier: 7.328A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD5, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.751A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD7, first strand: chain 'C' and resid 28 through 30 removed outlier: 7.990A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.319A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.181A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.744A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.042A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.660A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.376A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.978A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.837A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 452 through 453 Processing sheet with id=AE6, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE7, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.549A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.583A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA C1056 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.583A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.553A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.640A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 1044 hydrogen bonds defined for protein. 2826 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: 11.70 Time building geometry restraints manager: 7.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 6876 1.34 - 1.46: 4573 1.46 - 1.58: 13646 1.58 - 1.71: 0 1.71 - 1.83: 129 Bond restraints: 25224 Sorted by residual: bond pdb=" C4 NAG D 1 " pdb=" O4 NAG D 1 " ideal model delta sigma weight residual 1.409 1.491 -0.082 2.00e-02 2.50e+03 1.69e+01 bond pdb=" CA PRO C 862 " pdb=" C PRO C 862 " ideal model delta sigma weight residual 1.517 1.544 -0.027 6.70e-03 2.23e+04 1.66e+01 bond pdb=" C5 NAG O 2 " pdb=" O5 NAG O 2 " ideal model delta sigma weight residual 1.413 1.491 -0.078 2.00e-02 2.50e+03 1.51e+01 bond pdb=" C5 NAG A1311 " pdb=" O5 NAG A1311 " ideal model delta sigma weight residual 1.413 1.490 -0.077 2.00e-02 2.50e+03 1.49e+01 bond pdb=" C5 NAG I 2 " pdb=" O5 NAG I 2 " ideal model delta sigma weight residual 1.413 1.490 -0.077 2.00e-02 2.50e+03 1.48e+01 ... (remaining 25219 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.91: 33989 4.91 - 9.83: 318 9.83 - 14.74: 6 14.74 - 19.66: 0 19.66 - 24.57: 3 Bond angle restraints: 34316 Sorted by residual: angle pdb=" CA VAL B 622 " pdb=" CB VAL B 622 " pdb=" CG1 VAL B 622 " ideal model delta sigma weight residual 110.40 134.97 -24.57 1.70e+00 3.46e-01 2.09e+02 angle pdb=" CA VAL A 635 " pdb=" CB VAL A 635 " pdb=" CG1 VAL A 635 " ideal model delta sigma weight residual 110.40 132.38 -21.98 1.70e+00 3.46e-01 1.67e+02 angle pdb=" CB LEU C 629 " pdb=" CG LEU C 629 " pdb=" CD1 LEU C 629 " ideal model delta sigma weight residual 110.70 131.41 -20.71 3.00e+00 1.11e-01 4.76e+01 angle pdb=" N CYS C 391 " pdb=" CA CYS C 391 " pdb=" C CYS C 391 " ideal model delta sigma weight residual 108.96 118.98 -10.02 1.49e+00 4.50e-01 4.53e+01 angle pdb=" N CYS B 391 " pdb=" CA CYS B 391 " pdb=" C CYS B 391 " ideal model delta sigma weight residual 109.07 119.00 -9.93 1.52e+00 4.33e-01 4.26e+01 ... (remaining 34311 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.03: 14726 18.03 - 36.06: 841 36.06 - 54.09: 160 54.09 - 72.12: 53 72.12 - 90.15: 30 Dihedral angle restraints: 15810 sinusoidal: 6935 harmonic: 8875 Sorted by residual: dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual 93.00 -176.85 -90.15 1 1.00e+01 1.00e-02 9.62e+01 dihedral pdb=" CB CYS C1082 " pdb=" SG CYS C1082 " pdb=" SG CYS C1126 " pdb=" CB CYS C1126 " ideal model delta sinusoidal sigma weight residual -86.00 -168.46 82.46 1 1.00e+01 1.00e-02 8.34e+01 dihedral pdb=" C THR C 630 " pdb=" N THR C 630 " pdb=" CA THR C 630 " pdb=" CB THR C 630 " ideal model delta harmonic sigma weight residual -122.00 -138.70 16.70 0 2.50e+00 1.60e-01 4.46e+01 ... (remaining 15807 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.318: 4068 0.318 - 0.635: 16 0.635 - 0.953: 0 0.953 - 1.270: 0 1.270 - 1.588: 3 Chirality restraints: 4087 Sorted by residual: chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.60 0.20 2.00e-02 2.50e+03 1.02e+02 chirality pdb=" C1 NAG I 2 " pdb=" O4 NAG I 1 " pdb=" C2 NAG I 2 " pdb=" O5 NAG I 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.59 0.19 2.00e-02 2.50e+03 8.99e+01 chirality pdb=" C1 NAG N 2 " pdb=" O4 NAG N 1 " pdb=" C2 NAG N 2 " pdb=" O5 NAG N 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.58 0.18 2.00e-02 2.50e+03 7.68e+01 ... (remaining 4084 not shown) Planarity restraints: 4402 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C1074 " 0.137 2.00e-02 2.50e+03 1.46e-01 2.65e+02 pdb=" CG ASN C1074 " -0.078 2.00e-02 2.50e+03 pdb=" OD1 ASN C1074 " -0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN C1074 " -0.226 2.00e-02 2.50e+03 pdb=" C1 NAG C1305 " 0.174 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 165 " -0.135 2.00e-02 2.50e+03 1.40e-01 2.45e+02 pdb=" CG ASN C 165 " 0.079 2.00e-02 2.50e+03 pdb=" OD1 ASN C 165 " 0.016 2.00e-02 2.50e+03 pdb=" ND2 ASN C 165 " 0.210 2.00e-02 2.50e+03 pdb=" C1 NAG C1308 " -0.171 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 603 " -0.131 2.00e-02 2.50e+03 1.37e-01 2.36e+02 pdb=" CG ASN A 603 " 0.077 2.00e-02 2.50e+03 pdb=" OD1 ASN A 603 " 0.010 2.00e-02 2.50e+03 pdb=" ND2 ASN A 603 " 0.209 2.00e-02 2.50e+03 pdb=" C1 NAG A1306 " -0.166 2.00e-02 2.50e+03 ... (remaining 4399 not shown) Histogram of nonbonded interaction distances: 2.52 - 2.99: 12137 2.99 - 3.47: 23189 3.47 - 3.95: 40324 3.95 - 4.42: 44667 4.42 - 4.90: 76059 Nonbonded interactions: 196376 Sorted by model distance: nonbonded pdb=" OG SER A1123 " pdb=" OE2 GLU B 918 " model vdw 2.517 3.040 nonbonded pdb=" OE2 GLU A 918 " pdb=" OG SER C1123 " model vdw 2.530 3.040 nonbonded pdb=" OD1 ASP A 364 " pdb=" OG SER A 366 " model vdw 2.536 3.040 nonbonded pdb=" OG SER A 383 " pdb=" OE1 GLU B 988 " model vdw 2.540 3.040 nonbonded pdb=" OG SER B1123 " pdb=" OE2 GLU C 918 " model vdw 2.542 3.040 ... (remaining 196371 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' and (resid 27 through 624 or resid 633 through 1147 or resid 1301 thr \ ough 1311)) } 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' selection = chain 'P' selection = chain 'Q' } 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: 2.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.960 Check model and map are aligned: 0.190 Set scattering table: 0.250 Process input model: 58.360 Find NCS groups from input model: 1.370 Set up NCS constraints: 0.160 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: 0.000 Load rotamer database and sin/cos tables:3.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 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 : 0.014 0.082 25224 Z= 0.905 Angle : 1.819 24.573 34316 Z= 1.208 Chirality : 0.109 1.588 4087 Planarity : 0.014 0.217 4355 Dihedral : 12.991 89.697 9977 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 0.18 Ramachandran Plot: Outliers : 0.67 % Allowed : 6.16 % Favored : 93.18 % Rotamer: Outliers : 1.20 % Allowed : 3.38 % Favored : 95.42 % Cbeta Deviations : 0.28 % 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 (0.14), residues: 3004 helix: -0.94 (0.17), residues: 639 sheet: 0.38 (0.20), residues: 573 loop : -0.89 (0.14), residues: 1792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.159 0.023 TRP A 633 HIS 0.018 0.003 HIS B 519 PHE 0.082 0.011 PHE C 318 TYR 0.153 0.020 TYR C 495 ARG 0.014 0.001 ARG C 466 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6008 Ramachandran restraints generated. 3004 Oldfield, 0 Emsley, 3004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6008 Ramachandran restraints generated. 3004 Oldfield, 0 Emsley, 3004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 2665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 115 time to evaluate : 3.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 455 LEU cc_start: 0.7991 (tp) cc_final: 0.7710 (tt) REVERT: A 697 MET cc_start: 0.8897 (ptm) cc_final: 0.8636 (ptp) REVERT: A 869 MET cc_start: 0.8990 (mtt) cc_final: 0.8778 (mtt) REVERT: B 233 ILE cc_start: 0.6135 (mt) cc_final: 0.5913 (mt) REVERT: C 457 ARG cc_start: 0.4302 (OUTLIER) cc_final: 0.3902 (ptp90) REVERT: C 907 ASN cc_start: 0.8739 (OUTLIER) cc_final: 0.8536 (t0) outliers start: 32 outliers final: 10 residues processed: 145 average time/residue: 0.4426 time to fit residues: 100.0151 Evaluate side-chains 72 residues out of total 2665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 60 time to evaluate : 3.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 907 ASN Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain C residue 457 ARG Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 907 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 256 optimal weight: 0.8980 chunk 230 optimal weight: 10.0000 chunk 127 optimal weight: 5.9990 chunk 78 optimal weight: 0.9980 chunk 155 optimal weight: 0.8980 chunk 123 optimal weight: 8.9990 chunk 238 optimal weight: 6.9990 chunk 92 optimal weight: 2.9990 chunk 144 optimal weight: 8.9990 chunk 177 optimal weight: 0.6980 chunk 276 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 ASN A 607 GLN A1088 HIS B 955 ASN ** C 625 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 751 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.095401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.060750 restraints weight = 70118.217| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 2.56 r_work: 0.2960 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2826 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.1692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.092 25224 Z= 0.191 Angle : 0.693 13.889 34316 Z= 0.368 Chirality : 0.047 0.227 4087 Planarity : 0.004 0.037 4355 Dihedral : 6.817 55.850 4561 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.33 % Favored : 96.47 % Rotamer: Outliers : 1.31 % Allowed : 4.84 % Favored : 93.85 % 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: -0.16 (0.15), residues: 3004 helix: 1.06 (0.20), residues: 661 sheet: 0.36 (0.19), residues: 663 loop : -0.77 (0.15), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 633 HIS 0.006 0.001 HIS C 519 PHE 0.029 0.002 PHE C 338 TYR 0.018 0.002 TYR A 204 ARG 0.010 0.001 ARG B 237 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6008 Ramachandran restraints generated. 3004 Oldfield, 0 Emsley, 3004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6008 Ramachandran restraints generated. 3004 Oldfield, 0 Emsley, 3004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 2665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 67 time to evaluate : 2.786 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 318 PHE cc_start: 0.8227 (OUTLIER) cc_final: 0.7898 (t80) REVERT: A 697 MET cc_start: 0.9278 (ptm) cc_final: 0.9062 (ptp) REVERT: C 907 ASN cc_start: 0.9290 (OUTLIER) cc_final: 0.8987 (t0) REVERT: C 1029 MET cc_start: 0.9575 (tpp) cc_final: 0.9241 (tpp) outliers start: 35 outliers final: 13 residues processed: 102 average time/residue: 0.3925 time to fit residues: 66.3198 Evaluate side-chains 70 residues out of total 2665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 55 time to evaluate : 3.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 907 ASN Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 907 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 235 optimal weight: 5.9990 chunk 207 optimal weight: 9.9990 chunk 186 optimal weight: 2.9990 chunk 196 optimal weight: 0.8980 chunk 164 optimal weight: 6.9990 chunk 92 optimal weight: 2.9990 chunk 172 optimal weight: 4.9990 chunk 141 optimal weight: 20.0000 chunk 197 optimal weight: 0.9990 chunk 14 optimal weight: 8.9990 chunk 177 optimal weight: 4.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 ASN C 675 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.093960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.059101 restraints weight = 70139.094| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 2.52 r_work: 0.2918 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2786 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 25224 Z= 0.276 Angle : 0.632 10.151 34316 Z= 0.332 Chirality : 0.046 0.194 4087 Planarity : 0.004 0.039 4355 Dihedral : 6.098 50.661 4552 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.46 % Favored : 95.44 % Rotamer: Outliers : 1.46 % Allowed : 5.03 % Favored : 93.51 % 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: -0.05 (0.15), residues: 3004 helix: 1.38 (0.20), residues: 653 sheet: 0.41 (0.19), residues: 674 loop : -0.80 (0.15), residues: 1677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 633 HIS 0.006 0.001 HIS A1058 PHE 0.018 0.002 PHE B1121 TYR 0.023 0.002 TYR B 421 ARG 0.010 0.001 ARG C 457 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6008 Ramachandran restraints generated. 3004 Oldfield, 0 Emsley, 3004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6008 Ramachandran restraints generated. 3004 Oldfield, 0 Emsley, 3004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 2665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 61 time to evaluate : 2.817 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 461 LEU cc_start: 0.7074 (OUTLIER) cc_final: 0.6151 (mm) REVERT: A 902 MET cc_start: 0.8873 (tpp) cc_final: 0.8589 (mmt) REVERT: C 907 ASN cc_start: 0.9259 (OUTLIER) cc_final: 0.9010 (t0) outliers start: 39 outliers final: 23 residues processed: 98 average time/residue: 0.3659 time to fit residues: 59.6279 Evaluate side-chains 75 residues out of total 2665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 50 time to evaluate : 2.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 907 ASN Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 907 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 12 optimal weight: 30.0000 chunk 85 optimal weight: 5.9990 chunk 72 optimal weight: 5.9990 chunk 282 optimal weight: 5.9990 chunk 178 optimal weight: 3.9990 chunk 59 optimal weight: 0.9990 chunk 45 optimal weight: 9.9990 chunk 223 optimal weight: 2.9990 chunk 300 optimal weight: 4.9990 chunk 173 optimal weight: 0.0170 chunk 294 optimal weight: 0.9990 overall best weight: 1.8026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.094243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.059649 restraints weight = 70596.572| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 2.53 r_work: 0.2933 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2799 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.2563 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: