Starting phenix.real_space_refine on Sat Dec 28 20:58:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xu2_33456/12_2024/7xu2_33456_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xu2_33456/12_2024/7xu2_33456.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7xu2_33456/12_2024/7xu2_33456.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xu2_33456/12_2024/7xu2_33456.map" model { file = "/net/cci-nas-00/data/ceres_data/7xu2_33456/12_2024/7xu2_33456_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xu2_33456/12_2024/7xu2_33456_trim.cif" } resolution = 3.2 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= 0.000 sd= 0.005 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: 5 Type Number sf(0) Gaussians S 126 5.16 5 C 17166 2.51 5 N 4413 2.21 5 O 5265 1.98 5 H 25248 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.95s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 52218 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 17063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1107, 17063 Classifications: {'peptide': 1107} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 52, 'TRANS': 1054} Chain breaks: 3 Chain: "C" Number of atoms: 17063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1107, 17063 Classifications: {'peptide': 1107} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 52, 'TRANS': 1054} Chain breaks: 3 Chain: "B" Number of atoms: 17063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1107, 17063 Classifications: {'peptide': 1107} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 52, 'TRANS': 1054} Chain breaks: 3 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: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 231 Unusual residues: {'BLA': 1, 'EIC': 1, 'NAG': 12} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "C" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 231 Unusual residues: {'BLA': 1, 'EIC': 1, 'NAG': 12} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "B" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 231 Unusual residues: {'BLA': 1, 'EIC': 1, 'NAG': 12} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Time building chain proxies: 19.37, per 1000 atoms: 0.37 Number of scatterers: 52218 At special positions: 0 Unit cell: (137.93, 152.784, 167.638, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 126 16.00 O 5265 8.00 N 4413 7.00 C 17166 6.00 H 25248 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.06 Simple disulfide: pdb=" SG CYS A 427 " - pdb=" SG CYS B 987 " distance=2.02 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=2.04 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A 840 " - pdb=" SG CYS A 851 " distance=2.03 Simple disulfide: pdb=" SG CYS A 987 " - pdb=" SG CYS C 427 " distance=2.02 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.04 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " 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=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C 840 " - pdb=" SG CYS C 851 " distance=2.03 Simple disulfide: pdb=" SG CYS C 987 " - pdb=" SG CYS B 427 " 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=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " 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=2.04 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " 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=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B 840 " - pdb=" SG CYS B 851 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG 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 122 " " NAG A1303 " - " ASN A 331 " " NAG A1304 " - " ASN A 616 " " NAG A1305 " - " ASN A 657 " " NAG A1306 " - " ASN A 709 " " NAG A1307 " - " ASN A1074 " " NAG A1308 " - " ASN A1098 " " NAG A1309 " - " ASN A 165 " " NAG A1310 " - " ASN A 282 " " NAG A1311 " - " ASN A 343 " " NAG A1312 " - " ASN A 17 " " NAG B1802 " - " ASN B 61 " " NAG B1803 " - " ASN B 122 " " NAG B1804 " - " ASN B 331 " " NAG B1805 " - " ASN B 616 " " NAG B1806 " - " ASN B 657 " " NAG B1807 " - " ASN B 709 " " NAG B1808 " - " ASN B1074 " " NAG B1809 " - " ASN B1098 " " NAG B1810 " - " ASN B 165 " " NAG B1811 " - " ASN B 282 " " NAG B1812 " - " ASN B 343 " " NAG B1813 " - " ASN B 17 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 122 " " NAG C1303 " - " ASN C 331 " " NAG C1304 " - " ASN C 616 " " NAG C1305 " - " ASN C 657 " " NAG C1306 " - " ASN C 709 " " NAG C1307 " - " ASN C1074 " " NAG C1308 " - " ASN C1098 " " NAG C1309 " - " ASN C 165 " " NAG C1310 " - " ASN C 282 " " NAG C1311 " - " ASN C 343 " " NAG C1312 " - " ASN C 17 " " NAG D 1 " - " ASN A 234 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN A 801 " " NAG G 1 " - " ASN A1134 " " NAG H 1 " - " ASN C 234 " " NAG I 1 " - " ASN C 717 " " NAG J 1 " - " ASN C 801 " " NAG K 1 " - " ASN C1134 " " NAG L 1 " - " ASN B 234 " " NAG M 1 " - " ASN B 717 " " NAG N 1 " - " ASN B 801 " " NAG O 1 " - " ASN B1134 " Time building additional restraints: 10.49 Conformation dependent library (CDL) restraints added in 3.2 seconds 6594 Ramachandran restraints generated. 3297 Oldfield, 0 Emsley, 3297 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input volumes are d-peptide like pdb=" CB VAL C 70 " pdb=" CB VAL B 70 " Number of C-beta restraints generated: 6212 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 46 sheets defined 24.1% alpha, 22.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.59 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 342 removed outlier: 3.956A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 372 removed outlier: 4.426A pdb=" N SER A 371 " --> pdb=" O VAL A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 389 removed outlier: 4.221A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.336A 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 619 through 625 Processing helix chain 'A' and resid 630 through 635 removed outlier: 3.642A pdb=" N VAL A 635 " --> pdb=" O PRO A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 756 through 783 Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 848 through 856 removed outlier: 3.515A pdb=" N ALA A 852 " --> pdb=" O ASP A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 897 through 910 Processing helix chain 'A' and resid 913 through 941 removed outlier: 3.544A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N LYS A 921 " --> pdb=" O TYR A 917 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N LEU A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N SER A 939 " --> pdb=" O GLN A 935 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N THR A 941 " --> pdb=" O SER A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 5.421A pdb=" N VAL A 991 " --> pdb=" O CYS A 987 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 342 removed outlier: 3.944A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 372 removed outlier: 4.417A pdb=" N SER C 371 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 389 removed outlier: 4.219A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.336A 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 619 through 625 Processing helix chain 'C' and resid 630 through 635 removed outlier: 3.640A pdb=" N VAL C 635 " --> pdb=" O PRO C 631 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 756 through 783 Processing helix chain 'C' and resid 802 through 806 removed outlier: 3.667A pdb=" N LEU C 806 " --> pdb=" O SER C 803 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 825 Processing helix chain 'C' and resid 848 through 856 removed outlier: 3.517A pdb=" N ALA C 852 " --> pdb=" O ASP C 848 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 897 through 910 Processing helix chain 'C' and resid 913 through 941 removed outlier: 3.535A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N LYS C 921 " --> pdb=" O TYR C 917 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N LEU C 922 " --> pdb=" O GLU C 918 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N SER C 939 " --> pdb=" O GLN C 935 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N THR C 941 " --> pdb=" O SER C 937 " (cutoff:3.500A) 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 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 5.431A pdb=" N VAL C 991 " --> pdb=" O CYS C 987 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 342 removed outlier: 3.950A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 372 removed outlier: 4.414A pdb=" N SER B 371 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 389 removed outlier: 4.228A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.336A 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 619 through 625 Processing helix chain 'B' and resid 630 through 635 removed outlier: 3.640A pdb=" N VAL B 635 " --> pdb=" O PRO B 631 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 756 through 783 Processing helix chain 'B' and resid 802 through 806 removed outlier: 3.655A pdb=" N LEU B 806 " --> pdb=" O SER B 803 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 848 through 856 removed outlier: 3.517A pdb=" N ALA B 852 " --> pdb=" O ASP B 848 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 897 through 910 Processing helix chain 'B' and resid 913 through 941 removed outlier: 3.541A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N LYS B 921 " --> pdb=" O TYR B 917 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N LEU B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N SER B 939 " --> pdb=" O GLN B 935 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N THR B 941 " --> pdb=" O SER B 937 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 5.427A pdb=" N VAL B 991 " --> pdb=" O CYS B 987 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 31 removed outlier: 4.067A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.104A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.552A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ASN A 121 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N GLU A 132 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ALA A 163 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 311 through 314 Processing sheet with id=AA5, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.132A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.263A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA8, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA9, first strand: chain 'A' and resid 539 through 543 removed outlier: 4.126A pdb=" N GLU A 583 " --> pdb=" O ASP A 578 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.188A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.557A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.485A pdb=" N ALA A 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 712 through 715 removed outlier: 3.624A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 718 through 728 removed outlier: 7.051A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB6, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.532A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 27 through 31 removed outlier: 4.043A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 47 through 55 removed outlier: 4.116A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.568A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ASN C 121 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N GLU C 132 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ALA C 163 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 8.122A pdb=" N VAL C 159 " --> pdb=" O CYS C 136 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 311 through 314 Processing sheet with id=AC3, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.129A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.257A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AC6, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AC7, first strand: chain 'C' and resid 539 through 543 removed outlier: 4.116A pdb=" N GLU C 583 " --> pdb=" O ASP C 578 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.181A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.549A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 701 through 702 removed outlier: 6.489A pdb=" N ALA C 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'C' and resid 712 through 715 removed outlier: 3.629A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 718 through 728 removed outlier: 7.062A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AD4, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.533A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 27 through 31 removed outlier: 4.051A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.105A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.568A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASN B 121 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N GLU B 132 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ALA B 163 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N GLN B 134 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N VAL B 159 " --> pdb=" O CYS B 136 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 144 through 145 removed outlier: 3.513A pdb=" N TYR B 144 " --> pdb=" O MET B 153 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N MET B 153 " --> pdb=" O TYR B 144 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'B' and resid 311 through 314 Processing sheet with id=AE1, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.127A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.260A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AE4, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AE5, first strand: chain 'B' and resid 539 through 543 removed outlier: 4.131A pdb=" N GLU B 583 " --> pdb=" O ASP B 578 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.170A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.537A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'B' and resid 712 through 715 removed outlier: 3.638A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'B' and resid 718 through 728 removed outlier: 7.060A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AF1, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.547A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) 1029 hydrogen bonds defined for protein. 2802 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: 21.08 Time building geometry restraints manager: 12.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.05: 25242 1.05 - 1.26: 4359 1.26 - 1.48: 11457 1.48 - 1.69: 11610 1.69 - 1.91: 156 Bond restraints: 52824 Sorted by residual: bond pdb=" C4C BLA B1814 " pdb=" NC BLA B1814 " ideal model delta sigma weight residual 1.375 1.542 -0.167 2.00e-02 2.50e+03 6.99e+01 bond pdb=" C4C BLA C1313 " pdb=" NC BLA C1313 " ideal model delta sigma weight residual 1.375 1.542 -0.167 2.00e-02 2.50e+03 6.96e+01 bond pdb=" C4C BLA A1313 " pdb=" NC BLA A1313 " ideal model delta sigma weight residual 1.375 1.541 -0.166 2.00e-02 2.50e+03 6.93e+01 bond pdb=" NB BLA B1814 " pdb=" C4B BLA B1814 " ideal model delta sigma weight residual 1.371 1.532 -0.161 2.00e-02 2.50e+03 6.52e+01 bond pdb=" NB BLA C1313 " pdb=" C4B BLA C1313 " ideal model delta sigma weight residual 1.371 1.532 -0.161 2.00e-02 2.50e+03 6.49e+01 ... (remaining 52819 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.18: 94554 5.18 - 10.36: 104 10.36 - 15.54: 10 15.54 - 20.73: 12 20.73 - 25.91: 3 Bond angle restraints: 94683 Sorted by residual: angle pdb=" CA CYS B 432 " pdb=" CB CYS B 432 " pdb=" SG CYS B 432 " ideal model delta sigma weight residual 114.40 134.62 -20.22 2.30e+00 1.89e-01 7.73e+01 angle pdb=" CA CYS C 432 " pdb=" CB CYS C 432 " pdb=" SG CYS C 432 " ideal model delta sigma weight residual 114.40 134.48 -20.08 2.30e+00 1.89e-01 7.62e+01 angle pdb=" CA CYS A 432 " pdb=" CB CYS A 432 " pdb=" SG CYS A 432 " ideal model delta sigma weight residual 114.40 134.42 -20.02 2.30e+00 1.89e-01 7.57e+01 angle pdb=" CG2 THR C 95 " pdb=" CB THR C 95 " pdb=" HB THR C 95 " ideal model delta sigma weight residual 108.00 82.09 25.91 3.00e+00 1.11e-01 7.46e+01 angle pdb=" OG1 THR C 95 " pdb=" CB THR C 95 " pdb=" HB THR C 95 " ideal model delta sigma weight residual 109.00 83.37 25.63 3.00e+00 1.11e-01 7.30e+01 ... (remaining 94678 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.31: 24764 24.31 - 48.61: 1134 48.61 - 72.92: 280 72.92 - 97.22: 35 97.22 - 121.53: 3 Dihedral angle restraints: 26216 sinusoidal: 14613 harmonic: 11603 Sorted by residual: dihedral pdb=" CB CYS C 379 " pdb=" SG CYS C 379 " pdb=" SG CYS C 432 " pdb=" CB CYS C 432 " ideal model delta sinusoidal sigma weight residual 93.00 44.58 48.42 1 1.00e+01 1.00e-02 3.23e+01 dihedral pdb=" CB CYS A 379 " pdb=" SG CYS A 379 " pdb=" SG CYS A 432 " pdb=" CB CYS A 432 " ideal model delta sinusoidal sigma weight residual 93.00 44.84 48.16 1 1.00e+01 1.00e-02 3.20e+01 dihedral pdb=" CB CYS B 379 " pdb=" SG CYS B 379 " pdb=" SG CYS B 432 " pdb=" CB CYS B 432 " ideal model delta sinusoidal sigma weight residual 93.00 44.92 48.08 1 1.00e+01 1.00e-02 3.19e+01 ... (remaining 26213 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.544: 4392 0.544 - 1.087: 0 1.087 - 1.631: 1 1.631 - 2.174: 0 2.174 - 2.718: 2 Chirality restraints: 4395 Sorted by residual: chirality pdb=" CA VAL C 70 " pdb=" N VAL C 70 " pdb=" C VAL C 70 " pdb=" CB VAL C 70 " both_signs ideal model delta sigma weight residual False 2.44 -0.28 2.72 2.00e-01 2.50e+01 1.85e+02 chirality pdb=" CA VAL B 70 " pdb=" N VAL B 70 " pdb=" C VAL B 70 " pdb=" CB VAL B 70 " both_signs ideal model delta sigma weight residual False 2.44 -0.27 2.72 2.00e-01 2.50e+01 1.84e+02 chirality pdb=" CB THR C 95 " pdb=" CA THR C 95 " pdb=" OG1 THR C 95 " pdb=" CG2 THR C 95 " both_signs ideal model delta sigma weight residual False 2.55 1.00 1.55 2.00e-01 2.50e+01 6.02e+01 ... (remaining 4392 not shown) Planarity restraints: 7959 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" NB BLA C1313 " 0.070 2.00e-02 2.50e+03 7.51e-02 1.41e+02 pdb=" OB BLA C1313 " -0.004 2.00e-02 2.50e+03 pdb=" C1B BLA C1313 " 0.072 2.00e-02 2.50e+03 pdb=" C2B BLA C1313 " 0.007 2.00e-02 2.50e+03 pdb=" C3B BLA C1313 " -0.019 2.00e-02 2.50e+03 pdb=" C4A BLA C1313 " -0.170 2.00e-02 2.50e+03 pdb=" C4B BLA C1313 " 0.014 2.00e-02 2.50e+03 pdb=" CAB BLA C1313 " -0.075 2.00e-02 2.50e+03 pdb=" CHB BLA C1313 " 0.105 2.00e-02 2.50e+03 pdb=" CMB BLA C1313 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" NB BLA B1814 " 0.070 2.00e-02 2.50e+03 7.50e-02 1.40e+02 pdb=" OB BLA B1814 " -0.004 2.00e-02 2.50e+03 pdb=" C1B BLA B1814 " 0.072 2.00e-02 2.50e+03 pdb=" C2B BLA B1814 " 0.007 2.00e-02 2.50e+03 pdb=" C3B BLA B1814 " -0.019 2.00e-02 2.50e+03 pdb=" C4A BLA B1814 " -0.170 2.00e-02 2.50e+03 pdb=" C4B BLA B1814 " 0.013 2.00e-02 2.50e+03 pdb=" CAB BLA B1814 " -0.075 2.00e-02 2.50e+03 pdb=" CHB BLA B1814 " 0.106 2.00e-02 2.50e+03 pdb=" CMB BLA B1814 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" NB BLA A1313 " 0.070 2.00e-02 2.50e+03 7.49e-02 1.40e+02 pdb=" OB BLA A1313 " -0.004 2.00e-02 2.50e+03 pdb=" C1B BLA A1313 " 0.072 2.00e-02 2.50e+03 pdb=" C2B BLA A1313 " 0.007 2.00e-02 2.50e+03 pdb=" C3B BLA A1313 " -0.018 2.00e-02 2.50e+03 pdb=" C4A BLA A1313 " -0.170 2.00e-02 2.50e+03 pdb=" C4B BLA A1313 " 0.013 2.00e-02 2.50e+03 pdb=" CAB BLA A1313 " -0.075 2.00e-02 2.50e+03 pdb=" CHB BLA A1313 " 0.105 2.00e-02 2.50e+03 pdb=" CMB BLA A1313 " 0.001 2.00e-02 2.50e+03 ... (remaining 7956 not shown) Histogram of nonbonded interaction distances: 1.69 - 2.27: 7642 2.27 - 2.85: 114714 2.85 - 3.44: 130914 3.44 - 4.02: 189058 4.02 - 4.60: 284586 Nonbonded interactions: 726914 Sorted by model distance: nonbonded pdb=" HG1 THR B 22 " pdb=" O THR B 76 " model vdw 1.689 2.450 nonbonded pdb=" HH TYR B 37 " pdb=" O LEU B 54 " model vdw 1.717 2.450 nonbonded pdb=" HH TYR A 37 " pdb=" O LEU A 54 " model vdw 1.721 2.450 nonbonded pdb=" HH TYR C 37 " pdb=" O LEU C 54 " model vdw 1.726 2.450 nonbonded pdb=" H LYS B 462 " pdb=" OE1 GLU B 465 " model vdw 1.727 2.450 ... (remaining 726909 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' and (resid 14 through 1140 or resid 1302 through 1312)) selection = (chain 'B' and (resid 14 through 1140 or resid 1802 through 1812)) selection = (chain 'C' and (resid 14 through 1140 or resid 1302 through 1312)) } 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=0.00 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: 1.730 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: 0.660 Extract box with map and model: 1.390 Check model and map are aligned: 0.280 Set scattering table: 0.350 Process input model: 87.720 Find NCS groups from input model: 1.900 Set up NCS constraints: 0.240 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: 0.020 Load rotamer database and sin/cos tables:2.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 96.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 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 0.167 27576 Z= 0.807 Angle : 0.952 20.223 37524 Z= 0.445 Chirality : 0.082 2.718 4395 Planarity : 0.004 0.075 4776 Dihedral : 14.457 121.529 10866 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 0.86 % Allowed : 0.10 % Favored : 99.03 % Cbeta Deviations : 0.06 % 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: -1.37 (0.14), residues: 3297 helix: 0.68 (0.19), residues: 744 sheet: -0.85 (0.17), residues: 768 loop : -1.66 (0.13), residues: 1785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP B 152 HIS 0.022 0.001 HIS B 146 PHE 0.032 0.002 PHE B 318 TYR 0.025 0.002 TYR C 170 ARG 0.004 0.001 ARG B 454 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6594 Ramachandran restraints generated. 3297 Oldfield, 0 Emsley, 3297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6594 Ramachandran restraints generated. 3297 Oldfield, 0 Emsley, 3297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 2892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 122 time to evaluate : 3.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 TYR cc_start: 0.7473 (t80) cc_final: 0.7206 (t80) REVERT: A 153 MET cc_start: 0.6067 (OUTLIER) cc_final: 0.5766 (tmm) REVERT: A 731 MET cc_start: 0.8978 (ptt) cc_final: 0.8747 (ptt) REVERT: A 881 THR cc_start: 0.8347 (m) cc_final: 0.8109 (m) REVERT: C 144 TYR cc_start: 0.7282 (t80) cc_final: 0.7048 (t80) REVERT: C 170 TYR cc_start: 0.7013 (t80) cc_final: 0.6755 (t80) outliers start: 25 outliers final: 10 residues processed: 139 average time/residue: 0.6965 time to fit residues: 157.6133 Evaluate side-chains 106 residues out of total 2892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 95 time to evaluate : 2.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 725 GLU Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 725 GLU Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 725 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 278 optimal weight: 0.3980 chunk 250 optimal weight: 4.9990 chunk 138 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 168 optimal weight: 0.4980 chunk 133 optimal weight: 0.0050 chunk 258 optimal weight: 0.9990 chunk 100 optimal weight: 1.9990 chunk 157 optimal weight: 2.9990 chunk 192 optimal weight: 1.9990 chunk 299 optimal weight: 2.9990 overall best weight: 0.7798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN A 556 ASN ** C 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 556 ASN ** B 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.0686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 27576 Z= 0.195 Angle : 0.569 13.781 37524 Z= 0.295 Chirality : 0.062 1.768 4395 Planarity : 0.004 0.039 4776 Dihedral : 9.854 117.684 4975 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 1.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 0.76 % Allowed : 2.25 % Favored : 96.99 % Cbeta Deviations : 0.06 % 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: -1.08 (0.14), residues: 3297 helix: 1.00 (0.20), residues: 759 sheet: -0.64 (0.17), residues: 735 loop : -1.55 (0.13), residues: 1803 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 152 HIS 0.016 0.001 HIS B 146 PHE 0.023 0.001 PHE C 79 TYR 0.015 0.001 TYR C 365 ARG 0.003 0.000 ARG A 246 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6594 Ramachandran restraints generated. 3297 Oldfield, 0 Emsley, 3297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6594 Ramachandran restraints generated. 3297 Oldfield, 0 Emsley, 3297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 2892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 97 time to evaluate : 3.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 TYR cc_start: 0.7362 (t80) cc_final: 0.7150 (t80) REVERT: A 731 MET cc_start: 0.9011 (ptt) cc_final: 0.8774 (ptt) REVERT: A 881 THR cc_start: 0.8418 (m) cc_final: 0.8209 (m) REVERT: C 144 TYR cc_start: 0.7362 (t80) cc_final: 0.7121 (t80) outliers start: 22 outliers final: 14 residues processed: 113 average time/residue: 0.6384 time to fit residues: 122.1468 Evaluate side-chains 109 residues out of total 2892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 95 time to evaluate : 2.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 725 GLU Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 725 GLU Chi-restraints excluded: chain B residue 1050 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 166 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 249 optimal weight: 2.9990 chunk 204 optimal weight: 1.9990 chunk 82 optimal weight: 0.6980 chunk 300 optimal weight: 7.9990 chunk 324 optimal weight: 0.9990 chunk 267 optimal weight: 0.9990 chunk 297 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 240 optimal weight: 0.8980 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 556 ASN ** B 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.1002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 27576 Z= 0.237 Angle : 0.543 14.115 37524 Z= 0.280 Chirality : 0.062 1.835 4395 Planarity : 0.003 0.044 4776 Dihedral : 9.033 115.617 4972 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 1.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 0.76 % Allowed : 3.49 % Favored : 95.75 % Cbeta Deviations : 0.06 % 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: -0.97 (0.14), residues: 3297 helix: 1.03 (0.20), residues: 765 sheet: -0.52 (0.18), residues: 705 loop : -1.47 (0.13), residues: 1827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 436 HIS 0.012 0.001 HIS B 146 PHE 0.018 0.001 PHE C 318 TYR 0.018 0.001 TYR A 904 ARG 0.003 0.000 ARG C 102 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6594 Ramachandran restraints generated. 3297 Oldfield, 0 Emsley, 3297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6594 Ramachandran restraints generated. 3297 Oldfield, 0 Emsley, 3297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 2892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 98 time to evaluate : 3.026 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 TYR cc_start: 0.7434 (t80) cc_final: 0.7223 (t80) REVERT: A 881 THR cc_start: 0.8407 (m) cc_final: 0.8199 (m) REVERT: C 16 VAL cc_start: 0.8999 (OUTLIER) cc_final: 0.8762 (p) REVERT: C 170 TYR cc_start: 0.6808 (t80) cc_final: 0.6506 (t80) outliers start: 22 outliers final: 15 residues processed: 114 average time/residue: 0.6514 time to fit residues: 124.8170 Evaluate side-chains 111 residues out of total 2892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 95 time to evaluate : 3.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 725 GLU Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 725 GLU Chi-restraints excluded: chain B residue 1050 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 296 optimal weight: 1.9990 chunk 225 optimal weight: 5.9990 chunk 155 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 143 optimal weight: 0.9980 chunk 201 optimal weight: 2.9990 chunk 301 optimal weight: 3.9990 chunk 318 optimal weight: 1.9990 chunk 157 optimal weight: 1.9990 chunk 285 optimal weight: 3.9990 chunk 85 optimal weight: 0.0010 overall best weight: 1.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 556 ASN ** C 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 556 ASN B 69 HIS ** B 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.1199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 27576 Z= 0.266 Angle : 0.541 14.225 37524 Z= 0.279 Chirality : 0.062 1.813 4395 Planarity : 0.003 0.041 4776 Dihedral : 8.597 114.726 4971 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 2.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 0.69 % Allowed : 4.70 % Favored : 94.61 % Cbeta Deviations : 0.06 % 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: -0.92 (0.14), residues: 3297 helix: 1.05 (0.20), residues: 768 sheet: -0.42 (0.18), residues: 705 loop : -1.46 (0.13), residues: 1824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 436 HIS 0.008 0.001 HIS B 146 PHE 0.017 0.001 PHE C 318 TYR 0.016 0.001 TYR A 904 ARG 0.003 0.000 ARG B 403 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6594 Ramachandran restraints generated. 3297 Oldfield, 0 Emsley, 3297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6594 Ramachandran restraints generated. 3297 Oldfield, 0 Emsley, 3297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 2892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 96 time to evaluate : 3.059 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 TYR cc_start: 0.7464 (t80) cc_final: 0.7257 (t80) REVERT: A 731 MET cc_start: 0.9056 (ptt) cc_final: 0.8835 (ptt) REVERT: A 881 THR cc_start: 0.8425 (m) cc_final: 0.8220 (m) REVERT: C 16 VAL cc_start: 0.8945 (OUTLIER) cc_final: 0.8732 (p) REVERT: C 111 ASP cc_start: 0.7297 (t70) cc_final: 0.7065 (t0) outliers start: 20 outliers final: 10 residues processed: 112 average time/residue: 0.6545 time to fit residues: 123.0570 Evaluate side-chains 106 residues out of total 2892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 95 time to evaluate : 2.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 725 GLU Chi-restraints excluded: chain B residue 1050 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 265 optimal weight: 3.9990 chunk 181 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 237 optimal weight: 2.9990 chunk 131 optimal weight: 0.9980 chunk 272 optimal weight: 2.9990 chunk 220 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 162 optimal weight: 3.9990 chunk 286 optimal weight: 2.9990 chunk 80 optimal weight: 7.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1101 HIS ** C 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 556 ASN C1101 HIS ** B 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1101 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.1460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.088 27576 Z= 0.433 Angle : 0.594 15.009 37524 Z= 0.306 Chirality : 0.064 1.817 4395 Planarity : 0.004 0.053 4776 Dihedral : 8.397 115.500 4963 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 0.80 % Allowed : 5.50 % Favored : 93.71 % Cbeta Deviations : 0.06 % 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: -0.99 (0.14), residues: 3297 helix: 0.91 (0.20), residues: 768 sheet: -0.41 (0.18), residues: 729 loop : -1.49 (0.13), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 152 HIS 0.009 0.001 HIS B 146 PHE 0.022 0.001 PHE B 318 TYR 0.021 0.002 TYR A 904 ARG 0.004 0.000 ARG C 408 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6594 Ramachandran restraints generated. 3297 Oldfield, 0 Emsley, 3297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6594 Ramachandran restraints generated. 3297 Oldfield, 0 Emsley, 3297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 2892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 94 time to evaluate : 3.033 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 VAL cc_start: 0.7530 (OUTLIER) cc_final: 0.7183 (t) REVERT: A 170 TYR cc_start: 0.7584 (t80) cc_final: 0.7331 (t80) REVERT: A 881 THR cc_start: 0.8426 (m) cc_final: 0.8217 (m) REVERT: B 398 ASP cc_start: 0.8519 (OUTLIER) cc_final: 0.8294 (m-30) outliers start: 23 outliers final: 14 residues processed: 112 average time/residue: 0.6443 time to fit residues: 122.3523 Evaluate side-chains 108 residues out of total 2892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 92 time to evaluate : 3.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 725 GLU Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 1050 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 107 optimal weight: 0.9980 chunk 287 optimal weight: 3.9990 chunk 63 optimal weight: 0.9990 chunk 187 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 319 optimal weight: 1.9990 chunk 265 optimal weight: 3.9990 chunk 147 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 167 optimal weight: 2.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 556 ASN ** B 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.1510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 27576 Z= 0.266 Angle : 0.546 14.452 37524 Z= 0.281 Chirality : 0.062 1.809 4395 Planarity : 0.003 0.042 4776 Dihedral : 8.172 114.414 4962 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 0.76 % Allowed : 6.02 % Favored : 93.22 % Cbeta Deviations : 0.06 % 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: -0.94 (0.14), residues: 3297 helix: 0.99 (0.20), residues: 765 sheet: -0.48 (0.19), residues: 705 loop : -1.43 (0.13), residues: 1827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 152 HIS 0.010 0.001 HIS B 146 PHE 0.022 0.001 PHE B 318 TYR 0.017 0.001 TYR A 904 ARG 0.002 0.000 ARG C 403 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6594 Ramachandran restraints generated. 3297 Oldfield, 0 Emsley, 3297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6594 Ramachandran restraints generated. 3297 Oldfield, 0 Emsley, 3297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 2892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 90 time to evaluate : 3.039 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 VAL cc_start: 0.7485 (OUTLIER) cc_final: 0.7136 (t) REVERT: A 170 TYR cc_start: 0.7528 (t80) cc_final: 0.7295 (t80) REVERT: A 881 THR cc_start: 0.8455 (m) cc_final: 0.8253 (m) REVERT: C 170 TYR cc_start: 0.6985 (t80) cc_final: 0.6735 (t80) outliers start: 22 outliers final: 13 residues processed: 107 average time/residue: 0.6649 time to fit residues: 119.7539 Evaluate side-chains 104 residues out of total 2892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 90 time to evaluate : 3.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 1050 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 307 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 181 optimal weight: 1.9990 chunk 233 optimal weight: 5.9990 chunk 180 optimal weight: 1.9990 chunk 268 optimal weight: 0.6980 chunk 178 optimal weight: 2.9990 chunk 318 optimal weight: 1.9990 chunk 199 optimal weight: 2.9990 chunk 193 optimal weight: 0.7980 chunk 146 optimal weight: 0.6980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 556 ASN ** B 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.1570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 27576 Z= 0.255 Angle : 0.544 14.412 37524 Z= 0.279 Chirality : 0.062 1.808 4395 Planarity : 0.003 0.037 4776 Dihedral : 7.940 113.461 4959 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 0.62 % Allowed : 6.26 % Favored : 93.12 % Cbeta Deviations : 0.06 % 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: -0.86 (0.14), residues: 3297 helix: 1.05 (0.20), residues: 765 sheet: -0.43 (0.18), residues: 711 loop : -1.37 (0.13), residues: 1821 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 152 HIS 0.009 0.001 HIS B 146 PHE 0.029 0.001 PHE B 318 TYR 0.019 0.001 TYR A 904 ARG 0.002 0.000 ARG C 102 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6594 Ramachandran restraints generated. 3297 Oldfield, 0 Emsley, 3297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6594 Ramachandran restraints generated. 3297 Oldfield, 0 Emsley, 3297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 2892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 92 time to evaluate : 3.076 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 VAL cc_start: 0.7445 (OUTLIER) cc_final: 0.7091 (t) REVERT: A 170 TYR cc_start: 0.7555 (t80) cc_final: 0.7342 (t80) REVERT: A 881 THR cc_start: 0.8450 (m) cc_final: 0.8248 (m) outliers start: 18 outliers final: 14 residues processed: 106 average time/residue: 0.6671 time to fit residues: 119.4394 Evaluate side-chains 105 residues out of total 2892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 90 time to evaluate : 2.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 1050 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 196 optimal weight: 1.9990 chunk 127 optimal weight: 1.9990 chunk 189 optimal weight: 3.9990 chunk 95 optimal weight: 0.5980 chunk 62 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 202 optimal weight: 1.9990 chunk 216 optimal weight: 0.2980 chunk 157 optimal weight: 0.0970 chunk 29 optimal weight: 2.9990 chunk 250 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 556 ASN ** B 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 27576 Z= 0.220 Angle : 0.529 14.198 37524 Z= 0.271 Chirality : 0.062 1.804 4395 Planarity : 0.003 0.032 4776 Dihedral : 7.781 112.796 4959 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 0.59 % Allowed : 6.60 % Favored : 92.81 % Cbeta Deviations : 0.06 % 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: -0.80 (0.14), residues: 3297 helix: 1.12 (0.20), residues: 765 sheet: -0.41 (0.18), residues: 711 loop : -1.33 (0.14), residues: 1821 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 436 HIS 0.008 0.001 HIS B 146 PHE 0.030 0.001 PHE A 318 TYR 0.014 0.001 TYR A 904 ARG 0.002 0.000 ARG C 102 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6594 Ramachandran restraints generated. 3297 Oldfield, 0 Emsley, 3297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6594 Ramachandran restraints generated. 3297 Oldfield, 0 Emsley, 3297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 2892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 96 time to evaluate : 3.098 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 VAL cc_start: 0.7418 (OUTLIER) cc_final: 0.7066 (t) REVERT: A 881 THR cc_start: 0.8449 (m) cc_final: 0.8248 (m) REVERT: C 111 ASP cc_start: 0.7309 (t70) cc_final: 0.7086 (t0) outliers start: 17 outliers final: 14 residues processed: 110 average time/residue: 0.7525 time to fit residues: 135.9018 Evaluate side-chains 109 residues out of total 2892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 94 time to evaluate : 3.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 1050 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 289 optimal weight: 0.9980 chunk 304 optimal weight: 2.9990 chunk 278 optimal weight: 0.7980 chunk 296 optimal weight: 0.6980 chunk 178 optimal weight: 2.9990 chunk 129 optimal weight: 9.9990 chunk 232 optimal weight: 0.7980 chunk 90 optimal weight: 4.9990 chunk 267 optimal weight: 0.8980 chunk 280 optimal weight: 0.8980 chunk 295 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 556 ASN ** B 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 146 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.1646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 27576 Z= 0.187 Angle : 0.518 14.028 37524 Z= 0.265 Chirality : 0.062 1.802 4395 Planarity : 0.003 0.042 4776 Dihedral : 7.611 111.318 4959 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 2.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 0.55 % Allowed : 6.67 % Favored : 92.77 % Cbeta Deviations : 0.06 % 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: -0.71 (0.14), residues: 3297 helix: 1.20 (0.20), residues: 765 sheet: -0.37 (0.19), residues: 711 loop : -1.27 (0.14), residues: 1821 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 436 HIS 0.007 0.001 HIS B 146 PHE 0.034 0.001 PHE A 318 TYR 0.013 0.001 TYR A 904 ARG 0.003 0.000 ARG C 346 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6594 Ramachandran restraints generated. 3297 Oldfield, 0 Emsley, 3297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6594 Ramachandran restraints generated. 3297 Oldfield, 0 Emsley, 3297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 2892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 97 time to evaluate : 3.051 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 VAL cc_start: 0.7382 (OUTLIER) cc_final: 0.7021 (t) REVERT: C 111 ASP cc_start: 0.7246 (t70) cc_final: 0.7031 (t0) outliers start: 16 outliers final: 13 residues processed: 111 average time/residue: 0.6837 time to fit residues: 128.3442 Evaluate side-chains 105 residues out of total 2892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 91 time to evaluate : 3.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 1050 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 194 optimal weight: 1.9990 chunk 313 optimal weight: 1.9990 chunk 191 optimal weight: 2.9990 chunk 148 optimal weight: 1.9990 chunk 217 optimal weight: 0.9990 chunk 328 optimal weight: 0.6980 chunk 302 optimal weight: 1.9990 chunk 261 optimal weight: 0.9980 chunk 27 optimal weight: 0.6980 chunk 202 optimal weight: 1.9990 chunk 160 optimal weight: 0.0980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 556 ASN ** B 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.1710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 27576 Z= 0.179 Angle : 0.512 13.859 37524 Z= 0.262 Chirality : 0.062 1.798 4395 Planarity : 0.003 0.027 4776 Dihedral : 7.457 110.798 4959 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 0.55 % Allowed : 6.60 % Favored : 92.84 % Cbeta Deviations : 0.06 % 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: -0.65 (0.14), residues: 3297 helix: 1.26 (0.20), residues: 768 sheet: -0.30 (0.19), residues: 726 loop : -1.27 (0.14), residues: 1803 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 152 HIS 0.004 0.001 HIS B1048 PHE 0.023 0.001 PHE B 318 TYR 0.013 0.001 TYR C 365 ARG 0.002 0.000 ARG C 346 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6594 Ramachandran restraints generated. 3297 Oldfield, 0 Emsley, 3297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6594 Ramachandran restraints generated. 3297 Oldfield, 0 Emsley, 3297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 2892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 94 time to evaluate : 3.035 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 VAL cc_start: 0.7430 (OUTLIER) cc_final: 0.7070 (t) REVERT: B 900 MET cc_start: 0.8419 (mtp) cc_final: 0.8210 (mtp) outliers start: 16 outliers final: 14 residues processed: 108 average time/residue: 0.7608 time to fit residues: 139.0242 Evaluate side-chains 107 residues out of total 2892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 92 time to evaluate : 3.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 1050 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 207 optimal weight: 0.9980 chunk 278 optimal weight: 0.4980 chunk 80 optimal weight: 5.9990 chunk 241 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 262 optimal weight: 2.9990 chunk 109 optimal weight: 4.9990 chunk 269 optimal weight: 0.1980 chunk 33 optimal weight: 0.7980 chunk 48 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 556 ASN ** B 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.096593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.069690 restraints weight = 149058.303| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 2.80 r_work: 0.2813 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2668 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 27576 Z= 0.165 Angle : 0.504 13.762 37524 Z= 0.258 Chirality : 0.062 1.797 4395 Planarity : 0.003 0.029 4776 Dihedral : 7.319 109.213 4959 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 2.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 0.55 % Allowed : 6.67 % Favored : 92.77 % Cbeta Deviations : 0.06 % 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: -0.60 (0.14), residues: 3297 helix: 1.31 (0.20), residues: 768 sheet: -0.26 (0.19), residues: 726 loop : -1.23 (0.14), residues: 1803 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 436 HIS 0.003 0.001 HIS B1048 PHE 0.025 0.001 PHE A 318 TYR 0.012 0.001 TYR C 365 ARG 0.002 0.000 ARG C 346 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6356.83 seconds wall clock time: 112 minutes 13.61 seconds (6733.61 seconds total)