Starting phenix.real_space_refine on Sun Jun 22 05:33:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9eli_48150/06_2025/9eli_48150.cif Found real_map, /net/cci-nas-00/data/ceres_data/9eli_48150/06_2025/9eli_48150.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9eli_48150/06_2025/9eli_48150.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9eli_48150/06_2025/9eli_48150.map" model { file = "/net/cci-nas-00/data/ceres_data/9eli_48150/06_2025/9eli_48150.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9eli_48150/06_2025/9eli_48150.cif" } resolution = 2.82 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= 0.027 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 111 5.16 5 C 16275 2.51 5 N 4146 2.21 5 O 4977 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 25509 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 8243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1051, 8243 Classifications: {'peptide': 1051} Link IDs: {'PTRANS': 56, 'TRANS': 994} Chain breaks: 6 Chain: "B" Number of atoms: 8243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1051, 8243 Classifications: {'peptide': 1051} Link IDs: {'PTRANS': 56, 'TRANS': 994} Chain breaks: 6 Chain: "C" Number of atoms: 8243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1051, 8243 Classifications: {'peptide': 1051} Link IDs: {'PTRANS': 56, 'TRANS': 994} Chain breaks: 6 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: "R" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "B" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "C" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 17.56, per 1000 atoms: 0.69 Number of scatterers: 25509 At special positions: 0 Unit cell: (135.702, 135.702, 185.962, 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 111 16.00 O 4977 8.00 N 4146 7.00 C 16275 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 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=1.36 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.02 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 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=1.36 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.02 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 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=1.36 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=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " 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 H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " 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 M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " NAG-ASN " NAG A1301 " - " ASN A 616 " " NAG A1302 " - " ASN A 709 " " NAG A1303 " - " ASN A1074 " " NAG A1304 " - " ASN A 354 " " NAG A1305 " - " ASN A 343 " " NAG A1307 " - " ASN A 30 " " NAG B1301 " - " ASN B 616 " " NAG B1302 " - " ASN B 709 " " NAG B1303 " - " ASN B1074 " " NAG B1304 " - " ASN B 354 " " NAG B1305 " - " ASN B 343 " " NAG B1307 " - " ASN B 30 " " NAG C1301 " - " ASN C 616 " " NAG C1302 " - " ASN C 709 " " NAG C1303 " - " ASN C1074 " " NAG C1304 " - " ASN C 354 " " NAG C1305 " - " ASN C 343 " " NAG C1307 " - " ASN C 30 " " NAG D 1 " - " ASN A 717 " " NAG E 1 " - " ASN A1098 " " NAG F 1 " - " ASN A1134 " " NAG G 1 " - " ASN A 282 " " NAG H 1 " - " ASN A 801 " " NAG I 1 " - " ASN B 717 " " NAG J 1 " - " ASN B1098 " " NAG K 1 " - " ASN B1134 " " NAG L 1 " - " ASN B 282 " " NAG M 1 " - " ASN B 801 " " NAG N 1 " - " ASN C 717 " " NAG O 1 " - " ASN C1098 " " NAG P 1 " - " ASN C1134 " " NAG Q 1 " - " ASN C 282 " " NAG R 1 " - " ASN C 801 " NAG-THR " NAG A1306 " - " THR A 236 " " NAG B1306 " - " THR B 236 " " NAG C1306 " - " THR C 236 " Time building additional restraints: 7.05 Conformation dependent library (CDL) restraints added in 3.5 seconds 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5910 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 39 sheets defined 26.2% alpha, 27.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.79 Creating SS restraints... Processing helix chain 'A' and resid 69 through 72 Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 365 through 372 removed outlier: 3.555A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.101A pdb=" N SER A 408 " --> pdb=" O ASN A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 616 through 626 Processing helix chain 'A' and resid 737 through 742 Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.825A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.573A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 Processing helix chain 'A' and resid 897 through 910 Processing helix chain 'A' and resid 912 through 919 removed outlier: 3.921A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 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 1032 removed outlier: 4.671A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1139 through 1150 removed outlier: 3.856A pdb=" N LEU A1143 " --> pdb=" O ASP A1139 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 72 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 365 through 372 removed outlier: 3.556A pdb=" N TYR B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.100A pdb=" N SER B 408 " --> pdb=" O ASN B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 616 through 626 Processing helix chain 'B' and resid 737 through 742 Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.825A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.573A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 Processing helix chain 'B' and resid 897 through 910 Processing helix chain 'B' and resid 912 through 919 removed outlier: 3.921A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 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 1032 removed outlier: 4.671A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1139 through 1150 removed outlier: 3.856A pdb=" N LEU B1143 " --> pdb=" O ASP B1139 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 72 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 372 removed outlier: 3.555A pdb=" N TYR C 369 " --> pdb=" O TYR C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.100A pdb=" N SER C 408 " --> pdb=" O ASN C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 616 through 626 Processing helix chain 'C' and resid 737 through 742 Processing helix chain 'C' and resid 746 through 755 removed outlier: 3.825A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.573A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 Processing helix chain 'C' and resid 897 through 910 Processing helix chain 'C' and resid 912 through 919 removed outlier: 3.921A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 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 1032 removed outlier: 4.671A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1139 through 1150 removed outlier: 3.857A pdb=" N LEU C1143 " --> pdb=" O ASP C1139 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 32 removed outlier: 4.232A pdb=" N PHE A 32 " --> pdb=" O SER A 60 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N SER A 60 " --> pdb=" O PHE A 32 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 4.057A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 163 through 172 removed outlier: 7.055A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.973A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 324 through 328 removed outlier: 4.391A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 354 through 357 Processing sheet with id=AA7, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA8, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.383A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 701 through 704 Processing sheet with id=AB1, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.927A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.927A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.365A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 787 through 790 removed outlier: 6.070A pdb=" N ILE A 788 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.524A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 29 through 32 removed outlier: 4.232A pdb=" N PHE B 32 " --> pdb=" O SER B 60 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N SER B 60 " --> pdb=" O PHE B 32 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 48 through 55 removed outlier: 4.056A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 163 through 172 removed outlier: 7.054A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.972A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 324 through 328 removed outlier: 4.392A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 354 through 357 Processing sheet with id=AC3, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC4, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.384A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.927A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.927A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.366A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 787 through 790 removed outlier: 6.070A pdb=" N ILE B 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.524A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 29 through 32 removed outlier: 4.232A pdb=" N PHE C 32 " --> pdb=" O SER C 60 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N SER C 60 " --> pdb=" O PHE C 32 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 48 through 55 removed outlier: 4.057A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 163 through 172 removed outlier: 7.055A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.973A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 324 through 328 removed outlier: 4.392A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 354 through 357 Processing sheet with id=AD7, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AD8, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.383A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.927A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.927A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.365A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.524A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 1023 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: 12.44 Time building geometry restraints manager: 8.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.53: 24289 1.53 - 1.85: 1805 1.85 - 2.17: 0 2.17 - 2.49: 0 2.49 - 2.81: 3 Bond restraints: 26097 Sorted by residual: bond pdb=" C LYS C 679 " pdb=" N SER C 689 " ideal model delta sigma weight residual 1.332 2.808 -1.476 1.40e-02 5.10e+03 1.11e+04 bond pdb=" C LYS B 679 " pdb=" N SER B 689 " ideal model delta sigma weight residual 1.332 2.808 -1.476 1.40e-02 5.10e+03 1.11e+04 bond pdb=" C LYS A 679 " pdb=" N SER A 689 " ideal model delta sigma weight residual 1.332 2.808 -1.476 1.40e-02 5.10e+03 1.11e+04 bond pdb=" C1 NAG B1307 " pdb=" O5 NAG B1307 " ideal model delta sigma weight residual 1.406 1.519 -0.113 2.00e-02 2.50e+03 3.17e+01 bond pdb=" C1 NAG A1307 " pdb=" O5 NAG A1307 " ideal model delta sigma weight residual 1.406 1.519 -0.113 2.00e-02 2.50e+03 3.17e+01 ... (remaining 26092 not shown) Histogram of bond angle deviations from ideal: 0.00 - 11.98: 35484 11.98 - 23.96: 9 23.96 - 35.94: 3 35.94 - 47.92: 0 47.92 - 59.90: 3 Bond angle restraints: 35499 Sorted by residual: angle pdb=" O LYS C 679 " pdb=" C LYS C 679 " pdb=" N SER C 689 " ideal model delta sigma weight residual 122.59 62.69 59.90 1.33e+00 5.65e-01 2.03e+03 angle pdb=" O LYS B 679 " pdb=" C LYS B 679 " pdb=" N SER B 689 " ideal model delta sigma weight residual 122.59 62.72 59.87 1.33e+00 5.65e-01 2.03e+03 angle pdb=" O LYS A 679 " pdb=" C LYS A 679 " pdb=" N SER A 689 " ideal model delta sigma weight residual 122.59 62.72 59.87 1.33e+00 5.65e-01 2.03e+03 angle pdb=" C LYS C 679 " pdb=" N SER C 689 " pdb=" CA SER C 689 " ideal model delta sigma weight residual 121.54 148.49 -26.95 1.91e+00 2.74e-01 1.99e+02 angle pdb=" C LYS A 679 " pdb=" N SER A 689 " pdb=" CA SER A 689 " ideal model delta sigma weight residual 121.54 148.48 -26.94 1.91e+00 2.74e-01 1.99e+02 ... (remaining 35494 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 14950 17.92 - 35.84: 1007 35.84 - 53.76: 246 53.76 - 71.68: 51 71.68 - 89.60: 39 Dihedral angle restraints: 16293 sinusoidal: 7110 harmonic: 9183 Sorted by residual: dihedral pdb=" CA ALA B 372 " pdb=" C ALA B 372 " pdb=" N PRO B 373 " pdb=" CA PRO B 373 " ideal model delta harmonic sigma weight residual 180.00 146.94 33.06 0 5.00e+00 4.00e-02 4.37e+01 dihedral pdb=" CA ALA A 372 " pdb=" C ALA A 372 " pdb=" N PRO A 373 " pdb=" CA PRO A 373 " ideal model delta harmonic sigma weight residual 180.00 146.98 33.02 0 5.00e+00 4.00e-02 4.36e+01 dihedral pdb=" CA ALA C 372 " pdb=" C ALA C 372 " pdb=" N PRO C 373 " pdb=" CA PRO C 373 " ideal model delta harmonic sigma weight residual 180.00 147.00 33.00 0 5.00e+00 4.00e-02 4.36e+01 ... (remaining 16290 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 3024 0.053 - 0.106: 849 0.106 - 0.158: 264 0.158 - 0.211: 27 0.211 - 0.264: 15 Chirality restraints: 4179 Sorted by residual: chirality pdb=" CG LEU A 878 " pdb=" CB LEU A 878 " pdb=" CD1 LEU A 878 " pdb=" CD2 LEU A 878 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.74e+00 chirality pdb=" CG LEU B 878 " pdb=" CB LEU B 878 " pdb=" CD1 LEU B 878 " pdb=" CD2 LEU B 878 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" CG LEU C 878 " pdb=" CB LEU C 878 " pdb=" CD1 LEU C 878 " pdb=" CD2 LEU C 878 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.73e+00 ... (remaining 4176 not shown) Planarity restraints: 4533 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS B 679 " 0.189 2.00e-02 2.50e+03 2.84e-01 8.05e+02 pdb=" C LYS B 679 " -0.449 2.00e-02 2.50e+03 pdb=" O LYS B 679 " 0.289 2.00e-02 2.50e+03 pdb=" N SER B 689 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS C 679 " -0.189 2.00e-02 2.50e+03 2.84e-01 8.05e+02 pdb=" C LYS C 679 " 0.449 2.00e-02 2.50e+03 pdb=" O LYS C 679 " -0.289 2.00e-02 2.50e+03 pdb=" N SER C 689 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 679 " -0.189 2.00e-02 2.50e+03 2.84e-01 8.04e+02 pdb=" C LYS A 679 " 0.449 2.00e-02 2.50e+03 pdb=" O LYS A 679 " -0.289 2.00e-02 2.50e+03 pdb=" N SER A 689 " 0.029 2.00e-02 2.50e+03 ... (remaining 4530 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 168 2.63 - 3.20: 22573 3.20 - 3.77: 38022 3.77 - 4.33: 54740 4.33 - 4.90: 90477 Nonbonded interactions: 205980 Sorted by model distance: nonbonded pdb=" O ASN C 331 " pdb=" OD1 ASN C 331 " model vdw 2.066 3.040 nonbonded pdb=" O ASN B 331 " pdb=" OD1 ASN B 331 " model vdw 2.068 3.040 nonbonded pdb=" O ASN A 331 " pdb=" OD1 ASN A 331 " model vdw 2.068 3.040 nonbonded pdb=" O CYS C 851 " pdb=" CD2 PHE C 855 " model vdw 2.222 3.340 nonbonded pdb=" O CYS A 851 " pdb=" CD2 PHE A 855 " model vdw 2.223 3.340 ... (remaining 205975 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'I' selection = chain 'M' selection = chain 'N' selection = chain 'R' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'J' selection = chain 'K' selection = chain 'L' 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: 10.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.200 Check model and map are aligned: 0.180 Set scattering table: 0.250 Process input model: 64.280 Find NCS groups from input model: 1.300 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:16.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 94.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 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 : 0.019 1.476 26190 Z= 1.223 Angle : 1.303 59.903 35739 Z= 0.737 Chirality : 0.056 0.264 4179 Planarity : 0.011 0.284 4500 Dihedral : 13.854 89.603 10275 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 2.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 0.00 % Allowed : 9.74 % Favored : 90.26 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.79 % 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: 0.03 (0.14), residues: 3105 helix: 2.01 (0.20), residues: 693 sheet: -0.17 (0.20), residues: 561 loop : -0.69 (0.13), residues: 1851 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 436 HIS 0.003 0.001 HIS B 954 PHE 0.053 0.003 PHE A 92 TYR 0.031 0.002 TYR C 200 ARG 0.036 0.002 ARG A 567 Details of bonding type rmsd link_NAG-ASN : bond 0.00206 ( 33) link_NAG-ASN : angle 2.86143 ( 99) link_BETA1-4 : bond 0.00663 ( 21) link_BETA1-4 : angle 3.51278 ( 63) hydrogen bonds : bond 0.12499 ( 1008) hydrogen bonds : angle 6.94393 ( 2826) SS BOND : bond 0.19363 ( 36) SS BOND : angle 10.81232 ( 72) link_NAG-THR : bond 0.00598 ( 3) link_NAG-THR : angle 4.36338 ( 6) covalent geometry : bond 0.01724 (26097) covalent geometry : angle 1.19361 (35499) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 238 time to evaluate : 3.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 PRO cc_start: 0.6906 (Cg_endo) cc_final: 0.6068 (Cg_endo) REVERT: A 177 MET cc_start: 0.2420 (ptp) cc_final: 0.1902 (pp-130) REVERT: A 205 SER cc_start: 0.8905 (p) cc_final: 0.8437 (t) REVERT: B 85 PRO cc_start: 0.6964 (Cg_endo) cc_final: 0.5988 (Cg_endo) REVERT: B 177 MET cc_start: 0.2603 (ptp) cc_final: 0.1766 (pp-130) REVERT: B 205 SER cc_start: 0.8939 (p) cc_final: 0.8447 (t) REVERT: B 321 GLN cc_start: 0.8551 (mm-40) cc_final: 0.8341 (mm-40) REVERT: B 869 MET cc_start: 0.9150 (mtt) cc_final: 0.8882 (mtt) REVERT: C 177 MET cc_start: 0.2519 (ptp) cc_final: 0.1853 (pp-130) REVERT: C 205 SER cc_start: 0.8918 (p) cc_final: 0.8458 (t) REVERT: C 321 GLN cc_start: 0.8563 (mm-40) cc_final: 0.8352 (mm-40) outliers start: 0 outliers final: 0 residues processed: 238 average time/residue: 1.3316 time to fit residues: 385.4562 Evaluate side-chains 198 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 198 time to evaluate : 3.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 265 optimal weight: 2.9990 chunk 238 optimal weight: 5.9990 chunk 132 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 161 optimal weight: 0.7980 chunk 127 optimal weight: 0.6980 chunk 246 optimal weight: 6.9990 chunk 95 optimal weight: 0.5980 chunk 150 optimal weight: 0.0770 chunk 183 optimal weight: 2.9990 chunk 286 optimal weight: 0.5980 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 751 ASN B 751 ASN C 751 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.205504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.167135 restraints weight = 27523.263| |-----------------------------------------------------------------------------| r_work (start): 0.3866 rms_B_bonded: 1.57 r_work: 0.3390 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3247 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.1079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 26190 Z= 0.130 Angle : 0.634 10.844 35739 Z= 0.314 Chirality : 0.046 0.225 4179 Planarity : 0.004 0.039 4500 Dihedral : 6.118 46.788 4557 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.66 % Allowed : 9.05 % Favored : 89.29 % 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: 0.24 (0.14), residues: 3111 helix: 2.20 (0.19), residues: 726 sheet: 0.23 (0.20), residues: 588 loop : -0.74 (0.13), residues: 1797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 633 HIS 0.003 0.001 HIS C1058 PHE 0.018 0.001 PHE A1148 TYR 0.023 0.001 TYR A 170 ARG 0.007 0.001 ARG A 577 Details of bonding type rmsd link_NAG-ASN : bond 0.00572 ( 33) link_NAG-ASN : angle 2.60667 ( 99) link_BETA1-4 : bond 0.00655 ( 21) link_BETA1-4 : angle 3.20249 ( 63) hydrogen bonds : bond 0.04566 ( 1008) hydrogen bonds : angle 5.53656 ( 2826) SS BOND : bond 0.00457 ( 36) SS BOND : angle 0.95232 ( 72) link_NAG-THR : bond 0.00033 ( 3) link_NAG-THR : angle 1.99126 ( 6) covalent geometry : bond 0.00283 (26097) covalent geometry : angle 0.60467 (35499) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 223 time to evaluate : 2.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 ILE cc_start: 0.7071 (OUTLIER) cc_final: 0.6868 (mt) REVERT: A 205 SER cc_start: 0.8895 (p) cc_final: 0.8558 (t) REVERT: A 913 GLN cc_start: 0.8459 (mt0) cc_final: 0.8222 (mt0) REVERT: A 1119 ASN cc_start: 0.8012 (m-40) cc_final: 0.7676 (m-40) REVERT: B 170 TYR cc_start: 0.7092 (t80) cc_final: 0.6658 (t80) REVERT: B 205 SER cc_start: 0.8884 (p) cc_final: 0.8537 (t) REVERT: C 205 SER cc_start: 0.8895 (p) cc_final: 0.8584 (t) REVERT: C 314 GLN cc_start: 0.8396 (OUTLIER) cc_final: 0.7973 (tt0) outliers start: 46 outliers final: 18 residues processed: 254 average time/residue: 0.9875 time to fit residues: 307.1554 Evaluate side-chains 203 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 183 time to evaluate : 2.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 280 ASN Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 702 GLU Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 702 GLU Chi-restraints excluded: chain C residue 723 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 226 optimal weight: 0.1980 chunk 151 optimal weight: 7.9990 chunk 57 optimal weight: 0.8980 chunk 107 optimal weight: 8.9990 chunk 42 optimal weight: 10.0000 chunk 87 optimal weight: 3.9990 chunk 196 optimal weight: 2.9990 chunk 299 optimal weight: 4.9990 chunk 260 optimal weight: 6.9990 chunk 25 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 GLN B 280 ASN B 544 ASN B 613 GLN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN C 804 GLN C 935 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.200516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.161493 restraints weight = 27493.208| |-----------------------------------------------------------------------------| r_work (start): 0.3807 rms_B_bonded: 1.58 r_work: 0.3530 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3464 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.1729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 26190 Z= 0.221 Angle : 0.680 9.918 35739 Z= 0.340 Chirality : 0.048 0.213 4179 Planarity : 0.005 0.047 4500 Dihedral : 6.020 41.965 4557 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.31 % Allowed : 9.49 % Favored : 88.20 % 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: 0.11 (0.14), residues: 3111 helix: 1.85 (0.19), residues: 735 sheet: 0.35 (0.19), residues: 627 loop : -0.82 (0.13), residues: 1749 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 633 HIS 0.008 0.001 HIS B1058 PHE 0.019 0.002 PHE B 541 TYR 0.021 0.002 TYR A1067 ARG 0.005 0.001 ARG A 815 Details of bonding type rmsd link_NAG-ASN : bond 0.00420 ( 33) link_NAG-ASN : angle 2.85536 ( 99) link_BETA1-4 : bond 0.00500 ( 21) link_BETA1-4 : angle 3.13890 ( 63) hydrogen bonds : bond 0.05270 ( 1008) hydrogen bonds : angle 5.47298 ( 2826) SS BOND : bond 0.00415 ( 36) SS BOND : angle 1.67809 ( 72) link_NAG-THR : bond 0.00445 ( 3) link_NAG-THR : angle 2.17987 ( 6) covalent geometry : bond 0.00533 (26097) covalent geometry : angle 0.64738 (35499) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 198 time to evaluate : 2.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 314 GLN cc_start: 0.8182 (OUTLIER) cc_final: 0.7660 (tt0) REVERT: A 646 ARG cc_start: 0.8382 (mtp85) cc_final: 0.7865 (mtp-110) REVERT: B 177 MET cc_start: 0.2573 (ptp) cc_final: 0.0618 (pp-130) REVERT: B 304 LYS cc_start: 0.8683 (OUTLIER) cc_final: 0.7516 (mptp) REVERT: B 387 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.8285 (mt) REVERT: B 675 GLN cc_start: 0.7320 (OUTLIER) cc_final: 0.5988 (mp10) REVERT: C 314 GLN cc_start: 0.8169 (OUTLIER) cc_final: 0.7667 (tt0) REVERT: C 675 GLN cc_start: 0.7346 (OUTLIER) cc_final: 0.6067 (mp10) outliers start: 64 outliers final: 31 residues processed: 238 average time/residue: 0.8693 time to fit residues: 258.6180 Evaluate side-chains 220 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 183 time to evaluate : 2.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 304 LYS Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 738 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 282 optimal weight: 0.7980 chunk 98 optimal weight: 0.9980 chunk 241 optimal weight: 0.0170 chunk 168 optimal weight: 1.9990 chunk 194 optimal weight: 1.9990 chunk 221 optimal weight: 7.9990 chunk 43 optimal weight: 6.9990 chunk 30 optimal weight: 0.9990 chunk 304 optimal weight: 0.5980 chunk 178 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 overall best weight: 0.6818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 603 ASN A1119 ASN B 207 HIS B 751 ASN B 804 GLN B 935 GLN C 207 HIS C 751 ASN C1119 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.202696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.164674 restraints weight = 27867.511| |-----------------------------------------------------------------------------| r_work (start): 0.3841 rms_B_bonded: 1.59 r_work: 0.3541 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3414 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 26190 Z= 0.125 Angle : 0.584 10.043 35739 Z= 0.291 Chirality : 0.044 0.206 4179 Planarity : 0.004 0.043 4500 Dihedral : 5.591 40.629 4557 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.91 % Allowed : 10.61 % Favored : 87.48 % 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: 0.24 (0.14), residues: 3111 helix: 2.10 (0.19), residues: 735 sheet: 0.48 (0.19), residues: 627 loop : -0.83 (0.14), residues: 1749 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 633 HIS 0.003 0.001 HIS B1058 PHE 0.014 0.001 PHE B 371 TYR 0.018 0.001 TYR C 170 ARG 0.003 0.000 ARG C 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00329 ( 33) link_NAG-ASN : angle 2.43456 ( 99) link_BETA1-4 : bond 0.00488 ( 21) link_BETA1-4 : angle 2.88942 ( 63) hydrogen bonds : bond 0.04291 ( 1008) hydrogen bonds : angle 5.17912 ( 2826) SS BOND : bond 0.00222 ( 36) SS BOND : angle 1.62404 ( 72) link_NAG-THR : bond 0.00467 ( 3) link_NAG-THR : angle 1.85191 ( 6) covalent geometry : bond 0.00282 (26097) covalent geometry : angle 0.55279 (35499) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 193 time to evaluate : 4.028 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 THR cc_start: 0.5254 (OUTLIER) cc_final: 0.4777 (p) REVERT: A 153 MET cc_start: 0.1446 (OUTLIER) cc_final: 0.0528 (tpt) REVERT: A 203 ILE cc_start: 0.8467 (mp) cc_final: 0.8092 (mm) REVERT: A 646 ARG cc_start: 0.8432 (mtp85) cc_final: 0.7878 (mtp-110) REVERT: A 913 GLN cc_start: 0.8114 (mt0) cc_final: 0.7863 (mt0) REVERT: B 177 MET cc_start: 0.2597 (ptp) cc_final: 0.0602 (pp-130) REVERT: B 304 LYS cc_start: 0.8577 (OUTLIER) cc_final: 0.7283 (mptp) REVERT: B 675 GLN cc_start: 0.7366 (OUTLIER) cc_final: 0.6131 (mp10) REVERT: B 1119 ASN cc_start: 0.8140 (m-40) cc_final: 0.7912 (m110) REVERT: C 304 LYS cc_start: 0.8553 (OUTLIER) cc_final: 0.7947 (mptp) REVERT: C 646 ARG cc_start: 0.8427 (OUTLIER) cc_final: 0.8173 (mtp85) REVERT: C 675 GLN cc_start: 0.7360 (OUTLIER) cc_final: 0.6158 (mp10) outliers start: 53 outliers final: 24 residues processed: 231 average time/residue: 1.2186 time to fit residues: 358.8359 Evaluate side-chains 202 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 171 time to evaluate : 2.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 304 LYS Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 738 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 87 optimal weight: 4.9990 chunk 195 optimal weight: 2.9990 chunk 34 optimal weight: 10.0000 chunk 163 optimal weight: 4.9990 chunk 248 optimal weight: 1.9990 chunk 242 optimal weight: 7.9990 chunk 210 optimal weight: 9.9990 chunk 290 optimal weight: 0.9990 chunk 276 optimal weight: 0.5980 chunk 278 optimal weight: 1.9990 chunk 74 optimal weight: 5.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1119 ASN ** B 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS B 280 ASN ** C 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C 280 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.199099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.158331 restraints weight = 27692.731| |-----------------------------------------------------------------------------| r_work (start): 0.3775 rms_B_bonded: 1.68 r_work: 0.3472 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3314 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 26190 Z= 0.215 Angle : 0.650 10.064 35739 Z= 0.325 Chirality : 0.047 0.217 4179 Planarity : 0.004 0.046 4500 Dihedral : 5.731 39.514 4557 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.63 % Allowed : 10.64 % Favored : 86.72 % 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: 0.15 (0.14), residues: 3111 helix: 1.91 (0.18), residues: 735 sheet: 0.44 (0.20), residues: 621 loop : -0.84 (0.14), residues: 1755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 633 HIS 0.007 0.001 HIS C1058 PHE 0.018 0.002 PHE A 898 TYR 0.021 0.002 TYR A1067 ARG 0.004 0.001 ARG A 815 Details of bonding type rmsd link_NAG-ASN : bond 0.00335 ( 33) link_NAG-ASN : angle 2.65677 ( 99) link_BETA1-4 : bond 0.00418 ( 21) link_BETA1-4 : angle 2.93835 ( 63) hydrogen bonds : bond 0.05104 ( 1008) hydrogen bonds : angle 5.33003 ( 2826) SS BOND : bond 0.00344 ( 36) SS BOND : angle 1.70955 ( 72) link_NAG-THR : bond 0.00699 ( 3) link_NAG-THR : angle 2.23945 ( 6) covalent geometry : bond 0.00523 (26097) covalent geometry : angle 0.61965 (35499) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 193 time to evaluate : 3.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 THR cc_start: 0.5449 (OUTLIER) cc_final: 0.4995 (p) REVERT: A 646 ARG cc_start: 0.8528 (mtp85) cc_final: 0.7856 (mtp180) REVERT: A 657 ASN cc_start: 0.8481 (m-40) cc_final: 0.8278 (m110) REVERT: A 675 GLN cc_start: 0.7329 (OUTLIER) cc_final: 0.6001 (mp10) REVERT: B 177 MET cc_start: 0.2704 (ptp) cc_final: 0.0776 (pp-130) REVERT: B 675 GLN cc_start: 0.7502 (OUTLIER) cc_final: 0.5931 (mp10) REVERT: B 790 LYS cc_start: 0.8748 (OUTLIER) cc_final: 0.8515 (mttt) REVERT: B 1119 ASN cc_start: 0.8435 (m-40) cc_final: 0.8230 (m110) REVERT: C 304 LYS cc_start: 0.8689 (OUTLIER) cc_final: 0.8108 (mptp) REVERT: C 646 ARG cc_start: 0.8548 (OUTLIER) cc_final: 0.8277 (mtp85) REVERT: C 675 GLN cc_start: 0.7442 (OUTLIER) cc_final: 0.6133 (mp10) REVERT: C 1119 ASN cc_start: 0.8527 (m-40) cc_final: 0.8300 (m110) outliers start: 73 outliers final: 41 residues processed: 243 average time/residue: 0.9037 time to fit residues: 272.7357 Evaluate side-chains 219 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 171 time to evaluate : 2.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 790 LYS Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 994 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 162 optimal weight: 0.0770 chunk 69 optimal weight: 2.9990 chunk 217 optimal weight: 6.9990 chunk 196 optimal weight: 1.9990 chunk 212 optimal weight: 0.6980 chunk 34 optimal weight: 7.9990 chunk 240 optimal weight: 10.0000 chunk 167 optimal weight: 2.9990 chunk 294 optimal weight: 0.9980 chunk 248 optimal weight: 20.0000 chunk 121 optimal weight: 9.9990 overall best weight: 1.3542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 207 HIS A 321 GLN A 762 GLN ** B 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS B 280 ASN B 564 GLN B 955 ASN ** C 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS ** C 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 751 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.199967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.162946 restraints weight = 27572.554| |-----------------------------------------------------------------------------| r_work (start): 0.3819 rms_B_bonded: 1.56 r_work: 0.3513 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3382 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 26190 Z= 0.173 Angle : 0.602 9.571 35739 Z= 0.302 Chirality : 0.045 0.213 4179 Planarity : 0.004 0.044 4500 Dihedral : 5.585 40.425 4557 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.45 % Allowed : 11.54 % Favored : 86.00 % 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: 0.10 (0.14), residues: 3111 helix: 1.96 (0.18), residues: 735 sheet: 0.38 (0.20), residues: 597 loop : -0.89 (0.14), residues: 1779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 633 HIS 0.004 0.001 HIS C1058 PHE 0.016 0.001 PHE A 898 TYR 0.017 0.001 TYR A1067 ARG 0.003 0.000 ARG A 815 Details of bonding type rmsd link_NAG-ASN : bond 0.00301 ( 33) link_NAG-ASN : angle 2.49929 ( 99) link_BETA1-4 : bond 0.00438 ( 21) link_BETA1-4 : angle 2.81422 ( 63) hydrogen bonds : bond 0.04607 ( 1008) hydrogen bonds : angle 5.16090 ( 2826) SS BOND : bond 0.00296 ( 36) SS BOND : angle 1.61757 ( 72) link_NAG-THR : bond 0.00673 ( 3) link_NAG-THR : angle 1.84379 ( 6) covalent geometry : bond 0.00413 (26097) covalent geometry : angle 0.57242 (35499) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 181 time to evaluate : 2.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.2001 (tpt) cc_final: -0.0343 (mpm) REVERT: A 190 ARG cc_start: 0.7131 (mtt90) cc_final: 0.6836 (mtm-85) REVERT: A 646 ARG cc_start: 0.8496 (mtp85) cc_final: 0.7882 (mtp180) REVERT: A 675 GLN cc_start: 0.7356 (OUTLIER) cc_final: 0.6166 (mp10) REVERT: A 1119 ASN cc_start: 0.8299 (m-40) cc_final: 0.8082 (m110) REVERT: B 177 MET cc_start: 0.2732 (ptp) cc_final: 0.0879 (pp-130) REVERT: B 675 GLN cc_start: 0.7435 (OUTLIER) cc_final: 0.6150 (mp10) REVERT: B 1119 ASN cc_start: 0.8229 (m-40) cc_final: 0.8018 (m110) REVERT: C 153 MET cc_start: 0.2224 (tpt) cc_final: -0.0064 (mpt) REVERT: C 646 ARG cc_start: 0.8487 (OUTLIER) cc_final: 0.8204 (mtp85) REVERT: C 675 GLN cc_start: 0.7420 (OUTLIER) cc_final: 0.6241 (mp10) REVERT: C 1119 ASN cc_start: 0.8353 (m-40) cc_final: 0.8132 (m110) outliers start: 68 outliers final: 36 residues processed: 233 average time/residue: 0.8880 time to fit residues: 257.4115 Evaluate side-chains 210 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 170 time to evaluate : 2.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 994 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 214 optimal weight: 0.9980 chunk 105 optimal weight: 10.0000 chunk 169 optimal weight: 1.9990 chunk 300 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 314 optimal weight: 0.7980 chunk 33 optimal weight: 5.9990 chunk 204 optimal weight: 4.9990 chunk 11 optimal weight: 0.8980 chunk 131 optimal weight: 9.9990 chunk 218 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 207 HIS A 955 ASN A1011 GLN ** B 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS B 280 ASN ** C 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C 280 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.199272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.159244 restraints weight = 27793.500| |-----------------------------------------------------------------------------| r_work (start): 0.3763 rms_B_bonded: 1.67 r_work: 0.3309 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.2585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 26190 Z= 0.174 Angle : 0.609 9.477 35739 Z= 0.305 Chirality : 0.045 0.216 4179 Planarity : 0.004 0.044 4500 Dihedral : 5.499 38.873 4557 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.28 % Favored : 96.66 % Rotamer: Outliers : 2.42 % Allowed : 11.69 % Favored : 85.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.14), residues: 3111 helix: 1.87 (0.18), residues: 738 sheet: 0.42 (0.20), residues: 624 loop : -0.88 (0.14), residues: 1749 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 633 HIS 0.005 0.001 HIS A1058 PHE 0.017 0.002 PHE A 898 TYR 0.018 0.001 TYR A1067 ARG 0.003 0.000 ARG A 815 Details of bonding type rmsd link_NAG-ASN : bond 0.00309 ( 33) link_NAG-ASN : angle 2.47766 ( 99) link_BETA1-4 : bond 0.00410 ( 21) link_BETA1-4 : angle 2.78258 ( 63) hydrogen bonds : bond 0.04637 ( 1008) hydrogen bonds : angle 5.17494 ( 2826) SS BOND : bond 0.00339 ( 36) SS BOND : angle 1.61041 ( 72) link_NAG-THR : bond 0.00607 ( 3) link_NAG-THR : angle 1.84118 ( 6) covalent geometry : bond 0.00418 (26097) covalent geometry : angle 0.57991 (35499) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 184 time to evaluate : 2.979 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 THR cc_start: 0.5057 (OUTLIER) cc_final: 0.4534 (p) REVERT: A 153 MET cc_start: 0.1431 (tpt) cc_final: -0.0977 (mpm) REVERT: A 190 ARG cc_start: 0.7479 (mtt90) cc_final: 0.7171 (mtm-85) REVERT: A 269 TYR cc_start: 0.8409 (m-80) cc_final: 0.7907 (m-80) REVERT: A 646 ARG cc_start: 0.8535 (mtp85) cc_final: 0.7827 (mtp180) REVERT: A 675 GLN cc_start: 0.7416 (OUTLIER) cc_final: 0.6118 (mp10) REVERT: B 153 MET cc_start: 0.1368 (tpt) cc_final: -0.0564 (mpt) REVERT: B 190 ARG cc_start: 0.7600 (mtm-85) cc_final: 0.7209 (mtm110) REVERT: B 675 GLN cc_start: 0.7539 (OUTLIER) cc_final: 0.6056 (mp10) REVERT: B 790 LYS cc_start: 0.8787 (OUTLIER) cc_final: 0.8555 (mttt) REVERT: C 153 MET cc_start: 0.1917 (tpt) cc_final: -0.0386 (mpt) REVERT: C 314 GLN cc_start: 0.8504 (OUTLIER) cc_final: 0.8027 (tt0) REVERT: C 675 GLN cc_start: 0.7465 (OUTLIER) cc_final: 0.6146 (mp10) outliers start: 67 outliers final: 43 residues processed: 234 average time/residue: 0.9704 time to fit residues: 280.4335 Evaluate side-chains 223 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 174 time to evaluate : 2.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 790 LYS Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 994 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 97 optimal weight: 0.5980 chunk 5 optimal weight: 0.0000 chunk 49 optimal weight: 0.9980 chunk 174 optimal weight: 2.9990 chunk 272 optimal weight: 5.9990 chunk 124 optimal weight: 7.9990 chunk 26 optimal weight: 3.9990 chunk 126 optimal weight: 4.9990 chunk 107 optimal weight: 5.9990 chunk 172 optimal weight: 2.9990 chunk 105 optimal weight: 6.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 207 HIS A1119 ASN ** B 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS ** B 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 ASN B 474 GLN B1119 ASN ** C 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C 751 ASN C1119 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.198693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.158394 restraints weight = 27673.121| |-----------------------------------------------------------------------------| r_work (start): 0.3769 rms_B_bonded: 1.71 r_work: 0.3452 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3312 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.2761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 26190 Z= 0.190 Angle : 0.615 9.180 35739 Z= 0.309 Chirality : 0.046 0.218 4179 Planarity : 0.004 0.047 4500 Dihedral : 5.519 39.129 4557 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.76 % Favored : 97.04 % Rotamer: Outliers : 2.38 % Allowed : 11.94 % Favored : 85.68 % 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: 0.06 (0.14), residues: 3111 helix: 1.85 (0.18), residues: 738 sheet: 0.43 (0.20), residues: 633 loop : -0.94 (0.14), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 353 HIS 0.005 0.001 HIS A1058 PHE 0.017 0.002 PHE A 898 TYR 0.018 0.002 TYR A1067 ARG 0.004 0.000 ARG C 815 Details of bonding type rmsd link_NAG-ASN : bond 0.00322 ( 33) link_NAG-ASN : angle 2.50992 ( 99) link_BETA1-4 : bond 0.00384 ( 21) link_BETA1-4 : angle 2.75056 ( 63) hydrogen bonds : bond 0.04740 ( 1008) hydrogen bonds : angle 5.16206 ( 2826) SS BOND : bond 0.00328 ( 36) SS BOND : angle 1.61761 ( 72) link_NAG-THR : bond 0.00609 ( 3) link_NAG-THR : angle 1.77463 ( 6) covalent geometry : bond 0.00461 (26097) covalent geometry : angle 0.58696 (35499) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 188 time to evaluate : 2.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 THR cc_start: 0.5542 (OUTLIER) cc_final: 0.5075 (p) REVERT: A 153 MET cc_start: 0.2040 (tpt) cc_final: -0.0366 (mpm) REVERT: A 190 ARG cc_start: 0.7241 (mtt90) cc_final: 0.6931 (mtm-85) REVERT: A 269 TYR cc_start: 0.8208 (m-80) cc_final: 0.7926 (m-80) REVERT: A 646 ARG cc_start: 0.8559 (mtp85) cc_final: 0.7930 (mtp-110) REVERT: A 675 GLN cc_start: 0.7363 (OUTLIER) cc_final: 0.6070 (mp10) REVERT: A 1119 ASN cc_start: 0.8473 (m-40) cc_final: 0.8273 (m110) REVERT: B 59 PHE cc_start: 0.8532 (m-10) cc_final: 0.8315 (m-10) REVERT: B 153 MET cc_start: 0.2017 (tpt) cc_final: 0.0024 (mpt) REVERT: B 190 ARG cc_start: 0.7428 (mtm-85) cc_final: 0.7184 (mtm110) REVERT: B 675 GLN cc_start: 0.7511 (OUTLIER) cc_final: 0.6046 (mp10) REVERT: B 790 LYS cc_start: 0.8713 (OUTLIER) cc_final: 0.8469 (mttt) REVERT: B 1119 ASN cc_start: 0.8481 (m-40) cc_final: 0.8279 (m110) REVERT: C 153 MET cc_start: 0.2247 (tpt) cc_final: 0.0040 (mpt) REVERT: C 177 MET cc_start: 0.2713 (OUTLIER) cc_final: 0.1670 (ptp) REVERT: C 314 GLN cc_start: 0.8363 (OUTLIER) cc_final: 0.7867 (tt0) REVERT: C 675 GLN cc_start: 0.7458 (OUTLIER) cc_final: 0.6133 (mp10) REVERT: C 1119 ASN cc_start: 0.8515 (m-40) cc_final: 0.8313 (m110) outliers start: 66 outliers final: 44 residues processed: 234 average time/residue: 0.9659 time to fit residues: 278.4226 Evaluate side-chains 230 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 179 time to evaluate : 2.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 790 LYS Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 994 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 242 optimal weight: 1.9990 chunk 105 optimal weight: 10.0000 chunk 110 optimal weight: 5.9990 chunk 264 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 71 optimal weight: 0.9980 chunk 236 optimal weight: 5.9990 chunk 177 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 300 optimal weight: 0.9990 chunk 85 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 207 HIS A 321 GLN ** B 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS ** B 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 ASN ** C 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS ** C 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 474 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.199065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.157146 restraints weight = 27751.706| |-----------------------------------------------------------------------------| r_work (start): 0.3739 rms_B_bonded: 1.73 r_work: 0.3307 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.2822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 26190 Z= 0.175 Angle : 0.607 8.915 35739 Z= 0.304 Chirality : 0.045 0.310 4179 Planarity : 0.004 0.043 4500 Dihedral : 5.435 38.491 4557 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.15 % Favored : 96.66 % Rotamer: Outliers : 2.24 % Allowed : 12.37 % Favored : 85.39 % 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: 0.04 (0.15), residues: 3111 helix: 1.86 (0.18), residues: 738 sheet: 0.39 (0.19), residues: 648 loop : -0.97 (0.14), residues: 1725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 633 HIS 0.005 0.001 HIS B1058 PHE 0.016 0.001 PHE A 898 TYR 0.025 0.001 TYR B 170 ARG 0.009 0.000 ARG C 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00299 ( 33) link_NAG-ASN : angle 2.45089 ( 99) link_BETA1-4 : bond 0.00390 ( 21) link_BETA1-4 : angle 2.71170 ( 63) hydrogen bonds : bond 0.04601 ( 1008) hydrogen bonds : angle 5.12623 ( 2826) SS BOND : bond 0.00290 ( 36) SS BOND : angle 1.54888 ( 72) link_NAG-THR : bond 0.00576 ( 3) link_NAG-THR : angle 1.53904 ( 6) covalent geometry : bond 0.00421 (26097) covalent geometry : angle 0.57920 (35499) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 181 time to evaluate : 2.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 THR cc_start: 0.5250 (OUTLIER) cc_final: 0.4723 (p) REVERT: A 153 MET cc_start: 0.1717 (tpt) cc_final: -0.0675 (mpm) REVERT: A 190 ARG cc_start: 0.7506 (mtt90) cc_final: 0.7015 (mtm-85) REVERT: A 269 TYR cc_start: 0.8432 (m-80) cc_final: 0.7995 (m-80) REVERT: A 646 ARG cc_start: 0.8623 (mtp85) cc_final: 0.7873 (mtp-110) REVERT: A 675 GLN cc_start: 0.7396 (OUTLIER) cc_final: 0.6073 (mp10) REVERT: B 59 PHE cc_start: 0.8652 (m-10) cc_final: 0.8422 (m-10) REVERT: B 153 MET cc_start: 0.1578 (tpt) cc_final: -0.0290 (mpt) REVERT: B 190 ARG cc_start: 0.7640 (mtm-85) cc_final: 0.7385 (mtm110) REVERT: B 675 GLN cc_start: 0.7498 (OUTLIER) cc_final: 0.5985 (mp10) REVERT: B 790 LYS cc_start: 0.8795 (OUTLIER) cc_final: 0.8554 (mttt) REVERT: B 1119 ASN cc_start: 0.8493 (m-40) cc_final: 0.8268 (m110) REVERT: C 59 PHE cc_start: 0.8689 (m-10) cc_final: 0.8437 (m-10) REVERT: C 153 MET cc_start: 0.1735 (tpt) cc_final: -0.0400 (mpt) REVERT: C 314 GLN cc_start: 0.8532 (OUTLIER) cc_final: 0.8055 (tt0) REVERT: C 646 ARG cc_start: 0.8671 (OUTLIER) cc_final: 0.8395 (mtp85) REVERT: C 675 GLN cc_start: 0.7525 (OUTLIER) cc_final: 0.6246 (mp10) REVERT: C 1119 ASN cc_start: 0.8556 (m-40) cc_final: 0.8342 (m110) outliers start: 62 outliers final: 44 residues processed: 227 average time/residue: 0.9027 time to fit residues: 256.1220 Evaluate side-chains 228 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 177 time to evaluate : 2.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 790 LYS Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 994 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 135 optimal weight: 1.9990 chunk 203 optimal weight: 0.8980 chunk 173 optimal weight: 0.9990 chunk 263 optimal weight: 0.9980 chunk 291 optimal weight: 0.3980 chunk 184 optimal weight: 0.0370 chunk 21 optimal weight: 5.9990 chunk 32 optimal weight: 5.9990 chunk 288 optimal weight: 2.9990 chunk 16 optimal weight: 10.0000 chunk 10 optimal weight: 9.9990 overall best weight: 0.6660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 207 HIS ** B 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.201064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.162071 restraints weight = 27724.199| |-----------------------------------------------------------------------------| r_work (start): 0.3809 rms_B_bonded: 1.61 r_work: 0.3500 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.2867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 26190 Z= 0.119 Angle : 0.564 8.602 35739 Z= 0.282 Chirality : 0.044 0.325 4179 Planarity : 0.004 0.041 4500 Dihedral : 5.115 38.682 4557 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.23 % Allowed : 2.48 % Favored : 97.30 % Rotamer: Outliers : 1.37 % Allowed : 13.28 % Favored : 85.35 % 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: 0.12 (0.15), residues: 3111 helix: 2.02 (0.19), residues: 738 sheet: 0.42 (0.19), residues: 654 loop : -0.95 (0.14), residues: 1719 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 633 HIS 0.002 0.001 HIS B1058 PHE 0.015 0.001 PHE B 371 TYR 0.031 0.001 TYR C 170 ARG 0.008 0.000 ARG C 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00285 ( 33) link_NAG-ASN : angle 2.21806 ( 99) link_BETA1-4 : bond 0.00417 ( 21) link_BETA1-4 : angle 2.60469 ( 63) hydrogen bonds : bond 0.04059 ( 1008) hydrogen bonds : angle 4.95782 ( 2826) SS BOND : bond 0.00197 ( 36) SS BOND : angle 1.34562 ( 72) link_NAG-THR : bond 0.00466 ( 3) link_NAG-THR : angle 1.22824 ( 6) covalent geometry : bond 0.00274 (26097) covalent geometry : angle 0.53861 (35499) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 185 time to evaluate : 2.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 THR cc_start: 0.5479 (OUTLIER) cc_final: 0.5043 (p) REVERT: A 153 MET cc_start: 0.2290 (OUTLIER) cc_final: -0.0014 (mpm) REVERT: A 190 ARG cc_start: 0.7084 (mtt90) cc_final: 0.6830 (mtm-85) REVERT: A 646 ARG cc_start: 0.8329 (mtp85) cc_final: 0.7817 (mtp-110) REVERT: A 675 GLN cc_start: 0.7276 (OUTLIER) cc_final: 0.6166 (mp10) REVERT: B 153 MET cc_start: 0.2369 (tpt) cc_final: 0.0432 (mpt) REVERT: B 190 ARG cc_start: 0.7251 (mtm-85) cc_final: 0.7020 (mtm110) REVERT: B 675 GLN cc_start: 0.7385 (OUTLIER) cc_final: 0.6268 (mp10) REVERT: C 153 MET cc_start: 0.2128 (tpt) cc_final: 0.0108 (mpt) REVERT: C 646 ARG cc_start: 0.8311 (OUTLIER) cc_final: 0.8016 (mtp85) REVERT: C 675 GLN cc_start: 0.7378 (OUTLIER) cc_final: 0.6285 (mp10) outliers start: 38 outliers final: 27 residues processed: 212 average time/residue: 0.9473 time to fit residues: 246.2430 Evaluate side-chains 200 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 167 time to evaluate : 2.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 994 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 278 optimal weight: 0.8980 chunk 236 optimal weight: 6.9990 chunk 68 optimal weight: 2.9990 chunk 196 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 chunk 16 optimal weight: 10.0000 chunk 293 optimal weight: 0.0870 chunk 282 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 chunk 12 optimal weight: 0.0030 overall best weight: 0.5568 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 GLN C 207 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.202287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.164541 restraints weight = 27443.340| |-----------------------------------------------------------------------------| r_work (start): 0.3822 rms_B_bonded: 1.58 r_work: 0.3509 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.2913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 26190 Z= 0.115 Angle : 0.558 8.388 35739 Z= 0.279 Chirality : 0.044 0.275 4179 Planarity : 0.004 0.042 4500 Dihedral : 4.928 37.466 4557 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.60 % Favored : 97.14 % Rotamer: Outliers : 1.30 % Allowed : 13.64 % Favored : 85.06 % 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: 0.20 (0.15), residues: 3111 helix: 2.09 (0.19), residues: 738 sheet: 0.48 (0.20), residues: 639 loop : -0.90 (0.14), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 633 HIS 0.002 0.001 HIS C1058 PHE 0.015 0.001 PHE C 371 TYR 0.028 0.001 TYR B 170 ARG 0.009 0.000 ARG B 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00280 ( 33) link_NAG-ASN : angle 2.14643 ( 99) link_BETA1-4 : bond 0.00434 ( 21) link_BETA1-4 : angle 2.56659 ( 63) hydrogen bonds : bond 0.03989 ( 1008) hydrogen bonds : angle 4.90332 ( 2826) SS BOND : bond 0.00170 ( 36) SS BOND : angle 1.29909 ( 72) link_NAG-THR : bond 0.00414 ( 3) link_NAG-THR : angle 1.03606 ( 6) covalent geometry : bond 0.00262 (26097) covalent geometry : angle 0.53405 (35499) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16621.08 seconds wall clock time: 291 minutes 14.12 seconds (17474.12 seconds total)