Starting phenix.real_space_refine on Sun May 25 03:16:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uul_42589/05_2025/8uul_42589.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uul_42589/05_2025/8uul_42589.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8uul_42589/05_2025/8uul_42589.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uul_42589/05_2025/8uul_42589.map" model { file = "/net/cci-nas-00/data/ceres_data/8uul_42589/05_2025/8uul_42589.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uul_42589/05_2025/8uul_42589.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.017 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 117 5.16 5 C 16496 2.51 5 N 4270 2.21 5 O 5008 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 73 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 25891 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 8460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1083, 8460 Classifications: {'peptide': 1083} Link IDs: {'PTRANS': 57, 'TRANS': 1025} Chain breaks: 5 Chain: "B" Number of atoms: 8474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1084, 8474 Classifications: {'peptide': 1084} Link IDs: {'PTRANS': 57, 'TRANS': 1026} Chain breaks: 5 Chain: "C" Number of atoms: 8495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1087, 8495 Classifications: {'peptide': 1087} Link IDs: {'PTRANS': 58, 'TRANS': 1028} Chain breaks: 5 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "B" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 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: 14.84, per 1000 atoms: 0.57 Number of scatterers: 25891 At special positions: 0 Unit cell: (146.08, 154.933, 177.067, 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 117 16.00 O 5008 8.00 N 4270 7.00 C 16496 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=41, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 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=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.02 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.04 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.05 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.02 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 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 538 " - pdb=" SG CYS B 590 " 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=2.04 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=2.04 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 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=2.02 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.02 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.04 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=1, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " NAG-ASN " NAG A1303 " - " ASN A 709 " " NAG B1303 " - " ASN B 709 " " NAG B1305 " - " ASN B1074 " " NAG C1302 " - " ASN C 709 " " NAG C1307 " - " ASN C1074 " " NAG E 1 " - " ASN A1098 " " NAG F 1 " - " ASN B 717 " " NAG G 1 " - " ASN B 801 " " NAG H 1 " - " ASN B1098 " " NAG I 1 " - " ASN C 717 " " NAG J 1 " - " ASN C 801 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.82 Conformation dependent library (CDL) restraints added in 3.2 seconds 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6094 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 46 sheets defined 25.2% alpha, 26.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.64 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 removed outlier: 3.596A pdb=" N GLU A 298 " --> pdb=" O ASP A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.554A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 383 through 390 removed outlier: 4.207A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LEU A 390 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 411 removed outlier: 3.790A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA A 411 " --> pdb=" O ARG A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.740A pdb=" N ASP A 442 " --> pdb=" O SER A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 742 Processing helix chain 'A' and resid 747 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.622A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.783A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 849 through 855 Processing helix chain 'A' and resid 868 through 885 Processing helix chain 'A' and resid 886 through 890 removed outlier: 3.512A pdb=" N GLY A 889 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.688A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 918 Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.257A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 982 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 5.135A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL A1033 " --> pdb=" O MET A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 4.249A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ASP A1146 " --> pdb=" O GLN A1142 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.513A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 385 through 389 removed outlier: 3.868A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 411 removed outlier: 4.015A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ALA B 411 " --> pdb=" O ARG B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.953A pdb=" N ASP B 442 " --> pdb=" O SER B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 620 removed outlier: 3.606A pdb=" N GLU B 619 " --> pdb=" O ASN B 616 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.987A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.918A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 849 through 855 Processing helix chain 'B' and resid 866 through 885 removed outlier: 3.529A pdb=" N ALA B 871 " --> pdb=" O ASP B 867 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLN B 872 " --> pdb=" O GLU B 868 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.665A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 918 removed outlier: 4.014A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.157A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 982 Processing helix chain 'B' and resid 985 through 1032 removed outlier: 4.645A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1146 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.524A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 385 through 390 removed outlier: 3.580A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU C 390 " --> pdb=" O LEU C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 411 removed outlier: 4.084A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA C 411 " --> pdb=" O ARG C 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.539A pdb=" N ASP C 442 " --> pdb=" O SER C 438 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N SER C 443 " --> pdb=" O ASN C 439 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 438 through 443' Processing helix chain 'C' and resid 616 through 620 Processing helix chain 'C' and resid 635 through 639 removed outlier: 3.911A pdb=" N THR C 638 " --> pdb=" O VAL C 635 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLY C 639 " --> pdb=" O TYR C 636 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 635 through 639' Processing helix chain 'C' and resid 737 through 742 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.582A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.599A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.882A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 849 through 855 Processing helix chain 'C' and resid 866 through 885 removed outlier: 3.532A pdb=" N ILE C 870 " --> pdb=" O THR C 866 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA C 871 " --> pdb=" O ASP C 867 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLN C 872 " --> pdb=" O GLU C 868 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.676A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 918 removed outlier: 3.560A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.224A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.573A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1032 removed outlier: 5.026A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 4.195A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 31 removed outlier: 3.855A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N LYS A 187 " --> pdb=" O ILE A 210 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.837A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.667A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.076A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.562A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL A 130 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 9.790A pdb=" N GLN A 134 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 8.811A pdb=" N ASN A 164 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 8.995A pdb=" N CYS A 136 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 11.033A pdb=" N SER A 162 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 10.183A pdb=" N ASP A 138 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N TYR A 160 " --> pdb=" O ASP A 138 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.852A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.251A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA7, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA8, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA9, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.234A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.988A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 711 through 715 removed outlier: 4.335A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 718 through 728 removed outlier: 6.917A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB5, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AB6, first strand: chain 'A' and resid 1087 through 1088 Processing sheet with id=AB7, first strand: chain 'B' and resid 27 through 31 removed outlier: 3.883A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N LYS B 187 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.642A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.765A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.053A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.533A pdb=" N LEU B 241 " --> pdb=" O GLY B 103 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N VAL B 126 " --> pdb=" O SER B 172 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 154 through 158 removed outlier: 6.408A pdb=" N GLY B 142 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N PHE B 157 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N PHE B 140 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 311 through 319 removed outlier: 4.580A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 324 through 328 removed outlier: 6.793A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 8.304A pdb=" N ASN B 542 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AC5, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AC6, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC7, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.348A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.681A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 701 through 702 removed outlier: 6.940A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 715 Processing sheet with id=AD2, first strand: chain 'B' and resid 718 through 728 removed outlier: 6.941A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD4, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD5, first strand: chain 'B' and resid 1094 through 1096 Processing sheet with id=AD6, first strand: chain 'C' and resid 27 through 31 removed outlier: 3.944A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.821A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.492A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 47 through 55 removed outlier: 7.571A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 84 through 85 removed outlier: 7.155A pdb=" N ARG C 237 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N PHE C 106 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N GLN C 239 " --> pdb=" O TRP C 104 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N TRP C 104 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N LEU C 241 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 11.676A pdb=" N VAL C 126 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 10.220A pdb=" N GLU C 169 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 11.137A pdb=" N ILE C 128 " --> pdb=" O THR C 167 " (cutoff:3.500A) removed outlier: 8.897A pdb=" N THR C 167 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N VAL C 130 " --> pdb=" O ASN C 165 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N ASN C 165 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N GLU C 132 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ALA C 163 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N VAL C 159 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 10.867A pdb=" N ASP C 138 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 8.924A pdb=" N PHE C 157 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 10.977A pdb=" N PHE C 140 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 9.101A pdb=" N SER C 155 " --> pdb=" O PHE C 140 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 84 through 85 removed outlier: 13.897A pdb=" N PHE C 238 " --> pdb=" O PHE C 133 " (cutoff:3.500A) removed outlier: 12.988A pdb=" N PHE C 135 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 13.724A pdb=" N THR C 240 " --> pdb=" O PHE C 135 " (cutoff:3.500A) removed outlier: 11.643A pdb=" N ASN C 137 " --> pdb=" O THR C 240 " (cutoff:3.500A) removed outlier: 11.710A pdb=" N LEU C 242 " --> pdb=" O ASN C 137 " (cutoff:3.500A) removed outlier: 8.561A pdb=" N LEU C 244 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 11.676A pdb=" N VAL C 126 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 10.220A pdb=" N GLU C 169 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 11.137A pdb=" N ILE C 128 " --> pdb=" O THR C 167 " (cutoff:3.500A) removed outlier: 8.897A pdb=" N THR C 167 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N VAL C 130 " --> pdb=" O ASN C 165 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N ASN C 165 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N GLU C 132 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ALA C 163 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N VAL C 159 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 10.867A pdb=" N ASP C 138 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 8.924A pdb=" N PHE C 157 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 10.977A pdb=" N PHE C 140 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 9.101A pdb=" N SER C 155 " --> pdb=" O PHE C 140 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 311 through 319 removed outlier: 4.343A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 324 through 328 removed outlier: 4.244A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AE4, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE5, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE6, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.461A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 711 through 714 removed outlier: 3.578A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N GLN C1106 " --> pdb=" O GLU C1111 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N GLU C1111 " --> pdb=" O GLN C1106 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 717 through 728 removed outlier: 6.917A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AF1, first strand: chain 'C' and resid 1120 through 1122 1003 hydrogen bonds defined for protein. 2712 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 11.44 Time building geometry restraints manager: 6.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 8264 1.34 - 1.47: 6891 1.47 - 1.60: 11185 1.60 - 1.73: 2 1.73 - 1.86: 145 Bond restraints: 26487 Sorted by residual: bond pdb=" C1 NAG C1303 " pdb=" O5 NAG C1303 " ideal model delta sigma weight residual 1.406 1.545 -0.139 2.00e-02 2.50e+03 4.83e+01 bond pdb=" CB THR C 108 " pdb=" OG1 THR C 108 " ideal model delta sigma weight residual 1.433 1.485 -0.052 1.60e-02 3.91e+03 1.06e+01 bond pdb=" CG LEU A 916 " pdb=" CD1 LEU A 916 " ideal model delta sigma weight residual 1.521 1.417 0.104 3.30e-02 9.18e+02 1.00e+01 bond pdb=" CA THR C 108 " pdb=" CB THR C 108 " ideal model delta sigma weight residual 1.528 1.577 -0.048 1.59e-02 3.96e+03 9.27e+00 bond pdb=" CG LEU C 916 " pdb=" CD1 LEU C 916 " ideal model delta sigma weight residual 1.521 1.424 0.097 3.30e-02 9.18e+02 8.63e+00 ... (remaining 26482 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.94: 35247 2.94 - 5.88: 720 5.88 - 8.82: 77 8.82 - 11.76: 12 11.76 - 14.70: 1 Bond angle restraints: 36057 Sorted by residual: angle pdb=" N PRO A 986 " pdb=" CA PRO A 986 " pdb=" C PRO A 986 " ideal model delta sigma weight residual 110.70 117.76 -7.06 1.22e+00 6.72e-01 3.35e+01 angle pdb=" C LEU B 984 " pdb=" N ASP B 985 " pdb=" CA ASP B 985 " ideal model delta sigma weight residual 120.68 128.91 -8.23 1.52e+00 4.33e-01 2.93e+01 angle pdb=" N PRO B 986 " pdb=" CA PRO B 986 " pdb=" C PRO B 986 " ideal model delta sigma weight residual 110.70 117.19 -6.49 1.22e+00 6.72e-01 2.83e+01 angle pdb=" C GLY A 526 " pdb=" N PRO A 527 " pdb=" CA PRO A 527 " ideal model delta sigma weight residual 121.65 116.36 5.29 1.01e+00 9.80e-01 2.74e+01 angle pdb=" N CYS A 525 " pdb=" CA CYS A 525 " pdb=" C CYS A 525 " ideal model delta sigma weight residual 107.73 114.66 -6.93 1.34e+00 5.57e-01 2.67e+01 ... (remaining 36052 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.50: 15175 21.50 - 42.99: 866 42.99 - 64.49: 130 64.49 - 85.99: 33 85.99 - 107.48: 32 Dihedral angle restraints: 16236 sinusoidal: 6765 harmonic: 9471 Sorted by residual: dihedral pdb=" CB CYS B 291 " pdb=" SG CYS B 291 " pdb=" SG CYS B 301 " pdb=" CB CYS B 301 " ideal model delta sinusoidal sigma weight residual -86.00 -170.46 84.46 1 1.00e+01 1.00e-02 8.67e+01 dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual 93.00 14.20 78.80 1 1.00e+01 1.00e-02 7.73e+01 dihedral pdb=" CB CYS A 15 " pdb=" SG CYS A 15 " pdb=" SG CYS A 136 " pdb=" CB CYS A 136 " ideal model delta sinusoidal sigma weight residual 93.00 171.21 -78.21 1 1.00e+01 1.00e-02 7.64e+01 ... (remaining 16233 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.207: 4134 0.207 - 0.414: 25 0.414 - 0.621: 1 0.621 - 0.828: 1 0.828 - 1.034: 1 Chirality restraints: 4162 Sorted by residual: chirality pdb=" C1 NAG H 1 " pdb=" ND2 ASN B1098 " pdb=" C2 NAG H 1 " pdb=" O5 NAG H 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.37 -1.03 2.00e-01 2.50e+01 2.68e+01 chirality pdb=" CB THR C 108 " pdb=" CA THR C 108 " pdb=" OG1 THR C 108 " pdb=" CG2 THR C 108 " both_signs ideal model delta sigma weight residual False 2.55 1.75 0.80 2.00e-01 2.50e+01 1.60e+01 chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN A1098 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.90 -0.50 2.00e-01 2.50e+01 6.36e+00 ... (remaining 4159 not shown) Planarity restraints: 4648 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 24 " 0.057 5.00e-02 4.00e+02 8.77e-02 1.23e+01 pdb=" N PRO A 25 " -0.152 5.00e-02 4.00e+02 pdb=" CA PRO A 25 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO A 25 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN A1098 " 0.032 2.00e-02 2.50e+03 3.08e-02 1.19e+01 pdb=" CG ASN A1098 " -0.040 2.00e-02 2.50e+03 pdb=" OD1 ASN A1098 " 0.011 2.00e-02 2.50e+03 pdb=" ND2 ASN A1098 " -0.033 2.00e-02 2.50e+03 pdb=" C1 NAG E 1 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 906 " 0.021 2.00e-02 2.50e+03 2.41e-02 1.02e+01 pdb=" CG PHE A 906 " -0.055 2.00e-02 2.50e+03 pdb=" CD1 PHE A 906 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 PHE A 906 " 0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE A 906 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE A 906 " 0.010 2.00e-02 2.50e+03 pdb=" CZ PHE A 906 " -0.001 2.00e-02 2.50e+03 ... (remaining 4645 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 5717 2.78 - 3.31: 22321 3.31 - 3.84: 41023 3.84 - 4.37: 45893 4.37 - 4.90: 82082 Nonbonded interactions: 197036 Sorted by model distance: nonbonded pdb=" OH TYR B 37 " pdb=" OD2 ASP B 53 " model vdw 2.247 3.040 nonbonded pdb=" OH TYR C 37 " pdb=" OD2 ASP C 53 " model vdw 2.259 3.040 nonbonded pdb=" OD2 ASP B 398 " pdb=" OH TYR B 423 " model vdw 2.266 3.040 nonbonded pdb=" OH TYR A 37 " pdb=" OD2 ASP A 53 " model vdw 2.274 3.040 nonbonded pdb=" OD2 ASP C 398 " pdb=" OH TYR C 423 " model vdw 2.278 3.040 ... (remaining 197031 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' and (resid 14 through 623 or resid 634 through 1146 or resid 1301 thr \ ough 1306)) selection = (chain 'C' and (resid 14 through 623 or resid 634 through 1146 or resid 1301 thr \ ough 1306)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.780 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: 1.010 Check model and map are aligned: 0.170 Set scattering table: 0.240 Process input model: 56.660 Find NCS groups from input model: 1.510 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 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 : 0.009 0.139 26547 Z= 0.409 Angle : 1.057 19.018 36193 Z= 0.582 Chirality : 0.066 1.034 4162 Planarity : 0.007 0.088 4637 Dihedral : 14.634 107.484 10019 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 0.04 % Allowed : 0.49 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.58 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.96 (0.13), residues: 3218 helix: -0.75 (0.18), residues: 670 sheet: -0.09 (0.19), residues: 716 loop : -2.10 (0.12), residues: 1832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP B 633 HIS 0.009 0.002 HIS C 146 PHE 0.055 0.003 PHE A 906 TYR 0.031 0.003 TYR A 904 ARG 0.031 0.001 ARG A 346 Details of bonding type rmsd link_NAG-ASN : bond 0.01050 ( 11) link_NAG-ASN : angle 6.08978 ( 33) link_BETA1-4 : bond 0.01083 ( 7) link_BETA1-4 : angle 2.57046 ( 21) hydrogen bonds : bond 0.15108 ( 999) hydrogen bonds : angle 7.16885 ( 2712) SS BOND : bond 0.00592 ( 41) SS BOND : angle 2.33085 ( 82) covalent geometry : bond 0.00929 (26487) covalent geometry : angle 1.03552 (36057) Misc. bond : bond 0.00345 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 2846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 81 time to evaluate : 2.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.4830 (ptp) cc_final: 0.4605 (ptp) REVERT: A 801 ASN cc_start: 0.9269 (OUTLIER) cc_final: 0.8863 (t0) REVERT: B 177 MET cc_start: 0.5763 (pmm) cc_final: 0.5529 (pmm) REVERT: B 902 MET cc_start: 0.9207 (tpt) cc_final: 0.8875 (tpt) REVERT: C 177 MET cc_start: 0.5509 (pmm) cc_final: 0.5134 (pmm) REVERT: C 197 ILE cc_start: 0.7923 (mp) cc_final: 0.7608 (tp) REVERT: C 380 TYR cc_start: 0.8487 (m-10) cc_final: 0.8144 (m-10) REVERT: C 418 ILE cc_start: 0.9242 (pt) cc_final: 0.8882 (mm) outliers start: 1 outliers final: 0 residues processed: 82 average time/residue: 0.3821 time to fit residues: 51.4712 Evaluate side-chains 60 residues out of total 2846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 59 time to evaluate : 2.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 801 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 273 optimal weight: 2.9990 chunk 245 optimal weight: 3.9990 chunk 136 optimal weight: 0.7980 chunk 83 optimal weight: 1.9990 chunk 165 optimal weight: 5.9990 chunk 131 optimal weight: 6.9990 chunk 253 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 chunk 154 optimal weight: 0.9980 chunk 189 optimal weight: 0.8980 chunk 294 optimal weight: 9.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 519 HIS A 965 GLN B 69 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.079676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.052132 restraints weight = 90111.157| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 4.31 r_work: 0.2859 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.0966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 26547 Z= 0.143 Angle : 0.619 16.147 36193 Z= 0.316 Chirality : 0.046 0.648 4162 Planarity : 0.004 0.066 4637 Dihedral : 9.616 77.809 4180 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 0.07 % Allowed : 4.25 % Favored : 95.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.14), residues: 3218 helix: 1.04 (0.20), residues: 672 sheet: 0.06 (0.19), residues: 704 loop : -1.89 (0.13), residues: 1842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 633 HIS 0.007 0.001 HIS C 146 PHE 0.026 0.001 PHE C 168 TYR 0.019 0.001 TYR A1067 ARG 0.015 0.001 ARG C 214 Details of bonding type rmsd link_NAG-ASN : bond 0.00516 ( 11) link_NAG-ASN : angle 4.53012 ( 33) link_BETA1-4 : bond 0.00367 ( 7) link_BETA1-4 : angle 1.53087 ( 21) hydrogen bonds : bond 0.05726 ( 999) hydrogen bonds : angle 5.55453 ( 2712) SS BOND : bond 0.00320 ( 41) SS BOND : angle 1.49318 ( 82) covalent geometry : bond 0.00318 (26487) covalent geometry : angle 0.59907 (36057) Misc. bond : bond 0.00095 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 2846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 71 time to evaluate : 2.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 TYR cc_start: 0.8502 (m-10) cc_final: 0.8302 (m-80) REVERT: A 801 ASN cc_start: 0.8927 (OUTLIER) cc_final: 0.8679 (t0) REVERT: B 168 PHE cc_start: 0.6429 (t80) cc_final: 0.6221 (t80) REVERT: B 380 TYR cc_start: 0.8804 (m-10) cc_final: 0.8598 (m-10) REVERT: B 902 MET cc_start: 0.9282 (tpt) cc_final: 0.9071 (tpt) REVERT: C 177 MET cc_start: 0.5779 (pmm) cc_final: 0.5354 (pmm) REVERT: C 197 ILE cc_start: 0.7933 (mp) cc_final: 0.7541 (tp) REVERT: C 380 TYR cc_start: 0.8671 (m-10) cc_final: 0.8462 (m-10) REVERT: C 786 LYS cc_start: 0.8767 (mmtm) cc_final: 0.8444 (mmmt) outliers start: 2 outliers final: 1 residues processed: 73 average time/residue: 0.3752 time to fit residues: 45.7533 Evaluate side-chains 59 residues out of total 2846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 57 time to evaluate : 2.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 801 ASN Chi-restraints excluded: chain C residue 130 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 65 optimal weight: 4.9990 chunk 289 optimal weight: 5.9990 chunk 17 optimal weight: 8.9990 chunk 86 optimal weight: 4.9990 chunk 21 optimal weight: 9.9990 chunk 286 optimal weight: 0.0770 chunk 137 optimal weight: 8.9990 chunk 98 optimal weight: 2.9990 chunk 88 optimal weight: 5.9990 chunk 308 optimal weight: 2.9990 chunk 218 optimal weight: 9.9990 overall best weight: 3.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 957 GLN A1011 GLN ** A1134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 919 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.078083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.050424 restraints weight = 90484.369| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 4.30 r_work: 0.2815 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.1230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 26547 Z= 0.241 Angle : 0.649 15.706 36193 Z= 0.327 Chirality : 0.047 0.655 4162 Planarity : 0.004 0.058 4637 Dihedral : 7.800 74.956 4180 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 0.67 % Allowed : 6.68 % Favored : 92.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.14), residues: 3218 helix: 1.47 (0.20), residues: 677 sheet: -0.09 (0.19), residues: 728 loop : -1.83 (0.13), residues: 1813 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 633 HIS 0.006 0.001 HIS C 146 PHE 0.018 0.002 PHE C 92 TYR 0.022 0.001 TYR C1067 ARG 0.004 0.000 ARG B 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00538 ( 11) link_NAG-ASN : angle 4.33633 ( 33) link_BETA1-4 : bond 0.00285 ( 7) link_BETA1-4 : angle 1.64363 ( 21) hydrogen bonds : bond 0.05905 ( 999) hydrogen bonds : angle 5.36022 ( 2712) SS BOND : bond 0.00341 ( 41) SS BOND : angle 1.38193 ( 82) covalent geometry : bond 0.00559 (26487) covalent geometry : angle 0.63190 (36057) Misc. bond : bond 0.00089 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 2846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 68 time to evaluate : 3.052 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 197 ILE cc_start: 0.7396 (mp) cc_final: 0.6967 (tp) REVERT: A 200 TYR cc_start: 0.8543 (m-10) cc_final: 0.8262 (m-80) REVERT: A 801 ASN cc_start: 0.8897 (OUTLIER) cc_final: 0.8645 (t0) REVERT: B 168 PHE cc_start: 0.6445 (t80) cc_final: 0.6232 (t80) REVERT: B 197 ILE cc_start: 0.7945 (mp) cc_final: 0.7577 (tp) REVERT: B 408 ARG cc_start: 0.9401 (tmm160) cc_final: 0.9193 (ttp80) REVERT: C 177 MET cc_start: 0.5827 (pmm) cc_final: 0.5411 (pmm) REVERT: C 197 ILE cc_start: 0.7897 (mp) cc_final: 0.7469 (tp) REVERT: C 201 PHE cc_start: 0.6900 (t80) cc_final: 0.6313 (t80) REVERT: C 388 ASN cc_start: 0.9550 (t0) cc_final: 0.9201 (t0) REVERT: C 786 LYS cc_start: 0.8790 (mmtm) cc_final: 0.8465 (mmmt) REVERT: C 1066 THR cc_start: 0.9072 (OUTLIER) cc_final: 0.8779 (p) outliers start: 19 outliers final: 11 residues processed: 85 average time/residue: 0.3655 time to fit residues: 53.1679 Evaluate side-chains 73 residues out of total 2846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 60 time to evaluate : 3.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 801 ASN Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 1066 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 116 optimal weight: 8.9990 chunk 69 optimal weight: 0.7980 chunk 291 optimal weight: 0.7980 chunk 201 optimal weight: 0.9990 chunk 149 optimal weight: 0.9990 chunk 255 optimal weight: 10.0000 chunk 186 optimal weight: 20.0000 chunk 183 optimal weight: 0.8980 chunk 39 optimal weight: 8.9990 chunk 257 optimal weight: 0.0000 chunk 307 optimal weight: 0.0770 overall best weight: 0.5142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN A 804 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.080155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.052558 restraints weight = 89541.700| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 4.34 r_work: 0.2889 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.1577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 26547 Z= 0.100 Angle : 0.548 14.955 36193 Z= 0.274 Chirality : 0.045 0.630 4162 Planarity : 0.004 0.051 4637 Dihedral : 6.441 62.881 4180 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 0.53 % Allowed : 7.41 % Favored : 92.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.59 (0.14), residues: 3218 helix: 2.05 (0.21), residues: 670 sheet: 0.08 (0.19), residues: 721 loop : -1.62 (0.13), residues: 1827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 633 HIS 0.006 0.001 HIS A 519 PHE 0.024 0.001 PHE A 168 TYR 0.019 0.001 TYR A1067 ARG 0.003 0.000 ARG B 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00508 ( 11) link_NAG-ASN : angle 4.02044 ( 33) link_BETA1-4 : bond 0.00712 ( 7) link_BETA1-4 : angle 1.89067 ( 21) hydrogen bonds : bond 0.04483 ( 999) hydrogen bonds : angle 4.91178 ( 2712) SS BOND : bond 0.00271 ( 41) SS BOND : angle 1.08693 ( 82) covalent geometry : bond 0.00215 (26487) covalent geometry : angle 0.53090 (36057) Misc. bond : bond 0.00146 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 2846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 80 time to evaluate : 2.993 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 197 ILE cc_start: 0.7477 (mp) cc_final: 0.6983 (tp) REVERT: A 950 ASP cc_start: 0.8702 (t70) cc_final: 0.8270 (t0) REVERT: B 197 ILE cc_start: 0.7953 (mp) cc_final: 0.7589 (tp) REVERT: B 950 ASP cc_start: 0.8732 (t70) cc_final: 0.8374 (t0) REVERT: C 177 MET cc_start: 0.5731 (pmm) cc_final: 0.5359 (pmm) REVERT: C 197 ILE cc_start: 0.8027 (mp) cc_final: 0.7658 (tp) REVERT: C 786 LYS cc_start: 0.8738 (mmtm) cc_final: 0.8414 (mmmt) REVERT: C 1066 THR cc_start: 0.9078 (OUTLIER) cc_final: 0.8758 (p) outliers start: 15 outliers final: 7 residues processed: 93 average time/residue: 0.3442 time to fit residues: 55.5743 Evaluate side-chains 78 residues out of total 2846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 70 time to evaluate : 2.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 1066 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 135 optimal weight: 5.9990 chunk 59 optimal weight: 6.9990 chunk 281 optimal weight: 8.9990 chunk 16 optimal weight: 7.9990 chunk 111 optimal weight: 8.9990 chunk 115 optimal weight: 10.0000 chunk 121 optimal weight: 7.9990 chunk 21 optimal weight: 10.0000 chunk 24 optimal weight: 0.5980 chunk 226 optimal weight: 20.0000 chunk 26 optimal weight: 3.9990 overall best weight: 5.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 282 ASN A 801 ASN ** A1134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 655 HIS B 926 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.077152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.049989 restraints weight = 90994.741| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 4.07 r_work: 0.2827 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.1644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.084 26547 Z= 0.343 Angle : 0.709 15.881 36193 Z= 0.357 Chirality : 0.048 0.635 4162 Planarity : 0.004 0.050 4637 Dihedral : 6.650 67.047 4178 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 0.70 % Allowed : 9.42 % Favored : 89.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.14), residues: 3218 helix: 1.61 (0.20), residues: 683 sheet: -0.15 (0.19), residues: 739 loop : -1.82 (0.13), residues: 1796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 64 HIS 0.006 0.001 HIS C 146 PHE 0.023 0.002 PHE B 92 TYR 0.025 0.002 TYR A 279 ARG 0.004 0.001 ARG A 273 Details of bonding type rmsd link_NAG-ASN : bond 0.00601 ( 11) link_NAG-ASN : angle 4.34420 ( 33) link_BETA1-4 : bond 0.00352 ( 7) link_BETA1-4 : angle 1.72223 ( 21) hydrogen bonds : bond 0.06414 ( 999) hydrogen bonds : angle 5.36627 ( 2712) SS BOND : bond 0.00401 ( 41) SS BOND : angle 1.48354 ( 82) covalent geometry : bond 0.00802 (26487) covalent geometry : angle 0.69282 (36057) Misc. bond : bond 0.00120 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 2846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 65 time to evaluate : 2.936 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 197 ILE cc_start: 0.7553 (mp) cc_final: 0.7018 (tp) REVERT: A 636 TYR cc_start: 0.7865 (OUTLIER) cc_final: 0.6606 (t80) REVERT: A 801 ASN cc_start: 0.8934 (OUTLIER) cc_final: 0.8653 (t0) REVERT: A 950 ASP cc_start: 0.8818 (t70) cc_final: 0.8439 (t0) REVERT: B 168 PHE cc_start: 0.6370 (t80) cc_final: 0.6117 (t80) REVERT: B 197 ILE cc_start: 0.7999 (mp) cc_final: 0.7633 (tp) REVERT: B 950 ASP cc_start: 0.8891 (t70) cc_final: 0.8545 (t0) REVERT: C 141 LEU cc_start: 0.8417 (mm) cc_final: 0.7451 (tt) REVERT: C 177 MET cc_start: 0.5855 (pmm) cc_final: 0.5448 (pmm) REVERT: C 197 ILE cc_start: 0.7950 (mp) cc_final: 0.7511 (tp) REVERT: C 1066 THR cc_start: 0.9129 (OUTLIER) cc_final: 0.8842 (p) outliers start: 20 outliers final: 9 residues processed: 85 average time/residue: 0.3279 time to fit residues: 49.6101 Evaluate side-chains 72 residues out of total 2846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 60 time to evaluate : 2.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 636 TYR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 801 ASN Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 1066 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 132 optimal weight: 6.9990 chunk 94 optimal weight: 0.6980 chunk 156 optimal weight: 3.9990 chunk 199 optimal weight: 1.9990 chunk 76 optimal weight: 6.9990 chunk 82 optimal weight: 0.8980 chunk 168 optimal weight: 0.6980 chunk 263 optimal weight: 7.9990 chunk 51 optimal weight: 3.9990 chunk 150 optimal weight: 20.0000 chunk 313 optimal weight: 0.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.079176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.051813 restraints weight = 89536.199| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 4.27 r_work: 0.2855 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 26547 Z= 0.113 Angle : 0.550 14.816 36193 Z= 0.277 Chirality : 0.045 0.632 4162 Planarity : 0.003 0.047 4637 Dihedral : 5.924 55.409 4178 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 0.56 % Allowed : 10.01 % Favored : 89.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.56 (0.15), residues: 3218 helix: 2.14 (0.21), residues: 676 sheet: 0.03 (0.19), residues: 723 loop : -1.61 (0.13), residues: 1819 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 104 HIS 0.005 0.001 HIS A 519 PHE 0.021 0.001 PHE B 201 TYR 0.019 0.001 TYR A1067 ARG 0.003 0.000 ARG B 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00451 ( 11) link_NAG-ASN : angle 3.97782 ( 33) link_BETA1-4 : bond 0.00475 ( 7) link_BETA1-4 : angle 1.57924 ( 21) hydrogen bonds : bond 0.04847 ( 999) hydrogen bonds : angle 4.91788 ( 2712) SS BOND : bond 0.00274 ( 41) SS BOND : angle 1.16960 ( 82) covalent geometry : bond 0.00252 (26487) covalent geometry : angle 0.53386 (36057) Misc. bond : bond 0.00159 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 2846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 70 time to evaluate : 2.783 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 197 ILE cc_start: 0.7628 (mp) cc_final: 0.7119 (tp) REVERT: A 636 TYR cc_start: 0.7846 (OUTLIER) cc_final: 0.6378 (t80) REVERT: A 950 ASP cc_start: 0.8716 (t70) cc_final: 0.8330 (t0) REVERT: B 197 ILE cc_start: 0.8050 (mp) cc_final: 0.7705 (tp) REVERT: B 950 ASP cc_start: 0.8830 (t70) cc_final: 0.8503 (t0) REVERT: C 141 LEU cc_start: 0.8443 (mm) cc_final: 0.7493 (tt) REVERT: C 177 MET cc_start: 0.5859 (pmm) cc_final: 0.5438 (pmm) REVERT: C 197 ILE cc_start: 0.7960 (mp) cc_final: 0.7599 (tp) REVERT: C 380 TYR cc_start: 0.8590 (m-10) cc_final: 0.8264 (m-10) REVERT: C 725 GLU cc_start: 0.8861 (tt0) cc_final: 0.8607 (tt0) REVERT: C 786 LYS cc_start: 0.8732 (mmtm) cc_final: 0.8398 (mmmt) REVERT: C 1066 THR cc_start: 0.9085 (OUTLIER) cc_final: 0.8775 (p) outliers start: 16 outliers final: 11 residues processed: 84 average time/residue: 0.3348 time to fit residues: 49.3914 Evaluate side-chains 77 residues out of total 2846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 64 time to evaluate : 2.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 636 TYR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 1066 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 181 optimal weight: 5.9990 chunk 41 optimal weight: 20.0000 chunk 13 optimal weight: 20.0000 chunk 299 optimal weight: 0.7980 chunk 254 optimal weight: 4.9990 chunk 67 optimal weight: 6.9990 chunk 257 optimal weight: 10.0000 chunk 114 optimal weight: 10.0000 chunk 106 optimal weight: 0.0470 chunk 75 optimal weight: 5.9990 chunk 218 optimal weight: 7.9990 overall best weight: 3.5684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1011 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.077555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.050392 restraints weight = 90759.549| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 4.09 r_work: 0.2838 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.1895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 26547 Z= 0.252 Angle : 0.630 15.357 36193 Z= 0.317 Chirality : 0.046 0.628 4162 Planarity : 0.004 0.046 4637 Dihedral : 5.946 59.153 4178 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 0.67 % Allowed : 10.82 % Favored : 88.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.74 (0.14), residues: 3218 helix: 1.86 (0.20), residues: 690 sheet: -0.15 (0.19), residues: 736 loop : -1.67 (0.13), residues: 1792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 64 HIS 0.005 0.001 HIS C 146 PHE 0.026 0.002 PHE C 135 TYR 0.021 0.002 TYR B1067 ARG 0.004 0.000 ARG B 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00511 ( 11) link_NAG-ASN : angle 4.14560 ( 33) link_BETA1-4 : bond 0.00294 ( 7) link_BETA1-4 : angle 1.43716 ( 21) hydrogen bonds : bond 0.05762 ( 999) hydrogen bonds : angle 5.12212 ( 2712) SS BOND : bond 0.00337 ( 41) SS BOND : angle 1.33977 ( 82) covalent geometry : bond 0.00589 (26487) covalent geometry : angle 0.61420 (36057) Misc. bond : bond 0.00133 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 2846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 64 time to evaluate : 2.740 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 141 LEU cc_start: 0.8342 (mt) cc_final: 0.8120 (tp) REVERT: A 197 ILE cc_start: 0.7669 (mp) cc_final: 0.7173 (tp) REVERT: A 636 TYR cc_start: 0.7896 (OUTLIER) cc_final: 0.6603 (t80) REVERT: A 950 ASP cc_start: 0.8786 (t70) cc_final: 0.8408 (t0) REVERT: B 197 ILE cc_start: 0.8101 (mp) cc_final: 0.7849 (pt) REVERT: B 380 TYR cc_start: 0.8816 (m-10) cc_final: 0.8481 (m-10) REVERT: B 950 ASP cc_start: 0.8885 (t70) cc_final: 0.8546 (t0) REVERT: C 141 LEU cc_start: 0.8443 (mm) cc_final: 0.7422 (tt) REVERT: C 177 MET cc_start: 0.5950 (pmm) cc_final: 0.5496 (pmm) REVERT: C 197 ILE cc_start: 0.7887 (mp) cc_final: 0.7486 (tp) REVERT: C 380 TYR cc_start: 0.8605 (m-10) cc_final: 0.8261 (m-10) REVERT: C 786 LYS cc_start: 0.8804 (mmtm) cc_final: 0.8470 (mmmt) REVERT: C 1066 THR cc_start: 0.9123 (OUTLIER) cc_final: 0.8829 (p) outliers start: 19 outliers final: 11 residues processed: 80 average time/residue: 0.3294 time to fit residues: 46.6410 Evaluate side-chains 76 residues out of total 2846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 63 time to evaluate : 2.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 636 TYR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 1066 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 175 optimal weight: 2.9990 chunk 206 optimal weight: 1.9990 chunk 83 optimal weight: 0.7980 chunk 17 optimal weight: 5.9990 chunk 293 optimal weight: 3.9990 chunk 10 optimal weight: 10.0000 chunk 177 optimal weight: 1.9990 chunk 237 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 chunk 164 optimal weight: 5.9990 chunk 179 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 914 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.079176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.052270 restraints weight = 89841.175| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 4.14 r_work: 0.2871 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.2032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 26547 Z= 0.130 Angle : 0.544 14.742 36193 Z= 0.275 Chirality : 0.044 0.623 4162 Planarity : 0.003 0.043 4637 Dihedral : 5.499 55.865 4178 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 0.74 % Allowed : 10.65 % Favored : 88.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.52 (0.15), residues: 3218 helix: 2.15 (0.21), residues: 684 sheet: -0.01 (0.19), residues: 738 loop : -1.57 (0.14), residues: 1796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 633 HIS 0.004 0.001 HIS C 146 PHE 0.019 0.001 PHE C 135 TYR 0.019 0.001 TYR C1067 ARG 0.003 0.000 ARG B 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00414 ( 11) link_NAG-ASN : angle 3.90010 ( 33) link_BETA1-4 : bond 0.00426 ( 7) link_BETA1-4 : angle 1.41278 ( 21) hydrogen bonds : bond 0.04808 ( 999) hydrogen bonds : angle 4.84541 ( 2712) SS BOND : bond 0.00271 ( 41) SS BOND : angle 1.16522 ( 82) covalent geometry : bond 0.00297 (26487) covalent geometry : angle 0.52844 (36057) Misc. bond : bond 0.00155 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 2846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 72 time to evaluate : 2.780 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 141 LEU cc_start: 0.8318 (mt) cc_final: 0.8097 (tt) REVERT: A 197 ILE cc_start: 0.7663 (mp) cc_final: 0.7198 (tp) REVERT: A 636 TYR cc_start: 0.7849 (OUTLIER) cc_final: 0.6523 (t80) REVERT: A 950 ASP cc_start: 0.8707 (t70) cc_final: 0.8335 (t0) REVERT: B 197 ILE cc_start: 0.8112 (mp) cc_final: 0.7779 (tp) REVERT: B 380 TYR cc_start: 0.8768 (m-10) cc_final: 0.8471 (m-10) REVERT: B 950 ASP cc_start: 0.8802 (t70) cc_final: 0.8459 (t0) REVERT: C 141 LEU cc_start: 0.8481 (mm) cc_final: 0.7482 (tt) REVERT: C 177 MET cc_start: 0.5905 (pmm) cc_final: 0.5485 (pmm) REVERT: C 197 ILE cc_start: 0.7933 (mp) cc_final: 0.7587 (tp) REVERT: C 380 TYR cc_start: 0.8603 (m-10) cc_final: 0.8312 (m-10) REVERT: C 725 GLU cc_start: 0.8837 (tt0) cc_final: 0.8584 (tt0) REVERT: C 786 LYS cc_start: 0.8756 (mmtm) cc_final: 0.8421 (mmmt) REVERT: C 1066 THR cc_start: 0.9050 (OUTLIER) cc_final: 0.8743 (p) outliers start: 21 outliers final: 13 residues processed: 91 average time/residue: 0.3446 time to fit residues: 54.5999 Evaluate side-chains 83 residues out of total 2846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 68 time to evaluate : 2.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 636 TYR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 1066 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 115 optimal weight: 9.9990 chunk 37 optimal weight: 4.9990 chunk 268 optimal weight: 9.9990 chunk 160 optimal weight: 8.9990 chunk 13 optimal weight: 0.3980 chunk 289 optimal weight: 5.9990 chunk 186 optimal weight: 1.9990 chunk 227 optimal weight: 4.9990 chunk 147 optimal weight: 9.9990 chunk 43 optimal weight: 10.0000 chunk 219 optimal weight: 6.9990 overall best weight: 3.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.077632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.050279 restraints weight = 91278.959| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 4.14 r_work: 0.2832 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 26547 Z= 0.254 Angle : 0.629 15.264 36193 Z= 0.315 Chirality : 0.046 0.625 4162 Planarity : 0.004 0.045 4637 Dihedral : 5.686 58.572 4178 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 0.56 % Allowed : 11.24 % Favored : 88.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.72 (0.14), residues: 3218 helix: 1.88 (0.20), residues: 691 sheet: -0.16 (0.19), residues: 731 loop : -1.65 (0.13), residues: 1796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 64 HIS 0.005 0.001 HIS C 146 PHE 0.020 0.001 PHE B 201 TYR 0.022 0.002 TYR B1067 ARG 0.004 0.000 ARG B 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00505 ( 11) link_NAG-ASN : angle 4.07018 ( 33) link_BETA1-4 : bond 0.00273 ( 7) link_BETA1-4 : angle 1.28433 ( 21) hydrogen bonds : bond 0.05731 ( 999) hydrogen bonds : angle 5.09695 ( 2712) SS BOND : bond 0.00340 ( 41) SS BOND : angle 1.35628 ( 82) covalent geometry : bond 0.00598 (26487) covalent geometry : angle 0.61419 (36057) Misc. bond : bond 0.00159 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 2846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 67 time to evaluate : 2.681 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 141 LEU cc_start: 0.8351 (mt) cc_final: 0.8125 (tp) REVERT: A 197 ILE cc_start: 0.7667 (mp) cc_final: 0.7196 (tp) REVERT: A 636 TYR cc_start: 0.7924 (OUTLIER) cc_final: 0.6706 (t80) REVERT: A 950 ASP cc_start: 0.8778 (t70) cc_final: 0.8402 (t0) REVERT: A 1111 GLU cc_start: 0.9106 (tp30) cc_final: 0.8793 (tp30) REVERT: B 197 ILE cc_start: 0.8132 (mp) cc_final: 0.7876 (pt) REVERT: B 380 TYR cc_start: 0.8776 (m-10) cc_final: 0.8484 (m-10) REVERT: B 950 ASP cc_start: 0.8891 (t70) cc_final: 0.8573 (t0) REVERT: C 177 MET cc_start: 0.5887 (pmm) cc_final: 0.5432 (pmm) REVERT: C 197 ILE cc_start: 0.7892 (mp) cc_final: 0.7509 (tp) REVERT: C 380 TYR cc_start: 0.8633 (m-10) cc_final: 0.8307 (m-10) REVERT: C 786 LYS cc_start: 0.8821 (mmtm) cc_final: 0.8486 (mmmt) REVERT: C 1066 THR cc_start: 0.9118 (OUTLIER) cc_final: 0.8818 (p) outliers start: 16 outliers final: 14 residues processed: 81 average time/residue: 0.3269 time to fit residues: 46.4808 Evaluate side-chains 81 residues out of total 2846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 65 time to evaluate : 2.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 636 TYR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 1066 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 261 optimal weight: 0.0000 chunk 62 optimal weight: 0.9980 chunk 306 optimal weight: 0.9980 chunk 0 optimal weight: 40.0000 chunk 282 optimal weight: 0.7980 chunk 23 optimal weight: 6.9990 chunk 47 optimal weight: 6.9990 chunk 83 optimal weight: 0.5980 chunk 291 optimal weight: 0.9990 chunk 242 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.079968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.053124 restraints weight = 89247.881| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 4.14 r_work: 0.2898 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.2249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 26547 Z= 0.101 Angle : 0.539 14.683 36193 Z= 0.271 Chirality : 0.044 0.617 4162 Planarity : 0.003 0.043 4637 Dihedral : 5.169 54.978 4178 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 0.63 % Allowed : 11.21 % Favored : 88.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.40 (0.15), residues: 3218 helix: 2.28 (0.21), residues: 678 sheet: 0.03 (0.19), residues: 734 loop : -1.47 (0.14), residues: 1806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 104 HIS 0.004 0.001 HIS A 519 PHE 0.020 0.001 PHE C 201 TYR 0.018 0.001 TYR A1067 ARG 0.002 0.000 ARG B 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00476 ( 11) link_NAG-ASN : angle 3.77353 ( 33) link_BETA1-4 : bond 0.00502 ( 7) link_BETA1-4 : angle 1.38940 ( 21) hydrogen bonds : bond 0.04425 ( 999) hydrogen bonds : angle 4.71381 ( 2712) SS BOND : bond 0.00271 ( 41) SS BOND : angle 1.07404 ( 82) covalent geometry : bond 0.00220 (26487) covalent geometry : angle 0.52411 (36057) Misc. bond : bond 0.00152 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 2846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 77 time to evaluate : 3.057 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 141 LEU cc_start: 0.8353 (mt) cc_final: 0.8123 (tt) REVERT: A 197 ILE cc_start: 0.7681 (mp) cc_final: 0.7247 (tp) REVERT: A 380 TYR cc_start: 0.8776 (m-10) cc_final: 0.8468 (m-10) REVERT: A 636 TYR cc_start: 0.7850 (OUTLIER) cc_final: 0.6484 (t80) REVERT: A 950 ASP cc_start: 0.8683 (t70) cc_final: 0.8316 (t0) REVERT: B 153 MET cc_start: 0.8955 (mpp) cc_final: 0.8739 (mpp) REVERT: B 197 ILE cc_start: 0.8154 (mp) cc_final: 0.7817 (tp) REVERT: B 380 TYR cc_start: 0.8789 (m-10) cc_final: 0.8540 (m-10) REVERT: B 950 ASP cc_start: 0.8770 (t70) cc_final: 0.8401 (t0) REVERT: B 988 GLU cc_start: 0.9149 (mp0) cc_final: 0.8746 (mp0) REVERT: C 52 GLN cc_start: 0.9256 (tt0) cc_final: 0.8768 (tp-100) REVERT: C 141 LEU cc_start: 0.8497 (mm) cc_final: 0.7489 (tt) REVERT: C 177 MET cc_start: 0.5834 (pmm) cc_final: 0.5414 (pmm) REVERT: C 197 ILE cc_start: 0.7929 (mp) cc_final: 0.7602 (tp) REVERT: C 380 TYR cc_start: 0.8537 (m-10) cc_final: 0.8280 (m-10) REVERT: C 725 GLU cc_start: 0.8833 (tt0) cc_final: 0.8558 (tt0) REVERT: C 786 LYS cc_start: 0.8740 (mmtm) cc_final: 0.8438 (mmmt) REVERT: C 1066 THR cc_start: 0.9032 (OUTLIER) cc_final: 0.8714 (p) outliers start: 18 outliers final: 14 residues processed: 93 average time/residue: 0.3457 time to fit residues: 54.9958 Evaluate side-chains 90 residues out of total 2846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 74 time to evaluate : 3.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 636 TYR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 1066 THR Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 258 optimal weight: 8.9990 chunk 72 optimal weight: 5.9990 chunk 104 optimal weight: 0.0270 chunk 314 optimal weight: 3.9990 chunk 73 optimal weight: 0.9980 chunk 128 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 16 optimal weight: 20.0000 chunk 10 optimal weight: 9.9990 chunk 36 optimal weight: 9.9990 overall best weight: 2.0044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.079044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.052065 restraints weight = 90637.105| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 4.12 r_work: 0.2882 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.2271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 26547 Z= 0.154 Angle : 0.551 14.724 36193 Z= 0.275 Chirality : 0.044 0.612 4162 Planarity : 0.003 0.043 4637 Dihedral : 5.112 57.425 4178 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 0.63 % Allowed : 11.24 % Favored : 88.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.40 (0.15), residues: 3218 helix: 2.23 (0.21), residues: 686 sheet: 0.02 (0.19), residues: 722 loop : -1.46 (0.14), residues: 1810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 633 HIS 0.005 0.001 HIS C 146 PHE 0.023 0.001 PHE C 201 TYR 0.019 0.001 TYR B1067 ARG 0.004 0.000 ARG B 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00430 ( 11) link_NAG-ASN : angle 3.81193 ( 33) link_BETA1-4 : bond 0.00322 ( 7) link_BETA1-4 : angle 1.26133 ( 21) hydrogen bonds : bond 0.04773 ( 999) hydrogen bonds : angle 4.75264 ( 2712) SS BOND : bond 0.00266 ( 41) SS BOND : angle 1.11898 ( 82) covalent geometry : bond 0.00361 (26487) covalent geometry : angle 0.53599 (36057) Misc. bond : bond 0.00158 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11821.73 seconds wall clock time: 206 minutes 1.14 seconds (12361.14 seconds total)