Starting phenix.real_space_refine on Sun Sep 13 17:43:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6zoy_11330/09_2026/6zoy_11330.cif Found real_map, /net/cci-nas-00/data/ceres_data/6zoy_11330/09_2026/6zoy_11330.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6zoy_11330/09_2026/6zoy_11330.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6zoy_11330/09_2026/6zoy_11330.cif" model { file = "/net/cci-nas-00/data/ceres_data/6zoy_11330/09_2026/6zoy_11330.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6zoy_11330/09_2026/6zoy_11330.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6zoy_11330/09_2026/6zoy_11330.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6zoy_11330/09_2026/6zoy_11330.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 117 5.16 5 C 15744 2.51 5 N 4038 2.21 5 O 4854 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 159 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 24753 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 7971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1021, 7971 Classifications: {'peptide': 1021} Link IDs: {'PTRANS': 49, 'TRANS': 971} Chain breaks: 6 Chain: "B" Number of atoms: 7971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1021, 7971 Classifications: {'peptide': 1021} Link IDs: {'PTRANS': 49, 'TRANS': 971} Chain breaks: 6 Chain: "C" Number of atoms: 7971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1021, 7971 Classifications: {'peptide': 1021} Link IDs: {'PTRANS': 49, 'TRANS': 971} Chain breaks: 6 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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 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 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 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 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 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 chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen chiralities: 12 Chain: "B" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen chiralities: 12 Chain: "C" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen chiralities: 12 Time building chain proxies: 6.24, per 1000 atoms: 0.25 Number of scatterers: 24753 At special positions: 0 Unit cell: (132.625, 143.235, 162.333, 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 4854 8.00 N 4038 7.00 C 15744 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.04 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.02 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 383 " - pdb=" SG CYS B 985 " distance=2.07 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.05 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.05 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=2.04 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A 985 " - pdb=" SG CYS C 383 " distance=2.07 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.02 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.04 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.02 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 383 " - pdb=" SG CYS C 985 " distance=1.99 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.05 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=2.05 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=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.02 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.04 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.02 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.05 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.05 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=2.04 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 234 " " NAG A1304 " - " ASN A 282 " " NAG A1305 " - " ASN A 331 " " NAG A1306 " - " ASN A 343 " " NAG A1307 " - " ASN A 603 " " NAG A1308 " - " ASN A 616 " " NAG A1309 " - " ASN A 657 " " NAG A1310 " - " ASN A 709 " " NAG A1315 " - " ASN A1074 " " NAG A1320 " - " ASN A 165 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 234 " " NAG B1304 " - " ASN B 282 " " NAG B1305 " - " ASN B 331 " " NAG B1306 " - " ASN B 343 " " NAG B1307 " - " ASN B 603 " " NAG B1308 " - " ASN B 616 " " NAG B1309 " - " ASN B 657 " " NAG B1310 " - " ASN B 709 " " NAG B1315 " - " ASN B1074 " " NAG B1320 " - " ASN B 165 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 122 " " NAG C1303 " - " ASN C 234 " " NAG C1304 " - " ASN C 282 " " NAG C1305 " - " ASN C 331 " " NAG C1306 " - " ASN C 343 " " NAG C1307 " - " ASN C 603 " " NAG C1308 " - " ASN C 616 " " NAG C1309 " - " ASN C 657 " " NAG C1310 " - " ASN C 709 " " NAG C1315 " - " ASN C1074 " " NAG C1320 " - " ASN C 165 " " NAG D 1 " - " ASN A 717 " " NAG E 1 " - " ASN A 801 " " NAG F 1 " - " ASN A1098 " " NAG G 1 " - " ASN A1134 " " NAG H 1 " - " ASN B 717 " " NAG I 1 " - " ASN B 801 " " NAG J 1 " - " ASN B1098 " " NAG K 1 " - " ASN B1134 " " NAG L 1 " - " ASN C 717 " " NAG M 1 " - " ASN C 801 " " NAG N 1 " - " ASN C1098 " " NAG O 1 " - " ASN C1134 " Time building additional restraints: 2.45 Conformation dependent library (CDL) restraints added in 1.0 seconds 6042 Ramachandran restraints generated. 3021 Oldfield, 0 Emsley, 3021 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5736 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 42 sheets defined 24.8% alpha, 29.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.99 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.921A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 371 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.222A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 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: 3.675A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.688A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.509A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.175A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.734A pdb=" N ARG A 983 " --> pdb=" O ASP A 979 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 5.116A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (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: 3.920A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 371 Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.221A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.674A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.687A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.508A 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 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.174A 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 984 removed outlier: 3.733A pdb=" N ARG B 983 " --> pdb=" O ASP B 979 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 5.116A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) 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: 3.920A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 371 Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.222A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.674A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 824 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.688A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.509A 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 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.176A 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: 3.733A pdb=" N ARG C 983 " --> pdb=" O ASP C 979 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 5.117A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.364A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N VAL A 90 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N VAL A 193 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N PHE A 92 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N GLU A 191 " --> pdb=" O PHE A 92 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N SER A 94 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N LEU A 189 " --> pdb=" O SER A 94 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N GLU A 96 " --> pdb=" O LYS A 187 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N LYS A 187 " --> pdb=" O ILE A 210 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.279A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.367A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.836A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 52 removed outlier: 3.842A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.915A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 7.175A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.473A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.523A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.580A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.186A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.595A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.567A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.567A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.561A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.612A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.365A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N VAL B 90 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N VAL B 193 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N PHE B 92 " --> pdb=" O GLU B 191 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N GLU B 191 " --> pdb=" O PHE B 92 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N SER B 94 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N LEU B 189 " --> pdb=" O SER B 94 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N GLU B 96 " --> pdb=" O LYS B 187 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N LYS B 187 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.279A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.367A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.327A 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 52 removed outlier: 3.842A 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 Processing sheet with id=AC1, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.914A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 311 through 319 removed outlier: 7.175A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.473A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 6.813A 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 removed outlier: 3.523A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.581A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) 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 654 through 655 removed outlier: 6.185A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.595A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.567A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.567A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.561A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.612A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.365A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N VAL C 90 " --> pdb=" O VAL C 193 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N VAL C 193 " --> pdb=" O VAL C 90 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N PHE C 92 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N GLU C 191 " --> pdb=" O PHE C 92 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N SER C 94 " --> pdb=" O LEU C 189 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N LEU C 189 " --> pdb=" O SER C 94 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N GLU C 96 " --> pdb=" O LYS C 187 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N LYS C 187 " --> pdb=" O ILE C 210 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.278A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.367A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 47 through 52 removed outlier: 3.842A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AD6, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.915A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 311 through 319 removed outlier: 7.175A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.524A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.580A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE2, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.185A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.595A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.567A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.567A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.562A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.612A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 1010 hydrogen bonds defined for protein. 2805 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: 6.01 Time building geometry restraints manager: 3.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.35: 7864 1.35 - 1.48: 7082 1.48 - 1.62: 10200 1.62 - 1.75: 0 1.75 - 1.88: 147 Bond restraints: 25293 Sorted by residual: bond pdb=" CB ARG C 355 " pdb=" CG ARG C 355 " ideal model delta sigma weight residual 1.520 1.443 0.077 3.00e-02 1.11e+03 6.57e+00 bond pdb=" CB ARG B 355 " pdb=" CG ARG B 355 " ideal model delta sigma weight residual 1.520 1.444 0.076 3.00e-02 1.11e+03 6.39e+00 bond pdb=" CB ARG A 355 " pdb=" CG ARG A 355 " ideal model delta sigma weight residual 1.520 1.444 0.076 3.00e-02 1.11e+03 6.39e+00 bond pdb=" CA LEU C1063 " pdb=" CB LEU C1063 " ideal model delta sigma weight residual 1.527 1.497 0.030 1.30e-02 5.92e+03 5.28e+00 bond pdb=" C1 NAG B1309 " pdb=" O5 NAG B1309 " ideal model delta sigma weight residual 1.406 1.452 -0.046 2.00e-02 2.50e+03 5.26e+00 ... (remaining 25288 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.75: 32867 2.75 - 5.49: 1383 5.49 - 8.24: 130 8.24 - 10.98: 18 10.98 - 13.73: 6 Bond angle restraints: 34404 Sorted by residual: angle pdb=" N GLY C 700 " pdb=" CA GLY C 700 " pdb=" C GLY C 700 " ideal model delta sigma weight residual 111.85 105.24 6.61 1.06e+00 8.90e-01 3.89e+01 angle pdb=" N GLY A 700 " pdb=" CA GLY A 700 " pdb=" C GLY A 700 " ideal model delta sigma weight residual 111.85 105.24 6.61 1.06e+00 8.90e-01 3.88e+01 angle pdb=" N GLY B 700 " pdb=" CA GLY B 700 " pdb=" C GLY B 700 " ideal model delta sigma weight residual 111.85 105.26 6.59 1.06e+00 8.90e-01 3.87e+01 angle pdb=" CA GLY B 700 " pdb=" C GLY B 700 " pdb=" N ALA B 701 " ideal model delta sigma weight residual 114.23 119.68 -5.45 8.80e-01 1.29e+00 3.84e+01 angle pdb=" CA GLY A 700 " pdb=" C GLY A 700 " pdb=" N ALA A 701 " ideal model delta sigma weight residual 114.23 119.65 -5.42 8.80e-01 1.29e+00 3.80e+01 ... (remaining 34399 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 13676 17.93 - 35.86: 667 35.86 - 53.80: 156 53.80 - 71.73: 57 71.73 - 89.66: 39 Dihedral angle restraints: 14595 sinusoidal: 5685 harmonic: 8910 Sorted by residual: dihedral pdb=" CB CYS A 985 " pdb=" SG CYS A 985 " pdb=" SG CYS C 383 " pdb=" CB CYS C 383 " ideal model delta sinusoidal sigma weight residual 93.00 162.40 -69.40 1 1.00e+01 1.00e-02 6.22e+01 dihedral pdb=" CB CYS B 383 " pdb=" SG CYS B 383 " pdb=" SG CYS C 985 " pdb=" CB CYS C 985 " ideal model delta sinusoidal sigma weight residual 93.00 162.37 -69.37 1 1.00e+01 1.00e-02 6.22e+01 dihedral pdb=" CB CYS A 383 " pdb=" SG CYS A 383 " pdb=" SG CYS B 985 " pdb=" CB CYS B 985 " ideal model delta sinusoidal sigma weight residual 93.00 162.10 -69.10 1 1.00e+01 1.00e-02 6.18e+01 ... (remaining 14592 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.178: 4002 0.178 - 0.356: 63 0.356 - 0.533: 15 0.533 - 0.711: 0 0.711 - 0.889: 3 Chirality restraints: 4083 Sorted by residual: chirality pdb=" C1 NAG J 2 " pdb=" O4 NAG J 1 " pdb=" C2 NAG J 2 " pdb=" O5 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.51 -0.89 2.00e-02 2.50e+03 1.97e+03 chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.51 -0.89 2.00e-02 2.50e+03 1.96e+03 chirality pdb=" C1 NAG N 2 " pdb=" O4 NAG N 1 " pdb=" C2 NAG N 2 " pdb=" O5 NAG N 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.51 -0.89 2.00e-02 2.50e+03 1.96e+03 ... (remaining 4080 not shown) Planarity restraints: 4428 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A 759 " -0.022 2.00e-02 2.50e+03 4.32e-02 1.87e+01 pdb=" C PHE A 759 " 0.075 2.00e-02 2.50e+03 pdb=" O PHE A 759 " -0.028 2.00e-02 2.50e+03 pdb=" N CYS A 760 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 759 " 0.022 2.00e-02 2.50e+03 4.31e-02 1.85e+01 pdb=" C PHE B 759 " -0.074 2.00e-02 2.50e+03 pdb=" O PHE B 759 " 0.028 2.00e-02 2.50e+03 pdb=" N CYS B 760 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE C 759 " -0.021 2.00e-02 2.50e+03 4.28e-02 1.83e+01 pdb=" C PHE C 759 " 0.074 2.00e-02 2.50e+03 pdb=" O PHE C 759 " -0.028 2.00e-02 2.50e+03 pdb=" N CYS C 760 " -0.025 2.00e-02 2.50e+03 ... (remaining 4425 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 304 2.61 - 3.18: 22083 3.18 - 3.76: 36787 3.76 - 4.33: 52254 4.33 - 4.90: 88334 Nonbonded interactions: 199762 Sorted by model distance: nonbonded pdb=" OG1 THR B1116 " pdb=" OD1 ASP B1118 " model vdw 2.038 3.040 nonbonded pdb=" OG1 THR A1116 " pdb=" OD1 ASP A1118 " model vdw 2.039 3.040 nonbonded pdb=" OG1 THR C1116 " pdb=" OD1 ASP C1118 " model vdw 2.039 3.040 nonbonded pdb=" OE2 GLU B 654 " pdb=" OG SER B 691 " model vdw 2.087 3.040 nonbonded pdb=" OE2 GLU A 654 " pdb=" OG SER A 691 " model vdw 2.087 3.040 ... (remaining 199757 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.420 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 25.700 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.070 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:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 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 : 0.011 0.101 25395 Z= 0.472 Angle : 1.369 32.262 34668 Z= 0.757 Chirality : 0.077 0.889 4083 Planarity : 0.007 0.071 4380 Dihedral : 12.992 89.660 8733 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.30 % Allowed : 4.63 % Favored : 95.07 % Rotamer: Outliers : 0.22 % Allowed : 1.57 % Favored : 98.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.14), residues: 3021 helix: 0.17 (0.18), residues: 669 sheet: 0.65 (0.18), residues: 663 loop : -0.43 (0.14), residues: 1689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.002 ARG A 355 TYR 0.030 0.003 TYR C 421 PHE 0.035 0.004 PHE C 86 TRP 0.025 0.004 TRP A 436 HIS 0.013 0.003 HIS C1088 Details of bonding type rmsd/Z covalent geometry : bond 0.01075 / 0.47 (25293) covalent geometry : angle 1.24777 / 0.73 (34404) SS BOND : bond 0.01434 / 0.95 ( 42) SS BOND : angle 3.10829 / 2.08 ( 84) hydrogen bonds : bond 0.14511 / 9.59 ( 971) hydrogen bonds : angle 8.14625 / 5.64 ( 2805) link_BETA1-4 : bond 0.06582 / 3.98 ( 12) link_BETA1-4 : angle 12.91823 / 8.22 ( 36) link_NAG-ASN : bond 0.01221 / 0.64 ( 48) link_NAG-ASN : angle 5.64834 / 3.72 ( 144) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6042 Ramachandran restraints generated. 3021 Oldfield, 0 Emsley, 3021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6042 Ramachandran restraints generated. 3021 Oldfield, 0 Emsley, 3021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 278 time to evaluate : 1.028 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8197 (tm-30) cc_final: 0.7705 (tm-30) REVERT: A 455 LEU cc_start: 0.8732 (tp) cc_final: 0.8456 (tp) REVERT: A 1002 GLN cc_start: 0.8060 (tt0) cc_final: 0.7798 (tt0) REVERT: B 52 GLN cc_start: 0.8178 (tm-30) cc_final: 0.7681 (tm-30) REVERT: B 104 TRP cc_start: 0.6818 (m-90) cc_final: 0.6426 (m-90) REVERT: B 455 LEU cc_start: 0.8717 (tp) cc_final: 0.8412 (tp) REVERT: B 1092 GLU cc_start: 0.6229 (tp30) cc_final: 0.5974 (tp30) REVERT: C 52 GLN cc_start: 0.8269 (tm-30) cc_final: 0.7789 (tm-30) REVERT: C 455 LEU cc_start: 0.8653 (tp) cc_final: 0.8352 (tp) REVERT: C 569 ILE cc_start: 0.9423 (mm) cc_final: 0.8978 (mp) REVERT: C 582 LEU cc_start: 0.9436 (OUTLIER) cc_final: 0.9201 (mm) REVERT: C 1002 GLN cc_start: 0.8041 (tt0) cc_final: 0.7754 (tt0) outliers start: 6 outliers final: 0 residues processed: 281 average time/residue: 0.1808 time to fit residues: 78.9927 Evaluate side-chains 158 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 157 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 582 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 0.3980 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 0.8980 chunk 298 optimal weight: 0.9980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 607 GLN A 784 GLN A 824 ASN A 901 GLN A 957 GLN A1071 GLN A1101 HIS A1119 ASN B 314 GLN B 607 GLN B 824 ASN B 901 GLN B 926 GLN B 957 GLN B1071 GLN B1101 HIS B1119 ASN C 81 ASN C 314 GLN C 607 GLN C 824 ASN C 901 GLN C 926 GLN C1071 GLN C1101 HIS C1119 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.134322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.087554 restraints weight = 51171.847| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 3.14 r_work: 0.3066 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 25395 Z= 0.140 Angle : 0.691 9.461 34668 Z= 0.347 Chirality : 0.049 0.355 4083 Planarity : 0.004 0.036 4380 Dihedral : 4.756 26.907 3275 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 0.71 % Allowed : 6.17 % Favored : 93.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.14), residues: 3021 helix: 1.87 (0.20), residues: 645 sheet: 0.64 (0.18), residues: 687 loop : -0.43 (0.14), residues: 1689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A1107 TYR 0.024 0.002 TYR C 423 PHE 0.036 0.002 PHE A 220 TRP 0.014 0.002 TRP A 104 HIS 0.004 0.001 HIS B 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 (25293) covalent geometry : angle 0.64983 / 0.34 (34404) SS BOND : bond 0.00462 / 0.31 ( 42) SS BOND : angle 1.40979 / 0.95 ( 84) hydrogen bonds : bond 0.04470 / 2.94 ( 971) hydrogen bonds : angle 6.11747 / 4.22 ( 2805) link_BETA1-4 : bond 0.00515 / 0.31 ( 12) link_BETA1-4 : angle 1.16714 / 0.73 ( 36) link_NAG-ASN : bond 0.00679 / 0.40 ( 48) link_NAG-ASN : angle 3.52154 / 2.32 ( 144) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6042 Ramachandran restraints generated. 3021 Oldfield, 0 Emsley, 3021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6042 Ramachandran restraints generated. 3021 Oldfield, 0 Emsley, 3021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 181 time to evaluate : 1.074 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8473 (tm-30) cc_final: 0.7859 (tm-30) REVERT: A 360 ASN cc_start: 0.9135 (m110) cc_final: 0.8847 (t0) REVERT: A 950 ASP cc_start: 0.8173 (m-30) cc_final: 0.7905 (m-30) REVERT: A 979 ASP cc_start: 0.8350 (m-30) cc_final: 0.7633 (t0) REVERT: A 1045 LYS cc_start: 0.8390 (ptmm) cc_final: 0.7697 (tttm) REVERT: B 309 GLU cc_start: 0.8560 (mp0) cc_final: 0.8350 (mp0) REVERT: B 505 TYR cc_start: 0.8220 (t80) cc_final: 0.7905 (t80) REVERT: C 979 ASP cc_start: 0.8438 (m-30) cc_final: 0.7855 (t0) outliers start: 19 outliers final: 12 residues processed: 193 average time/residue: 0.1630 time to fit residues: 52.2068 Evaluate side-chains 147 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 135 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1092 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 146 optimal weight: 20.0000 chunk 140 optimal weight: 20.0000 chunk 210 optimal weight: 20.0000 chunk 74 optimal weight: 10.0000 chunk 129 optimal weight: 7.9990 chunk 221 optimal weight: 9.9990 chunk 267 optimal weight: 3.9990 chunk 277 optimal weight: 6.9990 chunk 186 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 183 optimal weight: 2.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 115 GLN A 784 GLN ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 926 GLN B 115 GLN ** B 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 GLN C 164 ASN C 314 GLN ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.128621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.079231 restraints weight = 51507.261| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 3.16 r_work: 0.2916 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.103 25395 Z= 0.319 Angle : 0.704 9.740 34668 Z= 0.355 Chirality : 0.051 0.355 4083 Planarity : 0.004 0.039 4380 Dihedral : 4.830 26.713 3273 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.80 % Allowed : 7.56 % Favored : 90.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.15), residues: 3021 helix: 1.48 (0.20), residues: 657 sheet: 0.62 (0.19), residues: 705 loop : -0.67 (0.14), residues: 1659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A1107 TYR 0.017 0.002 TYR A 200 PHE 0.026 0.002 PHE B 220 TRP 0.015 0.002 TRP A 886 HIS 0.006 0.001 HIS B1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00745 / 0.32 (25293) covalent geometry : angle 0.67564 / 0.35 (34404) SS BOND : bond 0.00446 / 0.30 ( 42) SS BOND : angle 1.46269 / 0.99 ( 84) hydrogen bonds : bond 0.04642 / 3.02 ( 971) hydrogen bonds : angle 5.93932 / 4.09 ( 2805) link_BETA1-4 : bond 0.00226 / 0.13 ( 12) link_BETA1-4 : angle 1.05664 / 0.67 ( 36) link_NAG-ASN : bond 0.00538 / 0.34 ( 48) link_NAG-ASN : angle 2.96214 / 1.93 ( 144) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6042 Ramachandran restraints generated. 3021 Oldfield, 0 Emsley, 3021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6042 Ramachandran restraints generated. 3021 Oldfield, 0 Emsley, 3021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 144 time to evaluate : 1.004 Fit side-chains REVERT: A 52 GLN cc_start: 0.8643 (tm-30) cc_final: 0.8030 (tm-30) REVERT: A 271 GLN cc_start: 0.7937 (mt0) cc_final: 0.7614 (mt0) REVERT: A 979 ASP cc_start: 0.8305 (m-30) cc_final: 0.7725 (t0) REVERT: A 1092 GLU cc_start: 0.7215 (tp30) cc_final: 0.6792 (tp30) REVERT: A 1107 ARG cc_start: 0.8768 (mtt90) cc_final: 0.8313 (mtm-85) REVERT: B 505 TYR cc_start: 0.8400 (t80) cc_final: 0.7497 (t80) REVERT: B 1092 GLU cc_start: 0.7390 (tp30) cc_final: 0.7114 (tp30) REVERT: C 52 GLN cc_start: 0.8669 (tm-30) cc_final: 0.8075 (tm-30) REVERT: C 271 GLN cc_start: 0.7742 (mt0) cc_final: 0.7500 (mt0) REVERT: C 314 GLN cc_start: 0.8940 (tt0) cc_final: 0.8682 (tt0) REVERT: C 979 ASP cc_start: 0.8370 (m-30) cc_final: 0.7979 (t0) outliers start: 48 outliers final: 29 residues processed: 182 average time/residue: 0.1513 time to fit residues: 46.8908 Evaluate side-chains 152 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 123 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1089 PHE Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1089 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 211 optimal weight: 0.4980 chunk 83 optimal weight: 0.9980 chunk 185 optimal weight: 0.8980 chunk 300 optimal weight: 7.9990 chunk 53 optimal weight: 3.9990 chunk 263 optimal weight: 0.8980 chunk 267 optimal weight: 0.7980 chunk 95 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 284 optimal weight: 0.6980 chunk 12 optimal weight: 9.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN ** B 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN C 99 ASN ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.131794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.083637 restraints weight = 51229.591| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 3.15 r_work: 0.2995 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.2610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 25395 Z= 0.111 Angle : 0.575 12.879 34668 Z= 0.286 Chirality : 0.046 0.354 4083 Planarity : 0.003 0.036 4380 Dihedral : 4.412 23.385 3273 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.35 % Allowed : 8.79 % Favored : 89.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.15), residues: 3021 helix: 1.87 (0.21), residues: 657 sheet: 0.56 (0.19), residues: 720 loop : -0.60 (0.14), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1107 TYR 0.018 0.001 TYR A 351 PHE 0.021 0.001 PHE B 220 TRP 0.014 0.001 TRP A 104 HIS 0.002 0.000 HIS C1083 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 (25293) covalent geometry : angle 0.54835 / 0.28 (34404) SS BOND : bond 0.00297 / 0.20 ( 42) SS BOND : angle 1.18001 / 0.79 ( 84) hydrogen bonds : bond 0.03644 / 2.37 ( 971) hydrogen bonds : angle 5.54684 / 3.82 ( 2805) link_BETA1-4 : bond 0.00359 / 0.21 ( 12) link_BETA1-4 : angle 0.85789 / 0.54 ( 36) link_NAG-ASN : bond 0.00568 / 0.37 ( 48) link_NAG-ASN : angle 2.62203 / 1.72 ( 144) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6042 Ramachandran restraints generated. 3021 Oldfield, 0 Emsley, 3021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6042 Ramachandran restraints generated. 3021 Oldfield, 0 Emsley, 3021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 140 time to evaluate : 0.992 Fit side-chains revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8631 (tm-30) cc_final: 0.8033 (tm-30) REVERT: A 271 GLN cc_start: 0.7876 (mt0) cc_final: 0.7602 (mt0) REVERT: A 979 ASP cc_start: 0.8224 (m-30) cc_final: 0.7683 (t0) REVERT: A 988 GLU cc_start: 0.8337 (pm20) cc_final: 0.7950 (pm20) REVERT: A 1045 LYS cc_start: 0.8427 (ptmm) cc_final: 0.7841 (tttm) REVERT: B 177 MET cc_start: 0.2503 (ptt) cc_final: 0.2126 (ptt) REVERT: B 271 GLN cc_start: 0.7918 (mt0) cc_final: 0.7605 (mt0) REVERT: B 988 GLU cc_start: 0.8351 (pm20) cc_final: 0.8074 (pm20) REVERT: B 1092 GLU cc_start: 0.7205 (tp30) cc_final: 0.6948 (tp30) REVERT: C 52 GLN cc_start: 0.8615 (tm-30) cc_final: 0.7959 (tm-30) REVERT: C 271 GLN cc_start: 0.7585 (mt0) cc_final: 0.7360 (mt0) REVERT: C 979 ASP cc_start: 0.8335 (m-30) cc_final: 0.7884 (t0) REVERT: C 988 GLU cc_start: 0.8330 (pm20) cc_final: 0.8084 (pm20) outliers start: 36 outliers final: 19 residues processed: 167 average time/residue: 0.1585 time to fit residues: 44.7077 Evaluate side-chains 147 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 128 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 1092 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 203 optimal weight: 3.9990 chunk 294 optimal weight: 0.7980 chunk 195 optimal weight: 4.9990 chunk 233 optimal weight: 10.0000 chunk 264 optimal weight: 7.9990 chunk 45 optimal weight: 5.9990 chunk 59 optimal weight: 0.0030 chunk 121 optimal weight: 7.9990 chunk 215 optimal weight: 30.0000 chunk 186 optimal weight: 0.8980 chunk 67 optimal weight: 3.9990 overall best weight: 1.9394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 99 ASN A 164 ASN ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.130549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.082046 restraints weight = 51130.992| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 3.14 r_work: 0.2958 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.2813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 25395 Z= 0.163 Angle : 0.572 9.747 34668 Z= 0.286 Chirality : 0.046 0.351 4083 Planarity : 0.003 0.039 4380 Dihedral : 4.429 32.251 3273 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.53 % Allowed : 9.39 % Favored : 89.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.36 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.15), residues: 3021 helix: 1.87 (0.21), residues: 657 sheet: 0.50 (0.19), residues: 717 loop : -0.54 (0.15), residues: 1647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1107 TYR 0.017 0.001 TYR C 505 PHE 0.016 0.001 PHE B 220 TRP 0.015 0.001 TRP A 104 HIS 0.003 0.001 HIS B1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.16 (25293) covalent geometry : angle 0.54696 / 0.28 (34404) SS BOND : bond 0.00611 / 0.41 ( 42) SS BOND : angle 1.47453 / 0.96 ( 84) hydrogen bonds : bond 0.03786 / 2.45 ( 971) hydrogen bonds : angle 5.45243 / 3.75 ( 2805) link_BETA1-4 : bond 0.00392 / 0.19 ( 12) link_BETA1-4 : angle 0.91747 / 0.59 ( 36) link_NAG-ASN : bond 0.00492 / 0.33 ( 48) link_NAG-ASN : angle 2.43862 / 1.60 ( 144) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6042 Ramachandran restraints generated. 3021 Oldfield, 0 Emsley, 3021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6042 Ramachandran restraints generated. 3021 Oldfield, 0 Emsley, 3021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 138 time to evaluate : 0.949 Fit side-chains revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8687 (tm-30) cc_final: 0.8202 (tm-30) REVERT: A 271 GLN cc_start: 0.7946 (mt0) cc_final: 0.7610 (mt0) REVERT: A 979 ASP cc_start: 0.8240 (m-30) cc_final: 0.7756 (t0) REVERT: B 52 GLN cc_start: 0.8567 (tm-30) cc_final: 0.7838 (tm-30) REVERT: B 271 GLN cc_start: 0.7950 (mt0) cc_final: 0.7610 (mt0) REVERT: B 988 GLU cc_start: 0.8451 (pm20) cc_final: 0.8238 (pm20) REVERT: B 1092 GLU cc_start: 0.7283 (tp30) cc_final: 0.7025 (tp30) REVERT: C 52 GLN cc_start: 0.8605 (tm-30) cc_final: 0.7930 (tm-30) REVERT: C 271 GLN cc_start: 0.7628 (mt0) cc_final: 0.7394 (mt0) REVERT: C 505 TYR cc_start: 0.7944 (t80) cc_final: 0.7610 (t80) REVERT: C 979 ASP cc_start: 0.8299 (m-30) cc_final: 0.7986 (t0) REVERT: C 988 GLU cc_start: 0.8426 (pm20) cc_final: 0.8173 (pm20) outliers start: 41 outliers final: 26 residues processed: 168 average time/residue: 0.1423 time to fit residues: 41.5477 Evaluate side-chains 150 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 124 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 1092 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 16 optimal weight: 30.0000 chunk 249 optimal weight: 5.9990 chunk 92 optimal weight: 5.9990 chunk 283 optimal weight: 0.9980 chunk 225 optimal weight: 10.0000 chunk 105 optimal weight: 10.0000 chunk 13 optimal weight: 8.9990 chunk 103 optimal weight: 8.9990 chunk 179 optimal weight: 3.9990 chunk 11 optimal weight: 30.0000 chunk 257 optimal weight: 3.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 655 HIS A 913 GLN A1005 GLN B 164 ASN B 655 HIS ** B 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 655 HIS ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1011 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.127761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.078669 restraints weight = 51555.144| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 3.15 r_work: 0.2893 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.3074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.087 25395 Z= 0.299 Angle : 0.646 9.662 34668 Z= 0.325 Chirality : 0.049 0.349 4083 Planarity : 0.004 0.038 4380 Dihedral : 4.676 29.849 3273 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.39 % Allowed : 9.39 % Favored : 88.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.15), residues: 3021 helix: 1.61 (0.20), residues: 657 sheet: 0.49 (0.19), residues: 708 loop : -0.58 (0.15), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C1014 TYR 0.014 0.002 TYR B 200 PHE 0.018 0.002 PHE B 220 TRP 0.013 0.002 TRP A 886 HIS 0.005 0.001 HIS B1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00702 / 0.30 (25293) covalent geometry : angle 0.62466 / 0.32 (34404) SS BOND : bond 0.00480 / 0.32 ( 42) SS BOND : angle 1.34092 / 0.87 ( 84) hydrogen bonds : bond 0.04381 / 2.83 ( 971) hydrogen bonds : angle 5.64456 / 3.88 ( 2805) link_BETA1-4 : bond 0.00175 / 0.09 ( 12) link_BETA1-4 : angle 0.90418 / 0.58 ( 36) link_NAG-ASN : bond 0.00459 / 0.31 ( 48) link_NAG-ASN : angle 2.42023 / 1.58 ( 144) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6042 Ramachandran restraints generated. 3021 Oldfield, 0 Emsley, 3021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6042 Ramachandran restraints generated. 3021 Oldfield, 0 Emsley, 3021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 127 time to evaluate : 0.994 Fit side-chains REVERT: A 52 GLN cc_start: 0.8733 (tm-30) cc_final: 0.8074 (tm-30) REVERT: A 902 MET cc_start: 0.8981 (mmm) cc_final: 0.8671 (tpt) REVERT: A 950 ASP cc_start: 0.8618 (m-30) cc_final: 0.8269 (m-30) REVERT: A 979 ASP cc_start: 0.8283 (m-30) cc_final: 0.7712 (t0) REVERT: A 988 GLU cc_start: 0.8463 (pm20) cc_final: 0.8195 (pm20) REVERT: B 52 GLN cc_start: 0.8661 (tm-30) cc_final: 0.7934 (tm-30) REVERT: B 505 TYR cc_start: 0.8608 (t80) cc_final: 0.7705 (t80) REVERT: B 950 ASP cc_start: 0.8620 (m-30) cc_final: 0.8262 (m-30) REVERT: B 988 GLU cc_start: 0.8413 (pm20) cc_final: 0.8179 (pm20) REVERT: B 1092 GLU cc_start: 0.7345 (tp30) cc_final: 0.7014 (tp30) REVERT: C 52 GLN cc_start: 0.8697 (tm-30) cc_final: 0.8024 (tm-30) REVERT: C 314 GLN cc_start: 0.8958 (tt0) cc_final: 0.8710 (tt0) REVERT: C 505 TYR cc_start: 0.8147 (t80) cc_final: 0.7867 (t80) REVERT: C 979 ASP cc_start: 0.8372 (m-30) cc_final: 0.8036 (t0) REVERT: C 988 GLU cc_start: 0.8369 (pm20) cc_final: 0.8107 (pm20) outliers start: 64 outliers final: 45 residues processed: 181 average time/residue: 0.1377 time to fit residues: 43.5859 Evaluate side-chains 165 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 120 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 1089 PHE Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1123 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 39 optimal weight: 20.0000 chunk 250 optimal weight: 20.0000 chunk 222 optimal weight: 20.0000 chunk 2 optimal weight: 8.9990 chunk 143 optimal weight: 7.9990 chunk 126 optimal weight: 0.6980 chunk 50 optimal weight: 8.9990 chunk 179 optimal weight: 0.7980 chunk 248 optimal weight: 20.0000 chunk 52 optimal weight: 0.9980 chunk 166 optimal weight: 2.9990 overall best weight: 2.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1135 ASN ** B 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 913 GLN ** 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 = 0.3998 r_free = 0.3998 target = 0.128493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.079793 restraints weight = 51102.853| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 3.14 r_work: 0.2930 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.3165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 25395 Z= 0.204 Angle : 0.587 9.648 34668 Z= 0.294 Chirality : 0.047 0.346 4083 Planarity : 0.003 0.040 4380 Dihedral : 4.530 27.273 3273 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.28 % Allowed : 9.84 % Favored : 87.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.15), residues: 3021 helix: 1.70 (0.20), residues: 657 sheet: 0.45 (0.19), residues: 717 loop : -0.59 (0.15), residues: 1647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1107 TYR 0.014 0.001 TYR A1067 PHE 0.017 0.001 PHE B 220 TRP 0.012 0.001 TRP A 104 HIS 0.003 0.001 HIS B1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00474 / 0.20 (25293) covalent geometry : angle 0.56646 / 0.29 (34404) SS BOND : bond 0.00430 / 0.29 ( 42) SS BOND : angle 1.15228 / 0.75 ( 84) hydrogen bonds : bond 0.03967 / 2.57 ( 971) hydrogen bonds : angle 5.51941 / 3.79 ( 2805) link_BETA1-4 : bond 0.00218 / 0.13 ( 12) link_BETA1-4 : angle 0.86837 / 0.55 ( 36) link_NAG-ASN : bond 0.00466 / 0.32 ( 48) link_NAG-ASN : angle 2.33552 / 1.53 ( 144) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6042 Ramachandran restraints generated. 3021 Oldfield, 0 Emsley, 3021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6042 Ramachandran restraints generated. 3021 Oldfield, 0 Emsley, 3021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 133 time to evaluate : 0.964 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8743 (tm-30) cc_final: 0.8055 (tm-30) REVERT: A 902 MET cc_start: 0.8973 (mmm) cc_final: 0.8665 (tpt) REVERT: A 979 ASP cc_start: 0.8310 (m-30) cc_final: 0.7866 (t0) REVERT: A 1123 SER cc_start: 0.8280 (t) cc_final: 0.8011 (m) REVERT: B 52 GLN cc_start: 0.8707 (tm-30) cc_final: 0.7969 (tm-30) REVERT: B 104 TRP cc_start: 0.6445 (m-90) cc_final: 0.6028 (m-90) REVERT: B 988 GLU cc_start: 0.8415 (pm20) cc_final: 0.8169 (pm20) REVERT: B 1092 GLU cc_start: 0.7414 (tp30) cc_final: 0.7086 (tp30) REVERT: C 52 GLN cc_start: 0.8718 (tm-30) cc_final: 0.8040 (tm-30) REVERT: C 104 TRP cc_start: 0.6378 (m-90) cc_final: 0.5976 (m-90) REVERT: C 505 TYR cc_start: 0.8150 (t80) cc_final: 0.7827 (t80) REVERT: C 957 GLN cc_start: 0.8883 (tt0) cc_final: 0.8655 (tt0) REVERT: C 979 ASP cc_start: 0.8346 (m-30) cc_final: 0.8045 (t0) REVERT: C 988 GLU cc_start: 0.8386 (pm20) cc_final: 0.8123 (pm20) outliers start: 61 outliers final: 44 residues processed: 186 average time/residue: 0.1385 time to fit residues: 44.7599 Evaluate side-chains 171 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 127 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 1092 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 166 optimal weight: 1.9990 chunk 108 optimal weight: 20.0000 chunk 124 optimal weight: 10.0000 chunk 136 optimal weight: 10.0000 chunk 270 optimal weight: 0.6980 chunk 181 optimal weight: 0.6980 chunk 25 optimal weight: 0.6980 chunk 46 optimal weight: 5.9990 chunk 303 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 291 optimal weight: 0.9980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 913 GLN B1135 ASN C 913 GLN C1135 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.130494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.082310 restraints weight = 51128.248| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 3.14 r_work: 0.2965 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.3276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 25395 Z= 0.115 Angle : 0.548 9.901 34668 Z= 0.272 Chirality : 0.045 0.343 4083 Planarity : 0.003 0.043 4380 Dihedral : 4.255 24.320 3273 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.87 % Allowed : 10.55 % Favored : 87.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.15), residues: 3021 helix: 1.93 (0.21), residues: 657 sheet: 0.41 (0.19), residues: 768 loop : -0.53 (0.15), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1107 TYR 0.015 0.001 TYR B1067 PHE 0.022 0.001 PHE C1089 TRP 0.015 0.001 TRP A 104 HIS 0.002 0.000 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.11 (25293) covalent geometry : angle 0.52790 / 0.27 (34404) SS BOND : bond 0.00412 / 0.28 ( 42) SS BOND : angle 0.99302 / 0.65 ( 84) hydrogen bonds : bond 0.03470 / 2.24 ( 971) hydrogen bonds : angle 5.27302 / 3.62 ( 2805) link_BETA1-4 : bond 0.00310 / 0.18 ( 12) link_BETA1-4 : angle 0.82220 / 0.52 ( 36) link_NAG-ASN : bond 0.00494 / 0.34 ( 48) link_NAG-ASN : angle 2.20110 / 1.44 ( 144) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6042 Ramachandran restraints generated. 3021 Oldfield, 0 Emsley, 3021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6042 Ramachandran restraints generated. 3021 Oldfield, 0 Emsley, 3021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 141 time to evaluate : 1.008 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8734 (tm-30) cc_final: 0.8237 (tm-30) REVERT: A 271 GLN cc_start: 0.7991 (mt0) cc_final: 0.7702 (mt0) REVERT: A 979 ASP cc_start: 0.8270 (m-30) cc_final: 0.7916 (t0) REVERT: A 988 GLU cc_start: 0.8438 (pm20) cc_final: 0.8121 (pm20) REVERT: A 1123 SER cc_start: 0.8062 (t) cc_final: 0.7754 (m) REVERT: B 52 GLN cc_start: 0.8681 (tm-30) cc_final: 0.7926 (tm-30) REVERT: B 104 TRP cc_start: 0.6286 (m-90) cc_final: 0.5797 (m-90) REVERT: B 271 GLN cc_start: 0.8029 (mt0) cc_final: 0.7680 (mt0) REVERT: B 1092 GLU cc_start: 0.7207 (tp30) cc_final: 0.6940 (tp30) REVERT: C 52 GLN cc_start: 0.8747 (tm-30) cc_final: 0.8015 (tm-30) REVERT: C 271 GLN cc_start: 0.7708 (mt0) cc_final: 0.7467 (mt0) REVERT: C 979 ASP cc_start: 0.8295 (m-30) cc_final: 0.7998 (t0) REVERT: C 988 GLU cc_start: 0.8348 (pm20) cc_final: 0.8060 (pm20) outliers start: 50 outliers final: 39 residues processed: 185 average time/residue: 0.1438 time to fit residues: 46.2517 Evaluate side-chains 166 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 127 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 619 GLU Chi-restraints excluded: chain C residue 1092 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 173 optimal weight: 6.9990 chunk 50 optimal weight: 8.9990 chunk 145 optimal weight: 2.9990 chunk 105 optimal weight: 5.9990 chunk 157 optimal weight: 6.9990 chunk 196 optimal weight: 5.9990 chunk 268 optimal weight: 0.9990 chunk 137 optimal weight: 9.9990 chunk 207 optimal weight: 7.9990 chunk 129 optimal weight: 0.4980 chunk 69 optimal weight: 0.9980 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.129363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.080697 restraints weight = 51027.140| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 3.19 r_work: 0.2940 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.3338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 25395 Z= 0.181 Angle : 0.574 9.684 34668 Z= 0.284 Chirality : 0.046 0.341 4083 Planarity : 0.003 0.042 4380 Dihedral : 4.320 23.977 3273 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.76 % Allowed : 11.15 % Favored : 87.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.15), residues: 3021 helix: 1.83 (0.21), residues: 660 sheet: 0.68 (0.20), residues: 672 loop : -0.57 (0.15), residues: 1689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1107 TYR 0.014 0.001 TYR A1138 PHE 0.016 0.001 PHE C 201 TRP 0.015 0.001 TRP A 104 HIS 0.003 0.001 HIS C1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.18 (25293) covalent geometry : angle 0.55496 / 0.28 (34404) SS BOND : bond 0.00347 / 0.24 ( 42) SS BOND : angle 1.07787 / 0.71 ( 84) hydrogen bonds : bond 0.03779 / 2.44 ( 971) hydrogen bonds : angle 5.31374 / 3.65 ( 2805) link_BETA1-4 : bond 0.00254 / 0.14 ( 12) link_BETA1-4 : angle 0.85959 / 0.55 ( 36) link_NAG-ASN : bond 0.00453 / 0.32 ( 48) link_NAG-ASN : angle 2.19239 / 1.44 ( 144) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6042 Ramachandran restraints generated. 3021 Oldfield, 0 Emsley, 3021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6042 Ramachandran restraints generated. 3021 Oldfield, 0 Emsley, 3021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 132 time to evaluate : 0.991 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8732 (tm-30) cc_final: 0.8229 (tm-30) REVERT: A 271 GLN cc_start: 0.8022 (mt0) cc_final: 0.7729 (mt0) REVERT: A 950 ASP cc_start: 0.8522 (m-30) cc_final: 0.8150 (m-30) REVERT: A 979 ASP cc_start: 0.8270 (m-30) cc_final: 0.7871 (t0) REVERT: A 988 GLU cc_start: 0.8373 (pm20) cc_final: 0.8076 (pm20) REVERT: A 1123 SER cc_start: 0.8070 (t) cc_final: 0.7841 (m) REVERT: B 52 GLN cc_start: 0.8707 (tm-30) cc_final: 0.7981 (tm-30) REVERT: B 104 TRP cc_start: 0.6375 (m-90) cc_final: 0.5917 (m-90) REVERT: B 271 GLN cc_start: 0.8065 (mt0) cc_final: 0.7682 (mt0) REVERT: B 988 GLU cc_start: 0.8317 (pm20) cc_final: 0.8013 (pm20) REVERT: B 1092 GLU cc_start: 0.7344 (tp30) cc_final: 0.7080 (tp30) REVERT: C 52 GLN cc_start: 0.8749 (tm-30) cc_final: 0.8012 (tm-30) REVERT: C 271 GLN cc_start: 0.7753 (mt0) cc_final: 0.7501 (mt0) REVERT: C 979 ASP cc_start: 0.8325 (m-30) cc_final: 0.8058 (t0) REVERT: C 988 GLU cc_start: 0.8288 (pm20) cc_final: 0.8043 (pm20) outliers start: 47 outliers final: 41 residues processed: 172 average time/residue: 0.1496 time to fit residues: 44.6007 Evaluate side-chains 164 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 123 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 619 GLU Chi-restraints excluded: chain C residue 1045 LYS Chi-restraints excluded: chain C residue 1092 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 2 optimal weight: 3.9990 chunk 121 optimal weight: 5.9990 chunk 282 optimal weight: 0.7980 chunk 179 optimal weight: 3.9990 chunk 144 optimal weight: 40.0000 chunk 239 optimal weight: 10.0000 chunk 48 optimal weight: 7.9990 chunk 112 optimal weight: 0.6980 chunk 223 optimal weight: 5.9990 chunk 302 optimal weight: 4.9990 chunk 137 optimal weight: 10.0000 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.128691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.079889 restraints weight = 51008.085| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 3.20 r_work: 0.2926 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.3419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 25395 Z= 0.217 Angle : 0.593 9.611 34668 Z= 0.296 Chirality : 0.047 0.338 4083 Planarity : 0.003 0.042 4380 Dihedral : 4.415 23.847 3273 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.76 % Allowed : 11.49 % Favored : 86.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.15), residues: 3021 helix: 1.74 (0.21), residues: 660 sheet: 0.66 (0.20), residues: 672 loop : -0.60 (0.15), residues: 1689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1107 TYR 0.014 0.001 TYR C 351 PHE 0.017 0.001 PHE C 201 TRP 0.013 0.001 TRP A 104 HIS 0.004 0.001 HIS B1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00505 / 0.22 (25293) covalent geometry : angle 0.57427 / 0.29 (34404) SS BOND : bond 0.00408 / 0.28 ( 42) SS BOND : angle 1.13936 / 0.75 ( 84) hydrogen bonds : bond 0.03909 / 2.53 ( 971) hydrogen bonds : angle 5.36047 / 3.68 ( 2805) link_BETA1-4 : bond 0.00196 / 0.12 ( 12) link_BETA1-4 : angle 0.84189 / 0.54 ( 36) link_NAG-ASN : bond 0.00443 / 0.31 ( 48) link_NAG-ASN : angle 2.22428 / 1.47 ( 144) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6042 Ramachandran restraints generated. 3021 Oldfield, 0 Emsley, 3021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6042 Ramachandran restraints generated. 3021 Oldfield, 0 Emsley, 3021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 127 time to evaluate : 1.020 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8758 (tm-30) cc_final: 0.8044 (tm-30) REVERT: A 271 GLN cc_start: 0.8054 (mt0) cc_final: 0.7738 (mt0) REVERT: A 902 MET cc_start: 0.8979 (mmm) cc_final: 0.8661 (tpt) REVERT: A 979 ASP cc_start: 0.8289 (m-30) cc_final: 0.7882 (t0) REVERT: A 988 GLU cc_start: 0.8353 (pm20) cc_final: 0.8032 (pm20) REVERT: A 1089 PHE cc_start: 0.8673 (OUTLIER) cc_final: 0.8109 (m-80) REVERT: B 52 GLN cc_start: 0.8767 (tm-30) cc_final: 0.8053 (tm-30) REVERT: B 104 TRP cc_start: 0.6376 (m-90) cc_final: 0.5924 (m-90) REVERT: B 271 GLN cc_start: 0.8075 (mt0) cc_final: 0.7718 (mt0) REVERT: B 988 GLU cc_start: 0.8404 (pm20) cc_final: 0.8123 (pm20) REVERT: B 1092 GLU cc_start: 0.7445 (tp30) cc_final: 0.7143 (tp30) REVERT: C 52 GLN cc_start: 0.8771 (tm-30) cc_final: 0.8027 (tm-30) REVERT: C 271 GLN cc_start: 0.7765 (mt0) cc_final: 0.7510 (mt0) REVERT: C 979 ASP cc_start: 0.8330 (m-30) cc_final: 0.8067 (t0) REVERT: C 988 GLU cc_start: 0.8290 (pm20) cc_final: 0.8057 (pm20) outliers start: 47 outliers final: 44 residues processed: 166 average time/residue: 0.1439 time to fit residues: 41.8839 Evaluate side-chains 168 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 123 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1089 PHE Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 619 GLU Chi-restraints excluded: chain C residue 1045 LYS Chi-restraints excluded: chain C residue 1092 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 35 optimal weight: 0.9980 chunk 189 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 289 optimal weight: 3.9990 chunk 113 optimal weight: 8.9990 chunk 78 optimal weight: 0.8980 chunk 299 optimal weight: 3.9990 chunk 206 optimal weight: 5.9990 chunk 48 optimal weight: 3.9990 chunk 5 optimal weight: 10.0000 chunk 4 optimal weight: 2.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C1002 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.128933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.080298 restraints weight = 50734.758| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 3.15 r_work: 0.2945 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.3487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 25395 Z= 0.173 Angle : 0.570 9.732 34668 Z= 0.283 Chirality : 0.046 0.336 4083 Planarity : 0.003 0.042 4380 Dihedral : 4.347 23.159 3273 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.68 % Allowed : 11.75 % Favored : 86.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.15), residues: 3021 helix: 1.77 (0.21), residues: 660 sheet: 0.64 (0.19), residues: 672 loop : -0.59 (0.15), residues: 1689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1107 TYR 0.016 0.001 TYR C 351 PHE 0.017 0.001 PHE C 201 TRP 0.017 0.001 TRP A 104 HIS 0.003 0.001 HIS B1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.17 (25293) covalent geometry : angle 0.55119 / 0.28 (34404) SS BOND : bond 0.00417 / 0.29 ( 42) SS BOND : angle 1.06243 / 0.70 ( 84) hydrogen bonds : bond 0.03718 / 2.41 ( 971) hydrogen bonds : angle 5.27961 / 3.62 ( 2805) link_BETA1-4 : bond 0.00246 / 0.14 ( 12) link_BETA1-4 : angle 0.84066 / 0.53 ( 36) link_NAG-ASN : bond 0.00452 / 0.32 ( 48) link_NAG-ASN : angle 2.17559 / 1.44 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6559.19 seconds wall clock time: 113 minutes 16.89 seconds (6796.89 seconds total)