Starting phenix.real_space_refine on Thu Mar 5 19:34:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6zoy_11330/03_2026/6zoy_11330.cif Found real_map, /net/cci-nas-00/data/ceres_data/6zoy_11330/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/6zoy_11330/03_2026/6zoy_11330.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6zoy_11330/03_2026/6zoy_11330.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6zoy_11330/03_2026/6zoy_11330.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6zoy_11330/03_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 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 dihedrals: 36 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 dihedrals: 36 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 dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Time building chain proxies: 5.29, per 1000 atoms: 0.21 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: 2.13 Conformation dependent library (CDL) restraints added in 990.1 milliseconds 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: 1.01 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: 6.48 Time building geometry restraints manager: 2.87 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: 14774 17.93 - 35.86: 754 35.86 - 53.80: 231 53.80 - 71.73: 57 71.73 - 89.66: 39 Dihedral angle restraints: 15855 sinusoidal: 6945 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 15852 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: 0.05 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: 1.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 23.720 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.060 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:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 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 : 13.073 89.660 9993 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 covalent geometry : bond 0.01075 (25293) covalent geometry : angle 1.24777 (34404) SS BOND : bond 0.01434 ( 42) SS BOND : angle 3.10829 ( 84) hydrogen bonds : bond 0.14511 ( 971) hydrogen bonds : angle 8.14625 ( 2805) link_BETA1-4 : bond 0.06582 ( 12) link_BETA1-4 : angle 12.91823 ( 36) link_NAG-ASN : bond 0.01221 ( 48) link_NAG-ASN : angle 5.64834 ( 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 : 0.699 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: 0.1613 time to fit residues: 70.1165 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 : 0.820 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 81 ASN 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: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.133937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.086988 restraints weight = 51120.465| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 3.13 r_work: 0.3068 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.1709 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 : 0.694 9.566 34668 Z= 0.348 Chirality : 0.049 0.369 4083 Planarity : 0.004 0.036 4380 Dihedral : 7.121 51.200 4535 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 0.67 % Allowed : 6.06 % Favored : 93.27 % 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: 0.49 (0.14), residues: 3021 helix: 1.88 (0.20), residues: 645 sheet: 0.67 (0.18), residues: 687 loop : -0.42 (0.14), residues: 1689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1107 TYR 0.026 0.002 TYR C 423 PHE 0.035 0.002 PHE A 220 TRP 0.014 0.002 TRP A 104 HIS 0.003 0.001 HIS B 66 Details of bonding type rmsd covalent geometry : bond 0.00309 (25293) covalent geometry : angle 0.64970 (34404) SS BOND : bond 0.00465 ( 42) SS BOND : angle 1.41738 ( 84) hydrogen bonds : bond 0.04558 ( 971) hydrogen bonds : angle 6.15942 ( 2805) link_BETA1-4 : bond 0.00437 ( 12) link_BETA1-4 : angle 1.27469 ( 36) link_NAG-ASN : bond 0.00642 ( 48) link_NAG-ASN : angle 3.66156 ( 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 199 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 181 time to evaluate : 0.782 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8470 (tm-30) cc_final: 0.7856 (tm-30) REVERT: A 360 ASN cc_start: 0.9140 (m110) cc_final: 0.8846 (t0) REVERT: A 950 ASP cc_start: 0.8167 (m-30) cc_final: 0.7910 (m-30) REVERT: A 979 ASP cc_start: 0.8355 (m-30) cc_final: 0.7636 (t0) REVERT: B 309 GLU cc_start: 0.8542 (mp0) cc_final: 0.8329 (mp0) REVERT: B 505 TYR cc_start: 0.8207 (t80) cc_final: 0.7911 (t80) REVERT: C 979 ASP cc_start: 0.8441 (m-30) cc_final: 0.7845 (t0) outliers start: 18 outliers final: 12 residues processed: 192 average time/residue: 0.1415 time to fit residues: 45.0967 Evaluate side-chains 148 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 136 time to evaluate : 0.698 ------------------------------------------------------------------------------- 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: 30.0000 chunk 210 optimal weight: 20.0000 chunk 74 optimal weight: 10.0000 chunk 129 optimal weight: 9.9990 chunk 221 optimal weight: 8.9990 chunk 267 optimal weight: 3.9990 chunk 277 optimal weight: 6.9990 chunk 186 optimal weight: 2.9990 chunk 10 optimal weight: 0.0770 chunk 183 optimal weight: 0.5980 overall best weight: 2.9344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 784 GLN ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 926 GLN A 957 GLN ** B 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN C 314 GLN ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.130713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.082045 restraints weight = 51302.361| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 3.15 r_work: 0.2956 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 25395 Z= 0.234 Angle : 0.649 9.736 34668 Z= 0.325 Chirality : 0.049 0.355 4083 Planarity : 0.004 0.037 4380 Dihedral : 6.260 53.184 4533 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.42 % Allowed : 7.71 % Favored : 90.87 % 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: 0.30 (0.15), residues: 3021 helix: 1.70 (0.20), residues: 657 sheet: 0.61 (0.19), residues: 690 loop : -0.58 (0.14), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A1107 TYR 0.014 0.002 TYR A1067 PHE 0.022 0.002 PHE B 220 TRP 0.014 0.002 TRP A 104 HIS 0.004 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00549 (25293) covalent geometry : angle 0.61727 (34404) SS BOND : bond 0.00416 ( 42) SS BOND : angle 1.34242 ( 84) hydrogen bonds : bond 0.04272 ( 971) hydrogen bonds : angle 5.79992 ( 2805) link_BETA1-4 : bond 0.00266 ( 12) link_BETA1-4 : angle 1.16716 ( 36) link_NAG-ASN : bond 0.00531 ( 48) link_NAG-ASN : angle 2.98422 ( 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 181 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 143 time to evaluate : 0.856 Fit side-chains REVERT: A 52 GLN cc_start: 0.8629 (tm-30) cc_final: 0.8119 (tm-30) REVERT: A 271 GLN cc_start: 0.7862 (mt0) cc_final: 0.7508 (mt0) REVERT: A 979 ASP cc_start: 0.8341 (m-30) cc_final: 0.7697 (t0) REVERT: A 988 GLU cc_start: 0.8313 (pm20) cc_final: 0.8024 (pm20) REVERT: A 1092 GLU cc_start: 0.7248 (tp30) cc_final: 0.6893 (tp30) REVERT: A 1107 ARG cc_start: 0.8786 (mtt90) cc_final: 0.8414 (mtm-85) REVERT: B 177 MET cc_start: 0.2403 (ptt) cc_final: 0.1981 (ptt) REVERT: B 271 GLN cc_start: 0.7981 (mt0) cc_final: 0.7741 (mt0) REVERT: B 505 TYR cc_start: 0.8344 (t80) cc_final: 0.7403 (t80) REVERT: B 1092 GLU cc_start: 0.7279 (tp30) cc_final: 0.7031 (tp30) REVERT: C 52 GLN cc_start: 0.8628 (tm-30) cc_final: 0.8030 (tm-30) REVERT: C 271 GLN cc_start: 0.7584 (mt0) cc_final: 0.7362 (mt0) REVERT: C 314 GLN cc_start: 0.8926 (tt0) cc_final: 0.8682 (tt0) REVERT: C 979 ASP cc_start: 0.8372 (m-30) cc_final: 0.7943 (t0) outliers start: 38 outliers final: 21 residues processed: 172 average time/residue: 0.1274 time to fit residues: 37.8116 Evaluate side-chains 150 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 129 time to evaluate : 0.631 ------------------------------------------------------------------------------- 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 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 524 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 915 VAL 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 277 LEU 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 994 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 211 optimal weight: 20.0000 chunk 83 optimal weight: 0.9990 chunk 185 optimal weight: 0.9990 chunk 300 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 263 optimal weight: 3.9990 chunk 267 optimal weight: 0.9990 chunk 95 optimal weight: 3.9990 chunk 73 optimal weight: 0.0670 chunk 284 optimal weight: 4.9990 chunk 12 optimal weight: 4.9990 overall best weight: 1.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN ** 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 = 0.4036 r_free = 0.4036 target = 0.131280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.082912 restraints weight = 51084.484| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 3.13 r_work: 0.2991 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.2561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 25395 Z= 0.133 Angle : 0.575 13.326 34668 Z= 0.287 Chirality : 0.046 0.337 4083 Planarity : 0.003 0.036 4380 Dihedral : 5.706 54.101 4533 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.50 % Allowed : 8.34 % Favored : 90.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.68 % 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: 0.41 (0.15), residues: 3021 helix: 1.94 (0.21), residues: 657 sheet: 0.55 (0.19), residues: 723 loop : -0.54 (0.15), residues: 1641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1107 TYR 0.014 0.001 TYR A1067 PHE 0.023 0.001 PHE A 490 TRP 0.019 0.001 TRP A 104 HIS 0.002 0.000 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00301 (25293) covalent geometry : angle 0.54774 (34404) SS BOND : bond 0.00508 ( 42) SS BOND : angle 1.24570 ( 84) hydrogen bonds : bond 0.03713 ( 971) hydrogen bonds : angle 5.51846 ( 2805) link_BETA1-4 : bond 0.00345 ( 12) link_BETA1-4 : angle 0.98449 ( 36) link_NAG-ASN : bond 0.00532 ( 48) link_NAG-ASN : angle 2.62161 ( 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 185 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 145 time to evaluate : 0.667 Fit side-chains revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8632 (tm-30) cc_final: 0.8138 (tm-30) REVERT: A 271 GLN cc_start: 0.7909 (mt0) cc_final: 0.7614 (mt0) REVERT: A 979 ASP cc_start: 0.8265 (m-30) cc_final: 0.7734 (t0) REVERT: A 988 GLU cc_start: 0.8436 (pm20) cc_final: 0.8200 (pm20) REVERT: A 1045 LYS cc_start: 0.8436 (ptmm) cc_final: 0.7842 (tttm) REVERT: B 52 GLN cc_start: 0.8510 (tm-30) cc_final: 0.7797 (tm-30) REVERT: B 271 GLN cc_start: 0.7918 (mt0) cc_final: 0.7616 (mt0) REVERT: B 988 GLU cc_start: 0.8234 (pm20) cc_final: 0.7997 (pm20) REVERT: B 1092 GLU cc_start: 0.7229 (tp30) cc_final: 0.6958 (tp30) REVERT: C 52 GLN cc_start: 0.8601 (tm-30) cc_final: 0.7965 (tm-30) REVERT: C 271 GLN cc_start: 0.7562 (mt0) cc_final: 0.7342 (mt0) REVERT: C 979 ASP cc_start: 0.8349 (m-30) cc_final: 0.7893 (t0) REVERT: C 988 GLU cc_start: 0.8239 (pm20) cc_final: 0.7969 (pm20) outliers start: 40 outliers final: 22 residues processed: 175 average time/residue: 0.1402 time to fit residues: 41.3320 Evaluate side-chains 153 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 131 time to evaluate : 0.857 ------------------------------------------------------------------------------- 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 581 THR Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain B residue 36 VAL 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 534 VAL Chi-restraints excluded: chain B residue 571 ASP 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 277 LEU 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 581 THR Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 975 SER 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: 4.9990 chunk 294 optimal weight: 3.9990 chunk 195 optimal weight: 4.9990 chunk 233 optimal weight: 9.9990 chunk 264 optimal weight: 9.9990 chunk 45 optimal weight: 7.9990 chunk 59 optimal weight: 0.6980 chunk 121 optimal weight: 5.9990 chunk 215 optimal weight: 30.0000 chunk 186 optimal weight: 0.7980 chunk 67 optimal weight: 3.9990 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 164 ASN ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.129758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.080946 restraints weight = 51102.826| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 3.14 r_work: 0.2934 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.2786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 25395 Z= 0.219 Angle : 0.598 9.867 34668 Z= 0.300 Chirality : 0.047 0.336 4083 Planarity : 0.004 0.038 4380 Dihedral : 5.586 54.521 4533 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.87 % Allowed : 9.09 % Favored : 89.04 % 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: 0.32 (0.15), residues: 3021 helix: 1.78 (0.21), residues: 657 sheet: 0.49 (0.18), residues: 747 loop : -0.58 (0.15), residues: 1617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1107 TYR 0.013 0.001 TYR A1067 PHE 0.019 0.001 PHE C 220 TRP 0.015 0.002 TRP A 104 HIS 0.004 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00511 (25293) covalent geometry : angle 0.57248 (34404) SS BOND : bond 0.00459 ( 42) SS BOND : angle 1.47649 ( 84) hydrogen bonds : bond 0.04023 ( 971) hydrogen bonds : angle 5.53843 ( 2805) link_BETA1-4 : bond 0.00236 ( 12) link_BETA1-4 : angle 1.00565 ( 36) link_NAG-ASN : bond 0.00478 ( 48) link_NAG-ASN : angle 2.49234 ( 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 189 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 139 time to evaluate : 0.917 Fit side-chains revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8697 (tm-30) cc_final: 0.8195 (tm-30) REVERT: A 271 GLN cc_start: 0.7981 (mt0) cc_final: 0.7640 (mt0) REVERT: A 902 MET cc_start: 0.8908 (mmm) cc_final: 0.8623 (tpt) REVERT: A 979 ASP cc_start: 0.8298 (m-30) cc_final: 0.7786 (t0) REVERT: A 988 GLU cc_start: 0.8478 (pm20) cc_final: 0.8242 (pm20) REVERT: B 52 GLN cc_start: 0.8584 (tm-30) cc_final: 0.7863 (tm-30) REVERT: B 271 GLN cc_start: 0.8030 (mt0) cc_final: 0.7693 (mt0) REVERT: B 988 GLU cc_start: 0.8513 (pm20) cc_final: 0.8276 (pm20) REVERT: B 1092 GLU cc_start: 0.7309 (tp30) cc_final: 0.7046 (tp30) REVERT: C 52 GLN cc_start: 0.8620 (tm-30) cc_final: 0.7957 (tm-30) REVERT: C 271 GLN cc_start: 0.7637 (mt0) cc_final: 0.7389 (mt0) REVERT: C 314 GLN cc_start: 0.8917 (tt0) cc_final: 0.8688 (tt0) REVERT: C 979 ASP cc_start: 0.8324 (m-30) cc_final: 0.7997 (t0) REVERT: C 988 GLU cc_start: 0.8431 (pm20) cc_final: 0.8080 (pm20) outliers start: 50 outliers final: 35 residues processed: 178 average time/residue: 0.1303 time to fit residues: 40.2783 Evaluate side-chains 161 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 126 time to evaluate : 0.860 ------------------------------------------------------------------------------- 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 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 975 SER 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 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 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 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 524 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 1045 LYS Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1123 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 16 optimal weight: 9.9990 chunk 249 optimal weight: 6.9990 chunk 92 optimal weight: 4.9990 chunk 283 optimal weight: 1.9990 chunk 225 optimal weight: 10.0000 chunk 105 optimal weight: 9.9990 chunk 13 optimal weight: 7.9990 chunk 103 optimal weight: 7.9990 chunk 179 optimal weight: 0.9980 chunk 11 optimal weight: 10.0000 chunk 257 optimal weight: 2.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 655 HIS ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN B 164 ASN ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.128428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.079565 restraints weight = 51198.174| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 3.18 r_work: 0.2916 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.3041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 25395 Z= 0.261 Angle : 0.619 9.804 34668 Z= 0.311 Chirality : 0.048 0.341 4083 Planarity : 0.004 0.038 4380 Dihedral : 5.607 54.651 4533 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.17 % Allowed : 9.35 % Favored : 88.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.27 (0.15), residues: 3021 helix: 1.68 (0.20), residues: 657 sheet: 0.50 (0.19), residues: 708 loop : -0.56 (0.15), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C1014 TYR 0.014 0.001 TYR A1067 PHE 0.019 0.002 PHE C 220 TRP 0.011 0.002 TRP B 436 HIS 0.004 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00607 (25293) covalent geometry : angle 0.59686 (34404) SS BOND : bond 0.00375 ( 42) SS BOND : angle 1.29929 ( 84) hydrogen bonds : bond 0.04196 ( 971) hydrogen bonds : angle 5.59572 ( 2805) link_BETA1-4 : bond 0.00187 ( 12) link_BETA1-4 : angle 0.98632 ( 36) link_NAG-ASN : bond 0.00469 ( 48) link_NAG-ASN : angle 2.43845 ( 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 186 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 128 time to evaluate : 0.875 Fit side-chains REVERT: A 52 GLN cc_start: 0.8702 (tm-30) cc_final: 0.8063 (tm-30) REVERT: A 902 MET cc_start: 0.8983 (mmm) cc_final: 0.8658 (tpt) REVERT: A 950 ASP cc_start: 0.8599 (m-30) cc_final: 0.8198 (m-30) REVERT: A 979 ASP cc_start: 0.8273 (m-30) cc_final: 0.7753 (t0) REVERT: B 52 GLN cc_start: 0.8678 (tm-30) cc_final: 0.7956 (tm-30) REVERT: B 369 TYR cc_start: 0.8590 (t80) cc_final: 0.8389 (t80) REVERT: B 505 TYR cc_start: 0.8582 (t80) cc_final: 0.7674 (t80) REVERT: B 988 GLU cc_start: 0.8479 (pm20) cc_final: 0.8231 (pm20) REVERT: B 1092 GLU cc_start: 0.7454 (tp30) cc_final: 0.7123 (tp30) REVERT: C 52 GLN cc_start: 0.8668 (tm-30) cc_final: 0.7984 (tm-30) REVERT: C 314 GLN cc_start: 0.8964 (tt0) cc_final: 0.8697 (tt0) REVERT: C 505 TYR cc_start: 0.8087 (t80) cc_final: 0.7723 (t80) REVERT: C 979 ASP cc_start: 0.8352 (m-30) cc_final: 0.8023 (t0) REVERT: C 988 GLU cc_start: 0.8381 (pm20) cc_final: 0.8098 (pm20) outliers start: 58 outliers final: 41 residues processed: 173 average time/residue: 0.1280 time to fit residues: 38.4885 Evaluate side-chains 161 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 120 time to evaluate : 0.847 ------------------------------------------------------------------------------- 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 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 731 MET 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 900 MET 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 39 optimal weight: 8.9990 chunk 250 optimal weight: 20.0000 chunk 222 optimal weight: 20.0000 chunk 2 optimal weight: 10.0000 chunk 143 optimal weight: 9.9990 chunk 126 optimal weight: 2.9990 chunk 50 optimal weight: 7.9990 chunk 179 optimal weight: 1.9990 chunk 248 optimal weight: 30.0000 chunk 52 optimal weight: 0.8980 chunk 166 optimal weight: 0.7980 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 913 GLN A1135 ASN B 655 HIS ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.128377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.079448 restraints weight = 50867.806| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 3.17 r_work: 0.2925 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.3139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 25395 Z= 0.220 Angle : 0.589 9.830 34668 Z= 0.296 Chirality : 0.047 0.340 4083 Planarity : 0.003 0.039 4380 Dihedral : 5.519 54.682 4533 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.06 % Allowed : 9.69 % Favored : 88.25 % 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: 1.72 (0.20), residues: 657 sheet: 0.46 (0.19), residues: 717 loop : -0.59 (0.15), residues: 1647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1107 TYR 0.014 0.001 TYR A1067 PHE 0.018 0.001 PHE C 220 TRP 0.012 0.001 TRP A 104 HIS 0.003 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00510 (25293) covalent geometry : angle 0.56755 (34404) SS BOND : bond 0.00430 ( 42) SS BOND : angle 1.18127 ( 84) hydrogen bonds : bond 0.03998 ( 971) hydrogen bonds : angle 5.51873 ( 2805) link_BETA1-4 : bond 0.00228 ( 12) link_BETA1-4 : angle 0.95080 ( 36) link_NAG-ASN : bond 0.00469 ( 48) link_NAG-ASN : angle 2.37596 ( 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 184 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 129 time to evaluate : 0.920 Fit side-chains revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8734 (tm-30) cc_final: 0.8230 (tm-30) REVERT: A 902 MET cc_start: 0.8977 (mmm) cc_final: 0.8652 (tpt) REVERT: A 950 ASP cc_start: 0.8573 (m-30) cc_final: 0.8174 (m-30) REVERT: A 979 ASP cc_start: 0.8303 (m-30) cc_final: 0.7833 (t0) REVERT: B 52 GLN cc_start: 0.8715 (tm-30) cc_final: 0.7979 (tm-30) REVERT: B 271 GLN cc_start: 0.8109 (mt0) cc_final: 0.7723 (mt0) REVERT: B 988 GLU cc_start: 0.8464 (pm20) cc_final: 0.8205 (pm20) REVERT: B 1092 GLU cc_start: 0.7445 (tp30) cc_final: 0.7125 (tp30) REVERT: C 52 GLN cc_start: 0.8712 (tm-30) cc_final: 0.8031 (tm-30) REVERT: C 314 GLN cc_start: 0.8946 (tt0) cc_final: 0.8676 (tt0) REVERT: C 505 TYR cc_start: 0.8080 (t80) cc_final: 0.7743 (t80) REVERT: C 979 ASP cc_start: 0.8344 (m-30) cc_final: 0.8020 (t0) REVERT: C 988 GLU cc_start: 0.8377 (pm20) cc_final: 0.8083 (pm20) outliers start: 55 outliers final: 37 residues processed: 174 average time/residue: 0.1284 time to fit residues: 39.0505 Evaluate side-chains 159 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 122 time to evaluate : 0.853 ------------------------------------------------------------------------------- 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 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 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 47 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 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 36 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 62 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 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: 2.9990 chunk 108 optimal weight: 20.0000 chunk 124 optimal weight: 10.0000 chunk 136 optimal weight: 7.9990 chunk 270 optimal weight: 0.6980 chunk 181 optimal weight: 0.9990 chunk 25 optimal weight: 0.0770 chunk 46 optimal weight: 5.9990 chunk 303 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 chunk 291 optimal weight: 2.9990 overall best weight: 0.9342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 913 GLN B1135 ASN ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1135 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.130751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.082489 restraints weight = 51164.032| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 3.14 r_work: 0.2967 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.3237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 25395 Z= 0.110 Angle : 0.547 10.172 34668 Z= 0.273 Chirality : 0.045 0.338 4083 Planarity : 0.003 0.042 4380 Dihedral : 5.261 55.392 4533 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.76 % Allowed : 10.33 % Favored : 87.92 % 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: 0.40 (0.15), residues: 3021 helix: 1.97 (0.21), residues: 657 sheet: 0.41 (0.18), residues: 768 loop : -0.51 (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 0.016 0.001 PHE B1089 TRP 0.015 0.001 TRP A 104 HIS 0.002 0.000 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00245 (25293) covalent geometry : angle 0.52630 (34404) SS BOND : bond 0.00470 ( 42) SS BOND : angle 1.00465 ( 84) hydrogen bonds : bond 0.03488 ( 971) hydrogen bonds : angle 5.27479 ( 2805) link_BETA1-4 : bond 0.00311 ( 12) link_BETA1-4 : angle 0.86669 ( 36) link_NAG-ASN : bond 0.00501 ( 48) link_NAG-ASN : angle 2.26259 ( 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 193 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 146 time to evaluate : 0.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8730 (tm-30) cc_final: 0.8230 (tm-30) REVERT: A 271 GLN cc_start: 0.8001 (mt0) cc_final: 0.7664 (mt0) REVERT: A 979 ASP cc_start: 0.8264 (m-30) cc_final: 0.7872 (t0) REVERT: A 1123 SER cc_start: 0.8047 (t) cc_final: 0.7720 (m) REVERT: B 52 GLN cc_start: 0.8684 (tm-30) cc_final: 0.7925 (tm-30) REVERT: B 271 GLN cc_start: 0.8027 (mt0) cc_final: 0.7676 (mt0) REVERT: B 1092 GLU cc_start: 0.7160 (tp30) cc_final: 0.6895 (tp30) REVERT: C 52 GLN cc_start: 0.8740 (tm-30) cc_final: 0.8014 (tm-30) REVERT: C 271 GLN cc_start: 0.7702 (mt0) cc_final: 0.7458 (mt0) REVERT: C 505 TYR cc_start: 0.8108 (t80) cc_final: 0.7668 (t80) REVERT: C 957 GLN cc_start: 0.8857 (tt0) cc_final: 0.8657 (tt0) REVERT: C 979 ASP cc_start: 0.8291 (m-30) cc_final: 0.7992 (t0) REVERT: C 988 GLU cc_start: 0.8422 (pm20) cc_final: 0.8113 (pm20) outliers start: 47 outliers final: 39 residues processed: 184 average time/residue: 0.1229 time to fit residues: 39.2004 Evaluate side-chains 168 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 129 time to evaluate : 0.884 ------------------------------------------------------------------------------- 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 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 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 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 571 ASP Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain C residue 36 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 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: 10.0000 chunk 50 optimal weight: 8.9990 chunk 145 optimal weight: 4.9990 chunk 105 optimal weight: 7.9990 chunk 157 optimal weight: 7.9990 chunk 196 optimal weight: 5.9990 chunk 268 optimal weight: 0.8980 chunk 137 optimal weight: 10.0000 chunk 207 optimal weight: 9.9990 chunk 129 optimal weight: 3.9990 chunk 69 optimal weight: 4.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN A 784 GLN B 115 GLN ** 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 = 0.3984 r_free = 0.3984 target = 0.127462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.078258 restraints weight = 51286.131| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 3.16 r_work: 0.2901 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.3344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.085 25395 Z= 0.296 Angle : 0.637 9.704 34668 Z= 0.319 Chirality : 0.048 0.338 4083 Planarity : 0.004 0.040 4380 Dihedral : 5.436 55.077 4533 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.83 % Allowed : 10.51 % Favored : 87.65 % 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: 0.20 (0.15), residues: 3021 helix: 1.65 (0.20), residues: 660 sheet: 0.43 (0.19), residues: 708 loop : -0.61 (0.15), residues: 1653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C1014 TYR 0.015 0.002 TYR A1067 PHE 0.017 0.002 PHE A1121 TRP 0.012 0.002 TRP C 436 HIS 0.006 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00690 (25293) covalent geometry : angle 0.61746 (34404) SS BOND : bond 0.00405 ( 42) SS BOND : angle 1.26324 ( 84) hydrogen bonds : bond 0.04266 ( 971) hydrogen bonds : angle 5.51747 ( 2805) link_BETA1-4 : bond 0.00161 ( 12) link_BETA1-4 : angle 0.93781 ( 36) link_NAG-ASN : bond 0.00463 ( 48) link_NAG-ASN : angle 2.34638 ( 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 176 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 127 time to evaluate : 0.806 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8759 (tm-30) cc_final: 0.8063 (tm-30) REVERT: A 560 LEU cc_start: 0.9378 (mp) cc_final: 0.9145 (mt) REVERT: A 697 MET cc_start: 0.8959 (ptm) cc_final: 0.8749 (ptp) REVERT: A 902 MET cc_start: 0.8957 (mmm) cc_final: 0.8637 (tpt) REVERT: A 979 ASP cc_start: 0.8309 (m-30) cc_final: 0.7821 (t0) REVERT: A 988 GLU cc_start: 0.8378 (pm20) cc_final: 0.8096 (pm20) REVERT: A 1089 PHE cc_start: 0.8738 (OUTLIER) cc_final: 0.8320 (m-80) REVERT: A 1092 GLU cc_start: 0.7351 (tp30) cc_final: 0.6838 (tp30) REVERT: B 52 GLN cc_start: 0.8776 (tm-30) cc_final: 0.8073 (tm-30) REVERT: B 271 GLN cc_start: 0.8140 (mt0) cc_final: 0.7742 (mt0) REVERT: B 950 ASP cc_start: 0.8636 (m-30) cc_final: 0.8257 (m-30) REVERT: B 988 GLU cc_start: 0.8388 (pm20) cc_final: 0.8073 (pm20) REVERT: B 1092 GLU cc_start: 0.7402 (tp30) cc_final: 0.7089 (tp30) REVERT: C 52 GLN cc_start: 0.8773 (tm-30) cc_final: 0.8044 (tm-30) REVERT: C 505 TYR cc_start: 0.8209 (t80) cc_final: 0.7849 (t80) REVERT: C 979 ASP cc_start: 0.8370 (m-30) cc_final: 0.8044 (t0) REVERT: C 988 GLU cc_start: 0.8336 (pm20) cc_final: 0.8051 (pm20) outliers start: 49 outliers final: 42 residues processed: 169 average time/residue: 0.1242 time to fit residues: 36.9715 Evaluate side-chains 161 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 118 time to evaluate : 0.829 ------------------------------------------------------------------------------- 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 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 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 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 391 CYS 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 915 VAL 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: 0.9980 chunk 121 optimal weight: 9.9990 chunk 282 optimal weight: 0.8980 chunk 179 optimal weight: 0.1980 chunk 144 optimal weight: 50.0000 chunk 239 optimal weight: 5.9990 chunk 48 optimal weight: 4.9990 chunk 112 optimal weight: 9.9990 chunk 223 optimal weight: 6.9990 chunk 302 optimal weight: 0.9990 chunk 137 optimal weight: 9.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.129430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.080795 restraints weight = 50858.561| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 3.16 r_work: 0.2946 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.3393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 25395 Z= 0.147 Angle : 0.565 10.059 34668 Z= 0.282 Chirality : 0.046 0.336 4083 Planarity : 0.003 0.042 4380 Dihedral : 5.286 54.703 4533 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.68 % Allowed : 10.92 % Favored : 87.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.85 (0.21), residues: 657 sheet: 0.64 (0.20), residues: 657 loop : -0.57 (0.15), residues: 1707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1107 TYR 0.014 0.001 TYR B1067 PHE 0.014 0.001 PHE C 220 TRP 0.019 0.001 TRP A 104 HIS 0.002 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00337 (25293) covalent geometry : angle 0.54465 (34404) SS BOND : bond 0.00427 ( 42) SS BOND : angle 1.04936 ( 84) hydrogen bonds : bond 0.03682 ( 971) hydrogen bonds : angle 5.32743 ( 2805) link_BETA1-4 : bond 0.00265 ( 12) link_BETA1-4 : angle 0.88383 ( 36) link_NAG-ASN : bond 0.00476 ( 48) link_NAG-ASN : angle 2.25050 ( 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 171 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 126 time to evaluate : 0.783 Fit side-chains revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8775 (tm-30) cc_final: 0.8061 (tm-30) REVERT: A 271 GLN cc_start: 0.8009 (mt0) cc_final: 0.7730 (mt0) REVERT: A 560 LEU cc_start: 0.9337 (mp) cc_final: 0.9103 (mt) REVERT: A 979 ASP cc_start: 0.8271 (m-30) cc_final: 0.7879 (t0) REVERT: B 52 GLN cc_start: 0.8782 (tm-30) cc_final: 0.8072 (tm-30) REVERT: B 271 GLN cc_start: 0.8094 (mt0) cc_final: 0.7738 (mt0) REVERT: B 988 GLU cc_start: 0.8437 (pm20) cc_final: 0.8127 (pm20) REVERT: B 1092 GLU cc_start: 0.7237 (tp30) cc_final: 0.6969 (tp30) REVERT: C 52 GLN cc_start: 0.8792 (tm-30) cc_final: 0.8067 (tm-30) REVERT: C 104 TRP cc_start: 0.6142 (m-90) cc_final: 0.5793 (m-90) REVERT: C 271 GLN cc_start: 0.7729 (mt0) cc_final: 0.7453 (mt0) REVERT: C 697 MET cc_start: 0.8763 (ptm) cc_final: 0.8500 (ptp) REVERT: C 957 GLN cc_start: 0.8844 (tt0) cc_final: 0.8632 (tt0) REVERT: C 979 ASP cc_start: 0.8281 (m-30) cc_final: 0.7994 (t0) outliers start: 45 outliers final: 40 residues processed: 162 average time/residue: 0.1235 time to fit residues: 34.9401 Evaluate side-chains 163 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 123 time to evaluate : 0.902 ------------------------------------------------------------------------------- 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 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 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 581 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 176 LEU 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 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 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: 0.7980 chunk 189 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 289 optimal weight: 4.9990 chunk 113 optimal weight: 6.9990 chunk 78 optimal weight: 2.9990 chunk 299 optimal weight: 2.9990 chunk 206 optimal weight: 7.9990 chunk 48 optimal weight: 8.9990 chunk 5 optimal weight: 10.0000 chunk 4 optimal weight: 0.9980 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 913 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.129136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.080599 restraints weight = 50896.360| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 3.17 r_work: 0.2939 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.3442 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= 0.175 Angle : 0.572 9.963 34668 Z= 0.285 Chirality : 0.046 0.337 4083 Planarity : 0.003 0.042 4380 Dihedral : 5.237 54.891 4533 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.61 % Allowed : 11.19 % Favored : 87.21 % 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: 0.34 (0.15), residues: 3021 helix: 1.81 (0.21), residues: 660 sheet: 0.56 (0.19), residues: 678 loop : -0.55 (0.15), residues: 1683 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1107 TYR 0.013 0.001 TYR A1067 PHE 0.015 0.001 PHE A 192 TRP 0.016 0.001 TRP A 104 HIS 0.003 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00405 (25293) covalent geometry : angle 0.55180 (34404) SS BOND : bond 0.00410 ( 42) SS BOND : angle 1.07660 ( 84) hydrogen bonds : bond 0.03761 ( 971) hydrogen bonds : angle 5.30397 ( 2805) link_BETA1-4 : bond 0.00280 ( 12) link_BETA1-4 : angle 0.90111 ( 36) link_NAG-ASN : bond 0.00465 ( 48) link_NAG-ASN : angle 2.25658 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6056.95 seconds wall clock time: 104 minutes 28.19 seconds (6268.19 seconds total)