Starting phenix.real_space_refine on Sun Sep 13 17:40:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6x6p_22078/09_2026/6x6p_22078.cif Found real_map, /net/cci-nas-00/data/ceres_data/6x6p_22078/09_2026/6x6p_22078.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6x6p_22078/09_2026/6x6p_22078.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6x6p_22078/09_2026/6x6p_22078.cif" model { file = "/net/cci-nas-00/data/ceres_data/6x6p_22078/09_2026/6x6p_22078.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6x6p_22078/09_2026/6x6p_22078.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6x6p_22078/09_2026/6x6p_22078.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6x6p_22078/09_2026/6x6p_22078.map" } resolution = 3.22 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= 0.001 sd= 0.020 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 105 5.16 5 C 15663 2.51 5 N 4014 2.21 5 O 4833 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 216 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 24615 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 7939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1017, 7939 Classifications: {'peptide': 1017} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 50, 'TRANS': 966} Chain breaks: 8 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 7939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1017, 7939 Classifications: {'peptide': 1017} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 50, 'TRANS': 966} Chain breaks: 8 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 7939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1017, 7939 Classifications: {'peptide': 1017} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 50, 'TRANS': 966} Chain breaks: 8 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen chiralities: 11 Chain: "C" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen chiralities: 11 Time building chain proxies: 5.78, per 1000 atoms: 0.23 Number of scatterers: 24615 At special positions: 0 Unit cell: (131.192, 140.714, 174.57, 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 105 16.00 O 4833 8.00 N 4014 7.00 C 15663 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.02 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.02 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.02 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.02 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.02 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.02 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.02 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.02 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 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=2.02 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=2.02 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.02 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.02 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.02 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.02 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.02 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.02 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 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=2.02 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=2.02 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.02 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.02 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.02 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.02 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.02 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.02 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 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 234 " " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A 331 " " NAG A1305 " - " ASN A 343 " " NAG A1306 " - " ASN A 603 " " NAG A1307 " - " ASN A 616 " " NAG A1308 " - " ASN A 657 " " NAG A1309 " - " ASN A 709 " " NAG A1314 " - " ASN A1074 " " NAG A1319 " - " ASN A 165 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 234 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B 331 " " NAG B1305 " - " ASN B 343 " " NAG B1306 " - " ASN B 603 " " NAG B1307 " - " ASN B 616 " " NAG B1308 " - " ASN B 657 " " NAG B1309 " - " ASN B 709 " " NAG B1314 " - " ASN B1074 " " NAG B1319 " - " ASN B 165 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 234 " " NAG C1303 " - " ASN C 282 " " NAG C1304 " - " ASN C 331 " " NAG C1305 " - " ASN C 343 " " NAG C1306 " - " ASN C 603 " " NAG C1307 " - " ASN C 616 " " NAG C1308 " - " ASN C 657 " " NAG C1309 " - " ASN C 709 " " NAG C1314 " - " ASN C1074 " " NAG C1319 " - " 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: 2.29 Conformation dependent library (CDL) restraints added in 969.1 milliseconds 5994 Ramachandran restraints generated. 2997 Oldfield, 0 Emsley, 2997 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5730 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 54 sheets defined 26.2% alpha, 24.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.18 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 364 through 370 removed outlier: 3.655A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 389 removed outlier: 3.943A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 410 removed outlier: 4.054A 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 438 through 443 Processing helix chain 'A' and resid 618 through 625 removed outlier: 4.017A pdb=" N VAL A 622 " --> pdb=" O THR A 618 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.800A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 756 through 759 removed outlier: 3.567A pdb=" N PHE A 759 " --> pdb=" O TYR A 756 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 756 through 759' Processing helix chain 'A' and resid 760 through 783 removed outlier: 3.778A pdb=" N ASN A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.507A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 941 removed outlier: 5.582A pdb=" N LYS A 921 " --> pdb=" O TYR A 917 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N LEU A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) 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 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 982 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.749A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1125 through 1129 removed outlier: 3.951A pdb=" N VAL A1128 " --> pdb=" O ASN A1125 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL A1129 " --> pdb=" O CYS A1126 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1125 through 1129' Processing helix chain 'A' and resid 1140 through 1145 removed outlier: 4.317A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 364 through 370 removed outlier: 3.655A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 389 removed outlier: 3.943A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 410 removed outlier: 4.055A 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 438 through 443 Processing helix chain 'B' and resid 618 through 625 removed outlier: 4.018A pdb=" N VAL B 622 " --> pdb=" O THR B 618 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.800A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 756 through 759 removed outlier: 3.568A pdb=" N PHE B 759 " --> pdb=" O TYR B 756 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 756 through 759' Processing helix chain 'B' and resid 760 through 783 removed outlier: 3.777A pdb=" N ASN B 764 " --> pdb=" O CYS B 760 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.508A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 913 through 941 removed outlier: 5.583A pdb=" N LYS B 921 " --> pdb=" O TYR B 917 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N LEU B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) 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 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 982 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.749A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1125 through 1129 removed outlier: 3.952A pdb=" N VAL B1128 " --> pdb=" O ASN B1125 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL B1129 " --> pdb=" O CYS B1126 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1125 through 1129' Processing helix chain 'B' and resid 1140 through 1145 removed outlier: 4.317A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 364 through 370 removed outlier: 3.654A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 389 removed outlier: 3.944A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 410 removed outlier: 4.054A 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 438 through 443 Processing helix chain 'C' and resid 618 through 625 removed outlier: 4.017A pdb=" N VAL C 622 " --> pdb=" O THR C 618 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 755 removed outlier: 3.799A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 756 through 759 removed outlier: 3.568A pdb=" N PHE C 759 " --> pdb=" O TYR C 756 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 756 through 759' Processing helix chain 'C' and resid 760 through 783 removed outlier: 3.777A pdb=" N ASN C 764 " --> pdb=" O CYS C 760 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.508A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 941 removed outlier: 5.583A pdb=" N LYS C 921 " --> pdb=" O TYR C 917 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N LEU C 922 " --> pdb=" O GLU C 918 " (cutoff:3.500A) 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 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 982 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.749A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1125 through 1129 removed outlier: 3.952A pdb=" N VAL C1128 " --> pdb=" O ASN C1125 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL C1129 " --> pdb=" O CYS C1126 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1125 through 1129' Processing helix chain 'C' and resid 1140 through 1145 removed outlier: 4.318A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.741A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 51 removed outlier: 3.862A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 54 through 55 Processing sheet with id=AA4, first strand: chain 'A' and resid 169 through 171 removed outlier: 5.780A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 171 removed outlier: 5.780A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 133 through 134 removed outlier: 3.638A pdb=" N SER A 162 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.468A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 324 through 328 removed outlier: 6.407A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N ASN A 542 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AB1, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.550A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB3, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB4, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.035A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 702 through 704 removed outlier: 3.596A pdb=" N LYS B 790 " --> pdb=" O ASN A 703 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 715 Processing sheet with id=AB7, first strand: chain 'A' and resid 718 through 728 removed outlier: 6.935A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB9, first strand: chain 'A' and resid 788 through 790 removed outlier: 5.633A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AC2, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.742A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 48 through 51 removed outlier: 3.863A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 54 through 55 Processing sheet with id=AC5, first strand: chain 'B' and resid 169 through 171 removed outlier: 5.780A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 169 through 171 removed outlier: 5.780A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 133 through 134 removed outlier: 3.637A pdb=" N SER B 162 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.467A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 324 through 328 removed outlier: 6.408A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N ASN B 542 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AD2, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.549A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD4, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD5, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.035A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 702 through 704 removed outlier: 3.565A pdb=" N LYS C 790 " --> pdb=" O ASN B 703 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 711 through 715 Processing sheet with id=AD8, first strand: chain 'B' and resid 718 through 728 removed outlier: 6.935A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AE1, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AE2, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.742A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 48 through 51 removed outlier: 3.862A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 54 through 55 Processing sheet with id=AE5, first strand: chain 'C' and resid 169 through 171 removed outlier: 5.780A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 169 through 171 removed outlier: 5.780A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 133 through 134 removed outlier: 3.638A pdb=" N SER C 162 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.467A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 324 through 328 removed outlier: 6.408A pdb=" N GLU C 324 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N ASN C 542 " --> pdb=" O GLU C 324 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AF2, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.549A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AF4, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AF5, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.035A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 711 through 715 Processing sheet with id=AF7, first strand: chain 'C' and resid 718 through 728 removed outlier: 6.935A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AF9, first strand: chain 'C' and resid 1120 through 1122 1007 hydrogen bonds defined for protein. 2733 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: 6.29 Time building geometry restraints manager: 2.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7211 1.33 - 1.45: 5600 1.45 - 1.58: 12209 1.58 - 1.70: 0 1.70 - 1.82: 132 Bond restraints: 25152 Sorted by residual: bond pdb=" C PHE C 559 " pdb=" N LEU C 560 " ideal model delta sigma weight residual 1.331 1.244 0.087 2.83e-02 1.25e+03 9.55e+00 bond pdb=" C PHE A 559 " pdb=" N LEU A 560 " ideal model delta sigma weight residual 1.331 1.244 0.087 2.83e-02 1.25e+03 9.51e+00 bond pdb=" C PHE B 559 " pdb=" N LEU B 560 " ideal model delta sigma weight residual 1.331 1.244 0.087 2.83e-02 1.25e+03 9.42e+00 bond pdb=" CA THR C1105 " pdb=" CB THR C1105 " ideal model delta sigma weight residual 1.535 1.480 0.055 1.93e-02 2.68e+03 7.98e+00 bond pdb=" CA THR A1105 " pdb=" CB THR A1105 " ideal model delta sigma weight residual 1.535 1.480 0.055 1.93e-02 2.68e+03 7.98e+00 ... (remaining 25147 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.05: 33475 3.05 - 6.10: 685 6.10 - 9.16: 58 9.16 - 12.21: 9 12.21 - 15.26: 6 Bond angle restraints: 34233 Sorted by residual: angle pdb=" N ILE C 100 " pdb=" CA ILE C 100 " pdb=" C ILE C 100 " ideal model delta sigma weight residual 112.96 105.96 7.00 1.00e+00 1.00e+00 4.90e+01 angle pdb=" N ILE A 100 " pdb=" CA ILE A 100 " pdb=" C ILE A 100 " ideal model delta sigma weight residual 112.96 105.99 6.97 1.00e+00 1.00e+00 4.86e+01 angle pdb=" N ILE B 100 " pdb=" CA ILE B 100 " pdb=" C ILE B 100 " ideal model delta sigma weight residual 112.96 106.01 6.95 1.00e+00 1.00e+00 4.84e+01 angle pdb=" CG ARG A 355 " pdb=" CD ARG A 355 " pdb=" NE ARG A 355 " ideal model delta sigma weight residual 112.00 96.74 15.26 2.20e+00 2.07e-01 4.81e+01 angle pdb=" CG ARG B 355 " pdb=" CD ARG B 355 " pdb=" NE ARG B 355 " ideal model delta sigma weight residual 112.00 96.77 15.23 2.20e+00 2.07e-01 4.79e+01 ... (remaining 34228 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.07: 12556 18.07 - 36.13: 1471 36.13 - 54.20: 396 54.20 - 72.27: 67 72.27 - 90.33: 24 Dihedral angle restraints: 14514 sinusoidal: 5625 harmonic: 8889 Sorted by residual: dihedral pdb=" CB CYS A1032 " pdb=" SG CYS A1032 " pdb=" SG CYS A1043 " pdb=" CB CYS A1043 " ideal model delta sinusoidal sigma weight residual 93.00 -176.67 -90.33 1 1.00e+01 1.00e-02 9.66e+01 dihedral pdb=" CB CYS C1032 " pdb=" SG CYS C1032 " pdb=" SG CYS C1043 " pdb=" CB CYS C1043 " ideal model delta sinusoidal sigma weight residual 93.00 -176.67 -90.33 1 1.00e+01 1.00e-02 9.65e+01 dihedral pdb=" CB CYS B1032 " pdb=" SG CYS B1032 " pdb=" SG CYS B1043 " pdb=" CB CYS B1043 " ideal model delta sinusoidal sigma weight residual 93.00 -176.67 -90.33 1 1.00e+01 1.00e-02 9.65e+01 ... (remaining 14511 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.136: 3971 0.136 - 0.273: 97 0.273 - 0.409: 0 0.409 - 0.546: 0 0.546 - 0.682: 6 Chirality restraints: 4074 Sorted by residual: chirality pdb=" C1 NAG B1306 " pdb=" ND2 ASN B 603 " pdb=" C2 NAG B1306 " pdb=" O5 NAG B1306 " both_signs ideal model delta sigma weight residual False -2.40 -1.72 -0.68 2.00e-01 2.50e+01 1.16e+01 chirality pdb=" C1 NAG C1306 " pdb=" ND2 ASN C 603 " pdb=" C2 NAG C1306 " pdb=" O5 NAG C1306 " both_signs ideal model delta sigma weight residual False -2.40 -1.72 -0.68 2.00e-01 2.50e+01 1.16e+01 chirality pdb=" C1 NAG A1306 " pdb=" ND2 ASN A 603 " pdb=" C2 NAG A1306 " pdb=" O5 NAG A1306 " both_signs ideal model delta sigma weight residual False -2.40 -1.72 -0.68 2.00e-01 2.50e+01 1.15e+01 ... (remaining 4071 not shown) Planarity restraints: 4395 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 904 " 0.038 2.00e-02 2.50e+03 3.06e-02 1.87e+01 pdb=" CG TYR C 904 " -0.074 2.00e-02 2.50e+03 pdb=" CD1 TYR C 904 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR C 904 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR C 904 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR C 904 " 0.007 2.00e-02 2.50e+03 pdb=" CZ TYR C 904 " 0.013 2.00e-02 2.50e+03 pdb=" OH TYR C 904 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 904 " -0.038 2.00e-02 2.50e+03 3.04e-02 1.85e+01 pdb=" CG TYR B 904 " 0.073 2.00e-02 2.50e+03 pdb=" CD1 TYR B 904 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 TYR B 904 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR B 904 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR B 904 " -0.007 2.00e-02 2.50e+03 pdb=" CZ TYR B 904 " -0.014 2.00e-02 2.50e+03 pdb=" OH TYR B 904 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 904 " 0.038 2.00e-02 2.50e+03 3.02e-02 1.83e+01 pdb=" CG TYR A 904 " -0.073 2.00e-02 2.50e+03 pdb=" CD1 TYR A 904 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR A 904 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR A 904 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR A 904 " 0.007 2.00e-02 2.50e+03 pdb=" CZ TYR A 904 " 0.013 2.00e-02 2.50e+03 pdb=" OH TYR A 904 " 0.001 2.00e-02 2.50e+03 ... (remaining 4392 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 559 2.63 - 3.20: 24479 3.20 - 3.76: 37989 3.76 - 4.33: 52705 4.33 - 4.90: 87457 Nonbonded interactions: 203189 Sorted by model distance: nonbonded pdb=" OH TYR A 369 " pdb=" OG1 THR C 415 " model vdw 2.062 3.040 nonbonded pdb=" O GLY A 496 " pdb=" OH TYR A 505 " model vdw 2.080 3.040 nonbonded pdb=" O GLY C 496 " pdb=" OH TYR C 505 " model vdw 2.080 3.040 nonbonded pdb=" O GLY B 496 " pdb=" OH TYR B 505 " model vdw 2.080 3.040 nonbonded pdb=" OH TYR B 170 " pdb=" OG SER B 172 " model vdw 2.082 3.040 ... (remaining 203184 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.790 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: 0.050 Extract box with map and model: 0.480 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 24.940 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.080 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:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.088 25245 Z= 0.523 Angle : 1.129 15.260 34476 Z= 0.587 Chirality : 0.064 0.682 4074 Planarity : 0.006 0.051 4350 Dihedral : 16.672 80.465 8676 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 25.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 3.15 % Allowed : 4.65 % Favored : 92.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -2.17 (0.14), residues: 2997 helix: -0.45 (0.18), residues: 729 sheet: -1.42 (0.18), residues: 612 loop : -1.93 (0.14), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.003 ARG C1107 TYR 0.074 0.004 TYR C 904 PHE 0.072 0.006 PHE C1052 TRP 0.027 0.005 TRP A 886 HIS 0.011 0.002 HIS B1064 Details of bonding type rmsd/Z covalent geometry : bond 0.01212 / 0.52 (25152) covalent geometry : angle 1.07195 / 0.57 (34233) SS BOND : bond 0.00884 / 0.57 ( 36) SS BOND : angle 3.24094 / 2.01 ( 72) hydrogen bonds : bond 0.13942 / 9.22 ( 974) hydrogen bonds : angle 8.59105 / 5.99 ( 2733) link_BETA1-4 : bond 0.00331 / 0.18 ( 12) link_BETA1-4 : angle 1.57638 / 1.00 ( 36) link_NAG-ASN : bond 0.00896 / 0.65 ( 45) link_NAG-ASN : angle 5.30631 / 3.42 ( 135) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5994 Ramachandran restraints generated. 2997 Oldfield, 0 Emsley, 2997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5994 Ramachandran restraints generated. 2997 Oldfield, 0 Emsley, 2997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 124 time to evaluate : 0.923 Fit side-chains REVERT: A 117 LEU cc_start: 0.7260 (tt) cc_final: 0.6388 (mp) REVERT: A 265 TYR cc_start: 0.5572 (p90) cc_final: 0.5324 (p90) REVERT: A 421 TYR cc_start: 0.7983 (m-80) cc_final: 0.7444 (m-80) REVERT: A 507 PRO cc_start: 0.5420 (Cg_endo) cc_final: 0.5196 (Cg_endo) REVERT: A 607 GLN cc_start: 0.8282 (OUTLIER) cc_final: 0.8036 (pt0) REVERT: A 1142 GLN cc_start: 0.8425 (OUTLIER) cc_final: 0.8194 (mm-40) REVERT: B 117 LEU cc_start: 0.7398 (tt) cc_final: 0.6532 (mp) REVERT: B 198 ASP cc_start: 0.7958 (OUTLIER) cc_final: 0.7494 (m-30) REVERT: B 396 TYR cc_start: 0.7220 (m-80) cc_final: 0.6717 (m-10) REVERT: B 473 TYR cc_start: 0.7708 (t80) cc_final: 0.7413 (t80) REVERT: C 117 LEU cc_start: 0.7183 (tt) cc_final: 0.6285 (mp) REVERT: C 198 ASP cc_start: 0.7902 (OUTLIER) cc_final: 0.7537 (m-30) REVERT: C 265 TYR cc_start: 0.5622 (p90) cc_final: 0.4918 (p90) REVERT: C 278 LYS cc_start: 0.7995 (OUTLIER) cc_final: 0.7790 (tmmt) REVERT: C 421 TYR cc_start: 0.8105 (m-80) cc_final: 0.7624 (m-80) REVERT: C 780 GLU cc_start: 0.8259 (tt0) cc_final: 0.7953 (tt0) REVERT: C 902 MET cc_start: 0.8729 (OUTLIER) cc_final: 0.8466 (tpt) outliers start: 84 outliers final: 21 residues processed: 199 average time/residue: 0.1738 time to fit residues: 54.3270 Evaluate side-chains 115 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 88 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 TYR Chi-restraints excluded: chain A residue 55 PHE Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 607 GLN Chi-restraints excluded: chain A residue 907 ASN Chi-restraints excluded: chain A residue 1142 GLN Chi-restraints excluded: chain B residue 37 TYR Chi-restraints excluded: chain B residue 55 PHE Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 1107 ARG Chi-restraints excluded: chain B residue 1142 GLN Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 278 LYS Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 1107 ARG Chi-restraints excluded: chain C residue 1142 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 197 optimal weight: 0.7980 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 0.8980 chunk 298 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 122 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 563 GLN A 755 GLN A 920 GLN ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 GLN A 955 ASN A1005 GLN A1048 HIS B 122 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 755 GLN B 920 GLN ** B 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 935 GLN B 955 ASN B1048 HIS C 122 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 607 GLN C 755 GLN C 920 GLN ** C 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 935 GLN C 955 ASN C1048 HIS Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.115049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.074118 restraints weight = 50371.056| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 3.17 r_work: 0.3040 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.1328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 25245 Z= 0.172 Angle : 0.764 9.171 34476 Z= 0.387 Chirality : 0.048 0.252 4074 Planarity : 0.006 0.107 4350 Dihedral : 7.028 59.307 3318 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 1.35 % Allowed : 11.79 % Favored : 86.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.30 (0.15), residues: 2997 helix: 0.90 (0.20), residues: 705 sheet: -1.11 (0.18), residues: 630 loop : -1.58 (0.14), residues: 1662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 403 TYR 0.031 0.002 TYR A 505 PHE 0.031 0.002 PHE C 347 TRP 0.015 0.003 TRP C 436 HIS 0.008 0.001 HIS B1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.17 (25152) covalent geometry : angle 0.73057 / 0.38 (34233) SS BOND : bond 0.00416 / 0.26 ( 36) SS BOND : angle 1.77362 / 1.14 ( 72) hydrogen bonds : bond 0.04472 / 2.94 ( 974) hydrogen bonds : angle 6.55469 / 4.48 ( 2733) link_BETA1-4 : bond 0.00405 / 0.27 ( 12) link_BETA1-4 : angle 1.09605 / 0.72 ( 36) link_NAG-ASN : bond 0.00430 / 0.27 ( 45) link_NAG-ASN : angle 3.40179 / 2.19 ( 135) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5994 Ramachandran restraints generated. 2997 Oldfield, 0 Emsley, 2997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5994 Ramachandran restraints generated. 2997 Oldfield, 0 Emsley, 2997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 103 time to evaluate : 1.005 Fit side-chains revert: symmetry clash REVERT: A 117 LEU cc_start: 0.7059 (tt) cc_final: 0.6343 (mp) REVERT: A 195 LYS cc_start: 0.8510 (OUTLIER) cc_final: 0.8310 (mtpt) REVERT: A 265 TYR cc_start: 0.5454 (p90) cc_final: 0.5011 (p90) REVERT: A 421 TYR cc_start: 0.7871 (m-80) cc_final: 0.7314 (m-80) REVERT: A 507 PRO cc_start: 0.5335 (Cg_endo) cc_final: 0.5086 (Cg_endo) REVERT: B 117 LEU cc_start: 0.7060 (tt) cc_final: 0.6224 (mp) REVERT: B 220 PHE cc_start: 0.6729 (t80) cc_final: 0.6457 (t80) REVERT: B 265 TYR cc_start: 0.5216 (p90) cc_final: 0.4959 (p90) REVERT: C 117 LEU cc_start: 0.7051 (tt) cc_final: 0.6132 (mp) REVERT: C 421 TYR cc_start: 0.7902 (m-80) cc_final: 0.7278 (m-80) REVERT: C 780 GLU cc_start: 0.8941 (tt0) cc_final: 0.8677 (tt0) outliers start: 36 outliers final: 22 residues processed: 135 average time/residue: 0.1606 time to fit residues: 35.6831 Evaluate side-chains 115 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 92 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 TYR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 1107 ARG Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 661 GLU Chi-restraints excluded: chain C residue 1107 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 207 optimal weight: 3.9990 chunk 145 optimal weight: 0.9990 chunk 215 optimal weight: 0.8980 chunk 190 optimal weight: 2.9990 chunk 178 optimal weight: 0.3980 chunk 5 optimal weight: 3.9990 chunk 47 optimal weight: 6.9990 chunk 147 optimal weight: 0.0040 chunk 213 optimal weight: 10.0000 chunk 67 optimal weight: 1.9990 chunk 144 optimal weight: 6.9990 overall best weight: 0.8596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 777 ASN A 907 ASN ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 777 ASN ** B 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 777 ASN C 901 GLN C 907 ASN ** C 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.115476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.073609 restraints weight = 50232.161| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 3.21 r_work: 0.3042 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 25245 Z= 0.151 Angle : 0.649 8.341 34476 Z= 0.329 Chirality : 0.046 0.198 4074 Planarity : 0.005 0.059 4350 Dihedral : 5.779 54.857 3280 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 2.29 % Allowed : 12.54 % Favored : 85.17 % 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: -0.94 (0.15), residues: 2997 helix: 1.39 (0.21), residues: 705 sheet: -0.88 (0.20), residues: 576 loop : -1.44 (0.14), residues: 1716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 403 TYR 0.026 0.002 TYR B 505 PHE 0.025 0.002 PHE B 347 TRP 0.015 0.002 TRP B 436 HIS 0.006 0.001 HIS B1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.15 (25152) covalent geometry : angle 0.62922 / 0.32 (34233) SS BOND : bond 0.00378 / 0.24 ( 36) SS BOND : angle 1.33644 / 0.84 ( 72) hydrogen bonds : bond 0.03912 / 2.56 ( 974) hydrogen bonds : angle 5.90217 / 4.01 ( 2733) link_BETA1-4 : bond 0.00253 / 0.15 ( 12) link_BETA1-4 : angle 1.01201 / 0.64 ( 36) link_NAG-ASN : bond 0.00350 / 0.22 ( 45) link_NAG-ASN : angle 2.47048 / 1.60 ( 135) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5994 Ramachandran restraints generated. 2997 Oldfield, 0 Emsley, 2997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5994 Ramachandran restraints generated. 2997 Oldfield, 0 Emsley, 2997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 113 time to evaluate : 0.882 Fit side-chains REVERT: A 117 LEU cc_start: 0.7116 (tt) cc_final: 0.6292 (mp) REVERT: A 265 TYR cc_start: 0.5308 (p90) cc_final: 0.5005 (p90) REVERT: A 357 ARG cc_start: 0.7531 (OUTLIER) cc_final: 0.6914 (mmm-85) REVERT: A 394 ASN cc_start: 0.8352 (m-40) cc_final: 0.8148 (m-40) REVERT: A 405 ASP cc_start: 0.7474 (OUTLIER) cc_final: 0.6552 (t0) REVERT: A 421 TYR cc_start: 0.7783 (m-80) cc_final: 0.7223 (m-80) REVERT: A 507 PRO cc_start: 0.5336 (Cg_endo) cc_final: 0.5090 (Cg_endo) REVERT: B 117 LEU cc_start: 0.7160 (tt) cc_final: 0.6331 (mp) REVERT: B 220 PHE cc_start: 0.6829 (t80) cc_final: 0.6442 (t80) REVERT: B 357 ARG cc_start: 0.7264 (OUTLIER) cc_final: 0.6827 (mmm-85) REVERT: B 405 ASP cc_start: 0.7283 (OUTLIER) cc_final: 0.6355 (t0) REVERT: C 54 LEU cc_start: 0.8661 (pt) cc_final: 0.8447 (pp) REVERT: C 117 LEU cc_start: 0.7194 (tt) cc_final: 0.6177 (mp) REVERT: C 265 TYR cc_start: 0.6592 (p90) cc_final: 0.5118 (p90) REVERT: C 346 ARG cc_start: 0.7559 (mmm160) cc_final: 0.7325 (mmm160) REVERT: C 353 TRP cc_start: 0.7014 (p-90) cc_final: 0.6615 (p-90) REVERT: C 357 ARG cc_start: 0.7583 (OUTLIER) cc_final: 0.7088 (mmm-85) REVERT: C 405 ASP cc_start: 0.7229 (OUTLIER) cc_final: 0.6304 (t0) REVERT: C 421 TYR cc_start: 0.7866 (m-80) cc_final: 0.7245 (m-80) REVERT: C 780 GLU cc_start: 0.8943 (tt0) cc_final: 0.8635 (tt0) outliers start: 61 outliers final: 33 residues processed: 164 average time/residue: 0.1729 time to fit residues: 44.6045 Evaluate side-chains 133 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 94 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 357 ARG Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 405 ASP Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 405 ASP Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 1107 ARG Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 220 PHE Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 405 ASP Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 661 GLU Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 1107 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 86 optimal weight: 2.9990 chunk 238 optimal weight: 20.0000 chunk 213 optimal weight: 7.9990 chunk 78 optimal weight: 0.3980 chunk 96 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 88 optimal weight: 0.6980 chunk 263 optimal weight: 0.9980 chunk 128 optimal weight: 2.9990 chunk 236 optimal weight: 7.9990 chunk 159 optimal weight: 6.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 196 ASN A 317 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN ** A 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN B 317 ASN B 394 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN ** B 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.114248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.072936 restraints weight = 50478.894| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 3.17 r_work: 0.3012 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.1975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.111 25245 Z= 0.211 Angle : 0.651 12.689 34476 Z= 0.329 Chirality : 0.046 0.189 4074 Planarity : 0.005 0.061 4350 Dihedral : 5.589 59.937 3270 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 2.63 % Allowed : 14.98 % Favored : 82.39 % 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: -0.89 (0.15), residues: 2997 helix: 1.35 (0.21), residues: 705 sheet: -0.87 (0.19), residues: 618 loop : -1.36 (0.14), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 403 TYR 0.020 0.002 TYR B 505 PHE 0.022 0.002 PHE C1052 TRP 0.013 0.002 TRP C 436 HIS 0.006 0.001 HIS B1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00503 / 0.21 (25152) covalent geometry : angle 0.63332 / 0.32 (34233) SS BOND : bond 0.00409 / 0.27 ( 36) SS BOND : angle 1.48133 / 0.93 ( 72) hydrogen bonds : bond 0.03875 / 2.55 ( 974) hydrogen bonds : angle 5.82428 / 3.97 ( 2733) link_BETA1-4 : bond 0.00270 / 0.16 ( 12) link_BETA1-4 : angle 1.02253 / 0.66 ( 36) link_NAG-ASN : bond 0.00301 / 0.20 ( 45) link_NAG-ASN : angle 2.26941 / 1.47 ( 135) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5994 Ramachandran restraints generated. 2997 Oldfield, 0 Emsley, 2997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5994 Ramachandran restraints generated. 2997 Oldfield, 0 Emsley, 2997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 104 time to evaluate : 0.921 Fit side-chains revert: symmetry clash REVERT: A 265 TYR cc_start: 0.5289 (p90) cc_final: 0.4986 (p90) REVERT: A 353 TRP cc_start: 0.7303 (p-90) cc_final: 0.6995 (p-90) REVERT: A 357 ARG cc_start: 0.7365 (OUTLIER) cc_final: 0.6905 (mmm-85) REVERT: A 421 TYR cc_start: 0.7818 (m-80) cc_final: 0.7267 (m-80) REVERT: B 117 LEU cc_start: 0.7148 (tt) cc_final: 0.6285 (mp) REVERT: B 220 PHE cc_start: 0.6894 (t80) cc_final: 0.6521 (t80) REVERT: B 357 ARG cc_start: 0.7440 (OUTLIER) cc_final: 0.7093 (mmm-85) REVERT: B 394 ASN cc_start: 0.8050 (OUTLIER) cc_final: 0.7829 (m-40) REVERT: C 54 LEU cc_start: 0.8819 (pt) cc_final: 0.8586 (pp) REVERT: C 357 ARG cc_start: 0.7314 (OUTLIER) cc_final: 0.6987 (mmm-85) REVERT: C 421 TYR cc_start: 0.7912 (m-80) cc_final: 0.7256 (m-80) REVERT: C 508 TYR cc_start: 0.7398 (OUTLIER) cc_final: 0.6858 (m-80) REVERT: C 780 GLU cc_start: 0.8947 (tt0) cc_final: 0.8643 (tt0) outliers start: 70 outliers final: 44 residues processed: 162 average time/residue: 0.1786 time to fit residues: 46.0131 Evaluate side-chains 139 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 90 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 357 ARG Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 1107 ARG Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 220 PHE Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 508 TYR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 661 GLU Chi-restraints excluded: chain C residue 1107 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 67 optimal weight: 0.8980 chunk 136 optimal weight: 0.0980 chunk 38 optimal weight: 9.9990 chunk 231 optimal weight: 4.9990 chunk 215 optimal weight: 5.9990 chunk 244 optimal weight: 5.9990 chunk 53 optimal weight: 5.9990 chunk 240 optimal weight: 9.9990 chunk 6 optimal weight: 0.7980 chunk 187 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 GLN A1002 GLN ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 628 GLN B 926 GLN C 196 ASN C 394 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 628 GLN ** C 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 935 GLN ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.114147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.073153 restraints weight = 50533.206| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 3.16 r_work: 0.3003 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.2096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 25245 Z= 0.220 Angle : 0.642 9.566 34476 Z= 0.325 Chirality : 0.045 0.182 4074 Planarity : 0.005 0.101 4350 Dihedral : 5.442 58.554 3268 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 3.27 % Allowed : 15.84 % Favored : 80.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.83 (0.15), residues: 2997 helix: 1.44 (0.21), residues: 687 sheet: -0.85 (0.19), residues: 618 loop : -1.31 (0.14), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 403 TYR 0.021 0.002 TYR C 505 PHE 0.028 0.002 PHE A 347 TRP 0.012 0.002 TRP C 436 HIS 0.006 0.001 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00521 / 0.22 (25152) covalent geometry : angle 0.62531 / 0.32 (34233) SS BOND : bond 0.00443 / 0.28 ( 36) SS BOND : angle 1.48518 / 0.91 ( 72) hydrogen bonds : bond 0.03856 / 2.54 ( 974) hydrogen bonds : angle 5.74550 / 3.91 ( 2733) link_BETA1-4 : bond 0.00218 / 0.13 ( 12) link_BETA1-4 : angle 1.01893 / 0.65 ( 36) link_NAG-ASN : bond 0.00298 / 0.20 ( 45) link_NAG-ASN : angle 2.17185 / 1.40 ( 135) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5994 Ramachandran restraints generated. 2997 Oldfield, 0 Emsley, 2997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5994 Ramachandran restraints generated. 2997 Oldfield, 0 Emsley, 2997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 97 time to evaluate : 0.921 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 LEU cc_start: 0.7182 (tt) cc_final: 0.6267 (mp) REVERT: A 265 TYR cc_start: 0.5276 (p90) cc_final: 0.4998 (p90) REVERT: A 353 TRP cc_start: 0.7377 (p-90) cc_final: 0.6835 (p-90) REVERT: A 357 ARG cc_start: 0.7500 (OUTLIER) cc_final: 0.7199 (mmm-85) REVERT: A 405 ASP cc_start: 0.7479 (OUTLIER) cc_final: 0.6609 (t0) REVERT: A 508 TYR cc_start: 0.7564 (OUTLIER) cc_final: 0.7040 (m-80) REVERT: A 1139 ASP cc_start: 0.8549 (OUTLIER) cc_final: 0.8301 (p0) REVERT: B 357 ARG cc_start: 0.7668 (OUTLIER) cc_final: 0.7376 (mmm-85) REVERT: B 405 ASP cc_start: 0.7109 (OUTLIER) cc_final: 0.6132 (t0) REVERT: B 508 TYR cc_start: 0.7688 (OUTLIER) cc_final: 0.7045 (m-80) REVERT: C 54 LEU cc_start: 0.8697 (pt) cc_final: 0.8444 (pp) REVERT: C 117 LEU cc_start: 0.7314 (tt) cc_final: 0.6316 (mp) REVERT: C 353 TRP cc_start: 0.7250 (p-90) cc_final: 0.6092 (p-90) REVERT: C 357 ARG cc_start: 0.7552 (OUTLIER) cc_final: 0.7139 (mmt90) REVERT: C 405 ASP cc_start: 0.7287 (OUTLIER) cc_final: 0.6264 (t0) REVERT: C 508 TYR cc_start: 0.7354 (OUTLIER) cc_final: 0.6824 (m-80) REVERT: C 780 GLU cc_start: 0.8905 (tt0) cc_final: 0.8620 (tt0) outliers start: 87 outliers final: 58 residues processed: 173 average time/residue: 0.1598 time to fit residues: 45.6245 Evaluate side-chains 159 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 91 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 357 ARG Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 405 ASP Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1139 ASP Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 405 ASP Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 508 TYR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1107 ARG Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 220 PHE Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 405 ASP Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 508 TYR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 661 GLU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1107 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 199 optimal weight: 0.5980 chunk 202 optimal weight: 7.9990 chunk 57 optimal weight: 0.4980 chunk 126 optimal weight: 4.9990 chunk 252 optimal weight: 0.9980 chunk 29 optimal weight: 4.9990 chunk 105 optimal weight: 10.0000 chunk 88 optimal weight: 2.9990 chunk 188 optimal weight: 0.6980 chunk 225 optimal weight: 2.9990 chunk 170 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 394 ASN ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 628 GLN ** A 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 926 GLN ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN B1005 GLN B1054 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 625 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN ** C 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.115269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.073302 restraints weight = 50178.344| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 3.22 r_work: 0.3033 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.2343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 25245 Z= 0.132 Angle : 0.595 8.783 34476 Z= 0.301 Chirality : 0.044 0.176 4074 Planarity : 0.004 0.086 4350 Dihedral : 5.197 59.882 3267 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.85 % Allowed : 16.67 % Favored : 80.48 % 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: -0.63 (0.15), residues: 2997 helix: 1.64 (0.21), residues: 684 sheet: -0.66 (0.20), residues: 597 loop : -1.23 (0.14), residues: 1716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 403 TYR 0.016 0.001 TYR C 505 PHE 0.021 0.001 PHE A 347 TRP 0.012 0.002 TRP B 436 HIS 0.005 0.001 HIS B1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 (25152) covalent geometry : angle 0.57979 / 0.30 (34233) SS BOND : bond 0.00419 / 0.24 ( 36) SS BOND : angle 1.28015 / 0.78 ( 72) hydrogen bonds : bond 0.03607 / 2.36 ( 974) hydrogen bonds : angle 5.52901 / 3.77 ( 2733) link_BETA1-4 : bond 0.00244 / 0.15 ( 12) link_BETA1-4 : angle 0.96881 / 0.61 ( 36) link_NAG-ASN : bond 0.00294 / 0.20 ( 45) link_NAG-ASN : angle 2.00139 / 1.29 ( 135) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5994 Ramachandran restraints generated. 2997 Oldfield, 0 Emsley, 2997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5994 Ramachandran restraints generated. 2997 Oldfield, 0 Emsley, 2997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 104 time to evaluate : 0.932 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 LEU cc_start: 0.7063 (tt) cc_final: 0.6210 (mp) REVERT: A 353 TRP cc_start: 0.7261 (p-90) cc_final: 0.6656 (p-90) REVERT: A 394 ASN cc_start: 0.8170 (OUTLIER) cc_final: 0.7890 (t0) REVERT: A 508 TYR cc_start: 0.7464 (OUTLIER) cc_final: 0.6945 (m-80) REVERT: A 1139 ASP cc_start: 0.8484 (OUTLIER) cc_final: 0.8230 (p0) REVERT: B 117 LEU cc_start: 0.7305 (tt) cc_final: 0.6418 (mp) REVERT: B 357 ARG cc_start: 0.7505 (OUTLIER) cc_final: 0.7237 (mmt90) REVERT: B 405 ASP cc_start: 0.7102 (OUTLIER) cc_final: 0.6097 (t0) REVERT: B 508 TYR cc_start: 0.7687 (OUTLIER) cc_final: 0.7166 (m-80) REVERT: C 54 LEU cc_start: 0.8723 (pt) cc_final: 0.8487 (pp) REVERT: C 117 LEU cc_start: 0.7297 (tt) cc_final: 0.6327 (mp) REVERT: C 353 TRP cc_start: 0.7109 (p-90) cc_final: 0.6519 (p-90) REVERT: C 357 ARG cc_start: 0.7541 (OUTLIER) cc_final: 0.7332 (mmt90) REVERT: C 405 ASP cc_start: 0.7264 (OUTLIER) cc_final: 0.6122 (t0) REVERT: C 759 PHE cc_start: 0.8690 (m-80) cc_final: 0.8016 (t80) REVERT: C 780 GLU cc_start: 0.8896 (tt0) cc_final: 0.8626 (tt0) outliers start: 76 outliers final: 55 residues processed: 169 average time/residue: 0.1603 time to fit residues: 44.4517 Evaluate side-chains 157 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 94 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1139 ASP Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 405 ASP Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 508 TYR Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 1107 ARG Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 405 ASP Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 661 GLU Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 1107 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 134 optimal weight: 8.9990 chunk 284 optimal weight: 2.9990 chunk 75 optimal weight: 0.0170 chunk 281 optimal weight: 0.5980 chunk 195 optimal weight: 2.9990 chunk 165 optimal weight: 1.9990 chunk 97 optimal weight: 0.6980 chunk 243 optimal weight: 10.0000 chunk 15 optimal weight: 9.9990 chunk 82 optimal weight: 1.9990 chunk 136 optimal weight: 10.0000 overall best weight: 1.0622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 625 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 625 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN ** C 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.114893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.072962 restraints weight = 50085.925| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 3.21 r_work: 0.3027 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.2415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 25245 Z= 0.154 Angle : 0.592 8.023 34476 Z= 0.299 Chirality : 0.044 0.177 4074 Planarity : 0.004 0.076 4350 Dihedral : 5.130 59.360 3267 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 3.34 % Allowed : 16.82 % Favored : 79.84 % 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: -0.57 (0.15), residues: 2997 helix: 1.63 (0.21), residues: 687 sheet: -0.61 (0.20), residues: 600 loop : -1.16 (0.14), residues: 1710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 34 TYR 0.017 0.001 TYR B 265 PHE 0.025 0.001 PHE A 347 TRP 0.011 0.002 TRP C 436 HIS 0.006 0.001 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.15 (25152) covalent geometry : angle 0.57694 / 0.30 (34233) SS BOND : bond 0.00347 / 0.21 ( 36) SS BOND : angle 1.30618 / 0.78 ( 72) hydrogen bonds : bond 0.03590 / 2.36 ( 974) hydrogen bonds : angle 5.46259 / 3.72 ( 2733) link_BETA1-4 : bond 0.00250 / 0.16 ( 12) link_BETA1-4 : angle 0.99386 / 0.63 ( 36) link_NAG-ASN : bond 0.00275 / 0.19 ( 45) link_NAG-ASN : angle 1.95963 / 1.26 ( 135) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5994 Ramachandran restraints generated. 2997 Oldfield, 0 Emsley, 2997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5994 Ramachandran restraints generated. 2997 Oldfield, 0 Emsley, 2997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 94 time to evaluate : 1.044 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 LEU cc_start: 0.7069 (tt) cc_final: 0.6203 (mp) REVERT: A 353 TRP cc_start: 0.7244 (p-90) cc_final: 0.6505 (p-90) REVERT: A 376 THR cc_start: 0.7545 (OUTLIER) cc_final: 0.7277 (p) REVERT: A 1139 ASP cc_start: 0.8466 (OUTLIER) cc_final: 0.8201 (p0) REVERT: B 34 ARG cc_start: 0.7597 (mmp80) cc_final: 0.6965 (mmt-90) REVERT: B 117 LEU cc_start: 0.7304 (tt) cc_final: 0.6394 (mp) REVERT: B 353 TRP cc_start: 0.6879 (p-90) cc_final: 0.5166 (p-90) REVERT: B 357 ARG cc_start: 0.7493 (OUTLIER) cc_final: 0.7264 (mmt90) REVERT: B 405 ASP cc_start: 0.7155 (OUTLIER) cc_final: 0.6099 (t0) REVERT: B 508 TYR cc_start: 0.7782 (OUTLIER) cc_final: 0.7284 (m-80) REVERT: C 54 LEU cc_start: 0.8766 (pt) cc_final: 0.8530 (pp) REVERT: C 117 LEU cc_start: 0.7278 (tt) cc_final: 0.6317 (mp) REVERT: C 353 TRP cc_start: 0.7129 (p-90) cc_final: 0.6624 (p-90) REVERT: C 357 ARG cc_start: 0.7627 (OUTLIER) cc_final: 0.7258 (mmm-85) REVERT: C 405 ASP cc_start: 0.7036 (OUTLIER) cc_final: 0.5966 (t0) REVERT: C 780 GLU cc_start: 0.8898 (tt0) cc_final: 0.8638 (tt0) outliers start: 89 outliers final: 65 residues processed: 174 average time/residue: 0.1625 time to fit residues: 47.0071 Evaluate side-chains 165 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 93 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1139 ASP Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 405 ASP Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 508 TYR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 1107 ARG Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 405 ASP Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 661 GLU Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 1107 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 171 optimal weight: 0.9990 chunk 42 optimal weight: 6.9990 chunk 253 optimal weight: 0.0970 chunk 54 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 199 optimal weight: 0.6980 chunk 249 optimal weight: 3.9990 chunk 82 optimal weight: 0.7980 chunk 35 optimal weight: 5.9990 chunk 40 optimal weight: 10.0000 chunk 147 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 394 ASN ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 625 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 625 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 625 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN ** C 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.115936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.074030 restraints weight = 50043.311| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 3.23 r_work: 0.3049 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.2596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 25245 Z= 0.123 Angle : 0.572 7.661 34476 Z= 0.290 Chirality : 0.044 0.201 4074 Planarity : 0.004 0.069 4350 Dihedral : 5.003 59.637 3267 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 3.00 % Allowed : 17.23 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.15), residues: 2997 helix: 1.71 (0.21), residues: 687 sheet: -0.28 (0.20), residues: 555 loop : -1.17 (0.14), residues: 1755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 403 TYR 0.016 0.001 TYR A1067 PHE 0.018 0.001 PHE B 855 TRP 0.012 0.001 TRP A 436 HIS 0.005 0.001 HIS B1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.12 (25152) covalent geometry : angle 0.55803 / 0.29 (34233) SS BOND : bond 0.00297 / 0.18 ( 36) SS BOND : angle 1.22249 / 0.74 ( 72) hydrogen bonds : bond 0.03472 / 2.27 ( 974) hydrogen bonds : angle 5.31650 / 3.62 ( 2733) link_BETA1-4 : bond 0.00295 / 0.18 ( 12) link_BETA1-4 : angle 0.96944 / 0.62 ( 36) link_NAG-ASN : bond 0.00292 / 0.20 ( 45) link_NAG-ASN : angle 1.84915 / 1.19 ( 135) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5994 Ramachandran restraints generated. 2997 Oldfield, 0 Emsley, 2997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5994 Ramachandran restraints generated. 2997 Oldfield, 0 Emsley, 2997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 104 time to evaluate : 0.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 353 TRP cc_start: 0.7170 (p-90) cc_final: 0.6493 (p-90) REVERT: A 376 THR cc_start: 0.7541 (OUTLIER) cc_final: 0.7258 (p) REVERT: A 1139 ASP cc_start: 0.8422 (OUTLIER) cc_final: 0.8139 (p0) REVERT: B 34 ARG cc_start: 0.7561 (mmp80) cc_final: 0.7121 (mmm160) REVERT: B 117 LEU cc_start: 0.7262 (tt) cc_final: 0.6370 (mp) REVERT: B 353 TRP cc_start: 0.6844 (p-90) cc_final: 0.5098 (p-90) REVERT: B 508 TYR cc_start: 0.7724 (OUTLIER) cc_final: 0.7218 (m-80) REVERT: B 902 MET cc_start: 0.8769 (tpp) cc_final: 0.8268 (tpt) REVERT: C 54 LEU cc_start: 0.8693 (pt) cc_final: 0.8471 (pp) REVERT: C 117 LEU cc_start: 0.7253 (tt) cc_final: 0.6301 (mp) REVERT: C 353 TRP cc_start: 0.6976 (p-90) cc_final: 0.6596 (p-90) REVERT: C 357 ARG cc_start: 0.7667 (OUTLIER) cc_final: 0.7258 (mmt90) REVERT: C 780 GLU cc_start: 0.8899 (tt0) cc_final: 0.8655 (tt0) outliers start: 80 outliers final: 64 residues processed: 174 average time/residue: 0.1604 time to fit residues: 46.2730 Evaluate side-chains 163 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 95 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1139 ASP Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 508 TYR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1107 ARG Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 1107 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 147 optimal weight: 0.6980 chunk 73 optimal weight: 2.9990 chunk 101 optimal weight: 8.9990 chunk 302 optimal weight: 0.4980 chunk 57 optimal weight: 0.0370 chunk 189 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 137 optimal weight: 30.0000 chunk 75 optimal weight: 0.0770 chunk 190 optimal weight: 0.9990 chunk 99 optimal weight: 1.9990 overall best weight: 0.4618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 625 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 ASN ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 625 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 625 HIS C 907 ASN ** C 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.117252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.076662 restraints weight = 50151.000| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 3.19 r_work: 0.3071 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.2754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 25245 Z= 0.110 Angle : 0.565 7.419 34476 Z= 0.286 Chirality : 0.044 0.172 4074 Planarity : 0.004 0.066 4350 Dihedral : 4.937 59.964 3267 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.85 % Allowed : 17.45 % Favored : 79.69 % 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: -0.33 (0.15), residues: 2997 helix: 1.78 (0.21), residues: 687 sheet: -0.17 (0.21), residues: 564 loop : -1.10 (0.14), residues: 1746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 34 TYR 0.015 0.001 TYR A1067 PHE 0.020 0.001 PHE B 855 TRP 0.012 0.001 TRP C 104 HIS 0.005 0.001 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 (25152) covalent geometry : angle 0.55188 / 0.28 (34233) SS BOND : bond 0.00255 / 0.15 ( 36) SS BOND : angle 1.18407 / 0.71 ( 72) hydrogen bonds : bond 0.03379 / 2.21 ( 974) hydrogen bonds : angle 5.19575 / 3.55 ( 2733) link_BETA1-4 : bond 0.00308 / 0.19 ( 12) link_BETA1-4 : angle 0.96241 / 0.61 ( 36) link_NAG-ASN : bond 0.00287 / 0.20 ( 45) link_NAG-ASN : angle 1.78644 / 1.15 ( 135) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5994 Ramachandran restraints generated. 2997 Oldfield, 0 Emsley, 2997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5994 Ramachandran restraints generated. 2997 Oldfield, 0 Emsley, 2997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 100 time to evaluate : 0.943 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 353 TRP cc_start: 0.7138 (p-90) cc_final: 0.6515 (p-90) REVERT: A 376 THR cc_start: 0.7613 (OUTLIER) cc_final: 0.7345 (p) REVERT: A 1139 ASP cc_start: 0.8388 (OUTLIER) cc_final: 0.8158 (p0) REVERT: B 34 ARG cc_start: 0.7474 (mmp80) cc_final: 0.6939 (mmt-90) REVERT: B 117 LEU cc_start: 0.7146 (tt) cc_final: 0.6242 (mp) REVERT: B 353 TRP cc_start: 0.6855 (p-90) cc_final: 0.5101 (p-90) REVERT: B 508 TYR cc_start: 0.7767 (OUTLIER) cc_final: 0.7232 (m-80) REVERT: C 54 LEU cc_start: 0.8692 (pt) cc_final: 0.8480 (pp) REVERT: C 117 LEU cc_start: 0.7205 (tt) cc_final: 0.6246 (mp) REVERT: C 121 ASN cc_start: 0.6576 (m110) cc_final: 0.4608 (t0) REVERT: C 353 TRP cc_start: 0.7018 (p-90) cc_final: 0.6695 (p-90) REVERT: C 357 ARG cc_start: 0.7701 (OUTLIER) cc_final: 0.7382 (mmt90) REVERT: C 780 GLU cc_start: 0.8886 (tt0) cc_final: 0.8637 (tt0) outliers start: 76 outliers final: 65 residues processed: 168 average time/residue: 0.1610 time to fit residues: 45.0763 Evaluate side-chains 167 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 98 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 907 ASN Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1139 ASP Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 508 TYR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1107 ARG Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 1107 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 254 optimal weight: 2.9990 chunk 251 optimal weight: 5.9990 chunk 207 optimal weight: 3.9990 chunk 149 optimal weight: 1.9990 chunk 236 optimal weight: 8.9990 chunk 230 optimal weight: 9.9990 chunk 301 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 181 optimal weight: 0.9990 chunk 215 optimal weight: 0.7980 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 448 ASN ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 625 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 ASN A1054 GLN B 448 ASN ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 625 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN ** C 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1054 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.113944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.071954 restraints weight = 50250.979| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 3.22 r_work: 0.3010 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.2638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 25245 Z= 0.221 Angle : 0.614 7.266 34476 Z= 0.310 Chirality : 0.045 0.315 4074 Planarity : 0.004 0.062 4350 Dihedral : 5.039 55.919 3267 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.70 % Allowed : 17.72 % Favored : 79.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.15), residues: 2997 helix: 1.61 (0.21), residues: 687 sheet: -0.46 (0.20), residues: 576 loop : -1.15 (0.14), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 34 TYR 0.021 0.002 TYR B 265 PHE 0.022 0.002 PHE C1121 TRP 0.010 0.002 TRP B 436 HIS 0.008 0.001 HIS B1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00524 / 0.22 (25152) covalent geometry : angle 0.59998 / 0.31 (34233) SS BOND : bond 0.00406 / 0.25 ( 36) SS BOND : angle 1.38050 / 0.84 ( 72) hydrogen bonds : bond 0.03676 / 2.41 ( 974) hydrogen bonds : angle 5.36828 / 3.66 ( 2733) link_BETA1-4 : bond 0.00180 / 0.12 ( 12) link_BETA1-4 : angle 0.98920 / 0.63 ( 36) link_NAG-ASN : bond 0.00274 / 0.19 ( 45) link_NAG-ASN : angle 1.92013 / 1.23 ( 135) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5994 Ramachandran restraints generated. 2997 Oldfield, 0 Emsley, 2997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5994 Ramachandran restraints generated. 2997 Oldfield, 0 Emsley, 2997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 102 time to evaluate : 0.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 353 TRP cc_start: 0.7314 (p-90) cc_final: 0.6596 (p-90) REVERT: A 376 THR cc_start: 0.7669 (OUTLIER) cc_final: 0.7390 (p) REVERT: A 1139 ASP cc_start: 0.8423 (OUTLIER) cc_final: 0.8193 (p0) REVERT: B 508 TYR cc_start: 0.7842 (OUTLIER) cc_final: 0.7288 (m-80) REVERT: C 54 LEU cc_start: 0.8697 (pt) cc_final: 0.8481 (pp) REVERT: C 353 TRP cc_start: 0.7069 (p-90) cc_final: 0.6460 (p-90) REVERT: C 780 GLU cc_start: 0.8897 (tt0) cc_final: 0.8648 (tt0) outliers start: 72 outliers final: 62 residues processed: 168 average time/residue: 0.1596 time to fit residues: 44.8743 Evaluate side-chains 165 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 100 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1139 ASP Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 508 TYR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1107 ARG Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1107 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 186 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 264 optimal weight: 0.9990 chunk 175 optimal weight: 0.6980 chunk 90 optimal weight: 0.5980 chunk 50 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 147 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 300 optimal weight: 0.4980 chunk 159 optimal weight: 4.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 625 HIS ** A 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 448 ASN ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 625 HIS ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN ** C 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.115806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.073936 restraints weight = 50071.095| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 3.23 r_work: 0.3049 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.2807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 25245 Z= 0.126 Angle : 0.571 7.216 34476 Z= 0.289 Chirality : 0.044 0.304 4074 Planarity : 0.004 0.061 4350 Dihedral : 4.921 57.154 3267 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.63 % Allowed : 17.76 % Favored : 79.62 % 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: 2997 helix: 1.74 (0.21), residues: 687 sheet: -0.22 (0.21), residues: 540 loop : -1.08 (0.14), residues: 1770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 34 TYR 0.015 0.001 TYR A1067 PHE 0.018 0.001 PHE B 855 TRP 0.012 0.001 TRP B 353 HIS 0.005 0.001 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (25152) covalent geometry : angle 0.55733 / 0.29 (34233) SS BOND : bond 0.00303 / 0.18 ( 36) SS BOND : angle 1.25429 / 0.73 ( 72) hydrogen bonds : bond 0.03446 / 2.26 ( 974) hydrogen bonds : angle 5.22345 / 3.57 ( 2733) link_BETA1-4 : bond 0.00272 / 0.17 ( 12) link_BETA1-4 : angle 0.97051 / 0.62 ( 36) link_NAG-ASN : bond 0.00270 / 0.19 ( 45) link_NAG-ASN : angle 1.82786 / 1.18 ( 135) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5313.24 seconds wall clock time: 92 minutes 31.14 seconds (5551.14 seconds total)