Starting phenix.real_space_refine on Thu Mar 5 19:32:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6x6p_22078/03_2026/6x6p_22078.cif Found real_map, /net/cci-nas-00/data/ceres_data/6x6p_22078/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/6x6p_22078/03_2026/6x6p_22078.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6x6p_22078/03_2026/6x6p_22078.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6x6p_22078/03_2026/6x6p_22078.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6x6p_22078/03_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 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 dihedrals: 33 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 dihedrals: 33 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 dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Time building chain proxies: 5.69, 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: 2.28 Conformation dependent library (CDL) restraints added in 972.3 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: 1.30 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: 6.01 Time building geometry restraints manager: 2.97 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: 13621 18.07 - 36.13: 1561 36.13 - 54.20: 424 54.20 - 72.27: 81 72.27 - 90.33: 24 Dihedral angle restraints: 15711 sinusoidal: 6822 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 15708 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: 0.06 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: 4.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.450 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 24.920 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 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 : 16.192 80.465 9873 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 covalent geometry : bond 0.01212 (25152) covalent geometry : angle 1.07195 (34233) SS BOND : bond 0.00884 ( 36) SS BOND : angle 3.24094 ( 72) hydrogen bonds : bond 0.13942 ( 974) hydrogen bonds : angle 8.59105 ( 2733) link_BETA1-4 : bond 0.00331 ( 12) link_BETA1-4 : angle 1.57638 ( 36) link_NAG-ASN : bond 0.00896 ( 45) link_NAG-ASN : angle 5.30631 ( 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 : 0.686 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: 0.1761 time to fit residues: 54.8291 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 : 0.894 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 122 ASN ** A 422 ASN ** 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 = 0.3852 r_free = 0.3852 target = 0.115200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.074236 restraints weight = 50424.835| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 3.18 r_work: 0.3041 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.1375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 25245 Z= 0.172 Angle : 0.758 9.115 34476 Z= 0.385 Chirality : 0.048 0.262 4074 Planarity : 0.006 0.104 4350 Dihedral : 7.847 58.912 4515 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 1.35 % Allowed : 11.60 % Favored : 87.05 % 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: -1.29 (0.15), residues: 2997 helix: 0.90 (0.20), residues: 705 sheet: -1.15 (0.18), residues: 645 loop : -1.55 (0.14), residues: 1647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 403 TYR 0.032 0.002 TYR B 505 PHE 0.029 0.002 PHE B 347 TRP 0.015 0.002 TRP C 436 HIS 0.008 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00399 (25152) covalent geometry : angle 0.72654 (34233) SS BOND : bond 0.00406 ( 36) SS BOND : angle 1.76038 ( 72) hydrogen bonds : bond 0.04426 ( 974) hydrogen bonds : angle 6.52109 ( 2733) link_BETA1-4 : bond 0.00464 ( 12) link_BETA1-4 : angle 0.99354 ( 36) link_NAG-ASN : bond 0.00446 ( 45) link_NAG-ASN : angle 3.32493 ( 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 141 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 105 time to evaluate : 0.685 Fit side-chains revert: symmetry clash REVERT: A 34 ARG cc_start: 0.7419 (mmp80) cc_final: 0.7109 (mmm160) REVERT: A 117 LEU cc_start: 0.7059 (tt) cc_final: 0.6340 (mp) REVERT: A 195 LYS cc_start: 0.8511 (OUTLIER) cc_final: 0.8302 (mtpt) REVERT: A 265 TYR cc_start: 0.5453 (p90) cc_final: 0.5006 (p90) REVERT: A 421 TYR cc_start: 0.7875 (m-80) cc_final: 0.7311 (m-80) REVERT: A 507 PRO cc_start: 0.5343 (Cg_endo) cc_final: 0.5091 (Cg_endo) REVERT: B 34 ARG cc_start: 0.7503 (mmp80) cc_final: 0.7205 (mmm160) REVERT: B 117 LEU cc_start: 0.7056 (tt) cc_final: 0.6220 (mp) REVERT: B 220 PHE cc_start: 0.6738 (t80) cc_final: 0.6423 (t80) REVERT: B 265 TYR cc_start: 0.5220 (p90) cc_final: 0.4958 (p90) REVERT: C 117 LEU cc_start: 0.7046 (tt) cc_final: 0.6125 (mp) REVERT: C 421 TYR cc_start: 0.7901 (m-80) cc_final: 0.7271 (m-80) REVERT: C 780 GLU cc_start: 0.8939 (tt0) cc_final: 0.8688 (tt0) outliers start: 36 outliers final: 23 residues processed: 137 average time/residue: 0.1567 time to fit residues: 35.4409 Evaluate side-chains 118 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 94 time to evaluate : 0.867 ------------------------------------------------------------------------------- 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 539 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: 9.9990 chunk 215 optimal weight: 0.7980 chunk 190 optimal weight: 2.9990 chunk 178 optimal weight: 0.3980 chunk 5 optimal weight: 3.9990 chunk 47 optimal weight: 7.9990 chunk 147 optimal weight: 0.0070 chunk 213 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 144 optimal weight: 6.9990 overall best weight: 1.2402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 317 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 777 ASN A 901 GLN ** A 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 901 GLN ** 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.114852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.073469 restraints weight = 50521.025| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 3.19 r_work: 0.3025 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.1774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 25245 Z= 0.185 Angle : 0.667 8.375 34476 Z= 0.338 Chirality : 0.046 0.206 4074 Planarity : 0.005 0.061 4350 Dihedral : 6.726 57.929 4478 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 2.36 % Allowed : 12.84 % Favored : 84.80 % 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: -1.01 (0.15), residues: 2997 helix: 1.32 (0.21), residues: 705 sheet: -1.02 (0.19), residues: 630 loop : -1.45 (0.14), residues: 1662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 403 TYR 0.024 0.002 TYR C 505 PHE 0.025 0.002 PHE B 347 TRP 0.015 0.002 TRP B 436 HIS 0.007 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00439 (25152) covalent geometry : angle 0.64524 (34233) SS BOND : bond 0.00371 ( 36) SS BOND : angle 1.45416 ( 72) hydrogen bonds : bond 0.04014 ( 974) hydrogen bonds : angle 5.98363 ( 2733) link_BETA1-4 : bond 0.00245 ( 12) link_BETA1-4 : angle 1.00945 ( 36) link_NAG-ASN : bond 0.00345 ( 45) link_NAG-ASN : angle 2.60090 ( 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 177 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 114 time to evaluate : 0.916 Fit side-chains revert: symmetry clash REVERT: A 117 LEU cc_start: 0.7157 (tt) cc_final: 0.6337 (mp) REVERT: A 265 TYR cc_start: 0.5333 (p90) cc_final: 0.5040 (p90) REVERT: A 357 ARG cc_start: 0.7531 (OUTLIER) cc_final: 0.6985 (mmm-85) REVERT: A 394 ASN cc_start: 0.8356 (m-40) cc_final: 0.8147 (m-40) REVERT: A 405 ASP cc_start: 0.7492 (OUTLIER) cc_final: 0.6574 (t0) REVERT: A 421 TYR cc_start: 0.7789 (m-80) cc_final: 0.7239 (m-80) REVERT: A 423 TYR cc_start: 0.6391 (t80) cc_final: 0.6153 (t80) REVERT: A 507 PRO cc_start: 0.5334 (Cg_endo) cc_final: 0.5080 (Cg_endo) REVERT: B 52 GLN cc_start: 0.8511 (tm-30) cc_final: 0.8135 (tm-30) REVERT: B 117 LEU cc_start: 0.7053 (tt) cc_final: 0.6233 (mp) REVERT: B 220 PHE cc_start: 0.6850 (t80) cc_final: 0.6455 (t80) REVERT: B 357 ARG cc_start: 0.7321 (OUTLIER) cc_final: 0.6912 (mmm-85) REVERT: B 405 ASP cc_start: 0.7312 (OUTLIER) cc_final: 0.6372 (t0) REVERT: C 54 LEU cc_start: 0.8732 (pt) cc_final: 0.8509 (pp) REVERT: C 117 LEU cc_start: 0.7142 (tt) cc_final: 0.6110 (mp) REVERT: C 265 TYR cc_start: 0.6601 (p90) cc_final: 0.5189 (p90) REVERT: C 346 ARG cc_start: 0.7514 (mmm160) cc_final: 0.7312 (mmm160) REVERT: C 353 TRP cc_start: 0.7088 (p-90) cc_final: 0.6677 (p-90) REVERT: C 357 ARG cc_start: 0.7468 (OUTLIER) cc_final: 0.7007 (mmt90) REVERT: C 405 ASP cc_start: 0.7124 (OUTLIER) cc_final: 0.6205 (t0) REVERT: C 421 TYR cc_start: 0.7852 (m-80) cc_final: 0.7247 (m-80) REVERT: C 780 GLU cc_start: 0.8942 (tt0) cc_final: 0.8619 (tt0) outliers start: 63 outliers final: 39 residues processed: 170 average time/residue: 0.1794 time to fit residues: 47.7610 Evaluate side-chains 135 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 90 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 267 VAL 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 90 VAL Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 267 VAL 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 524 VAL Chi-restraints excluded: chain C residue 539 VAL 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: 0.7980 chunk 96 optimal weight: 1.9990 chunk 9 optimal weight: 9.9990 chunk 88 optimal weight: 1.9990 chunk 263 optimal weight: 0.9980 chunk 128 optimal weight: 2.9990 chunk 236 optimal weight: 7.9990 chunk 159 optimal weight: 0.7980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN B 394 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 GLN ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.114634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.073346 restraints weight = 50328.492| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 3.17 r_work: 0.3022 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.096 25245 Z= 0.182 Angle : 0.639 12.458 34476 Z= 0.323 Chirality : 0.045 0.186 4074 Planarity : 0.004 0.058 4350 Dihedral : 6.297 59.708 4468 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 2.52 % Allowed : 15.13 % Favored : 82.36 % 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: -0.88 (0.15), residues: 2997 helix: 1.37 (0.21), residues: 705 sheet: -0.86 (0.19), residues: 618 loop : -1.37 (0.14), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 403 TYR 0.019 0.002 TYR B 505 PHE 0.020 0.002 PHE B 347 TRP 0.013 0.002 TRP C 436 HIS 0.005 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00432 (25152) covalent geometry : angle 0.62012 (34233) SS BOND : bond 0.00382 ( 36) SS BOND : angle 1.44171 ( 72) hydrogen bonds : bond 0.03818 ( 974) hydrogen bonds : angle 5.81851 ( 2733) link_BETA1-4 : bond 0.00281 ( 12) link_BETA1-4 : angle 0.99310 ( 36) link_NAG-ASN : bond 0.00303 ( 45) link_NAG-ASN : angle 2.35224 ( 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 171 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 104 time to evaluate : 1.170 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 265 TYR cc_start: 0.5292 (p90) cc_final: 0.5015 (p90) REVERT: A 357 ARG cc_start: 0.7374 (OUTLIER) cc_final: 0.6862 (mmm-85) REVERT: A 376 THR cc_start: 0.7479 (OUTLIER) cc_final: 0.7270 (p) REVERT: A 421 TYR cc_start: 0.7852 (m-80) cc_final: 0.7322 (m-80) REVERT: B 117 LEU cc_start: 0.7154 (tt) cc_final: 0.6312 (mp) REVERT: B 220 PHE cc_start: 0.6935 (t80) cc_final: 0.6535 (t80) REVERT: B 357 ARG cc_start: 0.7458 (OUTLIER) cc_final: 0.7125 (mmm-85) REVERT: C 54 LEU cc_start: 0.8793 (pt) cc_final: 0.8575 (pp) REVERT: C 117 LEU cc_start: 0.7252 (OUTLIER) cc_final: 0.6353 (mp) REVERT: C 357 ARG cc_start: 0.7603 (OUTLIER) cc_final: 0.7136 (mmm-85) REVERT: C 508 TYR cc_start: 0.7378 (OUTLIER) cc_final: 0.6835 (m-80) REVERT: C 780 GLU cc_start: 0.8920 (tt0) cc_final: 0.8599 (tt0) REVERT: C 900 MET cc_start: 0.8658 (mtp) cc_final: 0.8358 (mtp) outliers start: 67 outliers final: 47 residues processed: 160 average time/residue: 0.1721 time to fit residues: 44.4768 Evaluate side-chains 141 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 88 time to evaluate : 1.066 ------------------------------------------------------------------------------- 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 267 VAL 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 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 267 VAL 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 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 117 LEU 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 445 VAL Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 508 TYR Chi-restraints excluded: chain C residue 581 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 67 optimal weight: 0.5980 chunk 136 optimal weight: 0.0980 chunk 38 optimal weight: 3.9990 chunk 231 optimal weight: 6.9990 chunk 215 optimal weight: 5.9990 chunk 244 optimal weight: 0.0040 chunk 53 optimal weight: 4.9990 chunk 240 optimal weight: 10.0000 chunk 6 optimal weight: 0.7980 chunk 187 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 overall best weight: 0.8994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 628 GLN ** A 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 926 GLN A 935 GLN A1002 GLN ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 926 GLN 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** C 935 GLN ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.115955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.075015 restraints weight = 50253.657| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 3.19 r_work: 0.3039 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.2238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 25245 Z= 0.142 Angle : 0.600 9.521 34476 Z= 0.304 Chirality : 0.044 0.169 4074 Planarity : 0.004 0.054 4350 Dihedral : 5.850 59.885 4466 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 3.27 % Allowed : 15.69 % Favored : 81.04 % 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: -0.70 (0.15), residues: 2997 helix: 1.63 (0.21), residues: 684 sheet: -0.68 (0.19), residues: 624 loop : -1.30 (0.14), residues: 1689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 403 TYR 0.025 0.002 TYR C 505 PHE 0.017 0.002 PHE B 347 TRP 0.012 0.002 TRP C 436 HIS 0.005 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00332 (25152) covalent geometry : angle 0.58246 (34233) SS BOND : bond 0.00343 ( 36) SS BOND : angle 1.27903 ( 72) hydrogen bonds : bond 0.03608 ( 974) hydrogen bonds : angle 5.57263 ( 2733) link_BETA1-4 : bond 0.00310 ( 12) link_BETA1-4 : angle 1.00599 ( 36) link_NAG-ASN : bond 0.00298 ( 45) link_NAG-ASN : angle 2.16696 ( 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 190 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 103 time to evaluate : 0.800 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 117 LEU cc_start: 0.7241 (tt) cc_final: 0.6363 (mp) REVERT: A 265 TYR cc_start: 0.5208 (p90) cc_final: 0.4981 (p90) REVERT: A 353 TRP cc_start: 0.7231 (p-90) cc_final: 0.6915 (p-90) REVERT: A 357 ARG cc_start: 0.7487 (OUTLIER) cc_final: 0.7179 (mmm-85) REVERT: A 405 ASP cc_start: 0.7499 (OUTLIER) cc_final: 0.6567 (t0) REVERT: A 1139 ASP cc_start: 0.8487 (OUTLIER) cc_final: 0.8239 (p0) REVERT: B 220 PHE cc_start: 0.6839 (t80) cc_final: 0.6447 (t80) REVERT: B 357 ARG cc_start: 0.7464 (OUTLIER) cc_final: 0.7246 (mmm-85) REVERT: B 405 ASP cc_start: 0.7108 (OUTLIER) cc_final: 0.6088 (t0) REVERT: B 508 TYR cc_start: 0.7493 (OUTLIER) cc_final: 0.6923 (m-80) REVERT: C 54 LEU cc_start: 0.8733 (pt) cc_final: 0.8480 (pp) REVERT: C 117 LEU cc_start: 0.7211 (OUTLIER) cc_final: 0.6299 (mp) REVERT: C 353 TRP cc_start: 0.7110 (p-90) cc_final: 0.6337 (p-90) REVERT: C 357 ARG cc_start: 0.7569 (OUTLIER) cc_final: 0.7183 (mmt90) REVERT: C 405 ASP cc_start: 0.7274 (OUTLIER) cc_final: 0.6184 (t0) REVERT: C 421 TYR cc_start: 0.7833 (m-80) cc_final: 0.7240 (m-80) REVERT: C 780 GLU cc_start: 0.8912 (tt0) cc_final: 0.8633 (tt0) outliers start: 87 outliers final: 48 residues processed: 177 average time/residue: 0.1522 time to fit residues: 43.7287 Evaluate side-chains 150 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 93 time to evaluate : 0.823 ------------------------------------------------------------------------------- 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 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 524 VAL 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 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 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 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 117 LEU 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 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 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 524 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 661 GLU 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: 1.9990 chunk 202 optimal weight: 8.9990 chunk 57 optimal weight: 0.0870 chunk 126 optimal weight: 2.9990 chunk 252 optimal weight: 2.9990 chunk 29 optimal weight: 7.9990 chunk 105 optimal weight: 0.0570 chunk 88 optimal weight: 2.9990 chunk 188 optimal weight: 0.5980 chunk 225 optimal weight: 10.0000 chunk 170 optimal weight: 0.5980 overall best weight: 0.6678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 ASN ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 628 GLN B1002 GLN B1005 GLN B1054 GLN ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 625 HIS ** 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** ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.116169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.074970 restraints weight = 50198.008| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 3.20 r_work: 0.3048 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.2401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 25245 Z= 0.126 Angle : 0.583 8.648 34476 Z= 0.296 Chirality : 0.044 0.166 4074 Planarity : 0.005 0.104 4350 Dihedral : 5.561 59.212 4464 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 3.04 % Allowed : 16.14 % Favored : 80.82 % 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: -0.54 (0.15), residues: 2997 helix: 1.70 (0.21), residues: 684 sheet: -0.43 (0.20), residues: 576 loop : -1.22 (0.14), residues: 1737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 403 TYR 0.016 0.001 TYR C 505 PHE 0.015 0.001 PHE B 347 TRP 0.012 0.002 TRP B 436 HIS 0.005 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00292 (25152) covalent geometry : angle 0.56691 (34233) SS BOND : bond 0.00308 ( 36) SS BOND : angle 1.21321 ( 72) hydrogen bonds : bond 0.03542 ( 974) hydrogen bonds : angle 5.46497 ( 2733) link_BETA1-4 : bond 0.00340 ( 12) link_BETA1-4 : angle 1.02234 ( 36) link_NAG-ASN : bond 0.00293 ( 45) link_NAG-ASN : angle 2.07851 ( 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: 81 poor density : 99 time to evaluate : 0.893 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 LEU cc_start: 0.7034 (tt) cc_final: 0.6165 (mp) REVERT: A 353 TRP cc_start: 0.7199 (p-90) cc_final: 0.6752 (p-90) REVERT: A 394 ASN cc_start: 0.8194 (OUTLIER) cc_final: 0.7895 (t0) REVERT: A 1139 ASP cc_start: 0.8471 (OUTLIER) cc_final: 0.8218 (p0) REVERT: B 117 LEU cc_start: 0.7300 (tt) cc_final: 0.6413 (mp) REVERT: B 220 PHE cc_start: 0.6908 (t80) cc_final: 0.6460 (t80) REVERT: B 353 TRP cc_start: 0.6973 (p-90) cc_final: 0.5319 (p-90) REVERT: B 357 ARG cc_start: 0.7572 (OUTLIER) cc_final: 0.7353 (mmm-85) REVERT: B 405 ASP cc_start: 0.7035 (OUTLIER) cc_final: 0.6028 (t0) REVERT: B 508 TYR cc_start: 0.7678 (OUTLIER) cc_final: 0.7145 (m-80) REVERT: B 1107 ARG cc_start: 0.8585 (OUTLIER) cc_final: 0.6913 (mpp-170) REVERT: C 54 LEU cc_start: 0.8718 (pt) cc_final: 0.8456 (pp) REVERT: C 117 LEU cc_start: 0.7199 (OUTLIER) cc_final: 0.6288 (mp) REVERT: C 353 TRP cc_start: 0.7031 (p-90) cc_final: 0.6643 (p-90) REVERT: C 357 ARG cc_start: 0.7615 (OUTLIER) cc_final: 0.7351 (mmm-85) REVERT: C 405 ASP cc_start: 0.7065 (OUTLIER) cc_final: 0.6017 (t0) REVERT: C 759 PHE cc_start: 0.8673 (m-80) cc_final: 0.7959 (t80) REVERT: C 780 GLU cc_start: 0.8905 (tt0) cc_final: 0.8640 (tt0) REVERT: C 934 ILE cc_start: 0.8769 (OUTLIER) cc_final: 0.8563 (mm) outliers start: 81 outliers final: 55 residues processed: 168 average time/residue: 0.1580 time to fit residues: 43.7359 Evaluate side-chains 161 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 96 time to evaluate : 0.880 ------------------------------------------------------------------------------- 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 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 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 1139 ASP Chi-restraints excluded: chain B residue 47 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 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 117 LEU 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 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 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 739 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 934 ILE 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: 5.9990 chunk 284 optimal weight: 1.9990 chunk 75 optimal weight: 0.8980 chunk 281 optimal weight: 2.9990 chunk 195 optimal weight: 2.9990 chunk 165 optimal weight: 4.9990 chunk 97 optimal weight: 1.9990 chunk 243 optimal weight: 4.9990 chunk 15 optimal weight: 8.9990 chunk 82 optimal weight: 1.9990 chunk 136 optimal weight: 10.0000 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 B 317 ASN ** B 422 ASN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN C1054 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.113484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.071239 restraints weight = 50273.122| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 3.23 r_work: 0.2992 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 25245 Z= 0.238 Angle : 0.628 7.727 34476 Z= 0.318 Chirality : 0.045 0.176 4074 Planarity : 0.005 0.089 4350 Dihedral : 5.654 55.859 4464 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 3.34 % Allowed : 16.44 % Favored : 80.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.15), residues: 2997 helix: 1.49 (0.21), residues: 687 sheet: -0.56 (0.20), residues: 585 loop : -1.24 (0.14), residues: 1725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 403 TYR 0.022 0.002 TYR A 789 PHE 0.023 0.002 PHE C1121 TRP 0.011 0.002 TRP C 886 HIS 0.007 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00567 (25152) covalent geometry : angle 0.61048 (34233) SS BOND : bond 0.00453 ( 36) SS BOND : angle 1.43479 ( 72) hydrogen bonds : bond 0.03827 ( 974) hydrogen bonds : angle 5.60850 ( 2733) link_BETA1-4 : bond 0.00217 ( 12) link_BETA1-4 : angle 1.08441 ( 36) link_NAG-ASN : bond 0.00289 ( 45) link_NAG-ASN : angle 2.15731 ( 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 188 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 99 time to evaluate : 0.932 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 353 TRP cc_start: 0.7338 (p-90) cc_final: 0.6768 (p-90) REVERT: A 376 THR cc_start: 0.7575 (OUTLIER) cc_final: 0.7282 (p) REVERT: A 405 ASP cc_start: 0.7420 (OUTLIER) cc_final: 0.6347 (t0) REVERT: A 1139 ASP cc_start: 0.8516 (OUTLIER) cc_final: 0.8266 (p0) REVERT: B 117 LEU cc_start: 0.7417 (tt) cc_final: 0.6491 (mp) REVERT: B 353 TRP cc_start: 0.7049 (p-90) cc_final: 0.5314 (p-90) REVERT: B 357 ARG cc_start: 0.7548 (OUTLIER) cc_final: 0.7269 (mmm-85) REVERT: B 405 ASP cc_start: 0.7207 (OUTLIER) cc_final: 0.6117 (t0) REVERT: B 508 TYR cc_start: 0.7798 (OUTLIER) cc_final: 0.7232 (m-80) REVERT: C 54 LEU cc_start: 0.8770 (pt) cc_final: 0.8498 (pp) REVERT: C 353 TRP cc_start: 0.7215 (p-90) cc_final: 0.6530 (p-90) REVERT: C 357 ARG cc_start: 0.7601 (OUTLIER) cc_final: 0.7219 (mmm-85) REVERT: C 405 ASP cc_start: 0.7084 (OUTLIER) cc_final: 0.5965 (t0) REVERT: C 780 GLU cc_start: 0.8912 (tt0) cc_final: 0.8641 (tt0) outliers start: 89 outliers final: 63 residues processed: 179 average time/residue: 0.1612 time to fit residues: 47.4768 Evaluate side-chains 163 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 92 time to evaluate : 0.795 ------------------------------------------------------------------------------- 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 336 CYS 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 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 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 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 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 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 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 878 LEU 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: 0.1980 chunk 42 optimal weight: 6.9990 chunk 253 optimal weight: 4.9990 chunk 54 optimal weight: 0.1980 chunk 10 optimal weight: 8.9990 chunk 199 optimal weight: 0.6980 chunk 249 optimal weight: 3.9990 chunk 82 optimal weight: 0.5980 chunk 35 optimal weight: 5.9990 chunk 40 optimal weight: 8.9990 chunk 147 optimal weight: 0.0570 overall best weight: 0.3498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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** B 394 ASN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 926 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 = 0.3864 r_free = 0.3864 target = 0.116640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.074945 restraints weight = 49749.566| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 3.21 r_work: 0.3067 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.2687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.067 25245 Z= 0.104 Angle : 0.572 7.787 34476 Z= 0.290 Chirality : 0.044 0.191 4074 Planarity : 0.004 0.079 4350 Dihedral : 5.301 59.882 4464 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.70 % Allowed : 17.15 % Favored : 80.14 % 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: -0.44 (0.15), residues: 2997 helix: 1.78 (0.21), residues: 687 sheet: -0.22 (0.21), residues: 549 loop : -1.21 (0.14), residues: 1761 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 403 TYR 0.016 0.001 TYR A1067 PHE 0.019 0.001 PHE B 855 TRP 0.013 0.001 TRP C 104 HIS 0.004 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00231 (25152) covalent geometry : angle 0.55748 (34233) SS BOND : bond 0.00282 ( 36) SS BOND : angle 1.17640 ( 72) hydrogen bonds : bond 0.03431 ( 974) hydrogen bonds : angle 5.29644 ( 2733) link_BETA1-4 : bond 0.00371 ( 12) link_BETA1-4 : angle 1.01022 ( 36) link_NAG-ASN : bond 0.00356 ( 45) link_NAG-ASN : angle 1.96023 ( 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 183 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 111 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 353 TRP cc_start: 0.7141 (p-90) cc_final: 0.6522 (p-90) REVERT: A 376 THR cc_start: 0.7634 (OUTLIER) cc_final: 0.7363 (p) REVERT: A 405 ASP cc_start: 0.7328 (OUTLIER) cc_final: 0.6264 (t0) REVERT: A 1139 ASP cc_start: 0.8397 (OUTLIER) cc_final: 0.8126 (p0) REVERT: B 117 LEU cc_start: 0.7186 (tt) cc_final: 0.6292 (mp) REVERT: B 353 TRP cc_start: 0.6983 (p-90) cc_final: 0.5304 (p-90) REVERT: B 357 ARG cc_start: 0.7459 (OUTLIER) cc_final: 0.7233 (mmt90) REVERT: B 508 TYR cc_start: 0.7765 (OUTLIER) cc_final: 0.7256 (m-80) REVERT: B 1107 ARG cc_start: 0.8601 (OUTLIER) cc_final: 0.7101 (mpp-170) REVERT: C 54 LEU cc_start: 0.8694 (pt) cc_final: 0.8475 (pp) REVERT: C 117 LEU cc_start: 0.7180 (tt) cc_final: 0.6168 (mp) REVERT: C 353 TRP cc_start: 0.7033 (p-90) cc_final: 0.6685 (p-90) REVERT: C 357 ARG cc_start: 0.7674 (OUTLIER) cc_final: 0.7236 (mmt90) REVERT: C 394 ASN cc_start: 0.8221 (m-40) cc_final: 0.7764 (m-40) REVERT: C 780 GLU cc_start: 0.8881 (tt0) cc_final: 0.8623 (tt0) REVERT: C 1107 ARG cc_start: 0.8467 (OUTLIER) cc_final: 0.6928 (mpp-170) outliers start: 72 outliers final: 52 residues processed: 176 average time/residue: 0.1607 time to fit residues: 46.6644 Evaluate side-chains 159 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 99 time to evaluate : 1.071 ------------------------------------------------------------------------------- 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 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 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 524 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 1139 ASP Chi-restraints excluded: chain B residue 47 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 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 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 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 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 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 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 878 LEU 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: 0.9990 chunk 73 optimal weight: 1.9990 chunk 101 optimal weight: 8.9990 chunk 302 optimal weight: 0.9980 chunk 57 optimal weight: 0.0870 chunk 189 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 137 optimal weight: 9.9990 chunk 75 optimal weight: 0.0670 chunk 190 optimal weight: 1.9990 chunk 99 optimal weight: 0.7980 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 625 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 ASN B 164 ASN B 394 ASN ** B 506 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 ** C 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3862 r_free = 0.3862 target = 0.116398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.074543 restraints weight = 50114.260| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 3.23 r_work: 0.3057 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.2752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 25245 Z= 0.116 Angle : 0.565 7.389 34476 Z= 0.286 Chirality : 0.044 0.232 4074 Planarity : 0.004 0.074 4350 Dihedral : 5.208 59.960 4464 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.74 % Allowed : 17.42 % 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: -0.39 (0.15), residues: 2997 helix: 1.77 (0.21), residues: 687 sheet: -0.26 (0.21), residues: 570 loop : -1.12 (0.14), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 403 TYR 0.015 0.001 TYR A 265 PHE 0.019 0.001 PHE B 855 TRP 0.012 0.001 TRP B 436 HIS 0.005 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00269 (25152) covalent geometry : angle 0.54966 (34233) SS BOND : bond 0.00277 ( 36) SS BOND : angle 1.18908 ( 72) hydrogen bonds : bond 0.03384 ( 974) hydrogen bonds : angle 5.21913 ( 2733) link_BETA1-4 : bond 0.00343 ( 12) link_BETA1-4 : angle 1.01793 ( 36) link_NAG-ASN : bond 0.00280 ( 45) link_NAG-ASN : angle 1.95445 ( 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 174 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 101 time to evaluate : 0.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 353 TRP cc_start: 0.7183 (p-90) cc_final: 0.6535 (p-90) REVERT: A 376 THR cc_start: 0.7718 (OUTLIER) cc_final: 0.7472 (p) REVERT: A 405 ASP cc_start: 0.7319 (OUTLIER) cc_final: 0.6258 (t0) REVERT: A 506 GLN cc_start: 0.7338 (tp40) cc_final: 0.6780 (tp40) REVERT: A 1139 ASP cc_start: 0.8364 (OUTLIER) cc_final: 0.8134 (p0) REVERT: B 117 LEU cc_start: 0.7167 (tt) cc_final: 0.6288 (mp) REVERT: B 353 TRP cc_start: 0.6994 (p-90) cc_final: 0.5327 (p-90) REVERT: B 357 ARG cc_start: 0.7495 (OUTLIER) cc_final: 0.7260 (mmt90) REVERT: B 508 TYR cc_start: 0.7758 (OUTLIER) cc_final: 0.7234 (m-80) REVERT: B 1107 ARG cc_start: 0.8534 (OUTLIER) cc_final: 0.7112 (mpp-170) REVERT: C 54 LEU cc_start: 0.8700 (pt) cc_final: 0.8478 (pp) REVERT: C 117 LEU cc_start: 0.7173 (tt) cc_final: 0.6139 (mp) REVERT: C 121 ASN cc_start: 0.6595 (m110) cc_final: 0.4630 (t0) REVERT: C 353 TRP cc_start: 0.7045 (p-90) cc_final: 0.6699 (p-90) REVERT: C 357 ARG cc_start: 0.7665 (OUTLIER) cc_final: 0.7207 (mmt90) REVERT: C 394 ASN cc_start: 0.8201 (m-40) cc_final: 0.7717 (m-40) REVERT: C 780 GLU cc_start: 0.8894 (tt0) cc_final: 0.8645 (tt0) outliers start: 73 outliers final: 58 residues processed: 169 average time/residue: 0.1621 time to fit residues: 45.0236 Evaluate side-chains 163 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 98 time to evaluate : 0.929 ------------------------------------------------------------------------------- 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 326 ILE Chi-restraints excluded: chain A residue 336 CYS 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 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 1139 ASP Chi-restraints excluded: chain B residue 47 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 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 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 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 873 TYR 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 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 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 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 254 optimal weight: 2.9990 chunk 251 optimal weight: 0.0980 chunk 207 optimal weight: 4.9990 chunk 149 optimal weight: 0.6980 chunk 236 optimal weight: 8.9990 chunk 230 optimal weight: 9.9990 chunk 301 optimal weight: 1.9990 chunk 23 optimal weight: 5.9990 chunk 6 optimal weight: 3.9990 chunk 181 optimal weight: 0.9990 chunk 215 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 448 ASN ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 625 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 ASN B 394 ASN B 448 ASN ** B 506 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 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3855 r_free = 0.3855 target = 0.115121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.073767 restraints weight = 50335.424| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 3.19 r_work: 0.3030 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.2702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 25245 Z= 0.180 Angle : 0.589 7.341 34476 Z= 0.299 Chirality : 0.045 0.211 4074 Planarity : 0.004 0.072 4350 Dihedral : 5.267 56.595 4464 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.70 % Allowed : 17.45 % 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: -0.48 (0.15), residues: 2997 helix: 1.66 (0.21), residues: 687 sheet: -0.39 (0.20), residues: 576 loop : -1.15 (0.14), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 403 TYR 0.019 0.002 TYR B 265 PHE 0.018 0.002 PHE C1121 TRP 0.011 0.002 TRP B 436 HIS 0.007 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00427 (25152) covalent geometry : angle 0.57343 (34233) SS BOND : bond 0.00355 ( 36) SS BOND : angle 1.27691 ( 72) hydrogen bonds : bond 0.03570 ( 974) hydrogen bonds : angle 5.31562 ( 2733) link_BETA1-4 : bond 0.00253 ( 12) link_BETA1-4 : angle 1.03636 ( 36) link_NAG-ASN : bond 0.00265 ( 45) link_NAG-ASN : angle 2.00588 ( 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 179 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 107 time to evaluate : 0.937 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 353 TRP cc_start: 0.7285 (p-90) cc_final: 0.6653 (p-90) REVERT: A 376 THR cc_start: 0.7738 (OUTLIER) cc_final: 0.7486 (p) REVERT: A 405 ASP cc_start: 0.7319 (OUTLIER) cc_final: 0.6221 (t0) REVERT: A 1139 ASP cc_start: 0.8388 (OUTLIER) cc_final: 0.8158 (p0) REVERT: B 117 LEU cc_start: 0.7245 (tt) cc_final: 0.6363 (mp) REVERT: B 353 TRP cc_start: 0.7031 (p-90) cc_final: 0.5314 (p-90) REVERT: B 508 TYR cc_start: 0.7828 (OUTLIER) cc_final: 0.7262 (m-80) REVERT: B 1029 MET cc_start: 0.9089 (tpp) cc_final: 0.8868 (ttm) REVERT: C 54 LEU cc_start: 0.8688 (pt) cc_final: 0.8470 (pp) REVERT: C 96 GLU cc_start: 0.5398 (OUTLIER) cc_final: 0.5101 (tm-30) REVERT: C 117 LEU cc_start: 0.7143 (tt) cc_final: 0.6119 (mp) REVERT: C 353 TRP cc_start: 0.7013 (p-90) cc_final: 0.6560 (p-90) REVERT: C 357 ARG cc_start: 0.7677 (OUTLIER) cc_final: 0.7227 (mmt90) REVERT: C 780 GLU cc_start: 0.8896 (tt0) cc_final: 0.8650 (tt0) outliers start: 72 outliers final: 60 residues processed: 175 average time/residue: 0.1513 time to fit residues: 44.0615 Evaluate side-chains 167 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 101 time to evaluate : 0.888 ------------------------------------------------------------------------------- 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 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 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 1139 ASP Chi-restraints excluded: chain B residue 47 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 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 394 ASN 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 1107 ARG Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 96 GLU 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 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 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: 0.8980 chunk 30 optimal weight: 0.3980 chunk 264 optimal weight: 0.8980 chunk 175 optimal weight: 1.9990 chunk 90 optimal weight: 0.5980 chunk 50 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 147 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 300 optimal weight: 0.5980 chunk 159 optimal weight: 5.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 ASN ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 625 HIS A 907 ASN B 448 ASN ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 625 HIS C 164 ASN C 394 ASN ** 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** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.115936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.074088 restraints weight = 50001.046| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 3.22 r_work: 0.3052 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.2836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 25245 Z= 0.122 Angle : 0.567 7.248 34476 Z= 0.288 Chirality : 0.044 0.309 4074 Planarity : 0.004 0.070 4350 Dihedral : 5.173 57.592 4464 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.67 % Allowed : 17.68 % Favored : 79.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.15), residues: 2997 helix: 1.75 (0.21), residues: 687 sheet: -0.26 (0.21), residues: 555 loop : -1.05 (0.14), residues: 1755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 403 TYR 0.015 0.001 TYR A1067 PHE 0.020 0.001 PHE B 855 TRP 0.011 0.001 TRP B 436 HIS 0.005 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00283 (25152) covalent geometry : angle 0.55187 (34233) SS BOND : bond 0.00293 ( 36) SS BOND : angle 1.20988 ( 72) hydrogen bonds : bond 0.03398 ( 974) hydrogen bonds : angle 5.22463 ( 2733) link_BETA1-4 : bond 0.00333 ( 12) link_BETA1-4 : angle 1.00726 ( 36) link_NAG-ASN : bond 0.00280 ( 45) link_NAG-ASN : angle 1.92912 ( 135) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5140.83 seconds wall clock time: 89 minutes 30.07 seconds (5370.07 seconds total)