Starting phenix.real_space_refine on Thu Mar 5 16:17:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ke4_22831/03_2026/7ke4_22831.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ke4_22831/03_2026/7ke4_22831.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7ke4_22831/03_2026/7ke4_22831.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ke4_22831/03_2026/7ke4_22831.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ke4_22831/03_2026/7ke4_22831.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ke4_22831/03_2026/7ke4_22831.map" } resolution = 3.21 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= 0.049 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 99 5.16 5 C 15082 2.51 5 N 3852 2.21 5 O 4651 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 197 residue(s): 0.03s 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: 23684 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 7602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 972, 7602 Classifications: {'peptide': 972} Link IDs: {'PTRANS': 46, 'TRANS': 925} Chain breaks: 11 Chain: "B" Number of atoms: 7602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 972, 7602 Classifications: {'peptide': 972} Link IDs: {'PTRANS': 46, 'TRANS': 925} Chain breaks: 11 Chain: "C" Number of atoms: 7598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 972, 7598 Classifications: {'peptide': 972} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 46, 'TRANS': 925} Chain breaks: 11 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: "P" 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: "Q" 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: "R" 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: 5.31, per 1000 atoms: 0.22 Number of scatterers: 23684 At special positions: 0 Unit cell: (138.598, 131.192, 167.164, 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 99 16.00 O 4651 8.00 N 3852 7.00 C 15082 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=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.02 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.05 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=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.02 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.01 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.02 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.01 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.00 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.05 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=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.05 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.01 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.04 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.02 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.01 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 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 P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " 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 A1310 " - " ASN A1074 " " NAG A1311 " - " ASN A 165 " " NAG B1301 " - " ASN B 331 " " NAG B1302 " - " ASN B 343 " " NAG B1303 " - " ASN B 603 " " NAG B1304 " - " ASN B 709 " " NAG B1305 " - " ASN B1074 " " NAG B1306 " - " ASN B 616 " " NAG B1307 " - " ASN B 657 " " NAG B1308 " - " ASN B 122 " " NAG B1309 " - " ASN B 61 " " NAG B1310 " - " ASN B 282 " " NAG B1311 " - " ASN B 165 " " NAG C1301 " - " ASN C 603 " " NAG C1302 " - " ASN C 616 " " NAG C1303 " - " ASN C 709 " " NAG C1304 " - " ASN C 331 " " NAG C1305 " - " ASN C 657 " " NAG C1306 " - " ASN C1074 " " NAG C1307 " - " ASN C 165 " " NAG C1308 " - " ASN C 282 " " NAG C1309 " - " ASN C 61 " " NAG C1310 " - " ASN C 122 " " NAG C1311 " - " ASN C 343 " " NAG D 1 " - " ASN A 234 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN A 801 " " NAG G 1 " - " ASN A1098 " " NAG H 1 " - " ASN A1134 " " NAG I 1 " - " ASN B 717 " " NAG J 1 " - " ASN B 801 " " NAG K 1 " - " ASN B1098 " " NAG L 1 " - " ASN B 234 " " NAG M 1 " - " ASN B1134 " " NAG N 1 " - " ASN C1098 " " NAG O 1 " - " ASN C 717 " " NAG P 1 " - " ASN C1134 " " NAG Q 1 " - " ASN C 801 " " NAG R 1 " - " ASN C 234 " Time building additional restraints: 2.14 Conformation dependent library (CDL) restraints added in 1.2 seconds 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5478 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 48 sheets defined 27.2% alpha, 27.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.99 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.747A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 371 removed outlier: 4.012A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.972A 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 616 through 620 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.782A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.640A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 805 removed outlier: 4.535A pdb=" N GLN A 804 " --> pdb=" O ASN A 801 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.869A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.763A pdb=" N ALA A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASN A 907 " --> pdb=" O ALA A 903 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 918 removed outlier: 3.697A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.625A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 988 through 1033 removed outlier: 3.825A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1125 through 1129 removed outlier: 3.629A pdb=" N VAL A1128 " --> pdb=" O ASN A1125 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.767A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 383 through 387 removed outlier: 3.623A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.609A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.854A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 620 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.809A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.723A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 4.043A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.609A pdb=" N ALA B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ASN B 907 " --> pdb=" O ALA B 903 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.837A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.518A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.691A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 987 through 1033 removed outlier: 3.674A pdb=" N VAL B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1127 through 1129 No H-bonds generated for 'chain 'B' and resid 1127 through 1129' Processing helix chain 'B' and resid 1141 through 1147 removed outlier: 3.866A pdb=" N ASP B1146 " --> pdb=" O GLN B1142 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 337 through 342 Processing helix chain 'C' and resid 351 through 353 No H-bonds generated for 'chain 'C' and resid 351 through 353' Processing helix chain 'C' and resid 364 through 370 removed outlier: 4.013A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 390 Processing helix chain 'C' and resid 405 through 410 removed outlier: 5.065A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 616 through 620 removed outlier: 3.573A pdb=" N GLU C 619 " --> pdb=" O ASN C 616 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 removed outlier: 4.110A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.828A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 4.018A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.901A pdb=" N ALA C 903 " --> pdb=" O ALA C 899 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ASN C 907 " --> pdb=" O ALA C 903 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 918 removed outlier: 3.737A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.753A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.329A pdb=" N VAL C 991 " --> pdb=" O VAL C 987 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) Processing helix chain 'C' and resid 1127 through 1129 No H-bonds generated for 'chain 'C' and resid 1127 through 1129' Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 4.227A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ASP C1146 " --> pdb=" O GLN C1142 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.306A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.063A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.917A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA5, first strand: chain 'A' and resid 141 through 142 removed outlier: 5.945A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.306A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.758A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.857A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 448 through 453 removed outlier: 5.659A pdb=" N TYR A 449 " --> pdb=" O PHE A 497 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N PHE A 497 " --> pdb=" O TYR A 449 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N TYR A 451 " --> pdb=" O TYR A 495 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.907A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.390A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 701 through 704 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 715 removed outlier: 4.071A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N GLN A1106 " --> pdb=" O GLU A1111 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N GLU A1111 " --> pdb=" O GLN A1106 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 718 through 728 removed outlier: 3.513A pdb=" N HIS A1064 " --> pdb=" O THR A 723 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB7, first strand: chain 'A' and resid 787 through 790 removed outlier: 6.158A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1123 Processing sheet with id=AB9, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.226A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 8.647A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.891A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.398A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N VAL B 126 " --> pdb=" O SER B 172 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.777A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.508A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AC7, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.691A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'B' and resid 452 through 453 Processing sheet with id=AC9, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.876A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 701 through 704 Processing sheet with id=AD2, first strand: chain 'B' and resid 711 through 715 removed outlier: 4.114A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 718 through 722 Processing sheet with id=AD4, first strand: chain 'B' and resid 718 through 722 removed outlier: 7.155A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD6, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.654A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 28 through 30 removed outlier: 7.941A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA C 93 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 50 through 55 removed outlier: 3.869A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AE1, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.527A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.228A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 348 through 349 removed outlier: 6.535A pdb=" N ALA C 348 " --> pdb=" O VAL C 401 " (cutoff:3.500A) removed outlier: 8.893A pdb=" N ARG C 403 " --> pdb=" O ALA C 348 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 348 through 349 removed outlier: 6.535A pdb=" N ALA C 348 " --> pdb=" O VAL C 401 " (cutoff:3.500A) removed outlier: 8.893A pdb=" N ARG C 403 " --> pdb=" O ALA C 348 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.746A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'C' and resid 448 through 453 removed outlier: 5.473A pdb=" N TYR C 449 " --> pdb=" O PHE C 497 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N PHE C 497 " --> pdb=" O TYR C 449 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N TYR C 451 " --> pdb=" O TYR C 495 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.371A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 711 through 715 Processing sheet with id=AE9, first strand: chain 'C' and resid 718 through 728 removed outlier: 3.583A pdb=" N HIS C1064 " --> pdb=" O THR C 723 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AF2, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.896A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 1094 through 1097 1006 hydrogen bonds defined for protein. 2754 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: 5.57 Time building geometry restraints manager: 2.85 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: 6386 1.33 - 1.46: 4526 1.46 - 1.58: 13144 1.58 - 1.70: 3 1.70 - 1.82: 123 Bond restraints: 24182 Sorted by residual: bond pdb=" C5 NAG A1308 " pdb=" O5 NAG A1308 " ideal model delta sigma weight residual 1.413 1.489 -0.076 2.00e-02 2.50e+03 1.44e+01 bond pdb=" C5 NAG B1303 " pdb=" O5 NAG B1303 " ideal model delta sigma weight residual 1.413 1.488 -0.075 2.00e-02 2.50e+03 1.42e+01 bond pdb=" C5 NAG R 2 " pdb=" O5 NAG R 2 " ideal model delta sigma weight residual 1.413 1.488 -0.075 2.00e-02 2.50e+03 1.41e+01 bond pdb=" C5 NAG A1311 " pdb=" O5 NAG A1311 " ideal model delta sigma weight residual 1.413 1.488 -0.075 2.00e-02 2.50e+03 1.41e+01 bond pdb=" C5 NAG A1301 " pdb=" O5 NAG A1301 " ideal model delta sigma weight residual 1.413 1.488 -0.075 2.00e-02 2.50e+03 1.41e+01 ... (remaining 24177 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.54: 31293 3.54 - 7.09: 1570 7.09 - 10.63: 15 10.63 - 14.17: 2 14.17 - 17.72: 1 Bond angle restraints: 32881 Sorted by residual: angle pdb=" N CYS A 166 " pdb=" CA CYS A 166 " pdb=" C CYS A 166 " ideal model delta sigma weight residual 109.94 127.66 -17.72 1.57e+00 4.06e-01 1.27e+02 angle pdb=" N CYS B 391 " pdb=" CA CYS B 391 " pdb=" C CYS B 391 " ideal model delta sigma weight residual 108.96 119.87 -10.91 1.49e+00 4.50e-01 5.36e+01 angle pdb=" N CYS A 391 " pdb=" CA CYS A 391 " pdb=" C CYS A 391 " ideal model delta sigma weight residual 108.96 119.76 -10.80 1.49e+00 4.50e-01 5.26e+01 angle pdb=" N CYS C 391 " pdb=" CA CYS C 391 " pdb=" C CYS C 391 " ideal model delta sigma weight residual 108.96 119.41 -10.45 1.49e+00 4.50e-01 4.91e+01 angle pdb=" CA PHE C 559 " pdb=" CB PHE C 559 " pdb=" CG PHE C 559 " ideal model delta sigma weight residual 113.80 119.84 -6.04 1.00e+00 1.00e+00 3.65e+01 ... (remaining 32876 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 14018 17.93 - 35.87: 951 35.87 - 53.80: 146 53.80 - 71.74: 49 71.74 - 89.67: 46 Dihedral angle restraints: 15210 sinusoidal: 6726 harmonic: 8484 Sorted by residual: dihedral pdb=" CB CYS B1082 " pdb=" SG CYS B1082 " pdb=" SG CYS B1126 " pdb=" CB CYS B1126 " ideal model delta sinusoidal sigma weight residual -86.00 -173.26 87.26 1 1.00e+01 1.00e-02 9.14e+01 dihedral pdb=" CB CYS A1032 " pdb=" SG CYS A1032 " pdb=" SG CYS A1043 " pdb=" CB CYS A1043 " ideal model delta sinusoidal sigma weight residual 93.00 177.10 -84.10 1 1.00e+01 1.00e-02 8.61e+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 93.00 175.10 -82.10 1 1.00e+01 1.00e-02 8.28e+01 ... (remaining 15207 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.116: 2997 0.116 - 0.231: 861 0.231 - 0.346: 76 0.346 - 0.462: 9 0.462 - 0.577: 5 Chirality restraints: 3948 Sorted by residual: chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.59 0.19 2.00e-02 2.50e+03 8.98e+01 chirality pdb=" C1 NAG R 2 " pdb=" O4 NAG R 1 " pdb=" C2 NAG R 2 " pdb=" O5 NAG R 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.58 0.18 2.00e-02 2.50e+03 7.67e+01 chirality pdb=" C1 NAG L 2 " pdb=" O4 NAG L 1 " pdb=" C2 NAG L 2 " pdb=" O5 NAG L 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.55 0.15 2.00e-02 2.50e+03 5.91e+01 ... (remaining 3945 not shown) Planarity restraints: 4202 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 331 " 0.214 2.00e-02 2.50e+03 3.26e-01 1.33e+03 pdb=" CG ASN B 331 " -0.159 2.00e-02 2.50e+03 pdb=" OD1 ASN B 331 " 0.105 2.00e-02 2.50e+03 pdb=" ND2 ASN B 331 " -0.548 2.00e-02 2.50e+03 pdb=" C1 NAG B1301 " 0.387 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A1074 " -0.191 2.00e-02 2.50e+03 2.14e-01 5.74e+02 pdb=" CG ASN A1074 " 0.115 2.00e-02 2.50e+03 pdb=" OD1 ASN A1074 " -0.004 2.00e-02 2.50e+03 pdb=" ND2 ASN A1074 " 0.337 2.00e-02 2.50e+03 pdb=" C1 NAG A1310 " -0.257 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B1074 " 0.187 2.00e-02 2.50e+03 2.09e-01 5.47e+02 pdb=" CG ASN B1074 " -0.113 2.00e-02 2.50e+03 pdb=" OD1 ASN B1074 " 0.005 2.00e-02 2.50e+03 pdb=" ND2 ASN B1074 " -0.330 2.00e-02 2.50e+03 pdb=" C1 NAG B1305 " 0.250 2.00e-02 2.50e+03 ... (remaining 4199 not shown) Histogram of nonbonded interaction distances: 2.52 - 3.00: 11932 3.00 - 3.47: 22803 3.47 - 3.95: 39273 3.95 - 4.42: 43419 4.42 - 4.90: 73349 Nonbonded interactions: 190776 Sorted by model distance: nonbonded pdb=" OE2 GLU A 918 " pdb=" OG SER C1123 " model vdw 2.519 3.040 nonbonded pdb=" OG SER A1123 " pdb=" OE2 GLU B 918 " model vdw 2.541 3.040 nonbonded pdb=" OG SER B1123 " pdb=" OE2 GLU C 918 " model vdw 2.543 3.040 nonbonded pdb=" OD2 ASP A 398 " pdb=" OH TYR A 423 " model vdw 2.560 3.040 nonbonded pdb=" OD1 ASP B 294 " pdb=" OG SER B 297 " model vdw 2.575 3.040 ... (remaining 190771 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 131 or (resid 132 and (name N or name CA or nam \ e C or name O or name CB )) or resid 133 through 1311)) selection = (chain 'B' and (resid 27 through 131 or (resid 132 and (name N or name CA or nam \ e C or name O or name CB )) or resid 133 through 1311)) 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' selection = chain 'P' selection = chain 'Q' selection = chain 'R' } 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: 1.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 22.720 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7105 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 : 0.014 0.087 24281 Z= 0.774 Angle : 1.802 17.717 33142 Z= 1.179 Chirality : 0.101 0.577 3948 Planarity : 0.014 0.153 4154 Dihedral : 13.369 89.670 9624 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 0.15 Ramachandran Plot: Outliers : 0.35 % Allowed : 6.72 % Favored : 92.93 % Rotamer: Outliers : 1.06 % Allowed : 4.11 % Favored : 94.83 % Cbeta Deviations : 0.29 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.54 (0.14), residues: 2844 helix: -1.15 (0.16), residues: 644 sheet: 0.13 (0.23), residues: 470 loop : -1.33 (0.13), residues: 1730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 983 TYR 0.135 0.021 TYR A 423 PHE 0.075 0.012 PHE B 802 TRP 0.157 0.028 TRP A 886 HIS 0.012 0.003 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.01375 (24182) covalent geometry : angle 1.77637 (32881) SS BOND : bond 0.01200 ( 36) SS BOND : angle 1.97267 ( 72) hydrogen bonds : bond 0.14494 ( 998) hydrogen bonds : angle 8.79785 ( 2754) link_BETA1-4 : bond 0.02408 ( 15) link_BETA1-4 : angle 4.34078 ( 45) link_NAG-ASN : bond 0.02389 ( 48) link_NAG-ASN : angle 4.40467 ( 144) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 324 time to evaluate : 0.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 900 MET cc_start: 0.7180 (mtp) cc_final: 0.6826 (mtp) REVERT: A 1004 LEU cc_start: 0.8282 (OUTLIER) cc_final: 0.7816 (tt) REVERT: B 429 PHE cc_start: 0.8135 (OUTLIER) cc_final: 0.7190 (t80) outliers start: 27 outliers final: 2 residues processed: 348 average time/residue: 0.1735 time to fit residues: 91.7660 Evaluate side-chains 137 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 133 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 429 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 0.6980 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 0.7980 chunk 111 optimal weight: 4.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN A 121 ASN A 334 ASN A 394 ASN A 957 GLN A 969 ASN B 207 HIS ** B 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 498 GLN C 655 HIS C 675 GLN C 907 ASN C 969 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.115609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.082874 restraints weight = 49626.358| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 3.25 r_work: 0.3299 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 24281 Z= 0.165 Angle : 0.781 20.551 33142 Z= 0.387 Chirality : 0.048 0.319 3948 Planarity : 0.004 0.074 4154 Dihedral : 6.646 46.657 4430 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 1.21 % Allowed : 8.27 % Favored : 90.52 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.64 (0.15), residues: 2844 helix: 0.52 (0.19), residues: 665 sheet: -0.11 (0.19), residues: 642 loop : -0.96 (0.15), residues: 1537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 237 TYR 0.024 0.002 TYR B 453 PHE 0.026 0.002 PHE C 338 TRP 0.018 0.002 TRP C 64 HIS 0.005 0.001 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00352 (24182) covalent geometry : angle 0.70931 (32881) SS BOND : bond 0.00869 ( 36) SS BOND : angle 1.81375 ( 72) hydrogen bonds : bond 0.04559 ( 998) hydrogen bonds : angle 6.46143 ( 2754) link_BETA1-4 : bond 0.00399 ( 15) link_BETA1-4 : angle 1.92609 ( 45) link_NAG-ASN : bond 0.00646 ( 48) link_NAG-ASN : angle 4.76385 ( 144) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 179 time to evaluate : 0.837 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 TYR cc_start: 0.7651 (t80) cc_final: 0.7202 (t80) REVERT: A 100 ILE cc_start: 0.8371 (mm) cc_final: 0.8140 (tp) REVERT: A 129 LYS cc_start: 0.9002 (mmtt) cc_final: 0.8023 (tppt) REVERT: A 166 CYS cc_start: 0.6464 (OUTLIER) cc_final: 0.5869 (t) REVERT: A 169 GLU cc_start: 0.8855 (tt0) cc_final: 0.8376 (mp0) REVERT: A 202 LYS cc_start: 0.7534 (mptt) cc_final: 0.6881 (mmtm) REVERT: A 378 LYS cc_start: 0.8438 (tppp) cc_final: 0.8092 (tppt) REVERT: A 406 GLU cc_start: 0.8868 (mm-30) cc_final: 0.8190 (mp0) REVERT: A 1004 LEU cc_start: 0.9373 (OUTLIER) cc_final: 0.8768 (tt) REVERT: B 200 TYR cc_start: 0.6019 (m-80) cc_final: 0.5816 (m-80) REVERT: B 270 LEU cc_start: 0.7982 (mt) cc_final: 0.7363 (mp) REVERT: B 429 PHE cc_start: 0.8493 (OUTLIER) cc_final: 0.8014 (t80) REVERT: C 104 TRP cc_start: 0.7217 (m-90) cc_final: 0.6961 (m-90) REVERT: C 979 ASP cc_start: 0.8307 (m-30) cc_final: 0.7844 (m-30) outliers start: 31 outliers final: 11 residues processed: 202 average time/residue: 0.1573 time to fit residues: 51.8480 Evaluate side-chains 143 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 129 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 569 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 132 optimal weight: 8.9990 chunk 212 optimal weight: 10.0000 chunk 129 optimal weight: 9.9990 chunk 7 optimal weight: 20.0000 chunk 10 optimal weight: 6.9990 chunk 151 optimal weight: 0.9990 chunk 85 optimal weight: 2.9990 chunk 248 optimal weight: 7.9990 chunk 150 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 178 optimal weight: 6.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 755 GLN A 804 GLN A 901 GLN A 935 GLN ** B 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 ASN B 804 GLN B 901 GLN B 935 GLN B1058 HIS C 66 HIS C 207 HIS C 394 ASN C 607 GLN C 690 GLN C 804 GLN C 901 GLN C 935 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.113792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.079434 restraints weight = 50897.591| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 3.31 r_work: 0.3165 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.3041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.059 24281 Z= 0.292 Angle : 0.747 13.451 33142 Z= 0.377 Chirality : 0.049 0.459 3948 Planarity : 0.004 0.053 4154 Dihedral : 6.347 54.964 4428 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 1.72 % Allowed : 9.68 % Favored : 88.60 % 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: -0.62 (0.15), residues: 2844 helix: 0.64 (0.19), residues: 663 sheet: -0.44 (0.18), residues: 712 loop : -0.83 (0.15), residues: 1469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 983 TYR 0.024 0.002 TYR C1067 PHE 0.032 0.003 PHE A1089 TRP 0.013 0.002 TRP C 64 HIS 0.006 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00677 (24182) covalent geometry : angle 0.71277 (32881) SS BOND : bond 0.00585 ( 36) SS BOND : angle 1.93819 ( 72) hydrogen bonds : bond 0.04567 ( 998) hydrogen bonds : angle 6.34149 ( 2754) link_BETA1-4 : bond 0.00346 ( 15) link_BETA1-4 : angle 1.68028 ( 45) link_NAG-ASN : bond 0.00509 ( 48) link_NAG-ASN : angle 3.12204 ( 144) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 132 time to evaluate : 1.170 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.8994 (mmtt) cc_final: 0.8537 (tppt) REVERT: A 202 LYS cc_start: 0.7591 (mptt) cc_final: 0.6893 (mmtm) REVERT: A 378 LYS cc_start: 0.8490 (tppp) cc_final: 0.8118 (tppt) REVERT: A 406 GLU cc_start: 0.8779 (mm-30) cc_final: 0.8202 (mp0) REVERT: A 437 ASN cc_start: 0.9465 (OUTLIER) cc_final: 0.9035 (t0) REVERT: A 985 ASP cc_start: 0.8306 (t0) cc_final: 0.7802 (m-30) REVERT: B 200 TYR cc_start: 0.6574 (m-80) cc_final: 0.6172 (m-80) REVERT: B 347 PHE cc_start: 0.7902 (m-80) cc_final: 0.7665 (m-80) REVERT: B 399 SER cc_start: 0.7813 (OUTLIER) cc_final: 0.7584 (p) REVERT: B 429 PHE cc_start: 0.8579 (OUTLIER) cc_final: 0.7529 (t80) REVERT: B 873 TYR cc_start: 0.8533 (OUTLIER) cc_final: 0.7974 (m-10) REVERT: B 1141 LEU cc_start: 0.9345 (tt) cc_final: 0.9018 (tt) REVERT: C 198 ASP cc_start: 0.8998 (p0) cc_final: 0.8730 (m-30) REVERT: C 900 MET cc_start: 0.8574 (mtp) cc_final: 0.8364 (mtm) REVERT: C 979 ASP cc_start: 0.8401 (m-30) cc_final: 0.7983 (m-30) REVERT: C 1004 LEU cc_start: 0.9411 (OUTLIER) cc_final: 0.9194 (tt) outliers start: 44 outliers final: 25 residues processed: 170 average time/residue: 0.1467 time to fit residues: 40.7960 Evaluate side-chains 145 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 115 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 437 ASN Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 1004 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 134 optimal weight: 20.0000 chunk 263 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 279 optimal weight: 0.5980 chunk 287 optimal weight: 0.7980 chunk 168 optimal weight: 0.9990 chunk 30 optimal weight: 4.9990 chunk 28 optimal weight: 8.9990 chunk 151 optimal weight: 5.9990 chunk 153 optimal weight: 0.4980 chunk 144 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 317 ASN B 804 GLN B 935 GLN B1088 HIS C 901 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.116208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.081552 restraints weight = 50128.392| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 3.38 r_work: 0.3242 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.3268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 24281 Z= 0.121 Angle : 0.618 18.457 33142 Z= 0.309 Chirality : 0.044 0.195 3948 Planarity : 0.004 0.052 4154 Dihedral : 5.869 58.787 4426 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.53 % Allowed : 10.38 % Favored : 88.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.15), residues: 2844 helix: 1.20 (0.20), residues: 661 sheet: -0.31 (0.19), residues: 663 loop : -0.66 (0.15), residues: 1520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C1000 TYR 0.018 0.001 TYR C1067 PHE 0.026 0.001 PHE A 168 TRP 0.010 0.001 TRP B 104 HIS 0.004 0.001 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00262 (24182) covalent geometry : angle 0.58005 (32881) SS BOND : bond 0.00359 ( 36) SS BOND : angle 1.26596 ( 72) hydrogen bonds : bond 0.03823 ( 998) hydrogen bonds : angle 5.82912 ( 2754) link_BETA1-4 : bond 0.00329 ( 15) link_BETA1-4 : angle 1.40129 ( 45) link_NAG-ASN : bond 0.00335 ( 48) link_NAG-ASN : angle 3.09207 ( 144) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 139 time to evaluate : 0.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 LYS cc_start: 0.7495 (mptt) cc_final: 0.7167 (mptt) REVERT: A 437 ASN cc_start: 0.9461 (OUTLIER) cc_final: 0.9035 (t0) REVERT: A 869 MET cc_start: 0.8919 (mtm) cc_final: 0.8486 (ttm) REVERT: A 985 ASP cc_start: 0.8377 (t0) cc_final: 0.8025 (m-30) REVERT: B 200 TYR cc_start: 0.6403 (m-80) cc_final: 0.6098 (m-80) REVERT: B 429 PHE cc_start: 0.8559 (OUTLIER) cc_final: 0.7512 (t80) REVERT: B 957 GLN cc_start: 0.8930 (tt0) cc_final: 0.8698 (tt0) REVERT: B 988 GLU cc_start: 0.8312 (mp0) cc_final: 0.8103 (mp0) REVERT: B 1050 MET cc_start: 0.8342 (ptm) cc_final: 0.8068 (ptm) REVERT: C 52 GLN cc_start: 0.8668 (tm-30) cc_final: 0.8386 (tm-30) REVERT: C 198 ASP cc_start: 0.9028 (p0) cc_final: 0.8719 (m-30) REVERT: C 464 PHE cc_start: 0.8422 (m-80) cc_final: 0.8203 (m-80) REVERT: C 873 TYR cc_start: 0.8379 (m-80) cc_final: 0.7942 (m-10) REVERT: C 988 GLU cc_start: 0.8468 (mp0) cc_final: 0.7762 (mp0) outliers start: 39 outliers final: 26 residues processed: 171 average time/residue: 0.1405 time to fit residues: 40.3651 Evaluate side-chains 148 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 120 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 437 ASN Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain B residue 140 PHE Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 791 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 272 optimal weight: 4.9990 chunk 128 optimal weight: 5.9990 chunk 263 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 279 optimal weight: 4.9990 chunk 273 optimal weight: 3.9990 chunk 28 optimal weight: 10.0000 chunk 76 optimal weight: 9.9990 chunk 236 optimal weight: 9.9990 chunk 55 optimal weight: 0.0980 chunk 165 optimal weight: 5.9990 overall best weight: 3.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1002 GLN B 804 GLN B 935 GLN C 493 GLN C 762 GLN C 901 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.112864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.078182 restraints weight = 50412.570| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 3.32 r_work: 0.3171 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.3553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 24281 Z= 0.268 Angle : 0.686 16.481 33142 Z= 0.344 Chirality : 0.047 0.196 3948 Planarity : 0.004 0.051 4154 Dihedral : 5.806 58.673 4426 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 2.04 % Allowed : 11.48 % Favored : 86.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.15), residues: 2844 helix: 1.09 (0.20), residues: 655 sheet: -0.47 (0.18), residues: 688 loop : -0.74 (0.15), residues: 1501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B1107 TYR 0.021 0.002 TYR C1067 PHE 0.026 0.002 PHE B1089 TRP 0.008 0.001 TRP C 64 HIS 0.007 0.001 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00619 (24182) covalent geometry : angle 0.65219 (32881) SS BOND : bond 0.00696 ( 36) SS BOND : angle 1.98747 ( 72) hydrogen bonds : bond 0.04140 ( 998) hydrogen bonds : angle 6.04520 ( 2754) link_BETA1-4 : bond 0.00289 ( 15) link_BETA1-4 : angle 1.48308 ( 45) link_NAG-ASN : bond 0.00349 ( 48) link_NAG-ASN : angle 2.91347 ( 144) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 126 time to evaluate : 0.926 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.8063 (m-90) cc_final: 0.7548 (m-90) REVERT: A 202 LYS cc_start: 0.7512 (mptt) cc_final: 0.6804 (mmtm) REVERT: A 437 ASN cc_start: 0.9500 (OUTLIER) cc_final: 0.9082 (t0) REVERT: A 560 LEU cc_start: 0.9069 (OUTLIER) cc_final: 0.8693 (mp) REVERT: A 571 ASP cc_start: 0.7542 (t0) cc_final: 0.7330 (t0) REVERT: A 606 ASN cc_start: 0.8388 (m-40) cc_final: 0.7997 (t0) REVERT: A 985 ASP cc_start: 0.8305 (t0) cc_final: 0.7931 (m-30) REVERT: B 200 TYR cc_start: 0.6977 (m-80) cc_final: 0.6615 (m-80) REVERT: B 399 SER cc_start: 0.7941 (OUTLIER) cc_final: 0.7599 (p) REVERT: B 429 PHE cc_start: 0.8687 (OUTLIER) cc_final: 0.7672 (t80) REVERT: B 1050 MET cc_start: 0.8568 (ptm) cc_final: 0.8360 (ptm) REVERT: C 52 GLN cc_start: 0.8752 (tm-30) cc_final: 0.8458 (tm-30) REVERT: C 402 ILE cc_start: 0.8146 (pt) cc_final: 0.7924 (pt) REVERT: C 449 TYR cc_start: 0.8414 (m-80) cc_final: 0.8130 (m-80) REVERT: C 464 PHE cc_start: 0.8530 (m-80) cc_final: 0.8316 (m-80) REVERT: C 900 MET cc_start: 0.8546 (mtp) cc_final: 0.8262 (mtt) REVERT: C 988 GLU cc_start: 0.8560 (mp0) cc_final: 0.7856 (mp0) outliers start: 52 outliers final: 38 residues processed: 171 average time/residue: 0.1440 time to fit residues: 41.2943 Evaluate side-chains 157 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 115 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 437 ASN Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain B residue 140 PHE Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 1004 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 218 optimal weight: 0.4980 chunk 133 optimal weight: 20.0000 chunk 197 optimal weight: 6.9990 chunk 54 optimal weight: 7.9990 chunk 221 optimal weight: 10.0000 chunk 103 optimal weight: 10.0000 chunk 240 optimal weight: 5.9990 chunk 227 optimal weight: 8.9990 chunk 62 optimal weight: 0.9980 chunk 111 optimal weight: 5.9990 chunk 36 optimal weight: 10.0000 overall best weight: 4.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 607 GLN A 914 ASN B1088 HIS B1119 ASN C 901 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.108905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.075129 restraints weight = 51642.246| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 3.24 r_work: 0.3232 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.3863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.064 24281 Z= 0.340 Angle : 0.736 15.585 33142 Z= 0.368 Chirality : 0.048 0.212 3948 Planarity : 0.004 0.048 4154 Dihedral : 5.997 59.774 4426 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 2.78 % Allowed : 11.72 % Favored : 85.50 % 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: -0.69 (0.15), residues: 2844 helix: 0.86 (0.20), residues: 662 sheet: -0.66 (0.18), residues: 712 loop : -0.93 (0.15), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C1039 TYR 0.025 0.002 TYR A1067 PHE 0.030 0.002 PHE B1089 TRP 0.009 0.002 TRP A 64 HIS 0.009 0.001 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00786 (24182) covalent geometry : angle 0.70622 (32881) SS BOND : bond 0.00643 ( 36) SS BOND : angle 2.10646 ( 72) hydrogen bonds : bond 0.04377 ( 998) hydrogen bonds : angle 6.26120 ( 2754) link_BETA1-4 : bond 0.00298 ( 15) link_BETA1-4 : angle 1.48676 ( 45) link_NAG-ASN : bond 0.00395 ( 48) link_NAG-ASN : angle 2.80838 ( 144) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 117 time to evaluate : 0.876 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 318 PHE cc_start: 0.8314 (t80) cc_final: 0.8109 (t80) REVERT: A 378 LYS cc_start: 0.8657 (tppp) cc_final: 0.8390 (tppt) REVERT: A 437 ASN cc_start: 0.9510 (OUTLIER) cc_final: 0.9134 (t0) REVERT: A 606 ASN cc_start: 0.8308 (m-40) cc_final: 0.8056 (t0) REVERT: A 985 ASP cc_start: 0.8372 (t0) cc_final: 0.8011 (m-30) REVERT: B 429 PHE cc_start: 0.8902 (OUTLIER) cc_final: 0.7805 (t80) REVERT: B 873 TYR cc_start: 0.8699 (OUTLIER) cc_final: 0.8043 (m-10) REVERT: B 988 GLU cc_start: 0.8451 (mp0) cc_final: 0.7792 (mp0) REVERT: C 402 ILE cc_start: 0.8073 (pt) cc_final: 0.7856 (pt) REVERT: C 464 PHE cc_start: 0.8530 (m-80) cc_final: 0.8315 (m-80) REVERT: C 900 MET cc_start: 0.8627 (mtp) cc_final: 0.8421 (mtm) REVERT: C 988 GLU cc_start: 0.8556 (mp0) cc_final: 0.7846 (mp0) REVERT: C 1004 LEU cc_start: 0.9381 (OUTLIER) cc_final: 0.9172 (tt) outliers start: 71 outliers final: 45 residues processed: 174 average time/residue: 0.1447 time to fit residues: 41.9539 Evaluate side-chains 160 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 111 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 437 ASN Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain B residue 140 PHE Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 711 SER Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1031 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 204 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 124 optimal weight: 3.9990 chunk 76 optimal weight: 9.9990 chunk 142 optimal weight: 0.0870 chunk 110 optimal weight: 9.9990 chunk 177 optimal weight: 0.3980 chunk 271 optimal weight: 0.2980 chunk 37 optimal weight: 10.0000 chunk 229 optimal weight: 20.0000 chunk 136 optimal weight: 6.9990 overall best weight: 1.7562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1088 HIS C 125 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.112476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.079363 restraints weight = 51383.119| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 3.31 r_work: 0.3257 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.3976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 24281 Z= 0.174 Angle : 0.619 14.338 33142 Z= 0.310 Chirality : 0.045 0.193 3948 Planarity : 0.004 0.045 4154 Dihedral : 5.612 57.457 4426 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 1.92 % Allowed : 12.58 % Favored : 85.50 % 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: -0.43 (0.15), residues: 2844 helix: 1.20 (0.20), residues: 667 sheet: -0.55 (0.19), residues: 664 loop : -0.80 (0.15), residues: 1513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 509 TYR 0.020 0.001 TYR A 200 PHE 0.022 0.001 PHE B 347 TRP 0.009 0.001 TRP B 104 HIS 0.006 0.001 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00396 (24182) covalent geometry : angle 0.58736 (32881) SS BOND : bond 0.00460 ( 36) SS BOND : angle 2.19509 ( 72) hydrogen bonds : bond 0.03869 ( 998) hydrogen bonds : angle 5.91711 ( 2754) link_BETA1-4 : bond 0.00307 ( 15) link_BETA1-4 : angle 1.29888 ( 45) link_NAG-ASN : bond 0.00276 ( 48) link_NAG-ASN : angle 2.54516 ( 144) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 120 time to evaluate : 1.078 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 378 LYS cc_start: 0.8586 (tppp) cc_final: 0.8270 (tppt) REVERT: A 437 ASN cc_start: 0.9528 (OUTLIER) cc_final: 0.9141 (t0) REVERT: A 571 ASP cc_start: 0.7457 (t0) cc_final: 0.7249 (t0) REVERT: A 606 ASN cc_start: 0.8335 (m-40) cc_final: 0.8016 (t0) REVERT: A 869 MET cc_start: 0.8873 (OUTLIER) cc_final: 0.8533 (ttm) REVERT: A 985 ASP cc_start: 0.8311 (t0) cc_final: 0.7997 (m-30) REVERT: B 224 GLU cc_start: 0.7321 (OUTLIER) cc_final: 0.6519 (pp20) REVERT: B 429 PHE cc_start: 0.8826 (OUTLIER) cc_final: 0.7821 (t80) REVERT: B 988 GLU cc_start: 0.8237 (mp0) cc_final: 0.7610 (mp0) REVERT: C 52 GLN cc_start: 0.8787 (tm-30) cc_final: 0.8544 (tm-30) REVERT: C 110 LEU cc_start: 0.7426 (mp) cc_final: 0.6573 (tt) REVERT: C 464 PHE cc_start: 0.8432 (m-80) cc_final: 0.8228 (m-80) REVERT: C 900 MET cc_start: 0.8578 (mtp) cc_final: 0.8352 (mtm) REVERT: C 988 GLU cc_start: 0.8578 (mp0) cc_final: 0.7828 (mp0) REVERT: C 1004 LEU cc_start: 0.9349 (OUTLIER) cc_final: 0.9135 (tt) outliers start: 49 outliers final: 33 residues processed: 163 average time/residue: 0.1451 time to fit residues: 39.6431 Evaluate side-chains 149 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 111 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 437 ASN Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 140 PHE Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 1004 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 134 optimal weight: 9.9990 chunk 230 optimal weight: 5.9990 chunk 209 optimal weight: 6.9990 chunk 201 optimal weight: 1.9990 chunk 164 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 chunk 7 optimal weight: 20.0000 chunk 106 optimal weight: 2.9990 chunk 235 optimal weight: 4.9990 chunk 118 optimal weight: 1.9990 chunk 286 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN A 137 ASN C 137 ASN C 901 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.110219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.077932 restraints weight = 51106.402| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 3.37 r_work: 0.3235 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.4090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 24281 Z= 0.233 Angle : 0.650 14.425 33142 Z= 0.324 Chirality : 0.046 0.391 3948 Planarity : 0.004 0.051 4154 Dihedral : 5.553 56.172 4426 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 2.16 % Allowed : 12.74 % Favored : 85.11 % 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: 2844 helix: 1.10 (0.20), residues: 668 sheet: -0.50 (0.19), residues: 653 loop : -0.84 (0.15), residues: 1523 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C1000 TYR 0.024 0.002 TYR A 200 PHE 0.019 0.002 PHE B1089 TRP 0.007 0.001 TRP A 64 HIS 0.006 0.001 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00537 (24182) covalent geometry : angle 0.62053 (32881) SS BOND : bond 0.00512 ( 36) SS BOND : angle 2.19091 ( 72) hydrogen bonds : bond 0.04003 ( 998) hydrogen bonds : angle 5.97777 ( 2754) link_BETA1-4 : bond 0.00257 ( 15) link_BETA1-4 : angle 1.34681 ( 45) link_NAG-ASN : bond 0.00305 ( 48) link_NAG-ASN : angle 2.52240 ( 144) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 114 time to evaluate : 0.930 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 378 LYS cc_start: 0.8583 (tppp) cc_final: 0.8279 (tppt) REVERT: A 437 ASN cc_start: 0.9533 (OUTLIER) cc_final: 0.9153 (t0) REVERT: A 560 LEU cc_start: 0.9116 (OUTLIER) cc_final: 0.8768 (mp) REVERT: A 571 ASP cc_start: 0.7536 (t0) cc_final: 0.7295 (t0) REVERT: A 606 ASN cc_start: 0.8296 (m-40) cc_final: 0.7997 (t0) REVERT: A 985 ASP cc_start: 0.8369 (t0) cc_final: 0.8019 (m-30) REVERT: B 224 GLU cc_start: 0.7389 (OUTLIER) cc_final: 0.6581 (pp20) REVERT: B 429 PHE cc_start: 0.8848 (OUTLIER) cc_final: 0.7912 (t80) REVERT: B 873 TYR cc_start: 0.8602 (OUTLIER) cc_final: 0.7933 (m-10) REVERT: B 988 GLU cc_start: 0.8278 (mp0) cc_final: 0.7580 (mp0) REVERT: B 1050 MET cc_start: 0.8459 (ptp) cc_final: 0.8074 (ptp) REVERT: C 52 GLN cc_start: 0.8784 (tm-30) cc_final: 0.8546 (tm-30) REVERT: C 900 MET cc_start: 0.8594 (mtp) cc_final: 0.8382 (mtm) REVERT: C 988 GLU cc_start: 0.8585 (mp0) cc_final: 0.7833 (mp0) REVERT: C 1004 LEU cc_start: 0.9364 (OUTLIER) cc_final: 0.9150 (tt) outliers start: 55 outliers final: 38 residues processed: 164 average time/residue: 0.1460 time to fit residues: 40.2113 Evaluate side-chains 155 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 111 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 437 ASN Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 140 PHE Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 711 SER Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 1004 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 88 optimal weight: 0.9980 chunk 29 optimal weight: 3.9990 chunk 24 optimal weight: 0.6980 chunk 250 optimal weight: 0.8980 chunk 222 optimal weight: 0.7980 chunk 66 optimal weight: 0.6980 chunk 208 optimal weight: 8.9990 chunk 139 optimal weight: 2.9990 chunk 160 optimal weight: 3.9990 chunk 262 optimal weight: 0.2980 chunk 118 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 804 GLN B 935 GLN C 901 GLN C1088 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.115331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.081188 restraints weight = 50187.793| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 3.35 r_work: 0.3229 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.4196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 24281 Z= 0.115 Angle : 0.583 13.526 33142 Z= 0.290 Chirality : 0.044 0.228 3948 Planarity : 0.004 0.049 4154 Dihedral : 5.221 51.336 4426 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 1.72 % Allowed : 13.44 % Favored : 84.84 % 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: -0.21 (0.15), residues: 2844 helix: 1.37 (0.20), residues: 680 sheet: -0.38 (0.20), residues: 638 loop : -0.69 (0.15), residues: 1526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C1000 TYR 0.040 0.001 TYR B 369 PHE 0.024 0.001 PHE A 168 TRP 0.015 0.001 TRP B 104 HIS 0.004 0.001 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00255 (24182) covalent geometry : angle 0.55736 (32881) SS BOND : bond 0.00383 ( 36) SS BOND : angle 1.68575 ( 72) hydrogen bonds : bond 0.03632 ( 998) hydrogen bonds : angle 5.64871 ( 2754) link_BETA1-4 : bond 0.00333 ( 15) link_BETA1-4 : angle 1.19582 ( 45) link_NAG-ASN : bond 0.00302 ( 48) link_NAG-ASN : angle 2.32123 ( 144) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 127 time to evaluate : 0.917 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 378 LYS cc_start: 0.8456 (tppp) cc_final: 0.8138 (tppt) REVERT: A 437 ASN cc_start: 0.9528 (OUTLIER) cc_final: 0.9167 (t0) REVERT: A 560 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8641 (mp) REVERT: A 571 ASP cc_start: 0.7434 (t0) cc_final: 0.7178 (t0) REVERT: A 606 ASN cc_start: 0.8344 (m-40) cc_final: 0.7981 (t0) REVERT: A 869 MET cc_start: 0.8933 (OUTLIER) cc_final: 0.8511 (ttm) REVERT: A 985 ASP cc_start: 0.8325 (t0) cc_final: 0.7995 (m-30) REVERT: B 224 GLU cc_start: 0.6799 (OUTLIER) cc_final: 0.6217 (pp20) REVERT: B 429 PHE cc_start: 0.8669 (OUTLIER) cc_final: 0.7862 (t80) REVERT: B 900 MET cc_start: 0.8529 (mtp) cc_final: 0.8325 (mtp) REVERT: B 988 GLU cc_start: 0.8127 (mp0) cc_final: 0.7485 (mp0) REVERT: B 1050 MET cc_start: 0.8538 (ptp) cc_final: 0.8217 (ptp) REVERT: C 52 GLN cc_start: 0.8760 (tm-30) cc_final: 0.8489 (tm-30) REVERT: C 449 TYR cc_start: 0.8719 (m-10) cc_final: 0.8492 (m-80) REVERT: C 900 MET cc_start: 0.8438 (mtp) cc_final: 0.8135 (mtt) REVERT: C 988 GLU cc_start: 0.8521 (mp0) cc_final: 0.7711 (mp0) outliers start: 44 outliers final: 33 residues processed: 166 average time/residue: 0.1395 time to fit residues: 39.1925 Evaluate side-chains 150 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 112 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 437 ASN Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 140 PHE Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 791 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 270 optimal weight: 20.0000 chunk 12 optimal weight: 8.9990 chunk 218 optimal weight: 0.7980 chunk 101 optimal weight: 2.9990 chunk 130 optimal weight: 0.5980 chunk 236 optimal weight: 7.9990 chunk 188 optimal weight: 0.9980 chunk 263 optimal weight: 0.7980 chunk 104 optimal weight: 7.9990 chunk 118 optimal weight: 0.9990 chunk 124 optimal weight: 8.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.115793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.081154 restraints weight = 50380.021| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 3.39 r_work: 0.3235 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.4286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 24281 Z= 0.121 Angle : 0.583 13.393 33142 Z= 0.287 Chirality : 0.044 0.204 3948 Planarity : 0.004 0.048 4154 Dihedral : 5.041 50.221 4426 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 1.61 % Allowed : 13.64 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.15), residues: 2844 helix: 1.43 (0.20), residues: 677 sheet: -0.36 (0.19), residues: 662 loop : -0.67 (0.16), residues: 1505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C1000 TYR 0.035 0.001 TYR B 369 PHE 0.023 0.001 PHE A 168 TRP 0.012 0.001 TRP B 104 HIS 0.006 0.001 HIS A1083 Details of bonding type rmsd covalent geometry : bond 0.00271 (24182) covalent geometry : angle 0.55780 (32881) SS BOND : bond 0.00393 ( 36) SS BOND : angle 1.75994 ( 72) hydrogen bonds : bond 0.03583 ( 998) hydrogen bonds : angle 5.57124 ( 2754) link_BETA1-4 : bond 0.00349 ( 15) link_BETA1-4 : angle 1.20607 ( 45) link_NAG-ASN : bond 0.00276 ( 48) link_NAG-ASN : angle 2.26588 ( 144) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 123 time to evaluate : 0.874 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 346 ARG cc_start: 0.6626 (ttt180) cc_final: 0.6306 (tpt-90) REVERT: A 378 LYS cc_start: 0.8414 (tppp) cc_final: 0.8111 (tppt) REVERT: A 437 ASN cc_start: 0.9528 (OUTLIER) cc_final: 0.9181 (t0) REVERT: A 560 LEU cc_start: 0.9036 (OUTLIER) cc_final: 0.8638 (mp) REVERT: A 571 ASP cc_start: 0.7448 (t0) cc_final: 0.7189 (t0) REVERT: A 606 ASN cc_start: 0.8347 (m-40) cc_final: 0.7996 (t0) REVERT: A 869 MET cc_start: 0.8921 (OUTLIER) cc_final: 0.8520 (ttm) REVERT: A 985 ASP cc_start: 0.8282 (t0) cc_final: 0.7942 (m-30) REVERT: A 994 ASP cc_start: 0.8918 (m-30) cc_final: 0.8708 (m-30) REVERT: B 224 GLU cc_start: 0.6865 (OUTLIER) cc_final: 0.6318 (pp20) REVERT: B 429 PHE cc_start: 0.8687 (OUTLIER) cc_final: 0.7939 (t80) REVERT: B 873 TYR cc_start: 0.8467 (OUTLIER) cc_final: 0.7611 (m-10) REVERT: B 900 MET cc_start: 0.8554 (mtp) cc_final: 0.8351 (mtp) REVERT: B 988 GLU cc_start: 0.8144 (mp0) cc_final: 0.7495 (mp0) REVERT: B 1050 MET cc_start: 0.8554 (ptp) cc_final: 0.8270 (ptp) REVERT: C 52 GLN cc_start: 0.8759 (tm-30) cc_final: 0.8495 (tm-30) REVERT: C 354 ASN cc_start: 0.8037 (m-40) cc_final: 0.7825 (p0) REVERT: C 449 TYR cc_start: 0.8684 (m-10) cc_final: 0.8476 (m-80) REVERT: C 740 MET cc_start: 0.8836 (tpt) cc_final: 0.8600 (mmm) REVERT: C 900 MET cc_start: 0.8449 (mtp) cc_final: 0.8212 (mtm) REVERT: C 988 GLU cc_start: 0.8510 (mp0) cc_final: 0.7689 (mp0) outliers start: 41 outliers final: 32 residues processed: 158 average time/residue: 0.1474 time to fit residues: 39.2057 Evaluate side-chains 149 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 111 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 437 ASN Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 140 PHE Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 791 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 175 optimal weight: 5.9990 chunk 20 optimal weight: 0.7980 chunk 150 optimal weight: 7.9990 chunk 147 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 chunk 133 optimal weight: 0.9980 chunk 117 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 193 optimal weight: 3.9990 chunk 229 optimal weight: 30.0000 chunk 149 optimal weight: 0.6980 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 334 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.115220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.080881 restraints weight = 50407.112| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 3.34 r_work: 0.3220 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.4339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 24281 Z= 0.141 Angle : 0.592 13.256 33142 Z= 0.294 Chirality : 0.044 0.211 3948 Planarity : 0.004 0.051 4154 Dihedral : 4.916 50.388 4426 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 1.57 % Allowed : 14.07 % Favored : 84.37 % 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: -0.18 (0.15), residues: 2844 helix: 1.51 (0.20), residues: 661 sheet: -0.50 (0.19), residues: 688 loop : -0.63 (0.16), residues: 1495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 346 TYR 0.024 0.001 TYR B 369 PHE 0.040 0.001 PHE C 338 TRP 0.008 0.001 TRP A 104 HIS 0.004 0.001 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00322 (24182) covalent geometry : angle 0.56740 (32881) SS BOND : bond 0.00401 ( 36) SS BOND : angle 1.91312 ( 72) hydrogen bonds : bond 0.03615 ( 998) hydrogen bonds : angle 5.57255 ( 2754) link_BETA1-4 : bond 0.00318 ( 15) link_BETA1-4 : angle 1.21325 ( 45) link_NAG-ASN : bond 0.00274 ( 48) link_NAG-ASN : angle 2.22845 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5968.14 seconds wall clock time: 103 minutes 10.32 seconds (6190.32 seconds total)