Starting phenix.real_space_refine on Sun Sep 13 13:40:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7kdi_22823/09_2026/7kdi_22823.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kdi_22823/09_2026/7kdi_22823.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7kdi_22823/09_2026/7kdi_22823.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7kdi_22823/09_2026/7kdi_22823.cif" model { file = "/net/cci-nas-00/data/ceres_data/7kdi_22823/09_2026/7kdi_22823.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kdi_22823/09_2026/7kdi_22823.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7kdi_22823/09_2026/7kdi_22823.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kdi_22823/09_2026/7kdi_22823.map" } resolution = 3.26 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.051 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 15084 2.51 5 N 3852 2.21 5 O 4653 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 212 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 23688 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: 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: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "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 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 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 chiralities: 2 Chain: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen chiralities: 11 Chain: "C" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen chiralities: 11 Time building chain proxies: 4.63, per 1000 atoms: 0.20 Number of scatterers: 23688 At special positions: 0 Unit cell: (130.134, 138.598, 172.454, 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 4653 8.00 N 3852 7.00 C 15084 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 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=2.02 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.00 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.02 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 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=2.02 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=2.05 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.01 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=2.02 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.01 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.02 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.01 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=2.06 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.02 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.01 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG 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 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B 331 " " NAG B1305 " - " ASN B 343 " " NAG B1306 " - " ASN B 603 " " NAG B1307 " - " ASN B 616 " " NAG B1308 " - " ASN B 657 " " NAG B1309 " - " ASN B 709 " " NAG B1310 " - " ASN B1074 " " NAG B1311 " - " ASN B 165 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 122 " " NAG C1303 " - " ASN C 282 " " NAG C1304 " - " ASN C 331 " " NAG C1305 " - " ASN C 343 " " NAG C1306 " - " ASN C 603 " " NAG C1307 " - " ASN C 616 " " NAG C1308 " - " ASN C 657 " " NAG C1309 " - " ASN C 709 " " NAG C1310 " - " ASN C1074 " " NAG C1311 " - " ASN C 165 " " 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 234 " " NAG J 1 " - " ASN B 717 " " NAG K 1 " - " ASN B 801 " " NAG L 1 " - " ASN B1098 " " NAG M 1 " - " ASN B1134 " " NAG N 1 " - " ASN C 234 " " NAG O 1 " - " ASN C 717 " " NAG P 1 " - " ASN C 801 " " NAG Q 1 " - " ASN C1098 " " NAG R 1 " - " ASN C1134 " Time building additional restraints: 2.18 Conformation dependent library (CDL) restraints added in 826.7 milliseconds 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 27.5% alpha, 29.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.87 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 342 Processing helix chain 'A' and resid 351 through 353 No H-bonds generated for 'chain 'A' and resid 351 through 353' Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 383 through 387 Processing helix chain 'A' and resid 405 through 410 removed outlier: 3.947A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 616 through 620 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.839A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.587A pdb=" N GLY A 885 " --> pdb=" O THR A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.615A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 918 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 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.786A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.731A pdb=" N VAL A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 4.364A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.726A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.708A 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 405 through 410 removed outlier: 4.573A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.966A 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: 3.850A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.507A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 removed outlier: 3.566A pdb=" N GLY B 885 " --> pdb=" O THR B 881 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 891 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 918 Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.604A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.740A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.601A pdb=" N VAL B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 4.461A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.912A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 370 removed outlier: 4.170A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 389 removed outlier: 4.067A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.022A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.845A pdb=" N SER C 443 " --> pdb=" O ASN C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 616 through 620 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.623A 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: 3.923A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 801 through 805 removed outlier: 4.625A pdb=" N GLN C 804 " --> pdb=" O ASN C 801 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.630A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 removed outlier: 3.502A pdb=" N GLY C 885 " --> pdb=" O THR C 881 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.574A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 918 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: 3.719A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.566A pdb=" N VAL C 991 " --> pdb=" O VAL C 987 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) Processing helix chain 'C' and resid 1125 through 1129 removed outlier: 3.788A pdb=" N VAL C1128 " --> pdb=" O ASN C1125 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL C1129 " --> pdb=" O CYS C1126 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1125 through 1129' Processing helix chain 'C' and resid 1141 through 1146 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.275A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.387A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.590A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.172A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 5.445A 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: 3.934A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.764A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N VAL A 126 " --> pdb=" O SER A 172 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.281A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.391A 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 Processing sheet with id=AA8, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.416A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 348 through 349 removed outlier: 6.868A pdb=" N ALA A 348 " --> pdb=" O VAL A 401 " (cutoff:3.500A) removed outlier: 9.223A pdb=" N ARG A 403 " --> pdb=" O ALA A 348 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 348 through 349 removed outlier: 6.868A pdb=" N ALA A 348 " --> pdb=" O VAL A 401 " (cutoff:3.500A) removed outlier: 9.223A pdb=" N ARG A 403 " --> pdb=" O ALA A 348 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.669A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 452 through 453 Processing sheet with id=AB4, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.112A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.446A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.622A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 718 through 728 removed outlier: 5.816A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.370A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 787 through 790 removed outlier: 6.215A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AC2, first strand: chain 'B' and resid 28 through 30 removed outlier: 7.911A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.294A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 8.863A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.727A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC5, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.699A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.270A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 324 through 328 removed outlier: 4.225A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 324 through 328 removed outlier: 4.225A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AD1, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.729A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'B' and resid 452 through 453 Processing sheet with id=AD3, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.735A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 701 through 704 Processing sheet with id=AD5, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.532A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 718 through 728 removed outlier: 5.860A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD8, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.363A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.293A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.788A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AE3, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.702A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.343A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.883A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.753A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'C' and resid 452 through 453 Processing sheet with id=AE8, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.693A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.549A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.549A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AF3, first strand: chain 'C' and resid 1120 through 1122 1038 hydrogen bonds defined for protein. 2862 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: 5.82 Time building geometry restraints manager: 2.78 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: 6465 1.33 - 1.46: 4478 1.46 - 1.58: 13120 1.58 - 1.70: 0 1.70 - 1.83: 123 Bond restraints: 24186 Sorted by residual: bond pdb=" C5 NAG B1307 " pdb=" O5 NAG B1307 " ideal model delta sigma weight residual 1.413 1.492 -0.079 2.00e-02 2.50e+03 1.56e+01 bond pdb=" C5 NAG A1302 " pdb=" O5 NAG A1302 " ideal model delta sigma weight residual 1.413 1.489 -0.076 2.00e-02 2.50e+03 1.45e+01 bond pdb=" C5 NAG B1302 " pdb=" O5 NAG B1302 " ideal model delta sigma weight residual 1.413 1.489 -0.076 2.00e-02 2.50e+03 1.43e+01 bond pdb=" C5 NAG D 2 " pdb=" O5 NAG D 2 " ideal model delta sigma weight residual 1.413 1.487 -0.074 2.00e-02 2.50e+03 1.38e+01 bond pdb=" C5 NAG G 2 " pdb=" O5 NAG G 2 " ideal model delta sigma weight residual 1.413 1.487 -0.074 2.00e-02 2.50e+03 1.38e+01 ... (remaining 24181 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.14: 26143 2.14 - 4.28: 6316 4.28 - 6.43: 409 6.43 - 8.57: 11 8.57 - 10.71: 7 Bond angle restraints: 32886 Sorted by residual: angle pdb=" N CYS B 391 " pdb=" CA CYS B 391 " pdb=" C CYS B 391 " ideal model delta sigma weight residual 108.96 119.67 -10.71 1.49e+00 4.50e-01 5.17e+01 angle pdb=" N CYS A 391 " pdb=" CA CYS A 391 " pdb=" C CYS A 391 " ideal model delta sigma weight residual 108.96 119.30 -10.34 1.49e+00 4.50e-01 4.81e+01 angle pdb=" N CYS C 391 " pdb=" CA CYS C 391 " pdb=" C CYS C 391 " ideal model delta sigma weight residual 108.96 119.08 -10.12 1.49e+00 4.50e-01 4.61e+01 angle pdb=" CA PHE C 559 " pdb=" CB PHE C 559 " pdb=" CG PHE C 559 " ideal model delta sigma weight residual 113.80 119.52 -5.72 1.00e+00 1.00e+00 3.28e+01 angle pdb=" C PRO B 384 " pdb=" N THR B 385 " pdb=" CA THR B 385 " ideal model delta sigma weight residual 120.28 127.23 -6.95 1.34e+00 5.57e-01 2.69e+01 ... (remaining 32881 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 12973 17.97 - 35.94: 750 35.94 - 53.91: 96 53.91 - 71.88: 40 71.88 - 89.85: 31 Dihedral angle restraints: 13890 sinusoidal: 5406 harmonic: 8484 Sorted by residual: dihedral pdb=" CB CYS C1082 " pdb=" SG CYS C1082 " pdb=" SG CYS C1126 " pdb=" CB CYS C1126 " ideal model delta sinusoidal sigma weight residual -86.00 -174.86 88.86 1 1.00e+01 1.00e-02 9.41e+01 dihedral pdb=" CB CYS B1032 " pdb=" SG CYS B1032 " pdb=" SG CYS B1043 " pdb=" CB CYS B1043 " ideal model delta sinusoidal sigma weight residual -86.00 -174.28 88.28 1 1.00e+01 1.00e-02 9.31e+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 -86.00 -171.09 85.09 1 1.00e+01 1.00e-02 8.78e+01 ... (remaining 13887 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 2642 0.096 - 0.192: 1153 0.192 - 0.289: 130 0.289 - 0.385: 17 0.385 - 0.481: 6 Chirality restraints: 3948 Sorted by residual: 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 8.23e+01 chirality pdb=" C1 NAG N 2 " pdb=" O4 NAG N 1 " pdb=" C2 NAG N 2 " pdb=" O5 NAG N 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.57 0.17 2.00e-02 2.50e+03 7.63e+01 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 -2.57 0.17 2.00e-02 2.50e+03 7.49e+01 ... (remaining 3945 not shown) Planarity restraints: 4203 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 331 " -0.215 2.00e-02 2.50e+03 2.46e-01 7.54e+02 pdb=" CG ASN A 331 " 0.140 2.00e-02 2.50e+03 pdb=" OD1 ASN A 331 " -0.015 2.00e-02 2.50e+03 pdb=" ND2 ASN A 331 " 0.386 2.00e-02 2.50e+03 pdb=" C1 NAG A1304 " -0.295 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 657 " 0.140 2.00e-02 2.50e+03 1.48e-01 2.74e+02 pdb=" CG ASN A 657 " -0.089 2.00e-02 2.50e+03 pdb=" OD1 ASN A 657 " -0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN A 657 " -0.226 2.00e-02 2.50e+03 pdb=" C1 NAG A1308 " 0.175 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A1074 " -0.139 2.00e-02 2.50e+03 1.48e-01 2.73e+02 pdb=" CG ASN A1074 " 0.084 2.00e-02 2.50e+03 pdb=" OD1 ASN A1074 " 0.005 2.00e-02 2.50e+03 pdb=" ND2 ASN A1074 " 0.227 2.00e-02 2.50e+03 pdb=" C1 NAG A1310 " -0.176 2.00e-02 2.50e+03 ... (remaining 4200 not shown) Histogram of nonbonded interaction distances: 2.52 - 3.00: 12079 3.00 - 3.47: 22750 3.47 - 3.95: 38868 3.95 - 4.42: 43264 4.42 - 4.90: 73192 Nonbonded interactions: 190153 Sorted by model distance: nonbonded pdb=" OE2 GLU A 918 " pdb=" OG SER C1123 " model vdw 2.522 3.040 nonbonded pdb=" OG SER A1123 " pdb=" OE2 GLU B 918 " model vdw 2.530 3.040 nonbonded pdb=" OG SER B1123 " pdb=" OE2 GLU C 918 " model vdw 2.533 3.040 nonbonded pdb=" OH TYR C 91 " pdb=" OE1 GLU C 191 " model vdw 2.553 3.040 nonbonded pdb=" OH TYR B 91 " pdb=" OE1 GLU B 191 " model vdw 2.568 3.040 ... (remaining 190148 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' 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: 2.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.490 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 22.140 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.120 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:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 27.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 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 0.079 24285 Z= 0.761 Angle : 1.736 10.711 33147 Z= 1.142 Chirality : 0.096 0.481 3948 Planarity : 0.014 0.215 4155 Dihedral : 12.732 89.850 8304 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 0.15 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.12 % Favored : 93.81 % Rotamer: Outliers : 0.27 % Allowed : 0.51 % Favored : 99.22 % Cbeta Deviations : 0.07 % 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: -0.76 (0.14), residues: 2844 helix: -0.29 (0.18), residues: 666 sheet: 0.37 (0.22), residues: 488 loop : -0.84 (0.14), residues: 1690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B1019 TYR 0.124 0.020 TYR A 266 PHE 0.092 0.012 PHE B 718 TRP 0.135 0.022 TRP B 64 HIS 0.019 0.003 HIS B 519 Details of bonding type rmsd/Z covalent geometry : bond 0.01354 / 0.76 (24186) covalent geometry : angle 1.70471 / 1.14 (32886) SS BOND : bond 0.01266 / 0.82 ( 36) SS BOND : angle 2.09489 / 1.47 ( 72) hydrogen bonds : bond 0.14635 / 9.17 ( 1013) hydrogen bonds : angle 8.39610 / 5.79 ( 2862) link_BETA1-4 : bond 0.02531 / 1.49 ( 15) link_BETA1-4 : angle 4.49505 / 2.87 ( 45) link_NAG-ASN : bond 0.01086 / 0.71 ( 48) link_NAG-ASN : angle 4.61217 / 3.25 ( 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 260 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 253 time to evaluate : 0.869 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: B 367 VAL cc_start: 0.8010 (t) cc_final: 0.7295 (t) REVERT: B 994 ASP cc_start: 0.7134 (t70) cc_final: 0.6909 (t0) outliers start: 7 outliers final: 3 residues processed: 259 average time/residue: 0.1786 time to fit residues: 70.3867 Evaluate side-chains 115 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 112 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain C residue 603 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 0.0770 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 0.8980 chunk 111 optimal weight: 0.9990 overall best weight: 0.7542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 762 GLN A 913 GLN A 955 ASN A 957 GLN B 321 GLN B 394 ASN B 498 GLN B1088 HIS C 207 HIS C 957 GLN C1088 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.107759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.074657 restraints weight = 49976.822| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 3.41 r_work: 0.2992 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 24285 Z= 0.148 Angle : 0.698 13.736 33147 Z= 0.353 Chirality : 0.047 0.267 3948 Planarity : 0.004 0.037 4155 Dihedral : 5.948 57.434 3105 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 0.94 % Allowed : 4.78 % Favored : 94.28 % Cbeta Deviations : 0.00 % 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: -0.00 (0.15), residues: 2844 helix: 1.31 (0.20), residues: 673 sheet: 0.10 (0.19), residues: 671 loop : -0.62 (0.15), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 214 TYR 0.025 0.002 TYR C 495 PHE 0.027 0.002 PHE A 201 TRP 0.045 0.003 TRP B 64 HIS 0.008 0.001 HIS B 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.15 (24186) covalent geometry : angle 0.65218 / 0.34 (32886) SS BOND : bond 0.01077 / 0.57 ( 36) SS BOND : angle 2.11272 / 1.26 ( 72) hydrogen bonds : bond 0.04320 / 2.75 ( 1013) hydrogen bonds : angle 6.21011 / 4.30 ( 2862) link_BETA1-4 : bond 0.00336 / 0.21 ( 15) link_BETA1-4 : angle 1.45773 / 0.93 ( 45) link_NAG-ASN : bond 0.00355 / 0.25 ( 48) link_NAG-ASN : angle 3.50260 / 2.60 ( 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 181 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 157 time to evaluate : 0.958 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 64 TRP cc_start: 0.7789 (t60) cc_final: 0.7453 (t60) REVERT: B 200 TYR cc_start: 0.7808 (m-80) cc_final: 0.7300 (m-80) REVERT: B 578 ASP cc_start: 0.8176 (t0) cc_final: 0.7860 (t70) REVERT: B 878 LEU cc_start: 0.8387 (tp) cc_final: 0.8083 (tp) REVERT: B 882 ILE cc_start: 0.9060 (mt) cc_final: 0.8735 (mp) REVERT: B 988 GLU cc_start: 0.8512 (mt-10) cc_final: 0.8221 (mt-10) REVERT: B 994 ASP cc_start: 0.8707 (t70) cc_final: 0.8199 (t0) REVERT: C 357 ARG cc_start: 0.8406 (ttt180) cc_final: 0.8197 (ttt180) REVERT: C 390 LEU cc_start: 0.8961 (mt) cc_final: 0.8665 (mt) REVERT: C 643 PHE cc_start: 0.8034 (t80) cc_final: 0.7764 (t80) REVERT: C 988 GLU cc_start: 0.8750 (mt-10) cc_final: 0.8245 (tp30) outliers start: 24 outliers final: 12 residues processed: 177 average time/residue: 0.1522 time to fit residues: 42.9943 Evaluate side-chains 113 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 101 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 987 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 7 optimal weight: 10.0000 chunk 10 optimal weight: 20.0000 chunk 151 optimal weight: 2.9990 chunk 85 optimal weight: 0.4980 chunk 248 optimal weight: 4.9990 chunk 150 optimal weight: 2.9990 chunk 82 optimal weight: 4.9990 chunk 178 optimal weight: 5.9990 chunk 154 optimal weight: 0.6980 chunk 244 optimal weight: 0.7980 chunk 6 optimal weight: 7.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 HIS A1088 HIS B 207 HIS C 556 ASN C 762 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.105927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.072572 restraints weight = 50449.003| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 3.41 r_work: 0.2943 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.2549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 24285 Z= 0.159 Angle : 0.617 13.456 33147 Z= 0.313 Chirality : 0.045 0.232 3948 Planarity : 0.004 0.044 4155 Dihedral : 5.291 59.981 3101 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.25 % Allowed : 5.64 % Favored : 93.11 % 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: 0.14 (0.15), residues: 2844 helix: 1.61 (0.20), residues: 676 sheet: 0.02 (0.19), residues: 667 loop : -0.55 (0.15), residues: 1501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 214 TYR 0.025 0.001 TYR C1067 PHE 0.027 0.002 PHE C 400 TRP 0.030 0.002 TRP C 353 HIS 0.006 0.001 HIS B 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.16 (24186) covalent geometry : angle 0.58033 / 0.30 (32886) SS BOND : bond 0.00612 / 0.37 ( 36) SS BOND : angle 2.13312 / 1.09 ( 72) hydrogen bonds : bond 0.04029 / 2.57 ( 1013) hydrogen bonds : angle 5.81674 / 4.03 ( 2862) link_BETA1-4 : bond 0.00331 / 0.22 ( 15) link_BETA1-4 : angle 1.30632 / 0.88 ( 45) link_NAG-ASN : bond 0.00311 / 0.23 ( 48) link_NAG-ASN : angle 2.81880 / 2.15 ( 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 141 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 109 time to evaluate : 0.877 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 869 MET cc_start: 0.8898 (mtm) cc_final: 0.8643 (mtp) REVERT: A 994 ASP cc_start: 0.8913 (t70) cc_final: 0.8558 (t0) REVERT: A 1142 GLN cc_start: 0.9063 (tp40) cc_final: 0.8714 (tm-30) REVERT: B 53 ASP cc_start: 0.8225 (t0) cc_final: 0.7972 (t0) REVERT: B 64 TRP cc_start: 0.7923 (t60) cc_final: 0.7559 (t60) REVERT: B 200 TYR cc_start: 0.7743 (m-80) cc_final: 0.7209 (m-80) REVERT: B 421 TYR cc_start: 0.4500 (OUTLIER) cc_final: 0.3964 (m-10) REVERT: B 578 ASP cc_start: 0.8245 (t0) cc_final: 0.7871 (t70) REVERT: B 994 ASP cc_start: 0.8752 (t70) cc_final: 0.8380 (t0) REVERT: C 390 LEU cc_start: 0.9098 (mt) cc_final: 0.8813 (mt) REVERT: C 643 PHE cc_start: 0.8060 (t80) cc_final: 0.7744 (t80) REVERT: C 817 PHE cc_start: 0.8046 (t80) cc_final: 0.7602 (t80) REVERT: C 988 GLU cc_start: 0.8812 (mt-10) cc_final: 0.8285 (tp30) outliers start: 32 outliers final: 19 residues processed: 135 average time/residue: 0.1505 time to fit residues: 33.0414 Evaluate side-chains 114 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 94 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 979 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 30 optimal weight: 9.9990 chunk 28 optimal weight: 0.9990 chunk 151 optimal weight: 0.9980 chunk 153 optimal weight: 1.9990 chunk 144 optimal weight: 5.9990 chunk 131 optimal weight: 0.9980 chunk 32 optimal weight: 0.0060 chunk 208 optimal weight: 8.9990 chunk 99 optimal weight: 7.9990 chunk 179 optimal weight: 2.9990 chunk 194 optimal weight: 6.9990 overall best weight: 1.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 872 GLN B 394 ASN C 394 ASN C 556 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.106629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.073524 restraints weight = 49972.064| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 3.39 r_work: 0.2964 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.2822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 24285 Z= 0.123 Angle : 0.572 14.084 33147 Z= 0.287 Chirality : 0.044 0.282 3948 Planarity : 0.003 0.034 4155 Dihedral : 4.978 58.418 3101 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.33 % Allowed : 6.78 % Favored : 91.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.15), residues: 2844 helix: 1.80 (0.20), residues: 682 sheet: 0.13 (0.19), residues: 634 loop : -0.54 (0.15), residues: 1528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 214 TYR 0.022 0.001 TYR C1067 PHE 0.021 0.001 PHE A 168 TRP 0.041 0.002 TRP A 64 HIS 0.005 0.001 HIS B 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 (24186) covalent geometry : angle 0.53748 / 0.28 (32886) SS BOND : bond 0.00461 / 0.29 ( 36) SS BOND : angle 1.98192 / 1.16 ( 72) hydrogen bonds : bond 0.03571 / 2.27 ( 1013) hydrogen bonds : angle 5.56231 / 3.84 ( 2862) link_BETA1-4 : bond 0.00340 / 0.21 ( 15) link_BETA1-4 : angle 1.14975 / 0.76 ( 45) link_NAG-ASN : bond 0.00373 / 0.28 ( 48) link_NAG-ASN : angle 2.63436 / 2.03 ( 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 144 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 110 time to evaluate : 0.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 776 LYS cc_start: 0.8911 (tttt) cc_final: 0.8635 (tttm) REVERT: A 994 ASP cc_start: 0.8916 (t70) cc_final: 0.8551 (t0) REVERT: A 1142 GLN cc_start: 0.9046 (tp40) cc_final: 0.8720 (tm-30) REVERT: B 53 ASP cc_start: 0.8259 (t0) cc_final: 0.7974 (t70) REVERT: B 64 TRP cc_start: 0.7898 (t60) cc_final: 0.7551 (t60) REVERT: B 200 TYR cc_start: 0.7699 (m-80) cc_final: 0.7181 (m-80) REVERT: B 378 LYS cc_start: 0.8600 (ttmt) cc_final: 0.8258 (ptpp) REVERT: B 421 TYR cc_start: 0.4246 (OUTLIER) cc_final: 0.3752 (m-10) REVERT: B 578 ASP cc_start: 0.8228 (t0) cc_final: 0.7825 (t70) REVERT: B 988 GLU cc_start: 0.8593 (mt-10) cc_final: 0.8181 (mt-10) REVERT: B 994 ASP cc_start: 0.8738 (t70) cc_final: 0.8373 (t0) REVERT: C 340 GLU cc_start: 0.8879 (mp0) cc_final: 0.8672 (mp0) REVERT: C 390 LEU cc_start: 0.9053 (mt) cc_final: 0.8800 (mt) REVERT: C 441 LEU cc_start: 0.9415 (tt) cc_final: 0.9192 (pt) REVERT: C 452 LEU cc_start: 0.8792 (mt) cc_final: 0.8514 (tt) REVERT: C 571 ASP cc_start: 0.7754 (OUTLIER) cc_final: 0.7198 (t0) REVERT: C 643 PHE cc_start: 0.8097 (t80) cc_final: 0.7737 (t80) REVERT: C 817 PHE cc_start: 0.8079 (t80) cc_final: 0.7703 (t80) REVERT: C 988 GLU cc_start: 0.8842 (mt-10) cc_final: 0.8286 (tp30) outliers start: 34 outliers final: 19 residues processed: 139 average time/residue: 0.1496 time to fit residues: 34.1472 Evaluate side-chains 124 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 103 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 979 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 55 optimal weight: 8.9990 chunk 165 optimal weight: 5.9990 chunk 63 optimal weight: 4.9990 chunk 151 optimal weight: 0.9990 chunk 122 optimal weight: 0.9990 chunk 268 optimal weight: 1.9990 chunk 163 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 57.5566 > 50:) chunk 51 optimal weight: 0.8980 chunk 127 optimal weight: 0.8980 chunk 220 optimal weight: 7.9990 chunk 28 optimal weight: 0.5980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.107001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.073926 restraints weight = 49863.649| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 3.35 r_work: 0.2973 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.3033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 24285 Z= 0.114 Angle : 0.548 13.134 33147 Z= 0.275 Chirality : 0.043 0.254 3948 Planarity : 0.003 0.036 4155 Dihedral : 4.722 57.814 3101 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.49 % Allowed : 7.44 % Favored : 91.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.15), residues: 2844 helix: 2.03 (0.20), residues: 675 sheet: 0.22 (0.19), residues: 612 loop : -0.53 (0.15), residues: 1557 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 214 TYR 0.021 0.001 TYR C1067 PHE 0.019 0.001 PHE A 400 TRP 0.027 0.002 TRP C 353 HIS 0.004 0.001 HIS B 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.11 (24186) covalent geometry : angle 0.51776 / 0.27 (32886) SS BOND : bond 0.00530 / 0.29 ( 36) SS BOND : angle 1.84735 / 1.11 ( 72) hydrogen bonds : bond 0.03401 / 2.17 ( 1013) hydrogen bonds : angle 5.36314 / 3.72 ( 2862) link_BETA1-4 : bond 0.00332 / 0.20 ( 15) link_BETA1-4 : angle 1.06253 / 0.70 ( 45) link_NAG-ASN : bond 0.00316 / 0.24 ( 48) link_NAG-ASN : angle 2.39757 / 1.88 ( 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 153 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 115 time to evaluate : 0.871 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.9083 (tt0) cc_final: 0.8430 (tm-30) REVERT: A 776 LYS cc_start: 0.8980 (tttt) cc_final: 0.8615 (tttm) REVERT: A 994 ASP cc_start: 0.8906 (t70) cc_final: 0.8537 (t0) REVERT: A 1142 GLN cc_start: 0.9058 (tp40) cc_final: 0.8738 (tm-30) REVERT: B 53 ASP cc_start: 0.8288 (t0) cc_final: 0.8049 (t70) REVERT: B 64 TRP cc_start: 0.7909 (t60) cc_final: 0.7558 (t60) REVERT: B 200 TYR cc_start: 0.7586 (m-80) cc_final: 0.7104 (m-80) REVERT: B 378 LYS cc_start: 0.8629 (ttmt) cc_final: 0.8280 (ptpp) REVERT: B 421 TYR cc_start: 0.4158 (OUTLIER) cc_final: 0.3685 (m-10) REVERT: B 578 ASP cc_start: 0.8307 (t0) cc_final: 0.7803 (t70) REVERT: B 988 GLU cc_start: 0.8628 (mt-10) cc_final: 0.8245 (mt-10) REVERT: B 994 ASP cc_start: 0.8758 (t70) cc_final: 0.8428 (t0) REVERT: C 340 GLU cc_start: 0.8884 (mp0) cc_final: 0.8678 (mp0) REVERT: C 390 LEU cc_start: 0.9028 (mt) cc_final: 0.8780 (mt) REVERT: C 441 LEU cc_start: 0.9414 (tt) cc_final: 0.9206 (pt) REVERT: C 452 LEU cc_start: 0.8846 (mt) cc_final: 0.8589 (mm) REVERT: C 556 ASN cc_start: 0.9096 (p0) cc_final: 0.8768 (t0) REVERT: C 565 PHE cc_start: 0.8188 (m-10) cc_final: 0.7974 (m-10) REVERT: C 571 ASP cc_start: 0.7812 (OUTLIER) cc_final: 0.7351 (t0) REVERT: C 582 LEU cc_start: 0.9233 (OUTLIER) cc_final: 0.9027 (tt) REVERT: C 643 PHE cc_start: 0.8045 (t80) cc_final: 0.7644 (t80) REVERT: C 817 PHE cc_start: 0.8027 (t80) cc_final: 0.7660 (t80) REVERT: C 988 GLU cc_start: 0.8817 (mt-10) cc_final: 0.8229 (tp30) outliers start: 38 outliers final: 20 residues processed: 144 average time/residue: 0.1505 time to fit residues: 35.2912 Evaluate side-chains 124 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 101 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 582 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 36 optimal weight: 20.0000 chunk 65 optimal weight: 0.6980 chunk 282 optimal weight: 4.9990 chunk 158 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 147 optimal weight: 1.9990 chunk 1 optimal weight: 5.9990 chunk 14 optimal weight: 0.9980 chunk 69 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 394 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.106783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.073778 restraints weight = 49999.894| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 3.35 r_work: 0.2968 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.3196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 24285 Z= 0.127 Angle : 0.536 13.048 33147 Z= 0.270 Chirality : 0.043 0.256 3948 Planarity : 0.003 0.037 4155 Dihedral : 4.574 56.474 3101 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.57 % Allowed : 7.95 % Favored : 90.48 % 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: 0.36 (0.15), residues: 2844 helix: 2.00 (0.20), residues: 677 sheet: 0.18 (0.19), residues: 632 loop : -0.52 (0.15), residues: 1535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 214 TYR 0.022 0.001 TYR B 380 PHE 0.022 0.001 PHE A 168 TRP 0.031 0.002 TRP C 353 HIS 0.002 0.001 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (24186) covalent geometry : angle 0.50603 / 0.26 (32886) SS BOND : bond 0.00528 / 0.32 ( 36) SS BOND : angle 2.11780 / 1.26 ( 72) hydrogen bonds : bond 0.03410 / 2.16 ( 1013) hydrogen bonds : angle 5.35969 / 3.70 ( 2862) link_BETA1-4 : bond 0.00310 / 0.19 ( 15) link_BETA1-4 : angle 1.02361 / 0.67 ( 45) link_NAG-ASN : bond 0.00302 / 0.23 ( 48) link_NAG-ASN : angle 2.27510 / 1.80 ( 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 153 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 113 time to evaluate : 0.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.9066 (tt0) cc_final: 0.8444 (tm-30) REVERT: A 752 LEU cc_start: 0.8882 (mt) cc_final: 0.8548 (mp) REVERT: A 776 LYS cc_start: 0.8917 (tttt) cc_final: 0.8581 (tttm) REVERT: A 869 MET cc_start: 0.8834 (OUTLIER) cc_final: 0.8425 (mtm) REVERT: A 994 ASP cc_start: 0.8883 (t70) cc_final: 0.8526 (t0) REVERT: B 53 ASP cc_start: 0.8321 (t0) cc_final: 0.8070 (t0) REVERT: B 64 TRP cc_start: 0.7876 (t60) cc_final: 0.7546 (t60) REVERT: B 200 TYR cc_start: 0.7651 (m-80) cc_final: 0.7147 (m-80) REVERT: B 335 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8151 (tp) REVERT: B 421 TYR cc_start: 0.4319 (OUTLIER) cc_final: 0.3758 (m-10) REVERT: B 578 ASP cc_start: 0.8289 (t0) cc_final: 0.7772 (t70) REVERT: B 988 GLU cc_start: 0.8635 (mt-10) cc_final: 0.8242 (mt-10) REVERT: B 994 ASP cc_start: 0.8776 (t70) cc_final: 0.8444 (t0) REVERT: B 1096 VAL cc_start: 0.8665 (OUTLIER) cc_final: 0.8361 (m) REVERT: C 340 GLU cc_start: 0.8879 (mp0) cc_final: 0.8664 (mp0) REVERT: C 370 ASN cc_start: 0.8797 (m-40) cc_final: 0.8407 (p0) REVERT: C 390 LEU cc_start: 0.9011 (mt) cc_final: 0.8766 (mt) REVERT: C 441 LEU cc_start: 0.9367 (tt) cc_final: 0.9149 (pp) REVERT: C 452 LEU cc_start: 0.8754 (mt) cc_final: 0.8506 (mm) REVERT: C 556 ASN cc_start: 0.9120 (p0) cc_final: 0.8753 (t0) REVERT: C 565 PHE cc_start: 0.8195 (m-10) cc_final: 0.7964 (m-10) REVERT: C 571 ASP cc_start: 0.7853 (OUTLIER) cc_final: 0.7420 (t0) REVERT: C 582 LEU cc_start: 0.9257 (OUTLIER) cc_final: 0.9019 (tt) REVERT: C 643 PHE cc_start: 0.8051 (t80) cc_final: 0.7359 (t80) REVERT: C 817 PHE cc_start: 0.8078 (t80) cc_final: 0.7704 (t80) REVERT: C 988 GLU cc_start: 0.8818 (mt-10) cc_final: 0.8263 (tp30) outliers start: 40 outliers final: 21 residues processed: 143 average time/residue: 0.1438 time to fit residues: 33.7248 Evaluate side-chains 133 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 106 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 582 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 137 optimal weight: 0.8980 chunk 26 optimal weight: 9.9990 chunk 19 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 91 optimal weight: 0.6980 chunk 16 optimal weight: 7.9990 chunk 10 optimal weight: 0.0970 chunk 243 optimal weight: 0.0060 chunk 245 optimal weight: 5.9990 chunk 262 optimal weight: 0.0980 chunk 260 optimal weight: 0.0050 overall best weight: 0.1808 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 913 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.109034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.076221 restraints weight = 49682.625| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 3.40 r_work: 0.3025 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.3443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.076 24285 Z= 0.094 Angle : 0.526 12.708 33147 Z= 0.263 Chirality : 0.043 0.257 3948 Planarity : 0.003 0.038 4155 Dihedral : 4.360 56.028 3101 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.37 % Allowed : 8.34 % Favored : 90.29 % 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: 0.45 (0.15), residues: 2844 helix: 2.05 (0.21), residues: 676 sheet: 0.31 (0.20), residues: 615 loop : -0.47 (0.15), residues: 1553 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 214 TYR 0.025 0.001 TYR B 380 PHE 0.017 0.001 PHE C 515 TRP 0.031 0.002 TRP C 353 HIS 0.003 0.000 HIS B 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00206 / 0.09 (24186) covalent geometry : angle 0.49901 / 0.26 (32886) SS BOND : bond 0.00572 / 0.29 ( 36) SS BOND : angle 2.04329 / 1.11 ( 72) hydrogen bonds : bond 0.03206 / 2.03 ( 1013) hydrogen bonds : angle 5.15707 / 3.56 ( 2862) link_BETA1-4 : bond 0.00352 / 0.21 ( 15) link_BETA1-4 : angle 0.94063 / 0.62 ( 45) link_NAG-ASN : bond 0.00323 / 0.24 ( 48) link_NAG-ASN : angle 2.09064 / 1.68 ( 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 167 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 132 time to evaluate : 0.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.9062 (tt0) cc_final: 0.8482 (tm-30) REVERT: A 725 GLU cc_start: 0.8741 (tt0) cc_final: 0.8540 (tt0) REVERT: A 752 LEU cc_start: 0.8910 (mt) cc_final: 0.8584 (mp) REVERT: A 776 LYS cc_start: 0.8911 (tttt) cc_final: 0.8607 (tttm) REVERT: A 994 ASP cc_start: 0.8863 (t70) cc_final: 0.8496 (t0) REVERT: B 53 ASP cc_start: 0.8325 (t0) cc_final: 0.8072 (t0) REVERT: B 64 TRP cc_start: 0.7922 (t60) cc_final: 0.7576 (t60) REVERT: B 200 TYR cc_start: 0.7386 (m-80) cc_final: 0.6972 (m-80) REVERT: B 335 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8139 (tp) REVERT: B 421 TYR cc_start: 0.4537 (OUTLIER) cc_final: 0.3800 (m-10) REVERT: B 571 ASP cc_start: 0.8644 (OUTLIER) cc_final: 0.7697 (t0) REVERT: B 578 ASP cc_start: 0.8300 (t0) cc_final: 0.7770 (t70) REVERT: B 988 GLU cc_start: 0.8656 (mt-10) cc_final: 0.8302 (mt-10) REVERT: B 990 GLU cc_start: 0.8537 (tt0) cc_final: 0.7788 (pt0) REVERT: B 994 ASP cc_start: 0.8707 (t70) cc_final: 0.8356 (t0) REVERT: C 340 GLU cc_start: 0.8871 (mp0) cc_final: 0.8649 (mp0) REVERT: C 370 ASN cc_start: 0.8800 (m-40) cc_final: 0.8422 (p0) REVERT: C 390 LEU cc_start: 0.8969 (mt) cc_final: 0.8683 (mt) REVERT: C 452 LEU cc_start: 0.8711 (mt) cc_final: 0.8464 (mm) REVERT: C 556 ASN cc_start: 0.9100 (p0) cc_final: 0.8695 (t0) REVERT: C 565 PHE cc_start: 0.8140 (m-10) cc_final: 0.7913 (m-10) REVERT: C 571 ASP cc_start: 0.7929 (OUTLIER) cc_final: 0.7559 (t0) REVERT: C 582 LEU cc_start: 0.9302 (OUTLIER) cc_final: 0.9053 (tt) REVERT: C 643 PHE cc_start: 0.8013 (t80) cc_final: 0.7366 (t80) REVERT: C 786 LYS cc_start: 0.8754 (pttt) cc_final: 0.8290 (mmmt) REVERT: C 817 PHE cc_start: 0.8069 (t80) cc_final: 0.7757 (t80) REVERT: C 988 GLU cc_start: 0.8807 (mt-10) cc_final: 0.8215 (tp30) outliers start: 35 outliers final: 19 residues processed: 157 average time/residue: 0.1465 time to fit residues: 37.4003 Evaluate side-chains 140 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 116 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 916 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 28 optimal weight: 0.4980 chunk 274 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 chunk 186 optimal weight: 1.9990 chunk 133 optimal weight: 10.0000 chunk 235 optimal weight: 6.9990 chunk 222 optimal weight: 6.9990 chunk 290 optimal weight: 0.7980 chunk 203 optimal weight: 4.9990 chunk 84 optimal weight: 0.7980 chunk 202 optimal weight: 0.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.107434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.074454 restraints weight = 49796.235| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 3.35 r_work: 0.2986 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.3510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 24285 Z= 0.119 Angle : 0.530 12.819 33147 Z= 0.264 Chirality : 0.043 0.258 3948 Planarity : 0.003 0.037 4155 Dihedral : 4.329 55.934 3101 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.14 % Allowed : 8.89 % Favored : 89.97 % 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: 0.45 (0.16), residues: 2844 helix: 2.11 (0.21), residues: 672 sheet: 0.26 (0.19), residues: 627 loop : -0.48 (0.15), residues: 1545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 346 TYR 0.020 0.001 TYR C1067 PHE 0.044 0.001 PHE C 168 TRP 0.030 0.001 TRP C 353 HIS 0.002 0.000 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 (24186) covalent geometry : angle 0.50370 / 0.26 (32886) SS BOND : bond 0.00537 / 0.29 ( 36) SS BOND : angle 2.01201 / 1.17 ( 72) hydrogen bonds : bond 0.03224 / 2.05 ( 1013) hydrogen bonds : angle 5.14723 / 3.56 ( 2862) link_BETA1-4 : bond 0.00296 / 0.18 ( 15) link_BETA1-4 : angle 0.98262 / 0.65 ( 45) link_NAG-ASN : bond 0.00282 / 0.22 ( 48) link_NAG-ASN : angle 2.11122 / 1.69 ( 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 148 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 119 time to evaluate : 0.845 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.9066 (tt0) cc_final: 0.8542 (tm-30) REVERT: A 752 LEU cc_start: 0.8949 (mt) cc_final: 0.8620 (mp) REVERT: A 776 LYS cc_start: 0.8917 (tttt) cc_final: 0.8616 (tttm) REVERT: A 869 MET cc_start: 0.8850 (OUTLIER) cc_final: 0.8459 (mtm) REVERT: A 994 ASP cc_start: 0.8874 (t70) cc_final: 0.8509 (t0) REVERT: B 53 ASP cc_start: 0.8342 (t0) cc_final: 0.8133 (t0) REVERT: B 64 TRP cc_start: 0.7932 (t60) cc_final: 0.7601 (t60) REVERT: B 200 TYR cc_start: 0.7374 (m-80) cc_final: 0.6979 (m-80) REVERT: B 335 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8162 (tp) REVERT: B 421 TYR cc_start: 0.4516 (OUTLIER) cc_final: 0.3785 (m-10) REVERT: B 571 ASP cc_start: 0.8689 (OUTLIER) cc_final: 0.7888 (t0) REVERT: B 578 ASP cc_start: 0.8306 (t0) cc_final: 0.7779 (t70) REVERT: B 988 GLU cc_start: 0.8671 (mt-10) cc_final: 0.8315 (mt-10) REVERT: B 990 GLU cc_start: 0.8600 (tt0) cc_final: 0.7834 (pt0) REVERT: B 994 ASP cc_start: 0.8759 (t70) cc_final: 0.8407 (t0) REVERT: C 340 GLU cc_start: 0.8875 (mp0) cc_final: 0.8662 (mp0) REVERT: C 370 ASN cc_start: 0.8816 (m-40) cc_final: 0.8338 (p0) REVERT: C 390 LEU cc_start: 0.9008 (mt) cc_final: 0.8768 (mt) REVERT: C 400 PHE cc_start: 0.8565 (p90) cc_final: 0.8267 (p90) REVERT: C 452 LEU cc_start: 0.8696 (mt) cc_final: 0.8451 (mm) REVERT: C 556 ASN cc_start: 0.9083 (p0) cc_final: 0.8660 (t0) REVERT: C 565 PHE cc_start: 0.8119 (m-10) cc_final: 0.7896 (m-10) REVERT: C 571 ASP cc_start: 0.8052 (OUTLIER) cc_final: 0.7683 (t0) REVERT: C 582 LEU cc_start: 0.9337 (OUTLIER) cc_final: 0.9080 (tt) REVERT: C 643 PHE cc_start: 0.7952 (t80) cc_final: 0.7275 (t80) REVERT: C 786 LYS cc_start: 0.8751 (pttt) cc_final: 0.8297 (mmmt) REVERT: C 817 PHE cc_start: 0.8096 (t80) cc_final: 0.7778 (t80) REVERT: C 988 GLU cc_start: 0.8785 (mt-10) cc_final: 0.8238 (tp30) outliers start: 29 outliers final: 18 residues processed: 140 average time/residue: 0.1613 time to fit residues: 36.5350 Evaluate side-chains 136 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 112 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 977 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 170 optimal weight: 0.7980 chunk 112 optimal weight: 9.9990 chunk 206 optimal weight: 7.9990 chunk 63 optimal weight: 4.9990 chunk 223 optimal weight: 2.9990 chunk 27 optimal weight: 9.9990 chunk 5 optimal weight: 10.0000 chunk 230 optimal weight: 8.9990 chunk 224 optimal weight: 3.9990 chunk 196 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 804 GLN B 901 GLN C 655 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.104312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.070889 restraints weight = 50417.088| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 3.41 r_work: 0.2905 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.3471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 24285 Z= 0.243 Angle : 0.613 13.214 33147 Z= 0.306 Chirality : 0.045 0.269 3948 Planarity : 0.004 0.035 4155 Dihedral : 4.595 55.804 3101 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 1.02 % Allowed : 9.09 % Favored : 89.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.15), residues: 2844 helix: 1.75 (0.20), residues: 686 sheet: 0.13 (0.19), residues: 644 loop : -0.58 (0.15), residues: 1514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 346 TYR 0.029 0.001 TYR B 380 PHE 0.026 0.002 PHE C 168 TRP 0.032 0.002 TRP C 353 HIS 0.006 0.001 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00569 / 0.24 (24186) covalent geometry : angle 0.58523 / 0.30 (32886) SS BOND : bond 0.00537 / 0.34 ( 36) SS BOND : angle 2.32483 / 1.35 ( 72) hydrogen bonds : bond 0.03744 / 2.37 ( 1013) hydrogen bonds : angle 5.44236 / 3.77 ( 2862) link_BETA1-4 : bond 0.00213 / 0.13 ( 15) link_BETA1-4 : angle 1.06202 / 0.69 ( 45) link_NAG-ASN : bond 0.00376 / 0.26 ( 48) link_NAG-ASN : angle 2.28412 / 1.80 ( 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 133 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 107 time to evaluate : 0.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.9096 (tt0) cc_final: 0.8558 (tm-30) REVERT: A 776 LYS cc_start: 0.8927 (tttt) cc_final: 0.8568 (tttm) REVERT: A 869 MET cc_start: 0.8880 (OUTLIER) cc_final: 0.8483 (mtm) REVERT: A 994 ASP cc_start: 0.8960 (t70) cc_final: 0.8598 (t0) REVERT: B 64 TRP cc_start: 0.8089 (t60) cc_final: 0.7836 (t60) REVERT: B 200 TYR cc_start: 0.7600 (m-80) cc_final: 0.7173 (m-80) REVERT: B 335 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8107 (tp) REVERT: B 378 LYS cc_start: 0.8637 (ptpp) cc_final: 0.8332 (ptpp) REVERT: B 421 TYR cc_start: 0.4523 (OUTLIER) cc_final: 0.3787 (m-10) REVERT: B 571 ASP cc_start: 0.8757 (OUTLIER) cc_final: 0.7976 (t0) REVERT: B 578 ASP cc_start: 0.8377 (t0) cc_final: 0.7849 (t70) REVERT: B 988 GLU cc_start: 0.8648 (mt-10) cc_final: 0.8303 (mt-10) REVERT: B 990 GLU cc_start: 0.8604 (tt0) cc_final: 0.7815 (pt0) REVERT: B 994 ASP cc_start: 0.8807 (t70) cc_final: 0.8458 (t0) REVERT: B 1050 MET cc_start: 0.8102 (ptm) cc_final: 0.7840 (ptt) REVERT: C 340 GLU cc_start: 0.8881 (mp0) cc_final: 0.8671 (mp0) REVERT: C 357 ARG cc_start: 0.8170 (ttt180) cc_final: 0.7839 (tmt170) REVERT: C 390 LEU cc_start: 0.9053 (mt) cc_final: 0.8800 (mt) REVERT: C 400 PHE cc_start: 0.8589 (p90) cc_final: 0.8289 (p90) REVERT: C 452 LEU cc_start: 0.8723 (mt) cc_final: 0.8480 (mm) REVERT: C 556 ASN cc_start: 0.9210 (p0) cc_final: 0.8746 (t0) REVERT: C 565 PHE cc_start: 0.8111 (m-10) cc_final: 0.7856 (m-10) REVERT: C 571 ASP cc_start: 0.8235 (OUTLIER) cc_final: 0.7800 (t0) REVERT: C 817 PHE cc_start: 0.8239 (t80) cc_final: 0.7859 (t80) REVERT: C 988 GLU cc_start: 0.8753 (mt-10) cc_final: 0.8330 (tp30) outliers start: 26 outliers final: 18 residues processed: 126 average time/residue: 0.1499 time to fit residues: 30.4494 Evaluate side-chains 126 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 103 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 977 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 253 optimal weight: 2.9990 chunk 273 optimal weight: 3.9990 chunk 150 optimal weight: 6.9990 chunk 47 optimal weight: 10.0000 chunk 199 optimal weight: 0.6980 chunk 287 optimal weight: 0.2980 chunk 13 optimal weight: 9.9990 chunk 123 optimal weight: 4.9990 chunk 206 optimal weight: 4.9990 chunk 166 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 762 GLN B 901 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.104921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.071632 restraints weight = 50073.276| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 3.40 r_work: 0.2926 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.3548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.098 24285 Z= 0.184 Angle : 0.573 12.967 33147 Z= 0.287 Chirality : 0.044 0.261 3948 Planarity : 0.003 0.036 4155 Dihedral : 4.530 55.094 3101 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.02 % Allowed : 9.28 % Favored : 89.70 % 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: 1.74 (0.20), residues: 688 sheet: 0.09 (0.19), residues: 643 loop : -0.61 (0.15), residues: 1513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 346 TYR 0.022 0.001 TYR C1067 PHE 0.025 0.001 PHE C 168 TRP 0.030 0.002 TRP C 353 HIS 0.010 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.18 (24186) covalent geometry : angle 0.54544 / 0.28 (32886) SS BOND : bond 0.00484 / 0.31 ( 36) SS BOND : angle 2.27758 / 1.34 ( 72) hydrogen bonds : bond 0.03534 / 2.24 ( 1013) hydrogen bonds : angle 5.36340 / 3.71 ( 2862) link_BETA1-4 : bond 0.00305 / 0.18 ( 15) link_BETA1-4 : angle 1.00674 / 0.66 ( 45) link_NAG-ASN : bond 0.00304 / 0.23 ( 48) link_NAG-ASN : angle 2.18955 / 1.74 ( 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 131 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 105 time to evaluate : 0.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.9136 (tt0) cc_final: 0.8629 (tm-30) REVERT: A 346 ARG cc_start: 0.8234 (tpt170) cc_final: 0.8016 (tpt170) REVERT: A 776 LYS cc_start: 0.8939 (tttt) cc_final: 0.8562 (tttm) REVERT: A 869 MET cc_start: 0.8840 (OUTLIER) cc_final: 0.8448 (mtm) REVERT: A 994 ASP cc_start: 0.8956 (t70) cc_final: 0.8591 (t0) REVERT: B 64 TRP cc_start: 0.8056 (t60) cc_final: 0.7792 (t60) REVERT: B 200 TYR cc_start: 0.7602 (m-80) cc_final: 0.7189 (m-80) REVERT: B 335 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8104 (tp) REVERT: B 378 LYS cc_start: 0.8641 (ptpp) cc_final: 0.8339 (ptpp) REVERT: B 421 TYR cc_start: 0.4518 (OUTLIER) cc_final: 0.3753 (m-10) REVERT: B 571 ASP cc_start: 0.8742 (OUTLIER) cc_final: 0.7311 (t0) REVERT: B 578 ASP cc_start: 0.8370 (t0) cc_final: 0.7801 (t70) REVERT: B 988 GLU cc_start: 0.8659 (mt-10) cc_final: 0.8310 (mt-10) REVERT: B 990 GLU cc_start: 0.8567 (tt0) cc_final: 0.7776 (pt0) REVERT: B 994 ASP cc_start: 0.8781 (t70) cc_final: 0.8415 (t0) REVERT: C 340 GLU cc_start: 0.8849 (mp0) cc_final: 0.8631 (mp0) REVERT: C 357 ARG cc_start: 0.8081 (ttt180) cc_final: 0.7720 (tmt170) REVERT: C 390 LEU cc_start: 0.9055 (mt) cc_final: 0.8765 (mt) REVERT: C 400 PHE cc_start: 0.8591 (p90) cc_final: 0.8307 (p90) REVERT: C 556 ASN cc_start: 0.9209 (p0) cc_final: 0.8733 (t0) REVERT: C 565 PHE cc_start: 0.8084 (m-10) cc_final: 0.7819 (m-10) REVERT: C 571 ASP cc_start: 0.8278 (OUTLIER) cc_final: 0.7854 (t0) REVERT: C 817 PHE cc_start: 0.8174 (t80) cc_final: 0.7774 (t80) REVERT: C 988 GLU cc_start: 0.8739 (mt-10) cc_final: 0.8341 (tp30) outliers start: 26 outliers final: 20 residues processed: 125 average time/residue: 0.1522 time to fit residues: 30.7021 Evaluate side-chains 127 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 102 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 977 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 218 optimal weight: 0.6980 chunk 40 optimal weight: 8.9990 chunk 207 optimal weight: 4.9990 chunk 166 optimal weight: 3.9990 chunk 178 optimal weight: 0.9990 chunk 268 optimal weight: 0.9980 chunk 105 optimal weight: 9.9990 chunk 280 optimal weight: 2.9990 chunk 168 optimal weight: 3.9990 chunk 4 optimal weight: 10.0000 chunk 231 optimal weight: 20.0000 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.104897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.071591 restraints weight = 50118.099| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 3.40 r_work: 0.2924 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.3604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 24285 Z= 0.182 Angle : 0.574 12.925 33147 Z= 0.286 Chirality : 0.044 0.263 3948 Planarity : 0.003 0.036 4155 Dihedral : 4.515 54.968 3101 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.06 % Allowed : 9.44 % Favored : 89.50 % 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: 0.17 (0.15), residues: 2844 helix: 1.73 (0.20), residues: 688 sheet: 0.08 (0.19), residues: 636 loop : -0.61 (0.15), residues: 1520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 346 TYR 0.023 0.001 TYR C1067 PHE 0.022 0.001 PHE C 168 TRP 0.029 0.002 TRP C 353 HIS 0.009 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.18 (24186) covalent geometry : angle 0.54688 / 0.28 (32886) SS BOND : bond 0.00489 / 0.32 ( 36) SS BOND : angle 2.19466 / 1.29 ( 72) hydrogen bonds : bond 0.03517 / 2.23 ( 1013) hydrogen bonds : angle 5.35334 / 3.70 ( 2862) link_BETA1-4 : bond 0.00251 / 0.15 ( 15) link_BETA1-4 : angle 0.98441 / 0.64 ( 45) link_NAG-ASN : bond 0.00310 / 0.23 ( 48) link_NAG-ASN : angle 2.17879 / 1.73 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4587.15 seconds wall clock time: 79 minutes 48.86 seconds (4788.86 seconds total)