Starting phenix.real_space_refine on Thu Mar 5 16:16:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7kdi_22823/03_2026/7kdi_22823.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kdi_22823/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7kdi_22823/03_2026/7kdi_22823.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kdi_22823/03_2026/7kdi_22823.map" model { file = "/net/cci-nas-00/data/ceres_data/7kdi_22823/03_2026/7kdi_22823.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kdi_22823/03_2026/7kdi_22823.cif" } 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "C" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Time building chain proxies: 6.00, per 1000 atoms: 0.25 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 968.7 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: 1.09 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: 6.20 Time building geometry restraints manager: 2.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 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: 14240 17.97 - 35.94: 792 35.94 - 53.91: 110 53.91 - 71.88: 40 71.88 - 89.85: 31 Dihedral angle restraints: 15213 sinusoidal: 6729 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 15210 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: 1.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 24.790 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 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 : 12.192 89.850 9627 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 covalent geometry : bond 0.01354 (24186) covalent geometry : angle 1.70471 (32886) SS BOND : bond 0.01266 ( 36) SS BOND : angle 2.09489 ( 72) hydrogen bonds : bond 0.14635 ( 1013) hydrogen bonds : angle 8.39610 ( 2862) link_BETA1-4 : bond 0.02531 ( 15) link_BETA1-4 : angle 4.49505 ( 45) link_NAG-ASN : bond 0.01086 ( 48) link_NAG-ASN : angle 4.61217 ( 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 : 0.890 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: 0.1995 time to fit residues: 77.7495 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 : 0.894 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 762 GLN A 913 GLN A 955 ASN A 957 GLN B 321 GLN B 394 ASN B 498 GLN B1088 HIS C 957 GLN C1088 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.107602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.074422 restraints weight = 49945.369| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 3.41 r_work: 0.2978 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.2056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.095 24285 Z= 0.142 Angle : 0.702 14.062 33147 Z= 0.356 Chirality : 0.047 0.250 3948 Planarity : 0.004 0.037 4155 Dihedral : 6.121 56.938 4428 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 0.94 % Allowed : 4.74 % Favored : 94.32 % 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: 1.28 (0.20), residues: 673 sheet: 0.13 (0.19), residues: 665 loop : -0.61 (0.15), residues: 1506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 214 TYR 0.023 0.002 TYR C 495 PHE 0.024 0.002 PHE A 201 TRP 0.042 0.002 TRP B 64 HIS 0.007 0.001 HIS B 66 Details of bonding type rmsd covalent geometry : bond 0.00313 (24186) covalent geometry : angle 0.65055 (32886) SS BOND : bond 0.00721 ( 36) SS BOND : angle 2.16231 ( 72) hydrogen bonds : bond 0.04518 ( 1013) hydrogen bonds : angle 6.25821 ( 2862) link_BETA1-4 : bond 0.00389 ( 15) link_BETA1-4 : angle 1.65572 ( 45) link_NAG-ASN : bond 0.00355 ( 48) link_NAG-ASN : angle 3.67146 ( 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 177 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 153 time to evaluate : 0.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 64 TRP cc_start: 0.7760 (t60) cc_final: 0.7423 (t60) REVERT: B 200 TYR cc_start: 0.7829 (m-80) cc_final: 0.7297 (m-80) REVERT: B 578 ASP cc_start: 0.8154 (t0) cc_final: 0.7815 (t70) REVERT: B 878 LEU cc_start: 0.8382 (tp) cc_final: 0.8072 (tp) REVERT: B 882 ILE cc_start: 0.9050 (mt) cc_final: 0.8730 (mp) REVERT: B 994 ASP cc_start: 0.8688 (t70) cc_final: 0.8278 (t0) REVERT: C 314 GLN cc_start: 0.8452 (OUTLIER) cc_final: 0.8200 (mm-40) REVERT: C 357 ARG cc_start: 0.8431 (ttt180) cc_final: 0.8218 (ttt180) REVERT: C 390 LEU cc_start: 0.8945 (mt) cc_final: 0.8670 (mt) REVERT: C 643 PHE cc_start: 0.8011 (t80) cc_final: 0.7729 (t80) REVERT: C 988 GLU cc_start: 0.8733 (mt-10) cc_final: 0.8244 (tp30) outliers start: 24 outliers final: 15 residues processed: 173 average time/residue: 0.1692 time to fit residues: 46.4968 Evaluate side-chains 119 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 103 time to evaluate : 0.902 ------------------------------------------------------------------------------- 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 773 GLU 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 571 ASP Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 314 GLN 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: 9.9990 chunk 10 optimal weight: 20.0000 chunk 151 optimal weight: 2.9990 chunk 85 optimal weight: 0.5980 chunk 248 optimal weight: 4.9990 chunk 150 optimal weight: 3.9990 chunk 82 optimal weight: 4.9990 chunk 178 optimal weight: 1.9990 chunk 154 optimal weight: 0.9980 chunk 244 optimal weight: 0.0870 chunk 6 optimal weight: 7.9990 overall best weight: 1.3362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 804 GLN A1088 HIS B 207 HIS C 207 HIS C 556 ASN C 762 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.106467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.073174 restraints weight = 50346.502| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 3.42 r_work: 0.2954 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.2477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 24285 Z= 0.144 Angle : 0.612 13.536 33147 Z= 0.310 Chirality : 0.045 0.229 3948 Planarity : 0.004 0.046 4155 Dihedral : 5.441 59.438 4424 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.37 % Allowed : 5.41 % Favored : 93.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.15), residues: 2844 helix: 1.61 (0.20), residues: 675 sheet: 0.08 (0.19), residues: 656 loop : -0.53 (0.15), residues: 1513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 214 TYR 0.023 0.001 TYR C1067 PHE 0.026 0.001 PHE C 400 TRP 0.029 0.002 TRP C 353 HIS 0.006 0.001 HIS B 66 Details of bonding type rmsd covalent geometry : bond 0.00335 (24186) covalent geometry : angle 0.57124 (32886) SS BOND : bond 0.00521 ( 36) SS BOND : angle 2.10847 ( 72) hydrogen bonds : bond 0.04018 ( 1013) hydrogen bonds : angle 5.82989 ( 2862) link_BETA1-4 : bond 0.00316 ( 15) link_BETA1-4 : angle 1.41711 ( 45) link_NAG-ASN : bond 0.00285 ( 48) link_NAG-ASN : angle 2.98455 ( 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 146 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 111 time to evaluate : 0.771 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 346 ARG cc_start: 0.7980 (tpt170) cc_final: 0.7547 (tpt170) REVERT: A 869 MET cc_start: 0.8883 (mtm) cc_final: 0.8642 (mtp) REVERT: A 994 ASP cc_start: 0.8878 (t70) cc_final: 0.8633 (t0) REVERT: B 53 ASP cc_start: 0.8200 (t0) cc_final: 0.7961 (t0) REVERT: B 64 TRP cc_start: 0.7862 (t60) cc_final: 0.7523 (t60) REVERT: B 200 TYR cc_start: 0.7764 (m-80) cc_final: 0.7240 (m-80) REVERT: B 421 TYR cc_start: 0.4467 (OUTLIER) cc_final: 0.3946 (m-10) REVERT: B 578 ASP cc_start: 0.8180 (t0) cc_final: 0.7803 (t70) REVERT: B 994 ASP cc_start: 0.8722 (t70) cc_final: 0.8340 (t0) REVERT: C 390 LEU cc_start: 0.9101 (mt) cc_final: 0.8814 (mt) REVERT: C 643 PHE cc_start: 0.8052 (t80) cc_final: 0.7734 (t80) REVERT: C 817 PHE cc_start: 0.8023 (t80) cc_final: 0.7607 (t80) REVERT: C 988 GLU cc_start: 0.8802 (mt-10) cc_final: 0.8275 (tp30) outliers start: 35 outliers final: 18 residues processed: 141 average time/residue: 0.1682 time to fit residues: 38.1370 Evaluate side-chains 111 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 92 time to evaluate : 0.865 ------------------------------------------------------------------------------- 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 62 VAL Chi-restraints excluded: chain B residue 116 SER 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 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 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: 9.9990 chunk 131 optimal weight: 0.8980 chunk 32 optimal weight: 0.0570 chunk 208 optimal weight: 7.9990 chunk 99 optimal weight: 7.9990 chunk 179 optimal weight: 3.9990 chunk 194 optimal weight: 6.9990 overall best weight: 0.9902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 872 GLN A 935 GLN B 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 = 0.3705 r_free = 0.3705 target = 0.106911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.073940 restraints weight = 49918.272| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 3.34 r_work: 0.2973 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.2799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.093 24285 Z= 0.125 Angle : 0.578 13.598 33147 Z= 0.290 Chirality : 0.044 0.253 3948 Planarity : 0.003 0.036 4155 Dihedral : 5.043 58.593 4424 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.37 % Allowed : 6.54 % Favored : 92.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.15), residues: 2844 helix: 1.84 (0.20), residues: 676 sheet: 0.13 (0.19), residues: 639 loop : -0.51 (0.15), residues: 1529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 214 TYR 0.022 0.001 TYR C1067 PHE 0.021 0.001 PHE C 400 TRP 0.041 0.002 TRP A 64 HIS 0.006 0.001 HIS B 66 Details of bonding type rmsd covalent geometry : bond 0.00290 (24186) covalent geometry : angle 0.54049 (32886) SS BOND : bond 0.00540 ( 36) SS BOND : angle 2.07185 ( 72) hydrogen bonds : bond 0.03585 ( 1013) hydrogen bonds : angle 5.57341 ( 2862) link_BETA1-4 : bond 0.00428 ( 15) link_BETA1-4 : angle 1.25423 ( 45) link_NAG-ASN : bond 0.00420 ( 48) link_NAG-ASN : angle 2.72984 ( 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 147 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 112 time to evaluate : 0.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 346 ARG cc_start: 0.7989 (tpt170) cc_final: 0.7677 (tpt170) REVERT: A 776 LYS cc_start: 0.8916 (tttt) cc_final: 0.8604 (tttm) REVERT: A 935 GLN cc_start: 0.8694 (OUTLIER) cc_final: 0.8233 (mt0) REVERT: A 994 ASP cc_start: 0.8889 (t70) cc_final: 0.8515 (t0) REVERT: B 53 ASP cc_start: 0.8261 (t0) cc_final: 0.7994 (t70) REVERT: B 64 TRP cc_start: 0.7871 (t60) cc_final: 0.7511 (t60) REVERT: B 168 PHE cc_start: 0.7684 (t80) cc_final: 0.7469 (t80) REVERT: B 200 TYR cc_start: 0.7629 (m-80) cc_final: 0.7112 (m-80) REVERT: B 378 LYS cc_start: 0.8598 (ttmt) cc_final: 0.8271 (ptpp) REVERT: B 421 TYR cc_start: 0.4239 (OUTLIER) cc_final: 0.3758 (m-10) REVERT: B 578 ASP cc_start: 0.8199 (t0) cc_final: 0.7743 (t70) REVERT: B 988 GLU cc_start: 0.8546 (mt-10) cc_final: 0.8227 (mt-10) REVERT: B 994 ASP cc_start: 0.8746 (t70) cc_final: 0.8373 (t0) REVERT: C 340 GLU cc_start: 0.8888 (mp0) cc_final: 0.8668 (mp0) REVERT: C 390 LEU cc_start: 0.9045 (mt) cc_final: 0.8775 (mt) REVERT: C 452 LEU cc_start: 0.8842 (mt) cc_final: 0.8553 (tt) REVERT: C 571 ASP cc_start: 0.7703 (OUTLIER) cc_final: 0.7185 (t0) REVERT: C 643 PHE cc_start: 0.8051 (t80) cc_final: 0.7706 (t80) REVERT: C 817 PHE cc_start: 0.8078 (t80) cc_final: 0.7708 (t80) REVERT: C 988 GLU cc_start: 0.8826 (mt-10) cc_final: 0.8265 (tp30) outliers start: 35 outliers final: 21 residues processed: 140 average time/residue: 0.1630 time to fit residues: 36.8714 Evaluate side-chains 126 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 102 time to evaluate : 0.856 ------------------------------------------------------------------------------- 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 760 CYS Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1119 ASN 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 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 856 ASN 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: 7.9990 chunk 165 optimal weight: 5.9990 chunk 63 optimal weight: 4.9990 chunk 151 optimal weight: 0.9980 chunk 122 optimal weight: 3.9990 chunk 268 optimal weight: 3.9990 chunk 163 optimal weight: 0.0170 chunk 51 optimal weight: 0.9990 chunk 127 optimal weight: 0.5980 chunk 220 optimal weight: 8.9990 chunk 28 optimal weight: 0.0070 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 804 GLN A 935 GLN B 762 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.108023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.075091 restraints weight = 49652.172| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 3.34 r_work: 0.2995 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.3024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 24285 Z= 0.101 Angle : 0.540 13.140 33147 Z= 0.271 Chirality : 0.043 0.254 3948 Planarity : 0.003 0.036 4155 Dihedral : 4.746 57.831 4424 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.29 % Allowed : 7.29 % Favored : 91.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.15), residues: 2844 helix: 2.06 (0.20), residues: 675 sheet: 0.18 (0.19), residues: 629 loop : -0.50 (0.15), residues: 1540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 214 TYR 0.024 0.001 TYR B 380 PHE 0.019 0.001 PHE A 400 TRP 0.027 0.002 TRP C 353 HIS 0.004 0.000 HIS B 66 Details of bonding type rmsd covalent geometry : bond 0.00221 (24186) covalent geometry : angle 0.50891 (32886) SS BOND : bond 0.00667 ( 36) SS BOND : angle 1.74943 ( 72) hydrogen bonds : bond 0.03341 ( 1013) hydrogen bonds : angle 5.33607 ( 2862) link_BETA1-4 : bond 0.00385 ( 15) link_BETA1-4 : angle 1.14202 ( 45) link_NAG-ASN : bond 0.00310 ( 48) link_NAG-ASN : angle 2.47229 ( 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 151 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 118 time to evaluate : 0.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 346 ARG cc_start: 0.7950 (tpt170) cc_final: 0.7617 (tpt170) REVERT: A 752 LEU cc_start: 0.8851 (mt) cc_final: 0.8531 (mp) REVERT: A 776 LYS cc_start: 0.8952 (tttt) cc_final: 0.8592 (tttm) REVERT: A 994 ASP cc_start: 0.8873 (t70) cc_final: 0.8494 (t0) REVERT: B 53 ASP cc_start: 0.8273 (t0) cc_final: 0.8051 (t70) REVERT: B 64 TRP cc_start: 0.7872 (t60) cc_final: 0.7543 (t60) REVERT: B 200 TYR cc_start: 0.7560 (m-80) cc_final: 0.7088 (m-80) REVERT: B 421 TYR cc_start: 0.4035 (OUTLIER) cc_final: 0.3598 (m-10) REVERT: B 578 ASP cc_start: 0.8248 (t0) cc_final: 0.7762 (t70) REVERT: B 988 GLU cc_start: 0.8579 (mt-10) cc_final: 0.8199 (mt-10) REVERT: B 994 ASP cc_start: 0.8727 (t70) cc_final: 0.8351 (t0) REVERT: B 1096 VAL cc_start: 0.8639 (OUTLIER) cc_final: 0.8366 (m) REVERT: C 340 GLU cc_start: 0.8860 (mp0) cc_final: 0.8642 (mp0) REVERT: C 390 LEU cc_start: 0.9014 (mt) cc_final: 0.8750 (mt) REVERT: C 452 LEU cc_start: 0.8854 (mt) cc_final: 0.8599 (mm) REVERT: C 556 ASN cc_start: 0.8879 (t160) cc_final: 0.8580 (t0) REVERT: C 565 PHE cc_start: 0.8185 (m-10) cc_final: 0.7957 (m-10) REVERT: C 571 ASP cc_start: 0.7826 (OUTLIER) cc_final: 0.7398 (t0) REVERT: C 582 LEU cc_start: 0.9232 (OUTLIER) cc_final: 0.9002 (tt) REVERT: C 643 PHE cc_start: 0.8010 (t80) cc_final: 0.7642 (t80) REVERT: C 817 PHE cc_start: 0.8065 (t80) cc_final: 0.7690 (t80) REVERT: C 988 GLU cc_start: 0.8812 (mt-10) cc_final: 0.8194 (tp30) outliers start: 33 outliers final: 14 residues processed: 144 average time/residue: 0.1594 time to fit residues: 36.8546 Evaluate side-chains 123 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 105 time to evaluate : 0.947 ------------------------------------------------------------------------------- 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 1032 CYS Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain B residue 242 LEU 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 1096 VAL Chi-restraints excluded: chain C residue 48 LEU 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: 0.9990 chunk 57 optimal weight: 1.9990 chunk 39 optimal weight: 9.9990 chunk 147 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 chunk 14 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 46 optimal weight: 7.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 394 ASN B 762 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.106742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.073667 restraints weight = 49979.880| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 3.34 r_work: 0.2963 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.3147 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= 0.140 Angle : 0.546 13.091 33147 Z= 0.274 Chirality : 0.043 0.256 3948 Planarity : 0.003 0.036 4155 Dihedral : 4.635 56.606 4424 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.57 % Allowed : 7.52 % Favored : 90.91 % 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: 0.38 (0.15), residues: 2844 helix: 2.07 (0.21), residues: 673 sheet: 0.12 (0.19), residues: 639 loop : -0.50 (0.15), residues: 1532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 214 TYR 0.027 0.001 TYR B 380 PHE 0.024 0.001 PHE A 168 TRP 0.030 0.001 TRP C 353 HIS 0.002 0.001 HIS A1058 Details of bonding type rmsd covalent geometry : bond 0.00326 (24186) covalent geometry : angle 0.51517 (32886) SS BOND : bond 0.00575 ( 36) SS BOND : angle 1.95669 ( 72) hydrogen bonds : bond 0.03425 ( 1013) hydrogen bonds : angle 5.33624 ( 2862) link_BETA1-4 : bond 0.00323 ( 15) link_BETA1-4 : angle 1.12474 ( 45) link_NAG-ASN : bond 0.00295 ( 48) link_NAG-ASN : angle 2.38441 ( 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 149 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 109 time to evaluate : 0.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.9075 (tt0) cc_final: 0.8426 (tm-30) REVERT: A 200 TYR cc_start: 0.7169 (m-80) cc_final: 0.6892 (m-80) REVERT: A 346 ARG cc_start: 0.7929 (tpt170) cc_final: 0.7602 (tpt170) REVERT: A 752 LEU cc_start: 0.8871 (mt) cc_final: 0.8545 (mp) REVERT: A 776 LYS cc_start: 0.8952 (tttt) cc_final: 0.8583 (tttm) REVERT: A 869 MET cc_start: 0.8859 (OUTLIER) cc_final: 0.8463 (mtm) REVERT: A 994 ASP cc_start: 0.8897 (t70) cc_final: 0.8521 (t0) REVERT: B 53 ASP cc_start: 0.8280 (t0) cc_final: 0.8034 (t70) REVERT: B 64 TRP cc_start: 0.7888 (t60) cc_final: 0.7562 (t60) REVERT: B 200 TYR cc_start: 0.7660 (m-80) cc_final: 0.7167 (m-80) REVERT: B 335 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8189 (tp) REVERT: B 421 TYR cc_start: 0.4174 (OUTLIER) cc_final: 0.3657 (m-10) REVERT: B 578 ASP cc_start: 0.8296 (t0) cc_final: 0.7777 (t70) REVERT: B 988 GLU cc_start: 0.8583 (mt-10) cc_final: 0.8169 (mt-10) REVERT: B 994 ASP cc_start: 0.8762 (t70) cc_final: 0.8389 (t0) REVERT: B 1096 VAL cc_start: 0.8671 (OUTLIER) cc_final: 0.8371 (m) REVERT: C 340 GLU cc_start: 0.8902 (mp0) cc_final: 0.8682 (mp0) REVERT: C 390 LEU cc_start: 0.9006 (mt) cc_final: 0.8763 (mt) REVERT: C 556 ASN cc_start: 0.8914 (t160) cc_final: 0.8573 (t0) REVERT: C 565 PHE cc_start: 0.8173 (m-10) cc_final: 0.7946 (m-10) REVERT: C 571 ASP cc_start: 0.7882 (OUTLIER) cc_final: 0.7441 (t0) REVERT: C 582 LEU cc_start: 0.9263 (OUTLIER) cc_final: 0.9031 (tt) REVERT: C 643 PHE cc_start: 0.7995 (t80) cc_final: 0.7569 (t80) REVERT: C 817 PHE cc_start: 0.8095 (t80) cc_final: 0.7724 (t80) REVERT: C 988 GLU cc_start: 0.8809 (mt-10) cc_final: 0.8219 (tp30) REVERT: C 1050 MET cc_start: 0.8205 (ptt) cc_final: 0.7851 (ptt) outliers start: 40 outliers final: 20 residues processed: 139 average time/residue: 0.1615 time to fit residues: 35.9524 Evaluate side-chains 130 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 104 time to evaluate : 0.777 ------------------------------------------------------------------------------- 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 760 CYS 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 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 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 B residue 940 SER Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 242 LEU 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: 1.9990 chunk 26 optimal weight: 10.0000 chunk 19 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 chunk 16 optimal weight: 4.9990 chunk 10 optimal weight: 0.5980 chunk 243 optimal weight: 0.5980 chunk 245 optimal weight: 2.9990 chunk 262 optimal weight: 2.9990 chunk 260 optimal weight: 2.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.106870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.073614 restraints weight = 49927.860| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 3.41 r_work: 0.2962 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.3293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 24285 Z= 0.133 Angle : 0.539 12.951 33147 Z= 0.271 Chirality : 0.043 0.259 3948 Planarity : 0.003 0.036 4155 Dihedral : 4.524 56.119 4424 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.37 % Allowed : 8.15 % 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: 0.40 (0.15), residues: 2844 helix: 2.05 (0.21), residues: 673 sheet: 0.21 (0.19), residues: 624 loop : -0.49 (0.15), residues: 1547 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 214 TYR 0.021 0.001 TYR C1067 PHE 0.020 0.001 PHE C 515 TRP 0.031 0.002 TRP C 353 HIS 0.002 0.000 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00309 (24186) covalent geometry : angle 0.50966 (32886) SS BOND : bond 0.00614 ( 36) SS BOND : angle 2.02436 ( 72) hydrogen bonds : bond 0.03396 ( 1013) hydrogen bonds : angle 5.30035 ( 2862) link_BETA1-4 : bond 0.00303 ( 15) link_BETA1-4 : angle 1.04773 ( 45) link_NAG-ASN : bond 0.00290 ( 48) link_NAG-ASN : angle 2.28691 ( 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 147 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 112 time to evaluate : 0.928 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.9068 (tt0) cc_final: 0.8432 (tm-30) REVERT: A 200 TYR cc_start: 0.7136 (m-80) cc_final: 0.6860 (m-80) REVERT: A 346 ARG cc_start: 0.7892 (tpt170) cc_final: 0.7567 (tpt170) REVERT: A 776 LYS cc_start: 0.8905 (tttt) cc_final: 0.8567 (tttm) REVERT: A 994 ASP cc_start: 0.8881 (t70) cc_final: 0.8517 (t0) REVERT: B 53 ASP cc_start: 0.8319 (t0) cc_final: 0.8071 (t0) REVERT: B 64 TRP cc_start: 0.7971 (t60) cc_final: 0.7649 (t60) REVERT: B 200 TYR cc_start: 0.7625 (m-80) cc_final: 0.7191 (m-80) REVERT: B 335 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8177 (tp) REVERT: B 421 TYR cc_start: 0.4412 (OUTLIER) cc_final: 0.3721 (m-10) REVERT: B 578 ASP cc_start: 0.8357 (t0) cc_final: 0.7799 (t70) REVERT: B 752 LEU cc_start: 0.8840 (mt) cc_final: 0.8566 (mp) REVERT: B 988 GLU cc_start: 0.8646 (mt-10) cc_final: 0.8214 (mt-10) REVERT: B 994 ASP cc_start: 0.8766 (t70) cc_final: 0.8401 (t0) REVERT: C 340 GLU cc_start: 0.8910 (mp0) cc_final: 0.8681 (mp0) REVERT: C 390 LEU cc_start: 0.8996 (mt) cc_final: 0.8753 (mt) REVERT: C 556 ASN cc_start: 0.8934 (t160) cc_final: 0.8640 (t0) REVERT: C 565 PHE cc_start: 0.8127 (m-10) cc_final: 0.7894 (m-10) REVERT: C 571 ASP cc_start: 0.8158 (OUTLIER) cc_final: 0.7756 (t0) REVERT: C 582 LEU cc_start: 0.9267 (OUTLIER) cc_final: 0.9061 (tp) REVERT: C 643 PHE cc_start: 0.7984 (t80) cc_final: 0.7297 (t80) REVERT: C 817 PHE cc_start: 0.8085 (t80) cc_final: 0.7728 (t80) REVERT: C 988 GLU cc_start: 0.8802 (mt-10) cc_final: 0.8198 (tp30) REVERT: C 1050 MET cc_start: 0.8349 (ptt) cc_final: 0.8148 (ptt) outliers start: 35 outliers final: 20 residues processed: 137 average time/residue: 0.1759 time to fit residues: 38.5421 Evaluate side-chains 130 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 106 time to evaluate : 0.992 ------------------------------------------------------------------------------- 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 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 395 VAL Chi-restraints excluded: chain B residue 421 TYR 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 242 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 28 optimal weight: 10.0000 chunk 274 optimal weight: 5.9990 chunk 71 optimal weight: 0.9990 chunk 186 optimal weight: 2.9990 chunk 133 optimal weight: 10.0000 chunk 235 optimal weight: 0.3980 chunk 222 optimal weight: 0.8980 chunk 290 optimal weight: 6.9990 chunk 203 optimal weight: 6.9990 chunk 84 optimal weight: 3.9990 chunk 202 optimal weight: 3.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 804 GLN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.105532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.072250 restraints weight = 49986.781| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 3.40 r_work: 0.2937 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.3373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 24285 Z= 0.177 Angle : 0.571 13.071 33147 Z= 0.286 Chirality : 0.044 0.264 3948 Planarity : 0.003 0.036 4155 Dihedral : 4.539 55.585 4424 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.41 % Allowed : 8.19 % Favored : 90.40 % 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: 0.29 (0.15), residues: 2844 helix: 1.88 (0.21), residues: 674 sheet: 0.15 (0.19), residues: 635 loop : -0.53 (0.15), residues: 1535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 346 TYR 0.024 0.001 TYR B 380 PHE 0.020 0.001 PHE A 168 TRP 0.031 0.002 TRP C 353 HIS 0.003 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00419 (24186) covalent geometry : angle 0.53945 (32886) SS BOND : bond 0.00494 ( 36) SS BOND : angle 2.36818 ( 72) hydrogen bonds : bond 0.03528 ( 1013) hydrogen bonds : angle 5.37446 ( 2862) link_BETA1-4 : bond 0.00306 ( 15) link_BETA1-4 : angle 1.09694 ( 45) link_NAG-ASN : bond 0.00316 ( 48) link_NAG-ASN : angle 2.31202 ( 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 142 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 106 time to evaluate : 0.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.9065 (tt0) cc_final: 0.8536 (tm-30) REVERT: A 200 TYR cc_start: 0.7136 (m-80) cc_final: 0.6839 (m-80) REVERT: A 346 ARG cc_start: 0.7896 (tpt170) cc_final: 0.7586 (tpt170) REVERT: A 776 LYS cc_start: 0.8915 (tttt) cc_final: 0.8549 (tttm) REVERT: A 869 MET cc_start: 0.8854 (OUTLIER) cc_final: 0.8448 (mtm) REVERT: A 994 ASP cc_start: 0.8911 (t70) cc_final: 0.8540 (t0) REVERT: B 53 ASP cc_start: 0.8339 (t0) cc_final: 0.8129 (t0) REVERT: B 64 TRP cc_start: 0.7986 (t60) cc_final: 0.7706 (t60) REVERT: B 200 TYR cc_start: 0.7576 (m-80) cc_final: 0.7131 (m-80) REVERT: B 335 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8135 (tp) REVERT: B 421 TYR cc_start: 0.4498 (OUTLIER) cc_final: 0.3779 (m-10) REVERT: B 571 ASP cc_start: 0.8689 (OUTLIER) cc_final: 0.7727 (t0) REVERT: B 578 ASP cc_start: 0.8363 (t0) cc_final: 0.7785 (t70) REVERT: B 988 GLU cc_start: 0.8679 (mt-10) cc_final: 0.8259 (mt-10) REVERT: B 994 ASP cc_start: 0.8791 (t70) cc_final: 0.8423 (t0) REVERT: C 340 GLU cc_start: 0.8880 (mp0) cc_final: 0.8651 (mp0) REVERT: C 390 LEU cc_start: 0.9022 (mt) cc_final: 0.8784 (mt) REVERT: C 556 ASN cc_start: 0.8946 (t160) cc_final: 0.8677 (t0) REVERT: C 565 PHE cc_start: 0.8118 (m-10) cc_final: 0.7883 (m-10) REVERT: C 571 ASP cc_start: 0.8211 (OUTLIER) cc_final: 0.7773 (t0) REVERT: C 582 LEU cc_start: 0.9353 (OUTLIER) cc_final: 0.9138 (tp) REVERT: C 817 PHE cc_start: 0.8160 (t80) cc_final: 0.7794 (t80) REVERT: C 988 GLU cc_start: 0.8790 (mt-10) cc_final: 0.8209 (tp30) outliers start: 36 outliers final: 23 residues processed: 131 average time/residue: 0.1611 time to fit residues: 34.0950 Evaluate side-chains 131 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 102 time to evaluate : 0.845 ------------------------------------------------------------------------------- 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 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 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 571 ASP Chi-restraints excluded: chain B residue 581 THR 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 242 LEU 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 645 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 170 optimal weight: 0.9980 chunk 112 optimal weight: 1.9990 chunk 206 optimal weight: 6.9990 chunk 63 optimal weight: 2.9990 chunk 223 optimal weight: 2.9990 chunk 27 optimal weight: 6.9990 chunk 5 optimal weight: 9.9990 chunk 230 optimal weight: 10.0000 chunk 224 optimal weight: 5.9990 chunk 196 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 762 GLN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 655 HIS 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 = 0.104952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.071615 restraints weight = 50403.620| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 3.42 r_work: 0.2923 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.3422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.096 24285 Z= 0.201 Angle : 0.590 12.997 33147 Z= 0.294 Chirality : 0.044 0.261 3948 Planarity : 0.003 0.036 4155 Dihedral : 4.567 55.422 4424 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.41 % Allowed : 8.38 % Favored : 90.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.15), residues: 2844 helix: 1.66 (0.20), residues: 693 sheet: 0.13 (0.19), residues: 629 loop : -0.58 (0.15), residues: 1522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 346 TYR 0.023 0.001 TYR C1067 PHE 0.017 0.001 PHE B1121 TRP 0.032 0.002 TRP C 353 HIS 0.003 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00475 (24186) covalent geometry : angle 0.55795 (32886) SS BOND : bond 0.00533 ( 36) SS BOND : angle 2.55279 ( 72) hydrogen bonds : bond 0.03582 ( 1013) hydrogen bonds : angle 5.39615 ( 2862) link_BETA1-4 : bond 0.00273 ( 15) link_BETA1-4 : angle 1.08626 ( 45) link_NAG-ASN : bond 0.00322 ( 48) link_NAG-ASN : angle 2.30641 ( 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 141 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 105 time to evaluate : 0.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.9099 (tt0) cc_final: 0.8556 (tm-30) REVERT: A 346 ARG cc_start: 0.7883 (tpt170) cc_final: 0.7577 (tpt170) REVERT: A 776 LYS cc_start: 0.8920 (tttt) cc_final: 0.8545 (tttm) REVERT: A 869 MET cc_start: 0.8823 (OUTLIER) cc_final: 0.8419 (mtm) REVERT: A 994 ASP cc_start: 0.8942 (t70) cc_final: 0.8569 (t0) REVERT: B 64 TRP cc_start: 0.8059 (t60) cc_final: 0.7784 (t60) REVERT: B 200 TYR cc_start: 0.7605 (m-80) cc_final: 0.7156 (m-80) REVERT: B 335 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8130 (tp) REVERT: B 421 TYR cc_start: 0.4479 (OUTLIER) cc_final: 0.3751 (m-10) REVERT: B 571 ASP cc_start: 0.8691 (OUTLIER) cc_final: 0.7744 (t0) REVERT: B 578 ASP cc_start: 0.8421 (t0) cc_final: 0.7838 (t70) REVERT: B 988 GLU cc_start: 0.8701 (mt-10) cc_final: 0.8275 (mt-10) REVERT: B 994 ASP cc_start: 0.8790 (t70) cc_final: 0.8420 (t0) REVERT: C 340 GLU cc_start: 0.8887 (mp0) cc_final: 0.8654 (mp0) REVERT: C 390 LEU cc_start: 0.9015 (mt) cc_final: 0.8781 (mt) REVERT: C 556 ASN cc_start: 0.8989 (t160) cc_final: 0.8726 (t0) REVERT: C 565 PHE cc_start: 0.8104 (m-10) cc_final: 0.7870 (m-10) REVERT: C 571 ASP cc_start: 0.8256 (OUTLIER) cc_final: 0.7807 (t0) REVERT: C 582 LEU cc_start: 0.9358 (OUTLIER) cc_final: 0.9102 (tp) REVERT: C 643 PHE cc_start: 0.8159 (t80) cc_final: 0.7614 (t80) REVERT: C 817 PHE cc_start: 0.8188 (t80) cc_final: 0.7813 (t80) REVERT: C 988 GLU cc_start: 0.8798 (mt-10) cc_final: 0.8210 (tp30) outliers start: 36 outliers final: 27 residues processed: 130 average time/residue: 0.1679 time to fit residues: 35.0203 Evaluate side-chains 133 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 100 time to evaluate : 0.848 ------------------------------------------------------------------------------- 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 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 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 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 48 LEU Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 242 LEU 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 645 THR Chi-restraints excluded: chain C residue 810 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 253 optimal weight: 4.9990 chunk 273 optimal weight: 2.9990 chunk 150 optimal weight: 3.9990 chunk 47 optimal weight: 7.9990 chunk 199 optimal weight: 4.9990 chunk 287 optimal weight: 0.7980 chunk 13 optimal weight: 10.0000 chunk 123 optimal weight: 7.9990 chunk 206 optimal weight: 1.9990 chunk 166 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 519 HIS B1142 GLN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.104191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.070838 restraints weight = 50221.132| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 3.39 r_work: 0.2907 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.3497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 24285 Z= 0.226 Angle : 0.621 21.032 33147 Z= 0.307 Chirality : 0.045 0.268 3948 Planarity : 0.003 0.035 4155 Dihedral : 4.699 54.992 4424 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 1.37 % Allowed : 8.77 % Favored : 89.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.15), residues: 2844 helix: 1.57 (0.20), residues: 693 sheet: 0.02 (0.19), residues: 632 loop : -0.66 (0.15), residues: 1519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 346 TYR 0.024 0.001 TYR B 380 PHE 0.020 0.002 PHE A 168 TRP 0.033 0.002 TRP C 353 HIS 0.004 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00533 (24186) covalent geometry : angle 0.59167 (32886) SS BOND : bond 0.00530 ( 36) SS BOND : angle 2.45502 ( 72) hydrogen bonds : bond 0.03738 ( 1013) hydrogen bonds : angle 5.50004 ( 2862) link_BETA1-4 : bond 0.00242 ( 15) link_BETA1-4 : angle 1.10754 ( 45) link_NAG-ASN : bond 0.00358 ( 48) link_NAG-ASN : angle 2.35154 ( 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 140 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 105 time to evaluate : 0.870 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.9129 (tt0) cc_final: 0.8629 (tm-30) REVERT: A 346 ARG cc_start: 0.7907 (tpt170) cc_final: 0.7618 (tpt170) REVERT: A 776 LYS cc_start: 0.8946 (tttt) cc_final: 0.8570 (tttm) REVERT: A 869 MET cc_start: 0.8822 (OUTLIER) cc_final: 0.8410 (mtm) REVERT: A 994 ASP cc_start: 0.8968 (t70) cc_final: 0.8605 (t0) REVERT: A 1050 MET cc_start: 0.8263 (ptt) cc_final: 0.8001 (ptt) REVERT: B 200 TYR cc_start: 0.7748 (m-80) cc_final: 0.7304 (m-80) REVERT: B 335 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8125 (tp) REVERT: B 421 TYR cc_start: 0.4543 (OUTLIER) cc_final: 0.3781 (m-10) REVERT: B 571 ASP cc_start: 0.8685 (OUTLIER) cc_final: 0.7283 (t0) REVERT: B 578 ASP cc_start: 0.8395 (t0) cc_final: 0.7844 (t70) REVERT: B 988 GLU cc_start: 0.8722 (mt-10) cc_final: 0.8298 (mt-10) REVERT: B 994 ASP cc_start: 0.8803 (t70) cc_final: 0.8438 (t0) REVERT: C 340 GLU cc_start: 0.8870 (mp0) cc_final: 0.8649 (mp0) REVERT: C 390 LEU cc_start: 0.9034 (mt) cc_final: 0.8803 (mt) REVERT: C 556 ASN cc_start: 0.9013 (t160) cc_final: 0.8761 (t0) REVERT: C 565 PHE cc_start: 0.8104 (m-10) cc_final: 0.7873 (m-10) REVERT: C 571 ASP cc_start: 0.8357 (OUTLIER) cc_final: 0.7892 (t0) REVERT: C 582 LEU cc_start: 0.9331 (OUTLIER) cc_final: 0.9037 (tp) REVERT: C 817 PHE cc_start: 0.8221 (t80) cc_final: 0.7850 (t80) REVERT: C 988 GLU cc_start: 0.8800 (mt-10) cc_final: 0.8210 (tp30) outliers start: 35 outliers final: 26 residues processed: 128 average time/residue: 0.1685 time to fit residues: 34.8193 Evaluate side-chains 132 residues out of total 2553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 100 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU 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 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 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 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 48 LEU Chi-restraints excluded: chain C residue 242 LEU 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 645 THR Chi-restraints excluded: chain C residue 810 SER 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: 5.9990 chunk 207 optimal weight: 0.9990 chunk 166 optimal weight: 2.9990 chunk 178 optimal weight: 2.9990 chunk 268 optimal weight: 0.9990 chunk 105 optimal weight: 5.9990 chunk 280 optimal weight: 2.9990 chunk 168 optimal weight: 2.9990 chunk 4 optimal weight: 5.9990 chunk 231 optimal weight: 0.0270 overall best weight: 1.1444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 913 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.105883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.072787 restraints weight = 49894.902| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 3.40 r_work: 0.2948 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.3591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 24285 Z= 0.129 Angle : 0.557 12.782 33147 Z= 0.279 Chirality : 0.043 0.265 3948 Planarity : 0.003 0.036 4155 Dihedral : 4.482 54.298 4424 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.25 % Allowed : 8.85 % 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: 0.21 (0.15), residues: 2844 helix: 1.81 (0.21), residues: 686 sheet: 0.08 (0.19), residues: 629 loop : -0.59 (0.15), residues: 1529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 357 TYR 0.021 0.001 TYR C1067 PHE 0.018 0.001 PHE A 392 TRP 0.031 0.002 TRP C 353 HIS 0.004 0.000 HIS B 66 Details of bonding type rmsd covalent geometry : bond 0.00298 (24186) covalent geometry : angle 0.52648 (32886) SS BOND : bond 0.00481 ( 36) SS BOND : angle 2.44883 ( 72) hydrogen bonds : bond 0.03375 ( 1013) hydrogen bonds : angle 5.31109 ( 2862) link_BETA1-4 : bond 0.00333 ( 15) link_BETA1-4 : angle 0.98766 ( 45) link_NAG-ASN : bond 0.00301 ( 48) link_NAG-ASN : angle 2.19462 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4919.84 seconds wall clock time: 85 minutes 24.80 seconds (5124.80 seconds total)