Starting phenix.real_space_refine on Thu Mar 5 22:48:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7bbh_12130/03_2026/7bbh_12130.cif Found real_map, /net/cci-nas-00/data/ceres_data/7bbh_12130/03_2026/7bbh_12130.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7bbh_12130/03_2026/7bbh_12130.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7bbh_12130/03_2026/7bbh_12130.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7bbh_12130/03_2026/7bbh_12130.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7bbh_12130/03_2026/7bbh_12130.map" } resolution = 2.9 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= 0.003 sd= 0.083 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 120 5.16 5 C 16431 2.51 5 N 4173 2.21 5 O 5103 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 205 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: 25827 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 8287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1063, 8287 Classifications: {'peptide': 1063} Link IDs: {'PTRANS': 49, 'TRANS': 1013} Chain breaks: 9 Chain: "B" Number of atoms: 8287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1063, 8287 Classifications: {'peptide': 1063} Link IDs: {'PTRANS': 49, 'TRANS': 1013} Chain breaks: 9 Chain: "C" Number of atoms: 8287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1063, 8287 Classifications: {'peptide': 1063} Link IDs: {'PTRANS': 49, 'TRANS': 1013} Chain breaks: 9 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 15 Chain: "B" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 15 Chain: "C" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 15 Time building chain proxies: 6.29, per 1000 atoms: 0.24 Number of scatterers: 25827 At special positions: 0 Unit cell: (139.062, 130.438, 176.792, 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 120 16.00 O 5103 8.00 N 4173 7.00 C 16431 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 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=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A 840 " - pdb=" SG CYS A 851 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B 840 " - pdb=" SG CYS B 851 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 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=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C 840 " - pdb=" SG CYS C 851 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " NAG-ASN " NAG A1301 " - " ASN A 17 " " NAG A1302 " - " ASN A 30 " " NAG A1303 " - " ASN A 61 " " NAG A1304 " - " ASN A 122 " " NAG A1305 " - " ASN A 331 " " NAG A1306 " - " ASN A 343 " " NAG A1307 " - " ASN A 370 " " NAG A1308 " - " ASN A 709 " " NAG A1309 " - " ASN A 717 " " NAG A1310 " - " ASN A1134 " " NAG A1311 " - " ASN A 616 " " NAG A1312 " - " ASN A 112 " " NAG A1313 " - " ASN A 282 " " NAG A1314 " - " ASN A 657 " " NAG A1315 " - " ASN A1074 " " NAG B1301 " - " ASN B 17 " " NAG B1302 " - " ASN B 30 " " NAG B1303 " - " ASN B 61 " " NAG B1304 " - " ASN B 122 " " NAG B1305 " - " ASN B 331 " " NAG B1306 " - " ASN B 343 " " NAG B1307 " - " ASN B 370 " " NAG B1308 " - " ASN B 709 " " NAG B1309 " - " ASN B 717 " " NAG B1310 " - " ASN B1134 " " NAG B1311 " - " ASN B 616 " " NAG B1312 " - " ASN B 112 " " NAG B1313 " - " ASN B 282 " " NAG B1314 " - " ASN B 657 " " NAG B1315 " - " ASN B1074 " " NAG C1301 " - " ASN C 17 " " NAG C1302 " - " ASN C 30 " " NAG C1303 " - " ASN C 61 " " NAG C1304 " - " ASN C 122 " " NAG C1305 " - " ASN C 331 " " NAG C1306 " - " ASN C 343 " " NAG C1307 " - " ASN C 370 " " NAG C1308 " - " ASN C 709 " " NAG C1309 " - " ASN C 717 " " NAG C1310 " - " ASN C1134 " " NAG C1311 " - " ASN C 616 " " NAG C1312 " - " ASN C 112 " " NAG C1313 " - " ASN C 282 " " NAG C1314 " - " ASN C 657 " " NAG C1315 " - " ASN C1074 " " NAG D 1 " - " ASN A 165 " " NAG E 1 " - " ASN A 234 " " NAG F 1 " - " ASN A 801 " " NAG G 1 " - " ASN A1098 " " NAG H 1 " - " ASN B 165 " " NAG I 1 " - " ASN B 234 " " NAG J 1 " - " ASN B 801 " " NAG K 1 " - " ASN B1098 " " NAG L 1 " - " ASN C 165 " " NAG M 1 " - " ASN C 234 " " NAG N 1 " - " ASN C 801 " " NAG O 1 " - " ASN C1098 " Time building additional restraints: 2.38 Conformation dependent library (CDL) restraints added in 1.0 seconds 6258 Ramachandran restraints generated. 3129 Oldfield, 0 Emsley, 3129 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5982 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 42 sheets defined 24.8% alpha, 28.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.01 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 364 through 369 removed outlier: 4.050A pdb=" N VAL A 367 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 3.949A 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 619 through 624 Processing helix chain 'A' and resid 630 through 638 removed outlier: 3.768A pdb=" N VAL A 635 " --> pdb=" O PRO A 631 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N TYR A 636 " --> pdb=" O THR A 632 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N SER A 637 " --> pdb=" O TRP A 633 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR A 638 " --> pdb=" O ARG A 634 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 757 Processing helix chain 'A' and resid 759 through 783 removed outlier: 3.544A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE A 782 " --> pdb=" O THR A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.610A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 849 through 855 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 4.002A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLY A 891 " --> pdb=" O THR A 887 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 886 through 891' Processing helix chain 'A' and resid 897 through 910 Processing helix chain 'A' and resid 912 through 918 removed outlier: 4.059A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 940 Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.969A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL A 963 " --> pdb=" O LEU A 959 " (cutoff:3.500A) 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 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.418A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL A1033 " --> pdb=" O MET A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1145 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 364 through 369 removed outlier: 4.050A pdb=" N VAL B 367 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 3.948A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 619 through 624 Processing helix chain 'B' and resid 630 through 638 removed outlier: 3.769A pdb=" N VAL B 635 " --> pdb=" O PRO B 631 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N TYR B 636 " --> pdb=" O THR B 632 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N SER B 637 " --> pdb=" O TRP B 633 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR B 638 " --> pdb=" O ARG B 634 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 757 Processing helix chain 'B' and resid 759 through 783 removed outlier: 3.544A pdb=" N LEU B 763 " --> pdb=" O PHE B 759 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL B 781 " --> pdb=" O ASN B 777 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE B 782 " --> pdb=" O THR B 778 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.609A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 849 through 855 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 4.002A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLY B 891 " --> pdb=" O THR B 887 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 886 through 891' Processing helix chain 'B' and resid 897 through 910 Processing helix chain 'B' and resid 912 through 918 removed outlier: 4.060A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 940 Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.969A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL B 963 " --> pdb=" O LEU B 959 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.419A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL B1033 " --> pdb=" O MET B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1145 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 364 through 369 removed outlier: 4.050A pdb=" N VAL C 367 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 3.949A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 619 through 624 Processing helix chain 'C' and resid 630 through 638 removed outlier: 3.767A pdb=" N VAL C 635 " --> pdb=" O PRO C 631 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N TYR C 636 " --> pdb=" O THR C 632 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N SER C 637 " --> pdb=" O TRP C 633 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR C 638 " --> pdb=" O ARG C 634 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 757 Processing helix chain 'C' and resid 759 through 783 removed outlier: 3.545A pdb=" N LEU C 763 " --> pdb=" O PHE C 759 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL C 781 " --> pdb=" O ASN C 777 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N PHE C 782 " --> pdb=" O THR C 778 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.610A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 849 through 855 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 4.003A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLY C 891 " --> pdb=" O THR C 887 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 886 through 891' Processing helix chain 'C' and resid 897 through 910 Processing helix chain 'C' and resid 912 through 918 removed outlier: 4.060A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 940 Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.969A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL C 963 " --> pdb=" O LEU C 959 " (cutoff:3.500A) 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 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.418A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL C1033 " --> pdb=" O MET C1029 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1145 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 7.601A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.396A pdb=" N TYR A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.862A pdb=" N LEU A 223 " --> pdb=" O TYR A 207 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 4.262A pdb=" N ASP A 287 " --> pdb=" O ASN A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.685A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 11.409A pdb=" N VAL A 126 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 10.217A pdb=" N GLU A 169 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 11.485A pdb=" N ILE A 128 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 8.806A pdb=" N THR A 167 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N VAL A 130 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N ASN A 165 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ASN A 132 " --> pdb=" O TYR A 163 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N TYR A 163 " --> pdb=" O ASN A 132 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 311 through 314 Processing sheet with id=AA5, first strand: chain 'A' and resid 324 through 325 removed outlier: 6.887A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL A 539 " --> pdb=" O GLY A 550 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLU A 583 " --> pdb=" O ASP A 578 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 356 through 358 removed outlier: 4.422A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA8, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA9, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.127A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.583A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 701 through 703 removed outlier: 7.201A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 712 through 728 removed outlier: 6.782A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 712 through 728 removed outlier: 6.782A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N THR A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N PHE A1095 " --> pdb=" O THR A1078 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.526A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 787 through 789 Processing sheet with id=AB6, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB7, first strand: chain 'B' and resid 27 through 30 removed outlier: 7.602A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.396A pdb=" N TYR B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.862A pdb=" N LEU B 223 " --> pdb=" O TYR B 207 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 48 through 55 removed outlier: 4.262A pdb=" N ASP B 287 " --> pdb=" O ASN B 278 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.686A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 11.409A pdb=" N VAL B 126 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 10.218A pdb=" N GLU B 169 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 11.485A pdb=" N ILE B 128 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 8.806A pdb=" N THR B 167 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N VAL B 130 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N ASN B 165 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ASN B 132 " --> pdb=" O TYR B 163 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N TYR B 163 " --> pdb=" O ASN B 132 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N GLN B 134 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N VAL B 159 " --> pdb=" O CYS B 136 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 311 through 314 Processing sheet with id=AC2, first strand: chain 'B' and resid 324 through 325 removed outlier: 6.886A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL B 539 " --> pdb=" O GLY B 550 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLU B 583 " --> pdb=" O ASP B 578 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 356 through 358 removed outlier: 4.422A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC5, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC6, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.127A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.583A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 701 through 703 removed outlier: 7.128A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'B' and resid 712 through 728 removed outlier: 6.783A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 712 through 728 removed outlier: 6.783A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N THR B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N PHE B1095 " --> pdb=" O THR B1078 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.526A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD3, first strand: chain 'C' and resid 27 through 30 removed outlier: 7.601A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.396A pdb=" N TYR C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.862A pdb=" N LEU C 223 " --> pdb=" O TYR C 207 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 48 through 55 removed outlier: 4.261A pdb=" N ASP C 287 " --> pdb=" O ASN C 278 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.684A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 11.409A pdb=" N VAL C 126 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 10.217A pdb=" N GLU C 169 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 11.485A pdb=" N ILE C 128 " --> pdb=" O THR C 167 " (cutoff:3.500A) removed outlier: 8.806A pdb=" N THR C 167 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N VAL C 130 " --> pdb=" O ASN C 165 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N ASN C 165 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ASN C 132 " --> pdb=" O TYR C 163 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N TYR C 163 " --> pdb=" O ASN C 132 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N VAL C 159 " --> pdb=" O CYS C 136 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 311 through 314 Processing sheet with id=AD7, first strand: chain 'C' and resid 324 through 325 removed outlier: 6.886A pdb=" N GLU C 324 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL C 539 " --> pdb=" O GLY C 550 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLU C 583 " --> pdb=" O ASP C 578 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 356 through 358 removed outlier: 4.421A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE1, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE2, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.127A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.583A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 712 through 728 removed outlier: 6.782A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 712 through 728 removed outlier: 6.782A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N THR C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N PHE C1095 " --> pdb=" O THR C1078 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.526A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 1120 through 1122 1001 hydrogen bonds defined for protein. 2787 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.96 Time building geometry restraints manager: 3.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8137 1.34 - 1.47: 6639 1.47 - 1.59: 11447 1.59 - 1.71: 0 1.71 - 1.83: 150 Bond restraints: 26373 Sorted by residual: bond pdb=" N ILE A 332 " pdb=" CA ILE A 332 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.29e-02 6.01e+03 8.04e+00 bond pdb=" N ILE B 332 " pdb=" CA ILE B 332 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.29e-02 6.01e+03 7.85e+00 bond pdb=" N ILE C 332 " pdb=" CA ILE C 332 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.29e-02 6.01e+03 7.73e+00 bond pdb=" C1 NAG N 2 " pdb=" O5 NAG N 2 " ideal model delta sigma weight residual 1.406 1.448 -0.042 2.00e-02 2.50e+03 4.43e+00 bond pdb=" C ALA C 271 " pdb=" N PRO C 272 " ideal model delta sigma weight residual 1.335 1.353 -0.018 8.70e-03 1.32e+04 4.38e+00 ... (remaining 26368 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.86: 34558 1.86 - 3.73: 1253 3.73 - 5.59: 63 5.59 - 7.45: 15 7.45 - 9.31: 9 Bond angle restraints: 35898 Sorted by residual: angle pdb=" N PRO C1140 " pdb=" CA PRO C1140 " pdb=" C PRO C1140 " ideal model delta sigma weight residual 112.47 120.19 -7.72 2.06e+00 2.36e-01 1.41e+01 angle pdb=" N PRO B1140 " pdb=" CA PRO B1140 " pdb=" C PRO B1140 " ideal model delta sigma weight residual 112.47 120.18 -7.71 2.06e+00 2.36e-01 1.40e+01 angle pdb=" N PRO A1140 " pdb=" CA PRO A1140 " pdb=" C PRO A1140 " ideal model delta sigma weight residual 112.47 120.17 -7.70 2.06e+00 2.36e-01 1.40e+01 angle pdb=" N THR C 618 " pdb=" CA THR C 618 " pdb=" C THR C 618 " ideal model delta sigma weight residual 113.51 108.58 4.93 1.52e+00 4.33e-01 1.05e+01 angle pdb=" N THR B 618 " pdb=" CA THR B 618 " pdb=" C THR B 618 " ideal model delta sigma weight residual 113.51 108.59 4.92 1.52e+00 4.33e-01 1.05e+01 ... (remaining 35893 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.68: 15401 17.68 - 35.37: 924 35.37 - 53.05: 187 53.05 - 70.74: 63 70.74 - 88.42: 18 Dihedral angle restraints: 16593 sinusoidal: 7293 harmonic: 9300 Sorted by residual: dihedral pdb=" CB CYS B 538 " pdb=" SG CYS B 538 " pdb=" SG CYS B 590 " pdb=" CB CYS B 590 " ideal model delta sinusoidal sigma weight residual -86.00 -122.67 36.67 1 1.00e+01 1.00e-02 1.90e+01 dihedral pdb=" CB CYS A 538 " pdb=" SG CYS A 538 " pdb=" SG CYS A 590 " pdb=" CB CYS A 590 " ideal model delta sinusoidal sigma weight residual -86.00 -122.65 36.65 1 1.00e+01 1.00e-02 1.90e+01 dihedral pdb=" CB CYS C 538 " pdb=" SG CYS C 538 " pdb=" SG CYS C 590 " pdb=" CB CYS C 590 " ideal model delta sinusoidal sigma weight residual -86.00 -122.62 36.62 1 1.00e+01 1.00e-02 1.89e+01 ... (remaining 16590 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 3236 0.057 - 0.114: 949 0.114 - 0.170: 120 0.170 - 0.227: 3 0.227 - 0.284: 6 Chirality restraints: 4314 Sorted by residual: chirality pdb=" CA PRO B1140 " pdb=" N PRO B1140 " pdb=" C PRO B1140 " pdb=" CB PRO B1140 " both_signs ideal model delta sigma weight residual False 2.72 2.43 0.28 2.00e-01 2.50e+01 2.02e+00 chirality pdb=" CA PRO C1140 " pdb=" N PRO C1140 " pdb=" C PRO C1140 " pdb=" CB PRO C1140 " both_signs ideal model delta sigma weight residual False 2.72 2.44 0.28 2.00e-01 2.50e+01 2.00e+00 chirality pdb=" CA PRO A1140 " pdb=" N PRO A1140 " pdb=" C PRO A1140 " pdb=" CB PRO A1140 " both_signs ideal model delta sigma weight residual False 2.72 2.44 0.28 2.00e-01 2.50e+01 1.98e+00 ... (remaining 4311 not shown) Planarity restraints: 4590 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP B1139 " 0.065 5.00e-02 4.00e+02 9.84e-02 1.55e+01 pdb=" N PRO B1140 " -0.170 5.00e-02 4.00e+02 pdb=" CA PRO B1140 " 0.054 5.00e-02 4.00e+02 pdb=" CD PRO B1140 " 0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C1139 " 0.065 5.00e-02 4.00e+02 9.83e-02 1.55e+01 pdb=" N PRO C1140 " -0.170 5.00e-02 4.00e+02 pdb=" CA PRO C1140 " 0.054 5.00e-02 4.00e+02 pdb=" CD PRO C1140 " 0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A1139 " -0.064 5.00e-02 4.00e+02 9.81e-02 1.54e+01 pdb=" N PRO A1140 " 0.170 5.00e-02 4.00e+02 pdb=" CA PRO A1140 " -0.054 5.00e-02 4.00e+02 pdb=" CD PRO A1140 " -0.052 5.00e-02 4.00e+02 ... (remaining 4587 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 6249 2.80 - 3.32: 21591 3.32 - 3.85: 38961 3.85 - 4.37: 47162 4.37 - 4.90: 84244 Nonbonded interactions: 198207 Sorted by model distance: nonbonded pdb=" OD1 ASN C 125 " pdb=" O6 NAG C1304 " model vdw 2.270 3.040 nonbonded pdb=" OD1 ASN A 125 " pdb=" O6 NAG A1304 " model vdw 2.270 3.040 nonbonded pdb=" OD1 ASN B 125 " pdb=" O6 NAG B1304 " model vdw 2.270 3.040 nonbonded pdb=" OH TYR B 37 " pdb=" O TYR B 54 " model vdw 2.316 3.040 nonbonded pdb=" OH TYR C 37 " pdb=" O TYR C 54 " model vdw 2.316 3.040 ... (remaining 198202 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 0.340 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 25.010 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 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 : 0.006 0.042 26487 Z= 0.257 Angle : 0.778 9.315 36195 Z= 0.424 Chirality : 0.051 0.284 4314 Planarity : 0.006 0.098 4533 Dihedral : 12.295 88.423 10476 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 0.86 % Allowed : 3.57 % Favored : 95.57 % 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: -0.97 (0.14), residues: 3129 helix: 0.46 (0.19), residues: 750 sheet: -0.01 (0.19), residues: 726 loop : -1.49 (0.13), residues: 1653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 239 TYR 0.025 0.002 TYR A 265 PHE 0.023 0.002 PHE A1121 TRP 0.022 0.003 TRP C 886 HIS 0.004 0.001 HIS B1088 Details of bonding type rmsd covalent geometry : bond 0.00575 (26373) covalent geometry : angle 0.75623 (35898) SS BOND : bond 0.00403 ( 45) SS BOND : angle 1.61906 ( 90) hydrogen bonds : bond 0.13467 ( 965) hydrogen bonds : angle 6.37833 ( 2787) link_BETA1-4 : bond 0.00547 ( 12) link_BETA1-4 : angle 1.70053 ( 36) link_NAG-ASN : bond 0.00287 ( 57) link_NAG-ASN : angle 2.43467 ( 171) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6258 Ramachandran restraints generated. 3129 Oldfield, 0 Emsley, 3129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6258 Ramachandran restraints generated. 3129 Oldfield, 0 Emsley, 3129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 2775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 371 time to evaluate : 0.935 Fit side-chains REVERT: A 44 ARG cc_start: 0.7659 (mpp80) cc_final: 0.7303 (mtt180) REVERT: A 100 ILE cc_start: 0.8204 (mm) cc_final: 0.7968 (tt) REVERT: A 370 ASN cc_start: 0.8255 (t0) cc_final: 0.7290 (p0) REVERT: A 633 TRP cc_start: 0.7998 (OUTLIER) cc_final: 0.6428 (m100) REVERT: A 690 GLN cc_start: 0.8488 (mm-40) cc_final: 0.7982 (mm110) REVERT: A 836 GLN cc_start: 0.7818 (mt0) cc_final: 0.7467 (mt0) REVERT: B 44 ARG cc_start: 0.7821 (mpp80) cc_final: 0.7447 (mtt180) REVERT: B 370 ASN cc_start: 0.7950 (t0) cc_final: 0.7053 (p0) REVERT: B 529 GLN cc_start: 0.7431 (mt0) cc_final: 0.7225 (mm-40) REVERT: B 633 TRP cc_start: 0.8028 (OUTLIER) cc_final: 0.7024 (m100) REVERT: B 731 MET cc_start: 0.8779 (ptm) cc_final: 0.8558 (ptm) REVERT: C 44 ARG cc_start: 0.7659 (mpp80) cc_final: 0.7096 (mtt180) REVERT: C 54 TYR cc_start: 0.8277 (m-80) cc_final: 0.8038 (m-80) REVERT: C 77 LYS cc_start: 0.7443 (mttt) cc_final: 0.7012 (tptt) REVERT: C 370 ASN cc_start: 0.7733 (t0) cc_final: 0.6754 (p0) REVERT: C 486 PHE cc_start: 0.6996 (t80) cc_final: 0.6728 (t80) REVERT: C 567 ARG cc_start: 0.7551 (mtt90) cc_final: 0.7233 (mtt90) REVERT: C 675 GLN cc_start: 0.6885 (mt0) cc_final: 0.6649 (mp10) REVERT: C 731 MET cc_start: 0.8774 (ptm) cc_final: 0.8283 (ptm) REVERT: C 1101 HIS cc_start: 0.7536 (OUTLIER) cc_final: 0.7307 (m90) REVERT: C 1116 THR cc_start: 0.8120 (p) cc_final: 0.7557 (p) outliers start: 24 outliers final: 3 residues processed: 393 average time/residue: 0.6863 time to fit residues: 310.2208 Evaluate side-chains 252 residues out of total 2775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 246 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 353 TRP Chi-restraints excluded: chain A residue 633 TRP Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain C residue 1101 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 197 optimal weight: 0.9980 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 0.6980 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 0.0570 chunk 298 optimal weight: 3.9990 overall best weight: 0.6898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 ASN A 213 ASN A 360 ASN A 388 ASN A 501 ASN A 544 ASN A 804 GLN A 836 GLN A1010 GLN A1083 HIS A1119 ASN B 132 ASN B 360 ASN B 501 ASN B 544 ASN B 755 GLN B 804 GLN B1083 HIS B1119 ASN C 125 ASN C 132 ASN C 360 ASN C 388 ASN C 501 ASN C 544 ASN C 755 GLN C 804 GLN C1010 GLN C1083 HIS Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.159994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.130208 restraints weight = 30097.373| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 2.20 r_work: 0.3338 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3208 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.1302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 26487 Z= 0.138 Angle : 0.599 9.107 36195 Z= 0.318 Chirality : 0.046 0.221 4314 Planarity : 0.005 0.053 4533 Dihedral : 6.929 59.072 4884 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.62 % Allowed : 10.85 % Favored : 87.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.14), residues: 3129 helix: 1.11 (0.20), residues: 753 sheet: 0.49 (0.19), residues: 729 loop : -1.33 (0.13), residues: 1647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 273 TYR 0.016 0.001 TYR B1067 PHE 0.016 0.001 PHE A 133 TRP 0.010 0.001 TRP B 436 HIS 0.003 0.001 HIS B1088 Details of bonding type rmsd covalent geometry : bond 0.00307 (26373) covalent geometry : angle 0.57646 (35898) SS BOND : bond 0.00513 ( 45) SS BOND : angle 1.37686 ( 90) hydrogen bonds : bond 0.05683 ( 965) hydrogen bonds : angle 5.30367 ( 2787) link_BETA1-4 : bond 0.00380 ( 12) link_BETA1-4 : angle 1.28432 ( 36) link_NAG-ASN : bond 0.00320 ( 57) link_NAG-ASN : angle 2.20328 ( 171) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6258 Ramachandran restraints generated. 3129 Oldfield, 0 Emsley, 3129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6258 Ramachandran restraints generated. 3129 Oldfield, 0 Emsley, 3129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 2775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 258 time to evaluate : 0.890 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ARG cc_start: 0.7662 (mpp80) cc_final: 0.7305 (mtt180) REVERT: A 97 LYS cc_start: 0.8291 (pttt) cc_final: 0.7880 (ptpt) REVERT: A 100 ILE cc_start: 0.8135 (mm) cc_final: 0.7721 (tt) REVERT: A 298 GLU cc_start: 0.7617 (mt-10) cc_final: 0.7308 (tt0) REVERT: A 370 ASN cc_start: 0.8740 (t0) cc_final: 0.7564 (p0) REVERT: A 389 ASP cc_start: 0.7935 (p0) cc_final: 0.7663 (p0) REVERT: A 633 TRP cc_start: 0.7860 (OUTLIER) cc_final: 0.6285 (m100) REVERT: A 675 GLN cc_start: 0.7217 (mt0) cc_final: 0.6587 (mt0) REVERT: A 690 GLN cc_start: 0.8610 (mm-40) cc_final: 0.8169 (mm110) REVERT: A 814 LYS cc_start: 0.7274 (mptt) cc_final: 0.6576 (ptmt) REVERT: A 836 GLN cc_start: 0.7987 (mt0) cc_final: 0.7263 (mt0) REVERT: B 44 ARG cc_start: 0.7912 (mpp80) cc_final: 0.7568 (mtt180) REVERT: B 96 GLU cc_start: 0.6838 (OUTLIER) cc_final: 0.6158 (pt0) REVERT: B 298 GLU cc_start: 0.7785 (mt-10) cc_final: 0.7573 (tt0) REVERT: B 304 LYS cc_start: 0.7846 (tttt) cc_final: 0.7577 (mppt) REVERT: B 370 ASN cc_start: 0.8603 (t0) cc_final: 0.7489 (p0) REVERT: B 529 GLN cc_start: 0.8055 (mt0) cc_final: 0.7254 (mm-40) REVERT: B 619 GLU cc_start: 0.7829 (tt0) cc_final: 0.7495 (mt-10) REVERT: B 633 TRP cc_start: 0.7955 (OUTLIER) cc_final: 0.7165 (m100) REVERT: B 690 GLN cc_start: 0.8467 (mm-40) cc_final: 0.8096 (mm-40) REVERT: B 776 LYS cc_start: 0.8548 (tttt) cc_final: 0.8323 (ttpt) REVERT: B 836 GLN cc_start: 0.7752 (mt0) cc_final: 0.7349 (mt0) REVERT: C 44 ARG cc_start: 0.7888 (mpp80) cc_final: 0.7231 (mtt180) REVERT: C 54 TYR cc_start: 0.8464 (m-80) cc_final: 0.8235 (m-80) REVERT: C 96 GLU cc_start: 0.7044 (OUTLIER) cc_final: 0.6675 (pt0) REVERT: C 357 ARG cc_start: 0.8633 (OUTLIER) cc_final: 0.7859 (tpt-90) REVERT: C 370 ASN cc_start: 0.8489 (t0) cc_final: 0.7359 (p0) REVERT: C 417 ARG cc_start: 0.8723 (ptp90) cc_final: 0.8404 (ptt180) REVERT: C 521 PRO cc_start: 0.8795 (Cg_endo) cc_final: 0.8592 (Cg_exo) REVERT: C 567 ARG cc_start: 0.7576 (mtt90) cc_final: 0.7268 (mtt90) REVERT: C 675 GLN cc_start: 0.7214 (mt0) cc_final: 0.6781 (mp10) REVERT: C 731 MET cc_start: 0.9050 (ptm) cc_final: 0.8692 (ptm) REVERT: C 836 GLN cc_start: 0.7710 (mt0) cc_final: 0.7319 (mt0) REVERT: C 985 ASP cc_start: 0.7845 (OUTLIER) cc_final: 0.7621 (t0) REVERT: C 1101 HIS cc_start: 0.7737 (OUTLIER) cc_final: 0.7468 (m90) outliers start: 45 outliers final: 16 residues processed: 288 average time/residue: 0.6643 time to fit residues: 220.9763 Evaluate side-chains 248 residues out of total 2775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 225 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 353 TRP Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 633 TRP Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 207 TYR Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1101 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 15 optimal weight: 1.9990 chunk 218 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 267 optimal weight: 0.6980 chunk 88 optimal weight: 2.9990 chunk 296 optimal weight: 1.9990 chunk 225 optimal weight: 2.9990 chunk 1 optimal weight: 6.9990 chunk 253 optimal weight: 1.9990 chunk 262 optimal weight: 4.9990 chunk 117 optimal weight: 3.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 ASN A 804 GLN A1010 GLN B 544 ASN B 755 GLN C 544 ASN C 755 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.154377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.124149 restraints weight = 30307.955| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 2.19 r_work: 0.3259 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3124 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 26487 Z= 0.249 Angle : 0.706 7.691 36195 Z= 0.372 Chirality : 0.050 0.240 4314 Planarity : 0.005 0.045 4533 Dihedral : 7.024 57.676 4880 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.56 % Allowed : 12.22 % Favored : 85.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.14), residues: 3129 helix: 0.69 (0.19), residues: 777 sheet: 0.47 (0.20), residues: 708 loop : -1.47 (0.13), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 102 TYR 0.017 0.002 TYR A1067 PHE 0.023 0.002 PHE C 133 TRP 0.012 0.002 TRP A 436 HIS 0.006 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00614 (26373) covalent geometry : angle 0.68173 (35898) SS BOND : bond 0.00569 ( 45) SS BOND : angle 2.05220 ( 90) hydrogen bonds : bond 0.07353 ( 965) hydrogen bonds : angle 5.34801 ( 2787) link_BETA1-4 : bond 0.00323 ( 12) link_BETA1-4 : angle 1.27317 ( 36) link_NAG-ASN : bond 0.00370 ( 57) link_NAG-ASN : angle 2.30028 ( 171) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6258 Ramachandran restraints generated. 3129 Oldfield, 0 Emsley, 3129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6258 Ramachandran restraints generated. 3129 Oldfield, 0 Emsley, 3129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 236 time to evaluate : 1.077 Fit side-chains REVERT: A 96 GLU cc_start: 0.7430 (OUTLIER) cc_final: 0.6943 (pt0) REVERT: A 97 LYS cc_start: 0.8364 (pttt) cc_final: 0.7952 (ptpt) REVERT: A 218 ILE cc_start: 0.8597 (mp) cc_final: 0.8367 (mt) REVERT: A 298 GLU cc_start: 0.7741 (mt-10) cc_final: 0.7308 (tt0) REVERT: A 370 ASN cc_start: 0.8777 (t0) cc_final: 0.7632 (p0) REVERT: A 633 TRP cc_start: 0.7913 (OUTLIER) cc_final: 0.5846 (m100) REVERT: A 690 GLN cc_start: 0.8582 (mm-40) cc_final: 0.8096 (mm110) REVERT: A 697 MET cc_start: 0.8912 (OUTLIER) cc_final: 0.8652 (ptp) REVERT: A 814 LYS cc_start: 0.7286 (mptt) cc_final: 0.6560 (ptmt) REVERT: A 836 GLN cc_start: 0.8015 (mt0) cc_final: 0.7320 (mt0) REVERT: B 96 GLU cc_start: 0.7064 (OUTLIER) cc_final: 0.6494 (pt0) REVERT: B 97 LYS cc_start: 0.8230 (pttt) cc_final: 0.7935 (ptpt) REVERT: B 298 GLU cc_start: 0.7915 (mt-10) cc_final: 0.7651 (tt0) REVERT: B 304 LYS cc_start: 0.8093 (tttt) cc_final: 0.7673 (mppt) REVERT: B 370 ASN cc_start: 0.8697 (t0) cc_final: 0.7604 (p0) REVERT: B 529 GLN cc_start: 0.8128 (mt0) cc_final: 0.7301 (mm-40) REVERT: B 633 TRP cc_start: 0.8000 (OUTLIER) cc_final: 0.6970 (m100) REVERT: B 690 GLN cc_start: 0.8557 (mm-40) cc_final: 0.8219 (mm-40) REVERT: B 776 LYS cc_start: 0.8647 (tttt) cc_final: 0.8352 (ttpt) REVERT: B 796 ASP cc_start: 0.6671 (t0) cc_final: 0.6070 (p0) REVERT: B 836 GLN cc_start: 0.7919 (mt0) cc_final: 0.7519 (mt0) REVERT: B 900 MET cc_start: 0.8625 (mtt) cc_final: 0.8145 (mtt) REVERT: C 44 ARG cc_start: 0.8058 (mpp80) cc_final: 0.7233 (mtt180) REVERT: C 54 TYR cc_start: 0.8544 (m-80) cc_final: 0.8190 (m-80) REVERT: C 357 ARG cc_start: 0.8819 (OUTLIER) cc_final: 0.8035 (tpt-90) REVERT: C 370 ASN cc_start: 0.8751 (t0) cc_final: 0.7685 (p0) REVERT: C 567 ARG cc_start: 0.7634 (mtt90) cc_final: 0.7379 (mtt90) REVERT: C 690 GLN cc_start: 0.8416 (mm-40) cc_final: 0.8057 (mm-40) REVERT: C 697 MET cc_start: 0.8986 (OUTLIER) cc_final: 0.8663 (ptp) REVERT: C 776 LYS cc_start: 0.8715 (tttt) cc_final: 0.8461 (ttpm) REVERT: C 780 GLU cc_start: 0.8071 (mt-10) cc_final: 0.7763 (mm-30) REVERT: C 796 ASP cc_start: 0.7127 (t0) cc_final: 0.6295 (p0) REVERT: C 814 LYS cc_start: 0.7233 (mptt) cc_final: 0.6310 (ptmt) REVERT: C 985 ASP cc_start: 0.8066 (OUTLIER) cc_final: 0.7861 (t0) REVERT: C 1101 HIS cc_start: 0.7893 (OUTLIER) cc_final: 0.7598 (m90) outliers start: 71 outliers final: 31 residues processed: 288 average time/residue: 0.6864 time to fit residues: 228.4960 Evaluate side-chains 262 residues out of total 2775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 222 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 633 TRP Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 776 LYS Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1101 HIS Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 229 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 261 optimal weight: 0.6980 chunk 258 optimal weight: 0.8980 chunk 190 optimal weight: 1.9990 chunk 233 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 165 optimal weight: 0.8980 chunk 59 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 97 optimal weight: 0.3980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 ASN A 215 ASN A1010 GLN B 213 ASN B 544 ASN B 755 GLN C 755 GLN C 901 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.157422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.127316 restraints weight = 30074.376| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 2.15 r_work: 0.3308 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3173 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 26487 Z= 0.140 Angle : 0.589 11.199 36195 Z= 0.308 Chirality : 0.046 0.220 4314 Planarity : 0.004 0.038 4533 Dihedral : 6.781 59.770 4878 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.45 % Allowed : 13.26 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.14), residues: 3129 helix: 1.17 (0.20), residues: 756 sheet: 0.74 (0.20), residues: 711 loop : -1.48 (0.13), residues: 1662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 102 TYR 0.016 0.001 TYR B1067 PHE 0.014 0.001 PHE C 643 TRP 0.010 0.001 TRP A 436 HIS 0.003 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00323 (26373) covalent geometry : angle 0.56393 (35898) SS BOND : bond 0.00297 ( 45) SS BOND : angle 1.73096 ( 90) hydrogen bonds : bond 0.05529 ( 965) hydrogen bonds : angle 5.09663 ( 2787) link_BETA1-4 : bond 0.00343 ( 12) link_BETA1-4 : angle 1.39042 ( 36) link_NAG-ASN : bond 0.00367 ( 57) link_NAG-ASN : angle 2.14962 ( 171) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6258 Ramachandran restraints generated. 3129 Oldfield, 0 Emsley, 3129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6258 Ramachandran restraints generated. 3129 Oldfield, 0 Emsley, 3129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 246 time to evaluate : 1.041 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 GLU cc_start: 0.7360 (OUTLIER) cc_final: 0.6851 (pt0) REVERT: A 97 LYS cc_start: 0.8354 (pttt) cc_final: 0.7890 (ptpt) REVERT: A 298 GLU cc_start: 0.7538 (mt-10) cc_final: 0.7129 (tt0) REVERT: A 370 ASN cc_start: 0.8739 (t0) cc_final: 0.7638 (p0) REVERT: A 633 TRP cc_start: 0.7866 (OUTLIER) cc_final: 0.5872 (m100) REVERT: A 675 GLN cc_start: 0.7268 (mt0) cc_final: 0.6583 (mp10) REVERT: A 690 GLN cc_start: 0.8573 (mm-40) cc_final: 0.8063 (mm110) REVERT: A 697 MET cc_start: 0.8881 (OUTLIER) cc_final: 0.8619 (ptp) REVERT: A 796 ASP cc_start: 0.6814 (t0) cc_final: 0.6093 (p0) REVERT: A 814 LYS cc_start: 0.7246 (mptt) cc_final: 0.6501 (ptmt) REVERT: A 836 GLN cc_start: 0.7988 (mt0) cc_final: 0.7287 (mt0) REVERT: A 933 LYS cc_start: 0.8221 (mttt) cc_final: 0.7923 (mtpm) REVERT: B 21 ARG cc_start: 0.8557 (ptp90) cc_final: 0.8236 (ptm160) REVERT: B 96 GLU cc_start: 0.6995 (OUTLIER) cc_final: 0.6349 (pt0) REVERT: B 97 LYS cc_start: 0.8279 (pttt) cc_final: 0.8040 (ptpt) REVERT: B 304 LYS cc_start: 0.8089 (tttt) cc_final: 0.7704 (mppt) REVERT: B 357 ARG cc_start: 0.8512 (OUTLIER) cc_final: 0.7189 (tpt-90) REVERT: B 370 ASN cc_start: 0.8664 (t0) cc_final: 0.7587 (p0) REVERT: B 529 GLN cc_start: 0.8079 (mt0) cc_final: 0.7248 (mm-40) REVERT: B 633 TRP cc_start: 0.7984 (OUTLIER) cc_final: 0.6965 (m100) REVERT: B 690 GLN cc_start: 0.8643 (mm-40) cc_final: 0.8362 (mm-40) REVERT: B 776 LYS cc_start: 0.8629 (tttt) cc_final: 0.8341 (ttpt) REVERT: B 836 GLN cc_start: 0.7805 (mt0) cc_final: 0.7445 (mt0) REVERT: C 44 ARG cc_start: 0.8107 (mpp80) cc_final: 0.7377 (mtt180) REVERT: C 54 TYR cc_start: 0.8433 (m-80) cc_final: 0.8105 (m-80) REVERT: C 96 GLU cc_start: 0.7358 (OUTLIER) cc_final: 0.6974 (pt0) REVERT: C 370 ASN cc_start: 0.8729 (t0) cc_final: 0.7691 (p0) REVERT: C 675 GLN cc_start: 0.7254 (mt0) cc_final: 0.6717 (mp10) REVERT: C 690 GLN cc_start: 0.8576 (mm-40) cc_final: 0.8217 (mm-40) REVERT: C 697 MET cc_start: 0.8943 (OUTLIER) cc_final: 0.8622 (ptp) REVERT: C 780 GLU cc_start: 0.7819 (mt-10) cc_final: 0.7496 (mm-30) REVERT: C 796 ASP cc_start: 0.6872 (t0) cc_final: 0.6190 (p0) REVERT: C 814 LYS cc_start: 0.7246 (mptt) cc_final: 0.6351 (ptmt) REVERT: C 836 GLN cc_start: 0.7705 (mt0) cc_final: 0.7303 (mt0) REVERT: C 866 THR cc_start: 0.8622 (OUTLIER) cc_final: 0.8340 (m) REVERT: C 964 LYS cc_start: 0.8476 (OUTLIER) cc_final: 0.8095 (ttmm) REVERT: C 985 ASP cc_start: 0.8031 (OUTLIER) cc_final: 0.7819 (t0) REVERT: C 1101 HIS cc_start: 0.7845 (OUTLIER) cc_final: 0.7538 (m90) outliers start: 68 outliers final: 39 residues processed: 296 average time/residue: 0.6910 time to fit residues: 236.1893 Evaluate side-chains 278 residues out of total 2775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 227 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 353 TRP Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 633 TRP Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 776 LYS Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 207 TYR Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 964 LYS Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1101 HIS Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 112 optimal weight: 2.9990 chunk 169 optimal weight: 4.9990 chunk 184 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 265 optimal weight: 2.9990 chunk 143 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 174 optimal weight: 3.9990 chunk 277 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 ASN B 334 ASN B 544 ASN B 755 GLN C 132 ASN C 755 GLN C 901 GLN C1135 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.149435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.118695 restraints weight = 30287.669| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 2.17 r_work: 0.3239 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.091 26487 Z= 0.350 Angle : 0.803 10.986 36195 Z= 0.419 Chirality : 0.055 0.261 4314 Planarity : 0.006 0.048 4533 Dihedral : 7.239 59.802 4878 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 3.57 % Allowed : 13.30 % Favored : 83.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.14), residues: 3129 helix: 0.39 (0.19), residues: 762 sheet: 0.53 (0.20), residues: 696 loop : -1.71 (0.13), residues: 1671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 355 TYR 0.020 0.003 TYR A 495 PHE 0.026 0.003 PHE A1121 TRP 0.013 0.003 TRP A 886 HIS 0.008 0.002 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00886 (26373) covalent geometry : angle 0.77607 (35898) SS BOND : bond 0.00698 ( 45) SS BOND : angle 2.61985 ( 90) hydrogen bonds : bond 0.08339 ( 965) hydrogen bonds : angle 5.48264 ( 2787) link_BETA1-4 : bond 0.00253 ( 12) link_BETA1-4 : angle 1.47597 ( 36) link_NAG-ASN : bond 0.00541 ( 57) link_NAG-ASN : angle 2.44815 ( 171) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6258 Ramachandran restraints generated. 3129 Oldfield, 0 Emsley, 3129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6258 Ramachandran restraints generated. 3129 Oldfield, 0 Emsley, 3129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 2775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 224 time to evaluate : 0.982 Fit side-chains REVERT: A 21 ARG cc_start: 0.8901 (OUTLIER) cc_final: 0.7392 (ptp90) REVERT: A 52 GLN cc_start: 0.8505 (OUTLIER) cc_final: 0.7773 (tp40) REVERT: A 96 GLU cc_start: 0.7450 (OUTLIER) cc_final: 0.7022 (pt0) REVERT: A 97 LYS cc_start: 0.8452 (pttt) cc_final: 0.8078 (ptpt) REVERT: A 100 ILE cc_start: 0.8371 (mm) cc_final: 0.7862 (tt) REVERT: A 218 ILE cc_start: 0.8688 (mp) cc_final: 0.8460 (mt) REVERT: A 298 GLU cc_start: 0.7740 (mt-10) cc_final: 0.7314 (tt0) REVERT: A 370 ASN cc_start: 0.8812 (t0) cc_final: 0.7784 (p0) REVERT: A 577 ARG cc_start: 0.6608 (OUTLIER) cc_final: 0.6382 (ttp-170) REVERT: A 633 TRP cc_start: 0.8043 (OUTLIER) cc_final: 0.5865 (m100) REVERT: A 690 GLN cc_start: 0.8671 (mm-40) cc_final: 0.8025 (mm110) REVERT: A 697 MET cc_start: 0.8891 (OUTLIER) cc_final: 0.8684 (ptp) REVERT: A 796 ASP cc_start: 0.7018 (t0) cc_final: 0.6341 (p0) REVERT: A 814 LYS cc_start: 0.7332 (mptt) cc_final: 0.6608 (ptmt) REVERT: A 836 GLN cc_start: 0.8028 (mt0) cc_final: 0.7444 (mt0) REVERT: B 96 GLU cc_start: 0.7141 (OUTLIER) cc_final: 0.6622 (pt0) REVERT: B 97 LYS cc_start: 0.8427 (pttt) cc_final: 0.8045 (ptpt) REVERT: B 213 ASN cc_start: 0.7983 (p0) cc_final: 0.7714 (p0) REVERT: B 304 LYS cc_start: 0.8238 (tttt) cc_final: 0.7681 (mppt) REVERT: B 357 ARG cc_start: 0.8773 (OUTLIER) cc_final: 0.7575 (tpt-90) REVERT: B 370 ASN cc_start: 0.8779 (t0) cc_final: 0.7686 (p0) REVERT: B 633 TRP cc_start: 0.8157 (OUTLIER) cc_final: 0.6851 (m100) REVERT: B 690 GLN cc_start: 0.8579 (mm-40) cc_final: 0.8099 (mm-40) REVERT: B 697 MET cc_start: 0.8845 (OUTLIER) cc_final: 0.8631 (ptp) REVERT: B 796 ASP cc_start: 0.6956 (t0) cc_final: 0.6189 (p0) REVERT: B 836 GLN cc_start: 0.7906 (mt0) cc_final: 0.7525 (mt0) REVERT: B 900 MET cc_start: 0.8668 (mtt) cc_final: 0.8159 (mtt) REVERT: C 44 ARG cc_start: 0.8248 (mpp80) cc_final: 0.7275 (mtt180) REVERT: C 54 TYR cc_start: 0.8531 (m-80) cc_final: 0.8245 (m-80) REVERT: C 370 ASN cc_start: 0.8827 (t0) cc_final: 0.7782 (p0) REVERT: C 417 ARG cc_start: 0.8845 (OUTLIER) cc_final: 0.8486 (ptt180) REVERT: C 567 ARG cc_start: 0.7419 (OUTLIER) cc_final: 0.6337 (mtt90) REVERT: C 633 TRP cc_start: 0.8074 (OUTLIER) cc_final: 0.7605 (m100) REVERT: C 690 GLN cc_start: 0.8544 (mm-40) cc_final: 0.8322 (mm-40) REVERT: C 697 MET cc_start: 0.8968 (OUTLIER) cc_final: 0.8689 (ptp) REVERT: C 780 GLU cc_start: 0.8131 (mt-10) cc_final: 0.7841 (mm-30) REVERT: C 796 ASP cc_start: 0.6912 (t0) cc_final: 0.6371 (p0) REVERT: C 814 LYS cc_start: 0.7277 (mptt) cc_final: 0.6363 (ptmt) REVERT: C 836 GLN cc_start: 0.7676 (mt0) cc_final: 0.7391 (mt0) outliers start: 99 outliers final: 55 residues processed: 299 average time/residue: 0.6436 time to fit residues: 224.0970 Evaluate side-chains 283 residues out of total 2775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 214 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 577 ARG Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 633 TRP Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 417 ARG Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 567 ARG Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 633 TRP Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 964 LYS Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 271 optimal weight: 0.6980 chunk 51 optimal weight: 4.9990 chunk 231 optimal weight: 0.9980 chunk 199 optimal weight: 0.5980 chunk 83 optimal weight: 0.8980 chunk 96 optimal weight: 0.5980 chunk 228 optimal weight: 0.1980 chunk 113 optimal weight: 0.7980 chunk 36 optimal weight: 0.6980 chunk 118 optimal weight: 0.9980 chunk 134 optimal weight: 2.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 ASN A 215 ASN B 544 ASN B 755 GLN B 901 GLN C 544 ASN C 755 GLN C 901 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.157204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.127159 restraints weight = 30069.596| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 2.16 r_work: 0.3323 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 26487 Z= 0.125 Angle : 0.577 12.272 36195 Z= 0.302 Chirality : 0.045 0.217 4314 Planarity : 0.004 0.041 4533 Dihedral : 6.707 59.812 4876 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.31 % Allowed : 14.81 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.15), residues: 3129 helix: 1.12 (0.20), residues: 756 sheet: 0.76 (0.20), residues: 708 loop : -1.54 (0.13), residues: 1665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 102 TYR 0.017 0.001 TYR A1067 PHE 0.015 0.001 PHE B 643 TRP 0.010 0.001 TRP A 436 HIS 0.002 0.001 HIS C1088 Details of bonding type rmsd covalent geometry : bond 0.00281 (26373) covalent geometry : angle 0.55218 (35898) SS BOND : bond 0.00299 ( 45) SS BOND : angle 1.74488 ( 90) hydrogen bonds : bond 0.05150 ( 965) hydrogen bonds : angle 5.07011 ( 2787) link_BETA1-4 : bond 0.00364 ( 12) link_BETA1-4 : angle 1.31011 ( 36) link_NAG-ASN : bond 0.00333 ( 57) link_NAG-ASN : angle 2.14812 ( 171) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6258 Ramachandran restraints generated. 3129 Oldfield, 0 Emsley, 3129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6258 Ramachandran restraints generated. 3129 Oldfield, 0 Emsley, 3129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 232 time to evaluate : 0.887 Fit side-chains revert: symmetry clash REVERT: A 21 ARG cc_start: 0.8853 (OUTLIER) cc_final: 0.7125 (ptp90) REVERT: A 52 GLN cc_start: 0.8391 (OUTLIER) cc_final: 0.7672 (tp40) REVERT: A 96 GLU cc_start: 0.7423 (OUTLIER) cc_final: 0.6953 (pt0) REVERT: A 97 LYS cc_start: 0.8415 (pttt) cc_final: 0.7932 (ptpt) REVERT: A 177 LEU cc_start: 0.7890 (tp) cc_final: 0.7656 (pt) REVERT: A 298 GLU cc_start: 0.7527 (mt-10) cc_final: 0.7173 (tt0) REVERT: A 370 ASN cc_start: 0.8712 (t0) cc_final: 0.7638 (p0) REVERT: A 633 TRP cc_start: 0.7931 (OUTLIER) cc_final: 0.5946 (m100) REVERT: A 675 GLN cc_start: 0.7297 (mt0) cc_final: 0.6974 (mp10) REVERT: A 690 GLN cc_start: 0.8636 (mm-40) cc_final: 0.8004 (mm110) REVERT: A 796 ASP cc_start: 0.6905 (t0) cc_final: 0.6277 (p0) REVERT: A 814 LYS cc_start: 0.7252 (mptt) cc_final: 0.6517 (ptmt) REVERT: A 836 GLN cc_start: 0.8063 (mt0) cc_final: 0.7393 (mt0) REVERT: A 933 LYS cc_start: 0.8286 (mttt) cc_final: 0.8035 (mtpm) REVERT: B 96 GLU cc_start: 0.6997 (OUTLIER) cc_final: 0.6398 (pt0) REVERT: B 97 LYS cc_start: 0.8316 (pttt) cc_final: 0.8075 (ptpt) REVERT: B 99 ASN cc_start: 0.7023 (p0) cc_final: 0.6125 (m-40) REVERT: B 100 ILE cc_start: 0.8231 (OUTLIER) cc_final: 0.8009 (tt) REVERT: B 213 ASN cc_start: 0.7964 (p0) cc_final: 0.7698 (p0) REVERT: B 290 ASP cc_start: 0.8231 (t0) cc_final: 0.8011 (t0) REVERT: B 370 ASN cc_start: 0.8690 (t0) cc_final: 0.7644 (p0) REVERT: B 616 ASN cc_start: 0.8403 (t0) cc_final: 0.7609 (p0) REVERT: B 633 TRP cc_start: 0.8083 (OUTLIER) cc_final: 0.6979 (m100) REVERT: B 690 GLN cc_start: 0.8660 (mm-40) cc_final: 0.8304 (mm-40) REVERT: B 776 LYS cc_start: 0.8580 (tttt) cc_final: 0.8337 (ttpt) REVERT: B 796 ASP cc_start: 0.6843 (t0) cc_final: 0.6106 (p0) REVERT: B 836 GLN cc_start: 0.7726 (mt0) cc_final: 0.7341 (mt0) REVERT: B 866 THR cc_start: 0.8461 (OUTLIER) cc_final: 0.8191 (m) REVERT: C 44 ARG cc_start: 0.8177 (mpp80) cc_final: 0.7361 (mtt180) REVERT: C 52 GLN cc_start: 0.8275 (OUTLIER) cc_final: 0.8065 (tp40) REVERT: C 54 TYR cc_start: 0.8452 (m-80) cc_final: 0.8119 (m-80) REVERT: C 370 ASN cc_start: 0.8775 (t0) cc_final: 0.7734 (p0) REVERT: C 417 ARG cc_start: 0.8742 (OUTLIER) cc_final: 0.8412 (ptt180) REVERT: C 633 TRP cc_start: 0.8032 (OUTLIER) cc_final: 0.7600 (m100) REVERT: C 690 GLN cc_start: 0.8569 (mm-40) cc_final: 0.8209 (mm-40) REVERT: C 780 GLU cc_start: 0.7910 (mt-10) cc_final: 0.7617 (mm-30) REVERT: C 796 ASP cc_start: 0.6796 (t0) cc_final: 0.6230 (p0) REVERT: C 814 LYS cc_start: 0.7291 (mptt) cc_final: 0.6365 (ptmt) REVERT: C 836 GLN cc_start: 0.7496 (mt0) cc_final: 0.7098 (mt0) REVERT: C 964 LYS cc_start: 0.8450 (OUTLIER) cc_final: 0.8075 (ttmm) outliers start: 64 outliers final: 30 residues processed: 286 average time/residue: 0.6444 time to fit residues: 214.7568 Evaluate side-chains 260 residues out of total 2775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 218 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 353 TRP Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 633 TRP Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 52 GLN Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 207 TYR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 417 ARG Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 633 TRP Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 964 LYS Chi-restraints excluded: chain C residue 1114 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 105 optimal weight: 4.9990 chunk 266 optimal weight: 4.9990 chunk 233 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 42 optimal weight: 0.0020 chunk 35 optimal weight: 0.7980 chunk 270 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 184 optimal weight: 1.9990 chunk 215 optimal weight: 6.9990 chunk 18 optimal weight: 0.7980 overall best weight: 1.1192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 ASN A 334 ASN B 544 ASN B 755 GLN B 901 GLN B1135 ASN C 544 ASN C 755 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.155455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.125200 restraints weight = 30022.364| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 2.17 r_work: 0.3306 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.2366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 26487 Z= 0.174 Angle : 0.620 12.539 36195 Z= 0.323 Chirality : 0.047 0.232 4314 Planarity : 0.004 0.040 4533 Dihedral : 6.709 59.862 4876 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 2.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.49 % Allowed : 15.24 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.15), residues: 3129 helix: 0.95 (0.19), residues: 777 sheet: 0.67 (0.20), residues: 699 loop : -1.54 (0.13), residues: 1653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 102 TYR 0.016 0.002 TYR A1067 PHE 0.018 0.002 PHE B 643 TRP 0.012 0.002 TRP A 64 HIS 0.004 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00423 (26373) covalent geometry : angle 0.59674 (35898) SS BOND : bond 0.00361 ( 45) SS BOND : angle 1.93673 ( 90) hydrogen bonds : bond 0.05950 ( 965) hydrogen bonds : angle 5.08381 ( 2787) link_BETA1-4 : bond 0.00326 ( 12) link_BETA1-4 : angle 1.27969 ( 36) link_NAG-ASN : bond 0.00314 ( 57) link_NAG-ASN : angle 2.08712 ( 171) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6258 Ramachandran restraints generated. 3129 Oldfield, 0 Emsley, 3129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6258 Ramachandran restraints generated. 3129 Oldfield, 0 Emsley, 3129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 2775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 222 time to evaluate : 0.965 Fit side-chains revert: symmetry clash REVERT: A 21 ARG cc_start: 0.8849 (OUTLIER) cc_final: 0.7135 (ptp90) REVERT: A 52 GLN cc_start: 0.8267 (OUTLIER) cc_final: 0.7594 (tp40) REVERT: A 96 GLU cc_start: 0.7407 (OUTLIER) cc_final: 0.6925 (pt0) REVERT: A 97 LYS cc_start: 0.8425 (pttt) cc_final: 0.8025 (ptpt) REVERT: A 218 ILE cc_start: 0.8608 (mp) cc_final: 0.8356 (mt) REVERT: A 298 GLU cc_start: 0.7549 (mt-10) cc_final: 0.7195 (tt0) REVERT: A 370 ASN cc_start: 0.8754 (t0) cc_final: 0.7764 (p0) REVERT: A 633 TRP cc_start: 0.7923 (OUTLIER) cc_final: 0.5885 (m100) REVERT: A 675 GLN cc_start: 0.7222 (mt0) cc_final: 0.6920 (mp10) REVERT: A 690 GLN cc_start: 0.8626 (mm-40) cc_final: 0.7958 (mm110) REVERT: A 697 MET cc_start: 0.8915 (OUTLIER) cc_final: 0.8660 (ptp) REVERT: A 796 ASP cc_start: 0.7045 (t0) cc_final: 0.6360 (p0) REVERT: A 814 LYS cc_start: 0.7253 (mptt) cc_final: 0.6556 (ptmt) REVERT: A 836 GLN cc_start: 0.8078 (mt0) cc_final: 0.7406 (mt0) REVERT: A 988 GLU cc_start: 0.8026 (mt-10) cc_final: 0.7789 (mt-10) REVERT: B 96 GLU cc_start: 0.7055 (OUTLIER) cc_final: 0.6408 (pt0) REVERT: B 97 LYS cc_start: 0.8307 (pttt) cc_final: 0.7993 (ptpt) REVERT: B 99 ASN cc_start: 0.7004 (p0) cc_final: 0.6097 (m-40) REVERT: B 213 ASN cc_start: 0.7922 (p0) cc_final: 0.7665 (p0) REVERT: B 357 ARG cc_start: 0.8617 (OUTLIER) cc_final: 0.7566 (tpt-90) REVERT: B 370 ASN cc_start: 0.8718 (t0) cc_final: 0.7663 (p0) REVERT: B 633 TRP cc_start: 0.8112 (OUTLIER) cc_final: 0.6941 (m100) REVERT: B 675 GLN cc_start: 0.7400 (mt0) cc_final: 0.7147 (mt0) REVERT: B 690 GLN cc_start: 0.8543 (mm-40) cc_final: 0.8162 (mm-40) REVERT: B 776 LYS cc_start: 0.8609 (tttt) cc_final: 0.8327 (ttpt) REVERT: B 796 ASP cc_start: 0.6890 (t0) cc_final: 0.6137 (p0) REVERT: B 836 GLN cc_start: 0.7725 (mt0) cc_final: 0.7351 (mt0) REVERT: B 900 MET cc_start: 0.8604 (mtt) cc_final: 0.8088 (mtt) REVERT: B 1038 LYS cc_start: 0.8813 (OUTLIER) cc_final: 0.8150 (mmpt) REVERT: C 44 ARG cc_start: 0.8175 (mpp80) cc_final: 0.7326 (mtt180) REVERT: C 54 TYR cc_start: 0.8466 (m-80) cc_final: 0.8154 (m-80) REVERT: C 370 ASN cc_start: 0.8793 (t0) cc_final: 0.7772 (p0) REVERT: C 417 ARG cc_start: 0.8777 (OUTLIER) cc_final: 0.8433 (ptt180) REVERT: C 567 ARG cc_start: 0.7357 (OUTLIER) cc_final: 0.6449 (mtt90) REVERT: C 633 TRP cc_start: 0.8033 (OUTLIER) cc_final: 0.7612 (m100) REVERT: C 690 GLN cc_start: 0.8558 (mm-40) cc_final: 0.8187 (mm-40) REVERT: C 697 MET cc_start: 0.8951 (OUTLIER) cc_final: 0.8649 (ptp) REVERT: C 780 GLU cc_start: 0.7974 (mt-10) cc_final: 0.7649 (mm-30) REVERT: C 796 ASP cc_start: 0.6831 (t0) cc_final: 0.6325 (p0) REVERT: C 814 LYS cc_start: 0.7282 (mptt) cc_final: 0.6361 (ptmt) REVERT: C 836 GLN cc_start: 0.7458 (mt0) cc_final: 0.7151 (mt0) REVERT: C 866 THR cc_start: 0.8720 (OUTLIER) cc_final: 0.8349 (m) REVERT: C 964 LYS cc_start: 0.8487 (OUTLIER) cc_final: 0.8074 (ttmm) REVERT: C 1038 LYS cc_start: 0.8192 (OUTLIER) cc_final: 0.7806 (mmtt) outliers start: 69 outliers final: 38 residues processed: 278 average time/residue: 0.6518 time to fit residues: 211.8333 Evaluate side-chains 270 residues out of total 2775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 216 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 353 TRP Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 633 TRP Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 417 ARG Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 567 ARG Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 633 TRP Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 964 LYS Chi-restraints excluded: chain C residue 1038 LYS Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 277 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 199 optimal weight: 0.5980 chunk 237 optimal weight: 0.9980 chunk 290 optimal weight: 2.9990 chunk 227 optimal weight: 2.9990 chunk 224 optimal weight: 0.8980 chunk 251 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 167 optimal weight: 3.9990 chunk 168 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 ASN B 755 GLN B 901 GLN C 493 GLN C 755 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.156745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.126668 restraints weight = 30006.555| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 2.17 r_work: 0.3293 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3157 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 26487 Z= 0.140 Angle : 0.585 11.551 36195 Z= 0.305 Chirality : 0.045 0.225 4314 Planarity : 0.004 0.039 4533 Dihedral : 6.536 58.371 4876 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 2.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.52 % Allowed : 15.53 % Favored : 81.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.15), residues: 3129 helix: 1.22 (0.20), residues: 756 sheet: 0.73 (0.20), residues: 714 loop : -1.54 (0.13), residues: 1659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 102 TYR 0.017 0.001 TYR A1067 PHE 0.014 0.001 PHE B 643 TRP 0.013 0.002 TRP A 64 HIS 0.003 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00330 (26373) covalent geometry : angle 0.56240 (35898) SS BOND : bond 0.00323 ( 45) SS BOND : angle 1.69974 ( 90) hydrogen bonds : bond 0.05338 ( 965) hydrogen bonds : angle 4.98038 ( 2787) link_BETA1-4 : bond 0.00355 ( 12) link_BETA1-4 : angle 1.24764 ( 36) link_NAG-ASN : bond 0.00282 ( 57) link_NAG-ASN : angle 2.02373 ( 171) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6258 Ramachandran restraints generated. 3129 Oldfield, 0 Emsley, 3129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6258 Ramachandran restraints generated. 3129 Oldfield, 0 Emsley, 3129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 2775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 224 time to evaluate : 0.786 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 ARG cc_start: 0.8837 (OUTLIER) cc_final: 0.7110 (ptp90) REVERT: A 44 ARG cc_start: 0.8007 (OUTLIER) cc_final: 0.6530 (mpp80) REVERT: A 52 GLN cc_start: 0.8258 (OUTLIER) cc_final: 0.7674 (tp40) REVERT: A 96 GLU cc_start: 0.7283 (OUTLIER) cc_final: 0.6799 (pt0) REVERT: A 97 LYS cc_start: 0.8384 (pttt) cc_final: 0.7970 (ptpt) REVERT: A 177 LEU cc_start: 0.7874 (tp) cc_final: 0.7642 (pt) REVERT: A 298 GLU cc_start: 0.7510 (mt-10) cc_final: 0.7165 (tt0) REVERT: A 370 ASN cc_start: 0.8722 (t0) cc_final: 0.7652 (p0) REVERT: A 567 ARG cc_start: 0.7401 (OUTLIER) cc_final: 0.6522 (mtt90) REVERT: A 633 TRP cc_start: 0.7892 (OUTLIER) cc_final: 0.5893 (m100) REVERT: A 675 GLN cc_start: 0.7228 (mt0) cc_final: 0.6916 (mp10) REVERT: A 690 GLN cc_start: 0.8528 (mm-40) cc_final: 0.7906 (mm110) REVERT: A 697 MET cc_start: 0.8888 (OUTLIER) cc_final: 0.8638 (ptp) REVERT: A 796 ASP cc_start: 0.7035 (t0) cc_final: 0.6311 (p0) REVERT: A 814 LYS cc_start: 0.7237 (mptt) cc_final: 0.6474 (ptmt) REVERT: A 836 GLN cc_start: 0.8071 (mt0) cc_final: 0.7412 (mt0) REVERT: A 933 LYS cc_start: 0.8233 (mttt) cc_final: 0.7978 (mtpm) REVERT: B 96 GLU cc_start: 0.7161 (OUTLIER) cc_final: 0.6538 (pt0) REVERT: B 97 LYS cc_start: 0.8271 (pttt) cc_final: 0.7974 (ptpt) REVERT: B 99 ASN cc_start: 0.6927 (p0) cc_final: 0.5795 (m-40) REVERT: B 118 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8414 (tp) REVERT: B 213 ASN cc_start: 0.7875 (p0) cc_final: 0.7658 (p0) REVERT: B 370 ASN cc_start: 0.8710 (t0) cc_final: 0.7663 (p0) REVERT: B 633 TRP cc_start: 0.8075 (OUTLIER) cc_final: 0.6953 (m100) REVERT: B 675 GLN cc_start: 0.7274 (mt0) cc_final: 0.7047 (mt0) REVERT: B 690 GLN cc_start: 0.8461 (mm-40) cc_final: 0.8032 (mm-40) REVERT: B 776 LYS cc_start: 0.8561 (tttt) cc_final: 0.8308 (ttpt) REVERT: B 796 ASP cc_start: 0.6859 (t0) cc_final: 0.6070 (p0) REVERT: B 836 GLN cc_start: 0.7692 (mt0) cc_final: 0.7313 (mt0) REVERT: B 900 MET cc_start: 0.8521 (mtt) cc_final: 0.8036 (mtt) REVERT: B 1038 LYS cc_start: 0.8784 (OUTLIER) cc_final: 0.8127 (mmpt) REVERT: C 44 ARG cc_start: 0.8176 (mpp80) cc_final: 0.7338 (mtt180) REVERT: C 54 TYR cc_start: 0.8465 (m-80) cc_final: 0.8163 (m-80) REVERT: C 96 GLU cc_start: 0.7386 (OUTLIER) cc_final: 0.6938 (pt0) REVERT: C 357 ARG cc_start: 0.8874 (OUTLIER) cc_final: 0.7012 (tpp-160) REVERT: C 370 ASN cc_start: 0.8776 (t0) cc_final: 0.7760 (p0) REVERT: C 417 ARG cc_start: 0.8761 (OUTLIER) cc_final: 0.8451 (ptt180) REVERT: C 567 ARG cc_start: 0.7312 (OUTLIER) cc_final: 0.6430 (mtt90) REVERT: C 633 TRP cc_start: 0.8097 (OUTLIER) cc_final: 0.7642 (m100) REVERT: C 690 GLN cc_start: 0.8542 (mm-40) cc_final: 0.8146 (mm-40) REVERT: C 780 GLU cc_start: 0.7894 (mt-10) cc_final: 0.7567 (mm-30) REVERT: C 796 ASP cc_start: 0.6798 (t0) cc_final: 0.6282 (p0) REVERT: C 814 LYS cc_start: 0.7273 (mptt) cc_final: 0.6336 (ptmt) REVERT: C 836 GLN cc_start: 0.7345 (mt0) cc_final: 0.7027 (mt0) REVERT: C 866 THR cc_start: 0.8639 (OUTLIER) cc_final: 0.8291 (m) REVERT: C 964 LYS cc_start: 0.8449 (OUTLIER) cc_final: 0.8066 (ttmm) REVERT: C 1038 LYS cc_start: 0.8179 (OUTLIER) cc_final: 0.7814 (mmtt) outliers start: 70 outliers final: 40 residues processed: 284 average time/residue: 0.6757 time to fit residues: 223.1414 Evaluate side-chains 281 residues out of total 2775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 222 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 44 ARG Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 353 TRP Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 633 TRP Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 417 ARG Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 567 ARG Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 633 TRP Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 964 LYS Chi-restraints excluded: chain C residue 1038 LYS Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 185 optimal weight: 0.9980 chunk 171 optimal weight: 2.9990 chunk 236 optimal weight: 0.6980 chunk 2 optimal weight: 2.9990 chunk 215 optimal weight: 6.9990 chunk 254 optimal weight: 4.9990 chunk 311 optimal weight: 0.9990 chunk 99 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 273 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 ASN A 955 ASN B 388 ASN B 755 GLN B 787 GLN B 901 GLN C 755 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.154812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.124523 restraints weight = 30079.943| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 2.19 r_work: 0.3289 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 26487 Z= 0.197 Angle : 0.638 12.176 36195 Z= 0.333 Chirality : 0.048 0.236 4314 Planarity : 0.005 0.040 4533 Dihedral : 6.695 59.868 4876 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 2.45 % Allowed : 15.82 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.15), residues: 3129 helix: 0.90 (0.19), residues: 777 sheet: 0.60 (0.20), residues: 696 loop : -1.51 (0.14), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 102 TYR 0.016 0.002 TYR B1067 PHE 0.018 0.002 PHE A 643 TRP 0.016 0.002 TRP A 64 HIS 0.005 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00489 (26373) covalent geometry : angle 0.61574 (35898) SS BOND : bond 0.00395 ( 45) SS BOND : angle 1.95144 ( 90) hydrogen bonds : bond 0.06267 ( 965) hydrogen bonds : angle 5.09878 ( 2787) link_BETA1-4 : bond 0.00326 ( 12) link_BETA1-4 : angle 1.27534 ( 36) link_NAG-ASN : bond 0.00294 ( 57) link_NAG-ASN : angle 2.05035 ( 171) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6258 Ramachandran restraints generated. 3129 Oldfield, 0 Emsley, 3129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6258 Ramachandran restraints generated. 3129 Oldfield, 0 Emsley, 3129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 218 time to evaluate : 1.031 Fit side-chains revert: symmetry clash REVERT: A 21 ARG cc_start: 0.8857 (OUTLIER) cc_final: 0.7138 (ptp90) REVERT: A 44 ARG cc_start: 0.8035 (OUTLIER) cc_final: 0.6497 (mpp80) REVERT: A 52 GLN cc_start: 0.8245 (OUTLIER) cc_final: 0.7645 (tp40) REVERT: A 96 GLU cc_start: 0.7188 (OUTLIER) cc_final: 0.6735 (pt0) REVERT: A 97 LYS cc_start: 0.8414 (pttt) cc_final: 0.7999 (ptpt) REVERT: A 298 GLU cc_start: 0.7586 (mt-10) cc_final: 0.7229 (tt0) REVERT: A 370 ASN cc_start: 0.8781 (t0) cc_final: 0.7797 (p0) REVERT: A 567 ARG cc_start: 0.7276 (OUTLIER) cc_final: 0.6512 (mtt90) REVERT: A 633 TRP cc_start: 0.7936 (OUTLIER) cc_final: 0.6012 (m100) REVERT: A 675 GLN cc_start: 0.7251 (mt0) cc_final: 0.6941 (mp10) REVERT: A 690 GLN cc_start: 0.8636 (mm-40) cc_final: 0.7936 (mm110) REVERT: A 697 MET cc_start: 0.8877 (OUTLIER) cc_final: 0.8631 (ptp) REVERT: A 796 ASP cc_start: 0.7056 (t0) cc_final: 0.6361 (p0) REVERT: A 814 LYS cc_start: 0.7246 (mptt) cc_final: 0.6496 (ptmt) REVERT: A 836 GLN cc_start: 0.8116 (mt0) cc_final: 0.7455 (mt0) REVERT: A 988 GLU cc_start: 0.7905 (mt-10) cc_final: 0.7652 (mt-10) REVERT: B 96 GLU cc_start: 0.7195 (OUTLIER) cc_final: 0.6603 (pt0) REVERT: B 97 LYS cc_start: 0.8332 (pttt) cc_final: 0.8025 (ptpt) REVERT: B 99 ASN cc_start: 0.6952 (p0) cc_final: 0.5878 (m-40) REVERT: B 118 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8445 (tp) REVERT: B 213 ASN cc_start: 0.7882 (p0) cc_final: 0.7670 (p0) REVERT: B 357 ARG cc_start: 0.8671 (OUTLIER) cc_final: 0.7568 (tpt-90) REVERT: B 370 ASN cc_start: 0.8745 (t0) cc_final: 0.7687 (p0) REVERT: B 633 TRP cc_start: 0.8080 (OUTLIER) cc_final: 0.6968 (m100) REVERT: B 690 GLN cc_start: 0.8479 (mm-40) cc_final: 0.8042 (mm-40) REVERT: B 776 LYS cc_start: 0.8635 (tttt) cc_final: 0.8351 (ttpt) REVERT: B 796 ASP cc_start: 0.6985 (t0) cc_final: 0.6208 (p0) REVERT: B 836 GLN cc_start: 0.7736 (mt0) cc_final: 0.7359 (mt0) REVERT: B 900 MET cc_start: 0.8621 (mtt) cc_final: 0.8104 (mtt) REVERT: B 1038 LYS cc_start: 0.8804 (OUTLIER) cc_final: 0.8133 (mmpt) REVERT: C 44 ARG cc_start: 0.8229 (mpp80) cc_final: 0.7396 (mtt180) REVERT: C 54 TYR cc_start: 0.8490 (m-80) cc_final: 0.8190 (m-80) REVERT: C 96 GLU cc_start: 0.7395 (OUTLIER) cc_final: 0.6948 (pt0) REVERT: C 370 ASN cc_start: 0.8807 (t0) cc_final: 0.7798 (p0) REVERT: C 417 ARG cc_start: 0.8778 (OUTLIER) cc_final: 0.8423 (ptt180) REVERT: C 567 ARG cc_start: 0.7361 (OUTLIER) cc_final: 0.6482 (mtt90) REVERT: C 633 TRP cc_start: 0.8138 (OUTLIER) cc_final: 0.7700 (m100) REVERT: C 690 GLN cc_start: 0.8444 (mm-40) cc_final: 0.8180 (mm-40) REVERT: C 697 MET cc_start: 0.8958 (OUTLIER) cc_final: 0.8659 (ptp) REVERT: C 780 GLU cc_start: 0.8036 (mt-10) cc_final: 0.7709 (mm-30) REVERT: C 796 ASP cc_start: 0.6807 (t0) cc_final: 0.6407 (p0) REVERT: C 814 LYS cc_start: 0.7268 (mptt) cc_final: 0.6346 (ptmt) REVERT: C 836 GLN cc_start: 0.7468 (mt0) cc_final: 0.7195 (mt0) REVERT: C 964 LYS cc_start: 0.8524 (OUTLIER) cc_final: 0.8115 (ttmm) REVERT: C 1038 LYS cc_start: 0.8209 (OUTLIER) cc_final: 0.7819 (mmtt) outliers start: 68 outliers final: 43 residues processed: 273 average time/residue: 0.6655 time to fit residues: 211.0787 Evaluate side-chains 271 residues out of total 2775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 209 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 44 ARG Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 353 TRP Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 633 TRP Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 417 ARG Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 567 ARG Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 633 TRP Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 737 ASP Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 964 LYS Chi-restraints excluded: chain C residue 1038 LYS Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 156 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 256 optimal weight: 0.9980 chunk 3 optimal weight: 0.6980 chunk 102 optimal weight: 1.9990 chunk 179 optimal weight: 0.6980 chunk 47 optimal weight: 2.9990 chunk 260 optimal weight: 1.9990 chunk 141 optimal weight: 0.5980 chunk 56 optimal weight: 0.5980 chunk 20 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 955 ASN B 544 ASN B 755 GLN B 787 GLN B 901 GLN C 334 ASN C 544 ASN C 755 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.153494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.122100 restraints weight = 30021.195| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 2.22 r_work: 0.3291 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.2530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 26487 Z= 0.131 Angle : 0.585 17.423 36195 Z= 0.304 Chirality : 0.045 0.222 4314 Planarity : 0.004 0.039 4533 Dihedral : 6.478 58.063 4876 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.27 % Allowed : 16.22 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.15), residues: 3129 helix: 1.27 (0.20), residues: 756 sheet: 0.75 (0.20), residues: 714 loop : -1.50 (0.14), residues: 1659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 102 TYR 0.017 0.001 TYR A1067 PHE 0.022 0.001 PHE C 643 TRP 0.016 0.002 TRP C 886 HIS 0.003 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00303 (26373) covalent geometry : angle 0.56288 (35898) SS BOND : bond 0.00340 ( 45) SS BOND : angle 1.90364 ( 90) hydrogen bonds : bond 0.05159 ( 965) hydrogen bonds : angle 4.95553 ( 2787) link_BETA1-4 : bond 0.00346 ( 12) link_BETA1-4 : angle 1.34666 ( 36) link_NAG-ASN : bond 0.00282 ( 57) link_NAG-ASN : angle 1.91569 ( 171) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6258 Ramachandran restraints generated. 3129 Oldfield, 0 Emsley, 3129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6258 Ramachandran restraints generated. 3129 Oldfield, 0 Emsley, 3129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 221 time to evaluate : 0.982 Fit side-chains revert: symmetry clash REVERT: A 44 ARG cc_start: 0.7967 (OUTLIER) cc_final: 0.6454 (mpp80) REVERT: A 52 GLN cc_start: 0.8327 (OUTLIER) cc_final: 0.7805 (tp40) REVERT: A 96 GLU cc_start: 0.7151 (OUTLIER) cc_final: 0.6665 (pt0) REVERT: A 97 LYS cc_start: 0.8334 (pttt) cc_final: 0.7923 (ptpt) REVERT: A 177 LEU cc_start: 0.7884 (tp) cc_final: 0.7651 (pt) REVERT: A 218 ILE cc_start: 0.8649 (mp) cc_final: 0.8406 (mt) REVERT: A 298 GLU cc_start: 0.7442 (mt-10) cc_final: 0.7106 (tt0) REVERT: A 370 ASN cc_start: 0.8761 (t0) cc_final: 0.7771 (p0) REVERT: A 567 ARG cc_start: 0.7281 (OUTLIER) cc_final: 0.6496 (mtt90) REVERT: A 633 TRP cc_start: 0.7712 (OUTLIER) cc_final: 0.5849 (m100) REVERT: A 675 GLN cc_start: 0.7226 (mt0) cc_final: 0.6846 (mp10) REVERT: A 690 GLN cc_start: 0.8486 (mm-40) cc_final: 0.7828 (mm110) REVERT: A 697 MET cc_start: 0.8821 (OUTLIER) cc_final: 0.8591 (ptp) REVERT: A 796 ASP cc_start: 0.6956 (t0) cc_final: 0.6225 (p0) REVERT: A 814 LYS cc_start: 0.7232 (mptt) cc_final: 0.6391 (ptmt) REVERT: A 836 GLN cc_start: 0.8073 (mt0) cc_final: 0.7407 (mt0) REVERT: A 933 LYS cc_start: 0.8172 (mttt) cc_final: 0.7879 (mtpm) REVERT: A 988 GLU cc_start: 0.7837 (mt-10) cc_final: 0.7604 (mt-10) REVERT: B 96 GLU cc_start: 0.7210 (OUTLIER) cc_final: 0.6542 (pt0) REVERT: B 97 LYS cc_start: 0.8240 (pttt) cc_final: 0.7930 (ptpt) REVERT: B 99 ASN cc_start: 0.6891 (p0) cc_final: 0.5792 (m-40) REVERT: B 118 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8382 (tp) REVERT: B 370 ASN cc_start: 0.8734 (t0) cc_final: 0.7688 (p0) REVERT: B 633 TRP cc_start: 0.7896 (OUTLIER) cc_final: 0.6863 (m100) REVERT: B 690 GLN cc_start: 0.8417 (mm-40) cc_final: 0.8065 (mm-40) REVERT: B 776 LYS cc_start: 0.8473 (tttt) cc_final: 0.8160 (ttpt) REVERT: B 796 ASP cc_start: 0.6900 (t0) cc_final: 0.6075 (p0) REVERT: B 836 GLN cc_start: 0.7650 (mt0) cc_final: 0.7262 (mt0) REVERT: B 1038 LYS cc_start: 0.8739 (OUTLIER) cc_final: 0.7994 (mmpt) REVERT: C 44 ARG cc_start: 0.8147 (mpp80) cc_final: 0.7319 (mtt180) REVERT: C 54 TYR cc_start: 0.8407 (m-80) cc_final: 0.8039 (m-80) REVERT: C 96 GLU cc_start: 0.7390 (OUTLIER) cc_final: 0.6915 (pt0) REVERT: C 304 LYS cc_start: 0.8115 (OUTLIER) cc_final: 0.7530 (mtpt) REVERT: C 370 ASN cc_start: 0.8791 (t0) cc_final: 0.7767 (p0) REVERT: C 417 ARG cc_start: 0.8757 (OUTLIER) cc_final: 0.8437 (ptt180) REVERT: C 633 TRP cc_start: 0.7960 (OUTLIER) cc_final: 0.7496 (m100) REVERT: C 690 GLN cc_start: 0.8365 (mm-40) cc_final: 0.7968 (mm-40) REVERT: C 697 MET cc_start: 0.8904 (OUTLIER) cc_final: 0.8631 (ptp) REVERT: C 780 GLU cc_start: 0.7859 (mt-10) cc_final: 0.7515 (mm-30) REVERT: C 796 ASP cc_start: 0.6779 (t0) cc_final: 0.6344 (p0) REVERT: C 814 LYS cc_start: 0.7212 (mptt) cc_final: 0.6318 (ptmt) REVERT: C 836 GLN cc_start: 0.7367 (mt0) cc_final: 0.7141 (mt0) REVERT: C 866 THR cc_start: 0.8599 (OUTLIER) cc_final: 0.8280 (m) REVERT: C 933 LYS cc_start: 0.8117 (mttt) cc_final: 0.7681 (mtpm) REVERT: C 964 LYS cc_start: 0.8389 (OUTLIER) cc_final: 0.7991 (ttmm) REVERT: C 1038 LYS cc_start: 0.8201 (OUTLIER) cc_final: 0.7841 (mmtt) outliers start: 63 outliers final: 39 residues processed: 272 average time/residue: 0.6416 time to fit residues: 203.5440 Evaluate side-chains 274 residues out of total 2775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 217 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ARG Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 353 TRP Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 633 TRP Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 776 LYS Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 417 ARG Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 633 TRP Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 964 LYS Chi-restraints excluded: chain C residue 1038 LYS Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1114 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 248 optimal weight: 0.1980 chunk 210 optimal weight: 0.8980 chunk 288 optimal weight: 5.9990 chunk 264 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 110 optimal weight: 0.9990 chunk 113 optimal weight: 4.9990 chunk 219 optimal weight: 4.9990 chunk 245 optimal weight: 3.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 ASN A 955 ASN B 544 ASN B 755 GLN B 901 GLN B 955 ASN C 544 ASN C 755 GLN C 901 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.150488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.118761 restraints weight = 29914.416| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 2.23 r_work: 0.3201 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.2538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 26487 Z= 0.229 Angle : 0.682 15.486 36195 Z= 0.355 Chirality : 0.049 0.244 4314 Planarity : 0.005 0.041 4533 Dihedral : 6.782 59.520 4876 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 2.49 % Allowed : 15.93 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -0.65 (0.14), residues: 3129 helix: 0.81 (0.19), residues: 765 sheet: 0.58 (0.20), residues: 690 loop : -1.53 (0.13), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 102 TYR 0.016 0.002 TYR B1067 PHE 0.020 0.002 PHE B1121 TRP 0.022 0.002 TRP C 886 HIS 0.005 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00572 (26373) covalent geometry : angle 0.66008 (35898) SS BOND : bond 0.00441 ( 45) SS BOND : angle 2.16802 ( 90) hydrogen bonds : bond 0.06717 ( 965) hydrogen bonds : angle 5.16003 ( 2787) link_BETA1-4 : bond 0.00323 ( 12) link_BETA1-4 : angle 1.30822 ( 36) link_NAG-ASN : bond 0.00335 ( 57) link_NAG-ASN : angle 2.03775 ( 171) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8731.57 seconds wall clock time: 149 minutes 23.43 seconds (8963.43 seconds total)