Starting phenix.real_space_refine on Sun Sep 13 15:31:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6zwv_11497/09_2026/6zwv_11497.cif Found real_map, /net/cci-nas-00/data/ceres_data/6zwv_11497/09_2026/6zwv_11497.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6zwv_11497/09_2026/6zwv_11497.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6zwv_11497/09_2026/6zwv_11497.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6zwv_11497/09_2026/6zwv_11497.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6zwv_11497/09_2026/6zwv_11497.map" model { file = "/net/cci-nas-00/data/ceres_data/6zwv_11497/09_2026/6zwv_11497.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6zwv_11497/09_2026/6zwv_11497.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 99 5.16 5 C 15297 2.51 5 N 3909 2.21 5 O 4710 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 49 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 24015 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 7711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 985, 7711 Classifications: {'peptide': 985} Link IDs: {'PTRANS': 46, 'TRANS': 938} Chain breaks: 8 Chain: "B" Number of atoms: 7711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 985, 7711 Classifications: {'peptide': 985} Link IDs: {'PTRANS': 46, 'TRANS': 938} Chain breaks: 8 Chain: "C" Number of atoms: 7711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 985, 7711 Classifications: {'peptide': 985} Link IDs: {'PTRANS': 46, 'TRANS': 938} Chain breaks: 8 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "k" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "m" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "p" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "r" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "v" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "4" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "6" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "9" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "BA" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen chiralities: 11 Chain: "C" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen chiralities: 11 Time building chain proxies: 5.71, per 1000 atoms: 0.24 Number of scatterers: 24015 At special positions: 0 Unit cell: (130.503, 137.93, 180.37, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 99 16.00 O 4710 8.00 N 3909 7.00 C 15297 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.02 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.06 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=2.04 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.01 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.04 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=2.02 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.06 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 B1032 " - pdb=" SG CYS B1043 " distance=2.01 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.04 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=2.02 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.06 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 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 C1032 " - pdb=" SG CYS C1043 " distance=2.01 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.04 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 4 1 " - " NAG 4 2 " " NAG 6 1 " - " NAG 6 2 " " NAG 9 1 " - " NAG 9 2 " " NAG F 1 " - " NAG F 2 " " NAG Q 1 " - " NAG Q 2 " " NAG S 1 " - " NAG S 2 " " NAG V 1 " - " NAG V 2 " " NAG X 1 " - " NAG X 2 " " NAG b 1 " - " NAG b 2 " " NAG k 1 " - " NAG k 2 " " NAG m 1 " - " NAG m 2 " " NAG p 1 " - " NAG p 2 " " NAG r 1 " - " NAG r 2 " " NAG v 1 " - " NAG v 2 " " NAGBA 1 " - " NAGBA 2 " NAG-ASN " NAG 4 1 " - " ASN C 717 " " NAG 6 1 " - " ASN C 801 " " NAG 9 1 " - " ASN C1098 " " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A 331 " " NAG A1305 " - " ASN A 343 " " NAG A1306 " - " ASN A 603 " " NAG A1307 " - " ASN A 616 " " NAG A1308 " - " ASN A 657 " " NAG A1309 " - " ASN A 709 " " NAG A1310 " - " ASN A1074 " " NAG A1311 " - " ASN A 165 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B 331 " " NAG B1305 " - " ASN B 343 " " NAG B1306 " - " ASN B 603 " " NAG B1307 " - " ASN B 616 " " NAG B1308 " - " ASN B 657 " " NAG B1309 " - " ASN B 709 " " NAG B1310 " - " ASN B1074 " " NAG B1311 " - " ASN B 165 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 122 " " NAG C1303 " - " ASN C 282 " " NAG C1304 " - " ASN C 331 " " NAG C1305 " - " ASN C 343 " " NAG C1306 " - " ASN C 603 " " NAG C1307 " - " ASN C 616 " " NAG C1308 " - " ASN C 657 " " NAG C1309 " - " ASN C 709 " " NAG C1310 " - " ASN C1074 " " NAG C1311 " - " ASN C 165 " " NAG F 1 " - " ASN A 234 " " NAG Q 1 " - " ASN A 717 " " NAG S 1 " - " ASN A 801 " " NAG V 1 " - " ASN A1098 " " NAG X 1 " - " ASN A1134 " " NAG b 1 " - " ASN B 234 " " NAG k 1 " - " ASN B 717 " " NAG m 1 " - " ASN B 801 " " NAG p 1 " - " ASN B1098 " " NAG r 1 " - " ASN B1134 " " NAG v 1 " - " ASN C 234 " " NAGBA 1 " - " ASN C1134 " Time building additional restraints: 2.52 Conformation dependent library (CDL) restraints added in 1.2 seconds 5802 Ramachandran restraints generated. 2901 Oldfield, 0 Emsley, 2901 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5544 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 42 sheets defined 26.2% alpha, 28.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.00 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 364 through 371 removed outlier: 4.109A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.900A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 755 Processing helix chain 'A' and resid 758 through 783 removed outlier: 4.041A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASN A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.838A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.621A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.021A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.894A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (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 982 removed outlier: 3.885A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.192A pdb=" N VAL A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N GLY A 999 " --> pdb=" O ARG A 995 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N GLN A1002 " --> pdb=" O THR A 998 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1151 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 364 through 371 removed outlier: 4.108A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 387 removed outlier: 3.900A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 755 Processing helix chain 'B' and resid 758 through 783 removed outlier: 4.041A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU B 763 " --> pdb=" O PHE B 759 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASN B 764 " --> pdb=" O CYS B 760 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.838A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.623A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.020A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.894A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 982 removed outlier: 3.885A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.192A pdb=" N VAL B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N GLY B 999 " --> pdb=" O ARG B 995 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N GLN B1002 " --> pdb=" O THR B 998 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1151 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 364 through 371 removed outlier: 4.109A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 387 removed outlier: 3.900A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 755 Processing helix chain 'C' and resid 758 through 783 removed outlier: 4.041A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU C 763 " --> pdb=" O PHE C 759 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASN C 764 " --> pdb=" O CYS C 760 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 825 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.838A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.622A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.020A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.894A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (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 982 removed outlier: 3.884A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.193A pdb=" N VAL C 991 " --> pdb=" O VAL C 987 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N GLY C 999 " --> pdb=" O ARG C 995 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N GLN C1002 " --> pdb=" O THR C 998 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1151 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.915A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 8.675A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ALA A 93 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N SER A 94 " --> pdb=" O ARG A 190 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 5.164A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 4.363A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.586A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLY A 107 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE A 105 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER A 116 " --> pdb=" O CYS A 131 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.040A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.324A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 391 through 392 Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 538 through 543 removed outlier: 5.164A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N PHE A 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.823A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.342A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLN A 675 " --> pdb=" O SER A 691 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 702 through 703 Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 3.523A pdb=" N ILE A 714 " --> pdb=" O LYS A1073 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 3.523A pdb=" N ILE A 714 " --> pdb=" O LYS A1073 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 733 through 735 removed outlier: 4.094A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 788 through 789 removed outlier: 5.826A pdb=" N ILE A 788 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 3.555A pdb=" N SER A1123 " --> pdb=" O ALA A1087 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.915A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 8.675A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA B 93 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N SER B 94 " --> pdb=" O ARG B 190 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 42 through 43 removed outlier: 5.164A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 48 through 55 removed outlier: 4.363A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.586A pdb=" N LEU B 84 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLY B 107 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE B 105 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER B 116 " --> pdb=" O CYS B 131 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.041A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.325A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AC6, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC7, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.823A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.341A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLN B 675 " --> pdb=" O SER B 691 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 711 through 728 removed outlier: 3.523A pdb=" N ILE B 714 " --> pdb=" O LYS B1073 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 728 removed outlier: 3.523A pdb=" N ILE B 714 " --> pdb=" O LYS B1073 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 733 through 735 removed outlier: 4.095A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 788 through 789 removed outlier: 5.713A pdb=" N ILE B 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 3.555A pdb=" N SER B1123 " --> pdb=" O ALA B1087 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.915A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 8.676A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALA C 93 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N SER C 94 " --> pdb=" O ARG C 190 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 48 through 55 removed outlier: 4.362A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.585A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLY C 107 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE C 105 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER C 116 " --> pdb=" O CYS C 131 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 311 through 319 removed outlier: 7.236A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.325A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 391 through 392 Processing sheet with id=AE1, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE2, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.823A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.342A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLN C 675 " --> pdb=" O SER C 691 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 711 through 728 removed outlier: 3.523A pdb=" N ILE C 714 " --> pdb=" O LYS C1073 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 711 through 728 removed outlier: 3.523A pdb=" N ILE C 714 " --> pdb=" O LYS C1073 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 733 through 735 removed outlier: 4.095A 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 1125 removed outlier: 3.555A pdb=" N SER C1123 " --> pdb=" O ALA C1087 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 931 hydrogen bonds defined for protein. 2628 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: 5.48 Time building geometry restraints manager: 3.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 7591 1.35 - 1.48: 6585 1.48 - 1.60: 10226 1.60 - 1.73: 3 1.73 - 1.86: 123 Bond restraints: 24528 Sorted by residual: bond pdb=" CB GLN A 755 " pdb=" CG GLN A 755 " ideal model delta sigma weight residual 1.520 1.608 -0.088 3.00e-02 1.11e+03 8.51e+00 bond pdb=" CB GLN C 755 " pdb=" CG GLN C 755 " ideal model delta sigma weight residual 1.520 1.607 -0.087 3.00e-02 1.11e+03 8.49e+00 bond pdb=" CB GLN B 755 " pdb=" CG GLN B 755 " ideal model delta sigma weight residual 1.520 1.607 -0.087 3.00e-02 1.11e+03 8.37e+00 bond pdb=" CG1 ILE B 896 " pdb=" CD1 ILE B 896 " ideal model delta sigma weight residual 1.513 1.403 0.110 3.90e-02 6.57e+02 7.92e+00 bond pdb=" CG1 ILE C 896 " pdb=" CD1 ILE C 896 " ideal model delta sigma weight residual 1.513 1.403 0.110 3.90e-02 6.57e+02 7.92e+00 ... (remaining 24523 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.57: 33229 6.57 - 13.13: 89 13.13 - 19.70: 24 19.70 - 26.27: 0 26.27 - 32.83: 9 Bond angle restraints: 33351 Sorted by residual: angle pdb=" CB ARG A 214 " pdb=" CG ARG A 214 " pdb=" CD ARG A 214 " ideal model delta sigma weight residual 111.30 142.58 -31.28 2.30e+00 1.89e-01 1.85e+02 angle pdb=" CB ARG C 214 " pdb=" CG ARG C 214 " pdb=" CD ARG C 214 " ideal model delta sigma weight residual 111.30 142.58 -31.28 2.30e+00 1.89e-01 1.85e+02 angle pdb=" CB ARG B 214 " pdb=" CG ARG B 214 " pdb=" CD ARG B 214 " ideal model delta sigma weight residual 111.30 142.56 -31.26 2.30e+00 1.89e-01 1.85e+02 angle pdb=" CG ARG A1107 " pdb=" CD ARG A1107 " pdb=" NE ARG A1107 " ideal model delta sigma weight residual 112.00 140.16 -28.16 2.20e+00 2.07e-01 1.64e+02 angle pdb=" CG ARG B1107 " pdb=" CD ARG B1107 " pdb=" NE ARG B1107 " ideal model delta sigma weight residual 112.00 140.07 -28.07 2.20e+00 2.07e-01 1.63e+02 ... (remaining 33346 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 12878 17.91 - 35.83: 895 35.83 - 53.74: 198 53.74 - 71.66: 78 71.66 - 89.57: 48 Dihedral angle restraints: 14097 sinusoidal: 5499 harmonic: 8598 Sorted by residual: dihedral pdb=" CB CYS B 738 " pdb=" SG CYS B 738 " pdb=" SG CYS B 760 " pdb=" CB CYS B 760 " ideal model delta sinusoidal sigma weight residual 93.00 31.71 61.29 1 1.00e+01 1.00e-02 4.99e+01 dihedral pdb=" CB CYS C 738 " pdb=" SG CYS C 738 " pdb=" SG CYS C 760 " pdb=" CB CYS C 760 " ideal model delta sinusoidal sigma weight residual 93.00 31.73 61.27 1 1.00e+01 1.00e-02 4.98e+01 dihedral pdb=" CB CYS A 738 " pdb=" SG CYS A 738 " pdb=" SG CYS A 760 " pdb=" CB CYS A 760 " ideal model delta sinusoidal sigma weight residual 93.00 31.74 61.26 1 1.00e+01 1.00e-02 4.98e+01 ... (remaining 14094 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.292: 3954 0.292 - 0.584: 15 0.584 - 0.877: 9 0.877 - 1.169: 3 1.169 - 1.461: 9 Chirality restraints: 3990 Sorted by residual: chirality pdb=" C1 NAG A1301 " pdb=" ND2 ASN A 61 " pdb=" C2 NAG A1301 " pdb=" O5 NAG A1301 " both_signs ideal model delta sigma weight residual False -2.40 -0.94 -1.46 2.00e-01 2.50e+01 5.33e+01 chirality pdb=" C1 NAG B1301 " pdb=" ND2 ASN B 61 " pdb=" C2 NAG B1301 " pdb=" O5 NAG B1301 " both_signs ideal model delta sigma weight residual False -2.40 -0.94 -1.46 2.00e-01 2.50e+01 5.33e+01 chirality pdb=" C1 NAG C1301 " pdb=" ND2 ASN C 61 " pdb=" C2 NAG C1301 " pdb=" O5 NAG C1301 " both_signs ideal model delta sigma weight residual False -2.40 -0.94 -1.46 2.00e-01 2.50e+01 5.33e+01 ... (remaining 3987 not shown) Planarity restraints: 4269 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1304 " 0.086 2.00e-02 2.50e+03 7.55e-02 7.12e+01 pdb=" C7 NAG A1304 " -0.030 2.00e-02 2.50e+03 pdb=" C8 NAG A1304 " -0.013 2.00e-02 2.50e+03 pdb=" N2 NAG A1304 " -0.119 2.00e-02 2.50e+03 pdb=" O7 NAG A1304 " 0.076 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1304 " -0.086 2.00e-02 2.50e+03 7.53e-02 7.09e+01 pdb=" C7 NAG B1304 " 0.030 2.00e-02 2.50e+03 pdb=" C8 NAG B1304 " 0.013 2.00e-02 2.50e+03 pdb=" N2 NAG B1304 " 0.119 2.00e-02 2.50e+03 pdb=" O7 NAG B1304 " -0.076 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1304 " -0.086 2.00e-02 2.50e+03 7.52e-02 7.07e+01 pdb=" C7 NAG C1304 " 0.030 2.00e-02 2.50e+03 pdb=" C8 NAG C1304 " 0.013 2.00e-02 2.50e+03 pdb=" N2 NAG C1304 " 0.118 2.00e-02 2.50e+03 pdb=" O7 NAG C1304 " -0.076 2.00e-02 2.50e+03 ... (remaining 4266 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 274 2.60 - 3.18: 21137 3.18 - 3.75: 35686 3.75 - 4.33: 51272 4.33 - 4.90: 83714 Nonbonded interactions: 192083 Sorted by model distance: nonbonded pdb=" OG1 THR A 716 " pdb=" O GLN A1071 " model vdw 2.025 3.040 nonbonded pdb=" OG1 THR B 716 " pdb=" O GLN B1071 " model vdw 2.025 3.040 nonbonded pdb=" OG1 THR C 716 " pdb=" O GLN C1071 " model vdw 2.026 3.040 nonbonded pdb=" OG1 THR A1116 " pdb=" OD1 ASP A1118 " model vdw 2.068 3.040 nonbonded pdb=" OG1 THR C1116 " pdb=" OD1 ASP C1118 " model vdw 2.068 3.040 ... (remaining 192078 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: 0.07 Found NCS groups: ncs_group { reference = chain '4' selection = chain '6' selection = chain '9' selection = chain 'BA' selection = chain 'F' selection = chain 'Q' selection = chain 'S' selection = chain 'V' selection = chain 'X' selection = chain 'b' selection = chain 'k' selection = chain 'm' selection = chain 'p' selection = chain 'r' selection = chain 'v' } ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.070 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: 0.030 Extract box with map and model: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 24.760 Find NCS groups from input model: 0.750 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 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 : 0.010 0.110 24627 Z= 0.440 Angle : 1.436 32.832 33612 Z= 0.705 Chirality : 0.098 1.461 3990 Planarity : 0.008 0.132 4221 Dihedral : 14.896 89.569 8445 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 1.74 % Allowed : 0.89 % Favored : 97.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.71 (0.14), residues: 2901 helix: 0.40 (0.19), residues: 663 sheet: -1.32 (0.20), residues: 600 loop : -1.75 (0.13), residues: 1638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.083 0.004 ARG A1107 TYR 0.079 0.003 TYR C 904 PHE 0.059 0.004 PHE B 464 TRP 0.050 0.005 TRP C 104 HIS 0.008 0.002 HIS B 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00968 / 0.44 (24528) covalent geometry : angle 1.35403 / 0.69 (33351) SS BOND : bond 0.01015 / 0.67 ( 36) SS BOND : angle 2.06204 / 1.31 ( 72) hydrogen bonds : bond 0.19379 / 12.91 ( 919) hydrogen bonds : angle 8.76399 / 6.13 ( 2628) link_BETA1-4 : bond 0.00431 / 0.26 ( 15) link_BETA1-4 : angle 2.17889 / 1.57 ( 45) link_NAG-ASN : bond 0.01184 / 0.74 ( 48) link_NAG-ASN : angle 7.26846 / 4.99 ( 144) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5802 Ramachandran restraints generated. 2901 Oldfield, 0 Emsley, 2901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5802 Ramachandran restraints generated. 2901 Oldfield, 0 Emsley, 2901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 194 time to evaluate : 0.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 ASN cc_start: 0.8495 (m-40) cc_final: 0.7743 (p0) REVERT: A 104 TRP cc_start: 0.8391 (m-90) cc_final: 0.8022 (m-90) REVERT: A 239 GLN cc_start: 0.8200 (mm110) cc_final: 0.7984 (mm-40) REVERT: A 389 ASP cc_start: 0.8927 (m-30) cc_final: 0.8506 (m-30) REVERT: A 516 GLU cc_start: 0.7690 (OUTLIER) cc_final: 0.7453 (tp30) REVERT: A 517 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8173 (mm) REVERT: A 584 ILE cc_start: 0.8726 (OUTLIER) cc_final: 0.8482 (tp) REVERT: A 978 ASN cc_start: 0.8383 (OUTLIER) cc_final: 0.8155 (t0) REVERT: A 985 ASP cc_start: 0.8006 (m-30) cc_final: 0.7490 (m-30) REVERT: A 1107 ARG cc_start: 0.8204 (OUTLIER) cc_final: 0.7786 (ttm110) REVERT: B 87 ASN cc_start: 0.8338 (m-40) cc_final: 0.7944 (p0) REVERT: B 389 ASP cc_start: 0.8855 (m-30) cc_final: 0.8489 (m-30) REVERT: B 508 TYR cc_start: 0.7306 (m-80) cc_final: 0.6929 (m-80) REVERT: B 517 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8243 (mm) REVERT: B 584 ILE cc_start: 0.8866 (OUTLIER) cc_final: 0.8538 (tp) REVERT: B 598 ILE cc_start: 0.9166 (mt) cc_final: 0.8924 (mm) REVERT: B 869 MET cc_start: 0.8189 (mtt) cc_final: 0.7921 (mtt) REVERT: B 1107 ARG cc_start: 0.8200 (OUTLIER) cc_final: 0.7684 (ttm170) REVERT: C 87 ASN cc_start: 0.8539 (m-40) cc_final: 0.7801 (p0) REVERT: C 389 ASP cc_start: 0.8850 (m-30) cc_final: 0.8399 (m-30) REVERT: C 584 ILE cc_start: 0.8881 (OUTLIER) cc_final: 0.8606 (tp) REVERT: C 751 ASN cc_start: 0.8671 (m-40) cc_final: 0.8286 (m-40) outliers start: 45 outliers final: 11 residues processed: 220 average time/residue: 0.1555 time to fit residues: 56.0625 Evaluate side-chains 153 residues out of total 2589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 133 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 902 MET Chi-restraints excluded: chain A residue 978 ASN Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 465 GLU Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 755 GLN Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 1107 ARG Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 755 GLN Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 1107 ARG Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 197 optimal weight: 10.0000 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 0.9980 chunk 111 optimal weight: 3.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 HIS A 755 GLN A 901 GLN A 955 ASN A 957 GLN ** A 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1113 GLN B 66 HIS ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN B 955 ASN B1113 GLN C 66 HIS C 901 GLN C 955 ASN C 957 GLN C1113 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.099067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.061772 restraints weight = 64724.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.064485 restraints weight = 28243.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.066209 restraints weight = 17438.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.067245 restraints weight = 13214.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.067820 restraints weight = 11311.709| |-----------------------------------------------------------------------------| r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.2061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 24627 Z= 0.274 Angle : 0.925 22.060 33612 Z= 0.424 Chirality : 0.068 0.892 3990 Planarity : 0.005 0.048 4221 Dihedral : 6.807 72.893 3204 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 1.20 % Allowed : 7.26 % Favored : 91.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.15 (0.14), residues: 2901 helix: 0.80 (0.19), residues: 693 sheet: -1.05 (0.18), residues: 660 loop : -1.36 (0.14), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 357 TYR 0.014 0.002 TYR A 380 PHE 0.023 0.002 PHE C1148 TRP 0.023 0.002 TRP A 436 HIS 0.006 0.001 HIS B1058 Details of bonding type rmsd/Z covalent geometry : bond 0.00608 / 0.27 (24528) covalent geometry : angle 0.80384 / 0.40 (33351) SS BOND : bond 0.00569 / 0.37 ( 36) SS BOND : angle 1.37102 / 0.87 ( 72) hydrogen bonds : bond 0.04609 / 3.02 ( 919) hydrogen bonds : angle 6.18269 / 4.30 ( 2628) link_BETA1-4 : bond 0.00383 / 0.24 ( 15) link_BETA1-4 : angle 1.26503 / 0.77 ( 45) link_NAG-ASN : bond 0.00976 / 0.62 ( 48) link_NAG-ASN : angle 6.98187 / 4.77 ( 144) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5802 Ramachandran restraints generated. 2901 Oldfield, 0 Emsley, 2901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5802 Ramachandran restraints generated. 2901 Oldfield, 0 Emsley, 2901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 2589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 156 time to evaluate : 0.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 ASN cc_start: 0.8637 (m-40) cc_final: 0.7872 (p0) REVERT: A 104 TRP cc_start: 0.8504 (m-90) cc_final: 0.8188 (m-90) REVERT: A 369 TYR cc_start: 0.8110 (t80) cc_final: 0.7871 (t80) REVERT: A 389 ASP cc_start: 0.9048 (m-30) cc_final: 0.8687 (m-30) REVERT: A 508 TYR cc_start: 0.8324 (m-80) cc_final: 0.7943 (m-80) REVERT: A 584 ILE cc_start: 0.8976 (OUTLIER) cc_final: 0.8652 (tp) REVERT: A 751 ASN cc_start: 0.8789 (m-40) cc_final: 0.8582 (m-40) REVERT: A 985 ASP cc_start: 0.7818 (m-30) cc_final: 0.7222 (m-30) REVERT: B 87 ASN cc_start: 0.8522 (m-40) cc_final: 0.8029 (p0) REVERT: B 389 ASP cc_start: 0.8983 (m-30) cc_final: 0.8640 (m-30) REVERT: B 508 TYR cc_start: 0.8186 (m-80) cc_final: 0.7762 (m-80) REVERT: B 584 ILE cc_start: 0.9042 (OUTLIER) cc_final: 0.8565 (tt) REVERT: B 985 ASP cc_start: 0.7792 (m-30) cc_final: 0.7287 (m-30) REVERT: C 87 ASN cc_start: 0.8678 (m-40) cc_final: 0.7927 (p0) REVERT: C 508 TYR cc_start: 0.8296 (m-80) cc_final: 0.7872 (m-80) REVERT: C 584 ILE cc_start: 0.9091 (OUTLIER) cc_final: 0.8813 (tp) REVERT: C 985 ASP cc_start: 0.7712 (m-30) cc_final: 0.7120 (m-30) outliers start: 31 outliers final: 11 residues processed: 173 average time/residue: 0.1511 time to fit residues: 43.4049 Evaluate side-chains 147 residues out of total 2589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 133 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 214 ARG Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain C residue 214 ARG Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 1130 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 59 optimal weight: 0.9990 chunk 190 optimal weight: 3.9990 chunk 49 optimal weight: 6.9990 chunk 167 optimal weight: 0.6980 chunk 66 optimal weight: 0.8980 chunk 163 optimal weight: 2.9990 chunk 151 optimal weight: 4.9990 chunk 261 optimal weight: 4.9990 chunk 123 optimal weight: 0.1980 chunk 227 optimal weight: 9.9990 chunk 144 optimal weight: 9.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 978 ASN B 965 GLN ** B 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 965 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.100671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.063344 restraints weight = 64321.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.066163 restraints weight = 27679.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.067880 restraints weight = 16990.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.068971 restraints weight = 12910.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.069552 restraints weight = 11061.011| |-----------------------------------------------------------------------------| r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.2506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 24627 Z= 0.127 Angle : 0.764 18.907 33612 Z= 0.338 Chirality : 0.059 0.728 3990 Planarity : 0.004 0.045 4221 Dihedral : 5.122 48.477 3156 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 1.39 % Allowed : 9.73 % Favored : 88.88 % 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: -0.64 (0.15), residues: 2901 helix: 1.39 (0.20), residues: 687 sheet: -0.74 (0.19), residues: 666 loop : -1.12 (0.15), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 357 TYR 0.015 0.001 TYR C 380 PHE 0.018 0.001 PHE A 92 TRP 0.020 0.001 TRP C 436 HIS 0.002 0.001 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.13 (24528) covalent geometry : angle 0.65817 / 0.31 (33351) SS BOND : bond 0.00286 / 0.19 ( 36) SS BOND : angle 0.86198 / 0.54 ( 72) hydrogen bonds : bond 0.04038 / 2.63 ( 919) hydrogen bonds : angle 5.64995 / 3.93 ( 2628) link_BETA1-4 : bond 0.00338 / 0.20 ( 15) link_BETA1-4 : angle 1.03076 / 0.68 ( 45) link_NAG-ASN : bond 0.00833 / 0.52 ( 48) link_NAG-ASN : angle 5.92988 / 4.07 ( 144) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5802 Ramachandran restraints generated. 2901 Oldfield, 0 Emsley, 2901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5802 Ramachandran restraints generated. 2901 Oldfield, 0 Emsley, 2901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 2589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 159 time to evaluate : 0.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 ASN cc_start: 0.8629 (m-40) cc_final: 0.7918 (p0) REVERT: A 104 TRP cc_start: 0.8588 (m-90) cc_final: 0.8332 (m-90) REVERT: A 751 ASN cc_start: 0.8719 (m-40) cc_final: 0.8507 (m-40) REVERT: A 960 ASN cc_start: 0.8403 (m-40) cc_final: 0.7973 (t0) REVERT: A 985 ASP cc_start: 0.7771 (m-30) cc_final: 0.7306 (m-30) REVERT: B 87 ASN cc_start: 0.8483 (m-40) cc_final: 0.7993 (p0) REVERT: B 508 TYR cc_start: 0.8385 (m-80) cc_final: 0.7987 (m-80) REVERT: B 584 ILE cc_start: 0.9057 (OUTLIER) cc_final: 0.8594 (tt) REVERT: B 979 ASP cc_start: 0.8227 (t0) cc_final: 0.7844 (t0) REVERT: C 87 ASN cc_start: 0.8663 (m-40) cc_final: 0.7939 (p0) REVERT: C 508 TYR cc_start: 0.8465 (m-80) cc_final: 0.7991 (m-80) outliers start: 36 outliers final: 16 residues processed: 188 average time/residue: 0.1538 time to fit residues: 47.4882 Evaluate side-chains 151 residues out of total 2589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 134 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 1130 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 265 optimal weight: 0.9980 chunk 9 optimal weight: 0.3980 chunk 293 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 227 optimal weight: 7.9990 chunk 254 optimal weight: 3.9990 chunk 273 optimal weight: 7.9990 chunk 266 optimal weight: 0.9990 chunk 23 optimal weight: 9.9990 chunk 161 optimal weight: 1.9990 chunk 155 optimal weight: 3.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 978 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.099687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.062069 restraints weight = 64756.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.064869 restraints weight = 28237.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.066632 restraints weight = 17409.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.067653 restraints weight = 13221.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.068264 restraints weight = 11375.723| |-----------------------------------------------------------------------------| r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.2919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 24627 Z= 0.149 Angle : 0.718 17.650 33612 Z= 0.322 Chirality : 0.056 0.630 3990 Planarity : 0.004 0.059 4221 Dihedral : 4.699 36.679 3152 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 1.58 % Allowed : 11.66 % Favored : 86.75 % 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: -0.42 (0.15), residues: 2901 helix: 1.55 (0.20), residues: 687 sheet: -0.57 (0.19), residues: 639 loop : -0.97 (0.15), residues: 1575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C1107 TYR 0.013 0.001 TYR C 204 PHE 0.014 0.001 PHE A 92 TRP 0.018 0.001 TRP C 436 HIS 0.003 0.001 HIS B1058 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 (24528) covalent geometry : angle 0.62346 / 0.30 (33351) SS BOND : bond 0.00571 / 0.40 ( 36) SS BOND : angle 1.35303 / 0.83 ( 72) hydrogen bonds : bond 0.03654 / 2.37 ( 919) hydrogen bonds : angle 5.38239 / 3.75 ( 2628) link_BETA1-4 : bond 0.00317 / 0.19 ( 15) link_BETA1-4 : angle 0.90473 / 0.59 ( 45) link_NAG-ASN : bond 0.00787 / 0.50 ( 48) link_NAG-ASN : angle 5.41121 / 3.73 ( 144) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5802 Ramachandran restraints generated. 2901 Oldfield, 0 Emsley, 2901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5802 Ramachandran restraints generated. 2901 Oldfield, 0 Emsley, 2901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 2589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 144 time to evaluate : 0.946 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 THR cc_start: 0.9126 (OUTLIER) cc_final: 0.8872 (p) REVERT: A 87 ASN cc_start: 0.8632 (m-40) cc_final: 0.8060 (p0) REVERT: A 104 TRP cc_start: 0.8592 (m-90) cc_final: 0.8352 (m-90) REVERT: A 751 ASN cc_start: 0.8737 (m-40) cc_final: 0.8517 (m-40) REVERT: A 900 MET cc_start: 0.9053 (mtp) cc_final: 0.8781 (mtt) REVERT: A 960 ASN cc_start: 0.8386 (m-40) cc_final: 0.8025 (t0) REVERT: B 33 THR cc_start: 0.9186 (OUTLIER) cc_final: 0.8877 (p) REVERT: B 52 GLN cc_start: 0.8966 (tt0) cc_final: 0.8332 (tm-30) REVERT: B 87 ASN cc_start: 0.8500 (m-40) cc_final: 0.8032 (p0) REVERT: B 104 TRP cc_start: 0.8871 (m-90) cc_final: 0.8453 (m-90) REVERT: B 508 TYR cc_start: 0.8534 (m-80) cc_final: 0.8142 (m-80) REVERT: C 33 THR cc_start: 0.9163 (OUTLIER) cc_final: 0.8852 (p) REVERT: C 87 ASN cc_start: 0.8680 (m-40) cc_final: 0.7994 (p0) REVERT: C 568 ASP cc_start: 0.8419 (t0) cc_final: 0.7705 (p0) REVERT: C 740 MET cc_start: 0.8853 (tpp) cc_final: 0.8574 (tpp) REVERT: C 979 ASP cc_start: 0.8070 (t0) cc_final: 0.7616 (t0) REVERT: C 985 ASP cc_start: 0.7724 (m-30) cc_final: 0.7177 (m-30) outliers start: 41 outliers final: 16 residues processed: 176 average time/residue: 0.1394 time to fit residues: 42.0196 Evaluate side-chains 144 residues out of total 2589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 125 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 1130 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 175 optimal weight: 6.9990 chunk 226 optimal weight: 10.0000 chunk 249 optimal weight: 4.9990 chunk 2 optimal weight: 9.9990 chunk 75 optimal weight: 4.9990 chunk 286 optimal weight: 0.4980 chunk 112 optimal weight: 0.4980 chunk 229 optimal weight: 20.0000 chunk 101 optimal weight: 3.9990 chunk 167 optimal weight: 1.9990 chunk 149 optimal weight: 2.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 978 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.098610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.060945 restraints weight = 63933.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.063682 restraints weight = 28008.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.065413 restraints weight = 17339.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.066449 restraints weight = 13158.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.066993 restraints weight = 11301.972| |-----------------------------------------------------------------------------| r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.3280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 24627 Z= 0.161 Angle : 0.689 16.929 33612 Z= 0.312 Chirality : 0.054 0.550 3990 Planarity : 0.004 0.049 4221 Dihedral : 4.429 20.561 3150 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 1.51 % Allowed : 12.75 % Favored : 85.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.15), residues: 2901 helix: 1.38 (0.20), residues: 711 sheet: -0.43 (0.19), residues: 633 loop : -0.79 (0.15), residues: 1557 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C1107 TYR 0.022 0.001 TYR B 904 PHE 0.018 0.001 PHE B 464 TRP 0.013 0.001 TRP C 436 HIS 0.003 0.001 HIS C1058 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.16 (24528) covalent geometry : angle 0.60775 / 0.29 (33351) SS BOND : bond 0.00398 / 0.27 ( 36) SS BOND : angle 1.21896 / 0.75 ( 72) hydrogen bonds : bond 0.03669 / 2.38 ( 919) hydrogen bonds : angle 5.19638 / 3.62 ( 2628) link_BETA1-4 : bond 0.00374 / 0.23 ( 15) link_BETA1-4 : angle 0.88310 / 0.58 ( 45) link_NAG-ASN : bond 0.00715 / 0.45 ( 48) link_NAG-ASN : angle 4.91863 / 3.41 ( 144) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5802 Ramachandran restraints generated. 2901 Oldfield, 0 Emsley, 2901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5802 Ramachandran restraints generated. 2901 Oldfield, 0 Emsley, 2901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 2589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 140 time to evaluate : 0.923 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 THR cc_start: 0.9165 (OUTLIER) cc_final: 0.8901 (p) REVERT: A 87 ASN cc_start: 0.8667 (m-40) cc_final: 0.8086 (p0) REVERT: A 104 TRP cc_start: 0.8680 (m-90) cc_final: 0.8431 (m-90) REVERT: A 354 ASN cc_start: 0.9319 (t0) cc_final: 0.8995 (t0) REVERT: A 751 ASN cc_start: 0.8727 (m-40) cc_final: 0.8516 (m-40) REVERT: B 33 THR cc_start: 0.9210 (OUTLIER) cc_final: 0.8906 (p) REVERT: B 52 GLN cc_start: 0.8953 (tt0) cc_final: 0.8328 (tm-30) REVERT: B 87 ASN cc_start: 0.8482 (m-40) cc_final: 0.7993 (p0) REVERT: B 104 TRP cc_start: 0.8900 (m-90) cc_final: 0.8447 (m-90) REVERT: B 508 TYR cc_start: 0.8663 (m-80) cc_final: 0.8231 (m-80) REVERT: B 978 ASN cc_start: 0.8474 (t0) cc_final: 0.8187 (t0) REVERT: C 33 THR cc_start: 0.9195 (OUTLIER) cc_final: 0.8885 (p) REVERT: C 52 GLN cc_start: 0.8981 (tt0) cc_final: 0.8446 (tm-30) REVERT: C 87 ASN cc_start: 0.8716 (m-40) cc_final: 0.8026 (p0) REVERT: C 104 TRP cc_start: 0.8761 (m-90) cc_final: 0.8126 (m-90) REVERT: C 354 ASN cc_start: 0.9245 (t0) cc_final: 0.8857 (t0) REVERT: C 568 ASP cc_start: 0.8410 (t0) cc_final: 0.7745 (p0) REVERT: C 740 MET cc_start: 0.8845 (tpp) cc_final: 0.8566 (tpp) REVERT: C 978 ASN cc_start: 0.8624 (OUTLIER) cc_final: 0.8387 (t0) outliers start: 39 outliers final: 23 residues processed: 167 average time/residue: 0.1459 time to fit residues: 41.6128 Evaluate side-chains 154 residues out of total 2589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 127 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 449 TYR Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 92 PHE Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 978 ASN Chi-restraints excluded: chain C residue 1130 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 111 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 chunk 179 optimal weight: 6.9990 chunk 38 optimal weight: 2.9990 chunk 77 optimal weight: 0.0980 chunk 168 optimal weight: 2.9990 chunk 147 optimal weight: 3.9990 chunk 232 optimal weight: 50.0000 chunk 167 optimal weight: 0.0770 chunk 225 optimal weight: 5.9990 chunk 192 optimal weight: 2.9990 overall best weight: 0.9940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.099632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.062107 restraints weight = 64460.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.064909 restraints weight = 27992.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.066681 restraints weight = 17226.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.067742 restraints weight = 13036.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.068318 restraints weight = 11164.412| |-----------------------------------------------------------------------------| r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.3439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 24627 Z= 0.111 Angle : 0.650 16.762 33612 Z= 0.294 Chirality : 0.053 0.522 3990 Planarity : 0.003 0.048 4221 Dihedral : 4.257 19.212 3150 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 1.58 % Allowed : 13.13 % Favored : 85.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.15), residues: 2901 helix: 1.63 (0.20), residues: 705 sheet: -0.39 (0.19), residues: 639 loop : -0.76 (0.15), residues: 1557 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C1107 TYR 0.018 0.001 TYR B 904 PHE 0.013 0.001 PHE A 92 TRP 0.019 0.001 TRP C 436 HIS 0.001 0.000 HIS C1058 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (24528) covalent geometry : angle 0.57213 / 0.28 (33351) SS BOND : bond 0.00320 / 0.22 ( 36) SS BOND : angle 0.87350 / 0.55 ( 72) hydrogen bonds : bond 0.03408 / 2.21 ( 919) hydrogen bonds : angle 5.07185 / 3.53 ( 2628) link_BETA1-4 : bond 0.00384 / 0.24 ( 15) link_BETA1-4 : angle 0.80310 / 0.53 ( 45) link_NAG-ASN : bond 0.00770 / 0.49 ( 48) link_NAG-ASN : angle 4.72088 / 3.29 ( 144) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5802 Ramachandran restraints generated. 2901 Oldfield, 0 Emsley, 2901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5802 Ramachandran restraints generated. 2901 Oldfield, 0 Emsley, 2901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 2589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 143 time to evaluate : 1.020 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 THR cc_start: 0.9144 (OUTLIER) cc_final: 0.8878 (p) REVERT: A 87 ASN cc_start: 0.8647 (m-40) cc_final: 0.8037 (p0) REVERT: A 104 TRP cc_start: 0.8642 (m-90) cc_final: 0.8386 (m-90) REVERT: A 354 ASN cc_start: 0.9273 (t0) cc_final: 0.8964 (t0) REVERT: A 751 ASN cc_start: 0.8680 (m-40) cc_final: 0.8477 (m-40) REVERT: A 759 PHE cc_start: 0.8644 (OUTLIER) cc_final: 0.8303 (t80) REVERT: A 979 ASP cc_start: 0.8280 (t0) cc_final: 0.8048 (t0) REVERT: B 33 THR cc_start: 0.9185 (OUTLIER) cc_final: 0.8881 (p) REVERT: B 52 GLN cc_start: 0.8931 (tt0) cc_final: 0.8322 (tm-30) REVERT: B 87 ASN cc_start: 0.8467 (m-40) cc_final: 0.7966 (p0) REVERT: B 104 TRP cc_start: 0.8862 (m-90) cc_final: 0.8419 (m-90) REVERT: B 354 ASN cc_start: 0.9183 (t0) cc_final: 0.8135 (p0) REVERT: B 508 TYR cc_start: 0.8661 (m-80) cc_final: 0.8194 (m-80) REVERT: B 705 VAL cc_start: 0.9191 (OUTLIER) cc_final: 0.8949 (m) REVERT: B 759 PHE cc_start: 0.8592 (OUTLIER) cc_final: 0.8391 (t80) REVERT: B 978 ASN cc_start: 0.8468 (t0) cc_final: 0.8151 (t0) REVERT: B 985 ASP cc_start: 0.7619 (m-30) cc_final: 0.7183 (m-30) REVERT: B 1119 ASN cc_start: 0.8284 (m-40) cc_final: 0.8013 (m-40) REVERT: C 33 THR cc_start: 0.9165 (OUTLIER) cc_final: 0.8871 (p) REVERT: C 52 GLN cc_start: 0.8957 (tt0) cc_final: 0.8445 (tm-30) REVERT: C 87 ASN cc_start: 0.8719 (m-40) cc_final: 0.8029 (p0) REVERT: C 104 TRP cc_start: 0.8671 (m-90) cc_final: 0.8034 (m-90) REVERT: C 354 ASN cc_start: 0.9175 (t0) cc_final: 0.8807 (t0) REVERT: C 740 MET cc_start: 0.8824 (tpp) cc_final: 0.8567 (tpp) REVERT: C 985 ASP cc_start: 0.7839 (m-30) cc_final: 0.7313 (m-30) REVERT: C 1119 ASN cc_start: 0.8112 (m-40) cc_final: 0.7852 (m110) outliers start: 41 outliers final: 25 residues processed: 176 average time/residue: 0.1456 time to fit residues: 44.0793 Evaluate side-chains 161 residues out of total 2589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 130 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 568 ASP Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 1130 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 55 optimal weight: 9.9990 chunk 23 optimal weight: 5.9990 chunk 229 optimal weight: 20.0000 chunk 122 optimal weight: 9.9990 chunk 246 optimal weight: 2.9990 chunk 236 optimal weight: 9.9990 chunk 182 optimal weight: 1.9990 chunk 219 optimal weight: 10.0000 chunk 52 optimal weight: 5.9990 chunk 108 optimal weight: 5.9990 chunk 198 optimal weight: 9.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 271 GLN A 755 GLN A 919 ASN A1101 HIS B 271 GLN B1101 HIS C 271 GLN C1101 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.096040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.057545 restraints weight = 64837.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.060160 restraints weight = 29005.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.061833 restraints weight = 18223.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.062817 restraints weight = 13935.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.063361 restraints weight = 12019.152| |-----------------------------------------------------------------------------| r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.3803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.100 24627 Z= 0.321 Angle : 0.757 16.297 33612 Z= 0.354 Chirality : 0.055 0.569 3990 Planarity : 0.004 0.047 4221 Dihedral : 4.587 18.217 3150 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 2.24 % Allowed : 12.98 % Favored : 84.78 % 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: -0.32 (0.15), residues: 2901 helix: 1.19 (0.19), residues: 702 sheet: -0.41 (0.19), residues: 648 loop : -0.74 (0.15), residues: 1551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 815 TYR 0.019 0.001 TYR B 904 PHE 0.018 0.002 PHE B 464 TRP 0.018 0.001 TRP B 436 HIS 0.006 0.001 HIS C1058 Details of bonding type rmsd/Z covalent geometry : bond 0.00727 / 0.32 (24528) covalent geometry : angle 0.69578 / 0.34 (33351) SS BOND : bond 0.00525 / 0.35 ( 36) SS BOND : angle 1.25184 / 0.81 ( 72) hydrogen bonds : bond 0.04245 / 2.78 ( 919) hydrogen bonds : angle 5.34440 / 3.73 ( 2628) link_BETA1-4 : bond 0.00372 / 0.21 ( 15) link_BETA1-4 : angle 1.09919 / 0.73 ( 45) link_NAG-ASN : bond 0.00628 / 0.40 ( 48) link_NAG-ASN : angle 4.54245 / 3.16 ( 144) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5802 Ramachandran restraints generated. 2901 Oldfield, 0 Emsley, 2901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5802 Ramachandran restraints generated. 2901 Oldfield, 0 Emsley, 2901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 2589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 125 time to evaluate : 0.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 THR cc_start: 0.9284 (OUTLIER) cc_final: 0.8974 (p) REVERT: A 87 ASN cc_start: 0.8745 (m-40) cc_final: 0.8147 (p0) REVERT: A 104 TRP cc_start: 0.8798 (m-90) cc_final: 0.8461 (m-90) REVERT: A 751 ASN cc_start: 0.8727 (m-40) cc_final: 0.8487 (m-40) REVERT: A 985 ASP cc_start: 0.7708 (m-30) cc_final: 0.7091 (m-30) REVERT: B 33 THR cc_start: 0.9301 (OUTLIER) cc_final: 0.9025 (p) REVERT: B 52 GLN cc_start: 0.9001 (tt0) cc_final: 0.8362 (tm-30) REVERT: B 87 ASN cc_start: 0.8575 (m-40) cc_final: 0.8059 (p0) REVERT: B 104 TRP cc_start: 0.8977 (m-90) cc_final: 0.8563 (m-90) REVERT: B 508 TYR cc_start: 0.8810 (m-80) cc_final: 0.8297 (m-80) REVERT: B 759 PHE cc_start: 0.8751 (OUTLIER) cc_final: 0.8405 (t80) REVERT: B 978 ASN cc_start: 0.8535 (t0) cc_final: 0.8154 (t0) REVERT: C 33 THR cc_start: 0.9323 (OUTLIER) cc_final: 0.9039 (p) REVERT: C 87 ASN cc_start: 0.8760 (m-40) cc_final: 0.8034 (p0) REVERT: C 104 TRP cc_start: 0.8787 (m-90) cc_final: 0.8140 (m-90) REVERT: C 740 MET cc_start: 0.8901 (tpp) cc_final: 0.8688 (tpp) REVERT: C 985 ASP cc_start: 0.7711 (m-30) cc_final: 0.7032 (m-30) outliers start: 58 outliers final: 34 residues processed: 174 average time/residue: 0.1390 time to fit residues: 41.9643 Evaluate side-chains 159 residues out of total 2589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 121 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 755 GLN Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 449 TYR Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 568 ASP Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 449 TYR Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1130 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 199 optimal weight: 10.0000 chunk 96 optimal weight: 8.9990 chunk 27 optimal weight: 9.9990 chunk 55 optimal weight: 5.9990 chunk 31 optimal weight: 20.0000 chunk 241 optimal weight: 0.9980 chunk 207 optimal weight: 30.0000 chunk 65 optimal weight: 0.7980 chunk 41 optimal weight: 7.9990 chunk 245 optimal weight: 10.0000 chunk 11 optimal weight: 20.0000 overall best weight: 4.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 211 ASN A 422 ASN A 501 ASN B 239 GLN B 501 ASN ** B 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 501 ASN C 919 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.095487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.056365 restraints weight = 65063.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.059026 restraints weight = 29033.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.060712 restraints weight = 18251.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.061766 restraints weight = 13951.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.062333 restraints weight = 12010.864| |-----------------------------------------------------------------------------| r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.4132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 24627 Z= 0.332 Angle : 0.756 16.489 33612 Z= 0.355 Chirality : 0.055 0.560 3990 Planarity : 0.004 0.047 4221 Dihedral : 4.702 18.757 3150 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 1.97 % Allowed : 13.79 % Favored : 84.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.15), residues: 2901 helix: 1.02 (0.19), residues: 699 sheet: -0.46 (0.18), residues: 675 loop : -0.70 (0.15), residues: 1527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 815 TYR 0.032 0.001 TYR A 756 PHE 0.022 0.002 PHE B 970 TRP 0.011 0.001 TRP B 436 HIS 0.006 0.001 HIS A1058 Details of bonding type rmsd/Z covalent geometry : bond 0.00750 / 0.33 (24528) covalent geometry : angle 0.69636 / 0.34 (33351) SS BOND : bond 0.00540 / 0.36 ( 36) SS BOND : angle 1.32539 / 0.85 ( 72) hydrogen bonds : bond 0.04173 / 2.73 ( 919) hydrogen bonds : angle 5.35919 / 3.74 ( 2628) link_BETA1-4 : bond 0.00489 / 0.27 ( 15) link_BETA1-4 : angle 0.94583 / 0.63 ( 45) link_NAG-ASN : bond 0.00639 / 0.40 ( 48) link_NAG-ASN : angle 4.46537 / 3.12 ( 144) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5802 Ramachandran restraints generated. 2901 Oldfield, 0 Emsley, 2901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5802 Ramachandran restraints generated. 2901 Oldfield, 0 Emsley, 2901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 2589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 119 time to evaluate : 0.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 THR cc_start: 0.9349 (OUTLIER) cc_final: 0.9036 (p) REVERT: A 87 ASN cc_start: 0.8759 (m-40) cc_final: 0.8083 (p0) REVERT: A 104 TRP cc_start: 0.8735 (m-90) cc_final: 0.8449 (m-90) REVERT: A 423 TYR cc_start: 0.8379 (t80) cc_final: 0.8066 (t80) REVERT: A 751 ASN cc_start: 0.8719 (m-40) cc_final: 0.8437 (m-40) REVERT: A 755 GLN cc_start: 0.8875 (OUTLIER) cc_final: 0.8425 (pp30) REVERT: A 759 PHE cc_start: 0.8794 (OUTLIER) cc_final: 0.8336 (t80) REVERT: A 985 ASP cc_start: 0.7664 (m-30) cc_final: 0.7039 (m-30) REVERT: B 33 THR cc_start: 0.9333 (OUTLIER) cc_final: 0.9062 (p) REVERT: B 87 ASN cc_start: 0.8634 (m-40) cc_final: 0.8003 (p0) REVERT: B 104 TRP cc_start: 0.9004 (m-90) cc_final: 0.8596 (m-90) REVERT: B 200 TYR cc_start: 0.8711 (OUTLIER) cc_final: 0.8469 (m-10) REVERT: B 239 GLN cc_start: 0.8433 (mm110) cc_final: 0.8074 (mm110) REVERT: B 269 TYR cc_start: 0.8608 (m-80) cc_final: 0.7465 (m-10) REVERT: B 759 PHE cc_start: 0.8701 (OUTLIER) cc_final: 0.8478 (t80) REVERT: B 978 ASN cc_start: 0.8483 (m-40) cc_final: 0.8095 (t0) REVERT: C 33 THR cc_start: 0.9323 (OUTLIER) cc_final: 0.9044 (p) REVERT: C 87 ASN cc_start: 0.8734 (m-40) cc_final: 0.7996 (p0) REVERT: C 104 TRP cc_start: 0.8788 (m-90) cc_final: 0.8178 (m-90) REVERT: C 117 LEU cc_start: 0.9298 (OUTLIER) cc_final: 0.9013 (tp) REVERT: C 740 MET cc_start: 0.8914 (tpp) cc_final: 0.8679 (tpp) REVERT: C 759 PHE cc_start: 0.8826 (OUTLIER) cc_final: 0.8053 (t80) REVERT: C 985 ASP cc_start: 0.7780 (m-30) cc_final: 0.7052 (m-30) outliers start: 51 outliers final: 32 residues processed: 165 average time/residue: 0.1415 time to fit residues: 40.5751 Evaluate side-chains 152 residues out of total 2589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 111 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 755 GLN Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 449 TYR Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1130 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 142 optimal weight: 5.9990 chunk 33 optimal weight: 9.9990 chunk 32 optimal weight: 1.9990 chunk 134 optimal weight: 10.0000 chunk 163 optimal weight: 5.9990 chunk 259 optimal weight: 0.8980 chunk 118 optimal weight: 5.9990 chunk 57 optimal weight: 0.8980 chunk 115 optimal weight: 8.9990 chunk 198 optimal weight: 5.9990 chunk 209 optimal weight: 3.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 755 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.096584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.057632 restraints weight = 64891.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.060385 restraints weight = 28533.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.062153 restraints weight = 17772.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.063192 restraints weight = 13533.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.063763 restraints weight = 11645.106| |-----------------------------------------------------------------------------| r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.4224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 24627 Z= 0.201 Angle : 0.683 16.275 33612 Z= 0.316 Chirality : 0.053 0.538 3990 Planarity : 0.004 0.048 4221 Dihedral : 4.525 17.970 3150 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 1.74 % Allowed : 14.06 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.15), residues: 2901 helix: 1.20 (0.19), residues: 705 sheet: -0.35 (0.18), residues: 669 loop : -0.63 (0.15), residues: 1527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 815 TYR 0.015 0.001 TYR B 904 PHE 0.034 0.001 PHE B 855 TRP 0.013 0.001 TRP B 436 HIS 0.004 0.001 HIS C1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00454 / 0.20 (24528) covalent geometry : angle 0.61693 / 0.30 (33351) SS BOND : bond 0.00376 / 0.25 ( 36) SS BOND : angle 1.81147 / 1.13 ( 72) hydrogen bonds : bond 0.03814 / 2.49 ( 919) hydrogen bonds : angle 5.19956 / 3.63 ( 2628) link_BETA1-4 : bond 0.00360 / 0.21 ( 15) link_BETA1-4 : angle 0.83493 / 0.55 ( 45) link_NAG-ASN : bond 0.00674 / 0.43 ( 48) link_NAG-ASN : angle 4.35169 / 3.05 ( 144) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5802 Ramachandran restraints generated. 2901 Oldfield, 0 Emsley, 2901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5802 Ramachandran restraints generated. 2901 Oldfield, 0 Emsley, 2901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 2589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 121 time to evaluate : 0.924 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 THR cc_start: 0.9303 (OUTLIER) cc_final: 0.8988 (p) REVERT: A 87 ASN cc_start: 0.8780 (m-40) cc_final: 0.8126 (p0) REVERT: A 104 TRP cc_start: 0.8672 (m-90) cc_final: 0.8404 (m-90) REVERT: A 423 TYR cc_start: 0.8399 (t80) cc_final: 0.8079 (t80) REVERT: A 751 ASN cc_start: 0.8742 (m-40) cc_final: 0.8407 (m-40) REVERT: A 759 PHE cc_start: 0.8695 (OUTLIER) cc_final: 0.8243 (t80) REVERT: B 33 THR cc_start: 0.9296 (OUTLIER) cc_final: 0.9022 (p) REVERT: B 87 ASN cc_start: 0.8631 (m-40) cc_final: 0.7957 (p0) REVERT: B 104 TRP cc_start: 0.8967 (m-90) cc_final: 0.8518 (m-90) REVERT: B 269 TYR cc_start: 0.8588 (m-80) cc_final: 0.7413 (m-10) REVERT: B 584 ILE cc_start: 0.9099 (OUTLIER) cc_final: 0.8785 (pt) REVERT: B 759 PHE cc_start: 0.8488 (OUTLIER) cc_final: 0.8282 (t80) REVERT: B 978 ASN cc_start: 0.8445 (m-40) cc_final: 0.8022 (t0) REVERT: C 33 THR cc_start: 0.9332 (OUTLIER) cc_final: 0.9045 (p) REVERT: C 87 ASN cc_start: 0.8743 (m-40) cc_final: 0.7999 (p0) REVERT: C 104 TRP cc_start: 0.8752 (m-90) cc_final: 0.8176 (m-90) REVERT: C 740 MET cc_start: 0.8878 (tpp) cc_final: 0.8654 (tpp) outliers start: 45 outliers final: 30 residues processed: 160 average time/residue: 0.1431 time to fit residues: 39.5786 Evaluate side-chains 155 residues out of total 2589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 119 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 755 GLN Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 449 TYR Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1130 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 293 optimal weight: 5.9990 chunk 29 optimal weight: 9.9990 chunk 267 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 127 optimal weight: 3.9990 chunk 162 optimal weight: 2.9990 chunk 244 optimal weight: 6.9990 chunk 263 optimal weight: 0.9980 chunk 155 optimal weight: 1.9990 chunk 256 optimal weight: 0.9980 chunk 62 optimal weight: 0.6980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 30 ASN A 196 ASN A 422 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.097312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.059250 restraints weight = 64314.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.062006 restraints weight = 27991.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.063752 restraints weight = 17291.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.064777 restraints weight = 13127.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.065383 restraints weight = 11267.293| |-----------------------------------------------------------------------------| r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.4288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 24627 Z= 0.140 Angle : 0.649 15.961 33612 Z= 0.300 Chirality : 0.052 0.518 3990 Planarity : 0.004 0.048 4221 Dihedral : 4.404 18.434 3150 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 1.54 % Allowed : 14.37 % Favored : 84.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.15), residues: 2901 helix: 1.37 (0.20), residues: 705 sheet: -0.30 (0.19), residues: 630 loop : -0.62 (0.15), residues: 1566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 466 TYR 0.013 0.001 TYR B 904 PHE 0.044 0.001 PHE A 201 TRP 0.013 0.001 TRP B 436 HIS 0.002 0.001 HIS C1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 (24528) covalent geometry : angle 0.58444 / 0.28 (33351) SS BOND : bond 0.00305 / 0.20 ( 36) SS BOND : angle 1.53705 / 0.94 ( 72) hydrogen bonds : bond 0.03569 / 2.32 ( 919) hydrogen bonds : angle 5.09787 / 3.55 ( 2628) link_BETA1-4 : bond 0.00338 / 0.21 ( 15) link_BETA1-4 : angle 0.77096 / 0.50 ( 45) link_NAG-ASN : bond 0.00720 / 0.46 ( 48) link_NAG-ASN : angle 4.24023 / 2.98 ( 144) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5802 Ramachandran restraints generated. 2901 Oldfield, 0 Emsley, 2901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5802 Ramachandran restraints generated. 2901 Oldfield, 0 Emsley, 2901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 2589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 126 time to evaluate : 1.022 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 THR cc_start: 0.9308 (OUTLIER) cc_final: 0.9007 (p) REVERT: A 87 ASN cc_start: 0.8786 (m-40) cc_final: 0.8140 (p0) REVERT: A 104 TRP cc_start: 0.8609 (m-90) cc_final: 0.8371 (m-90) REVERT: A 423 TYR cc_start: 0.8346 (t80) cc_final: 0.8036 (t80) REVERT: A 751 ASN cc_start: 0.8707 (m-40) cc_final: 0.8506 (m-40) REVERT: A 759 PHE cc_start: 0.8717 (OUTLIER) cc_final: 0.8249 (t80) REVERT: B 33 THR cc_start: 0.9268 (OUTLIER) cc_final: 0.9003 (p) REVERT: B 52 GLN cc_start: 0.9007 (tt0) cc_final: 0.8402 (tm-30) REVERT: B 87 ASN cc_start: 0.8629 (m-40) cc_final: 0.7950 (p0) REVERT: B 104 TRP cc_start: 0.8970 (m-90) cc_final: 0.8493 (m-90) REVERT: B 269 TYR cc_start: 0.8544 (m-80) cc_final: 0.7264 (m-10) REVERT: B 354 ASN cc_start: 0.9177 (t0) cc_final: 0.8868 (t0) REVERT: B 584 ILE cc_start: 0.9107 (OUTLIER) cc_final: 0.8795 (pt) REVERT: B 978 ASN cc_start: 0.8409 (m-40) cc_final: 0.8029 (t0) REVERT: C 33 THR cc_start: 0.9309 (OUTLIER) cc_final: 0.9037 (p) REVERT: C 87 ASN cc_start: 0.8715 (m-40) cc_final: 0.8318 (m-40) REVERT: C 104 TRP cc_start: 0.8716 (m-90) cc_final: 0.8213 (m-90) REVERT: C 269 TYR cc_start: 0.8694 (m-80) cc_final: 0.8116 (m-80) REVERT: C 389 ASP cc_start: 0.9082 (m-30) cc_final: 0.8805 (m-30) REVERT: C 423 TYR cc_start: 0.8094 (t80) cc_final: 0.7803 (t80) outliers start: 40 outliers final: 29 residues processed: 161 average time/residue: 0.1414 time to fit residues: 39.2608 Evaluate side-chains 160 residues out of total 2589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 126 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 449 TYR Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 449 TYR Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1130 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 232 optimal weight: 40.0000 chunk 198 optimal weight: 9.9990 chunk 280 optimal weight: 0.9990 chunk 250 optimal weight: 9.9990 chunk 277 optimal weight: 0.5980 chunk 171 optimal weight: 0.8980 chunk 39 optimal weight: 0.0170 chunk 189 optimal weight: 5.9990 chunk 130 optimal weight: 0.9990 chunk 53 optimal weight: 0.9980 chunk 137 optimal weight: 0.8980 overall best weight: 0.6818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 755 GLN B 30 ASN B 239 GLN C 30 ASN C 965 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.098588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.061271 restraints weight = 64215.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.064050 restraints weight = 27786.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.065838 restraints weight = 17083.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.066892 restraints weight = 12879.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.067405 restraints weight = 11015.692| |-----------------------------------------------------------------------------| r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.4378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 24627 Z= 0.104 Angle : 0.615 15.453 33612 Z= 0.285 Chirality : 0.051 0.495 3990 Planarity : 0.003 0.048 4221 Dihedral : 4.148 19.560 3150 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.12 % Allowed : 14.91 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.15), residues: 2901 helix: 1.62 (0.20), residues: 705 sheet: -0.21 (0.20), residues: 615 loop : -0.59 (0.15), residues: 1581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 357 TYR 0.014 0.001 TYR B 369 PHE 0.039 0.001 PHE A 201 TRP 0.014 0.001 TRP B 436 HIS 0.002 0.000 HIS B 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.10 (24528) covalent geometry : angle 0.55394 / 0.27 (33351) SS BOND : bond 0.00221 / 0.15 ( 36) SS BOND : angle 1.05019 / 0.63 ( 72) hydrogen bonds : bond 0.03246 / 2.10 ( 919) hydrogen bonds : angle 4.92368 / 3.42 ( 2628) link_BETA1-4 : bond 0.00352 / 0.21 ( 15) link_BETA1-4 : angle 0.73443 / 0.48 ( 45) link_NAG-ASN : bond 0.00781 / 0.50 ( 48) link_NAG-ASN : angle 4.04495 / 2.84 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4400.21 seconds wall clock time: 76 minutes 54.56 seconds (4614.56 seconds total)