Starting phenix.real_space_refine on Tue Aug 26 07:59:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8h08_34411/08_2025/8h08_34411_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h08_34411/08_2025/8h08_34411.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8h08_34411/08_2025/8h08_34411_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h08_34411/08_2025/8h08_34411_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8h08_34411/08_2025/8h08_34411.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h08_34411/08_2025/8h08_34411.map" } resolution = 3.2 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= 0.054 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 4614 atoms to isotropic. 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 111 5.16 5 C 19833 2.51 5 N 5334 2.21 5 O 5999 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 58 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 31277 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 7138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 948, 7138 Classifications: {'peptide': 948} Incomplete info: {'truncation_to_alanine': 93} Link IDs: {'PTRANS': 53, 'TRANS': 894} Chain breaks: 10 Unresolved non-hydrogen bonds: 300 Unresolved non-hydrogen angles: 378 Unresolved non-hydrogen dihedrals: 230 Unresolved non-hydrogen chiralities: 42 Planarities with less than four sites: {'PHE:plan': 4, 'ASN:plan1': 7, 'ARG:plan': 3, 'GLN:plan1': 8, 'GLU:plan': 3, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 125 Chain: "B" Number of atoms: 7024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 933, 7024 Classifications: {'peptide': 933} Incomplete info: {'truncation_to_alanine': 97} Link IDs: {'PTRANS': 50, 'TRANS': 882} Chain breaks: 14 Unresolved non-hydrogen bonds: 314 Unresolved non-hydrogen angles: 406 Unresolved non-hydrogen dihedrals: 243 Unresolved non-hydrogen chiralities: 50 Planarities with less than four sites: {'PHE:plan': 6, 'ARG:plan': 3, 'GLU:plan': 6, 'ASN:plan1': 2, 'GLN:plan1': 4, 'TYR:plan': 3, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 136 Chain: "C" Number of atoms: 7125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 948, 7125 Classifications: {'peptide': 948} Incomplete info: {'truncation_to_alanine': 96} Link IDs: {'PTRANS': 53, 'TRANS': 894} Chain breaks: 11 Unresolved non-hydrogen bonds: 319 Unresolved non-hydrogen angles: 409 Unresolved non-hydrogen dihedrals: 245 Unresolved non-hydrogen chiralities: 51 Planarities with less than four sites: {'PHE:plan': 3, 'HIS:plan': 2, 'ARG:plan': 5, 'ASN:plan1': 2, 'GLU:plan': 7, 'TYR:plan': 2, 'GLN:plan1': 4, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 132 Chain: "D" Number of atoms: 839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 839 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 2, 'TRANS': 113} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "J" Number of atoms: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 738 Classifications: {'peptide': 104} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 95} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'PHE:plan': 2} Unresolved non-hydrogen planarities: 12 Chain: "N" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 945 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 4, 'TRANS': 117} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "O" Number of atoms: 794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 794 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 6, 'TRANS': 99} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "F" Number of atoms: 839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 839 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 2, 'TRANS': 113} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "H" Number of atoms: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 738 Classifications: {'peptide': 104} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 95} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'PHE:plan': 2} Unresolved non-hydrogen planarities: 12 Chain: "I" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 945 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 4, 'TRANS': 117} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "K" Number of atoms: 794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 794 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 6, 'TRANS': 99} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "L" Number of atoms: 839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 839 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 2, 'TRANS': 113} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "P" Number of atoms: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 738 Classifications: {'peptide': 104} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 95} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'PHE:plan': 2} Unresolved non-hydrogen planarities: 12 Chain: "Q" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 945 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 4, 'TRANS': 117} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "R" Number of atoms: 794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 794 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 6, 'TRANS': 99} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 7.87, per 1000 atoms: 0.25 Number of scatterers: 31277 At special positions: 0 Unit cell: (161.99, 172.66, 226.01, 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 111 16.00 O 5999 8.00 N 5334 7.00 C 19833 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=33, symmetry=0 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=1.29 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.05 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=2.05 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.06 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=1.76 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " 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=2.05 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.05 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.04 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 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=1.96 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.02 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.02 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=1.97 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.05 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.02 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.01 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.05 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.04 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=1.97 Simple disulfide: pdb=" SG CYS O 23 " - pdb=" SG CYS O 88 " distance=2.08 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.07 Simple disulfide: pdb=" SG CYS R 23 " - pdb=" SG CYS R 88 " distance=2.07 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 NAG-ASN " NAG A1401 " - " ASN A 343 " " NAG B1401 " - " ASN B 343 " " NAG C1401 " - " ASN C 343 " Time building additional restraints: 2.59 Conformation dependent library (CDL) restraints added in 1.4 seconds Enol-peptide restraints added in 1.2 microseconds 8146 Ramachandran restraints generated. 4073 Oldfield, 0 Emsley, 4073 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7714 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 76 sheets defined 17.4% alpha, 23.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.55 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 384 through 389 removed outlier: 3.547A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 408 removed outlier: 3.968A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 405 through 408' Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 616 through 620 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 757 removed outlier: 3.501A pdb=" N ASN A 751 " --> pdb=" O THR A 747 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N TYR A 756 " --> pdb=" O LEU A 752 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 782 removed outlier: 3.635A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LYS A 776 " --> pdb=" O VAL A 772 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLN A 779 " --> pdb=" O ASP A 775 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N PHE A 782 " --> pdb=" O THR A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.567A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 869 through 880 removed outlier: 3.507A pdb=" N THR A 874 " --> pdb=" O ILE A 870 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER A 875 " --> pdb=" O ALA A 871 " (cutoff:3.500A) Processing helix chain 'A' and resid 885 through 890 removed outlier: 4.127A pdb=" N PHE A 888 " --> pdb=" O GLY A 885 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA A 890 " --> pdb=" O THR A 887 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 902 Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.648A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.599A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR A 941 " --> pdb=" O SER A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.544A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.724A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1022 removed outlier: 3.581A pdb=" N GLU A 990 " --> pdb=" O PRO A 986 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1116 through 1118 No H-bonds generated for 'chain 'A' and resid 1116 through 1118' Processing helix chain 'B' and resid 294 through 304 removed outlier: 3.587A pdb=" N GLU B 298 " --> pdb=" O ASP B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 384 through 389 removed outlier: 3.548A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 408 removed outlier: 3.969A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 405 through 408' Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 616 through 620 removed outlier: 3.548A pdb=" N VAL B 620 " --> pdb=" O CYS B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 757 removed outlier: 3.561A pdb=" N LEU B 754 " --> pdb=" O SER B 750 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 771 removed outlier: 3.552A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) Processing helix chain 'B' and resid 773 through 782 removed outlier: 3.529A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.855A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 869 through 884 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.802A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 901 Processing helix chain 'B' and resid 905 through 909 Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.664A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 939 removed outlier: 3.793A pdb=" N ILE B 923 " --> pdb=" O ASN B 919 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 967 removed outlier: 3.600A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.672A pdb=" N GLU B 990 " --> pdb=" O PRO B 986 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA B1020 " --> pdb=" O ALA B1016 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 4.016A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 384 through 389 removed outlier: 3.548A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 408 removed outlier: 3.969A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 405 through 408' Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 755 removed outlier: 4.209A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 774 Processing helix chain 'C' and resid 776 through 783 removed outlier: 3.879A pdb=" N PHE C 782 " --> pdb=" O THR C 778 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 827 Processing helix chain 'C' and resid 866 through 878 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.874A pdb=" N GLY C 891 " --> pdb=" O PHE C 888 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 907 removed outlier: 4.172A pdb=" N ALA C 903 " --> pdb=" O PRO C 899 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 918 removed outlier: 3.523A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 940 removed outlier: 4.087A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 946 through 965 removed outlier: 3.553A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1022 removed outlier: 3.718A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1145 removed outlier: 4.113A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.540A pdb=" N THR N 91 " --> pdb=" O ALA N 88 " (cutoff:3.500A) Processing helix chain 'O' and resid 79 through 83 removed outlier: 3.536A pdb=" N PHE O 83 " --> pdb=" O PRO O 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 87 through 91 removed outlier: 3.539A pdb=" N THR I 91 " --> pdb=" O ALA I 88 " (cutoff:3.500A) Processing helix chain 'K' and resid 79 through 83 removed outlier: 3.536A pdb=" N PHE K 83 " --> pdb=" O PRO K 80 " (cutoff:3.500A) Processing helix chain 'Q' and resid 87 through 91 removed outlier: 3.539A pdb=" N THR Q 91 " --> pdb=" O ALA Q 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 79 through 83 removed outlier: 3.536A pdb=" N PHE R 83 " --> pdb=" O PRO R 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 30 through 31 Processing sheet with id=AA2, first strand: chain 'A' and resid 36 through 37 removed outlier: 7.426A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.747A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 65 through 66 Processing sheet with id=AA5, first strand: chain 'A' and resid 89 through 92 removed outlier: 4.146A pdb=" N PHE A 92 " --> pdb=" O PHE A 192 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 89 through 92 removed outlier: 4.146A pdb=" N PHE A 92 " --> pdb=" O PHE A 192 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 127 through 129 Processing sheet with id=AA8, first strand: chain 'A' and resid 311 through 314 Processing sheet with id=AA9, first strand: chain 'A' and resid 318 through 319 Processing sheet with id=AB1, first strand: chain 'A' and resid 324 through 328 removed outlier: 3.956A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ASP A 574 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 361 through 362 removed outlier: 7.132A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 399 through 403 removed outlier: 3.590A pdb=" N ILE A 434 " --> pdb=" O VAL A 511 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB5, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB6, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.049A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.402A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ILE A 664 " --> pdb=" O ALA A 672 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 715 through 722 removed outlier: 6.422A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 715 through 722 removed outlier: 6.422A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLY A1059 " --> pdb=" O ALA A1056 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.564A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1076 through 1077 removed outlier: 3.824A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 5.328A pdb=" N VAL A1122 " --> pdb=" O PHE A1089 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N PHE A1089 " --> pdb=" O VAL A1122 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N GLY A1124 " --> pdb=" O ALA A1087 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 27 through 31 removed outlier: 3.843A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.930A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 90 through 94 removed outlier: 3.825A pdb=" N PHE B 92 " --> pdb=" O PHE B 192 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL B 193 " --> pdb=" O TYR B 204 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 128 through 129 removed outlier: 3.548A pdb=" N GLY B 107 " --> pdb=" O ARG B 237 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 311 through 316 removed outlier: 6.101A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 326 through 327 removed outlier: 4.880A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 399 through 403 removed outlier: 3.591A pdb=" N ILE B 434 " --> pdb=" O VAL B 511 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD2, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD3, first strand: chain 'B' and resid 654 through 660 removed outlier: 4.908A pdb=" N THR B 696 " --> pdb=" O VAL B 656 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N ASN B 658 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 703 through 704 removed outlier: 7.129A pdb=" N ASN B 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'B' and resid 711 through 713 removed outlier: 3.733A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N GLN B1106 " --> pdb=" O GLU B1111 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N GLU B1111 " --> pdb=" O GLN B1106 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 717 through 720 removed outlier: 7.083A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 725 through 728 removed outlier: 3.631A pdb=" N GLY B1059 " --> pdb=" O ALA B1056 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.600A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 1120 through 1121 Processing sheet with id=AE1, first strand: chain 'C' and resid 27 through 30 removed outlier: 3.934A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.626A pdb=" N VAL C 47 " --> pdb=" O TYR C 279 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N PHE C 275 " --> pdb=" O THR C 51 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.562A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 190 through 195 removed outlier: 5.509A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 311 through 313 Processing sheet with id=AE6, first strand: chain 'C' and resid 318 through 319 Processing sheet with id=AE7, first strand: chain 'C' and resid 324 through 327 removed outlier: 4.270A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 399 through 403 removed outlier: 3.590A pdb=" N ILE C 434 " --> pdb=" O VAL C 511 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AF1, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AF2, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.985A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.609A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 711 through 720 removed outlier: 3.617A pdb=" N LYS C1073 " --> pdb=" O ILE C 714 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N THR C 723 " --> pdb=" O HIS C1064 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 711 through 720 removed outlier: 3.617A pdb=" N LYS C1073 " --> pdb=" O ILE C 714 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 734 through 735 Processing sheet with id=AF6, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AF7, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AF8, first strand: chain 'D' and resid 5 through 7 Processing sheet with id=AF9, first strand: chain 'D' and resid 55 through 57 removed outlier: 5.145A pdb=" N CYS D 45 " --> pdb=" O ARG D 36 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N ARG D 36 " --> pdb=" O CYS D 45 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N SER D 47 " --> pdb=" O TRP D 34 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N MET D 32 " --> pdb=" O ILE D 49 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'J' and resid 5 through 7 Processing sheet with id=AG2, first strand: chain 'J' and resid 45 through 46 removed outlier: 3.855A pdb=" N ALA J 34 " --> pdb=" O GLN J 89 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'N' and resid 18 through 22 removed outlier: 3.591A pdb=" N LEU N 81 " --> pdb=" O LEU N 20 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL N 79 " --> pdb=" O CYS N 22 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR N 69 " --> pdb=" O GLN N 82 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'N' and resid 58 through 60 removed outlier: 6.294A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N PHE N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N MET N 34 " --> pdb=" O PHE N 50 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N TYR N 94 " --> pdb=" O THR N 116 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'O' and resid 4 through 6 removed outlier: 3.510A pdb=" N ILE O 21 " --> pdb=" O LEU O 73 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'O' and resid 10 through 13 removed outlier: 6.224A pdb=" N LEU O 11 " --> pdb=" O ASP O 105 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLN O 38 " --> pdb=" O THR O 85 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N TRP O 35 " --> pdb=" O LEU O 47 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'F' and resid 5 through 7 Processing sheet with id=AG8, first strand: chain 'F' and resid 55 through 57 removed outlier: 5.146A pdb=" N CYS F 45 " --> pdb=" O ARG F 36 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N ARG F 36 " --> pdb=" O CYS F 45 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N SER F 47 " --> pdb=" O TRP F 34 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N MET F 32 " --> pdb=" O ILE F 49 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'H' and resid 5 through 7 Processing sheet with id=AH1, first strand: chain 'H' and resid 45 through 46 removed outlier: 3.855A pdb=" N ALA H 34 " --> pdb=" O GLN H 89 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'I' and resid 18 through 22 removed outlier: 3.592A pdb=" N LEU I 81 " --> pdb=" O LEU I 20 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL I 79 " --> pdb=" O CYS I 22 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR I 69 " --> pdb=" O GLN I 82 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'I' and resid 58 through 60 removed outlier: 6.295A pdb=" N TRP I 36 " --> pdb=" O VAL I 48 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N PHE I 50 " --> pdb=" O MET I 34 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N MET I 34 " --> pdb=" O PHE I 50 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N TYR I 94 " --> pdb=" O THR I 116 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'K' and resid 4 through 6 removed outlier: 3.510A pdb=" N ILE K 21 " --> pdb=" O LEU K 73 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'K' and resid 10 through 13 removed outlier: 6.226A pdb=" N LEU K 11 " --> pdb=" O ASP K 105 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLN K 38 " --> pdb=" O THR K 85 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'L' and resid 5 through 7 Processing sheet with id=AH7, first strand: chain 'L' and resid 55 through 57 removed outlier: 5.145A pdb=" N CYS L 45 " --> pdb=" O ARG L 36 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N ARG L 36 " --> pdb=" O CYS L 45 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N SER L 47 " --> pdb=" O TRP L 34 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N MET L 32 " --> pdb=" O ILE L 49 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'P' and resid 5 through 7 Processing sheet with id=AH9, first strand: chain 'P' and resid 45 through 46 removed outlier: 3.855A pdb=" N ALA P 34 " --> pdb=" O GLN P 89 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'Q' and resid 18 through 22 removed outlier: 3.592A pdb=" N LEU Q 81 " --> pdb=" O LEU Q 20 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL Q 79 " --> pdb=" O CYS Q 22 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR Q 69 " --> pdb=" O GLN Q 82 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'Q' and resid 58 through 60 removed outlier: 6.294A pdb=" N TRP Q 36 " --> pdb=" O VAL Q 48 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N PHE Q 50 " --> pdb=" O MET Q 34 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N MET Q 34 " --> pdb=" O PHE Q 50 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N TYR Q 94 " --> pdb=" O THR Q 116 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'R' and resid 4 through 6 removed outlier: 3.511A pdb=" N ILE R 21 " --> pdb=" O LEU R 73 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'R' and resid 10 through 13 removed outlier: 6.226A pdb=" N LEU R 11 " --> pdb=" O ASP R 105 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLN R 38 " --> pdb=" O THR R 85 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N TRP R 35 " --> pdb=" O LEU R 47 " (cutoff:3.500A) 1023 hydrogen bonds defined for protein. 2649 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: 8.63 Time building geometry restraints manager: 3.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.30: 5131 1.30 - 1.44: 9129 1.44 - 1.59: 17604 1.59 - 1.73: 0 1.73 - 1.88: 147 Bond restraints: 32011 Sorted by residual: bond pdb=" C ASN I 57 " pdb=" N TYR I 58 " ideal model delta sigma weight residual 1.331 1.485 -0.155 1.32e-02 5.74e+03 1.37e+02 bond pdb=" C ASN N 57 " pdb=" N TYR N 58 " ideal model delta sigma weight residual 1.331 1.485 -0.154 1.32e-02 5.74e+03 1.37e+02 bond pdb=" C ASN Q 57 " pdb=" N TYR Q 58 " ideal model delta sigma weight residual 1.331 1.484 -0.154 1.32e-02 5.74e+03 1.35e+02 bond pdb=" C TYR N 58 " pdb=" N TYR N 59 " ideal model delta sigma weight residual 1.331 1.483 -0.152 1.55e-02 4.16e+03 9.59e+01 bond pdb=" C TYR Q 58 " pdb=" N TYR Q 59 " ideal model delta sigma weight residual 1.331 1.483 -0.152 1.55e-02 4.16e+03 9.59e+01 ... (remaining 32006 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.69: 40711 3.69 - 7.38: 2684 7.38 - 11.08: 175 11.08 - 14.77: 22 14.77 - 18.46: 1 Bond angle restraints: 43593 Sorted by residual: angle pdb=" N PRO B 812 " pdb=" CA PRO B 812 " pdb=" C PRO B 812 " ideal model delta sigma weight residual 113.47 95.01 18.46 1.43e+00 4.89e-01 1.67e+02 angle pdb=" N ILE A 909 " pdb=" CA ILE A 909 " pdb=" C ILE A 909 " ideal model delta sigma weight residual 113.10 104.63 8.47 9.70e-01 1.06e+00 7.63e+01 angle pdb=" C ILE P 29 " pdb=" N SER P 30 " pdb=" CA SER P 30 " ideal model delta sigma weight residual 122.30 110.53 11.77 1.35e+00 5.49e-01 7.61e+01 angle pdb=" N PRO A 337 " pdb=" CA PRO A 337 " pdb=" C PRO A 337 " ideal model delta sigma weight residual 112.48 124.25 -11.77 1.35e+00 5.49e-01 7.60e+01 angle pdb=" C ILE H 29 " pdb=" N SER H 30 " pdb=" CA SER H 30 " ideal model delta sigma weight residual 122.30 110.57 11.73 1.35e+00 5.49e-01 7.55e+01 ... (remaining 43588 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 17216 17.71 - 35.43: 1334 35.43 - 53.14: 284 53.14 - 70.85: 57 70.85 - 88.56: 17 Dihedral angle restraints: 18908 sinusoidal: 6875 harmonic: 12033 Sorted by residual: dihedral pdb=" C TYR K 94 " pdb=" N TYR K 94 " pdb=" CA TYR K 94 " pdb=" CB TYR K 94 " ideal model delta harmonic sigma weight residual -122.60 -153.55 30.95 0 2.50e+00 1.60e-01 1.53e+02 dihedral pdb=" C TYR R 94 " pdb=" N TYR R 94 " pdb=" CA TYR R 94 " pdb=" CB TYR R 94 " ideal model delta harmonic sigma weight residual -122.60 -153.51 30.91 0 2.50e+00 1.60e-01 1.53e+02 dihedral pdb=" C TYR O 94 " pdb=" N TYR O 94 " pdb=" CA TYR O 94 " pdb=" CB TYR O 94 " ideal model delta harmonic sigma weight residual -122.60 -153.49 30.89 0 2.50e+00 1.60e-01 1.53e+02 ... (remaining 18905 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.267: 4553 0.267 - 0.535: 298 0.535 - 0.802: 10 0.802 - 1.070: 0 1.070 - 1.337: 3 Chirality restraints: 4864 Sorted by residual: chirality pdb=" CA TYR K 94 " pdb=" N TYR K 94 " pdb=" C TYR K 94 " pdb=" CB TYR K 94 " both_signs ideal model delta sigma weight residual False 2.51 1.17 1.34 2.00e-01 2.50e+01 4.47e+01 chirality pdb=" CA TYR R 94 " pdb=" N TYR R 94 " pdb=" C TYR R 94 " pdb=" CB TYR R 94 " both_signs ideal model delta sigma weight residual False 2.51 1.18 1.34 2.00e-01 2.50e+01 4.46e+01 chirality pdb=" CA TYR O 94 " pdb=" N TYR O 94 " pdb=" C TYR O 94 " pdb=" CB TYR O 94 " both_signs ideal model delta sigma weight residual False 2.51 1.18 1.33 2.00e-01 2.50e+01 4.45e+01 ... (remaining 4861 not shown) Planarity restraints: 5698 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP L 107 " -0.018 2.00e-02 2.50e+03 2.29e-02 1.31e+01 pdb=" CG TRP L 107 " 0.059 2.00e-02 2.50e+03 pdb=" CD1 TRP L 107 " -0.035 2.00e-02 2.50e+03 pdb=" CD2 TRP L 107 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP L 107 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP L 107 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP L 107 " -0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP L 107 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP L 107 " -0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP L 107 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 107 " 0.018 2.00e-02 2.50e+03 2.28e-02 1.29e+01 pdb=" CG TRP D 107 " -0.059 2.00e-02 2.50e+03 pdb=" CD1 TRP D 107 " 0.035 2.00e-02 2.50e+03 pdb=" CD2 TRP D 107 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP D 107 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP D 107 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP D 107 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 107 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 107 " 0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP D 107 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP F 107 " -0.018 2.00e-02 2.50e+03 2.28e-02 1.29e+01 pdb=" CG TRP F 107 " 0.059 2.00e-02 2.50e+03 pdb=" CD1 TRP F 107 " -0.036 2.00e-02 2.50e+03 pdb=" CD2 TRP F 107 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP F 107 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP F 107 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP F 107 " -0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 107 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 107 " -0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP F 107 " -0.000 2.00e-02 2.50e+03 ... (remaining 5695 not shown) Histogram of nonbonded interaction distances: 1.52 - 2.19: 4 2.19 - 2.87: 12219 2.87 - 3.55: 40255 3.55 - 4.22: 69859 4.22 - 4.90: 121541 Nonbonded interactions: 243878 Sorted by model distance: nonbonded pdb=" OE1 GLN B 965 " pdb=" OG SER B1003 " model vdw 1.518 3.040 nonbonded pdb=" CG1 VAL A 483 " pdb=" OD1 ASN L 54 " model vdw 2.107 3.460 nonbonded pdb=" CG1 VAL B 483 " pdb=" OD1 ASN F 54 " model vdw 2.107 3.460 nonbonded pdb=" CG1 VAL C 483 " pdb=" OD1 ASN D 54 " model vdw 2.107 3.460 nonbonded pdb=" O ASP B 574 " pdb=" OD1 ASP B 586 " model vdw 2.229 3.040 ... (remaining 243873 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 29 through 33 or (resid 34 and (name N or name CA or name \ C or name O or name CB )) or resid 35 through 40 or (resid 41 through 43 and (na \ me N or name CA or name C or name O or name CB )) or resid 44 through 46 or (res \ id 47 and (name N or name CA or name C or name O or name CB )) or resid 48 throu \ gh 53 or (resid 54 and (name N or name CA or name C or name O or name CB )) or r \ esid 55 or (resid 56 and (name N or name CA or name C or name O or name CB )) or \ resid 57 through 61 or (resid 62 through 63 and (name N or name CA or name C or \ name O or name CB )) or resid 64 through 65 or resid 88 through 89 or (resid 90 \ and (name N or name CA or name C or name O or name CB )) or resid 91 through 94 \ or (resid 95 and (name N or name CA or name C or name O or name CB )) or (resid \ 100 and (name N or name CA or name C or name O or name CB )) or resid 101 or (r \ esid 102 and (name N or name CA or name C or name O or name CB )) or resid 103 t \ hrough 107 or (resid 121 and (name N or name CA or name C or name O or name CB ) \ ) or resid 126 or (resid 127 and (name N or name CA or name C or name O or name \ CB )) or resid 128 through 130 or (resid 189 through 191 and (name N or name CA \ or name C or name O or name CB )) or resid 192 through 194 or (resid 195 through \ 196 and (name N or name CA or name C or name O or name CB )) or resid 201 throu \ gh 208 or resid 220 through 222 or (resid 223 and (name N or name CA or name C o \ r name O or name CB )) or resid 224 through 230 or resid 236 through 240 or (res \ id 241 through 242 and (name N or name CA or name C or name O or name CB )) or r \ esid 265 or (resid 266 through 267 and (name N or name CA or name C or name O or \ name CB )) or resid 268 or (resid 269 and (name N or name CA or name C or name \ O or name CB )) or resid 270 through 285 or (resid 286 and (name N or name CA or \ name C or name O or name CB )) or resid 287 through 290 or (resid 291 through 2 \ 92 and (name N or name CA or name C or name O or name CB )) or resid 293 through \ 300 or (resid 301 and (name N or name CA or name C or name O or name CB )) or r \ esid 302 through 307 or (resid 308 and (name N or name CA or name C or name O or \ name CB )) or resid 309 or (resid 310 and (name N or name CA or name C or name \ O or name CB )) or resid 311 through 318 or (resid 319 and (name N or name CA or \ name C or name O or name CB )) or resid 320 through 530 or (resid 531 and (name \ N or name CA or name C or name O or name CB )) or resid 532 or (resid 533 and ( \ name N or name CA or name C or name O or name CB )) or resid 534 through 548 or \ (resid 549 and (name N or name CA or name C or name O or name CB )) or resid 550 \ through 564 or (resid 565 and (name N or name CA or name C or name O or name CB \ )) or resid 566 through 567 or (resid 568 and (name N or name CA or name C or n \ ame O or name CB )) or resid 569 through 577 or (resid 578 and (name N or name C \ A or name C or name O or name CB )) or resid 579 through 582 or (resid 583 throu \ gh 584 and (name N or name CA or name C or name O or name CB )) or resid 585 thr \ ough 590 or (resid 591 through 592 and (name N or name CA or name C or name O or \ name CB )) or resid 593 through 594 or (resid 595 and (name N or name CA or nam \ e C or name O or name CB )) or resid 596 or (resid 597 through 598 and (name N o \ r name CA or name C or name O or name CB )) or resid 599 through 601 or (resid 6 \ 02 and (name N or name CA or name C or name O or name CB )) or resid 603 through \ 605 or (resid 606 and (name N or name CA or name C or name O or name CB )) or r \ esid 607 through 609 or (resid 610 and (name N or name CA or name C or name O or \ name CB )) or resid 611 through 621 or resid 641 through 644 or (resid 645 and \ (name N or name CA or name C or name O or name CB )) or resid 646 through 659 or \ (resid 660 and (name N or name CA or name C or name O or name CB )) or resid 66 \ 1 through 662 or (resid 663 and (name N or name CA or name C or name O or name C \ B )) or resid 664 through 669 or (resid 670 and (name N or name CA or name C or \ name O or name CB )) or resid 671 through 675 or resid 691 or (resid 692 through \ 694 and (name N or name CA or name C or name O or name CB )) or resid 695 throu \ gh 701 or (resid 702 and (name N or name CA or name C or name O or name CB )) or \ resid 703 through 704 or (resid 705 through 706 and (name N or name CA or name \ C or name O or name CB )) or resid 707 through 721 or (resid 722 and (name N or \ name CA or name C or name O or name CB )) or resid 723 or (resid 724 and (name N \ or name CA or name C or name O or name CB )) or resid 725 through 737 or (resid \ 738 and (name N or name CA or name C or name O or name CB )) or resid 739 throu \ gh 741 or (resid 742 and (name N or name CA or name C or name O or name CB )) or \ resid 743 through 745 or (resid 746 and (name N or name CA or name C or name O \ or name CB )) or resid 747 or (resid 748 and (name N or name CA or name C or nam \ e O or name CB )) or resid 749 through 754 or (resid 755 and (name N or name CA \ or name C or name O or name CB )) or resid 756 through 759 or (resid 760 and (na \ me N or name CA or name C or name O or name CB )) or resid 761 through 790 or (r \ esid 791 and (name N or name CA or name C or name O or name CB )) or resid 792 t \ hrough 812 or (resid 813 through 814 and (name N or name CA or name C or name O \ or name CB )) or resid 815 through 820 or (resid 821 and (name N or name CA or n \ ame C or name O or name CB )) or resid 822 through 825 or (resid 826 through 856 \ and (name N or name CA or name C or name O or name CB )) or resid 857 or (resid \ 858 and (name N or name CA or name C or name O or name CB )) or resid 859 throu \ gh 877 or (resid 878 through 879 and (name N or name CA or name C or name O or n \ ame CB )) or resid 880 through 903 or (resid 904 and (name N or name CA or name \ C or name O or name CB )) or resid 905 through 914 or (resid 915 through 916 and \ (name N or name CA or name C or name O or name CB )) or resid 917 through 920 o \ r (resid 921 and (name N or name CA or name C or name O or name CB )) or resid 9 \ 22 or (resid 923 through 924 and (name N or name CA or name C or name O or name \ CB )) or resid 925 through 930 or (resid 931 and (name N or name CA or name C or \ name O or name CB )) or (resid 932 through 934 and (name N or name CA or name C \ or name O or name CB )) or resid 935 through 940 or resid 944 through 949 or (r \ esid 950 and (name N or name CA or name C or name O or name CB )) or resid 951 t \ hrough 953 or (resid 954 and (name N or name CA or name C or name O or name CB ) \ ) or resid 955 through 964 or (resid 965 and (name N or name CA or name C or nam \ e O or name CB )) or resid 966 through 972 or (resid 973 and (name N or name CA \ or name C or name O or name CB )) or resid 974 through 976 or (resid 977 through \ 980 and (name N or name CA or name C or name O or name CB )) or resid 981 throu \ gh 993 or (resid 994 and (name N or name CA or name C or name O or name CB )) or \ resid 995 or (resid 996 through 997 and (name N or name CA or name C or name O \ or name CB )) or resid 998 through 1017 or (resid 1018 and (name N or name CA or \ name C or name O or name CB )) or resid 1019 through 1071 or (resid 1072 and (n \ ame N or name CA or name C or name O or name CB )) or resid 1073 through 1080 or \ (resid 1081 through 1082 and (name N or name CA or name C or name O or name CB \ )) or resid 1083 through 1091 or (resid 1092 and (name N or name CA or name C or \ name O or name CB )) or resid 1093 or (resid 1094 and (name N or name CA or nam \ e C or name O or name CB )) or resid 1095 through 1103 or (resid 1104 and (name \ N or name CA or name C or name O or name CB )) or resid 1105 through 1110 or (re \ sid 1111 and (name N or name CA or name C or name O or name CB )) or resid 1112 \ through 1121 or (resid 1122 through 1123 and (name N or name CA or name C or nam \ e O or name CB )) or resid 1124 through 1125 or (resid 1126 through 1127 and (na \ me N or name CA or name C or name O or name CB )) or resid 1128 through 1138 or \ (resid 1139 and (name N or name CA or name C or name O or name CB )) or resid 11 \ 40 through 1401)) selection = (chain 'B' and (resid 29 through 60 or (resid 61 through 63 and (name N or name \ CA or name C or name O or name CB )) or resid 64 through 95 or (resid 100 and (n \ ame N or name CA or name C or name O or name CB )) or resid 101 through 107 or ( \ resid 121 and (name N or name CA or name C or name O or name CB )) or resid 126 \ through 128 or (resid 129 through 130 and (name N or name CA or name C or name O \ or name CB )) or (resid 189 through 191 and (name N or name CA or name C or nam \ e O or name CB )) or resid 192 through 196 or (resid 201 through 203 and (name N \ or name CA or name C or name O or name CB )) or resid 204 or (resid 205 and (na \ me N or name CA or name C or name O or name CB )) or resid 206 through 208 or re \ sid 220 through 226 or (resid 227 and (name N or name CA or name C or name O or \ name CB )) or resid 228 or (resid 229 and (name N or name CA or name C or name O \ or name CB )) or resid 230 or resid 236 through 239 or (resid 240 through 242 a \ nd (name N or name CA or name C or name O or name CB )) or resid 265 through 270 \ or (resid 271 and (name N or name CA or name C or name O or name CB )) or resid \ 272 through 285 or (resid 286 and (name N or name CA or name C or name O or nam \ e CB )) or resid 287 through 318 or (resid 319 and (name N or name CA or name C \ or name O or name CB )) or resid 320 through 323 or (resid 324 and (name N or na \ me CA or name C or name O or name CB )) or resid 325 through 331 or (resid 332 a \ nd (name N or name CA or name C or name O or name CB )) or resid 333 through 527 \ or (resid 528 and (name N or name CA or name C or name O or name CB )) or resid \ 529 through 543 or (resid 544 and (name N or name CA or name C or name O or nam \ e CB )) or resid 545 through 571 or (resid 572 and (name N or name CA or name C \ or name O or name CB )) or resid 573 through 581 or (resid 582 through 584 and ( \ name N or name CA or name C or name O or name CB )) or resid 585 or (resid 586 a \ nd (name N or name CA or name C or name O or name CB )) or resid 587 through 596 \ or (resid 597 through 598 and (name N or name CA or name C or name O or name CB \ )) or resid 599 through 618 or (resid 619 and (name N or name CA or name C or n \ ame O or name CB )) or resid 620 through 621 or resid 641 through 644 or (resid \ 645 and (name N or name CA or name C or name O or name CB )) or resid 646 throug \ h 659 or (resid 660 and (name N or name CA or name C or name O or name CB )) or \ resid 661 through 674 or (resid 675 and (name N or name CA or name C or name O o \ r name CB )) or resid 691 or (resid 692 through 694 and (name N or name CA or na \ me C or name O or name CB )) or resid 695 or (resid 696 and (name N or name CA o \ r name C or name O or name CB )) or resid 697 through 701 or (resid 702 and (nam \ e N or name CA or name C or name O or name CB )) or resid 703 through 709 or (re \ sid 710 and (name N or name CA or name C or name O or name CB )) or resid 711 th \ rough 713 or (resid 714 and (name N or name CA or name C or name O or name CB )) \ or resid 715 through 721 or (resid 722 and (name N or name CA or name C or name \ O or name CB )) or resid 723 through 741 or (resid 742 and (name N or name CA o \ r name C or name O or name CB )) or resid 743 through 752 or (resid 753 through \ 755 and (name N or name CA or name C or name O or name CB )) or resid 756 throug \ h 784 or (resid 785 through 786 and (name N or name CA or name C or name O or na \ me CB )) or resid 787 through 810 or (resid 811 and (name N or name CA or name C \ or name O or name CB )) or resid 812 through 813 or (resid 814 and (name N or n \ ame CA or name C or name O or name CB )) or resid 815 through 819 or (resid 820 \ through 821 and (name N or name CA or name C or name O or name CB )) or resid 82 \ 2 through 824 or (resid 825 through 826 and (name N or name CA or name C or name \ O or name CB )) or (resid 855 through 856 and (name N or name CA or name C or n \ ame O or name CB )) or resid 857 or (resid 858 and (name N or name CA or name C \ or name O or name CB )) or resid 859 through 866 or (resid 867 and (name N or na \ me CA or name C or name O or name CB )) or resid 868 through 883 or (resid 884 a \ nd (name N or name CA or name C or name O or name CB )) or resid 885 through 893 \ or (resid 894 through 895 and (name N or name CA or name C or name O or name CB \ )) or resid 896 through 901 or (resid 902 through 904 and (name N or name CA or \ name C or name O or name CB )) or resid 905 through 913 or (resid 914 through 9 \ 16 and (name N or name CA or name C or name O or name CB )) or resid 917 through \ 932 or (resid 933 through 934 and (name N or name CA or name C or name O or nam \ e CB )) or resid 935 or (resid 936 and (name N or name CA or name C or name O or \ name CB )) or resid 937 through 953 or (resid 954 and (name N or name CA or nam \ e C or name O or name CB )) or resid 955 through 964 or (resid 965 and (name N o \ r name CA or name C or name O or name CB )) or resid 966 through 972 or (resid 9 \ 73 and (name N or name CA or name C or name O or name CB )) or resid 974 through \ 977 or (resid 978 through 980 and (name N or name CA or name C or name O or nam \ e CB )) or resid 981 through 983 or (resid 984 and (name N or name CA or name C \ or name O or name CB )) or resid 985 through 993 or (resid 994 and (name N or na \ me CA or name C or name O or name CB )) or resid 995 or (resid 996 through 997 a \ nd (name N or name CA or name C or name O or name CB )) or resid 998 through 100 \ 9 or (resid 1010 and (name N or name CA or name C or name O or name CB )) or res \ id 1011 through 1028 or (resid 1029 and (name N or name CA or name C or name O o \ r name CB )) or resid 1030 through 1033 or (resid 1034 and (name N or name CA or \ name C or name O or name CB )) or resid 1035 through 1081 or (resid 1082 and (n \ ame N or name CA or name C or name O or name CB )) or resid 1083 through 1103 or \ (resid 1104 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 105 through 1106 or (resid 1107 and (name N or name CA or name C or name O or na \ me CB )) or resid 1108 through 1110 or (resid 1111 and (name N or name CA or nam \ e C or name O or name CB )) or resid 1112 through 1122 or (resid 1123 and (name \ N or name CA or name C or name O or name CB )) or resid 1124 through 1125 or (re \ sid 1126 through 1127 and (name N or name CA or name C or name O or name CB )) o \ r resid 1128 through 1138 or (resid 1139 and (name N or name CA or name C or nam \ e O or name CB )) or resid 1140 through 1141 or resid 1401)) selection = (chain 'C' and (resid 29 through 33 or (resid 34 and (name N or name CA or name \ C or name O or name CB )) or resid 35 through 40 or (resid 41 through 43 and (na \ me N or name CA or name C or name O or name CB )) or resid 44 through 46 or (res \ id 47 and (name N or name CA or name C or name O or name CB )) or resid 48 throu \ gh 53 or (resid 54 and (name N or name CA or name C or name O or name CB )) or r \ esid 55 or (resid 56 and (name N or name CA or name C or name O or name CB )) or \ resid 57 through 60 or (resid 61 through 63 and (name N or name CA or name C or \ name O or name CB )) or resid 64 through 65 or resid 88 through 107 or resid 12 \ 5 through 126 or (resid 127 and (name N or name CA or name C or name O or name C \ B )) or resid 128 through 129 or (resid 130 and (name N or name CA or name C or \ name O or name CB )) or (resid 189 through 191 and (name N or name CA or name C \ or name O or name CB )) or resid 192 through 194 or (resid 195 through 196 and ( \ name N or name CA or name C or name O or name CB )) or (resid 201 through 203 an \ d (name N or name CA or name C or name O or name CB )) or resid 204 or (resid 20 \ 5 and (name N or name CA or name C or name O or name CB )) or resid 206 through \ 208 or resid 220 through 228 or (resid 229 and (name N or name CA or name C or n \ ame O or name CB )) or resid 230 through 237 or (resid 238 through 242 and (name \ N or name CA or name C or name O or name CB )) or resid 265 or (resid 266 throu \ gh 267 and (name N or name CA or name C or name O or name CB )) or resid 268 or \ (resid 269 and (name N or name CA or name C or name O or name CB )) or resid 270 \ or (resid 271 and (name N or name CA or name C or name O or name CB )) or resid \ 272 through 290 or (resid 291 through 292 and (name N or name CA or name C or n \ ame O or name CB )) or resid 293 through 300 or (resid 301 and (name N or name C \ A or name C or name O or name CB )) or resid 302 through 323 or (resid 324 and ( \ name N or name CA or name C or name O or name CB )) or resid 325 through 331 or \ (resid 332 and (name N or name CA or name C or name O or name CB )) or resid 333 \ through 530 or (resid 531 and (name N or name CA or name C or name O or name CB \ )) or resid 532 or (resid 533 and (name N or name CA or name C or name O or nam \ e CB )) or resid 534 through 548 or (resid 549 and (name N or name CA or name C \ or name O or name CB )) or resid 550 through 564 or (resid 565 and (name N or na \ me CA or name C or name O or name CB )) or resid 566 through 567 or (resid 568 a \ nd (name N or name CA or name C or name O or name CB )) or resid 569 through 571 \ or (resid 572 and (name N or name CA or name C or name O or name CB )) or resid \ 573 through 577 or (resid 578 and (name N or name CA or name C or name O or nam \ e CB )) or resid 579 or (resid 580 through 584 and (name N or name CA or name C \ or name O or name CB )) or resid 585 or (resid 586 and (name N or name CA or nam \ e C or name O or name CB )) or resid 587 through 590 or (resid 591 through 592 a \ nd (name N or name CA or name C or name O or name CB )) or resid 593 through 594 \ or (resid 595 and (name N or name CA or name C or name O or name CB )) or resid \ 596 through 605 or (resid 606 and (name N or name CA or name C or name O or nam \ e CB )) or resid 607 or (resid 608 through 610 and (name N or name CA or name C \ or name O or name CB )) or resid 611 through 618 or (resid 619 and (name N or na \ me CA or name C or name O or name CB )) or resid 620 through 662 or (resid 663 a \ nd (name N or name CA or name C or name O or name CB )) or resid 664 through 665 \ or (resid 666 and (name N or name CA or name C or name O or name CB )) or (resi \ d 667 through 670 and (name N or name CA or name C or name O or name CB )) or re \ sid 671 through 704 or (resid 705 through 706 and (name N or name CA or name C o \ r name O or name CB )) or resid 707 through 709 or (resid 710 and (name N or nam \ e CA or name C or name O or name CB )) or resid 711 through 725 or (resid 726 an \ d (name N or name CA or name C or name O or name CB )) or resid 727 through 737 \ or (resid 738 and (name N or name CA or name C or name O or name CB )) or resid \ 739 through 745 or (resid 746 and (name N or name CA or name C or name O or name \ CB )) or resid 747 through 753 or (resid 754 through 755 and (name N or name CA \ or name C or name O or name CB )) or resid 756 through 759 or (resid 760 and (n \ ame N or name CA or name C or name O or name CB )) or resid 761 through 778 or ( \ resid 779 and (name N or name CA or name C or name O or name CB )) or resid 780 \ through 812 or (resid 813 through 814 and (name N or name CA or name C or name O \ or name CB )) or resid 815 through 826 or (resid 855 through 856 and (name N or \ name CA or name C or name O or name CB )) or resid 857 through 866 or (resid 86 \ 7 and (name N or name CA or name C or name O or name CB )) or resid 868 through \ 877 or (resid 878 through 879 and (name N or name CA or name C or name O or name \ CB )) or resid 880 through 882 or (resid 883 through 884 and (name N or name CA \ or name C or name O or name CB )) or resid 885 through 893 or (resid 894 throug \ h 895 and (name N or name CA or name C or name O or name CB )) or resid 896 thro \ ugh 901 or (resid 902 through 904 and (name N or name CA or name C or name O or \ name CB )) or resid 905 through 911 or (resid 912 and (name N or name CA or name \ C or name O or name CB )) or resid 913 or (resid 914 through 916 and (name N or \ name CA or name C or name O or name CB )) or resid 917 through 922 or (resid 92 \ 3 through 924 and (name N or name CA or name C or name O or name CB )) or resid \ 925 through 932 or (resid 933 through 934 and (name N or name CA or name C or na \ me O or name CB )) or resid 935 or (resid 936 and (name N or name CA or name C o \ r name O or name CB )) or resid 937 through 940 or resid 944 through 949 or (res \ id 950 and (name N or name CA or name C or name O or name CB )) or resid 951 thr \ ough 976 or (resid 977 through 980 and (name N or name CA or name C or name O or \ name CB )) or resid 981 through 1009 or (resid 1010 and (name N or name CA or n \ ame C or name O or name CB )) or resid 1011 through 1017 or (resid 1018 and (nam \ e N or name CA or name C or name O or name CB )) or resid 1019 through 1080 or ( \ resid 1081 through 1082 and (name N or name CA or name C or name O or name CB )) \ or resid 1083 through 1091 or (resid 1092 and (name N or name CA or name C or n \ ame O or name CB )) or resid 1093 through 1114 or (resid 1115 and (name N or nam \ e CA or name C or name O or name CB )) or resid 1116 through 1121 or (resid 1122 \ through 1123 and (name N or name CA or name C or name O or name CB )) or resid \ 1124 through 1126 or (resid 1127 and (name N or name CA or name C or name O or n \ ame CB )) or resid 1128 or (resid 1129 and (name N or name CA or name C or name \ O or name CB )) or resid 1130 through 1141 or resid 1401)) } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'L' } ncs_group { reference = chain 'H' selection = chain 'J' selection = chain 'P' } ncs_group { reference = chain 'I' selection = chain 'N' selection = chain 'Q' } ncs_group { reference = chain 'K' selection = chain 'O' selection = chain 'R' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.030 Extract box with map and model: 0.550 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 32.370 Find NCS groups from input model: 0.840 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6537 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.014 0.742 32047 Z= 1.031 Angle : 2.039 50.828 43668 Z= 1.480 Chirality : 0.150 1.337 4864 Planarity : 0.007 0.059 5695 Dihedral : 13.411 88.564 11095 Min Nonbonded Distance : 1.518 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.61 % Allowed : 5.13 % Favored : 94.25 % Rotamer: Outliers : 1.16 % Allowed : 12.93 % Favored : 85.92 % Cbeta Deviations : 2.88 % Peptide Plane: Cis-proline : 2.78 % 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 aren not related in a simple way. whole: -0.73 (0.13), residues: 4073 helix: 0.60 (0.21), residues: 573 sheet: -0.11 (0.16), residues: 1050 loop : -0.92 (0.12), residues: 2450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 577 TYR 0.046 0.004 TYR C 707 PHE 0.046 0.004 PHE A1121 TRP 0.059 0.004 TRP L 107 HIS 0.013 0.003 HIS N 104 Details of bonding type rmsd covalent geometry : bond 0.01374 (32011) covalent geometry : angle 2.00682 (43593) SS BOND : bond 0.14013 ( 33) SS BOND : angle 9.19836 ( 66) hydrogen bonds : bond 0.25081 ( 1010) hydrogen bonds : angle 10.11067 ( 2649) link_NAG-ASN : bond 0.05560 ( 3) link_NAG-ASN : angle 7.03025 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8146 Ramachandran restraints generated. 4073 Oldfield, 0 Emsley, 4073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8146 Ramachandran restraints generated. 4073 Oldfield, 0 Emsley, 4073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 3606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 343 time to evaluate : 1.215 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: A 563 GLN cc_start: 0.7745 (OUTLIER) cc_final: 0.7337 (mt0) REVERT: B 347 PHE cc_start: 0.3610 (OUTLIER) cc_final: 0.1575 (m-80) REVERT: C 106 PHE cc_start: 0.5995 (m-80) cc_final: 0.4209 (t80) REVERT: C 759 PHE cc_start: 0.6964 (m-80) cc_final: 0.6733 (m-80) REVERT: J 46 VAL cc_start: 0.4134 (OUTLIER) cc_final: 0.3743 (m) outliers start: 37 outliers final: 9 residues processed: 376 average time/residue: 0.1769 time to fit residues: 112.3797 Evaluate side-chains 209 residues out of total 3606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 197 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 563 GLN Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain J residue 46 VAL Chi-restraints excluded: chain N residue 104 HIS Chi-restraints excluded: chain I residue 104 HIS Chi-restraints excluded: chain Q residue 104 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 197 optimal weight: 1.9990 chunk 388 optimal weight: 5.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 0.1980 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 6.9990 chunk 401 optimal weight: 30.0000 chunk 155 optimal weight: 0.5980 chunk 244 optimal weight: 2.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 481 ASN A 540 ASN A 907 ASN A 919 ASN A 935 GLN A 965 GLN A1005 GLN A1113 GLN B 49 HIS B 52 GLN B 536 ASN B 751 ASN B 762 GLN B 787 GLN B 992 GLN B1005 GLN B1083 HIS B1088 HIS B1106 GLN C 87 ASN C 207 HIS C 239 GLN C 481 ASN C 658 ASN C 762 GLN ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 949 GLN C 953 ASN C 955 ASN C1002 GLN C1023 ASN C1106 GLN D 79 GLN F 79 GLN L 79 GLN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4801 r_free = 0.4801 target = 0.229763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4415 r_free = 0.4415 target = 0.189533 restraints weight = 53072.022| |-----------------------------------------------------------------------------| r_work (start): 0.4395 rms_B_bonded: 3.22 r_work: 0.3677 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 32047 Z= 0.165 Angle : 0.666 12.034 43668 Z= 0.358 Chirality : 0.047 0.205 4864 Planarity : 0.005 0.045 5695 Dihedral : 6.245 55.503 4555 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.70 % Favored : 97.20 % Rotamer: Outliers : 2.68 % Allowed : 14.70 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.46 % 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 aren not related in a simple way. whole: -0.67 (0.13), residues: 4073 helix: 0.50 (0.21), residues: 605 sheet: -0.14 (0.15), residues: 1177 loop : -0.84 (0.12), residues: 2291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 64 TYR 0.036 0.002 TYR K 87 PHE 0.032 0.002 PHE B 377 TRP 0.030 0.002 TRP A 353 HIS 0.009 0.001 HIS N 104 Details of bonding type rmsd covalent geometry : bond 0.00338 (32011) covalent geometry : angle 0.66151 (43593) SS BOND : bond 0.00649 ( 33) SS BOND : angle 1.88176 ( 66) hydrogen bonds : bond 0.04267 ( 1010) hydrogen bonds : angle 6.58708 ( 2649) link_NAG-ASN : bond 0.00120 ( 3) link_NAG-ASN : angle 2.75308 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8146 Ramachandran restraints generated. 4073 Oldfield, 0 Emsley, 4073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8146 Ramachandran restraints generated. 4073 Oldfield, 0 Emsley, 4073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 3606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 220 time to evaluate : 1.190 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 361 CYS cc_start: 0.4050 (OUTLIER) cc_final: 0.1915 (m) REVERT: A 969 LYS cc_start: 0.7696 (OUTLIER) cc_final: 0.7219 (mmtt) REVERT: B 436 TRP cc_start: 0.6624 (p90) cc_final: 0.6368 (p90) REVERT: C 707 TYR cc_start: 0.7788 (t80) cc_final: 0.7396 (t80) REVERT: J 46 VAL cc_start: 0.4451 (OUTLIER) cc_final: 0.3985 (m) REVERT: F 80 MET cc_start: -0.2708 (mtp) cc_final: -0.3589 (tpp) REVERT: I 70 ILE cc_start: 0.3197 (OUTLIER) cc_final: 0.2996 (pt) REVERT: I 109 PHE cc_start: 0.7373 (m-80) cc_final: 0.6595 (t80) REVERT: I 112 TRP cc_start: 0.3700 (m-90) cc_final: 0.2386 (m-90) REVERT: P 4 MET cc_start: -0.0190 (tpp) cc_final: -0.0942 (tmm) REVERT: Q 33 HIS cc_start: 0.3434 (m90) cc_final: 0.3185 (m170) outliers start: 86 outliers final: 30 residues processed: 295 average time/residue: 0.1797 time to fit residues: 90.8962 Evaluate side-chains 210 residues out of total 3606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 176 time to evaluate : 1.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 969 LYS Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 711 SER Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain J residue 46 VAL Chi-restraints excluded: chain N residue 58 TYR Chi-restraints excluded: chain N residue 104 HIS Chi-restraints excluded: chain H residue 46 VAL Chi-restraints excluded: chain H residue 58 VAL Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 70 ILE Chi-restraints excluded: chain I residue 104 HIS Chi-restraints excluded: chain K residue 60 SER Chi-restraints excluded: chain R residue 38 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 333 optimal weight: 50.0000 chunk 104 optimal weight: 8.9990 chunk 77 optimal weight: 0.9990 chunk 290 optimal weight: 50.0000 chunk 317 optimal weight: 20.0000 chunk 193 optimal weight: 0.0170 chunk 91 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 246 optimal weight: 0.7980 chunk 320 optimal weight: 8.9990 overall best weight: 1.5624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 52 GLN B 919 ASN C 87 ASN ** C 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 755 GLN C 762 GLN C 935 GLN C 949 GLN C 953 ASN C1002 GLN ** I 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 57 ASN ** Q 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4782 r_free = 0.4782 target = 0.228900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.186576 restraints weight = 53528.262| |-----------------------------------------------------------------------------| r_work (start): 0.4326 rms_B_bonded: 3.23 r_work: 0.3600 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.2673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 32047 Z= 0.149 Angle : 0.606 10.341 43668 Z= 0.322 Chirality : 0.046 0.216 4864 Planarity : 0.004 0.047 5695 Dihedral : 5.551 57.246 4546 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.81 % Favored : 96.10 % Rotamer: Outliers : 2.72 % Allowed : 14.70 % Favored : 82.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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 aren not related in a simple way. whole: -0.76 (0.13), residues: 4073 helix: 0.48 (0.22), residues: 594 sheet: -0.22 (0.15), residues: 1141 loop : -0.89 (0.12), residues: 2338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 509 TYR 0.023 0.001 TYR R 49 PHE 0.039 0.002 PHE A 565 TRP 0.025 0.002 TRP A 353 HIS 0.008 0.001 HIS B 505 Details of bonding type rmsd covalent geometry : bond 0.00330 (32011) covalent geometry : angle 0.60200 (43593) SS BOND : bond 0.00652 ( 33) SS BOND : angle 1.69835 ( 66) hydrogen bonds : bond 0.03800 ( 1010) hydrogen bonds : angle 6.01341 ( 2649) link_NAG-ASN : bond 0.00507 ( 3) link_NAG-ASN : angle 2.16250 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8146 Ramachandran restraints generated. 4073 Oldfield, 0 Emsley, 4073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8146 Ramachandran restraints generated. 4073 Oldfield, 0 Emsley, 4073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 3606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 198 time to evaluate : 1.209 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: A 361 CYS cc_start: 0.3775 (OUTLIER) cc_final: 0.0852 (m) REVERT: A 563 GLN cc_start: 0.7621 (OUTLIER) cc_final: 0.7018 (mt0) REVERT: A 1134 ASN cc_start: 0.7007 (OUTLIER) cc_final: 0.6802 (m-40) REVERT: B 714 ILE cc_start: 0.8163 (OUTLIER) cc_final: 0.7882 (mm) REVERT: C 92 PHE cc_start: 0.6672 (t80) cc_final: 0.6343 (t80) REVERT: C 1043 CYS cc_start: 0.8733 (OUTLIER) cc_final: 0.8177 (m) REVERT: F 80 MET cc_start: -0.2818 (mtp) cc_final: -0.3619 (tpp) REVERT: H 4 MET cc_start: 0.2535 (OUTLIER) cc_final: 0.2242 (ttt) REVERT: I 80 TYR cc_start: 0.6925 (m-80) cc_final: 0.6647 (m-80) REVERT: I 109 PHE cc_start: 0.7477 (m-80) cc_final: 0.6860 (t80) REVERT: I 112 TRP cc_start: 0.3661 (m-90) cc_final: 0.2492 (m-90) REVERT: K 53 ASN cc_start: 0.7396 (t0) cc_final: 0.7102 (t0) REVERT: P 4 MET cc_start: -0.0084 (tpp) cc_final: -0.0964 (tmm) REVERT: Q 104 HIS cc_start: 0.3887 (OUTLIER) cc_final: 0.3661 (p-80) outliers start: 87 outliers final: 48 residues processed: 272 average time/residue: 0.1753 time to fit residues: 83.2204 Evaluate side-chains 230 residues out of total 3606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 175 time to evaluate : 1.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 563 GLN Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 751 ASN Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1134 ASN Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 711 SER Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 929 SER Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain J residue 4 MET Chi-restraints excluded: chain J residue 46 VAL Chi-restraints excluded: chain N residue 58 TYR Chi-restraints excluded: chain N residue 104 HIS Chi-restraints excluded: chain F residue 32 MET Chi-restraints excluded: chain H residue 4 MET Chi-restraints excluded: chain H residue 23 CYS Chi-restraints excluded: chain H residue 46 VAL Chi-restraints excluded: chain H residue 58 VAL Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 104 HIS Chi-restraints excluded: chain K residue 79 GLN Chi-restraints excluded: chain Q residue 104 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 402 optimal weight: 50.0000 chunk 224 optimal weight: 9.9990 chunk 370 optimal weight: 9.9990 chunk 200 optimal weight: 1.9990 chunk 93 optimal weight: 9.9990 chunk 331 optimal weight: 50.0000 chunk 281 optimal weight: 50.0000 chunk 18 optimal weight: 0.9990 chunk 102 optimal weight: 4.9990 chunk 38 optimal weight: 9.9990 chunk 358 optimal weight: 30.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 414 GLN A 762 GLN A 926 GLN A 965 GLN A1036 GLN C 196 ASN C 207 HIS C 334 ASN C 414 GLN C 564 GLN C 762 GLN C 955 ASN H 55 GLN I 3 GLN I 33 HIS K 38 GLN K 53 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4726 r_free = 0.4726 target = 0.219919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.175758 restraints weight = 52838.137| |-----------------------------------------------------------------------------| r_work (start): 0.4257 rms_B_bonded: 3.27 r_work: 0.3544 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.3178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.089 32047 Z= 0.401 Angle : 0.779 10.532 43668 Z= 0.419 Chirality : 0.053 0.301 4864 Planarity : 0.006 0.054 5695 Dihedral : 6.150 57.179 4546 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.66 % Favored : 95.24 % Rotamer: Outliers : 3.87 % Allowed : 14.83 % Favored : 81.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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 aren not related in a simple way. whole: -1.29 (0.13), residues: 4073 helix: -0.60 (0.20), residues: 605 sheet: -0.50 (0.15), residues: 1219 loop : -1.09 (0.13), residues: 2249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 403 TYR 0.037 0.002 TYR C 707 PHE 0.031 0.003 PHE A1121 TRP 0.031 0.002 TRP K 35 HIS 0.011 0.002 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00948 (32011) covalent geometry : angle 0.77550 (43593) SS BOND : bond 0.00994 ( 33) SS BOND : angle 1.95727 ( 66) hydrogen bonds : bond 0.04974 ( 1010) hydrogen bonds : angle 6.45211 ( 2649) link_NAG-ASN : bond 0.00541 ( 3) link_NAG-ASN : angle 2.30724 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8146 Ramachandran restraints generated. 4073 Oldfield, 0 Emsley, 4073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8146 Ramachandran restraints generated. 4073 Oldfield, 0 Emsley, 4073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 3606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 184 time to evaluate : 1.246 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: symmetry clash revert: symmetry clash REVERT: B 347 PHE cc_start: 0.5800 (OUTLIER) cc_final: 0.3958 (m-80) REVERT: B 772 VAL cc_start: 0.9329 (OUTLIER) cc_final: 0.9074 (p) REVERT: C 452 LEU cc_start: 0.6403 (OUTLIER) cc_final: 0.6149 (tt) REVERT: N 34 MET cc_start: 0.2994 (tmm) cc_final: 0.2589 (tmm) REVERT: H 4 MET cc_start: 0.2381 (OUTLIER) cc_final: 0.2005 (ttt) REVERT: I 109 PHE cc_start: 0.7310 (m-80) cc_final: 0.6891 (t80) REVERT: I 112 TRP cc_start: 0.4261 (m-90) cc_final: 0.3159 (m-90) REVERT: L 80 MET cc_start: -0.1876 (mmt) cc_final: -0.3272 (tpp) REVERT: Q 83 MET cc_start: 0.1556 (mtp) cc_final: 0.1150 (mmp) outliers start: 124 outliers final: 85 residues processed: 290 average time/residue: 0.1766 time to fit residues: 88.4414 Evaluate side-chains 261 residues out of total 3606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 172 time to evaluate : 1.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 450 ASN Chi-restraints excluded: chain A residue 498 ARG Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 751 ASN Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 498 ARG Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 711 SER Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 929 SER Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1021 SER Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 101 HIS Chi-restraints excluded: chain D residue 112 MET Chi-restraints excluded: chain J residue 46 VAL Chi-restraints excluded: chain N residue 58 TYR Chi-restraints excluded: chain N residue 104 HIS Chi-restraints excluded: chain F residue 32 MET Chi-restraints excluded: chain H residue 4 MET Chi-restraints excluded: chain H residue 23 CYS Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 104 HIS Chi-restraints excluded: chain K residue 22 THR Chi-restraints excluded: chain K residue 38 GLN Chi-restraints excluded: chain K residue 60 SER Chi-restraints excluded: chain K residue 79 GLN Chi-restraints excluded: chain P residue 4 MET Chi-restraints excluded: chain P residue 67 SER Chi-restraints excluded: chain Q residue 78 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 401 optimal weight: 5.9990 chunk 349 optimal weight: 20.0000 chunk 172 optimal weight: 0.9990 chunk 90 optimal weight: 0.9980 chunk 313 optimal weight: 50.0000 chunk 156 optimal weight: 0.9990 chunk 286 optimal weight: 8.9990 chunk 274 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 302 optimal weight: 6.9990 chunk 141 optimal weight: 1.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1058 HIS C 196 ASN H 55 GLN I 33 HIS K 38 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4746 r_free = 0.4746 target = 0.222503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.178341 restraints weight = 52986.013| |-----------------------------------------------------------------------------| r_work (start): 0.4282 rms_B_bonded: 3.29 r_work: 0.3568 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.3382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 32047 Z= 0.131 Angle : 0.576 10.255 43668 Z= 0.304 Chirality : 0.045 0.191 4864 Planarity : 0.004 0.052 5695 Dihedral : 5.524 57.847 4546 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.56 % Favored : 96.34 % Rotamer: Outliers : 2.28 % Allowed : 17.27 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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 aren not related in a simple way. whole: -0.97 (0.13), residues: 4073 helix: 0.04 (0.21), residues: 608 sheet: -0.35 (0.15), residues: 1221 loop : -0.96 (0.13), residues: 2244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG Q 98 TYR 0.023 0.001 TYR C 707 PHE 0.023 0.001 PHE I 50 TRP 0.020 0.001 TRP A 353 HIS 0.007 0.001 HIS N 104 Details of bonding type rmsd covalent geometry : bond 0.00294 (32011) covalent geometry : angle 0.57353 (43593) SS BOND : bond 0.00480 ( 33) SS BOND : angle 1.32735 ( 66) hydrogen bonds : bond 0.03387 ( 1010) hydrogen bonds : angle 5.79815 ( 2649) link_NAG-ASN : bond 0.00431 ( 3) link_NAG-ASN : angle 1.78906 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8146 Ramachandran restraints generated. 4073 Oldfield, 0 Emsley, 4073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8146 Ramachandran restraints generated. 4073 Oldfield, 0 Emsley, 4073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 3606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 189 time to evaluate : 1.194 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: symmetry clash REVERT: B 347 PHE cc_start: 0.5763 (OUTLIER) cc_final: 0.3207 (m-80) REVERT: B 560 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8344 (mp) REVERT: H 4 MET cc_start: 0.2267 (OUTLIER) cc_final: 0.1935 (ttt) REVERT: I 112 TRP cc_start: 0.4074 (m-90) cc_final: 0.3741 (m-90) REVERT: Q 83 MET cc_start: 0.1466 (mtp) cc_final: 0.1065 (mmp) outliers start: 73 outliers final: 59 residues processed: 248 average time/residue: 0.1866 time to fit residues: 79.2024 Evaluate side-chains 242 residues out of total 3606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 180 time to evaluate : 1.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 450 ASN Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 498 ARG Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 711 SER Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 929 SER Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain D residue 101 HIS Chi-restraints excluded: chain D residue 112 MET Chi-restraints excluded: chain J residue 46 VAL Chi-restraints excluded: chain N residue 58 TYR Chi-restraints excluded: chain N residue 104 HIS Chi-restraints excluded: chain F residue 32 MET Chi-restraints excluded: chain H residue 4 MET Chi-restraints excluded: chain H residue 23 CYS Chi-restraints excluded: chain H residue 58 VAL Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 99 ASP Chi-restraints excluded: chain I residue 104 HIS Chi-restraints excluded: chain P residue 67 SER Chi-restraints excluded: chain Q residue 78 THR Chi-restraints excluded: chain R residue 38 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 196 optimal weight: 0.2980 chunk 274 optimal weight: 0.9980 chunk 49 optimal weight: 5.9990 chunk 346 optimal weight: 40.0000 chunk 89 optimal weight: 0.6980 chunk 399 optimal weight: 5.9990 chunk 183 optimal weight: 0.9990 chunk 51 optimal weight: 0.0170 chunk 283 optimal weight: 30.0000 chunk 138 optimal weight: 0.9990 chunk 215 optimal weight: 40.0000 overall best weight: 0.6020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1058 HIS A1106 GLN B 121 ASN C 196 ASN H 89 GLN I 33 HIS ** Q 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4760 r_free = 0.4760 target = 0.223870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.179789 restraints weight = 53194.522| |-----------------------------------------------------------------------------| r_work (start): 0.4298 rms_B_bonded: 3.32 r_work: 0.3615 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.3638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 32047 Z= 0.097 Angle : 0.529 10.082 43668 Z= 0.275 Chirality : 0.043 0.196 4864 Planarity : 0.004 0.051 5695 Dihedral : 5.020 58.976 4546 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.58 % Favored : 96.34 % Rotamer: Outliers : 2.12 % Allowed : 17.45 % Favored : 80.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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 aren not related in a simple way. whole: -0.67 (0.13), residues: 4073 helix: 0.59 (0.22), residues: 601 sheet: -0.22 (0.15), residues: 1190 loop : -0.82 (0.13), residues: 2282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 31 TYR 0.017 0.001 TYR A1138 PHE 0.016 0.001 PHE C 565 TRP 0.022 0.001 TRP I 36 HIS 0.006 0.001 HIS Q 104 Details of bonding type rmsd covalent geometry : bond 0.00211 (32011) covalent geometry : angle 0.52767 (43593) SS BOND : bond 0.00306 ( 33) SS BOND : angle 0.99210 ( 66) hydrogen bonds : bond 0.02911 ( 1010) hydrogen bonds : angle 5.34685 ( 2649) link_NAG-ASN : bond 0.00336 ( 3) link_NAG-ASN : angle 1.47189 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8146 Ramachandran restraints generated. 4073 Oldfield, 0 Emsley, 4073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8146 Ramachandran restraints generated. 4073 Oldfield, 0 Emsley, 4073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 3606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 204 time to evaluate : 1.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 118 LEU cc_start: 0.8792 (mt) cc_final: 0.8589 (mm) REVERT: B 347 PHE cc_start: 0.5482 (OUTLIER) cc_final: 0.3373 (m-80) REVERT: C 92 PHE cc_start: 0.6720 (t80) cc_final: 0.6462 (t80) REVERT: C 452 LEU cc_start: 0.6357 (OUTLIER) cc_final: 0.6116 (tt) REVERT: C 1043 CYS cc_start: 0.8709 (OUTLIER) cc_final: 0.8220 (m) REVERT: F 80 MET cc_start: -0.2785 (OUTLIER) cc_final: -0.3585 (tmm) REVERT: H 4 MET cc_start: 0.2810 (OUTLIER) cc_final: 0.2524 (ttt) REVERT: I 109 PHE cc_start: 0.7420 (m-80) cc_final: 0.6656 (t80) REVERT: L 80 MET cc_start: -0.2669 (mmt) cc_final: -0.3388 (tpp) REVERT: Q 83 MET cc_start: 0.1395 (mtp) cc_final: 0.1020 (mmp) outliers start: 68 outliers final: 47 residues processed: 253 average time/residue: 0.1856 time to fit residues: 80.1665 Evaluate side-chains 237 residues out of total 3606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 185 time to evaluate : 1.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 498 ARG Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 711 SER Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 929 SER Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain D residue 112 MET Chi-restraints excluded: chain J residue 46 VAL Chi-restraints excluded: chain N residue 58 TYR Chi-restraints excluded: chain N residue 104 HIS Chi-restraints excluded: chain F residue 32 MET Chi-restraints excluded: chain F residue 80 MET Chi-restraints excluded: chain H residue 4 MET Chi-restraints excluded: chain H residue 23 CYS Chi-restraints excluded: chain H residue 58 VAL Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 99 ASP Chi-restraints excluded: chain I residue 104 HIS Chi-restraints excluded: chain P residue 4 MET Chi-restraints excluded: chain P residue 67 SER Chi-restraints excluded: chain Q residue 78 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 148 optimal weight: 0.9980 chunk 255 optimal weight: 2.9990 chunk 362 optimal weight: 30.0000 chunk 154 optimal weight: 5.9990 chunk 191 optimal weight: 6.9990 chunk 315 optimal weight: 40.0000 chunk 258 optimal weight: 3.9990 chunk 287 optimal weight: 50.0000 chunk 30 optimal weight: 9.9990 chunk 278 optimal weight: 3.9990 chunk 178 optimal weight: 0.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1106 GLN C 703 ASN ** J 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 33 HIS ** Q 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4739 r_free = 0.4739 target = 0.221349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.177588 restraints weight = 53189.791| |-----------------------------------------------------------------------------| r_work (start): 0.4269 rms_B_bonded: 3.26 r_work: 0.3549 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.3738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 32047 Z= 0.197 Angle : 0.594 10.264 43668 Z= 0.311 Chirality : 0.046 0.184 4864 Planarity : 0.004 0.051 5695 Dihedral : 5.124 59.615 4541 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.35 % Favored : 95.58 % Rotamer: Outliers : 2.62 % Allowed : 16.98 % Favored : 80.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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 aren not related in a simple way. whole: -0.86 (0.13), residues: 4073 helix: 0.24 (0.22), residues: 602 sheet: -0.36 (0.15), residues: 1210 loop : -0.87 (0.13), residues: 2261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 983 TYR 0.020 0.002 TYR C 741 PHE 0.027 0.002 PHE C 375 TRP 0.014 0.001 TRP A 353 HIS 0.011 0.001 HIS N 104 Details of bonding type rmsd covalent geometry : bond 0.00459 (32011) covalent geometry : angle 0.59011 (43593) SS BOND : bond 0.00671 ( 33) SS BOND : angle 1.68424 ( 66) hydrogen bonds : bond 0.03553 ( 1010) hydrogen bonds : angle 5.59557 ( 2649) link_NAG-ASN : bond 0.00341 ( 3) link_NAG-ASN : angle 1.49292 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8146 Ramachandran restraints generated. 4073 Oldfield, 0 Emsley, 4073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8146 Ramachandran restraints generated. 4073 Oldfield, 0 Emsley, 4073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 3606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 187 time to evaluate : 1.201 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: B 338 PHE cc_start: 0.8470 (m-80) cc_final: 0.7956 (m-10) REVERT: C 92 PHE cc_start: 0.6907 (t80) cc_final: 0.6633 (t80) REVERT: C 452 LEU cc_start: 0.6293 (OUTLIER) cc_final: 0.6041 (tt) REVERT: F 80 MET cc_start: -0.2745 (OUTLIER) cc_final: -0.3589 (tmm) REVERT: H 4 MET cc_start: 0.2642 (OUTLIER) cc_final: 0.2335 (ttt) REVERT: I 83 MET cc_start: 0.3500 (ppp) cc_final: 0.3105 (ttp) REVERT: I 109 PHE cc_start: 0.7332 (m-80) cc_final: 0.6571 (t80) REVERT: L 80 MET cc_start: -0.2141 (mmt) cc_final: -0.3206 (tpp) REVERT: Q 83 MET cc_start: 0.1393 (mtp) cc_final: 0.0996 (mmp) outliers start: 84 outliers final: 66 residues processed: 252 average time/residue: 0.1794 time to fit residues: 78.4307 Evaluate side-chains 248 residues out of total 3606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 179 time to evaluate : 1.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 711 SER Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 929 SER Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain D residue 112 MET Chi-restraints excluded: chain J residue 46 VAL Chi-restraints excluded: chain N residue 58 TYR Chi-restraints excluded: chain N residue 104 HIS Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 32 MET Chi-restraints excluded: chain F residue 80 MET Chi-restraints excluded: chain H residue 4 MET Chi-restraints excluded: chain H residue 23 CYS Chi-restraints excluded: chain H residue 58 VAL Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 99 ASP Chi-restraints excluded: chain I residue 104 HIS Chi-restraints excluded: chain P residue 4 MET Chi-restraints excluded: chain P residue 67 SER Chi-restraints excluded: chain Q residue 78 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 16 optimal weight: 3.9990 chunk 107 optimal weight: 8.9990 chunk 394 optimal weight: 20.0000 chunk 56 optimal weight: 0.8980 chunk 93 optimal weight: 7.9990 chunk 361 optimal weight: 0.5980 chunk 393 optimal weight: 30.0000 chunk 300 optimal weight: 20.0000 chunk 408 optimal weight: 30.0000 chunk 277 optimal weight: 0.9980 chunk 87 optimal weight: 0.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 33 HIS I 39 GLN ** Q 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4773 r_free = 0.4773 target = 0.227680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.184906 restraints weight = 53098.474| |-----------------------------------------------------------------------------| r_work (start): 0.4304 rms_B_bonded: 3.31 r_work: 0.3588 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.3904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 32047 Z= 0.132 Angle : 0.549 10.281 43668 Z= 0.285 Chirality : 0.044 0.171 4864 Planarity : 0.004 0.057 5695 Dihedral : 4.939 59.427 4541 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.68 % Favored : 96.27 % Rotamer: Outliers : 2.22 % Allowed : 17.55 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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 aren not related in a simple way. whole: -0.76 (0.13), residues: 4073 helix: 0.40 (0.22), residues: 609 sheet: -0.31 (0.15), residues: 1215 loop : -0.82 (0.13), residues: 2249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 38 TYR 0.017 0.001 TYR B1067 PHE 0.028 0.001 PHE I 50 TRP 0.022 0.001 TRP B 436 HIS 0.010 0.001 HIS N 104 Details of bonding type rmsd covalent geometry : bond 0.00302 (32011) covalent geometry : angle 0.54637 (43593) SS BOND : bond 0.00424 ( 33) SS BOND : angle 1.32289 ( 66) hydrogen bonds : bond 0.03105 ( 1010) hydrogen bonds : angle 5.38652 ( 2649) link_NAG-ASN : bond 0.00324 ( 3) link_NAG-ASN : angle 1.38870 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8146 Ramachandran restraints generated. 4073 Oldfield, 0 Emsley, 4073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8146 Ramachandran restraints generated. 4073 Oldfield, 0 Emsley, 4073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 3606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 182 time to evaluate : 1.239 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 870 ILE cc_start: 0.9045 (OUTLIER) cc_final: 0.8601 (mm) REVERT: B 118 LEU cc_start: 0.8808 (mt) cc_final: 0.8597 (mm) REVERT: B 338 PHE cc_start: 0.8515 (m-80) cc_final: 0.8035 (m-10) REVERT: B 347 PHE cc_start: 0.5696 (OUTLIER) cc_final: 0.2880 (m-80) REVERT: C 92 PHE cc_start: 0.6809 (t80) cc_final: 0.6574 (t80) REVERT: C 452 LEU cc_start: 0.6242 (OUTLIER) cc_final: 0.5995 (tt) REVERT: C 759 PHE cc_start: 0.7617 (m-80) cc_final: 0.7296 (m-80) REVERT: F 80 MET cc_start: -0.2758 (OUTLIER) cc_final: -0.3587 (tmm) REVERT: H 4 MET cc_start: 0.2767 (OUTLIER) cc_final: 0.2547 (ttt) REVERT: I 68 PHE cc_start: 0.1495 (m-80) cc_final: 0.1283 (m-80) REVERT: I 83 MET cc_start: 0.3513 (ppp) cc_final: 0.3136 (ttp) REVERT: I 109 PHE cc_start: 0.7322 (m-80) cc_final: 0.6580 (t80) REVERT: L 80 MET cc_start: -0.2114 (mmt) cc_final: -0.3143 (tpp) REVERT: Q 83 MET cc_start: 0.1434 (mtp) cc_final: 0.1034 (mmp) outliers start: 71 outliers final: 59 residues processed: 235 average time/residue: 0.1796 time to fit residues: 73.3981 Evaluate side-chains 238 residues out of total 3606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 174 time to evaluate : 1.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 498 ARG Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 870 ILE Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 711 SER Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 929 SER Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain D residue 112 MET Chi-restraints excluded: chain J residue 46 VAL Chi-restraints excluded: chain N residue 58 TYR Chi-restraints excluded: chain N residue 104 HIS Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 32 MET Chi-restraints excluded: chain F residue 80 MET Chi-restraints excluded: chain H residue 4 MET Chi-restraints excluded: chain H residue 23 CYS Chi-restraints excluded: chain H residue 58 VAL Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 99 ASP Chi-restraints excluded: chain I residue 104 HIS Chi-restraints excluded: chain K residue 22 THR Chi-restraints excluded: chain P residue 4 MET Chi-restraints excluded: chain P residue 67 SER Chi-restraints excluded: chain Q residue 78 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 275 optimal weight: 0.0870 chunk 311 optimal weight: 30.0000 chunk 397 optimal weight: 20.0000 chunk 26 optimal weight: 7.9990 chunk 210 optimal weight: 9.9990 chunk 408 optimal weight: 30.0000 chunk 193 optimal weight: 8.9990 chunk 323 optimal weight: 9.9990 chunk 334 optimal weight: 40.0000 chunk 343 optimal weight: 30.0000 chunk 232 optimal weight: 0.6980 overall best weight: 5.5564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 658 ASN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 92 HIS ** F 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4738 r_free = 0.4738 target = 0.220326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.180427 restraints weight = 52665.466| |-----------------------------------------------------------------------------| r_work (start): 0.4334 rms_B_bonded: 2.99 r_work: 0.3691 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.4140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.080 32047 Z= 0.381 Angle : 0.743 12.257 43668 Z= 0.396 Chirality : 0.051 0.243 4864 Planarity : 0.006 0.058 5695 Dihedral : 5.712 59.273 4540 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.02 % Favored : 93.91 % Rotamer: Outliers : 2.72 % Allowed : 17.51 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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 aren not related in a simple way. whole: -1.33 (0.13), residues: 4073 helix: -0.58 (0.20), residues: 619 sheet: -0.54 (0.15), residues: 1212 loop : -1.12 (0.13), residues: 2242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 905 TYR 0.025 0.002 TYR A 279 PHE 0.031 0.003 PHE A1121 TRP 0.029 0.003 TRP F 107 HIS 0.010 0.002 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00902 (32011) covalent geometry : angle 0.73999 (43593) SS BOND : bond 0.01051 ( 33) SS BOND : angle 1.72890 ( 66) hydrogen bonds : bond 0.04623 ( 1010) hydrogen bonds : angle 6.12598 ( 2649) link_NAG-ASN : bond 0.00432 ( 3) link_NAG-ASN : angle 1.59189 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8146 Ramachandran restraints generated. 4073 Oldfield, 0 Emsley, 4073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8146 Ramachandran restraints generated. 4073 Oldfield, 0 Emsley, 4073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 3606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 174 time to evaluate : 1.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 338 PHE cc_start: 0.8132 (m-80) cc_final: 0.7626 (m-10) REVERT: B 347 PHE cc_start: 0.5253 (OUTLIER) cc_final: 0.3664 (m-80) REVERT: B 560 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8431 (mp) REVERT: C 759 PHE cc_start: 0.7695 (m-80) cc_final: 0.7235 (m-80) REVERT: F 32 MET cc_start: 0.2525 (OUTLIER) cc_final: 0.2289 (mmm) REVERT: F 80 MET cc_start: -0.2425 (OUTLIER) cc_final: -0.3461 (tmm) REVERT: H 4 MET cc_start: 0.2263 (OUTLIER) cc_final: 0.1991 (ttt) REVERT: I 83 MET cc_start: 0.3753 (ppp) cc_final: 0.3211 (ttp) REVERT: I 109 PHE cc_start: 0.6808 (m-80) cc_final: 0.6318 (t80) REVERT: L 80 MET cc_start: -0.1507 (mmt) cc_final: -0.2805 (tpp) outliers start: 87 outliers final: 68 residues processed: 242 average time/residue: 0.1753 time to fit residues: 74.2420 Evaluate side-chains 241 residues out of total 3606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 168 time to evaluate : 1.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 711 SER Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 929 SER Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1134 ASN Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain J residue 46 VAL Chi-restraints excluded: chain N residue 104 HIS Chi-restraints excluded: chain F residue 32 MET Chi-restraints excluded: chain F residue 80 MET Chi-restraints excluded: chain H residue 4 MET Chi-restraints excluded: chain H residue 23 CYS Chi-restraints excluded: chain H residue 58 VAL Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain I residue 34 MET Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 99 ASP Chi-restraints excluded: chain I residue 104 HIS Chi-restraints excluded: chain K residue 22 THR Chi-restraints excluded: chain P residue 4 MET Chi-restraints excluded: chain P residue 67 SER Chi-restraints excluded: chain Q residue 78 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 208 optimal weight: 20.0000 chunk 155 optimal weight: 0.8980 chunk 21 optimal weight: 4.9990 chunk 279 optimal weight: 0.9990 chunk 235 optimal weight: 0.3980 chunk 277 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 146 optimal weight: 0.9990 chunk 394 optimal weight: 20.0000 chunk 220 optimal weight: 20.0000 chunk 307 optimal weight: 30.0000 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 505 HIS ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 751 ASN C 955 ASN ** J 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 33 HIS K 53 ASN ** K 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 38 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4774 r_free = 0.4774 target = 0.224070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.182217 restraints weight = 52660.324| |-----------------------------------------------------------------------------| r_work (start): 0.4332 rms_B_bonded: 3.10 r_work: 0.3645 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.4248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 32047 Z= 0.109 Angle : 0.557 11.376 43668 Z= 0.289 Chirality : 0.044 0.167 4864 Planarity : 0.004 0.060 5695 Dihedral : 5.077 59.759 4540 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.49 % Favored : 96.44 % Rotamer: Outliers : 1.84 % Allowed : 18.36 % Favored : 79.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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 aren not related in a simple way. whole: -0.93 (0.13), residues: 4073 helix: 0.15 (0.21), residues: 627 sheet: -0.37 (0.15), residues: 1232 loop : -0.94 (0.13), residues: 2214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 328 TYR 0.019 0.001 TYR B1067 PHE 0.016 0.001 PHE I 50 TRP 0.035 0.002 TRP B 436 HIS 0.006 0.001 HIS N 104 Details of bonding type rmsd covalent geometry : bond 0.00242 (32011) covalent geometry : angle 0.55562 (43593) SS BOND : bond 0.00375 ( 33) SS BOND : angle 1.05517 ( 66) hydrogen bonds : bond 0.03090 ( 1010) hydrogen bonds : angle 5.47278 ( 2649) link_NAG-ASN : bond 0.00314 ( 3) link_NAG-ASN : angle 1.34892 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8146 Ramachandran restraints generated. 4073 Oldfield, 0 Emsley, 4073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8146 Ramachandran restraints generated. 4073 Oldfield, 0 Emsley, 4073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 3606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 177 time to evaluate : 1.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 338 PHE cc_start: 0.8389 (m-80) cc_final: 0.7917 (m-10) REVERT: B 436 TRP cc_start: 0.7366 (p90) cc_final: 0.7120 (p90) REVERT: F 32 MET cc_start: 0.2771 (OUTLIER) cc_final: 0.2526 (mmm) REVERT: F 80 MET cc_start: -0.2752 (OUTLIER) cc_final: -0.3543 (tmm) REVERT: I 68 PHE cc_start: 0.1546 (m-80) cc_final: 0.1316 (m-80) REVERT: I 83 MET cc_start: 0.3530 (ppp) cc_final: 0.3141 (ttp) REVERT: I 109 PHE cc_start: 0.7206 (m-80) cc_final: 0.6485 (t80) REVERT: K 32 TYR cc_start: 0.6684 (m-80) cc_final: 0.6481 (m-80) REVERT: L 80 MET cc_start: -0.2018 (mmt) cc_final: -0.2998 (tpp) outliers start: 59 outliers final: 46 residues processed: 217 average time/residue: 0.1816 time to fit residues: 68.0141 Evaluate side-chains 217 residues out of total 3606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 169 time to evaluate : 1.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 505 HIS Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 711 SER Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 929 SER Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain J residue 46 VAL Chi-restraints excluded: chain N residue 104 HIS Chi-restraints excluded: chain F residue 32 MET Chi-restraints excluded: chain F residue 80 MET Chi-restraints excluded: chain H residue 23 CYS Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 99 ASP Chi-restraints excluded: chain I residue 104 HIS Chi-restraints excluded: chain K residue 22 THR Chi-restraints excluded: chain P residue 4 MET Chi-restraints excluded: chain P residue 67 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 408 optimal weight: 10.0000 chunk 32 optimal weight: 30.0000 chunk 385 optimal weight: 40.0000 chunk 252 optimal weight: 6.9990 chunk 93 optimal weight: 7.9990 chunk 357 optimal weight: 0.6980 chunk 208 optimal weight: 10.0000 chunk 17 optimal weight: 4.9990 chunk 83 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 107 optimal weight: 10.0000 overall best weight: 3.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 505 HIS ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 33 HIS ** K 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4725 r_free = 0.4725 target = 0.220604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.176885 restraints weight = 52240.625| |-----------------------------------------------------------------------------| r_work (start): 0.4320 rms_B_bonded: 3.22 r_work: 0.3664 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.4313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 32047 Z= 0.240 Angle : 0.625 12.107 43668 Z= 0.327 Chirality : 0.047 0.219 4864 Planarity : 0.005 0.055 5695 Dihedral : 5.242 59.417 4540 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.08 % Favored : 94.87 % Rotamer: Outliers : 2.06 % Allowed : 18.17 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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 aren not related in a simple way. whole: -1.05 (0.13), residues: 4073 helix: -0.09 (0.21), residues: 627 sheet: -0.39 (0.15), residues: 1224 loop : -1.01 (0.13), residues: 2222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 509 TYR 0.020 0.002 TYR A 279 PHE 0.026 0.002 PHE B1121 TRP 0.020 0.002 TRP B 436 HIS 0.006 0.001 HIS N 104 Details of bonding type rmsd covalent geometry : bond 0.00563 (32011) covalent geometry : angle 0.62300 (43593) SS BOND : bond 0.00689 ( 33) SS BOND : angle 1.32862 ( 66) hydrogen bonds : bond 0.03711 ( 1010) hydrogen bonds : angle 5.66208 ( 2649) link_NAG-ASN : bond 0.00319 ( 3) link_NAG-ASN : angle 1.40553 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8981.34 seconds wall clock time: 154 minutes 44.03 seconds (9284.03 seconds total)