Starting phenix.real_space_refine on Wed Jun 18 13:45:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6crv_7573/06_2025/6crv_7573.cif Found real_map, /net/cci-nas-00/data/ceres_data/6crv_7573/06_2025/6crv_7573.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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6crv_7573/06_2025/6crv_7573.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6crv_7573/06_2025/6crv_7573.map" model { file = "/net/cci-nas-00/data/ceres_data/6crv_7573/06_2025/6crv_7573.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6crv_7573/06_2025/6crv_7573.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 111 5.16 5 C 13362 2.51 5 N 3438 2.21 5 O 4125 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 21036 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 6833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 881, 6833 Classifications: {'peptide': 881} Link IDs: {'PCIS': 1, 'PTRANS': 38, 'TRANS': 841} Chain breaks: 5 Chain: "B" Number of atoms: 6833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 881, 6833 Classifications: {'peptide': 881} Link IDs: {'PCIS': 1, 'PTRANS': 38, 'TRANS': 841} Chain breaks: 5 Chain: "C" Number of atoms: 6833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 881, 6833 Classifications: {'peptide': 881} Link IDs: {'PCIS': 1, 'PTRANS': 38, 'TRANS': 841} Chain breaks: 5 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "B" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "C" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 11.60, per 1000 atoms: 0.55 Number of scatterers: 21036 At special positions: 0 Unit cell: (146.26, 149.35, 144.2, 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 4125 8.00 N 3438 7.00 C 13362 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=33, symmetry=0 Simple disulfide: pdb=" SG CYS A 19 " - pdb=" SG CYS A 133 " distance=2.03 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 159 " distance=2.02 Simple disulfide: pdb=" SG CYS A 278 " - pdb=" SG CYS A 288 " distance=2.02 Simple disulfide: pdb=" SG CYS A 524 " - pdb=" SG CYS A 576 " distance=2.03 Simple disulfide: pdb=" SG CYS A 603 " - pdb=" SG CYS A 635 " distance=2.03 Simple disulfide: pdb=" SG CYS A 648 " - pdb=" SG CYS A 657 " distance=2.03 Simple disulfide: pdb=" SG CYS A 720 " - pdb=" SG CYS A 742 " distance=2.03 Simple disulfide: pdb=" SG CYS A 725 " - pdb=" SG CYS A 731 " distance=2.04 Simple disulfide: pdb=" SG CYS A 822 " - pdb=" SG CYS A 833 " distance=2.03 Simple disulfide: pdb=" SG CYS A1014 " - pdb=" SG CYS A1025 " distance=2.00 Simple disulfide: pdb=" SG CYS A1064 " - pdb=" SG CYS A1108 " distance=2.03 Simple disulfide: pdb=" SG CYS B 19 " - pdb=" SG CYS B 133 " distance=2.03 Simple disulfide: pdb=" SG CYS B 128 " - pdb=" SG CYS B 159 " distance=2.02 Simple disulfide: pdb=" SG CYS B 278 " - pdb=" SG CYS B 288 " distance=2.02 Simple disulfide: pdb=" SG CYS B 524 " - pdb=" SG CYS B 576 " distance=2.03 Simple disulfide: pdb=" SG CYS B 603 " - pdb=" SG CYS B 635 " distance=2.03 Simple disulfide: pdb=" SG CYS B 648 " - pdb=" SG CYS B 657 " distance=2.03 Simple disulfide: pdb=" SG CYS B 720 " - pdb=" SG CYS B 742 " distance=2.03 Simple disulfide: pdb=" SG CYS B 725 " - pdb=" SG CYS B 731 " distance=2.03 Simple disulfide: pdb=" SG CYS B 822 " - pdb=" SG CYS B 833 " distance=2.03 Simple disulfide: pdb=" SG CYS B1014 " - pdb=" SG CYS B1025 " distance=2.00 Simple disulfide: pdb=" SG CYS B1064 " - pdb=" SG CYS B1108 " distance=2.02 Simple disulfide: pdb=" SG CYS C 19 " - pdb=" SG CYS C 133 " distance=2.03 Simple disulfide: pdb=" SG CYS C 128 " - pdb=" SG CYS C 159 " distance=2.02 Simple disulfide: pdb=" SG CYS C 278 " - pdb=" SG CYS C 288 " distance=2.02 Simple disulfide: pdb=" SG CYS C 524 " - pdb=" SG CYS C 576 " distance=2.03 Simple disulfide: pdb=" SG CYS C 603 " - pdb=" SG CYS C 635 " distance=2.03 Simple disulfide: pdb=" SG CYS C 648 " - pdb=" SG CYS C 657 " distance=2.03 Simple disulfide: pdb=" SG CYS C 720 " - pdb=" SG CYS C 742 " distance=2.03 Simple disulfide: pdb=" SG CYS C 725 " - pdb=" SG CYS C 731 " distance=2.03 Simple disulfide: pdb=" SG CYS C 822 " - pdb=" SG CYS C 833 " distance=2.03 Simple disulfide: pdb=" SG CYS C1014 " - pdb=" SG CYS C1025 " distance=2.00 Simple disulfide: pdb=" SG CYS C1064 " - pdb=" SG CYS C1108 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " NAG-ASN " NAG A1301 " - " ASN A 65 " " NAG A1304 " - " ASN A 691 " " NAG A1308 " - " ASN A1080 " " NAG A1309 " - " ASN A1116 " " NAG A1310 " - " ASN A1056 " " NAG A1311 " - " ASN A 602 " " NAG B1301 " - " ASN B 65 " " NAG B1304 " - " ASN B 691 " " NAG B1308 " - " ASN B1080 " " NAG B1309 " - " ASN B1116 " " NAG B1310 " - " ASN B1056 " " NAG B1311 " - " ASN B 602 " " NAG C1301 " - " ASN C 65 " " NAG C1304 " - " ASN C 691 " " NAG C1308 " - " ASN C1080 " " NAG C1309 " - " ASN C1116 " " NAG C1310 " - " ASN C1056 " " NAG C1311 " - " ASN C 602 " " NAG D 1 " - " ASN A 269 " " NAG E 1 " - " ASN A 783 " " NAG F 1 " - " ASN A 699 " " NAG G 1 " - " ASN B 269 " " NAG H 1 " - " ASN B 783 " " NAG I 1 " - " ASN B 699 " " NAG J 1 " - " ASN C 269 " " NAG K 1 " - " ASN C 783 " " NAG L 1 " - " ASN C 699 " Time building additional restraints: 4.74 Conformation dependent library (CDL) restraints added in 2.4 seconds 5214 Ramachandran restraints generated. 2607 Oldfield, 0 Emsley, 2607 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4950 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 45 sheets defined 24.9% alpha, 42.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.10 Creating SS restraints... Processing helix chain 'A' and resid 281 through 291 Processing helix chain 'A' and resid 602 through 612 Processing helix chain 'A' and resid 719 through 724 Processing helix chain 'A' and resid 728 through 735 Processing helix chain 'A' and resid 736 through 739 Processing helix chain 'A' and resid 740 through 765 removed outlier: 3.534A pdb=" N GLN A 744 " --> pdb=" O SER A 740 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASP A 757 " --> pdb=" O ALA A 753 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N THR A 760 " --> pdb=" O GLN A 756 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL A 763 " --> pdb=" O ASN A 759 " (cutoff:3.500A) Processing helix chain 'A' and resid 798 through 805 removed outlier: 3.584A pdb=" N LEU A 803 " --> pdb=" O PHE A 799 " (cutoff:3.500A) Processing helix chain 'A' and resid 848 through 866 removed outlier: 3.536A pdb=" N THR A 865 " --> pdb=" O SER A 861 " (cutoff:3.500A) Processing helix chain 'A' and resid 867 through 871 removed outlier: 3.550A pdb=" N PHE A 870 " --> pdb=" O GLY A 867 " (cutoff:3.500A) Processing helix chain 'A' and resid 879 through 890 Processing helix chain 'A' and resid 895 through 900 removed outlier: 3.576A pdb=" N TYR A 899 " --> pdb=" O GLN A 895 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 923 Processing helix chain 'A' and resid 927 through 947 removed outlier: 3.587A pdb=" N VAL A 933 " --> pdb=" O LYS A 929 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASN A 937 " --> pdb=" O VAL A 933 " (cutoff:3.500A) Processing helix chain 'A' and resid 948 through 950 No H-bonds generated for 'chain 'A' and resid 948 through 950' Processing helix chain 'A' and resid 958 through 966 Processing helix chain 'A' and resid 967 through 1013 removed outlier: 3.569A pdb=" N THR A 980 " --> pdb=" O ASP A 976 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA A 998 " --> pdb=" O LEU A 994 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLU A 999 " --> pdb=" O ILE A 995 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 291 Processing helix chain 'B' and resid 602 through 612 Processing helix chain 'B' and resid 719 through 724 Processing helix chain 'B' and resid 728 through 735 Processing helix chain 'B' and resid 736 through 739 Processing helix chain 'B' and resid 740 through 765 removed outlier: 3.534A pdb=" N GLN B 744 " --> pdb=" O SER B 740 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASP B 757 " --> pdb=" O ALA B 753 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR B 760 " --> pdb=" O GLN B 756 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL B 763 " --> pdb=" O ASN B 759 " (cutoff:3.500A) Processing helix chain 'B' and resid 798 through 805 removed outlier: 3.584A pdb=" N LEU B 803 " --> pdb=" O PHE B 799 " (cutoff:3.500A) Processing helix chain 'B' and resid 848 through 866 removed outlier: 3.536A pdb=" N THR B 865 " --> pdb=" O SER B 861 " (cutoff:3.500A) Processing helix chain 'B' and resid 867 through 871 removed outlier: 3.550A pdb=" N PHE B 870 " --> pdb=" O GLY B 867 " (cutoff:3.500A) Processing helix chain 'B' and resid 879 through 890 Processing helix chain 'B' and resid 895 through 900 removed outlier: 3.576A pdb=" N TYR B 899 " --> pdb=" O GLN B 895 " (cutoff:3.500A) Processing helix chain 'B' and resid 901 through 923 Processing helix chain 'B' and resid 927 through 947 removed outlier: 3.588A pdb=" N VAL B 933 " --> pdb=" O LYS B 929 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASN B 937 " --> pdb=" O VAL B 933 " (cutoff:3.500A) Processing helix chain 'B' and resid 948 through 950 No H-bonds generated for 'chain 'B' and resid 948 through 950' Processing helix chain 'B' and resid 958 through 966 Processing helix chain 'B' and resid 967 through 1013 removed outlier: 3.569A pdb=" N THR B 980 " --> pdb=" O ASP B 976 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA B 998 " --> pdb=" O LEU B 994 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLU B 999 " --> pdb=" O ILE B 995 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 291 Processing helix chain 'C' and resid 602 through 612 Processing helix chain 'C' and resid 719 through 724 Processing helix chain 'C' and resid 728 through 735 Processing helix chain 'C' and resid 736 through 739 Processing helix chain 'C' and resid 740 through 765 removed outlier: 3.534A pdb=" N GLN C 744 " --> pdb=" O SER C 740 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASP C 757 " --> pdb=" O ALA C 753 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N THR C 760 " --> pdb=" O GLN C 756 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL C 763 " --> pdb=" O ASN C 759 " (cutoff:3.500A) Processing helix chain 'C' and resid 798 through 805 removed outlier: 3.584A pdb=" N LEU C 803 " --> pdb=" O PHE C 799 " (cutoff:3.500A) Processing helix chain 'C' and resid 848 through 866 removed outlier: 3.536A pdb=" N THR C 865 " --> pdb=" O SER C 861 " (cutoff:3.500A) Processing helix chain 'C' and resid 867 through 871 removed outlier: 3.550A pdb=" N PHE C 870 " --> pdb=" O GLY C 867 " (cutoff:3.500A) Processing helix chain 'C' and resid 879 through 890 Processing helix chain 'C' and resid 895 through 900 removed outlier: 3.575A pdb=" N TYR C 899 " --> pdb=" O GLN C 895 " (cutoff:3.500A) Processing helix chain 'C' and resid 901 through 923 Processing helix chain 'C' and resid 927 through 947 removed outlier: 3.587A pdb=" N VAL C 933 " --> pdb=" O LYS C 929 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASN C 937 " --> pdb=" O VAL C 933 " (cutoff:3.500A) Processing helix chain 'C' and resid 948 through 950 No H-bonds generated for 'chain 'C' and resid 948 through 950' Processing helix chain 'C' and resid 958 through 966 Processing helix chain 'C' and resid 967 through 1013 removed outlier: 3.568A pdb=" N THR C 980 " --> pdb=" O ASP C 976 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA C 998 " --> pdb=" O LEU C 994 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLU C 999 " --> pdb=" O ILE C 995 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 31 through 35 Processing sheet with id=AA2, first strand: chain 'A' and resid 31 through 35 removed outlier: 7.800A pdb=" N ASN A 65 " --> pdb=" O TYR A 256 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N TYR A 256 " --> pdb=" O ASN A 65 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA A 251 " --> pdb=" O THR A 92 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N HIS A 181 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N ILE A 203 " --> pdb=" O HIS A 181 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N ARG A 183 " --> pdb=" O GLN A 201 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N GLN A 201 " --> pdb=" O ARG A 183 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N PHE A 185 " --> pdb=" O GLY A 199 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N GLY A 199 " --> pdb=" O PHE A 185 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N PHE A 187 " --> pdb=" O TYR A 197 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N TYR A 197 " --> pdb=" O PHE A 187 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N ASN A 189 " --> pdb=" O TYR A 195 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N TYR A 195 " --> pdb=" O ASN A 189 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N LEU A 194 " --> pdb=" O LYS A 221 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N LYS A 221 " --> pdb=" O LEU A 194 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N VAL A 196 " --> pdb=" O ILE A 219 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 46 through 47 removed outlier: 6.490A pdb=" N PHE A 47 " --> pdb=" O ARG C 553 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N SER C 561 " --> pdb=" O GLY C 552 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N ASP C 560 " --> pdb=" O ILE C 573 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N VAL C 313 " --> pdb=" O ASN C 528 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 51 through 59 removed outlier: 3.813A pdb=" N ASP A 274 " --> pdb=" O LYS A 265 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 81 through 82 removed outlier: 6.587A pdb=" N VAL A 123 " --> pdb=" O ILE A 164 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ILE A 164 " --> pdb=" O VAL A 123 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ILE A 125 " --> pdb=" O GLU A 162 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N GLU A 162 " --> pdb=" O ILE A 125 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ALA A 127 " --> pdb=" O THR A 160 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ASN A 129 " --> pdb=" O ASN A 158 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N ASN A 158 " --> pdb=" O ASN A 129 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N GLU A 131 " --> pdb=" O ALA A 156 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ALA A 156 " --> pdb=" O GLU A 131 " (cutoff:3.500A) removed outlier: 9.237A pdb=" N CYS A 133 " --> pdb=" O ASP A 154 " (cutoff:3.500A) removed outlier: 8.431A pdb=" N ASP A 154 " --> pdb=" O CYS A 133 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ASN A 135 " --> pdb=" O ILE A 152 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N ILE A 152 " --> pdb=" O ASN A 135 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N PHE A 137 " --> pdb=" O THR A 150 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N THR A 150 " --> pdb=" O PHE A 137 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ALA A 139 " --> pdb=" O THR A 148 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 81 through 82 removed outlier: 13.934A pdb=" N PHE A 231 " --> pdb=" O PHE A 130 " (cutoff:3.500A) removed outlier: 13.514A pdb=" N LEU A 132 " --> pdb=" O PHE A 231 " (cutoff:3.500A) removed outlier: 13.118A pdb=" N ALA A 233 " --> pdb=" O LEU A 132 " (cutoff:3.500A) removed outlier: 10.294A pdb=" N ASP A 134 " --> pdb=" O ALA A 233 " (cutoff:3.500A) removed outlier: 9.998A pdb=" N LEU A 235 " --> pdb=" O ASP A 134 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N ALA A 237 " --> pdb=" O PRO A 136 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N PHE A 138 " --> pdb=" O ALA A 237 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N SER A 239 " --> pdb=" O PHE A 138 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N VAL A 140 " --> pdb=" O SER A 239 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N VAL A 123 " --> pdb=" O ILE A 164 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ILE A 164 " --> pdb=" O VAL A 123 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ILE A 125 " --> pdb=" O GLU A 162 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N GLU A 162 " --> pdb=" O ILE A 125 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ALA A 127 " --> pdb=" O THR A 160 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ASN A 129 " --> pdb=" O ASN A 158 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N ASN A 158 " --> pdb=" O ASN A 129 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N GLU A 131 " --> pdb=" O ALA A 156 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ALA A 156 " --> pdb=" O GLU A 131 " (cutoff:3.500A) removed outlier: 9.237A pdb=" N CYS A 133 " --> pdb=" O ASP A 154 " (cutoff:3.500A) removed outlier: 8.431A pdb=" N ASP A 154 " --> pdb=" O CYS A 133 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ASN A 135 " --> pdb=" O ILE A 152 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N ILE A 152 " --> pdb=" O ASN A 135 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N PHE A 137 " --> pdb=" O THR A 150 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N THR A 150 " --> pdb=" O PHE A 137 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ALA A 139 " --> pdb=" O THR A 148 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 615 through 616 removed outlier: 3.952A pdb=" N VAL A 581 " --> pdb=" O THR A 302 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N ASN A 304 " --> pdb=" O GLY A 579 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N GLY A 579 " --> pdb=" O ASN A 304 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N GLY A 580 " --> pdb=" O GLN A 599 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 312 through 314 removed outlier: 6.550A pdb=" N VAL A 313 " --> pdb=" O ASN A 528 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N ASP A 560 " --> pdb=" O ILE A 573 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N SER A 561 " --> pdb=" O GLY A 552 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N PHE A 551 " --> pdb=" O PHE B 47 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 640 through 646 removed outlier: 6.060A pdb=" N GLU A 640 " --> pdb=" O ALA A 676 " (cutoff:3.500A) removed outlier: 8.429A pdb=" N THR A 678 " --> pdb=" O GLU A 640 " (cutoff:3.500A) removed outlier: 8.847A pdb=" N VAL A 642 " --> pdb=" O THR A 678 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ILE A 656 " --> pdb=" O ILE A 652 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 683 through 685 removed outlier: 6.225A pdb=" N ALA A 683 " --> pdb=" O MET B 770 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 693 through 710 removed outlier: 6.627A pdb=" N THR A 693 " --> pdb=" O THR A1058 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N THR A1058 " --> pdb=" O THR A 693 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ALA A 695 " --> pdb=" O ASN A1056 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N ASN A1056 " --> pdb=" O ALA A 695 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N GLU A1054 " --> pdb=" O PRO A 697 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLY A1041 " --> pdb=" O ALA A1038 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N TYR A1049 " --> pdb=" O HIS A1030 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N HIS A1030 " --> pdb=" O TYR A1049 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 693 through 710 removed outlier: 6.627A pdb=" N THR A 693 " --> pdb=" O THR A1058 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N THR A1058 " --> pdb=" O THR A 693 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ALA A 695 " --> pdb=" O ASN A1056 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N ASN A1056 " --> pdb=" O ALA A 695 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N GLU A1054 " --> pdb=" O PRO A 697 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N THR A1058 " --> pdb=" O PHE A1079 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ALA A1060 " --> pdb=" O PHE A1077 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N PHE A1077 " --> pdb=" O ALA A1060 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 716 through 718 Processing sheet with id=AB5, first strand: chain 'A' and resid 769 through 771 Processing sheet with id=AB6, first strand: chain 'A' and resid 778 through 779 removed outlier: 3.678A pdb=" N PHE A 782 " --> pdb=" O PHE A 779 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 821 through 823 Processing sheet with id=AB8, first strand: chain 'A' and resid 1102 through 1107 removed outlier: 4.366A pdb=" N ALA A1069 " --> pdb=" O SER A1105 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 31 through 35 Processing sheet with id=AC1, first strand: chain 'B' and resid 31 through 35 removed outlier: 7.801A pdb=" N ASN B 65 " --> pdb=" O TYR B 256 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N TYR B 256 " --> pdb=" O ASN B 65 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA B 251 " --> pdb=" O THR B 92 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N HIS B 181 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N ILE B 203 " --> pdb=" O HIS B 181 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N ARG B 183 " --> pdb=" O GLN B 201 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N GLN B 201 " --> pdb=" O ARG B 183 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N PHE B 185 " --> pdb=" O GLY B 199 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N GLY B 199 " --> pdb=" O PHE B 185 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N PHE B 187 " --> pdb=" O TYR B 197 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N TYR B 197 " --> pdb=" O PHE B 187 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N ASN B 189 " --> pdb=" O TYR B 195 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N TYR B 195 " --> pdb=" O ASN B 189 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N LEU B 194 " --> pdb=" O LYS B 221 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N LYS B 221 " --> pdb=" O LEU B 194 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N VAL B 196 " --> pdb=" O ILE B 219 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 51 through 59 removed outlier: 3.813A pdb=" N ASP B 274 " --> pdb=" O LYS B 265 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 81 through 82 removed outlier: 6.587A pdb=" N VAL B 123 " --> pdb=" O ILE B 164 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ILE B 164 " --> pdb=" O VAL B 123 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ILE B 125 " --> pdb=" O GLU B 162 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N GLU B 162 " --> pdb=" O ILE B 125 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ALA B 127 " --> pdb=" O THR B 160 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ASN B 129 " --> pdb=" O ASN B 158 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N ASN B 158 " --> pdb=" O ASN B 129 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N GLU B 131 " --> pdb=" O ALA B 156 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ALA B 156 " --> pdb=" O GLU B 131 " (cutoff:3.500A) removed outlier: 9.236A pdb=" N CYS B 133 " --> pdb=" O ASP B 154 " (cutoff:3.500A) removed outlier: 8.430A pdb=" N ASP B 154 " --> pdb=" O CYS B 133 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ASN B 135 " --> pdb=" O ILE B 152 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N ILE B 152 " --> pdb=" O ASN B 135 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N PHE B 137 " --> pdb=" O THR B 150 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N THR B 150 " --> pdb=" O PHE B 137 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ALA B 139 " --> pdb=" O THR B 148 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 81 through 82 removed outlier: 13.934A pdb=" N PHE B 231 " --> pdb=" O PHE B 130 " (cutoff:3.500A) removed outlier: 13.515A pdb=" N LEU B 132 " --> pdb=" O PHE B 231 " (cutoff:3.500A) removed outlier: 13.119A pdb=" N ALA B 233 " --> pdb=" O LEU B 132 " (cutoff:3.500A) removed outlier: 10.294A pdb=" N ASP B 134 " --> pdb=" O ALA B 233 " (cutoff:3.500A) removed outlier: 9.997A pdb=" N LEU B 235 " --> pdb=" O ASP B 134 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N ALA B 237 " --> pdb=" O PRO B 136 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N PHE B 138 " --> pdb=" O ALA B 237 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N SER B 239 " --> pdb=" O PHE B 138 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N VAL B 140 " --> pdb=" O SER B 239 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N VAL B 123 " --> pdb=" O ILE B 164 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ILE B 164 " --> pdb=" O VAL B 123 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ILE B 125 " --> pdb=" O GLU B 162 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N GLU B 162 " --> pdb=" O ILE B 125 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ALA B 127 " --> pdb=" O THR B 160 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ASN B 129 " --> pdb=" O ASN B 158 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N ASN B 158 " --> pdb=" O ASN B 129 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N GLU B 131 " --> pdb=" O ALA B 156 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ALA B 156 " --> pdb=" O GLU B 131 " (cutoff:3.500A) removed outlier: 9.236A pdb=" N CYS B 133 " --> pdb=" O ASP B 154 " (cutoff:3.500A) removed outlier: 8.430A pdb=" N ASP B 154 " --> pdb=" O CYS B 133 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ASN B 135 " --> pdb=" O ILE B 152 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N ILE B 152 " --> pdb=" O ASN B 135 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N PHE B 137 " --> pdb=" O THR B 150 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N THR B 150 " --> pdb=" O PHE B 137 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ALA B 139 " --> pdb=" O THR B 148 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 615 through 616 removed outlier: 3.952A pdb=" N VAL B 581 " --> pdb=" O THR B 302 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N ASN B 304 " --> pdb=" O GLY B 579 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N GLY B 579 " --> pdb=" O ASN B 304 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N GLY B 580 " --> pdb=" O GLN B 599 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 312 through 314 removed outlier: 6.550A pdb=" N VAL B 313 " --> pdb=" O ASN B 528 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N ASP B 560 " --> pdb=" O ILE B 573 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N SER B 561 " --> pdb=" O GLY B 552 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 640 through 646 removed outlier: 6.060A pdb=" N GLU B 640 " --> pdb=" O ALA B 676 " (cutoff:3.500A) removed outlier: 8.429A pdb=" N THR B 678 " --> pdb=" O GLU B 640 " (cutoff:3.500A) removed outlier: 8.847A pdb=" N VAL B 642 " --> pdb=" O THR B 678 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ILE B 656 " --> pdb=" O ILE B 652 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 683 through 685 removed outlier: 6.196A pdb=" N ALA B 683 " --> pdb=" O MET C 770 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'B' and resid 693 through 710 removed outlier: 6.627A pdb=" N THR B 693 " --> pdb=" O THR B1058 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N THR B1058 " --> pdb=" O THR B 693 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ALA B 695 " --> pdb=" O ASN B1056 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N ASN B1056 " --> pdb=" O ALA B 695 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N GLU B1054 " --> pdb=" O PRO B 697 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLY B1041 " --> pdb=" O ALA B1038 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N TYR B1049 " --> pdb=" O HIS B1030 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N HIS B1030 " --> pdb=" O TYR B1049 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 693 through 710 removed outlier: 6.627A pdb=" N THR B 693 " --> pdb=" O THR B1058 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N THR B1058 " --> pdb=" O THR B 693 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ALA B 695 " --> pdb=" O ASN B1056 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N ASN B1056 " --> pdb=" O ALA B 695 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N GLU B1054 " --> pdb=" O PRO B 697 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N THR B1058 " --> pdb=" O PHE B1079 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ALA B1060 " --> pdb=" O PHE B1077 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N PHE B1077 " --> pdb=" O ALA B1060 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 716 through 718 Processing sheet with id=AD3, first strand: chain 'B' and resid 778 through 779 removed outlier: 3.678A pdb=" N PHE B 782 " --> pdb=" O PHE B 779 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 821 through 823 Processing sheet with id=AD5, first strand: chain 'B' and resid 1102 through 1107 removed outlier: 4.366A pdb=" N ALA B1069 " --> pdb=" O SER B1105 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 31 through 35 Processing sheet with id=AD7, first strand: chain 'C' and resid 31 through 35 removed outlier: 7.801A pdb=" N ASN C 65 " --> pdb=" O TYR C 256 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N TYR C 256 " --> pdb=" O ASN C 65 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA C 251 " --> pdb=" O THR C 92 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N HIS C 181 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N ILE C 203 " --> pdb=" O HIS C 181 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N ARG C 183 " --> pdb=" O GLN C 201 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N GLN C 201 " --> pdb=" O ARG C 183 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N PHE C 185 " --> pdb=" O GLY C 199 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N GLY C 199 " --> pdb=" O PHE C 185 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N PHE C 187 " --> pdb=" O TYR C 197 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N TYR C 197 " --> pdb=" O PHE C 187 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N ASN C 189 " --> pdb=" O TYR C 195 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N TYR C 195 " --> pdb=" O ASN C 189 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N LEU C 194 " --> pdb=" O LYS C 221 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N LYS C 221 " --> pdb=" O LEU C 194 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N VAL C 196 " --> pdb=" O ILE C 219 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 51 through 59 removed outlier: 3.813A pdb=" N ASP C 274 " --> pdb=" O LYS C 265 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 81 through 82 removed outlier: 6.587A pdb=" N VAL C 123 " --> pdb=" O ILE C 164 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ILE C 164 " --> pdb=" O VAL C 123 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ILE C 125 " --> pdb=" O GLU C 162 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N GLU C 162 " --> pdb=" O ILE C 125 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ALA C 127 " --> pdb=" O THR C 160 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ASN C 129 " --> pdb=" O ASN C 158 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N ASN C 158 " --> pdb=" O ASN C 129 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N GLU C 131 " --> pdb=" O ALA C 156 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ALA C 156 " --> pdb=" O GLU C 131 " (cutoff:3.500A) removed outlier: 9.237A pdb=" N CYS C 133 " --> pdb=" O ASP C 154 " (cutoff:3.500A) removed outlier: 8.430A pdb=" N ASP C 154 " --> pdb=" O CYS C 133 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ASN C 135 " --> pdb=" O ILE C 152 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N ILE C 152 " --> pdb=" O ASN C 135 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N PHE C 137 " --> pdb=" O THR C 150 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N THR C 150 " --> pdb=" O PHE C 137 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ALA C 139 " --> pdb=" O THR C 148 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 81 through 82 removed outlier: 13.935A pdb=" N PHE C 231 " --> pdb=" O PHE C 130 " (cutoff:3.500A) removed outlier: 13.514A pdb=" N LEU C 132 " --> pdb=" O PHE C 231 " (cutoff:3.500A) removed outlier: 13.119A pdb=" N ALA C 233 " --> pdb=" O LEU C 132 " (cutoff:3.500A) removed outlier: 10.293A pdb=" N ASP C 134 " --> pdb=" O ALA C 233 " (cutoff:3.500A) removed outlier: 9.998A pdb=" N LEU C 235 " --> pdb=" O ASP C 134 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N ALA C 237 " --> pdb=" O PRO C 136 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N PHE C 138 " --> pdb=" O ALA C 237 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N SER C 239 " --> pdb=" O PHE C 138 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N VAL C 140 " --> pdb=" O SER C 239 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N VAL C 123 " --> pdb=" O ILE C 164 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ILE C 164 " --> pdb=" O VAL C 123 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ILE C 125 " --> pdb=" O GLU C 162 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N GLU C 162 " --> pdb=" O ILE C 125 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ALA C 127 " --> pdb=" O THR C 160 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ASN C 129 " --> pdb=" O ASN C 158 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N ASN C 158 " --> pdb=" O ASN C 129 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N GLU C 131 " --> pdb=" O ALA C 156 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ALA C 156 " --> pdb=" O GLU C 131 " (cutoff:3.500A) removed outlier: 9.237A pdb=" N CYS C 133 " --> pdb=" O ASP C 154 " (cutoff:3.500A) removed outlier: 8.430A pdb=" N ASP C 154 " --> pdb=" O CYS C 133 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ASN C 135 " --> pdb=" O ILE C 152 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N ILE C 152 " --> pdb=" O ASN C 135 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N PHE C 137 " --> pdb=" O THR C 150 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N THR C 150 " --> pdb=" O PHE C 137 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ALA C 139 " --> pdb=" O THR C 148 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 615 through 616 removed outlier: 3.953A pdb=" N VAL C 581 " --> pdb=" O THR C 302 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N ASN C 304 " --> pdb=" O GLY C 579 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N GLY C 579 " --> pdb=" O ASN C 304 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N GLY C 580 " --> pdb=" O GLN C 599 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 640 through 646 removed outlier: 6.060A pdb=" N GLU C 640 " --> pdb=" O ALA C 676 " (cutoff:3.500A) removed outlier: 8.429A pdb=" N THR C 678 " --> pdb=" O GLU C 640 " (cutoff:3.500A) removed outlier: 8.847A pdb=" N VAL C 642 " --> pdb=" O THR C 678 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ILE C 656 " --> pdb=" O ILE C 652 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 693 through 710 removed outlier: 6.627A pdb=" N THR C 693 " --> pdb=" O THR C1058 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N THR C1058 " --> pdb=" O THR C 693 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ALA C 695 " --> pdb=" O ASN C1056 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N ASN C1056 " --> pdb=" O ALA C 695 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N GLU C1054 " --> pdb=" O PRO C 697 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLY C1041 " --> pdb=" O ALA C1038 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N TYR C1049 " --> pdb=" O HIS C1030 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N HIS C1030 " --> pdb=" O TYR C1049 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 693 through 710 removed outlier: 6.627A pdb=" N THR C 693 " --> pdb=" O THR C1058 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N THR C1058 " --> pdb=" O THR C 693 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ALA C 695 " --> pdb=" O ASN C1056 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N ASN C1056 " --> pdb=" O ALA C 695 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N GLU C1054 " --> pdb=" O PRO C 697 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N THR C1058 " --> pdb=" O PHE C1079 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ALA C1060 " --> pdb=" O PHE C1077 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N PHE C1077 " --> pdb=" O ALA C1060 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 716 through 718 Processing sheet with id=AE7, first strand: chain 'C' and resid 778 through 779 removed outlier: 3.678A pdb=" N PHE C 782 " --> pdb=" O PHE C 779 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 821 through 823 Processing sheet with id=AE9, first strand: chain 'C' and resid 1102 through 1107 removed outlier: 4.367A pdb=" N ALA C1069 " --> pdb=" O SER C1105 " (cutoff:3.500A) 955 hydrogen bonds defined for protein. 2604 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: 8.54 Time building geometry restraints manager: 5.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6362 1.33 - 1.46: 5223 1.46 - 1.58: 9742 1.58 - 1.71: 3 1.71 - 1.83: 153 Bond restraints: 21483 Sorted by residual: bond pdb=" CB CYS B1014 " pdb=" SG CYS B1014 " ideal model delta sigma weight residual 1.808 1.658 0.150 3.30e-02 9.18e+02 2.06e+01 bond pdb=" CB CYS C1014 " pdb=" SG CYS C1014 " ideal model delta sigma weight residual 1.808 1.658 0.150 3.30e-02 9.18e+02 2.06e+01 bond pdb=" CB CYS A1014 " pdb=" SG CYS A1014 " ideal model delta sigma weight residual 1.808 1.658 0.150 3.30e-02 9.18e+02 2.06e+01 bond pdb=" CA TYR A 300 " pdb=" CB TYR A 300 " ideal model delta sigma weight residual 1.532 1.483 0.048 1.58e-02 4.01e+03 9.42e+00 bond pdb=" CA TYR C 300 " pdb=" CB TYR C 300 " ideal model delta sigma weight residual 1.532 1.484 0.048 1.58e-02 4.01e+03 9.38e+00 ... (remaining 21478 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.20: 27652 2.20 - 4.41: 1340 4.41 - 6.61: 180 6.61 - 8.82: 24 8.82 - 11.02: 15 Bond angle restraints: 29211 Sorted by residual: angle pdb=" N GLY C 867 " pdb=" CA GLY C 867 " pdb=" C GLY C 867 " ideal model delta sigma weight residual 110.95 119.29 -8.34 1.70e+00 3.46e-01 2.40e+01 angle pdb=" N GLY B 867 " pdb=" CA GLY B 867 " pdb=" C GLY B 867 " ideal model delta sigma weight residual 110.95 119.27 -8.32 1.70e+00 3.46e-01 2.40e+01 angle pdb=" N GLY A 867 " pdb=" CA GLY A 867 " pdb=" C GLY A 867 " ideal model delta sigma weight residual 110.95 119.26 -8.31 1.70e+00 3.46e-01 2.39e+01 angle pdb=" C PHE C 83 " pdb=" N LYS C 84 " pdb=" CA LYS C 84 " ideal model delta sigma weight residual 121.54 130.52 -8.98 1.91e+00 2.74e-01 2.21e+01 angle pdb=" C PHE A 83 " pdb=" N LYS A 84 " pdb=" CA LYS A 84 " ideal model delta sigma weight residual 121.54 130.52 -8.98 1.91e+00 2.74e-01 2.21e+01 ... (remaining 29206 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.45: 12941 21.45 - 42.89: 256 42.89 - 64.34: 69 64.34 - 85.78: 27 85.78 - 107.23: 12 Dihedral angle restraints: 13305 sinusoidal: 5631 harmonic: 7674 Sorted by residual: dihedral pdb=" CB CYS B1014 " pdb=" SG CYS B1014 " pdb=" SG CYS B1025 " pdb=" CB CYS B1025 " ideal model delta sinusoidal sigma weight residual -86.00 -169.27 83.27 1 1.00e+01 1.00e-02 8.48e+01 dihedral pdb=" CB CYS A1014 " pdb=" SG CYS A1014 " pdb=" SG CYS A1025 " pdb=" CB CYS A1025 " ideal model delta sinusoidal sigma weight residual -86.00 -169.26 83.26 1 1.00e+01 1.00e-02 8.47e+01 dihedral pdb=" CB CYS C1014 " pdb=" SG CYS C1014 " pdb=" SG CYS C1025 " pdb=" CB CYS C1025 " ideal model delta sinusoidal sigma weight residual -86.00 -169.25 83.25 1 1.00e+01 1.00e-02 8.47e+01 ... (remaining 13302 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 2221 0.057 - 0.115: 1021 0.115 - 0.172: 180 0.172 - 0.230: 31 0.230 - 0.287: 12 Chirality restraints: 3465 Sorted by residual: chirality pdb=" CB VAL A 711 " pdb=" CA VAL A 711 " pdb=" CG1 VAL A 711 " pdb=" CG2 VAL A 711 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" CB VAL C 711 " pdb=" CA VAL C 711 " pdb=" CG1 VAL C 711 " pdb=" CG2 VAL C 711 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.28 2.00e-01 2.50e+01 2.02e+00 chirality pdb=" CB VAL B 711 " pdb=" CA VAL B 711 " pdb=" CG1 VAL B 711 " pdb=" CG2 VAL B 711 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.28 2.00e-01 2.50e+01 2.02e+00 ... (remaining 3462 not shown) Planarity restraints: 3753 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 868 " 0.017 2.00e-02 2.50e+03 1.95e-02 9.50e+00 pdb=" CG TRP B 868 " -0.047 2.00e-02 2.50e+03 pdb=" CD1 TRP B 868 " 0.033 2.00e-02 2.50e+03 pdb=" CD2 TRP B 868 " -0.009 2.00e-02 2.50e+03 pdb=" NE1 TRP B 868 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP B 868 " -0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP B 868 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 868 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 868 " 0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP B 868 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 868 " 0.017 2.00e-02 2.50e+03 1.94e-02 9.38e+00 pdb=" CG TRP A 868 " -0.046 2.00e-02 2.50e+03 pdb=" CD1 TRP A 868 " 0.033 2.00e-02 2.50e+03 pdb=" CD2 TRP A 868 " -0.009 2.00e-02 2.50e+03 pdb=" NE1 TRP A 868 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP A 868 " -0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP A 868 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 868 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 868 " 0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP A 868 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 868 " 0.017 2.00e-02 2.50e+03 1.93e-02 9.31e+00 pdb=" CG TRP C 868 " -0.046 2.00e-02 2.50e+03 pdb=" CD1 TRP C 868 " 0.033 2.00e-02 2.50e+03 pdb=" CD2 TRP C 868 " -0.009 2.00e-02 2.50e+03 pdb=" NE1 TRP C 868 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP C 868 " -0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP C 868 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 868 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 868 " 0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP C 868 " 0.005 2.00e-02 2.50e+03 ... (remaining 3750 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 1339 2.72 - 3.26: 18996 3.26 - 3.81: 32848 3.81 - 4.35: 40034 4.35 - 4.90: 71121 Nonbonded interactions: 164338 Sorted by model distance: nonbonded pdb=" NH2 ARG A 306 " pdb=" OD1 ASP B 727 " model vdw 2.170 3.120 nonbonded pdb=" NH2 ARG B 306 " pdb=" OD1 ASP C 727 " model vdw 2.183 3.120 nonbonded pdb=" OE1 GLU B 999 " pdb=" NH2 ARG C1001 " model vdw 2.209 3.120 nonbonded pdb=" OE1 GLU A 999 " pdb=" NH2 ARG B1001 " model vdw 2.278 3.120 nonbonded pdb=" O GLY C 77 " pdb=" OH TYR C 252 " model vdw 2.302 3.040 ... (remaining 164333 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' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'L' } ncs_group { reference = chain 'E' selection = chain 'H' selection = chain 'K' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.720 Check model and map are aligned: 0.140 Set scattering table: 0.170 Process input model: 46.600 Find NCS groups from input model: 0.750 Set up NCS constraints: 0.110 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 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 : 0.013 0.150 21555 Z= 0.536 Angle : 1.120 11.019 29394 Z= 0.603 Chirality : 0.064 0.287 3465 Planarity : 0.007 0.073 3726 Dihedral : 11.023 107.227 8256 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 0.26 % Allowed : 0.66 % Favored : 99.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.09 (0.13), residues: 2607 helix: -3.57 (0.10), residues: 600 sheet: -0.70 (0.19), residues: 642 loop : -1.98 (0.14), residues: 1365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.008 TRP B 868 HIS 0.017 0.004 HIS A 33 PHE 0.051 0.005 PHE C 870 TYR 0.051 0.006 TYR C 197 ARG 0.013 0.002 ARG B1089 Details of bonding type rmsd link_NAG-ASN : bond 0.00550 ( 27) link_NAG-ASN : angle 3.51141 ( 81) link_BETA1-4 : bond 0.01156 ( 12) link_BETA1-4 : angle 4.15933 ( 36) hydrogen bonds : bond 0.26465 ( 889) hydrogen bonds : angle 8.47344 ( 2604) SS BOND : bond 0.00976 ( 33) SS BOND : angle 2.59868 ( 66) covalent geometry : bond 0.01282 (21483) covalent geometry : angle 1.09104 (29211) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5214 Ramachandran restraints generated. 2607 Oldfield, 0 Emsley, 2607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5214 Ramachandran restraints generated. 2607 Oldfield, 0 Emsley, 2607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 2283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 339 time to evaluate : 2.162 Fit side-chains revert: symmetry clash REVERT: A 67 THR cc_start: 0.7688 (m) cc_final: 0.7314 (p) REVERT: A 89 PHE cc_start: 0.6290 (t80) cc_final: 0.5806 (t80) REVERT: A 868 TRP cc_start: 0.5200 (t-100) cc_final: 0.4887 (t-100) REVERT: A 932 ASP cc_start: 0.7695 (t70) cc_final: 0.7483 (t0) REVERT: B 78 ASN cc_start: 0.6603 (p0) cc_final: 0.6034 (m110) REVERT: B 89 PHE cc_start: 0.6198 (t80) cc_final: 0.5882 (t80) REVERT: B 932 ASP cc_start: 0.7793 (t70) cc_final: 0.7519 (t0) REVERT: C 87 ILE cc_start: 0.8520 (pt) cc_final: 0.8314 (mm) REVERT: C 932 ASP cc_start: 0.7957 (t70) cc_final: 0.7666 (t0) outliers start: 6 outliers final: 2 residues processed: 345 average time/residue: 0.4041 time to fit residues: 207.9682 Evaluate side-chains 181 residues out of total 2283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 179 time to evaluate : 2.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1022 VAL Chi-restraints excluded: chain B residue 1022 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 222 optimal weight: 0.9980 chunk 200 optimal weight: 0.9990 chunk 111 optimal weight: 9.9990 chunk 68 optimal weight: 4.9990 chunk 134 optimal weight: 0.9990 chunk 106 optimal weight: 9.9990 chunk 206 optimal weight: 2.9990 chunk 80 optimal weight: 0.9990 chunk 125 optimal weight: 2.9990 chunk 154 optimal weight: 0.8980 chunk 239 optimal weight: 0.3980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 818 GLN A 883 GLN A1030 HIS A1046 HIS A1095 GLN B 33 HIS B 721 ASN B 756 GLN B 786 GLN B 818 GLN B1030 HIS B1046 HIS C 33 HIS C 721 ASN C 818 GLN C1030 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.163812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.122916 restraints weight = 31141.828| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 3.15 r_work: 0.3239 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 21555 Z= 0.147 Angle : 0.655 9.719 29394 Z= 0.342 Chirality : 0.046 0.287 3465 Planarity : 0.005 0.050 3726 Dihedral : 9.293 62.134 3623 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.18 % Allowed : 4.86 % Favored : 93.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.15), residues: 2607 helix: -0.33 (0.19), residues: 612 sheet: -0.52 (0.19), residues: 660 loop : -1.71 (0.14), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 868 HIS 0.004 0.001 HIS A 33 PHE 0.023 0.002 PHE C 83 TYR 0.014 0.002 TYR A 886 ARG 0.003 0.000 ARG C 758 Details of bonding type rmsd link_NAG-ASN : bond 0.00311 ( 27) link_NAG-ASN : angle 2.09888 ( 81) link_BETA1-4 : bond 0.00398 ( 12) link_BETA1-4 : angle 2.38425 ( 36) hydrogen bonds : bond 0.05941 ( 889) hydrogen bonds : angle 5.30638 ( 2604) SS BOND : bond 0.00514 ( 33) SS BOND : angle 1.87896 ( 66) covalent geometry : bond 0.00326 (21483) covalent geometry : angle 0.63621 (29211) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5214 Ramachandran restraints generated. 2607 Oldfield, 0 Emsley, 2607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5214 Ramachandran restraints generated. 2607 Oldfield, 0 Emsley, 2607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 2283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 224 time to evaluate : 2.523 Fit side-chains REVERT: A 67 THR cc_start: 0.7008 (m) cc_final: 0.6380 (p) REVERT: A 99 ARG cc_start: 0.6127 (mmt90) cc_final: 0.5849 (mmt90) REVERT: A 721 ASN cc_start: 0.7642 (m-40) cc_final: 0.7376 (m-40) REVERT: A 819 TYR cc_start: 0.8036 (p90) cc_final: 0.7567 (p90) REVERT: A 932 ASP cc_start: 0.8367 (t70) cc_final: 0.8077 (t0) REVERT: B 78 ASN cc_start: 0.7108 (p0) cc_final: 0.6097 (m110) REVERT: B 89 PHE cc_start: 0.6841 (t80) cc_final: 0.6377 (t80) REVERT: B 99 ARG cc_start: 0.6058 (mmt90) cc_final: 0.5683 (mtt90) REVERT: B 758 ARG cc_start: 0.7756 (tmm160) cc_final: 0.7540 (ttp80) REVERT: B 932 ASP cc_start: 0.8371 (t70) cc_final: 0.8142 (t0) REVERT: C 37 MET cc_start: 0.8303 (mtp) cc_final: 0.8097 (mmm) REVERT: C 89 PHE cc_start: 0.6691 (t80) cc_final: 0.6411 (t80) REVERT: C 99 ARG cc_start: 0.6226 (mmt90) cc_final: 0.5792 (mtt90) REVERT: C 294 GLU cc_start: 0.7522 (pm20) cc_final: 0.7265 (pm20) REVERT: C 758 ARG cc_start: 0.7687 (tmm160) cc_final: 0.7409 (ttp80) REVERT: C 932 ASP cc_start: 0.8446 (t70) cc_final: 0.8160 (t0) outliers start: 27 outliers final: 13 residues processed: 245 average time/residue: 0.4166 time to fit residues: 155.0116 Evaluate side-chains 178 residues out of total 2283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 165 time to evaluate : 2.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain A residue 1022 VAL Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 756 GLN Chi-restraints excluded: chain B residue 937 ASN Chi-restraints excluded: chain B residue 963 LEU Chi-restraints excluded: chain B residue 1022 VAL Chi-restraints excluded: chain C residue 532 LEU Chi-restraints excluded: chain C residue 643 ASP Chi-restraints excluded: chain C residue 1022 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 183 optimal weight: 1.9990 chunk 134 optimal weight: 0.9990 chunk 182 optimal weight: 0.0870 chunk 153 optimal weight: 0.8980 chunk 162 optimal weight: 0.6980 chunk 213 optimal weight: 4.9990 chunk 176 optimal weight: 20.0000 chunk 108 optimal weight: 10.0000 chunk 2 optimal weight: 6.9990 chunk 246 optimal weight: 0.9990 chunk 225 optimal weight: 0.9990 overall best weight: 0.7362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1095 GLN C1046 HIS C1053 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.163293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.123165 restraints weight = 30991.437| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 3.12 r_work: 0.3227 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.2603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 21555 Z= 0.125 Angle : 0.590 7.530 29394 Z= 0.308 Chirality : 0.046 0.270 3465 Planarity : 0.004 0.039 3726 Dihedral : 8.103 59.584 3623 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.27 % Allowed : 6.26 % Favored : 92.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.15), residues: 2607 helix: 1.15 (0.21), residues: 615 sheet: -0.39 (0.19), residues: 666 loop : -1.36 (0.15), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 868 HIS 0.004 0.001 HIS B 33 PHE 0.024 0.001 PHE A 83 TYR 0.014 0.001 TYR A 886 ARG 0.004 0.000 ARG C 306 Details of bonding type rmsd link_NAG-ASN : bond 0.00159 ( 27) link_NAG-ASN : angle 1.88095 ( 81) link_BETA1-4 : bond 0.00576 ( 12) link_BETA1-4 : angle 2.33734 ( 36) hydrogen bonds : bond 0.05035 ( 889) hydrogen bonds : angle 5.05534 ( 2604) SS BOND : bond 0.00457 ( 33) SS BOND : angle 1.73776 ( 66) covalent geometry : bond 0.00282 (21483) covalent geometry : angle 0.57196 (29211) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5214 Ramachandran restraints generated. 2607 Oldfield, 0 Emsley, 2607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5214 Ramachandran restraints generated. 2607 Oldfield, 0 Emsley, 2607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 2283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 185 time to evaluate : 2.098 Fit side-chains revert: symmetry clash REVERT: A 67 THR cc_start: 0.6986 (m) cc_final: 0.6397 (p) REVERT: A 89 PHE cc_start: 0.6911 (t80) cc_final: 0.6369 (t80) REVERT: A 296 ASP cc_start: 0.7615 (OUTLIER) cc_final: 0.7365 (m-30) REVERT: A 721 ASN cc_start: 0.7558 (m-40) cc_final: 0.7160 (m-40) REVERT: A 819 TYR cc_start: 0.7979 (p90) cc_final: 0.7503 (p90) REVERT: A 932 ASP cc_start: 0.8242 (t70) cc_final: 0.8007 (t0) REVERT: B 78 ASN cc_start: 0.7218 (p0) cc_final: 0.6233 (m110) REVERT: B 89 PHE cc_start: 0.6908 (t80) cc_final: 0.6355 (t80) REVERT: B 99 ARG cc_start: 0.5879 (mmt90) cc_final: 0.5452 (mtt90) REVERT: B 932 ASP cc_start: 0.8264 (t70) cc_final: 0.7995 (t0) REVERT: C 89 PHE cc_start: 0.6661 (t80) cc_final: 0.6324 (t80) REVERT: C 99 ARG cc_start: 0.6282 (mmt90) cc_final: 0.5770 (mtt90) REVERT: C 306 ARG cc_start: 0.7877 (tpp-160) cc_final: 0.7499 (mpt-90) REVERT: C 758 ARG cc_start: 0.7608 (tmm160) cc_final: 0.7365 (ttp80) REVERT: C 932 ASP cc_start: 0.8266 (t70) cc_final: 0.7936 (t0) outliers start: 29 outliers final: 18 residues processed: 209 average time/residue: 0.3102 time to fit residues: 101.3435 Evaluate side-chains 181 residues out of total 2283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 162 time to evaluate : 2.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 296 ASP Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain A residue 1022 VAL Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain B residue 1111 VAL Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 532 LEU Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 606 VAL Chi-restraints excluded: chain C residue 963 LEU Chi-restraints excluded: chain C residue 1022 VAL Chi-restraints excluded: chain C residue 1111 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 244 optimal weight: 7.9990 chunk 28 optimal weight: 2.9990 chunk 258 optimal weight: 0.7980 chunk 3 optimal weight: 5.9990 chunk 36 optimal weight: 0.4980 chunk 61 optimal weight: 3.9990 chunk 130 optimal weight: 8.9990 chunk 62 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 68 optimal weight: 0.5980 chunk 92 optimal weight: 6.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 947 GLN B 599 GLN B 756 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.160375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.121016 restraints weight = 31270.571| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 3.31 r_work: 0.3186 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.2976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 21555 Z= 0.156 Angle : 0.602 9.487 29394 Z= 0.315 Chirality : 0.046 0.281 3465 Planarity : 0.004 0.037 3726 Dihedral : 7.122 59.650 3622 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.49 % Allowed : 6.57 % Favored : 91.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.16), residues: 2607 helix: 1.81 (0.21), residues: 609 sheet: -0.23 (0.20), residues: 645 loop : -1.25 (0.15), residues: 1353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 868 HIS 0.004 0.001 HIS B1046 PHE 0.030 0.002 PHE C 83 TYR 0.015 0.002 TYR A 886 ARG 0.004 0.000 ARG B 758 Details of bonding type rmsd link_NAG-ASN : bond 0.00186 ( 27) link_NAG-ASN : angle 1.87586 ( 81) link_BETA1-4 : bond 0.00560 ( 12) link_BETA1-4 : angle 2.32711 ( 36) hydrogen bonds : bond 0.05142 ( 889) hydrogen bonds : angle 4.98078 ( 2604) SS BOND : bond 0.00460 ( 33) SS BOND : angle 2.47212 ( 66) covalent geometry : bond 0.00372 (21483) covalent geometry : angle 0.57867 (29211) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5214 Ramachandran restraints generated. 2607 Oldfield, 0 Emsley, 2607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5214 Ramachandran restraints generated. 2607 Oldfield, 0 Emsley, 2607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 190 time to evaluate : 2.076 Fit side-chains REVERT: A 37 MET cc_start: 0.8088 (mmm) cc_final: 0.7704 (mmt) REVERT: A 67 THR cc_start: 0.7094 (m) cc_final: 0.6465 (p) REVERT: A 89 PHE cc_start: 0.6875 (t80) cc_final: 0.6305 (t80) REVERT: A 99 ARG cc_start: 0.6119 (mmt90) cc_final: 0.5821 (mmt90) REVERT: A 296 ASP cc_start: 0.7710 (OUTLIER) cc_final: 0.7458 (m-30) REVERT: A 819 TYR cc_start: 0.8044 (p90) cc_final: 0.7455 (p90) REVERT: A 932 ASP cc_start: 0.8286 (t70) cc_final: 0.7998 (t0) REVERT: B 78 ASN cc_start: 0.7467 (p0) cc_final: 0.6706 (m-40) REVERT: B 87 ILE cc_start: 0.8418 (OUTLIER) cc_final: 0.8193 (mp) REVERT: B 89 PHE cc_start: 0.6967 (t80) cc_final: 0.6388 (t80) REVERT: B 99 ARG cc_start: 0.6180 (mmt90) cc_final: 0.5827 (mtt90) REVERT: B 109 ASN cc_start: 0.6580 (p0) cc_final: 0.6375 (p0) REVERT: B 932 ASP cc_start: 0.8215 (t70) cc_final: 0.7971 (t0) REVERT: C 37 MET cc_start: 0.8229 (mmm) cc_final: 0.7850 (mmt) REVERT: C 89 PHE cc_start: 0.6869 (t80) cc_final: 0.6378 (t80) REVERT: C 99 ARG cc_start: 0.6536 (mmt90) cc_final: 0.6050 (mtt90) REVERT: C 109 ASN cc_start: 0.6829 (p0) cc_final: 0.6622 (p0) REVERT: C 758 ARG cc_start: 0.7715 (tmm160) cc_final: 0.7403 (ttp80) REVERT: C 932 ASP cc_start: 0.8238 (t70) cc_final: 0.7891 (t0) outliers start: 34 outliers final: 21 residues processed: 216 average time/residue: 0.3382 time to fit residues: 113.8711 Evaluate side-chains 191 residues out of total 2283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 168 time to evaluate : 2.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 296 ASP Chi-restraints excluded: chain A residue 518 ASP Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain A residue 1022 VAL Chi-restraints excluded: chain A residue 1023 ASP Chi-restraints excluded: chain A residue 1111 VAL Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain B residue 709 MET Chi-restraints excluded: chain B residue 1098 THR Chi-restraints excluded: chain B residue 1111 VAL Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 606 VAL Chi-restraints excluded: chain C residue 643 ASP Chi-restraints excluded: chain C residue 963 LEU Chi-restraints excluded: chain C residue 1022 VAL Chi-restraints excluded: chain C residue 1098 THR Chi-restraints excluded: chain C residue 1111 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 64 optimal weight: 1.9990 chunk 167 optimal weight: 0.7980 chunk 38 optimal weight: 0.1980 chunk 80 optimal weight: 4.9990 chunk 189 optimal weight: 7.9990 chunk 100 optimal weight: 30.0000 chunk 163 optimal weight: 2.9990 chunk 144 optimal weight: 1.9990 chunk 104 optimal weight: 8.9990 chunk 214 optimal weight: 3.9990 chunk 257 optimal weight: 2.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 661 HIS A1088 GLN ** B 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1088 GLN ** C 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 947 GLN C1053 GLN C1088 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.158888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.118959 restraints weight = 31170.882| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 3.25 r_work: 0.3150 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.3323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 21555 Z= 0.170 Angle : 0.601 8.671 29394 Z= 0.315 Chirality : 0.046 0.289 3465 Planarity : 0.004 0.037 3726 Dihedral : 6.694 59.284 3622 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.88 % Allowed : 7.36 % Favored : 90.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.16), residues: 2607 helix: 2.04 (0.21), residues: 609 sheet: -0.27 (0.20), residues: 663 loop : -1.19 (0.15), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 868 HIS 0.005 0.001 HIS B1046 PHE 0.027 0.002 PHE A 83 TYR 0.016 0.002 TYR A 886 ARG 0.003 0.000 ARG B1089 Details of bonding type rmsd link_NAG-ASN : bond 0.00144 ( 27) link_NAG-ASN : angle 1.80854 ( 81) link_BETA1-4 : bond 0.00573 ( 12) link_BETA1-4 : angle 2.07372 ( 36) hydrogen bonds : bond 0.05097 ( 889) hydrogen bonds : angle 4.91736 ( 2604) SS BOND : bond 0.00465 ( 33) SS BOND : angle 2.44874 ( 66) covalent geometry : bond 0.00409 (21483) covalent geometry : angle 0.57890 (29211) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5214 Ramachandran restraints generated. 2607 Oldfield, 0 Emsley, 2607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5214 Ramachandran restraints generated. 2607 Oldfield, 0 Emsley, 2607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 2283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 187 time to evaluate : 2.228 Fit side-chains REVERT: A 67 THR cc_start: 0.7179 (m) cc_final: 0.6559 (p) REVERT: A 89 PHE cc_start: 0.7000 (t80) cc_final: 0.6389 (t80) REVERT: A 99 ARG cc_start: 0.6126 (mmt90) cc_final: 0.5885 (mmt90) REVERT: A 256 TYR cc_start: 0.7828 (m-80) cc_final: 0.7627 (m-80) REVERT: A 296 ASP cc_start: 0.7791 (OUTLIER) cc_final: 0.7570 (m-30) REVERT: A 932 ASP cc_start: 0.8345 (t70) cc_final: 0.8088 (t0) REVERT: B 78 ASN cc_start: 0.7567 (p0) cc_final: 0.6847 (m-40) REVERT: B 87 ILE cc_start: 0.8477 (OUTLIER) cc_final: 0.8217 (mp) REVERT: B 89 PHE cc_start: 0.7109 (t80) cc_final: 0.6488 (t80) REVERT: B 99 ARG cc_start: 0.6124 (mmt90) cc_final: 0.5741 (mtt90) REVERT: B 107 MET cc_start: 0.4124 (mpp) cc_final: 0.3307 (mtp) REVERT: B 109 ASN cc_start: 0.6978 (p0) cc_final: 0.6682 (p0) REVERT: B 932 ASP cc_start: 0.8210 (t70) cc_final: 0.7979 (t0) REVERT: C 37 MET cc_start: 0.8222 (mmm) cc_final: 0.7801 (mmt) REVERT: C 99 ARG cc_start: 0.6671 (mmt90) cc_final: 0.6290 (mtt90) REVERT: C 107 MET cc_start: 0.4570 (mpp) cc_final: 0.4292 (mtp) REVERT: C 109 ASN cc_start: 0.7005 (p0) cc_final: 0.6693 (p0) REVERT: C 758 ARG cc_start: 0.7765 (tmm160) cc_final: 0.7424 (ttp80) REVERT: C 932 ASP cc_start: 0.8372 (t70) cc_final: 0.8057 (t0) outliers start: 43 outliers final: 28 residues processed: 220 average time/residue: 0.3443 time to fit residues: 118.3312 Evaluate side-chains 194 residues out of total 2283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 164 time to evaluate : 2.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 PHE Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 296 ASP Chi-restraints excluded: chain A residue 518 ASP Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 711 VAL Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain A residue 1022 VAL Chi-restraints excluded: chain A residue 1023 ASP Chi-restraints excluded: chain A residue 1111 VAL Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 231 PHE Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain B residue 711 VAL Chi-restraints excluded: chain B residue 1098 THR Chi-restraints excluded: chain B residue 1111 VAL Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 606 VAL Chi-restraints excluded: chain C residue 643 ASP Chi-restraints excluded: chain C residue 711 VAL Chi-restraints excluded: chain C residue 720 CYS Chi-restraints excluded: chain C residue 916 ILE Chi-restraints excluded: chain C residue 963 LEU Chi-restraints excluded: chain C residue 1022 VAL Chi-restraints excluded: chain C residue 1023 ASP Chi-restraints excluded: chain C residue 1098 THR Chi-restraints excluded: chain C residue 1111 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 173 optimal weight: 0.6980 chunk 97 optimal weight: 10.0000 chunk 241 optimal weight: 0.9990 chunk 261 optimal weight: 3.9990 chunk 132 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 156 optimal weight: 7.9990 chunk 244 optimal weight: 6.9990 chunk 8 optimal weight: 8.9990 chunk 178 optimal weight: 4.9990 chunk 259 optimal weight: 0.7980 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 818 GLN ** A 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 189 ASN B1095 GLN C 756 GLN C1053 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.157943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.118001 restraints weight = 31097.322| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 3.27 r_work: 0.3138 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.3580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 21555 Z= 0.174 Angle : 0.597 8.534 29394 Z= 0.312 Chirality : 0.046 0.240 3465 Planarity : 0.004 0.036 3726 Dihedral : 6.272 59.354 3622 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 2.06 % Allowed : 7.84 % Favored : 90.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.16), residues: 2607 helix: 2.12 (0.21), residues: 606 sheet: -0.23 (0.20), residues: 630 loop : -1.16 (0.15), residues: 1371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 868 HIS 0.005 0.001 HIS B1046 PHE 0.028 0.002 PHE C 83 TYR 0.017 0.002 TYR A 886 ARG 0.002 0.000 ARG C 965 Details of bonding type rmsd link_NAG-ASN : bond 0.00132 ( 27) link_NAG-ASN : angle 1.78083 ( 81) link_BETA1-4 : bond 0.00573 ( 12) link_BETA1-4 : angle 2.07462 ( 36) hydrogen bonds : bond 0.05065 ( 889) hydrogen bonds : angle 4.86871 ( 2604) SS BOND : bond 0.00464 ( 33) SS BOND : angle 2.32546 ( 66) covalent geometry : bond 0.00421 (21483) covalent geometry : angle 0.57673 (29211) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5214 Ramachandran restraints generated. 2607 Oldfield, 0 Emsley, 2607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5214 Ramachandran restraints generated. 2607 Oldfield, 0 Emsley, 2607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 2283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 189 time to evaluate : 2.425 Fit side-chains REVERT: A 67 THR cc_start: 0.7168 (m) cc_final: 0.6536 (p) REVERT: A 99 ARG cc_start: 0.6142 (mmt90) cc_final: 0.5913 (mmt90) REVERT: A 107 MET cc_start: 0.4927 (mpp) cc_final: 0.4627 (mtt) REVERT: A 256 TYR cc_start: 0.7853 (m-80) cc_final: 0.7616 (m-80) REVERT: A 296 ASP cc_start: 0.7830 (OUTLIER) cc_final: 0.7611 (m-30) REVERT: A 932 ASP cc_start: 0.8389 (t70) cc_final: 0.8109 (t0) REVERT: A 965 ARG cc_start: 0.7759 (mmm-85) cc_final: 0.7313 (tpp-160) REVERT: B 67 THR cc_start: 0.7060 (m) cc_final: 0.6432 (p) REVERT: B 78 ASN cc_start: 0.7583 (p0) cc_final: 0.6867 (m-40) REVERT: B 87 ILE cc_start: 0.8523 (OUTLIER) cc_final: 0.8304 (mp) REVERT: B 89 PHE cc_start: 0.7213 (t80) cc_final: 0.6533 (t80) REVERT: B 99 ARG cc_start: 0.6203 (mmt90) cc_final: 0.5797 (mtt90) REVERT: B 107 MET cc_start: 0.4844 (mpp) cc_final: 0.3901 (mtt) REVERT: B 109 ASN cc_start: 0.7089 (p0) cc_final: 0.6735 (p0) REVERT: B 198 LYS cc_start: 0.8559 (OUTLIER) cc_final: 0.8129 (tttp) REVERT: B 932 ASP cc_start: 0.8219 (t70) cc_final: 0.7983 (t0) REVERT: C 37 MET cc_start: 0.8299 (OUTLIER) cc_final: 0.8052 (mmm) REVERT: C 99 ARG cc_start: 0.6632 (mmt90) cc_final: 0.6226 (mtt90) REVERT: C 107 MET cc_start: 0.4603 (mpp) cc_final: 0.4274 (mtt) REVERT: C 109 ASN cc_start: 0.7123 (p0) cc_final: 0.6818 (p0) REVERT: C 151 MET cc_start: 0.4126 (mmm) cc_final: 0.2708 (ttm) REVERT: C 756 GLN cc_start: 0.8999 (OUTLIER) cc_final: 0.8118 (mp-120) REVERT: C 758 ARG cc_start: 0.7797 (tmm160) cc_final: 0.7489 (ttp80) REVERT: C 932 ASP cc_start: 0.8383 (t70) cc_final: 0.8069 (t0) outliers start: 47 outliers final: 31 residues processed: 223 average time/residue: 0.3293 time to fit residues: 115.0028 Evaluate side-chains 198 residues out of total 2283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 162 time to evaluate : 2.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 138 PHE Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 296 ASP Chi-restraints excluded: chain A residue 518 ASP Chi-restraints excluded: chain A residue 576 CYS Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 711 VAL Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain A residue 1022 VAL Chi-restraints excluded: chain A residue 1023 ASP Chi-restraints excluded: chain A residue 1111 VAL Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 198 LYS Chi-restraints excluded: chain B residue 231 PHE Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain B residue 711 VAL Chi-restraints excluded: chain B residue 937 ASN Chi-restraints excluded: chain B residue 955 ILE Chi-restraints excluded: chain B residue 1098 THR Chi-restraints excluded: chain B residue 1111 VAL Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain C residue 37 MET Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 606 VAL Chi-restraints excluded: chain C residue 643 ASP Chi-restraints excluded: chain C residue 711 VAL Chi-restraints excluded: chain C residue 720 CYS Chi-restraints excluded: chain C residue 756 GLN Chi-restraints excluded: chain C residue 916 ILE Chi-restraints excluded: chain C residue 1022 VAL Chi-restraints excluded: chain C residue 1098 THR Chi-restraints excluded: chain C residue 1111 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 70.1249 > 50: distance: 49 - 79: 35.605 distance: 52 - 76: 31.817 distance: 64 - 71: 34.899 distance: 72 - 73: 63.632 distance: 73 - 74: 10.636 distance: 73 - 76: 48.182 distance: 74 - 235: 36.983 distance: 76 - 77: 14.942 distance: 77 - 78: 44.344 distance: 77 - 80: 21.368 distance: 78 - 79: 53.942 distance: 78 - 88: 9.108 distance: 81 - 82: 12.004 distance: 82 - 84: 21.051 distance: 83 - 85: 28.645 distance: 84 - 86: 17.900 distance: 85 - 86: 13.625 distance: 86 - 87: 27.938 distance: 88 - 89: 28.750 distance: 88 - 224: 32.258 distance: 89 - 90: 13.574 distance: 89 - 92: 37.811 distance: 90 - 91: 59.350 distance: 90 - 99: 22.355 distance: 91 - 221: 36.196 distance: 92 - 93: 17.714 distance: 93 - 94: 20.552 distance: 93 - 95: 26.229 distance: 94 - 96: 26.786 distance: 95 - 97: 29.444 distance: 96 - 98: 29.590 distance: 97 - 98: 39.431 distance: 99 - 100: 27.997 distance: 99 - 105: 19.006 distance: 100 - 101: 31.976 distance: 100 - 103: 49.380 distance: 101 - 102: 4.044 distance: 101 - 106: 50.721 distance: 103 - 104: 37.376 distance: 104 - 105: 37.802 distance: 106 - 107: 6.063 distance: 107 - 108: 17.846 distance: 107 - 110: 6.235 distance: 108 - 109: 29.117 distance: 108 - 117: 20.765 distance: 110 - 111: 19.798 distance: 111 - 112: 21.889 distance: 112 - 113: 25.762 distance: 113 - 114: 4.951 distance: 114 - 115: 5.172 distance: 117 - 118: 12.449 distance: 118 - 119: 15.156 distance: 118 - 121: 14.674 distance: 119 - 120: 9.421 distance: 119 - 126: 26.117 distance: 121 - 122: 14.416 distance: 122 - 123: 18.470 distance: 123 - 124: 5.232 distance: 123 - 125: 19.453 distance: 126 - 127: 43.693 distance: 127 - 128: 44.744 distance: 128 - 129: 27.608 distance: 128 - 130: 45.041 distance: 130 - 131: 42.800 distance: 130 - 189: 37.543 distance: 131 - 132: 33.444 distance: 131 - 134: 31.389 distance: 132 - 133: 11.158 distance: 132 - 137: 16.821 distance: 133 - 186: 30.627 distance: 134 - 135: 25.826 distance: 134 - 136: 16.055 distance: 137 - 138: 23.462 distance: 138 - 139: 40.378 distance: 138 - 141: 17.562 distance: 139 - 140: 10.701 distance: 139 - 148: 41.521 distance: 141 - 142: 15.634 distance: 142 - 143: 13.845 distance: 142 - 144: 16.767 distance: 143 - 145: 11.387 distance: 144 - 146: 27.828 distance: 145 - 147: 23.253 distance: 146 - 147: 22.884 distance: 148 - 177: 36.818 distance: 149 - 150: 19.195 distance: 149 - 152: 17.615 distance: 150 - 151: 43.196 distance: 150 - 155: 25.668 distance: 151 - 174: 36.083 distance: 152 - 153: 12.051 distance: 152 - 154: 22.568