Starting phenix.real_space_refine on Mon May 26 11:13:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6wps_21864/05_2025/6wps_21864.cif Found real_map, /net/cci-nas-00/data/ceres_data/6wps_21864/05_2025/6wps_21864.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6wps_21864/05_2025/6wps_21864.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6wps_21864/05_2025/6wps_21864.map" model { file = "/net/cci-nas-00/data/ceres_data/6wps_21864/05_2025/6wps_21864.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6wps_21864/05_2025/6wps_21864.cif" } resolution = 3.1 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= 0.004 sd= 0.066 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 117 5.16 5 C 17909 2.51 5 N 4593 2.21 5 O 5497 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 200 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 28116 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 7386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 955, 7386 Classifications: {'peptide': 955} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 45, 'TRANS': 909} Chain breaks: 13 Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 104 Unresolved non-hydrogen dihedrals: 62 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 2, 'ASN:plan1': 2, 'GLU:plan': 5, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 68 Chain: "H" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 937 Classifications: {'peptide': 123} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 3, 'TRANS': 119} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "L" Number of atoms: 706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 706 Classifications: {'peptide': 102} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 5, 'TRANS': 96} Chain breaks: 1 Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ARG:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 33 Chain: "B" Number of atoms: 7395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 955, 7395 Classifications: {'peptide': 955} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 45, 'TRANS': 909} Chain breaks: 13 Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 2, 'ASN:plan1': 2, 'GLU:plan': 4, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 61 Chain: "C" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 937 Classifications: {'peptide': 123} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 3, 'TRANS': 119} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "D" Number of atoms: 706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 706 Classifications: {'peptide': 102} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 5, 'TRANS': 96} Chain breaks: 1 Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ARG:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 33 Chain: "E" Number of atoms: 7395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 955, 7395 Classifications: {'peptide': 955} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 45, 'TRANS': 909} Chain breaks: 13 Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 2, 'ASN:plan1': 2, 'GLU:plan': 4, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 61 Chain: "F" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 937 Classifications: {'peptide': 123} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 3, 'TRANS': 119} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "G" Number of atoms: 706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 706 Classifications: {'peptide': 102} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 5, 'TRANS': 96} Chain breaks: 1 Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ARG:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 33 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 71 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 2, 'NAG': 2} 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: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 71 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 2, 'NAG': 2} 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: "T" 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: "U" 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: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" 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: "X" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 71 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 2, 'NAG': 2} 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: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "E" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Time building chain proxies: 17.19, per 1000 atoms: 0.61 Number of scatterers: 28116 At special positions: 0 Unit cell: (148.05, 144.9, 179.55, 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 117 16.00 O 5497 8.00 N 4593 7.00 C 17909 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.09 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.23 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.02 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.02 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.02 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.09 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.23 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.02 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.04 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.02 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 89 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 166 " distance=2.03 Simple disulfide: pdb=" SG CYS E 291 " - pdb=" SG CYS E 301 " distance=2.02 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.02 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.10 Simple disulfide: pdb=" SG CYS E 391 " - pdb=" SG CYS E 525 " distance=2.23 Simple disulfide: pdb=" SG CYS E 538 " - pdb=" SG CYS E 590 " distance=2.02 Simple disulfide: pdb=" SG CYS E 617 " - pdb=" SG CYS E 649 " distance=2.03 Simple disulfide: pdb=" SG CYS E 662 " - pdb=" SG CYS E 671 " distance=2.04 Simple disulfide: pdb=" SG CYS E 738 " - pdb=" SG CYS E 760 " distance=2.03 Simple disulfide: pdb=" SG CYS E 743 " - pdb=" SG CYS E 749 " distance=2.03 Simple disulfide: pdb=" SG CYS E1032 " - pdb=" SG CYS E1043 " distance=2.02 Simple disulfide: pdb=" SG CYS E1082 " - pdb=" SG CYS E1126 " distance=2.02 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 89 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA N 3 " - " MAN N 4 " " BMA S 3 " - " MAN S 4 " " BMA X 3 " - " MAN X 4 " ALPHA1-6 " BMA N 3 " - " MAN N 5 " " BMA S 3 " - " MAN S 5 " " BMA X 3 " - " MAN X 5 " BETA1-4 " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " BETA1-6 " NAG N 1 " - " FUC N 6 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG S 1 " - " FUC S 6 " " NAG X 1 " - " FUC X 6 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 234 " " NAG A1304 " - " ASN A 282 " " NAG A1305 " - " ASN A 331 " " NAG A1306 " - " ASN A 603 " " NAG A1307 " - " ASN A 616 " " NAG A1308 " - " ASN A 657 " " NAG A1309 " - " ASN A 709 " " NAG A1314 " - " ASN A1074 " " NAG A1319 " - " ASN A 165 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 234 " " NAG B1304 " - " ASN B 282 " " NAG B1305 " - " ASN B 331 " " NAG B1306 " - " ASN B 603 " " NAG B1307 " - " ASN B 616 " " NAG B1308 " - " ASN B 657 " " NAG B1309 " - " ASN B 709 " " NAG B1314 " - " ASN B1074 " " NAG B1319 " - " ASN B 165 " " NAG E1301 " - " ASN E 61 " " NAG E1302 " - " ASN E 122 " " NAG E1303 " - " ASN E 234 " " NAG E1304 " - " ASN E 282 " " NAG E1305 " - " ASN E 331 " " NAG E1306 " - " ASN E 603 " " NAG E1307 " - " ASN E 616 " " NAG E1308 " - " ASN E 657 " " NAG E1309 " - " ASN E 709 " " NAG E1314 " - " ASN E1074 " " NAG E1319 " - " ASN E 165 " " NAG I 1 " - " ASN A 717 " " NAG J 1 " - " ASN A 801 " " NAG K 1 " - " ASN A1098 " " NAG M 1 " - " ASN A1134 " " NAG N 1 " - " ASN A 343 " " NAG O 1 " - " ASN B 717 " " NAG P 1 " - " ASN B 801 " " NAG Q 1 " - " ASN B1098 " " NAG R 1 " - " ASN B1134 " " NAG S 1 " - " ASN B 343 " " NAG T 1 " - " ASN E 717 " " NAG U 1 " - " ASN E 801 " " NAG V 1 " - " ASN E1098 " " NAG W 1 " - " ASN E1134 " " NAG X 1 " - " ASN E 343 " Time building additional restraints: 8.12 Conformation dependent library (CDL) restraints added in 3.6 seconds 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6576 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 69 sheets defined 21.8% alpha, 36.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.53 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 351 through 353 No H-bonds generated for 'chain 'A' and resid 351 through 353' Processing helix chain 'A' and resid 365 through 371 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.359A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 759 removed outlier: 6.935A pdb=" N SER A 758 " --> pdb=" O GLN A 755 " (cutoff:3.500A) Processing helix chain 'A' and resid 760 through 783 removed outlier: 3.541A pdb=" N GLN A 774 " --> pdb=" O ILE A 770 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.541A pdb=" N GLY A 885 " --> pdb=" O THR A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 891 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.196A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.530A pdb=" N SER A 940 " --> pdb=" O ASP A 936 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.993A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 982 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 5.038A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 62 through 65 Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'L' and resid 80 through 84 removed outlier: 3.770A pdb=" N PHE L 84 " --> pdb=" O PRO L 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 351 through 353 No H-bonds generated for 'chain 'B' and resid 351 through 353' Processing helix chain 'B' and resid 365 through 371 Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.359A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 759 removed outlier: 6.935A pdb=" N SER B 758 " --> pdb=" O GLN B 755 " (cutoff:3.500A) Processing helix chain 'B' and resid 760 through 783 removed outlier: 3.541A pdb=" N GLN B 774 " --> pdb=" O ILE B 770 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 Processing helix chain 'B' and resid 866 through 885 removed outlier: 3.540A pdb=" N GLY B 885 " --> pdb=" O THR B 881 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 891 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.196A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.530A pdb=" N SER B 940 " --> pdb=" O ASP B 936 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.993A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 982 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 5.038A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 32 Processing helix chain 'C' and resid 62 through 65 Processing helix chain 'C' and resid 87 through 91 Processing helix chain 'D' and resid 80 through 84 removed outlier: 3.770A pdb=" N PHE D 84 " --> pdb=" O PRO D 81 " (cutoff:3.500A) Processing helix chain 'E' and resid 294 through 303 Processing helix chain 'E' and resid 338 through 343 Processing helix chain 'E' and resid 351 through 353 No H-bonds generated for 'chain 'E' and resid 351 through 353' Processing helix chain 'E' and resid 365 through 371 Processing helix chain 'E' and resid 405 through 410 removed outlier: 4.359A pdb=" N ARG E 408 " --> pdb=" O ASP E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 737 through 743 Processing helix chain 'E' and resid 746 through 754 Processing helix chain 'E' and resid 755 through 759 removed outlier: 6.935A pdb=" N SER E 758 " --> pdb=" O GLN E 755 " (cutoff:3.500A) Processing helix chain 'E' and resid 760 through 783 removed outlier: 3.541A pdb=" N GLN E 774 " --> pdb=" O ILE E 770 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ASP E 775 " --> pdb=" O ALA E 771 " (cutoff:3.500A) Processing helix chain 'E' and resid 816 through 824 Processing helix chain 'E' and resid 866 through 885 removed outlier: 3.542A pdb=" N GLY E 885 " --> pdb=" O THR E 881 " (cutoff:3.500A) Processing helix chain 'E' and resid 886 through 891 Processing helix chain 'E' and resid 897 through 908 Processing helix chain 'E' and resid 912 through 919 removed outlier: 4.196A pdb=" N LEU E 916 " --> pdb=" O THR E 912 " (cutoff:3.500A) Processing helix chain 'E' and resid 919 through 941 removed outlier: 3.530A pdb=" N SER E 940 " --> pdb=" O ASP E 936 " (cutoff:3.500A) Processing helix chain 'E' and resid 942 through 944 No H-bonds generated for 'chain 'E' and resid 942 through 944' Processing helix chain 'E' and resid 945 through 965 removed outlier: 3.993A pdb=" N VAL E 951 " --> pdb=" O LYS E 947 " (cutoff:3.500A) Processing helix chain 'E' and resid 966 through 968 No H-bonds generated for 'chain 'E' and resid 966 through 968' Processing helix chain 'E' and resid 976 through 982 Processing helix chain 'E' and resid 985 through 1033 removed outlier: 5.038A pdb=" N VAL E 991 " --> pdb=" O PRO E 987 " (cutoff:3.500A) Processing helix chain 'F' and resid 28 through 32 Processing helix chain 'F' and resid 62 through 65 Processing helix chain 'F' and resid 87 through 91 Processing helix chain 'G' and resid 80 through 84 removed outlier: 3.769A pdb=" N PHE G 84 " --> pdb=" O PRO G 81 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 7.866A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.368A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.489A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 4.091A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 7.399A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 83 through 85 removed outlier: 6.661A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 83 through 85 removed outlier: 6.736A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASN A 122 " --> pdb=" O ASN A 125 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.287A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 324 through 328 removed outlier: 4.423A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N PHE A 565 " --> pdb=" O PHE E 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 348 through 349 removed outlier: 7.160A pdb=" N ALA A 348 " --> pdb=" O VAL A 401 " (cutoff:3.500A) removed outlier: 9.460A pdb=" N ARG A 403 " --> pdb=" O ALA A 348 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 348 through 349 removed outlier: 7.160A pdb=" N ALA A 348 " --> pdb=" O VAL A 401 " (cutoff:3.500A) removed outlier: 9.460A pdb=" N ARG A 403 " --> pdb=" O ALA A 348 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.294A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 452 through 453 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.898A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.275A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N TYR A 660 " --> pdb=" O SER A 698 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.898A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.275A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.651A pdb=" N ALA A 701 " --> pdb=" O ILE E 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.466A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.466A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB9, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AC1, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.836A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AC3, first strand: chain 'H' and resid 10 through 11 removed outlier: 7.079A pdb=" N GLU H 10 " --> pdb=" O THR H 124 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ILE H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N TRP H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 10 through 11 removed outlier: 7.079A pdb=" N GLU H 10 " --> pdb=" O THR H 124 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASN H 116 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 4 through 5 Processing sheet with id=AC6, first strand: chain 'L' and resid 10 through 11 removed outlier: 6.412A pdb=" N LEU L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N TYR L 50 " --> pdb=" O LEU L 34 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'L' and resid 10 through 11 Processing sheet with id=AC8, first strand: chain 'B' and resid 28 through 30 removed outlier: 7.866A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.368A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.489A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 42 through 43 removed outlier: 4.091A pdb=" N ALA E 575 " --> pdb=" O GLY E 566 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N ASP E 574 " --> pdb=" O ILE E 587 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N GLU E 324 " --> pdb=" O CYS E 538 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 47 through 55 removed outlier: 7.399A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 83 through 85 removed outlier: 6.660A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 83 through 85 removed outlier: 6.736A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASN B 122 " --> pdb=" O ASN B 125 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.288A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 348 through 349 removed outlier: 7.161A pdb=" N ALA B 348 " --> pdb=" O VAL B 401 " (cutoff:3.500A) removed outlier: 9.460A pdb=" N ARG B 403 " --> pdb=" O ALA B 348 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 348 through 349 removed outlier: 7.161A pdb=" N ALA B 348 " --> pdb=" O VAL B 401 " (cutoff:3.500A) removed outlier: 9.460A pdb=" N ARG B 403 " --> pdb=" O ALA B 348 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.294A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'B' and resid 452 through 453 Processing sheet with id=AD9, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.898A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.275A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N TYR B 660 " --> pdb=" O SER B 698 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.898A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.275A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.467A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.467A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AE5, first strand: chain 'B' and resid 787 through 788 Processing sheet with id=AE6, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.837A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 3 through 6 Processing sheet with id=AE8, first strand: chain 'C' and resid 10 through 11 removed outlier: 7.078A pdb=" N GLU C 10 " --> pdb=" O THR C 124 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ILE C 34 " --> pdb=" O TRP C 50 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N TRP C 50 " --> pdb=" O ILE C 34 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N TRP C 36 " --> pdb=" O MET C 48 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 10 through 11 removed outlier: 7.078A pdb=" N GLU C 10 " --> pdb=" O THR C 124 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASN C 116 " --> pdb=" O ARG C 98 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 4 through 5 Processing sheet with id=AF2, first strand: chain 'D' and resid 10 through 11 removed outlier: 6.413A pdb=" N LEU D 34 " --> pdb=" O TYR D 50 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N TYR D 50 " --> pdb=" O LEU D 34 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N TRP D 36 " --> pdb=" O LEU D 48 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'D' and resid 10 through 11 Processing sheet with id=AF4, first strand: chain 'E' and resid 28 through 30 removed outlier: 7.866A pdb=" N ASN E 61 " --> pdb=" O TYR E 269 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N TYR E 269 " --> pdb=" O ASN E 61 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N SER E 205 " --> pdb=" O PRO E 225 " (cutoff:3.500A) removed outlier: 9.368A pdb=" N HIS E 207 " --> pdb=" O LEU E 223 " (cutoff:3.500A) removed outlier: 9.488A pdb=" N LEU E 223 " --> pdb=" O HIS E 207 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N VAL E 36 " --> pdb=" O LEU E 223 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'E' and resid 47 through 55 removed outlier: 7.399A pdb=" N THR E 274 " --> pdb=" O ASP E 290 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N ASP E 290 " --> pdb=" O THR E 274 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N LEU E 276 " --> pdb=" O ALA E 288 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ALA E 288 " --> pdb=" O LEU E 276 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N LYS E 278 " --> pdb=" O THR E 286 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'E' and resid 83 through 85 removed outlier: 6.661A pdb=" N LEU E 141 " --> pdb=" O LEU E 244 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'E' and resid 83 through 85 removed outlier: 6.736A pdb=" N ALA E 243 " --> pdb=" O ILE E 101 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ILE E 101 " --> pdb=" O ALA E 243 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N ARG E 102 " --> pdb=" O ASN E 121 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASN E 122 " --> pdb=" O ASN E 125 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N PHE E 168 " --> pdb=" O VAL E 130 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'E' and resid 311 through 319 removed outlier: 5.288A pdb=" N ILE E 312 " --> pdb=" O THR E 599 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N THR E 599 " --> pdb=" O ILE E 312 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N GLN E 314 " --> pdb=" O VAL E 597 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N VAL E 597 " --> pdb=" O GLN E 314 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N GLY E 594 " --> pdb=" O GLN E 613 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'E' and resid 348 through 349 removed outlier: 7.160A pdb=" N ALA E 348 " --> pdb=" O VAL E 401 " (cutoff:3.500A) removed outlier: 9.459A pdb=" N ARG E 403 " --> pdb=" O ALA E 348 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'E' and resid 348 through 349 removed outlier: 7.160A pdb=" N ALA E 348 " --> pdb=" O VAL E 401 " (cutoff:3.500A) removed outlier: 9.459A pdb=" N ARG E 403 " --> pdb=" O ALA E 348 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASN E 394 " --> pdb=" O GLU E 516 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'E' and resid 361 through 362 removed outlier: 6.293A pdb=" N CYS E 361 " --> pdb=" O CYS E 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG2 Processing sheet with id=AG3, first strand: chain 'E' and resid 452 through 453 Processing sheet with id=AG4, first strand: chain 'E' and resid 654 through 655 removed outlier: 5.899A pdb=" N GLU E 654 " --> pdb=" O ALA E 694 " (cutoff:3.500A) removed outlier: 8.276A pdb=" N THR E 696 " --> pdb=" O GLU E 654 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N TYR E 660 " --> pdb=" O SER E 698 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG4 Processing sheet with id=AG5, first strand: chain 'E' and resid 654 through 655 removed outlier: 5.899A pdb=" N GLU E 654 " --> pdb=" O ALA E 694 " (cutoff:3.500A) removed outlier: 8.276A pdb=" N THR E 696 " --> pdb=" O GLU E 654 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ILE E 670 " --> pdb=" O ILE E 666 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'E' and resid 711 through 728 removed outlier: 6.466A pdb=" N SER E 711 " --> pdb=" O THR E1076 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N THR E1076 " --> pdb=" O SER E 711 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ALA E 713 " --> pdb=" O ASN E1074 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ASN E1074 " --> pdb=" O ALA E 713 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N GLU E1072 " --> pdb=" O PRO E 715 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ASN E 717 " --> pdb=" O ALA E1070 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N TYR E1067 " --> pdb=" O HIS E1048 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N HIS E1048 " --> pdb=" O TYR E1067 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'E' and resid 711 through 728 removed outlier: 6.466A pdb=" N SER E 711 " --> pdb=" O THR E1076 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N THR E1076 " --> pdb=" O SER E 711 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ALA E 713 " --> pdb=" O ASN E1074 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ASN E1074 " --> pdb=" O ALA E 713 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N GLU E1072 " --> pdb=" O PRO E 715 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ASN E 717 " --> pdb=" O ALA E1070 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ALA E1078 " --> pdb=" O PHE E1095 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N PHE E1095 " --> pdb=" O ALA E1078 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'E' and resid 734 through 736 Processing sheet with id=AG9, first strand: chain 'E' and resid 1120 through 1125 removed outlier: 4.836A pdb=" N ALA E1087 " --> pdb=" O SER E1123 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'F' and resid 3 through 6 Processing sheet with id=AH2, first strand: chain 'F' and resid 10 through 11 removed outlier: 7.079A pdb=" N GLU F 10 " --> pdb=" O THR F 124 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ILE F 34 " --> pdb=" O TRP F 50 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N TRP F 50 " --> pdb=" O ILE F 34 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N TRP F 36 " --> pdb=" O MET F 48 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'F' and resid 10 through 11 removed outlier: 7.079A pdb=" N GLU F 10 " --> pdb=" O THR F 124 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASN F 116 " --> pdb=" O ARG F 98 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'G' and resid 4 through 5 Processing sheet with id=AH5, first strand: chain 'G' and resid 10 through 11 removed outlier: 6.413A pdb=" N LEU G 34 " --> pdb=" O TYR G 50 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N TYR G 50 " --> pdb=" O LEU G 34 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N TRP G 36 " --> pdb=" O LEU G 48 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'G' and resid 10 through 11 1242 hydrogen bonds defined for protein. 3312 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: 14.60 Time building geometry restraints manager: 9.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.33: 7795 1.33 - 1.48: 8760 1.48 - 1.62: 11999 1.62 - 1.76: 9 1.76 - 1.90: 150 Bond restraints: 28713 Sorted by residual: bond pdb=" NE ARG A 454 " pdb=" CZ ARG A 454 " ideal model delta sigma weight residual 1.326 1.379 -0.053 1.10e-02 8.26e+03 2.29e+01 bond pdb=" NE ARG B 454 " pdb=" CZ ARG B 454 " ideal model delta sigma weight residual 1.326 1.379 -0.053 1.10e-02 8.26e+03 2.29e+01 bond pdb=" NE ARG E 454 " pdb=" CZ ARG E 454 " ideal model delta sigma weight residual 1.326 1.378 -0.052 1.10e-02 8.26e+03 2.28e+01 bond pdb=" CB ILE B 468 " pdb=" CG1 ILE B 468 " ideal model delta sigma weight residual 1.530 1.622 -0.092 2.00e-02 2.50e+03 2.14e+01 bond pdb=" CB ILE A 468 " pdb=" CG1 ILE A 468 " ideal model delta sigma weight residual 1.530 1.622 -0.092 2.00e-02 2.50e+03 2.13e+01 ... (remaining 28708 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.73: 32852 1.73 - 3.46: 5287 3.46 - 5.18: 709 5.18 - 6.91: 212 6.91 - 8.64: 18 Bond angle restraints: 39078 Sorted by residual: angle pdb=" C ILE G 59 " pdb=" N PRO G 60 " pdb=" CA PRO G 60 " ideal model delta sigma weight residual 119.78 127.24 -7.46 1.03e+00 9.43e-01 5.25e+01 angle pdb=" C ILE D 59 " pdb=" N PRO D 60 " pdb=" CA PRO D 60 " ideal model delta sigma weight residual 119.78 127.22 -7.44 1.03e+00 9.43e-01 5.22e+01 angle pdb=" C ILE L 59 " pdb=" N PRO L 60 " pdb=" CA PRO L 60 " ideal model delta sigma weight residual 119.78 127.22 -7.44 1.03e+00 9.43e-01 5.22e+01 angle pdb=" C ASP E 808 " pdb=" N PRO E 809 " pdb=" CA PRO E 809 " ideal model delta sigma weight residual 119.56 126.88 -7.32 1.02e+00 9.61e-01 5.16e+01 angle pdb=" C ASP A 808 " pdb=" N PRO A 809 " pdb=" CA PRO A 809 " ideal model delta sigma weight residual 119.56 126.86 -7.30 1.02e+00 9.61e-01 5.12e+01 ... (remaining 39073 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.48: 17339 21.48 - 42.95: 398 42.95 - 64.43: 89 64.43 - 85.90: 45 85.90 - 107.38: 18 Dihedral angle restraints: 17889 sinusoidal: 7665 harmonic: 10224 Sorted by residual: dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual -86.00 -153.38 67.38 1 1.00e+01 1.00e-02 5.91e+01 dihedral pdb=" CB CYS E1082 " pdb=" SG CYS E1082 " pdb=" SG CYS E1126 " pdb=" CB CYS E1126 " ideal model delta sinusoidal sigma weight residual -86.00 -153.37 67.37 1 1.00e+01 1.00e-02 5.91e+01 dihedral pdb=" CB CYS B1082 " pdb=" SG CYS B1082 " pdb=" SG CYS B1126 " pdb=" CB CYS B1126 " ideal model delta sinusoidal sigma weight residual -86.00 -153.37 67.37 1 1.00e+01 1.00e-02 5.91e+01 ... (remaining 17886 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 3292 0.085 - 0.169: 1048 0.169 - 0.254: 289 0.254 - 0.339: 68 0.339 - 0.423: 12 Chirality restraints: 4709 Sorted by residual: chirality pdb=" C1 NAG R 2 " pdb=" O4 NAG R 1 " pdb=" C2 NAG R 2 " pdb=" O5 NAG R 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.49 0.09 2.00e-02 2.50e+03 2.01e+01 chirality pdb=" C1 NAG M 2 " pdb=" O4 NAG M 1 " pdb=" C2 NAG M 2 " pdb=" O5 NAG M 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.49 0.09 2.00e-02 2.50e+03 1.97e+01 chirality pdb=" C1 NAG W 2 " pdb=" O4 NAG W 1 " pdb=" C2 NAG W 2 " pdb=" O5 NAG W 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.49 0.09 2.00e-02 2.50e+03 1.93e+01 ... (remaining 4706 not shown) Planarity restraints: 4951 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN E 331 " 0.046 2.00e-02 2.50e+03 4.62e-02 2.66e+01 pdb=" CG ASN E 331 " -0.029 2.00e-02 2.50e+03 pdb=" OD1 ASN E 331 " -0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN E 331 " -0.067 2.00e-02 2.50e+03 pdb=" C1 NAG E1305 " 0.056 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 331 " 0.046 2.00e-02 2.50e+03 4.59e-02 2.64e+01 pdb=" CG ASN B 331 " -0.028 2.00e-02 2.50e+03 pdb=" OD1 ASN B 331 " -0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN B 331 " -0.067 2.00e-02 2.50e+03 pdb=" C1 NAG B1305 " 0.056 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 331 " -0.046 2.00e-02 2.50e+03 4.58e-02 2.62e+01 pdb=" CG ASN A 331 " 0.028 2.00e-02 2.50e+03 pdb=" OD1 ASN A 331 " 0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN A 331 " 0.067 2.00e-02 2.50e+03 pdb=" C1 NAG A1305 " -0.055 2.00e-02 2.50e+03 ... (remaining 4948 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.87: 9505 2.87 - 3.38: 24884 3.38 - 3.89: 48554 3.89 - 4.39: 55527 4.39 - 4.90: 91903 Nonbonded interactions: 230373 Sorted by model distance: nonbonded pdb=" NZ LYS B 557 " pdb=" OD2 ASP B 574 " model vdw 2.364 3.120 nonbonded pdb=" NZ LYS A 557 " pdb=" OD2 ASP A 574 " model vdw 2.364 3.120 nonbonded pdb=" NZ LYS E 557 " pdb=" OD2 ASP E 574 " model vdw 2.365 3.120 nonbonded pdb=" NH1 ARG B 346 " pdb=" OD1 ASP D 93 " model vdw 2.430 3.120 nonbonded pdb=" NH1 ARG E 346 " pdb=" OD1 ASP G 93 " model vdw 2.430 3.120 ... (remaining 230368 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' and (resid 27 through 419 or (resid 420 and (name N or name CA or nam \ e C or name O or name CB )) or resid 421 through 499 or (resid 500 and (name N o \ r name CA or name C or name O or name CB )) or resid 501 through 772 or (resid 7 \ 73 and (name N or name CA or name C or name O or name CB )) or resid 774 through \ 1140 or resid 1301 through 1319)) selection = (chain 'E' and (resid 27 through 419 or (resid 420 and (name N or name CA or nam \ e C or name O or name CB )) or resid 421 through 499 or (resid 500 and (name N o \ r name CA or name C or name O or name CB )) or resid 501 through 772 or (resid 7 \ 73 and (name N or name CA or name C or name O or name CB )) or resid 774 through \ 1140 or resid 1301 through 1319)) } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'D' selection = chain 'G' selection = chain 'L' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' } ncs_group { reference = chain 'N' selection = chain 'S' selection = chain 'X' } 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: 3.320 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: 0.030 Extract box with map and model: 1.220 Check model and map are aligned: 0.220 Set scattering table: 0.290 Process input model: 71.220 Find NCS groups from input model: 1.410 Set up NCS constraints: 0.180 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: 0.010 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 80.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7107 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 0.202 28830 Z= 0.710 Angle : 1.357 9.892 39387 Z= 0.903 Chirality : 0.092 0.423 4709 Planarity : 0.005 0.028 4903 Dihedral : 11.022 107.375 11187 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 0.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 0.10 % Allowed : 0.82 % Favored : 99.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.67 (0.13), residues: 3438 helix: -0.00 (0.18), residues: 666 sheet: 0.96 (0.17), residues: 858 loop : 0.51 (0.14), residues: 1914 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.007 TRP C 47 HIS 0.006 0.001 HIS E1048 PHE 0.020 0.004 PHE B 497 TYR 0.037 0.005 TYR B 495 ARG 0.003 0.000 ARG E 509 Details of bonding type rmsd link_NAG-ASN : bond 0.05574 ( 48) link_NAG-ASN : angle 2.25174 ( 144) link_ALPHA1-6 : bond 0.04740 ( 3) link_ALPHA1-6 : angle 1.76105 ( 9) link_BETA1-4 : bond 0.05624 ( 18) link_BETA1-4 : angle 3.19735 ( 54) link_ALPHA1-3 : bond 0.05488 ( 3) link_ALPHA1-3 : angle 2.56284 ( 9) hydrogen bonds : bond 0.16827 ( 1182) hydrogen bonds : angle 8.03509 ( 3312) link_BETA1-6 : bond 0.04228 ( 3) link_BETA1-6 : angle 2.12290 ( 9) SS BOND : bond 0.05689 ( 42) SS BOND : angle 3.58240 ( 84) covalent geometry : bond 0.01305 (28713) covalent geometry : angle 1.33886 (39078) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 748 residues out of total 3057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 745 time to evaluate : 3.079 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 453 TYR cc_start: 0.6989 (p90) cc_final: 0.6757 (p90) REVERT: A 764 ASN cc_start: 0.8251 (m-40) cc_final: 0.7901 (m-40) REVERT: A 1105 THR cc_start: 0.7429 (t) cc_final: 0.6505 (m) REVERT: D 50 TYR cc_start: 0.8084 (p90) cc_final: 0.7883 (p90) REVERT: D 55 ARG cc_start: 0.6313 (ttm110) cc_final: 0.5867 (ttm110) REVERT: E 95 THR cc_start: 0.7552 (p) cc_final: 0.7304 (p) REVERT: E 764 ASN cc_start: 0.8225 (m-40) cc_final: 0.7903 (m-40) REVERT: G 36 TRP cc_start: 0.7775 (m100) cc_final: 0.7324 (m100) outliers start: 3 outliers final: 3 residues processed: 748 average time/residue: 0.4360 time to fit residues: 505.2766 Evaluate side-chains 401 residues out of total 3057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 398 time to evaluate : 2.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain E residue 603 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 296 optimal weight: 0.9980 chunk 266 optimal weight: 0.9990 chunk 147 optimal weight: 0.6980 chunk 90 optimal weight: 0.9990 chunk 179 optimal weight: 0.5980 chunk 142 optimal weight: 0.9990 chunk 275 optimal weight: 0.7980 chunk 106 optimal weight: 0.7980 chunk 167 optimal weight: 0.9980 chunk 204 optimal weight: 0.9980 chunk 318 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 519 HIS A 914 ASN A 935 GLN A1054 GLN H 3 GLN H 59 ASN B 196 ASN B 703 ASN B 764 ASN B 935 GLN C 3 GLN C 39 GLN C 59 ASN E 66 HIS E 218 GLN E 519 HIS E 914 ASN E 935 GLN E1054 GLN E1101 HIS F 3 GLN F 59 ASN F 116 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4390 r_free = 0.4390 target = 0.177480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.152516 restraints weight = 40858.578| |-----------------------------------------------------------------------------| r_work (start): 0.4083 rms_B_bonded: 2.61 r_work: 0.3752 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.2473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.112 28830 Z= 0.166 Angle : 0.649 8.699 39387 Z= 0.341 Chirality : 0.046 0.206 4709 Planarity : 0.004 0.047 4903 Dihedral : 6.891 74.328 5313 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 1.95 % Allowed : 7.67 % Favored : 90.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.68 (0.14), residues: 3438 helix: 1.40 (0.21), residues: 627 sheet: 0.53 (0.16), residues: 951 loop : 0.18 (0.14), residues: 1860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B1102 HIS 0.009 0.001 HIS G 92 PHE 0.028 0.002 PHE D 72 TYR 0.023 0.002 TYR G 50 ARG 0.008 0.001 ARG C 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00518 ( 48) link_NAG-ASN : angle 1.98012 ( 144) link_ALPHA1-6 : bond 0.00681 ( 3) link_ALPHA1-6 : angle 1.62170 ( 9) link_BETA1-4 : bond 0.00688 ( 18) link_BETA1-4 : angle 2.13402 ( 54) link_ALPHA1-3 : bond 0.01216 ( 3) link_ALPHA1-3 : angle 2.69618 ( 9) hydrogen bonds : bond 0.04970 ( 1182) hydrogen bonds : angle 6.30638 ( 3312) link_BETA1-6 : bond 0.00239 ( 3) link_BETA1-6 : angle 1.98830 ( 9) SS BOND : bond 0.00482 ( 42) SS BOND : angle 1.86556 ( 84) covalent geometry : bond 0.00381 (28713) covalent geometry : angle 0.62658 (39078) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 3057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 439 time to evaluate : 3.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 421 TYR cc_start: 0.4151 (OUTLIER) cc_final: 0.3172 (t80) REVERT: A 423 TYR cc_start: 0.7234 (t80) cc_final: 0.7033 (t80) REVERT: A 453 TYR cc_start: 0.7421 (p90) cc_final: 0.6973 (p90) REVERT: H 116 ASN cc_start: 0.7565 (m-40) cc_final: 0.7191 (m-40) REVERT: L 55 ARG cc_start: 0.7477 (mtm-85) cc_final: 0.6935 (mtm-85) REVERT: L 83 ASP cc_start: 0.6514 (m-30) cc_final: 0.6283 (m-30) REVERT: B 140 PHE cc_start: 0.8287 (p90) cc_final: 0.7972 (p90) REVERT: B 376 THR cc_start: 0.7740 (t) cc_final: 0.7460 (p) REVERT: B 421 TYR cc_start: 0.4313 (OUTLIER) cc_final: 0.3160 (t80) REVERT: B 808 ASP cc_start: 0.6698 (OUTLIER) cc_final: 0.6302 (m-30) REVERT: D 50 TYR cc_start: 0.8176 (p90) cc_final: 0.7763 (p90) REVERT: D 55 ARG cc_start: 0.6760 (ttm110) cc_final: 0.6517 (mtm-85) REVERT: D 72 PHE cc_start: 0.8212 (m-80) cc_final: 0.7891 (m-10) REVERT: D 73 THR cc_start: 0.7637 (p) cc_final: 0.7223 (p) REVERT: D 80 GLU cc_start: 0.7877 (tp30) cc_final: 0.7323 (mp0) REVERT: D 90 GLN cc_start: 0.7585 (OUTLIER) cc_final: 0.7308 (tp40) REVERT: E 95 THR cc_start: 0.7640 (p) cc_final: 0.7246 (p) REVERT: E 421 TYR cc_start: 0.4657 (m-80) cc_final: 0.3653 (t80) REVERT: G 55 ARG cc_start: 0.6817 (ttp-110) cc_final: 0.6258 (mtm-85) outliers start: 57 outliers final: 34 residues processed: 475 average time/residue: 0.3854 time to fit residues: 293.9594 Evaluate side-chains 391 residues out of total 3057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 353 time to evaluate : 3.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 371 SER Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 808 ASP Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 90 GLN Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 302 THR Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain E residue 574 ASP Chi-restraints excluded: chain E residue 603 ASN Chi-restraints excluded: chain E residue 738 CYS Chi-restraints excluded: chain E residue 747 THR Chi-restraints excluded: chain E residue 759 PHE Chi-restraints excluded: chain E residue 791 THR Chi-restraints excluded: chain E residue 808 ASP Chi-restraints excluded: chain E residue 980 ILE Chi-restraints excluded: chain E residue 1117 THR Chi-restraints excluded: chain F residue 101 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 19 optimal weight: 1.9990 chunk 323 optimal weight: 0.6980 chunk 96 optimal weight: 50.0000 chunk 29 optimal weight: 0.9990 chunk 71 optimal weight: 0.5980 chunk 177 optimal weight: 0.7980 chunk 7 optimal weight: 0.7980 chunk 99 optimal weight: 6.9990 chunk 130 optimal weight: 9.9990 chunk 176 optimal weight: 0.6980 chunk 178 optimal weight: 0.4980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 658 ASN A 955 ASN H 3 GLN H 65 GLN B 207 HIS B 658 ASN B 935 GLN C 3 GLN E 207 HIS F 3 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.175529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.151511 restraints weight = 40666.237| |-----------------------------------------------------------------------------| r_work (start): 0.4068 rms_B_bonded: 2.69 r_work: 0.3695 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.3126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 28830 Z= 0.143 Angle : 0.572 8.124 39387 Z= 0.297 Chirality : 0.045 0.248 4709 Planarity : 0.004 0.065 4903 Dihedral : 6.172 64.952 5313 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.50 % Allowed : 8.74 % Favored : 88.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.68 (0.14), residues: 3438 helix: 1.50 (0.21), residues: 645 sheet: 0.50 (0.16), residues: 948 loop : 0.15 (0.14), residues: 1845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP G 36 HIS 0.007 0.001 HIS D 92 PHE 0.021 0.002 PHE E 497 TYR 0.020 0.001 TYR B1067 ARG 0.006 0.000 ARG F 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00463 ( 48) link_NAG-ASN : angle 1.88443 ( 144) link_ALPHA1-6 : bond 0.00510 ( 3) link_ALPHA1-6 : angle 1.56209 ( 9) link_BETA1-4 : bond 0.00597 ( 18) link_BETA1-4 : angle 1.62203 ( 54) link_ALPHA1-3 : bond 0.01180 ( 3) link_ALPHA1-3 : angle 1.62958 ( 9) hydrogen bonds : bond 0.04312 ( 1182) hydrogen bonds : angle 5.72139 ( 3312) link_BETA1-6 : bond 0.00115 ( 3) link_BETA1-6 : angle 1.61793 ( 9) SS BOND : bond 0.00426 ( 42) SS BOND : angle 1.63143 ( 84) covalent geometry : bond 0.00327 (28713) covalent geometry : angle 0.55304 (39078) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 3057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 369 time to evaluate : 2.968 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 340 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7781 (mt-10) REVERT: A 421 TYR cc_start: 0.4157 (OUTLIER) cc_final: 0.3116 (t80) REVERT: A 453 TYR cc_start: 0.7541 (p90) cc_final: 0.7085 (p90) REVERT: A 1029 MET cc_start: 0.8705 (tpp) cc_final: 0.8184 (tpp) REVERT: H 80 TYR cc_start: 0.7224 (m-80) cc_final: 0.7008 (m-80) REVERT: H 98 ARG cc_start: 0.8290 (tmm-80) cc_final: 0.7976 (tmm-80) REVERT: H 116 ASN cc_start: 0.7698 (m-40) cc_final: 0.7382 (m-40) REVERT: L 55 ARG cc_start: 0.7487 (mtm-85) cc_final: 0.6903 (mtm-85) REVERT: L 90 GLN cc_start: 0.7781 (OUTLIER) cc_final: 0.7487 (tt0) REVERT: B 140 PHE cc_start: 0.8296 (p90) cc_final: 0.8002 (p90) REVERT: B 421 TYR cc_start: 0.4492 (OUTLIER) cc_final: 0.3288 (t80) REVERT: B 808 ASP cc_start: 0.6821 (OUTLIER) cc_final: 0.6446 (m-30) REVERT: B 984 LEU cc_start: 0.8197 (OUTLIER) cc_final: 0.7946 (mt) REVERT: D 50 TYR cc_start: 0.8098 (p90) cc_final: 0.7778 (p90) REVERT: D 80 GLU cc_start: 0.7934 (tp30) cc_final: 0.7637 (mp0) REVERT: E 95 THR cc_start: 0.7442 (p) cc_final: 0.7089 (p) REVERT: E 421 TYR cc_start: 0.4604 (m-80) cc_final: 0.3566 (t80) REVERT: E 453 TYR cc_start: 0.7211 (p90) cc_final: 0.6958 (p90) REVERT: E 904 TYR cc_start: 0.7577 (m-10) cc_final: 0.7170 (m-10) REVERT: F 81 MET cc_start: 0.7519 (ttp) cc_final: 0.7287 (ttp) REVERT: F 98 ARG cc_start: 0.8285 (tmm-80) cc_final: 0.7752 (ttp-170) outliers start: 73 outliers final: 41 residues processed: 422 average time/residue: 0.3718 time to fit residues: 254.4789 Evaluate side-chains 372 residues out of total 3057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 325 time to evaluate : 2.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 31 SER Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 808 ASP Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 302 THR Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain E residue 603 ASN Chi-restraints excluded: chain E residue 747 THR Chi-restraints excluded: chain E residue 752 LEU Chi-restraints excluded: chain E residue 759 PHE Chi-restraints excluded: chain E residue 761 THR Chi-restraints excluded: chain E residue 791 THR Chi-restraints excluded: chain E residue 808 ASP Chi-restraints excluded: chain E residue 1117 THR Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 31 SER Chi-restraints excluded: chain F residue 121 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 1 optimal weight: 1.9990 chunk 221 optimal weight: 2.9990 chunk 164 optimal weight: 0.5980 chunk 346 optimal weight: 9.9990 chunk 236 optimal weight: 2.9990 chunk 304 optimal weight: 0.0980 chunk 345 optimal weight: 0.9990 chunk 336 optimal weight: 5.9990 chunk 52 optimal weight: 0.8980 chunk 102 optimal weight: 8.9990 chunk 337 optimal weight: 10.0000 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 935 GLN H 3 GLN H 39 GLN E 658 ASN E 935 GLN E1054 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.173806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.147631 restraints weight = 41237.977| |-----------------------------------------------------------------------------| r_work (start): 0.4004 rms_B_bonded: 2.86 r_work: 0.3673 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.3541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 28830 Z= 0.164 Angle : 0.580 9.361 39387 Z= 0.297 Chirality : 0.046 0.392 4709 Planarity : 0.004 0.064 4903 Dihedral : 5.827 55.906 5313 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.36 % Allowed : 9.63 % Favored : 88.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.52 (0.14), residues: 3438 helix: 1.45 (0.21), residues: 648 sheet: 0.32 (0.16), residues: 978 loop : 0.05 (0.14), residues: 1812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 105 HIS 0.006 0.001 HIS D 92 PHE 0.019 0.002 PHE A 306 TYR 0.019 0.002 TYR B1067 ARG 0.006 0.000 ARG G 55 Details of bonding type rmsd link_NAG-ASN : bond 0.00410 ( 48) link_NAG-ASN : angle 1.98376 ( 144) link_ALPHA1-6 : bond 0.00516 ( 3) link_ALPHA1-6 : angle 1.49580 ( 9) link_BETA1-4 : bond 0.00479 ( 18) link_BETA1-4 : angle 1.62395 ( 54) link_ALPHA1-3 : bond 0.01207 ( 3) link_ALPHA1-3 : angle 2.13298 ( 9) hydrogen bonds : bond 0.04089 ( 1182) hydrogen bonds : angle 5.53006 ( 3312) link_BETA1-6 : bond 0.00277 ( 3) link_BETA1-6 : angle 1.85607 ( 9) SS BOND : bond 0.00426 ( 42) SS BOND : angle 2.08883 ( 84) covalent geometry : bond 0.00385 (28713) covalent geometry : angle 0.55622 (39078) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 3057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 341 time to evaluate : 3.010 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 390 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.8500 (pp) REVERT: A 421 TYR cc_start: 0.4246 (OUTLIER) cc_final: 0.3156 (t80) REVERT: A 453 TYR cc_start: 0.7594 (p90) cc_final: 0.7097 (p90) REVERT: A 759 PHE cc_start: 0.8295 (OUTLIER) cc_final: 0.7735 (m-10) REVERT: A 993 ILE cc_start: 0.9435 (OUTLIER) cc_final: 0.9216 (mp) REVERT: A 1029 MET cc_start: 0.8713 (tpp) cc_final: 0.8238 (tpp) REVERT: H 80 TYR cc_start: 0.7371 (m-80) cc_final: 0.7116 (m-80) REVERT: H 98 ARG cc_start: 0.8406 (tmm-80) cc_final: 0.7828 (ttp-170) REVERT: H 116 ASN cc_start: 0.7689 (m-40) cc_final: 0.7373 (m-40) REVERT: L 55 ARG cc_start: 0.7504 (mtm-85) cc_final: 0.6895 (mtm-85) REVERT: L 80 GLU cc_start: 0.7483 (tp30) cc_final: 0.7272 (mp0) REVERT: L 90 GLN cc_start: 0.7828 (OUTLIER) cc_final: 0.7466 (tt0) REVERT: B 421 TYR cc_start: 0.4449 (m-80) cc_final: 0.3141 (t80) REVERT: B 453 TYR cc_start: 0.7359 (p90) cc_final: 0.7046 (p90) REVERT: B 759 PHE cc_start: 0.8276 (OUTLIER) cc_final: 0.7677 (t80) REVERT: B 808 ASP cc_start: 0.7011 (OUTLIER) cc_final: 0.6640 (m-30) REVERT: B 984 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.7909 (mt) REVERT: D 50 TYR cc_start: 0.8115 (p90) cc_final: 0.7770 (p90) REVERT: E 95 THR cc_start: 0.7512 (p) cc_final: 0.7160 (p) REVERT: E 421 TYR cc_start: 0.4690 (m-80) cc_final: 0.3419 (t80) REVERT: E 453 TYR cc_start: 0.7216 (p90) cc_final: 0.6947 (p90) REVERT: F 98 ARG cc_start: 0.8283 (tmm-80) cc_final: 0.7635 (ttp-170) REVERT: G 80 GLU cc_start: 0.7458 (tp30) cc_final: 0.7249 (mp0) outliers start: 69 outliers final: 46 residues processed: 391 average time/residue: 0.3633 time to fit residues: 231.4183 Evaluate side-chains 366 residues out of total 3057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 312 time to evaluate : 2.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 31 SER Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 808 ASP Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 205 SER Chi-restraints excluded: chain E residue 302 THR Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain E residue 371 SER Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain E residue 571 ASP Chi-restraints excluded: chain E residue 603 ASN Chi-restraints excluded: chain E residue 743 CYS Chi-restraints excluded: chain E residue 759 PHE Chi-restraints excluded: chain E residue 791 THR Chi-restraints excluded: chain E residue 808 ASP Chi-restraints excluded: chain E residue 1117 THR Chi-restraints excluded: chain E residue 1128 VAL Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 31 SER Chi-restraints excluded: chain F residue 101 THR Chi-restraints excluded: chain G residue 5 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 332 optimal weight: 6.9990 chunk 203 optimal weight: 1.9990 chunk 239 optimal weight: 3.9990 chunk 107 optimal weight: 9.9990 chunk 205 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 41 optimal weight: 0.9990 chunk 196 optimal weight: 0.4980 chunk 130 optimal weight: 3.9990 chunk 65 optimal weight: 0.6980 chunk 315 optimal weight: 2.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN A 703 ASN H 3 GLN L 91 GLN B 519 HIS D 90 GLN E 935 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.171775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.147211 restraints weight = 40708.634| |-----------------------------------------------------------------------------| r_work (start): 0.4000 rms_B_bonded: 2.61 r_work: 0.3638 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.3929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 28830 Z= 0.197 Angle : 0.601 8.805 39387 Z= 0.307 Chirality : 0.046 0.371 4709 Planarity : 0.004 0.058 4903 Dihedral : 5.747 48.670 5313 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.33 % Favored : 97.64 % Rotamer: Outliers : 2.60 % Allowed : 10.83 % Favored : 86.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.27 (0.14), residues: 3438 helix: 1.27 (0.21), residues: 651 sheet: 0.17 (0.15), residues: 972 loop : -0.12 (0.14), residues: 1815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 105 HIS 0.006 0.001 HIS D 92 PHE 0.021 0.002 PHE C 106 TYR 0.021 0.002 TYR A1067 ARG 0.006 0.001 ARG H 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00415 ( 48) link_NAG-ASN : angle 2.12615 ( 144) link_ALPHA1-6 : bond 0.00796 ( 3) link_ALPHA1-6 : angle 1.43491 ( 9) link_BETA1-4 : bond 0.00433 ( 18) link_BETA1-4 : angle 1.65518 ( 54) link_ALPHA1-3 : bond 0.01226 ( 3) link_ALPHA1-3 : angle 1.84260 ( 9) hydrogen bonds : bond 0.04224 ( 1182) hydrogen bonds : angle 5.49976 ( 3312) link_BETA1-6 : bond 0.00295 ( 3) link_BETA1-6 : angle 1.81323 ( 9) SS BOND : bond 0.00480 ( 42) SS BOND : angle 1.85688 ( 84) covalent geometry : bond 0.00470 (28713) covalent geometry : angle 0.57855 (39078) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 3057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 334 time to evaluate : 3.112 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 390 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8549 (pp) REVERT: A 421 TYR cc_start: 0.4494 (m-80) cc_final: 0.4242 (m-80) REVERT: A 453 TYR cc_start: 0.7712 (p90) cc_final: 0.7180 (p90) REVERT: A 759 PHE cc_start: 0.8314 (OUTLIER) cc_final: 0.7799 (m-10) REVERT: A 977 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8723 (mp) REVERT: A 1029 MET cc_start: 0.8802 (tpp) cc_final: 0.8319 (tpp) REVERT: H 80 TYR cc_start: 0.7408 (m-80) cc_final: 0.7150 (m-80) REVERT: H 116 ASN cc_start: 0.7717 (m-40) cc_final: 0.7343 (m-40) REVERT: L 90 GLN cc_start: 0.7888 (OUTLIER) cc_final: 0.7659 (tt0) REVERT: B 410 ILE cc_start: 0.8285 (mm) cc_final: 0.8006 (mt) REVERT: B 421 TYR cc_start: 0.4662 (m-80) cc_final: 0.3174 (t80) REVERT: B 453 TYR cc_start: 0.7475 (p90) cc_final: 0.7081 (p90) REVERT: B 646 ARG cc_start: 0.7791 (mtm-85) cc_final: 0.7586 (mtm180) REVERT: B 759 PHE cc_start: 0.8023 (OUTLIER) cc_final: 0.7400 (t80) REVERT: B 808 ASP cc_start: 0.7170 (OUTLIER) cc_final: 0.6646 (m-30) REVERT: B 984 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.8063 (mt) REVERT: D 50 TYR cc_start: 0.8070 (p90) cc_final: 0.7422 (p90) REVERT: E 95 THR cc_start: 0.7623 (p) cc_final: 0.7281 (p) REVERT: E 421 TYR cc_start: 0.5093 (m-80) cc_final: 0.3483 (t80) REVERT: E 453 TYR cc_start: 0.7369 (p90) cc_final: 0.7101 (p90) REVERT: E 758 SER cc_start: 0.8506 (m) cc_final: 0.8243 (t) REVERT: F 98 ARG cc_start: 0.8426 (tmm-80) cc_final: 0.7778 (tmm160) REVERT: G 80 GLU cc_start: 0.7634 (tp30) cc_final: 0.7427 (mp0) outliers start: 76 outliers final: 47 residues processed: 395 average time/residue: 0.3988 time to fit residues: 259.7949 Evaluate side-chains 353 residues out of total 3057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 299 time to evaluate : 3.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 31 SER Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 808 ASP Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 90 GLN Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 205 SER Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 302 THR Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain E residue 371 SER Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain E residue 588 THR Chi-restraints excluded: chain E residue 603 ASN Chi-restraints excluded: chain E residue 747 THR Chi-restraints excluded: chain E residue 752 LEU Chi-restraints excluded: chain E residue 791 THR Chi-restraints excluded: chain E residue 808 ASP Chi-restraints excluded: chain E residue 1072 GLU Chi-restraints excluded: chain E residue 1117 THR Chi-restraints excluded: chain E residue 1128 VAL Chi-restraints excluded: chain F residue 31 SER Chi-restraints excluded: chain F residue 101 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 333 optimal weight: 5.9990 chunk 35 optimal weight: 7.9990 chunk 121 optimal weight: 3.9990 chunk 295 optimal weight: 0.8980 chunk 262 optimal weight: 3.9990 chunk 215 optimal weight: 1.9990 chunk 107 optimal weight: 9.9990 chunk 211 optimal weight: 0.8980 chunk 94 optimal weight: 0.5980 chunk 68 optimal weight: 1.9990 chunk 209 optimal weight: 0.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1101 HIS B 954 GLN ** D 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 196 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.171238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.146793 restraints weight = 41063.149| |-----------------------------------------------------------------------------| r_work (start): 0.3975 rms_B_bonded: 2.60 r_work: 0.3614 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.4143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 28830 Z= 0.178 Angle : 0.587 8.919 39387 Z= 0.299 Chirality : 0.046 0.373 4709 Planarity : 0.004 0.057 4903 Dihedral : 5.572 46.391 5313 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.43 % Allowed : 11.85 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.20 (0.14), residues: 3438 helix: 1.28 (0.21), residues: 651 sheet: 0.10 (0.15), residues: 972 loop : -0.18 (0.14), residues: 1815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 105 HIS 0.009 0.001 HIS D 92 PHE 0.028 0.002 PHE L 72 TYR 0.021 0.002 TYR A1067 ARG 0.008 0.000 ARG C 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00386 ( 48) link_NAG-ASN : angle 2.09862 ( 144) link_ALPHA1-6 : bond 0.00828 ( 3) link_ALPHA1-6 : angle 1.37884 ( 9) link_BETA1-4 : bond 0.00409 ( 18) link_BETA1-4 : angle 1.57943 ( 54) link_ALPHA1-3 : bond 0.01192 ( 3) link_ALPHA1-3 : angle 1.88552 ( 9) hydrogen bonds : bond 0.04048 ( 1182) hydrogen bonds : angle 5.47926 ( 3312) link_BETA1-6 : bond 0.00291 ( 3) link_BETA1-6 : angle 1.73558 ( 9) SS BOND : bond 0.00400 ( 42) SS BOND : angle 1.84943 ( 84) covalent geometry : bond 0.00423 (28713) covalent geometry : angle 0.56406 (39078) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 3057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 325 time to evaluate : 2.919 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 453 TYR cc_start: 0.7773 (p90) cc_final: 0.7180 (p90) REVERT: A 759 PHE cc_start: 0.8463 (OUTLIER) cc_final: 0.7722 (m-10) REVERT: A 1029 MET cc_start: 0.8796 (tpp) cc_final: 0.8302 (tpp) REVERT: H 80 TYR cc_start: 0.7426 (m-80) cc_final: 0.7137 (m-80) REVERT: H 116 ASN cc_start: 0.7789 (m-40) cc_final: 0.7463 (m-40) REVERT: L 90 GLN cc_start: 0.7998 (OUTLIER) cc_final: 0.7729 (tt0) REVERT: B 410 ILE cc_start: 0.8332 (mm) cc_final: 0.8068 (mt) REVERT: B 421 TYR cc_start: 0.4647 (m-80) cc_final: 0.4296 (m-80) REVERT: B 759 PHE cc_start: 0.7919 (OUTLIER) cc_final: 0.7292 (t80) REVERT: B 808 ASP cc_start: 0.7198 (OUTLIER) cc_final: 0.6668 (m-30) REVERT: B 977 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8605 (mp) REVERT: B 984 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8219 (mt) REVERT: D 50 TYR cc_start: 0.8038 (p90) cc_final: 0.7163 (p90) REVERT: D 90 GLN cc_start: 0.7314 (tp40) cc_final: 0.6748 (tp40) REVERT: E 95 THR cc_start: 0.7618 (p) cc_final: 0.7290 (p) REVERT: E 421 TYR cc_start: 0.5151 (m-80) cc_final: 0.3454 (t80) REVERT: E 453 TYR cc_start: 0.7426 (p90) cc_final: 0.7121 (p90) REVERT: F 43 GLN cc_start: 0.5618 (mp10) cc_final: 0.5377 (mp10) REVERT: G 80 GLU cc_start: 0.7695 (tp30) cc_final: 0.7485 (mp0) outliers start: 71 outliers final: 51 residues processed: 381 average time/residue: 0.3547 time to fit residues: 222.2334 Evaluate side-chains 356 residues out of total 3057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 299 time to evaluate : 3.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 371 SER Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 31 SER Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 808 ASP Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 302 THR Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain E residue 371 SER Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain E residue 588 THR Chi-restraints excluded: chain E residue 603 ASN Chi-restraints excluded: chain E residue 747 THR Chi-restraints excluded: chain E residue 752 LEU Chi-restraints excluded: chain E residue 791 THR Chi-restraints excluded: chain E residue 808 ASP Chi-restraints excluded: chain E residue 1072 GLU Chi-restraints excluded: chain E residue 1104 VAL Chi-restraints excluded: chain E residue 1117 THR Chi-restraints excluded: chain E residue 1128 VAL Chi-restraints excluded: chain F residue 31 SER Chi-restraints excluded: chain F residue 101 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 223 optimal weight: 3.9990 chunk 178 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 72 optimal weight: 0.5980 chunk 67 optimal weight: 5.9990 chunk 27 optimal weight: 0.9990 chunk 109 optimal weight: 5.9990 chunk 265 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 113 optimal weight: 0.2980 chunk 188 optimal weight: 0.3980 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 90 GLN E 196 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.170220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 106)---------------| | r_work = 0.3852 r_free = 0.3852 target = 0.135560 restraints weight = 41733.117| |-----------------------------------------------------------------------------| r_work (start): 0.3852 rms_B_bonded: 2.11 r_work: 0.3712 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3580 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.4278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 28830 Z= 0.129 Angle : 0.534 6.721 39387 Z= 0.274 Chirality : 0.044 0.327 4709 Planarity : 0.004 0.056 4903 Dihedral : 5.152 45.944 5313 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.30 % Allowed : 12.78 % Favored : 84.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.31 (0.14), residues: 3438 helix: 1.37 (0.21), residues: 657 sheet: 0.11 (0.15), residues: 969 loop : -0.07 (0.14), residues: 1812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP F 105 HIS 0.005 0.001 HIS D 92 PHE 0.022 0.001 PHE L 72 TYR 0.021 0.001 TYR H 95 ARG 0.009 0.000 ARG C 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00343 ( 48) link_NAG-ASN : angle 1.95586 ( 144) link_ALPHA1-6 : bond 0.00844 ( 3) link_ALPHA1-6 : angle 1.30236 ( 9) link_BETA1-4 : bond 0.00427 ( 18) link_BETA1-4 : angle 1.39681 ( 54) link_ALPHA1-3 : bond 0.01188 ( 3) link_ALPHA1-3 : angle 1.69795 ( 9) hydrogen bonds : bond 0.03713 ( 1182) hydrogen bonds : angle 5.30825 ( 3312) link_BETA1-6 : bond 0.00056 ( 3) link_BETA1-6 : angle 1.57533 ( 9) SS BOND : bond 0.00360 ( 42) SS BOND : angle 1.49562 ( 84) covalent geometry : bond 0.00297 (28713) covalent geometry : angle 0.51411 (39078) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 3057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 324 time to evaluate : 3.085 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 340 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.8025 (mt-10) REVERT: A 453 TYR cc_start: 0.7816 (p90) cc_final: 0.7224 (p90) REVERT: A 759 PHE cc_start: 0.8407 (OUTLIER) cc_final: 0.7630 (m-10) REVERT: A 1029 MET cc_start: 0.8856 (tpp) cc_final: 0.8334 (tpp) REVERT: H 25 SER cc_start: 0.7223 (OUTLIER) cc_final: 0.7019 (p) REVERT: H 80 TYR cc_start: 0.7209 (m-80) cc_final: 0.6896 (m-80) REVERT: H 116 ASN cc_start: 0.7761 (m-40) cc_final: 0.7414 (m-40) REVERT: L 90 GLN cc_start: 0.8013 (OUTLIER) cc_final: 0.7653 (tt0) REVERT: B 269 TYR cc_start: 0.7421 (m-10) cc_final: 0.7203 (m-10) REVERT: B 390 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8447 (pp) REVERT: B 421 TYR cc_start: 0.4712 (m-80) cc_final: 0.4304 (m-80) REVERT: B 453 TYR cc_start: 0.7463 (p90) cc_final: 0.6995 (p90) REVERT: B 493 GLN cc_start: 0.6956 (mp10) cc_final: 0.6659 (mp10) REVERT: B 759 PHE cc_start: 0.7792 (OUTLIER) cc_final: 0.7045 (t80) REVERT: B 808 ASP cc_start: 0.7219 (OUTLIER) cc_final: 0.6696 (m-30) REVERT: B 977 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8632 (mp) REVERT: B 984 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8299 (mt) REVERT: C 80 TYR cc_start: 0.7045 (m-80) cc_final: 0.6817 (m-80) REVERT: C 84 ARG cc_start: 0.6948 (mmm-85) cc_final: 0.6592 (mtt180) REVERT: D 50 TYR cc_start: 0.7915 (p90) cc_final: 0.6913 (p90) REVERT: E 95 THR cc_start: 0.7539 (p) cc_final: 0.7192 (p) REVERT: E 421 TYR cc_start: 0.5226 (m-80) cc_final: 0.3419 (t80) REVERT: E 453 TYR cc_start: 0.7531 (p90) cc_final: 0.7219 (p90) REVERT: E 1002 GLN cc_start: 0.8110 (tt0) cc_final: 0.7655 (tt0) REVERT: G 80 GLU cc_start: 0.7838 (tp30) cc_final: 0.7615 (mp0) outliers start: 67 outliers final: 47 residues processed: 378 average time/residue: 0.3542 time to fit residues: 219.1578 Evaluate side-chains 358 residues out of total 3057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 302 time to evaluate : 2.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 371 SER Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 31 SER Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 808 ASP Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 90 GLN Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 196 ASN Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain E residue 371 SER Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain E residue 588 THR Chi-restraints excluded: chain E residue 603 ASN Chi-restraints excluded: chain E residue 747 THR Chi-restraints excluded: chain E residue 752 LEU Chi-restraints excluded: chain E residue 791 THR Chi-restraints excluded: chain E residue 808 ASP Chi-restraints excluded: chain E residue 1117 THR Chi-restraints excluded: chain E residue 1128 VAL Chi-restraints excluded: chain F residue 31 SER Chi-restraints excluded: chain F residue 101 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 130 optimal weight: 0.6980 chunk 126 optimal weight: 0.6980 chunk 57 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 248 optimal weight: 1.9990 chunk 297 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 128 optimal weight: 3.9990 chunk 338 optimal weight: 3.9990 chunk 181 optimal weight: 0.0270 chunk 52 optimal weight: 0.9990 overall best weight: 0.8842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 91 GLN C 39 GLN D 90 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.169183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.136922 restraints weight = 41788.089| |-----------------------------------------------------------------------------| r_work (start): 0.3871 rms_B_bonded: 1.82 r_work: 0.3739 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3622 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.4385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 28830 Z= 0.155 Angle : 0.554 8.340 39387 Z= 0.282 Chirality : 0.045 0.349 4709 Planarity : 0.004 0.054 4903 Dihedral : 5.103 46.003 5313 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.33 % Allowed : 13.05 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.25 (0.14), residues: 3438 helix: 1.34 (0.21), residues: 657 sheet: 0.08 (0.15), residues: 972 loop : -0.13 (0.14), residues: 1809 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP F 105 HIS 0.016 0.001 HIS E 655 PHE 0.014 0.001 PHE E 759 TYR 0.020 0.001 TYR A1067 ARG 0.007 0.000 ARG L 55 Details of bonding type rmsd link_NAG-ASN : bond 0.00356 ( 48) link_NAG-ASN : angle 2.00968 ( 144) link_ALPHA1-6 : bond 0.00887 ( 3) link_ALPHA1-6 : angle 1.24218 ( 9) link_BETA1-4 : bond 0.00403 ( 18) link_BETA1-4 : angle 1.43584 ( 54) link_ALPHA1-3 : bond 0.01176 ( 3) link_ALPHA1-3 : angle 1.68333 ( 9) hydrogen bonds : bond 0.03797 ( 1182) hydrogen bonds : angle 5.31114 ( 3312) link_BETA1-6 : bond 0.00112 ( 3) link_BETA1-6 : angle 1.62751 ( 9) SS BOND : bond 0.00384 ( 42) SS BOND : angle 1.46974 ( 84) covalent geometry : bond 0.00365 (28713) covalent geometry : angle 0.53440 (39078) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 3057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 308 time to evaluate : 3.163 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 340 GLU cc_start: 0.8222 (OUTLIER) cc_final: 0.8014 (mt-10) REVERT: A 453 TYR cc_start: 0.7737 (p90) cc_final: 0.7117 (p90) REVERT: A 505 TYR cc_start: 0.6695 (t80) cc_final: 0.6234 (t80) REVERT: A 759 PHE cc_start: 0.8410 (OUTLIER) cc_final: 0.7523 (m-10) REVERT: A 1029 MET cc_start: 0.8815 (tpp) cc_final: 0.8327 (tpp) REVERT: H 80 TYR cc_start: 0.7208 (m-80) cc_final: 0.6986 (m-80) REVERT: H 116 ASN cc_start: 0.7782 (m-40) cc_final: 0.7417 (m-40) REVERT: L 90 GLN cc_start: 0.7988 (OUTLIER) cc_final: 0.7665 (tt0) REVERT: B 390 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8438 (pp) REVERT: B 421 TYR cc_start: 0.4646 (m-80) cc_final: 0.4340 (m-80) REVERT: B 453 TYR cc_start: 0.7484 (p90) cc_final: 0.7190 (p90) REVERT: B 759 PHE cc_start: 0.7859 (OUTLIER) cc_final: 0.7250 (t80) REVERT: B 808 ASP cc_start: 0.7182 (OUTLIER) cc_final: 0.6647 (m-30) REVERT: B 977 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8607 (mp) REVERT: B 984 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8325 (mt) REVERT: C 80 TYR cc_start: 0.7047 (m-80) cc_final: 0.6801 (m-80) REVERT: C 84 ARG cc_start: 0.7011 (mmm-85) cc_final: 0.6689 (mtt180) REVERT: D 36 TRP cc_start: 0.8253 (m-90) cc_final: 0.7831 (m-90) REVERT: D 50 TYR cc_start: 0.7946 (p90) cc_final: 0.7442 (p90) REVERT: E 95 THR cc_start: 0.7637 (p) cc_final: 0.7303 (p) REVERT: E 421 TYR cc_start: 0.5244 (m-80) cc_final: 0.3394 (t80) REVERT: E 453 TYR cc_start: 0.7484 (p90) cc_final: 0.7181 (p90) outliers start: 68 outliers final: 51 residues processed: 364 average time/residue: 0.3649 time to fit residues: 218.5398 Evaluate side-chains 357 residues out of total 3057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 298 time to evaluate : 2.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 371 SER Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain H residue 31 SER Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 808 ASP Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 90 GLN Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain E residue 371 SER Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain E residue 588 THR Chi-restraints excluded: chain E residue 603 ASN Chi-restraints excluded: chain E residue 747 THR Chi-restraints excluded: chain E residue 752 LEU Chi-restraints excluded: chain E residue 791 THR Chi-restraints excluded: chain E residue 808 ASP Chi-restraints excluded: chain E residue 1081 ILE Chi-restraints excluded: chain E residue 1117 THR Chi-restraints excluded: chain E residue 1128 VAL Chi-restraints excluded: chain F residue 31 SER Chi-restraints excluded: chain F residue 101 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 255 optimal weight: 0.0060 chunk 278 optimal weight: 2.9990 chunk 101 optimal weight: 10.0000 chunk 327 optimal weight: 2.9990 chunk 336 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 293 optimal weight: 0.9990 chunk 8 optimal weight: 0.7980 chunk 267 optimal weight: 0.4980 chunk 83 optimal weight: 2.9990 overall best weight: 0.8600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN E 196 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.169077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 109)---------------| | r_work = 0.3844 r_free = 0.3844 target = 0.134683 restraints weight = 41739.693| |-----------------------------------------------------------------------------| r_work (start): 0.3858 rms_B_bonded: 2.03 r_work: 0.3711 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3579 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.4461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 28830 Z= 0.152 Angle : 0.553 8.354 39387 Z= 0.283 Chirality : 0.045 0.411 4709 Planarity : 0.004 0.051 4903 Dihedral : 5.046 45.919 5313 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.33 % Allowed : 13.50 % Favored : 84.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.22 (0.14), residues: 3438 helix: 1.33 (0.21), residues: 669 sheet: 0.08 (0.15), residues: 972 loop : -0.17 (0.14), residues: 1797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP F 105 HIS 0.017 0.001 HIS E 655 PHE 0.018 0.001 PHE E 643 TYR 0.020 0.001 TYR A1067 ARG 0.007 0.000 ARG C 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00349 ( 48) link_NAG-ASN : angle 2.02465 ( 144) link_ALPHA1-6 : bond 0.00893 ( 3) link_ALPHA1-6 : angle 1.21513 ( 9) link_BETA1-4 : bond 0.00399 ( 18) link_BETA1-4 : angle 1.41954 ( 54) link_ALPHA1-3 : bond 0.01142 ( 3) link_ALPHA1-3 : angle 1.63495 ( 9) hydrogen bonds : bond 0.03769 ( 1182) hydrogen bonds : angle 5.30513 ( 3312) link_BETA1-6 : bond 0.00089 ( 3) link_BETA1-6 : angle 1.60967 ( 9) SS BOND : bond 0.00367 ( 42) SS BOND : angle 1.40520 ( 84) covalent geometry : bond 0.00359 (28713) covalent geometry : angle 0.53319 (39078) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 3057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 305 time to evaluate : 3.002 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 340 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.8010 (mt-10) REVERT: A 453 TYR cc_start: 0.7724 (p90) cc_final: 0.7082 (p90) REVERT: A 505 TYR cc_start: 0.6847 (t80) cc_final: 0.6341 (t80) REVERT: A 759 PHE cc_start: 0.8405 (OUTLIER) cc_final: 0.7526 (m-10) REVERT: A 1029 MET cc_start: 0.8855 (tpp) cc_final: 0.8379 (tpp) REVERT: H 116 ASN cc_start: 0.7872 (m-40) cc_final: 0.7477 (m-40) REVERT: L 90 GLN cc_start: 0.7969 (OUTLIER) cc_final: 0.7696 (tt0) REVERT: B 390 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8401 (pp) REVERT: B 421 TYR cc_start: 0.4704 (m-80) cc_final: 0.4412 (m-80) REVERT: B 453 TYR cc_start: 0.7527 (p90) cc_final: 0.7244 (p90) REVERT: B 759 PHE cc_start: 0.7915 (OUTLIER) cc_final: 0.7155 (t80) REVERT: B 808 ASP cc_start: 0.7234 (OUTLIER) cc_final: 0.6685 (m-30) REVERT: B 977 LEU cc_start: 0.8975 (OUTLIER) cc_final: 0.8639 (mp) REVERT: B 984 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8385 (mt) REVERT: C 57 ASN cc_start: 0.7961 (t0) cc_final: 0.7275 (m110) REVERT: C 80 TYR cc_start: 0.7080 (m-80) cc_final: 0.6842 (m-80) REVERT: C 84 ARG cc_start: 0.7096 (mmm-85) cc_final: 0.6737 (mtt180) REVERT: D 50 TYR cc_start: 0.7857 (p90) cc_final: 0.7561 (p90) REVERT: E 95 THR cc_start: 0.7693 (p) cc_final: 0.7367 (p) REVERT: E 453 TYR cc_start: 0.7597 (p90) cc_final: 0.7277 (p90) REVERT: E 804 GLN cc_start: 0.7982 (mt0) cc_final: 0.7642 (mp10) REVERT: E 1002 GLN cc_start: 0.8140 (tt0) cc_final: 0.7758 (tt0) outliers start: 68 outliers final: 52 residues processed: 359 average time/residue: 0.3586 time to fit residues: 210.3044 Evaluate side-chains 353 residues out of total 3057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 293 time to evaluate : 2.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 371 SER Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 31 SER Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 808 ASP Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 196 ASN Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain E residue 371 SER Chi-restraints excluded: chain E residue 392 PHE Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain E residue 588 THR Chi-restraints excluded: chain E residue 603 ASN Chi-restraints excluded: chain E residue 747 THR Chi-restraints excluded: chain E residue 752 LEU Chi-restraints excluded: chain E residue 791 THR Chi-restraints excluded: chain E residue 808 ASP Chi-restraints excluded: chain E residue 1081 ILE Chi-restraints excluded: chain E residue 1117 THR Chi-restraints excluded: chain E residue 1128 VAL Chi-restraints excluded: chain F residue 31 SER Chi-restraints excluded: chain F residue 101 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/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-5687/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-5687/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-5687/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-5687/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-5687/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-5687/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-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/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-5687/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-5687/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-5687/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: 50.3977 > 50: distance: 11 - 19: 9.847 distance: 19 - 20: 5.037 distance: 20 - 21: 5.908 distance: 20 - 23: 9.194 distance: 21 - 22: 5.794 distance: 21 - 29: 7.065 distance: 23 - 24: 3.790 distance: 24 - 25: 11.555 distance: 24 - 26: 7.065 distance: 25 - 27: 5.129 distance: 26 - 28: 8.989 distance: 27 - 28: 13.639 distance: 29 - 30: 8.077 distance: 30 - 31: 16.118 distance: 30 - 33: 11.828 distance: 31 - 32: 12.270 distance: 31 - 34: 16.812 distance: 34 - 35: 6.840 distance: 35 - 36: 13.176 distance: 35 - 38: 4.554 distance: 36 - 37: 16.080 distance: 36 - 42: 36.791 distance: 38 - 39: 8.815 distance: 38 - 40: 10.264 distance: 39 - 41: 7.558 distance: 42 - 43: 14.931 distance: 43 - 44: 26.823 distance: 43 - 46: 16.365 distance: 44 - 45: 19.699 distance: 46 - 47: 7.854 distance: 47 - 48: 14.804 distance: 47 - 49: 22.366 distance: 48 - 50: 13.664 distance: 49 - 51: 7.678 distance: 50 - 51: 21.868 distance: 52 - 53: 16.791 distance: 53 - 54: 12.595 distance: 53 - 56: 9.286 distance: 54 - 55: 19.546 distance: 54 - 60: 16.313 distance: 56 - 57: 24.871 distance: 57 - 58: 15.940 distance: 57 - 59: 17.933 distance: 60 - 61: 9.152 distance: 61 - 62: 4.089 distance: 61 - 64: 11.545 distance: 62 - 63: 6.354 distance: 64 - 65: 7.526 distance: 65 - 66: 4.891 distance: 65 - 67: 11.875 distance: 68 - 69: 6.909 distance: 68 - 74: 6.372 distance: 69 - 70: 11.209 distance: 69 - 72: 7.887 distance: 70 - 71: 5.809 distance: 70 - 75: 5.329 distance: 72 - 73: 14.253 distance: 73 - 74: 6.041 distance: 75 - 76: 9.452 distance: 76 - 77: 10.046 distance: 76 - 79: 11.001 distance: 77 - 78: 17.958 distance: 77 - 82: 12.816 distance: 79 - 80: 3.165 distance: 79 - 81: 14.888 distance: 82 - 83: 18.699 distance: 82 - 127: 22.698 distance: 83 - 84: 10.231 distance: 83 - 86: 14.836 distance: 84 - 85: 8.191 distance: 84 - 90: 8.438 distance: 85 - 124: 8.961 distance: 86 - 87: 14.541 distance: 87 - 88: 13.469 distance: 87 - 89: 20.109 distance: 90 - 91: 10.003 distance: 90 - 96: 10.587 distance: 91 - 92: 9.226 distance: 91 - 94: 10.835 distance: 92 - 93: 7.134 distance: 92 - 97: 5.301 distance: 94 - 95: 25.726 distance: 95 - 96: 17.363