Starting phenix.real_space_refine on Fri Mar 6 04:35:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6wps_21864/03_2026/6wps_21864.cif Found real_map, /net/cci-nas-00/data/ceres_data/6wps_21864/03_2026/6wps_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 { model { file = "/net/cci-nas-00/data/ceres_data/6wps_21864/03_2026/6wps_21864.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6wps_21864/03_2026/6wps_21864.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6wps_21864/03_2026/6wps_21864.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6wps_21864/03_2026/6wps_21864.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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, 'ASP:plan': 8, 'ASN:plan1': 2, 'ARG:plan': 2, 'GLU:plan': 5} 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: {'ARG:plan': 3, 'GLN:plan1': 2, 'ASP:plan': 2, 'GLU:plan': 1} 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, 'ASP:plan': 7, 'ASN:plan1': 2, 'ARG:plan': 2, 'GLU:plan': 4} 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: {'ARG:plan': 3, 'GLN:plan1': 2, 'ASP:plan': 2, 'GLU:plan': 1} 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, 'ASP:plan': 7, 'ASN:plan1': 2, 'ARG:plan': 2, 'GLU:plan': 4} 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: {'ARG:plan': 3, 'GLN:plan1': 2, 'ASP:plan': 2, 'GLU:plan': 1} 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: 6.72, per 1000 atoms: 0.24 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: 2.58 Conformation dependent library (CDL) restraints added in 1.2 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: 1.43 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: 7.03 Time building geometry restraints manager: 3.43 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 \ 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 \ 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: 6.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.480 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 27.930 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.070 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (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 ARG 0.003 0.000 ARG E 509 TYR 0.037 0.005 TYR B 495 PHE 0.020 0.004 PHE B 497 TRP 0.025 0.007 TRP C 47 HIS 0.006 0.001 HIS E1048 Details of bonding type rmsd covalent geometry : bond 0.01305 (28713) covalent geometry : angle 1.33886 (39078) SS BOND : bond 0.05689 ( 42) SS BOND : angle 3.58240 ( 84) hydrogen bonds : bond 0.16827 ( 1182) hydrogen bonds : angle 8.03509 ( 3312) link_ALPHA1-3 : bond 0.05488 ( 3) link_ALPHA1-3 : angle 2.56284 ( 9) 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_BETA1-6 : bond 0.04228 ( 3) link_BETA1-6 : angle 2.12290 ( 9) link_NAG-ASN : bond 0.05574 ( 48) link_NAG-ASN : angle 2.25174 ( 144) *********************** 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 : 1.117 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: 0.6756 (p90) REVERT: A 764 ASN cc_start: 0.8251 (m-40) cc_final: 0.7902 (m-40) REVERT: A 1105 THR cc_start: 0.7429 (t) cc_final: 0.6503 (m) REVERT: D 50 TYR cc_start: 0.8084 (p90) cc_final: 0.7884 (p90) REVERT: D 55 ARG cc_start: 0.6312 (ttm110) cc_final: 0.5866 (ttm110) REVERT: E 95 THR cc_start: 0.7552 (p) cc_final: 0.7303 (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: 0.7325 (m100) outliers start: 3 outliers final: 3 residues processed: 748 average time/residue: 0.1917 time to fit residues: 222.5546 Evaluate side-chains 399 residues out of total 3057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 396 time to evaluate : 0.902 ------------------------------------------------------------------------------- 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 197 optimal weight: 0.8980 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 0.7980 chunk 298 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 39 GLN H 59 ASN B 196 ASN B 703 ASN B 764 ASN B 914 ASN B 935 GLN C 3 GLN C 39 GLN C 59 ASN E 66 HIS 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: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.176704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.150673 restraints weight = 40874.517| |-----------------------------------------------------------------------------| r_work (start): 0.4055 rms_B_bonded: 2.79 r_work: 0.3736 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.2486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 28830 Z= 0.178 Angle : 0.660 10.173 39387 Z= 0.344 Chirality : 0.046 0.196 4709 Planarity : 0.005 0.051 4903 Dihedral : 6.935 75.123 5313 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 2.23 % Allowed : 7.50 % Favored : 90.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.14), residues: 3438 helix: 1.31 (0.20), residues: 645 sheet: 0.52 (0.16), residues: 951 loop : 0.16 (0.14), residues: 1842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 102 TYR 0.024 0.002 TYR G 50 PHE 0.030 0.002 PHE D 72 TRP 0.013 0.001 TRP B1102 HIS 0.010 0.001 HIS G 92 Details of bonding type rmsd covalent geometry : bond 0.00411 (28713) covalent geometry : angle 0.63699 (39078) SS BOND : bond 0.00504 ( 42) SS BOND : angle 2.04600 ( 84) hydrogen bonds : bond 0.04883 ( 1182) hydrogen bonds : angle 6.28307 ( 3312) link_ALPHA1-3 : bond 0.01110 ( 3) link_ALPHA1-3 : angle 2.61126 ( 9) link_ALPHA1-6 : bond 0.00613 ( 3) link_ALPHA1-6 : angle 1.52648 ( 9) link_BETA1-4 : bond 0.00570 ( 18) link_BETA1-4 : angle 2.15941 ( 54) link_BETA1-6 : bond 0.00302 ( 3) link_BETA1-6 : angle 1.99271 ( 9) link_NAG-ASN : bond 0.00492 ( 48) link_NAG-ASN : angle 2.03157 ( 144) *********************** 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 499 residues out of total 3057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 434 time to evaluate : 0.943 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: 0.4218 (OUTLIER) cc_final: 0.3215 (t80) REVERT: A 423 TYR cc_start: 0.7323 (t80) cc_final: 0.7116 (t80) REVERT: A 453 TYR cc_start: 0.7416 (p90) cc_final: 0.6903 (p90) REVERT: H 116 ASN cc_start: 0.7566 (m-40) cc_final: 0.7182 (m-40) REVERT: L 55 ARG cc_start: 0.7492 (mtm-85) cc_final: 0.6924 (mtm-85) REVERT: L 79 LEU cc_start: 0.5627 (OUTLIER) cc_final: 0.5417 (tp) REVERT: L 83 ASP cc_start: 0.6499 (m-30) cc_final: 0.6262 (m-30) REVERT: B 140 PHE cc_start: 0.8334 (p90) cc_final: 0.8000 (p90) REVERT: B 376 THR cc_start: 0.7745 (t) cc_final: 0.7460 (p) REVERT: B 421 TYR cc_start: 0.4352 (OUTLIER) cc_final: 0.3183 (t80) REVERT: B 808 ASP cc_start: 0.6730 (OUTLIER) cc_final: 0.6303 (m-30) REVERT: B 1138 TYR cc_start: 0.7492 (t80) cc_final: 0.7274 (m-10) REVERT: D 50 TYR cc_start: 0.8171 (p90) cc_final: 0.7771 (p90) REVERT: D 55 ARG cc_start: 0.6762 (ttm110) cc_final: 0.6511 (mtm-85) REVERT: D 73 THR cc_start: 0.7685 (p) cc_final: 0.7268 (p) REVERT: D 80 GLU cc_start: 0.7931 (tp30) cc_final: 0.7372 (mp0) REVERT: D 90 GLN cc_start: 0.7972 (OUTLIER) cc_final: 0.7527 (tt0) REVERT: E 95 THR cc_start: 0.7635 (p) cc_final: 0.7329 (p) REVERT: E 421 TYR cc_start: 0.4716 (m-80) cc_final: 0.3686 (t80) REVERT: G 55 ARG cc_start: 0.6825 (ttp-110) cc_final: 0.6272 (mtm-85) outliers start: 65 outliers final: 41 residues processed: 475 average time/residue: 0.1731 time to fit residues: 132.4108 Evaluate side-chains 399 residues out of total 3057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 353 time to evaluate : 0.858 ------------------------------------------------------------------------------- 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 276 LEU Chi-restraints excluded: chain A residue 302 THR 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 761 THR Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 66 HIS 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 302 THR 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 C residue 122 LEU 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 371 SER 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 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 101 THR Chi-restraints excluded: chain G residue 89 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 233 optimal weight: 9.9990 chunk 129 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 93 optimal weight: 0.8980 chunk 173 optimal weight: 0.5980 chunk 196 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 235 optimal weight: 1.9990 chunk 152 optimal weight: 8.9990 chunk 56 optimal weight: 0.8980 chunk 204 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: A 207 HIS A 658 ASN A 703 ASN A 935 GLN 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 F 119 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.172753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.148177 restraints weight = 40780.908| |-----------------------------------------------------------------------------| r_work (start): 0.4024 rms_B_bonded: 2.60 r_work: 0.3659 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.3265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 28830 Z= 0.186 Angle : 0.615 8.272 39387 Z= 0.318 Chirality : 0.046 0.191 4709 Planarity : 0.005 0.063 4903 Dihedral : 6.382 66.211 5313 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.64 % Allowed : 8.91 % Favored : 88.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.14), residues: 3438 helix: 1.27 (0.20), residues: 663 sheet: 0.45 (0.16), residues: 933 loop : 0.04 (0.14), residues: 1842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 983 TYR 0.020 0.002 TYR B1067 PHE 0.023 0.002 PHE D 72 TRP 0.017 0.001 TRP F 105 HIS 0.007 0.001 HIS G 92 Details of bonding type rmsd covalent geometry : bond 0.00435 (28713) covalent geometry : angle 0.59270 (39078) SS BOND : bond 0.00783 ( 42) SS BOND : angle 1.94777 ( 84) hydrogen bonds : bond 0.04530 ( 1182) hydrogen bonds : angle 5.82048 ( 3312) link_ALPHA1-3 : bond 0.01032 ( 3) link_ALPHA1-3 : angle 1.66937 ( 9) link_ALPHA1-6 : bond 0.00641 ( 3) link_ALPHA1-6 : angle 1.49310 ( 9) link_BETA1-4 : bond 0.00599 ( 18) link_BETA1-4 : angle 1.77750 ( 54) link_BETA1-6 : bond 0.00177 ( 3) link_BETA1-6 : angle 1.79045 ( 9) link_NAG-ASN : bond 0.00501 ( 48) link_NAG-ASN : angle 2.04030 ( 144) *********************** 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 436 residues out of total 3057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 359 time to evaluate : 0.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 421 TYR cc_start: 0.4271 (OUTLIER) cc_final: 0.3187 (t80) REVERT: A 453 TYR cc_start: 0.7601 (p90) cc_final: 0.7081 (p90) REVERT: A 588 THR cc_start: 0.8127 (m) cc_final: 0.7909 (p) REVERT: A 1029 MET cc_start: 0.8776 (tpp) cc_final: 0.8255 (tpp) REVERT: H 80 TYR cc_start: 0.7229 (m-80) cc_final: 0.7013 (m-80) REVERT: H 116 ASN cc_start: 0.7699 (m-40) cc_final: 0.7317 (m-40) REVERT: L 55 ARG cc_start: 0.7515 (mtm-85) cc_final: 0.6910 (mtm-85) REVERT: L 79 LEU cc_start: 0.5319 (OUTLIER) cc_final: 0.5030 (tp) REVERT: L 83 ASP cc_start: 0.6778 (m-30) cc_final: 0.6556 (m-30) REVERT: L 90 GLN cc_start: 0.7980 (OUTLIER) cc_final: 0.7688 (tt0) REVERT: B 421 TYR cc_start: 0.4468 (OUTLIER) cc_final: 0.3166 (t80) REVERT: B 759 PHE cc_start: 0.7178 (OUTLIER) cc_final: 0.6613 (t80) REVERT: B 808 ASP cc_start: 0.6995 (OUTLIER) cc_final: 0.6527 (m-30) REVERT: B 977 LEU cc_start: 0.8875 (OUTLIER) cc_final: 0.8444 (mp) REVERT: B 984 LEU cc_start: 0.8372 (OUTLIER) cc_final: 0.7939 (mt) REVERT: C 45 LEU cc_start: 0.7515 (mt) cc_final: 0.7302 (mt) REVERT: D 50 TYR cc_start: 0.8201 (p90) cc_final: 0.7824 (p90) REVERT: D 55 ARG cc_start: 0.6887 (ttm110) cc_final: 0.6681 (mtm-85) REVERT: D 80 GLU cc_start: 0.7976 (tp30) cc_final: 0.7680 (mp0) REVERT: D 90 GLN cc_start: 0.7961 (OUTLIER) cc_final: 0.7433 (tp40) REVERT: E 95 THR cc_start: 0.7555 (p) cc_final: 0.7219 (p) REVERT: E 421 TYR cc_start: 0.4682 (m-80) cc_final: 0.3610 (t80) REVERT: E 904 TYR cc_start: 0.7600 (m-10) cc_final: 0.7166 (m-10) REVERT: E 1002 GLN cc_start: 0.7914 (tt0) cc_final: 0.7691 (tt0) REVERT: F 81 MET cc_start: 0.7591 (ttp) cc_final: 0.7365 (ttp) REVERT: F 116 ASN cc_start: 0.7550 (m110) cc_final: 0.7285 (m-40) outliers start: 77 outliers final: 42 residues processed: 418 average time/residue: 0.1670 time to fit residues: 113.8933 Evaluate side-chains 370 residues out of total 3057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 319 time to evaluate : 1.021 ------------------------------------------------------------------------------- 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 205 SER Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 421 TYR 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 747 THR Chi-restraints excluded: chain A residue 761 THR 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 79 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 367 VAL Chi-restraints excluded: chain B residue 371 SER 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 977 LEU 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 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 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 791 THR Chi-restraints excluded: chain E residue 808 ASP Chi-restraints excluded: chain E residue 858 LEU Chi-restraints excluded: chain E residue 1117 THR 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 139 optimal weight: 7.9990 chunk 324 optimal weight: 0.0970 chunk 204 optimal weight: 0.9980 chunk 221 optimal weight: 2.9990 chunk 206 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 165 optimal weight: 0.5980 chunk 262 optimal weight: 0.0030 chunk 227 optimal weight: 0.8980 chunk 45 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 overall best weight: 0.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 3 GLN E 935 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.173001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.146552 restraints weight = 41754.676| |-----------------------------------------------------------------------------| r_work (start): 0.4024 rms_B_bonded: 2.99 r_work: 0.3672 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.3535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 28830 Z= 0.117 Angle : 0.553 9.239 39387 Z= 0.284 Chirality : 0.045 0.354 4709 Planarity : 0.004 0.062 4903 Dihedral : 5.796 56.483 5313 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.09 % Allowed : 10.24 % Favored : 87.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.14), residues: 3438 helix: 1.64 (0.21), residues: 630 sheet: 0.31 (0.16), residues: 981 loop : 0.01 (0.14), residues: 1827 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 102 TYR 0.019 0.001 TYR A1067 PHE 0.018 0.001 PHE D 72 TRP 0.014 0.001 TRP G 36 HIS 0.006 0.001 HIS D 92 Details of bonding type rmsd covalent geometry : bond 0.00263 (28713) covalent geometry : angle 0.52803 (39078) SS BOND : bond 0.00387 ( 42) SS BOND : angle 2.28579 ( 84) hydrogen bonds : bond 0.03898 ( 1182) hydrogen bonds : angle 5.54162 ( 3312) link_ALPHA1-3 : bond 0.01100 ( 3) link_ALPHA1-3 : angle 1.97801 ( 9) link_ALPHA1-6 : bond 0.00475 ( 3) link_ALPHA1-6 : angle 1.54549 ( 9) link_BETA1-4 : bond 0.00484 ( 18) link_BETA1-4 : angle 1.53669 ( 54) link_BETA1-6 : bond 0.00119 ( 3) link_BETA1-6 : angle 1.66287 ( 9) link_NAG-ASN : bond 0.00385 ( 48) link_NAG-ASN : angle 1.88996 ( 144) *********************** 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 418 residues out of total 3057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 357 time to evaluate : 0.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 421 TYR cc_start: 0.4274 (OUTLIER) cc_final: 0.3180 (t80) REVERT: A 453 TYR cc_start: 0.7600 (p90) cc_final: 0.7087 (p90) REVERT: A 588 THR cc_start: 0.7788 (m) cc_final: 0.7571 (p) REVERT: A 754 LEU cc_start: 0.8307 (mp) cc_final: 0.8104 (mp) REVERT: A 759 PHE cc_start: 0.8130 (OUTLIER) cc_final: 0.7705 (m-10) REVERT: A 1029 MET cc_start: 0.8727 (tpp) cc_final: 0.8190 (tpp) REVERT: H 80 TYR cc_start: 0.7287 (m-80) cc_final: 0.7010 (m-80) REVERT: H 98 ARG cc_start: 0.8417 (tmm-80) cc_final: 0.7745 (ttp-170) REVERT: H 116 ASN cc_start: 0.7659 (m-40) cc_final: 0.7335 (m-40) REVERT: L 72 PHE cc_start: 0.8195 (m-10) cc_final: 0.7917 (m-10) REVERT: L 79 LEU cc_start: 0.5347 (OUTLIER) cc_final: 0.5108 (tp) REVERT: L 80 GLU cc_start: 0.7495 (tp30) cc_final: 0.7287 (mp0) REVERT: L 90 GLN cc_start: 0.8040 (OUTLIER) cc_final: 0.7743 (tt0) REVERT: B 421 TYR cc_start: 0.4429 (m-80) cc_final: 0.3102 (t80) REVERT: B 453 TYR cc_start: 0.7389 (p90) cc_final: 0.7084 (p90) REVERT: B 759 PHE cc_start: 0.7344 (OUTLIER) cc_final: 0.6769 (t80) REVERT: B 808 ASP cc_start: 0.6976 (OUTLIER) cc_final: 0.6585 (m-30) REVERT: B 984 LEU cc_start: 0.8435 (OUTLIER) cc_final: 0.7914 (mt) REVERT: D 50 TYR cc_start: 0.8104 (p90) cc_final: 0.7796 (p90) REVERT: D 80 GLU cc_start: 0.7988 (tp30) cc_final: 0.7745 (mp0) REVERT: D 90 GLN cc_start: 0.7954 (OUTLIER) cc_final: 0.7564 (tt0) REVERT: E 95 THR cc_start: 0.7403 (p) cc_final: 0.7044 (p) REVERT: E 421 TYR cc_start: 0.4786 (m-80) cc_final: 0.3304 (t80) REVERT: E 453 TYR cc_start: 0.7122 (p90) cc_final: 0.6707 (p90) REVERT: E 1002 GLN cc_start: 0.7924 (tt0) cc_final: 0.7696 (tt0) REVERT: F 98 ARG cc_start: 0.8352 (tmm-80) cc_final: 0.7736 (ttp-170) REVERT: G 80 GLU cc_start: 0.7449 (tp30) cc_final: 0.7223 (mp0) outliers start: 61 outliers final: 35 residues processed: 398 average time/residue: 0.1600 time to fit residues: 105.5848 Evaluate side-chains 356 residues out of total 3057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 313 time to evaluate : 0.994 ------------------------------------------------------------------------------- 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 382 VAL Chi-restraints excluded: chain A residue 421 TYR 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 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 79 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 371 SER 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 B residue 1128 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain D residue 90 GLN Chi-restraints excluded: chain E residue 48 LEU 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 759 PHE Chi-restraints excluded: chain E residue 791 THR Chi-restraints excluded: chain E residue 808 ASP Chi-restraints excluded: chain E residue 858 LEU 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 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 45 optimal weight: 0.6980 chunk 173 optimal weight: 0.6980 chunk 188 optimal weight: 0.5980 chunk 126 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 270 optimal weight: 6.9990 chunk 294 optimal weight: 0.9980 chunk 200 optimal weight: 3.9990 chunk 230 optimal weight: 9.9990 chunk 23 optimal weight: 3.9990 chunk 256 optimal weight: 4.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 39 GLN L 91 GLN B 519 HIS E 935 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.171331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.145138 restraints weight = 40591.982| |-----------------------------------------------------------------------------| r_work (start): 0.3995 rms_B_bonded: 2.84 r_work: 0.3627 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.3857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 28830 Z= 0.171 Angle : 0.581 8.748 39387 Z= 0.296 Chirality : 0.046 0.331 4709 Planarity : 0.004 0.058 4903 Dihedral : 5.603 48.804 5313 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.77 % Allowed : 11.24 % Favored : 85.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.14), residues: 3438 helix: 1.60 (0.21), residues: 630 sheet: 0.19 (0.15), residues: 987 loop : -0.10 (0.14), residues: 1821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 102 TYR 0.020 0.002 TYR A1067 PHE 0.022 0.002 PHE D 72 TRP 0.015 0.001 TRP C 47 HIS 0.006 0.001 HIS D 92 Details of bonding type rmsd covalent geometry : bond 0.00408 (28713) covalent geometry : angle 0.55812 (39078) SS BOND : bond 0.00466 ( 42) SS BOND : angle 1.99700 ( 84) hydrogen bonds : bond 0.04030 ( 1182) hydrogen bonds : angle 5.45126 ( 3312) link_ALPHA1-3 : bond 0.01232 ( 3) link_ALPHA1-3 : angle 1.85846 ( 9) link_ALPHA1-6 : bond 0.00746 ( 3) link_ALPHA1-6 : angle 1.44969 ( 9) link_BETA1-4 : bond 0.00437 ( 18) link_BETA1-4 : angle 1.58144 ( 54) link_BETA1-6 : bond 0.00225 ( 3) link_BETA1-6 : angle 1.76838 ( 9) link_NAG-ASN : bond 0.00401 ( 48) link_NAG-ASN : angle 2.02908 ( 144) *********************** 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 407 residues out of total 3057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 326 time to evaluate : 0.960 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: 0.4473 (OUTLIER) cc_final: 0.4219 (m-80) REVERT: A 453 TYR cc_start: 0.7730 (p90) cc_final: 0.7222 (p90) REVERT: A 588 THR cc_start: 0.8044 (m) cc_final: 0.7815 (p) REVERT: A 759 PHE cc_start: 0.8281 (OUTLIER) cc_final: 0.7755 (m-10) REVERT: A 1029 MET cc_start: 0.8802 (tpp) cc_final: 0.8290 (tpp) REVERT: H 80 TYR cc_start: 0.7342 (m-80) cc_final: 0.6953 (m-80) REVERT: H 116 ASN cc_start: 0.7710 (m-40) cc_final: 0.7345 (m-40) REVERT: L 74 LEU cc_start: 0.7701 (OUTLIER) cc_final: 0.7483 (tp) REVERT: L 90 GLN cc_start: 0.7997 (OUTLIER) cc_final: 0.7709 (tt0) REVERT: B 410 ILE cc_start: 0.8254 (mm) cc_final: 0.7975 (mt) REVERT: B 421 TYR cc_start: 0.4628 (m-80) cc_final: 0.3157 (t80) REVERT: B 453 TYR cc_start: 0.7486 (p90) cc_final: 0.7141 (p90) REVERT: B 759 PHE cc_start: 0.7647 (OUTLIER) cc_final: 0.7126 (t80) REVERT: B 808 ASP cc_start: 0.7166 (OUTLIER) cc_final: 0.6667 (m-30) REVERT: B 984 LEU cc_start: 0.8588 (OUTLIER) cc_final: 0.7960 (mt) REVERT: D 50 TYR cc_start: 0.8123 (p90) cc_final: 0.7619 (p90) REVERT: D 90 GLN cc_start: 0.8011 (OUTLIER) cc_final: 0.7597 (tt0) REVERT: E 95 THR cc_start: 0.7562 (p) cc_final: 0.7225 (p) REVERT: E 421 TYR cc_start: 0.4987 (m-80) cc_final: 0.3419 (t80) REVERT: F 98 ARG cc_start: 0.8438 (tmm-80) cc_final: 0.7858 (tmm160) REVERT: G 80 GLU cc_start: 0.7645 (tp30) cc_final: 0.7292 (mp0) outliers start: 81 outliers final: 49 residues processed: 387 average time/residue: 0.1611 time to fit residues: 103.4758 Evaluate side-chains 361 residues out of total 3057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 304 time to evaluate : 0.735 ------------------------------------------------------------------------------- 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 421 TYR Chi-restraints excluded: chain A residue 514 SER 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 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 47 LEU Chi-restraints excluded: chain L residue 74 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 367 VAL Chi-restraints excluded: chain B residue 371 SER 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 B residue 1128 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 73 THR 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 302 THR Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain E residue 571 ASP Chi-restraints excluded: chain E residue 588 THR Chi-restraints excluded: chain E residue 603 ASN 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 858 LEU 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 Chi-restraints excluded: chain F residue 121 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 263 optimal weight: 6.9990 chunk 266 optimal weight: 2.9990 chunk 257 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 14 optimal weight: 0.6980 chunk 167 optimal weight: 5.9990 chunk 298 optimal weight: 0.0670 chunk 238 optimal weight: 3.9990 chunk 175 optimal weight: 0.9990 chunk 312 optimal weight: 2.9990 chunk 211 optimal weight: 0.3980 overall best weight: 1.0322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN H 3 GLN L 91 GLN D 39 GLN E 196 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.169177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.142446 restraints weight = 41634.942| |-----------------------------------------------------------------------------| r_work (start): 0.3971 rms_B_bonded: 3.05 r_work: 0.3616 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.4094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 28830 Z= 0.171 Angle : 0.576 9.330 39387 Z= 0.294 Chirality : 0.045 0.305 4709 Planarity : 0.004 0.055 4903 Dihedral : 5.446 46.069 5313 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.50 % Allowed : 12.13 % Favored : 85.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.14), residues: 3438 helix: 1.42 (0.21), residues: 648 sheet: 0.11 (0.15), residues: 990 loop : -0.11 (0.14), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 102 TYR 0.021 0.002 TYR C 95 PHE 0.022 0.002 PHE L 72 TRP 0.018 0.001 TRP F 105 HIS 0.006 0.001 HIS D 92 Details of bonding type rmsd covalent geometry : bond 0.00404 (28713) covalent geometry : angle 0.55228 (39078) SS BOND : bond 0.00417 ( 42) SS BOND : angle 2.04895 ( 84) hydrogen bonds : bond 0.03978 ( 1182) hydrogen bonds : angle 5.41847 ( 3312) link_ALPHA1-3 : bond 0.01219 ( 3) link_ALPHA1-3 : angle 1.87772 ( 9) link_ALPHA1-6 : bond 0.00810 ( 3) link_ALPHA1-6 : angle 1.37702 ( 9) link_BETA1-4 : bond 0.00412 ( 18) link_BETA1-4 : angle 1.54774 ( 54) link_BETA1-6 : bond 0.00349 ( 3) link_BETA1-6 : angle 1.67983 ( 9) link_NAG-ASN : bond 0.00381 ( 48) link_NAG-ASN : angle 2.04936 ( 144) *********************** 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 399 residues out of total 3057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 326 time to evaluate : 0.971 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 453 TYR cc_start: 0.7768 (p90) cc_final: 0.7211 (p90) REVERT: A 588 THR cc_start: 0.8085 (m) cc_final: 0.7855 (p) REVERT: A 759 PHE cc_start: 0.8467 (OUTLIER) cc_final: 0.7818 (m-10) REVERT: A 1029 MET cc_start: 0.8835 (tpp) cc_final: 0.8325 (tpp) REVERT: H 80 TYR cc_start: 0.7341 (m-80) cc_final: 0.7078 (m-80) REVERT: H 116 ASN cc_start: 0.7772 (m-40) cc_final: 0.7473 (m-40) REVERT: L 90 GLN cc_start: 0.8099 (OUTLIER) cc_final: 0.7780 (tt0) REVERT: B 410 ILE cc_start: 0.8322 (mm) cc_final: 0.8055 (mt) REVERT: B 421 TYR cc_start: 0.4790 (m-80) cc_final: 0.4367 (m-80) REVERT: B 643 PHE cc_start: 0.8328 (t80) cc_final: 0.8038 (t80) REVERT: B 759 PHE cc_start: 0.7682 (OUTLIER) cc_final: 0.6961 (t80) REVERT: B 808 ASP cc_start: 0.7212 (OUTLIER) cc_final: 0.6673 (m-30) REVERT: B 984 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8189 (mt) REVERT: C 84 ARG cc_start: 0.6788 (mmm-85) cc_final: 0.6435 (mtt180) REVERT: D 36 TRP cc_start: 0.8327 (m-90) cc_final: 0.7811 (m-90) REVERT: D 50 TYR cc_start: 0.8045 (p90) cc_final: 0.7171 (p90) REVERT: D 90 GLN cc_start: 0.8079 (OUTLIER) cc_final: 0.7736 (tt0) REVERT: E 95 THR cc_start: 0.7618 (p) cc_final: 0.7287 (p) REVERT: E 421 TYR cc_start: 0.5130 (m-80) cc_final: 0.3428 (t80) REVERT: E 993 ILE cc_start: 0.9336 (OUTLIER) cc_final: 0.9130 (mp) REVERT: E 1002 GLN cc_start: 0.8057 (tt0) cc_final: 0.7654 (tt0) REVERT: F 43 GLN cc_start: 0.5658 (mp10) cc_final: 0.5419 (mp10) REVERT: F 98 ARG cc_start: 0.8456 (tmm-80) cc_final: 0.7839 (tmm160) REVERT: G 80 GLU cc_start: 0.7673 (tp30) cc_final: 0.7468 (mp0) outliers start: 73 outliers final: 51 residues processed: 380 average time/residue: 0.1651 time to fit residues: 104.1326 Evaluate side-chains 356 residues out of total 3057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 298 time to evaluate : 0.904 ------------------------------------------------------------------------------- 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 514 SER Chi-restraints excluded: chain A residue 603 ASN 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 31 SER Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain L residue 91 GLN Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 110 LEU 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 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 90 GLN Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 110 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 571 ASP Chi-restraints excluded: chain E residue 588 THR Chi-restraints excluded: chain E residue 603 ASN Chi-restraints excluded: chain E residue 752 LEU 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 977 LEU Chi-restraints excluded: chain E residue 993 ILE 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 Chi-restraints excluded: chain G residue 89 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 131 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 310 optimal weight: 0.7980 chunk 75 optimal weight: 0.0970 chunk 6 optimal weight: 3.9990 chunk 276 optimal weight: 3.9990 chunk 235 optimal weight: 3.9990 chunk 163 optimal weight: 1.9990 chunk 147 optimal weight: 4.9990 chunk 32 optimal weight: 9.9990 chunk 285 optimal weight: 0.0970 overall best weight: 1.1980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1002 GLN L 91 GLN E 196 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.168054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 120)---------------| | r_work = 0.3820 r_free = 0.3820 target = 0.132784 restraints weight = 41663.953| |-----------------------------------------------------------------------------| r_work (start): 0.3833 rms_B_bonded: 1.98 r_work: 0.3688 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3554 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.4271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 28830 Z= 0.190 Angle : 0.592 9.759 39387 Z= 0.301 Chirality : 0.046 0.277 4709 Planarity : 0.004 0.052 4903 Dihedral : 5.423 46.239 5313 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.54 % Allowed : 13.02 % Favored : 84.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.14), residues: 3438 helix: 1.33 (0.21), residues: 654 sheet: 0.08 (0.15), residues: 975 loop : -0.18 (0.14), residues: 1809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 102 TYR 0.021 0.002 TYR A1067 PHE 0.016 0.002 PHE E 92 TRP 0.022 0.002 TRP F 105 HIS 0.012 0.001 HIS L 92 Details of bonding type rmsd covalent geometry : bond 0.00452 (28713) covalent geometry : angle 0.56763 (39078) SS BOND : bond 0.00464 ( 42) SS BOND : angle 2.10685 ( 84) hydrogen bonds : bond 0.04086 ( 1182) hydrogen bonds : angle 5.42861 ( 3312) link_ALPHA1-3 : bond 0.01234 ( 3) link_ALPHA1-3 : angle 1.79953 ( 9) link_ALPHA1-6 : bond 0.00889 ( 3) link_ALPHA1-6 : angle 1.31444 ( 9) link_BETA1-4 : bond 0.00420 ( 18) link_BETA1-4 : angle 1.57865 ( 54) link_BETA1-6 : bond 0.00208 ( 3) link_BETA1-6 : angle 1.73469 ( 9) link_NAG-ASN : bond 0.00399 ( 48) link_NAG-ASN : angle 2.11728 ( 144) *********************** 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 384 residues out of total 3057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 310 time to evaluate : 0.941 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 453 TYR cc_start: 0.7856 (p90) cc_final: 0.7225 (p90) REVERT: A 588 THR cc_start: 0.8053 (m) cc_final: 0.7828 (p) REVERT: A 759 PHE cc_start: 0.8503 (OUTLIER) cc_final: 0.7873 (m-10) REVERT: A 1029 MET cc_start: 0.8887 (tpp) cc_final: 0.8377 (tpp) REVERT: H 80 TYR cc_start: 0.7369 (m-80) cc_final: 0.6956 (m-80) REVERT: H 116 ASN cc_start: 0.7878 (m-40) cc_final: 0.7459 (m-40) REVERT: L 90 GLN cc_start: 0.8121 (OUTLIER) cc_final: 0.7662 (tt0) REVERT: B 421 TYR cc_start: 0.4845 (m-80) cc_final: 0.4372 (m-80) REVERT: B 453 TYR cc_start: 0.7507 (p90) cc_final: 0.7050 (p90) REVERT: B 493 GLN cc_start: 0.6901 (mp10) cc_final: 0.6621 (mp10) REVERT: B 759 PHE cc_start: 0.7839 (OUTLIER) cc_final: 0.7284 (t80) REVERT: B 808 ASP cc_start: 0.7248 (OUTLIER) cc_final: 0.6677 (m-30) REVERT: B 984 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8246 (mt) REVERT: C 84 ARG cc_start: 0.6934 (mmm-85) cc_final: 0.6586 (mtt180) REVERT: D 36 TRP cc_start: 0.8411 (m-90) cc_final: 0.7875 (m-90) REVERT: D 50 TYR cc_start: 0.7996 (p90) cc_final: 0.7196 (p90) REVERT: D 90 GLN cc_start: 0.8109 (OUTLIER) cc_final: 0.7812 (tt0) REVERT: E 95 THR cc_start: 0.7676 (p) cc_final: 0.7346 (p) REVERT: E 421 TYR cc_start: 0.5280 (m-80) cc_final: 0.3482 (t80) REVERT: G 80 GLU cc_start: 0.7806 (tp30) cc_final: 0.7561 (mp0) outliers start: 74 outliers final: 57 residues processed: 370 average time/residue: 0.1657 time to fit residues: 101.7076 Evaluate side-chains 362 residues out of total 3057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 299 time to evaluate : 1.012 ------------------------------------------------------------------------------- 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 298 GLU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 371 SER Chi-restraints excluded: chain A residue 495 TYR 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 975 SER 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 31 SER Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain L residue 91 GLN Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 110 LEU 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 723 THR 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 90 GLN Chi-restraints excluded: chain E residue 48 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 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 752 LEU Chi-restraints excluded: chain E residue 791 THR Chi-restraints excluded: chain E residue 808 ASP Chi-restraints excluded: chain E residue 977 LEU Chi-restraints excluded: chain E residue 1072 GLU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 327 optimal weight: 2.9990 chunk 222 optimal weight: 1.9990 chunk 44 optimal weight: 6.9990 chunk 251 optimal weight: 4.9990 chunk 243 optimal weight: 3.9990 chunk 192 optimal weight: 3.9990 chunk 267 optimal weight: 4.9990 chunk 288 optimal weight: 3.9990 chunk 90 optimal weight: 0.7980 chunk 342 optimal weight: 6.9990 chunk 334 optimal weight: 1.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN ** A1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 116 ASN ** E1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.165500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 103)---------------| | r_work = 0.3770 r_free = 0.3770 target = 0.129746 restraints weight = 42322.030| |-----------------------------------------------------------------------------| r_work (start): 0.3744 rms_B_bonded: 2.08 r_work: 0.3589 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3455 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.4617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.117 28830 Z= 0.338 Angle : 0.743 10.989 39387 Z= 0.374 Chirality : 0.051 0.388 4709 Planarity : 0.005 0.051 4903 Dihedral : 6.171 46.882 5313 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.57 % Allowed : 13.16 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.14), residues: 3438 helix: 0.95 (0.20), residues: 651 sheet: -0.25 (0.15), residues: 963 loop : -0.48 (0.14), residues: 1824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 102 TYR 0.026 0.002 TYR E 265 PHE 0.028 0.003 PHE E 92 TRP 0.031 0.003 TRP F 105 HIS 0.010 0.002 HIS L 92 Details of bonding type rmsd covalent geometry : bond 0.00809 (28713) covalent geometry : angle 0.71325 (39078) SS BOND : bond 0.00585 ( 42) SS BOND : angle 2.54190 ( 84) hydrogen bonds : bond 0.04852 ( 1182) hydrogen bonds : angle 5.75055 ( 3312) link_ALPHA1-3 : bond 0.01349 ( 3) link_ALPHA1-3 : angle 1.85823 ( 9) link_ALPHA1-6 : bond 0.01134 ( 3) link_ALPHA1-6 : angle 1.32372 ( 9) link_BETA1-4 : bond 0.00402 ( 18) link_BETA1-4 : angle 2.00618 ( 54) link_BETA1-6 : bond 0.00456 ( 3) link_BETA1-6 : angle 2.09429 ( 9) link_NAG-ASN : bond 0.00544 ( 48) link_NAG-ASN : angle 2.67959 ( 144) *********************** 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 385 residues out of total 3057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 310 time to evaluate : 0.917 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 453 TYR cc_start: 0.7852 (p90) cc_final: 0.7160 (p90) REVERT: A 505 TYR cc_start: 0.7052 (t80) cc_final: 0.6491 (t80) REVERT: A 586 ASP cc_start: 0.7849 (m-30) cc_final: 0.7521 (t70) REVERT: A 588 THR cc_start: 0.8210 (m) cc_final: 0.7931 (p) REVERT: A 759 PHE cc_start: 0.8629 (OUTLIER) cc_final: 0.7944 (m-10) REVERT: A 1029 MET cc_start: 0.8977 (tpp) cc_final: 0.8468 (tpp) REVERT: H 65 GLN cc_start: 0.8361 (tp-100) cc_final: 0.8099 (tp-100) REVERT: H 116 ASN cc_start: 0.7934 (m-40) cc_final: 0.7533 (m-40) REVERT: L 90 GLN cc_start: 0.8229 (OUTLIER) cc_final: 0.7659 (tt0) REVERT: L 91 GLN cc_start: 0.7752 (tm-30) cc_final: 0.7368 (pp30) REVERT: B 453 TYR cc_start: 0.7666 (p90) cc_final: 0.7297 (p90) REVERT: B 759 PHE cc_start: 0.8468 (OUTLIER) cc_final: 0.7800 (t80) REVERT: B 808 ASP cc_start: 0.7514 (OUTLIER) cc_final: 0.7046 (m-30) REVERT: B 977 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8636 (mp) REVERT: B 984 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8440 (mt) REVERT: B 1138 TYR cc_start: 0.7783 (t80) cc_final: 0.7560 (t80) REVERT: C 57 ASN cc_start: 0.8090 (t0) cc_final: 0.7418 (m110) REVERT: D 50 TYR cc_start: 0.8107 (p90) cc_final: 0.7173 (p90) REVERT: D 90 GLN cc_start: 0.8183 (OUTLIER) cc_final: 0.7652 (tt0) REVERT: E 95 THR cc_start: 0.8036 (p) cc_final: 0.7761 (p) REVERT: E 759 PHE cc_start: 0.8581 (OUTLIER) cc_final: 0.8172 (m-10) REVERT: G 80 GLU cc_start: 0.7940 (tp30) cc_final: 0.7674 (mp0) outliers start: 75 outliers final: 57 residues processed: 371 average time/residue: 0.1642 time to fit residues: 100.4306 Evaluate side-chains 364 residues out of total 3057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 299 time to evaluate : 1.005 ------------------------------------------------------------------------------- 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 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 747 THR Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 975 SER 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 31 SER 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 63 THR Chi-restraints excluded: chain B residue 110 LEU 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 367 VAL Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 514 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 931 ILE Chi-restraints excluded: chain B residue 975 SER 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 90 GLN Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 143 VAL 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 553 THR Chi-restraints excluded: chain E residue 571 ASP 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 759 PHE Chi-restraints excluded: chain E residue 791 THR Chi-restraints excluded: chain E residue 808 ASP Chi-restraints excluded: chain E residue 977 LEU Chi-restraints excluded: chain E residue 1072 GLU 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 G residue 89 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 72 optimal weight: 0.5980 chunk 134 optimal weight: 0.7980 chunk 184 optimal weight: 1.9990 chunk 261 optimal weight: 2.9990 chunk 288 optimal weight: 0.8980 chunk 8 optimal weight: 6.9990 chunk 222 optimal weight: 0.6980 chunk 108 optimal weight: 10.0000 chunk 114 optimal weight: 0.0370 chunk 201 optimal weight: 0.5980 chunk 60 optimal weight: 0.9980 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1101 HIS H 3 GLN ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 91 GLN B1101 HIS ** E1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 91 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.170915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 117)---------------| | r_work = 0.3831 r_free = 0.3831 target = 0.134320 restraints weight = 42410.438| |-----------------------------------------------------------------------------| r_work (start): 0.3797 rms_B_bonded: 2.10 r_work: 0.3675 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3544 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.4607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 28830 Z= 0.128 Angle : 0.565 7.715 39387 Z= 0.290 Chirality : 0.045 0.451 4709 Planarity : 0.004 0.053 4903 Dihedral : 5.415 46.413 5313 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.85 % Allowed : 14.18 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.14), residues: 3438 helix: 1.40 (0.21), residues: 639 sheet: -0.11 (0.16), residues: 876 loop : -0.33 (0.14), residues: 1923 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 102 TYR 0.021 0.001 TYR B 269 PHE 0.017 0.001 PHE B 400 TRP 0.019 0.001 TRP F 105 HIS 0.006 0.001 HIS D 92 Details of bonding type rmsd covalent geometry : bond 0.00294 (28713) covalent geometry : angle 0.54205 (39078) SS BOND : bond 0.00407 ( 42) SS BOND : angle 1.88812 ( 84) hydrogen bonds : bond 0.03807 ( 1182) hydrogen bonds : angle 5.41335 ( 3312) link_ALPHA1-3 : bond 0.01185 ( 3) link_ALPHA1-3 : angle 1.72597 ( 9) link_ALPHA1-6 : bond 0.00823 ( 3) link_ALPHA1-6 : angle 1.26326 ( 9) link_BETA1-4 : bond 0.00430 ( 18) link_BETA1-4 : angle 1.42017 ( 54) link_BETA1-6 : bond 0.00107 ( 3) link_BETA1-6 : angle 1.47435 ( 9) link_NAG-ASN : bond 0.00346 ( 48) link_NAG-ASN : angle 2.08529 ( 144) *********************** 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 380 residues out of total 3057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 326 time to evaluate : 0.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 453 TYR cc_start: 0.7798 (p90) cc_final: 0.7128 (p90) REVERT: A 505 TYR cc_start: 0.7021 (t80) cc_final: 0.6426 (t80) REVERT: A 584 ILE cc_start: 0.8600 (mm) cc_final: 0.8185 (mm) REVERT: A 588 THR cc_start: 0.8099 (m) cc_final: 0.7879 (p) REVERT: A 759 PHE cc_start: 0.8386 (OUTLIER) cc_final: 0.7551 (m-10) REVERT: A 990 GLU cc_start: 0.7506 (mt-10) cc_final: 0.7237 (mt-10) REVERT: A 1029 MET cc_start: 0.8869 (tpp) cc_final: 0.8357 (tpp) REVERT: H 80 TYR cc_start: 0.7277 (m-80) cc_final: 0.6994 (m-80) REVERT: H 116 ASN cc_start: 0.7849 (m-40) cc_final: 0.7416 (m-40) REVERT: L 90 GLN cc_start: 0.8404 (OUTLIER) cc_final: 0.8081 (tt0) REVERT: B 453 TYR cc_start: 0.7653 (p90) cc_final: 0.7163 (p90) REVERT: B 759 PHE cc_start: 0.8078 (OUTLIER) cc_final: 0.7126 (t80) REVERT: B 808 ASP cc_start: 0.7321 (OUTLIER) cc_final: 0.6707 (m-30) REVERT: B 984 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8424 (mt) REVERT: C 57 ASN cc_start: 0.7970 (t0) cc_final: 0.7214 (m110) REVERT: C 80 TYR cc_start: 0.7389 (m-80) cc_final: 0.7108 (m-80) REVERT: D 90 GLN cc_start: 0.8068 (OUTLIER) cc_final: 0.7638 (tt0) REVERT: E 95 THR cc_start: 0.7848 (p) cc_final: 0.7513 (p) REVERT: E 804 GLN cc_start: 0.8043 (mt0) cc_final: 0.7739 (mp10) REVERT: E 1002 GLN cc_start: 0.8125 (tt0) cc_final: 0.7742 (tt0) outliers start: 54 outliers final: 40 residues processed: 373 average time/residue: 0.1635 time to fit residues: 101.1468 Evaluate side-chains 346 residues out of total 3057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 300 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 309 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 977 LEU 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 L residue 73 THR Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 514 SER 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 D residue 90 GLN Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 371 SER 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 791 THR Chi-restraints excluded: chain E residue 808 ASP Chi-restraints excluded: chain E residue 1032 CYS 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 G residue 89 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 130 optimal weight: 0.6980 chunk 197 optimal weight: 0.3980 chunk 243 optimal weight: 2.9990 chunk 71 optimal weight: 0.0970 chunk 236 optimal weight: 1.9990 chunk 99 optimal weight: 6.9990 chunk 325 optimal weight: 0.9990 chunk 161 optimal weight: 6.9990 chunk 245 optimal weight: 5.9990 chunk 326 optimal weight: 0.9990 chunk 90 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1002 GLN L 39 GLN C 39 GLN ** E1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.170303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 114)---------------| | r_work = 0.3839 r_free = 0.3839 target = 0.134005 restraints weight = 41982.168| |-----------------------------------------------------------------------------| r_work (start): 0.3803 rms_B_bonded: 1.98 r_work: 0.3691 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3569 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.4681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 28830 Z= 0.128 Angle : 0.552 9.493 39387 Z= 0.282 Chirality : 0.044 0.363 4709 Planarity : 0.004 0.046 4903 Dihedral : 5.073 45.839 5313 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.58 % Allowed : 14.87 % Favored : 83.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.14), residues: 3438 helix: 1.44 (0.21), residues: 657 sheet: 0.01 (0.16), residues: 918 loop : -0.28 (0.14), residues: 1863 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 102 TYR 0.021 0.001 TYR D 50 PHE 0.020 0.001 PHE B 643 TRP 0.020 0.001 TRP F 105 HIS 0.006 0.001 HIS D 92 Details of bonding type rmsd covalent geometry : bond 0.00295 (28713) covalent geometry : angle 0.53113 (39078) SS BOND : bond 0.00382 ( 42) SS BOND : angle 1.73824 ( 84) hydrogen bonds : bond 0.03698 ( 1182) hydrogen bonds : angle 5.26594 ( 3312) link_ALPHA1-3 : bond 0.01048 ( 3) link_ALPHA1-3 : angle 1.55920 ( 9) link_ALPHA1-6 : bond 0.00890 ( 3) link_ALPHA1-6 : angle 1.19230 ( 9) link_BETA1-4 : bond 0.00415 ( 18) link_BETA1-4 : angle 1.38326 ( 54) link_BETA1-6 : bond 0.00308 ( 3) link_BETA1-6 : angle 1.43740 ( 9) link_NAG-ASN : bond 0.00345 ( 48) link_NAG-ASN : angle 2.02002 ( 144) ********************** REFINEMENT MACRO_CYCLE 10 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 371 residues out of total 3057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 325 time to evaluate : 0.706 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: 0.7774 (p90) cc_final: 0.7119 (p90) REVERT: A 505 TYR cc_start: 0.6968 (t80) cc_final: 0.6496 (t80) REVERT: A 584 ILE cc_start: 0.8613 (mm) cc_final: 0.8194 (mm) REVERT: A 588 THR cc_start: 0.8113 (m) cc_final: 0.7903 (p) REVERT: A 643 PHE cc_start: 0.8253 (t80) cc_final: 0.8001 (t80) REVERT: A 759 PHE cc_start: 0.8329 (OUTLIER) cc_final: 0.7554 (m-10) REVERT: A 990 GLU cc_start: 0.7542 (mt-10) cc_final: 0.7286 (mt-10) REVERT: A 1029 MET cc_start: 0.8851 (tpp) cc_final: 0.8323 (tpp) REVERT: H 80 TYR cc_start: 0.7169 (m-80) cc_final: 0.6905 (m-80) REVERT: H 116 ASN cc_start: 0.7835 (m-40) cc_final: 0.7430 (m-40) REVERT: L 80 GLU cc_start: 0.6352 (mp0) cc_final: 0.6093 (mp0) REVERT: B 453 TYR cc_start: 0.7818 (p90) cc_final: 0.7468 (p90) REVERT: B 759 PHE cc_start: 0.8038 (OUTLIER) cc_final: 0.7105 (t80) REVERT: B 808 ASP cc_start: 0.7187 (OUTLIER) cc_final: 0.6761 (m-30) REVERT: B 984 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8435 (mt) REVERT: C 57 ASN cc_start: 0.7953 (t0) cc_final: 0.7202 (m110) REVERT: C 80 TYR cc_start: 0.7192 (m-80) cc_final: 0.6904 (m-80) REVERT: C 84 ARG cc_start: 0.7212 (mmm-85) cc_final: 0.6842 (mtm180) REVERT: D 90 GLN cc_start: 0.8097 (OUTLIER) cc_final: 0.7688 (tt0) REVERT: E 95 THR cc_start: 0.7860 (p) cc_final: 0.7518 (p) REVERT: E 804 GLN cc_start: 0.7994 (mt0) cc_final: 0.7714 (mp10) REVERT: E 1002 GLN cc_start: 0.8096 (tt0) cc_final: 0.7713 (tt0) outliers start: 46 outliers final: 36 residues processed: 364 average time/residue: 0.1597 time to fit residues: 96.1392 Evaluate side-chains 351 residues out of total 3057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 310 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 309 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 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 31 SER Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 428 ASP 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 D residue 90 GLN Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain E residue 603 ASN 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 977 LEU Chi-restraints excluded: chain E residue 1032 CYS Chi-restraints excluded: chain E residue 1117 THR Chi-restraints excluded: chain E residue 1128 VAL Chi-restraints excluded: chain F residue 31 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 104 optimal weight: 3.9990 chunk 191 optimal weight: 0.9990 chunk 99 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 269 optimal weight: 9.9990 chunk 6 optimal weight: 0.9990 chunk 59 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 176 optimal weight: 0.9990 chunk 237 optimal weight: 1.9990 chunk 341 optimal weight: 9.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1002 GLN ** B1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.168396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 95)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.133060 restraints weight = 41934.177| |-----------------------------------------------------------------------------| r_work (start): 0.3800 rms_B_bonded: 1.94 r_work: 0.3650 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3520 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.4772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 28830 Z= 0.190 Angle : 0.599 8.620 39387 Z= 0.304 Chirality : 0.046 0.337 4709 Planarity : 0.004 0.050 4903 Dihedral : 5.203 45.834 5313 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.95 % Allowed : 14.49 % Favored : 83.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.14), residues: 3438 helix: 1.41 (0.21), residues: 639 sheet: -0.07 (0.16), residues: 939 loop : -0.38 (0.14), residues: 1860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 102 TYR 0.027 0.002 TYR D 50 PHE 0.025 0.002 PHE B 643 TRP 0.021 0.002 TRP F 105 HIS 0.007 0.001 HIS D 92 Details of bonding type rmsd covalent geometry : bond 0.00454 (28713) covalent geometry : angle 0.57624 (39078) SS BOND : bond 0.00410 ( 42) SS BOND : angle 1.81834 ( 84) hydrogen bonds : bond 0.03979 ( 1182) hydrogen bonds : angle 5.39407 ( 3312) link_ALPHA1-3 : bond 0.01026 ( 3) link_ALPHA1-3 : angle 1.55406 ( 9) link_ALPHA1-6 : bond 0.00944 ( 3) link_ALPHA1-6 : angle 1.11880 ( 9) link_BETA1-4 : bond 0.00399 ( 18) link_BETA1-4 : angle 1.50853 ( 54) link_BETA1-6 : bond 0.00045 ( 3) link_BETA1-6 : angle 1.61004 ( 9) link_NAG-ASN : bond 0.00369 ( 48) link_NAG-ASN : angle 2.18792 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7793.96 seconds wall clock time: 133 minutes 45.39 seconds (8025.39 seconds total)