Starting phenix.real_space_refine on Sat Mar 7 01:41:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wn3_32620/03_2026/7wn3_32620_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wn3_32620/03_2026/7wn3_32620.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wn3_32620/03_2026/7wn3_32620.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wn3_32620/03_2026/7wn3_32620.map" model { file = "/net/cci-nas-00/data/ceres_data/7wn3_32620/03_2026/7wn3_32620_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wn3_32620/03_2026/7wn3_32620_neut.cif" } resolution = 3.29 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= 0.001 sd= 0.002 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: 5 Type Number sf(0) Gaussians Ca 16 9.91 5 S 560 5.16 5 C 22568 2.51 5 N 6260 2.21 5 O 7180 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.02s 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: 36584 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 5421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 711, 5421 Classifications: {'peptide': 711} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 2, 'PTRANS': 33, 'TRANS': 675} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "F" Number of atoms: 3651 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 478, 3645 Classifications: {'peptide': 478} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 28, 'TRANS': 449} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 478, 3645 Classifications: {'peptide': 478} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 28, 'TRANS': 449} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 3714 Chain: "B" Number of atoms: 5421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 711, 5421 Classifications: {'peptide': 711} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 2, 'PTRANS': 33, 'TRANS': 675} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "H" Number of atoms: 3651 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 478, 3645 Classifications: {'peptide': 478} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 28, 'TRANS': 449} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 478, 3645 Classifications: {'peptide': 478} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 28, 'TRANS': 449} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 3714 Chain: "E" Number of atoms: 5421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 711, 5421 Classifications: {'peptide': 711} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 2, 'PTRANS': 33, 'TRANS': 675} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "G" Number of atoms: 5421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 711, 5421 Classifications: {'peptide': 711} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 2, 'PTRANS': 33, 'TRANS': 675} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "C" Number of atoms: 3651 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 478, 3645 Classifications: {'peptide': 478} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 28, 'TRANS': 449} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 478, 3645 Classifications: {'peptide': 478} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 28, 'TRANS': 449} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 3714 Chain: "D" Number of atoms: 3651 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 478, 3645 Classifications: {'peptide': 478} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 28, 'TRANS': 449} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 478, 3645 Classifications: {'peptide': 478} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 28, 'TRANS': 449} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 3714 Chain: "A" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 30 Unusual residues: {' CA': 2, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 44 Unusual residues: {' CA': 2, 'NAG': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 30 Unusual residues: {' CA': 2, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 44 Unusual residues: {' CA': 2, 'NAG': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 30 Unusual residues: {' CA': 2, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 30 Unusual residues: {' CA': 2, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 44 Unusual residues: {' CA': 2, 'NAG': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 44 Unusual residues: {' CA': 2, 'NAG': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 10.91, per 1000 atoms: 0.30 Number of scatterers: 36584 At special positions: 0 Unit cell: (161.02, 246.38, 176.54, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 16 19.99 S 560 16.00 O 7180 8.00 N 6260 7.00 C 22568 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=230, symmetry=0 Simple disulfide: pdb=" SG CYS A 35 " - pdb=" SG CYS A 162 " distance=2.03 Simple disulfide: pdb=" SG CYS A 57 " - pdb=" SG CYS A 200 " distance=2.03 Simple disulfide: pdb=" SG CYS A 65 " - pdb=" SG CYS A 159 " distance=2.02 Simple disulfide: pdb=" SG CYS A 210 " - pdb=" SG CYS A 255 " distance=2.03 Simple disulfide: pdb=" SG CYS A 225 " - pdb=" SG CYS A 250 " distance=2.02 Simple disulfide: pdb=" SG CYS A 237 " - pdb=" SG CYS A 275 " distance=2.03 Simple disulfide: pdb=" SG CYS A 257 " - pdb=" SG CYS A 263 " distance=2.03 Simple disulfide: pdb=" SG CYS A 265 " - pdb=" SG CYS A 291 " distance=2.03 Simple disulfide: pdb=" SG CYS A 295 " - pdb=" SG CYS A 329 " distance=2.02 Simple disulfide: pdb=" SG CYS A 304 " - pdb=" SG CYS A 325 " distance=2.03 Simple disulfide: pdb=" SG CYS A 308 " - pdb=" SG CYS A 321 " distance=2.02 Simple disulfide: pdb=" SG CYS A 312 " - pdb=" SG CYS A 348 " distance=2.03 Simple disulfide: pdb=" SG CYS A 331 " - pdb=" SG CYS A 342 " distance=2.03 Simple disulfide: pdb=" SG CYS A 350 " - pdb=" SG CYS A 372 " distance=2.03 Simple disulfide: pdb=" SG CYS A 367 " - pdb=" SG CYS A 384 " distance=2.03 Simple disulfide: pdb=" SG CYS A 370 " - pdb=" SG CYS A 379 " distance=2.03 Simple disulfide: pdb=" SG CYS A 388 " - pdb=" SG CYS A 524 " distance=2.03 Simple disulfide: pdb=" SG CYS A 410 " - pdb=" SG CYS A 559 " distance=2.03 Simple disulfide: pdb=" SG CYS A 418 " - pdb=" SG CYS A 521 " distance=2.03 Simple disulfide: pdb=" SG CYS A 432 " - pdb=" SG CYS A 440 " distance=2.03 Simple disulfide: pdb=" SG CYS A 570 " - pdb=" SG CYS A 613 " distance=2.03 Simple disulfide: pdb=" SG CYS A 584 " - pdb=" SG CYS A 608 " distance=2.02 Simple disulfide: pdb=" SG CYS A 595 " - pdb=" SG CYS A 633 " distance=2.04 Simple disulfide: pdb=" SG CYS A 615 " - pdb=" SG CYS A 621 " distance=2.03 Simple disulfide: pdb=" SG CYS A 623 " - pdb=" SG CYS A 648 " distance=2.02 Simple disulfide: pdb=" SG CYS A 652 " - pdb=" SG CYS A 687 " distance=2.03 Simple disulfide: pdb=" SG CYS A 661 " - pdb=" SG CYS A 683 " distance=2.03 Simple disulfide: pdb=" SG CYS A 665 " - pdb=" SG CYS A 679 " distance=2.03 Simple disulfide: pdb=" SG CYS A 669 " - pdb=" SG CYS A 707 " distance=2.03 Simple disulfide: pdb=" SG CYS A 689 " - pdb=" SG CYS A 701 " distance=2.04 Simple disulfide: pdb=" SG CYS A 709 " - pdb=" SG CYS A 731 " distance=2.03 Simple disulfide: pdb=" SG CYS A 729 " - pdb=" SG CYS A 738 " distance=2.03 Simple disulfide: pdb=" SG CYS F 767 " - pdb=" SG CYS F 808 " distance=2.03 Simple disulfide: pdb=" SG CYS F 776 " - pdb=" SG CYS F 804 " distance=2.03 Simple disulfide: pdb=" SG CYS F 788 " - pdb=" SG CYS F 799 " distance=2.03 Simple disulfide: pdb=" SG CYS F 792 " - pdb=" SG CYS F 827 " distance=2.03 Simple disulfide: pdb=" SG CYS F 810 " - pdb=" SG CYS F 821 " distance=2.03 Simple disulfide: pdb=" SG CYS F 829 " - pdb=" SG CYS F 851 " distance=2.03 Simple disulfide: pdb=" SG CYS F 846 " - pdb=" SG CYS F 863 " distance=2.03 Simple disulfide: pdb=" SG CYS F 849 " - pdb=" SG CYS F 858 " distance=2.03 Simple disulfide: pdb=" SG CYS F 867 " - pdb=" SG CYS F 996 " distance=2.03 Simple disulfide: pdb=" SG CYS F 889 " - pdb=" SG CYS F1031 " distance=2.02 Simple disulfide: pdb=" SG CYS F 898 " - pdb=" SG CYS F 993 " distance=2.03 Simple disulfide: pdb=" SG CYS F 914 " - pdb=" SG CYS F 921 " distance=2.03 Simple disulfide: pdb=" SG CYS F1046 " - pdb=" SG CYS F1089 " distance=2.03 Simple disulfide: pdb=" SG CYS F1060 " - pdb=" SG CYS F1084 " distance=2.04 Simple disulfide: pdb=" SG CYS F1071 " - pdb=" SG CYS F1111 " distance=2.03 Simple disulfide: pdb=" SG CYS F1091 " - pdb=" SG CYS F1099 " distance=2.03 Simple disulfide: pdb=" SG CYS F1097 " - pdb=" SG CYS H1097 " distance=1.99 Simple disulfide: pdb=" SG CYS F1101 " - pdb=" SG CYS F1126 " distance=2.02 Simple disulfide: pdb=" SG CYS F1130 " - pdb=" SG CYS F1173 " distance=2.02 Simple disulfide: pdb=" SG CYS F1149 " - pdb=" SG CYS F1169 " distance=2.03 Simple disulfide: pdb=" SG CYS F1153 " - pdb=" SG CYS F1165 " distance=2.03 Simple disulfide: pdb=" SG CYS F1157 " - pdb=" SG CYS F1196 " distance=2.03 Simple disulfide: pdb=" SG CYS F1177 " - pdb=" SG CYS F1190 " distance=2.03 Simple disulfide: pdb=" SG CYS F1199 " - pdb=" SG CYS F1227 " distance=2.03 Simple disulfide: pdb=" SG CYS F1222 " - pdb=" SG CYS F1237 " distance=2.03 Simple disulfide: pdb=" SG CYS F1225 " - pdb=" SG CYS F1234 " distance=2.03 Simple disulfide: pdb=" SG CYS B 35 " - pdb=" SG CYS B 162 " distance=2.03 Simple disulfide: pdb=" SG CYS B 57 " - pdb=" SG CYS B 200 " distance=2.03 Simple disulfide: pdb=" SG CYS B 65 " - pdb=" SG CYS B 159 " distance=2.03 Simple disulfide: pdb=" SG CYS B 210 " - pdb=" SG CYS B 255 " distance=2.03 Simple disulfide: pdb=" SG CYS B 225 " - pdb=" SG CYS B 250 " distance=2.02 Simple disulfide: pdb=" SG CYS B 237 " - pdb=" SG CYS B 275 " distance=2.03 Simple disulfide: pdb=" SG CYS B 257 " - pdb=" SG CYS B 263 " distance=2.03 Simple disulfide: pdb=" SG CYS B 265 " - pdb=" SG CYS B 291 " distance=2.03 Simple disulfide: pdb=" SG CYS B 295 " - pdb=" SG CYS B 329 " distance=2.02 Simple disulfide: pdb=" SG CYS B 304 " - pdb=" SG CYS B 325 " distance=2.03 Simple disulfide: pdb=" SG CYS B 308 " - pdb=" SG CYS B 321 " distance=2.02 Simple disulfide: pdb=" SG CYS B 312 " - pdb=" SG CYS B 348 " distance=2.03 Simple disulfide: pdb=" SG CYS B 331 " - pdb=" SG CYS B 342 " distance=2.03 Simple disulfide: pdb=" SG CYS B 350 " - pdb=" SG CYS B 372 " distance=2.03 Simple disulfide: pdb=" SG CYS B 367 " - pdb=" SG CYS B 384 " distance=2.03 Simple disulfide: pdb=" SG CYS B 370 " - pdb=" SG CYS B 379 " distance=2.03 Simple disulfide: pdb=" SG CYS B 388 " - pdb=" SG CYS B 524 " distance=2.03 Simple disulfide: pdb=" SG CYS B 410 " - pdb=" SG CYS B 559 " distance=2.03 Simple disulfide: pdb=" SG CYS B 418 " - pdb=" SG CYS B 521 " distance=2.03 Simple disulfide: pdb=" SG CYS B 432 " - pdb=" SG CYS B 440 " distance=2.03 Simple disulfide: pdb=" SG CYS B 570 " - pdb=" SG CYS B 613 " distance=2.03 Simple disulfide: pdb=" SG CYS B 584 " - pdb=" SG CYS B 608 " distance=2.02 Simple disulfide: pdb=" SG CYS B 595 " - pdb=" SG CYS B 633 " distance=2.03 Simple disulfide: pdb=" SG CYS B 615 " - pdb=" SG CYS B 621 " distance=2.03 Simple disulfide: pdb=" SG CYS B 623 " - pdb=" SG CYS B 648 " distance=2.02 Simple disulfide: pdb=" SG CYS B 652 " - pdb=" SG CYS B 687 " distance=2.03 Simple disulfide: pdb=" SG CYS B 661 " - pdb=" SG CYS B 683 " distance=2.03 Simple disulfide: pdb=" SG CYS B 665 " - pdb=" SG CYS B 679 " distance=2.03 Simple disulfide: pdb=" SG CYS B 669 " - pdb=" SG CYS B 707 " distance=2.03 Simple disulfide: pdb=" SG CYS B 689 " - pdb=" SG CYS B 701 " distance=2.04 Simple disulfide: pdb=" SG CYS B 709 " - pdb=" SG CYS B 731 " distance=2.03 Simple disulfide: pdb=" SG CYS B 729 " - pdb=" SG CYS B 738 " distance=2.03 Simple disulfide: pdb=" SG CYS H 767 " - pdb=" SG CYS H 808 " distance=2.03 Simple disulfide: pdb=" SG CYS H 776 " - pdb=" SG CYS H 804 " distance=2.03 Simple disulfide: pdb=" SG CYS H 788 " - pdb=" SG CYS H 799 " distance=2.03 Simple disulfide: pdb=" SG CYS H 792 " - pdb=" SG CYS H 827 " distance=2.03 Simple disulfide: pdb=" SG CYS H 810 " - pdb=" SG CYS H 821 " distance=2.03 Simple disulfide: pdb=" SG CYS H 829 " - pdb=" SG CYS H 851 " distance=2.03 Simple disulfide: pdb=" SG CYS H 846 " - pdb=" SG CYS H 863 " distance=2.03 Simple disulfide: pdb=" SG CYS H 849 " - pdb=" SG CYS H 858 " distance=2.04 Simple disulfide: pdb=" SG CYS H 867 " - pdb=" SG CYS H 996 " distance=2.03 Simple disulfide: pdb=" SG CYS H 889 " - pdb=" SG CYS H1031 " distance=2.03 Simple disulfide: pdb=" SG CYS H 898 " - pdb=" SG CYS H 993 " distance=2.03 Simple disulfide: pdb=" SG CYS H 914 " - pdb=" SG CYS H 921 " distance=2.03 Simple disulfide: pdb=" SG CYS H1046 " - pdb=" SG CYS H1089 " distance=2.03 Simple disulfide: pdb=" SG CYS H1060 " - pdb=" SG CYS H1084 " distance=2.04 Simple disulfide: pdb=" SG CYS H1071 " - pdb=" SG CYS H1111 " distance=2.03 Simple disulfide: pdb=" SG CYS H1091 " - pdb=" SG CYS H1099 " distance=2.03 Simple disulfide: pdb=" SG CYS H1101 " - pdb=" SG CYS H1126 " distance=2.02 Simple disulfide: pdb=" SG CYS H1130 " - pdb=" SG CYS H1173 " distance=2.02 Simple disulfide: pdb=" SG CYS H1149 " - pdb=" SG CYS H1169 " distance=2.03 Simple disulfide: pdb=" SG CYS H1153 " - pdb=" SG CYS H1165 " distance=2.03 Simple disulfide: pdb=" SG CYS H1157 " - pdb=" SG CYS H1196 " distance=2.03 Simple disulfide: pdb=" SG CYS H1177 " - pdb=" SG CYS H1190 " distance=2.03 Simple disulfide: pdb=" SG CYS H1199 " - pdb=" SG CYS H1227 " distance=2.03 Simple disulfide: pdb=" SG CYS H1222 " - pdb=" SG CYS H1237 " distance=2.04 Simple disulfide: pdb=" SG CYS H1225 " - pdb=" SG CYS H1234 " distance=2.03 Simple disulfide: pdb=" SG CYS E 35 " - pdb=" SG CYS E 162 " distance=2.03 Simple disulfide: pdb=" SG CYS E 57 " - pdb=" SG CYS E 200 " distance=2.03 Simple disulfide: pdb=" SG CYS E 65 " - pdb=" SG CYS E 159 " distance=2.02 Simple disulfide: pdb=" SG CYS E 210 " - pdb=" SG CYS E 255 " distance=2.03 Simple disulfide: pdb=" SG CYS E 225 " - pdb=" SG CYS E 250 " distance=2.02 Simple disulfide: pdb=" SG CYS E 237 " - pdb=" SG CYS E 275 " distance=2.03 Simple disulfide: pdb=" SG CYS E 257 " - pdb=" SG CYS E 263 " distance=2.03 Simple disulfide: pdb=" SG CYS E 265 " - pdb=" SG CYS E 291 " distance=2.03 Simple disulfide: pdb=" SG CYS E 295 " - pdb=" SG CYS E 329 " distance=2.02 Simple disulfide: pdb=" SG CYS E 304 " - pdb=" SG CYS E 325 " distance=2.03 Simple disulfide: pdb=" SG CYS E 308 " - pdb=" SG CYS E 321 " distance=2.02 Simple disulfide: pdb=" SG CYS E 312 " - pdb=" SG CYS E 348 " distance=2.03 Simple disulfide: pdb=" SG CYS E 331 " - pdb=" SG CYS E 342 " distance=2.03 Simple disulfide: pdb=" SG CYS E 350 " - pdb=" SG CYS E 372 " distance=2.03 Simple disulfide: pdb=" SG CYS E 367 " - pdb=" SG CYS E 384 " distance=2.03 Simple disulfide: pdb=" SG CYS E 370 " - pdb=" SG CYS E 379 " distance=2.03 Simple disulfide: pdb=" SG CYS E 388 " - pdb=" SG CYS E 524 " distance=2.03 Simple disulfide: pdb=" SG CYS E 410 " - pdb=" SG CYS E 559 " distance=2.03 Simple disulfide: pdb=" SG CYS E 418 " - pdb=" SG CYS E 521 " distance=2.03 Simple disulfide: pdb=" SG CYS E 432 " - pdb=" SG CYS E 440 " distance=2.03 Simple disulfide: pdb=" SG CYS E 570 " - pdb=" SG CYS E 613 " distance=2.03 Simple disulfide: pdb=" SG CYS E 584 " - pdb=" SG CYS E 608 " distance=2.02 Simple disulfide: pdb=" SG CYS E 595 " - pdb=" SG CYS E 633 " distance=2.03 Simple disulfide: pdb=" SG CYS E 615 " - pdb=" SG CYS E 621 " distance=2.03 Simple disulfide: pdb=" SG CYS E 623 " - pdb=" SG CYS E 648 " distance=2.02 Simple disulfide: pdb=" SG CYS E 652 " - pdb=" SG CYS E 687 " distance=2.03 Simple disulfide: pdb=" SG CYS E 661 " - pdb=" SG CYS E 683 " distance=2.03 Simple disulfide: pdb=" SG CYS E 665 " - pdb=" SG CYS E 679 " distance=2.03 Simple disulfide: pdb=" SG CYS E 669 " - pdb=" SG CYS E 707 " distance=2.03 Simple disulfide: pdb=" SG CYS E 689 " - pdb=" SG CYS E 701 " distance=2.04 Simple disulfide: pdb=" SG CYS E 709 " - pdb=" SG CYS E 731 " distance=2.03 Simple disulfide: pdb=" SG CYS E 729 " - pdb=" SG CYS E 738 " distance=2.03 Simple disulfide: pdb=" SG CYS G 35 " - pdb=" SG CYS G 162 " distance=2.04 Simple disulfide: pdb=" SG CYS G 57 " - pdb=" SG CYS G 200 " distance=2.04 Simple disulfide: pdb=" SG CYS G 65 " - pdb=" SG CYS G 159 " distance=2.03 Simple disulfide: pdb=" SG CYS G 210 " - pdb=" SG CYS G 255 " distance=2.03 Simple disulfide: pdb=" SG CYS G 225 " - pdb=" SG CYS G 250 " distance=2.02 Simple disulfide: pdb=" SG CYS G 237 " - pdb=" SG CYS G 275 " distance=2.03 Simple disulfide: pdb=" SG CYS G 257 " - pdb=" SG CYS G 263 " distance=2.03 Simple disulfide: pdb=" SG CYS G 265 " - pdb=" SG CYS G 291 " distance=2.03 Simple disulfide: pdb=" SG CYS G 295 " - pdb=" SG CYS G 329 " distance=2.02 Simple disulfide: pdb=" SG CYS G 304 " - pdb=" SG CYS G 325 " distance=2.03 Simple disulfide: pdb=" SG CYS G 308 " - pdb=" SG CYS G 321 " distance=2.02 Simple disulfide: pdb=" SG CYS G 312 " - pdb=" SG CYS G 348 " distance=2.03 Simple disulfide: pdb=" SG CYS G 331 " - pdb=" SG CYS G 342 " distance=2.03 Simple disulfide: pdb=" SG CYS G 350 " - pdb=" SG CYS G 372 " distance=2.03 Simple disulfide: pdb=" SG CYS G 367 " - pdb=" SG CYS G 384 " distance=2.03 Simple disulfide: pdb=" SG CYS G 370 " - pdb=" SG CYS G 379 " distance=2.03 Simple disulfide: pdb=" SG CYS G 388 " - pdb=" SG CYS G 524 " distance=2.03 Simple disulfide: pdb=" SG CYS G 410 " - pdb=" SG CYS G 559 " distance=2.03 Simple disulfide: pdb=" SG CYS G 418 " - pdb=" SG CYS G 521 " distance=2.03 Simple disulfide: pdb=" SG CYS G 432 " - pdb=" SG CYS G 440 " distance=2.03 Simple disulfide: pdb=" SG CYS G 570 " - pdb=" SG CYS G 613 " distance=2.03 Simple disulfide: pdb=" SG CYS G 584 " - pdb=" SG CYS G 608 " distance=2.02 Simple disulfide: pdb=" SG CYS G 595 " - pdb=" SG CYS G 633 " distance=2.03 Simple disulfide: pdb=" SG CYS G 615 " - pdb=" SG CYS G 621 " distance=2.03 Simple disulfide: pdb=" SG CYS G 623 " - pdb=" SG CYS G 648 " distance=2.02 Simple disulfide: pdb=" SG CYS G 652 " - pdb=" SG CYS G 687 " distance=2.03 Simple disulfide: pdb=" SG CYS G 661 " - pdb=" SG CYS G 683 " distance=2.03 Simple disulfide: pdb=" SG CYS G 665 " - pdb=" SG CYS G 679 " distance=2.03 Simple disulfide: pdb=" SG CYS G 669 " - pdb=" SG CYS G 707 " distance=2.03 Simple disulfide: pdb=" SG CYS G 689 " - pdb=" SG CYS G 701 " distance=2.04 Simple disulfide: pdb=" SG CYS G 709 " - pdb=" SG CYS G 731 " distance=2.03 Simple disulfide: pdb=" SG CYS G 729 " - pdb=" SG CYS G 738 " distance=2.03 Simple disulfide: pdb=" SG CYS C 767 " - pdb=" SG CYS C 808 " distance=2.03 Simple disulfide: pdb=" SG CYS C 776 " - pdb=" SG CYS C 804 " distance=2.03 Simple disulfide: pdb=" SG CYS C 788 " - pdb=" SG CYS C 799 " distance=2.03 Simple disulfide: pdb=" SG CYS C 792 " - pdb=" SG CYS C 827 " distance=2.03 Simple disulfide: pdb=" SG CYS C 810 " - pdb=" SG CYS C 821 " distance=2.03 Simple disulfide: pdb=" SG CYS C 829 " - pdb=" SG CYS C 851 " distance=2.03 Simple disulfide: pdb=" SG CYS C 846 " - pdb=" SG CYS C 863 " distance=2.03 Simple disulfide: pdb=" SG CYS C 849 " - pdb=" SG CYS C 858 " distance=2.03 Simple disulfide: pdb=" SG CYS C 867 " - pdb=" SG CYS C 996 " distance=2.03 Simple disulfide: pdb=" SG CYS C 889 " - pdb=" SG CYS C1031 " distance=2.03 Simple disulfide: pdb=" SG CYS C 898 " - pdb=" SG CYS C 993 " distance=2.03 Simple disulfide: pdb=" SG CYS C 914 " - pdb=" SG CYS C 921 " distance=2.03 Simple disulfide: pdb=" SG CYS C1046 " - pdb=" SG CYS C1089 " distance=2.03 Simple disulfide: pdb=" SG CYS C1060 " - pdb=" SG CYS C1084 " distance=2.04 Simple disulfide: pdb=" SG CYS C1071 " - pdb=" SG CYS C1111 " distance=2.02 Simple disulfide: pdb=" SG CYS C1091 " - pdb=" SG CYS C1099 " distance=2.03 Simple disulfide: pdb=" SG CYS C1097 " - pdb=" SG CYS D1097 " distance=2.08 Simple disulfide: pdb=" SG CYS C1101 " - pdb=" SG CYS C1126 " distance=2.02 Simple disulfide: pdb=" SG CYS C1130 " - pdb=" SG CYS C1173 " distance=2.02 Simple disulfide: pdb=" SG CYS C1149 " - pdb=" SG CYS C1169 " distance=2.04 Simple disulfide: pdb=" SG CYS C1153 " - pdb=" SG CYS C1165 " distance=2.03 Simple disulfide: pdb=" SG CYS C1157 " - pdb=" SG CYS C1196 " distance=2.03 Simple disulfide: pdb=" SG CYS C1177 " - pdb=" SG CYS C1190 " distance=2.03 Simple disulfide: pdb=" SG CYS C1199 " - pdb=" SG CYS C1227 " distance=2.03 Simple disulfide: pdb=" SG CYS C1222 " - pdb=" SG CYS C1237 " distance=2.03 Simple disulfide: pdb=" SG CYS C1225 " - pdb=" SG CYS C1234 " distance=2.03 Simple disulfide: pdb=" SG CYS D 767 " - pdb=" SG CYS D 808 " distance=2.03 Simple disulfide: pdb=" SG CYS D 776 " - pdb=" SG CYS D 804 " distance=2.03 Simple disulfide: pdb=" SG CYS D 788 " - pdb=" SG CYS D 799 " distance=2.03 Simple disulfide: pdb=" SG CYS D 792 " - pdb=" SG CYS D 827 " distance=2.03 Simple disulfide: pdb=" SG CYS D 810 " - pdb=" SG CYS D 821 " distance=2.03 Simple disulfide: pdb=" SG CYS D 829 " - pdb=" SG CYS D 851 " distance=2.03 Simple disulfide: pdb=" SG CYS D 846 " - pdb=" SG CYS D 863 " distance=2.03 Simple disulfide: pdb=" SG CYS D 849 " - pdb=" SG CYS D 858 " distance=2.03 Simple disulfide: pdb=" SG CYS D 867 " - pdb=" SG CYS D 996 " distance=2.03 Simple disulfide: pdb=" SG CYS D 889 " - pdb=" SG CYS D1031 " distance=2.03 Simple disulfide: pdb=" SG CYS D 898 " - pdb=" SG CYS D 993 " distance=2.03 Simple disulfide: pdb=" SG CYS D 914 " - pdb=" SG CYS D 921 " distance=2.03 Simple disulfide: pdb=" SG CYS D1046 " - pdb=" SG CYS D1089 " distance=2.03 Simple disulfide: pdb=" SG CYS D1060 " - pdb=" SG CYS D1084 " distance=2.04 Simple disulfide: pdb=" SG CYS D1071 " - pdb=" SG CYS D1111 " distance=2.03 Simple disulfide: pdb=" SG CYS D1091 " - pdb=" SG CYS D1099 " distance=2.03 Simple disulfide: pdb=" SG CYS D1101 " - pdb=" SG CYS D1126 " distance=2.02 Simple disulfide: pdb=" SG CYS D1130 " - pdb=" SG CYS D1173 " distance=2.03 Simple disulfide: pdb=" SG CYS D1149 " - pdb=" SG CYS D1169 " distance=2.03 Simple disulfide: pdb=" SG CYS D1153 " - pdb=" SG CYS D1165 " distance=2.03 Simple disulfide: pdb=" SG CYS D1157 " - pdb=" SG CYS D1196 " distance=2.03 Simple disulfide: pdb=" SG CYS D1177 " - pdb=" SG CYS D1190 " distance=2.03 Simple disulfide: pdb=" SG CYS D1199 " - pdb=" SG CYS D1227 " distance=2.03 Simple disulfide: pdb=" SG CYS D1222 " - pdb=" SG CYS D1237 " distance=2.04 Simple disulfide: pdb=" SG CYS D1225 " - pdb=" SG CYS D1234 " 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 Atom "HETATM36582 O5 NAG D1305 .*. O " rejected from bonding due to valence issues. Atom "HETATM36434 O5 NAG H1305 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 803 " - " ASN A 156 " " NAG A 804 " - " ASN A 99 " " NAG B 803 " - " ASN B 156 " " NAG B 804 " - " ASN B 99 " " NAG C1301 " - " ASN C1231 " " NAG C1304 " - " ASN C 857 " " NAG C1305 " - " ASN C1147 " " NAG D1301 " - " ASN D1231 " " NAG D1304 " - " ASN D 857 " " NAG D1305 " - " ASN D1147 " " NAG E 803 " - " ASN E 156 " " NAG E 804 " - " ASN E 99 " " NAG F1301 " - " ASN F1231 " " NAG F1304 " - " ASN F 857 " " NAG F1305 " - " ASN F1147 " " NAG G 803 " - " ASN G 156 " " NAG G 804 " - " ASN G 99 " " NAG H1301 " - " ASN H1231 " " NAG H1304 " - " ASN H 857 " " NAG H1305 " - " ASN H1147 " Time building additional restraints: 3.11 Conformation dependent library (CDL) restraints added in 2.4 seconds 9488 Ramachandran restraints generated. 4744 Oldfield, 0 Emsley, 4744 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8768 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 98 sheets defined 17.9% alpha, 13.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.51 Creating SS restraints... Processing helix chain 'A' and resid 114 through 118 removed outlier: 3.923A pdb=" N GLY A 117 " --> pdb=" O ALA A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 191 removed outlier: 3.504A pdb=" N TRP A 191 " --> pdb=" O PHE A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 212 removed outlier: 3.758A pdb=" N ASN A 211 " --> pdb=" O SER A 208 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE A 212 " --> pdb=" O SER A 209 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 208 through 212' Processing helix chain 'A' and resid 216 through 221 removed outlier: 3.757A pdb=" N LEU A 221 " --> pdb=" O MET A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 231 removed outlier: 4.279A pdb=" N CYS A 225 " --> pdb=" O LEU A 221 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N LEU A 228 " --> pdb=" O GLN A 224 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N LYS A 229 " --> pdb=" O CYS A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 235 Processing helix chain 'A' and resid 243 through 251 removed outlier: 3.585A pdb=" N GLU A 251 " --> pdb=" O VAL A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 263 removed outlier: 3.881A pdb=" N CYS A 263 " --> pdb=" O GLY A 260 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 260 through 263' Processing helix chain 'A' and resid 264 through 278 removed outlier: 3.710A pdb=" N TYR A 271 " --> pdb=" O ALA A 267 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ARG A 273 " --> pdb=" O LEU A 269 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLU A 278 " --> pdb=" O THR A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 348 Processing helix chain 'A' and resid 514 through 517 Processing helix chain 'A' and resid 545 through 550 removed outlier: 3.505A pdb=" N PHE A 549 " --> pdb=" O ARG A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 554 removed outlier: 3.783A pdb=" N LYS A 554 " --> pdb=" O ASN A 551 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 551 through 554' Processing helix chain 'A' and resid 568 through 572 Processing helix chain 'A' and resid 573 through 574 No H-bonds generated for 'chain 'A' and resid 573 through 574' Processing helix chain 'A' and resid 575 through 584 removed outlier: 4.825A pdb=" N PHE A 579 " --> pdb=" O ARG A 575 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLU A 581 " --> pdb=" O THR A 577 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N CYS A 584 " --> pdb=" O SER A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 589 through 596 removed outlier: 4.902A pdb=" N ALA A 594 " --> pdb=" O THR A 591 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N HIS A 596 " --> pdb=" O GLU A 593 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 613 removed outlier: 3.819A pdb=" N CYS A 608 " --> pdb=" O TYR A 604 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG A 609 " --> pdb=" O LEU A 605 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N TYR A 610 " --> pdb=" O ARG A 606 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ASP A 611 " --> pdb=" O ASN A 607 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N CYS A 613 " --> pdb=" O ARG A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 617 through 623 removed outlier: 3.720A pdb=" N CYS A 621 " --> pdb=" O ASP A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 635 removed outlier: 3.657A pdb=" N ALA A 632 " --> pdb=" O SER A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 668 through 674 removed outlier: 4.235A pdb=" N LEU A 672 " --> pdb=" O THR A 668 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N SER A 673 " --> pdb=" O CYS A 669 " (cutoff:3.500A) Processing helix chain 'F' and resid 1017 through 1023 removed outlier: 3.544A pdb=" N PHE F1021 " --> pdb=" O ASP F1017 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ASN F1023 " --> pdb=" O VAL F1019 " (cutoff:3.500A) Processing helix chain 'F' and resid 1049 through 1060 removed outlier: 3.549A pdb=" N MET F1055 " --> pdb=" O MET F1051 " (cutoff:3.500A) Processing helix chain 'F' and resid 1061 through 1065 Processing helix chain 'F' and resid 1068 through 1075 removed outlier: 3.869A pdb=" N LYS F1073 " --> pdb=" O GLN F1069 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LEU F1074 " --> pdb=" O ASP F1070 " (cutoff:3.500A) Processing helix chain 'F' and resid 1077 through 1091 removed outlier: 3.625A pdb=" N VAL F1083 " --> pdb=" O PRO F1079 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N CYS F1084 " --> pdb=" O TYR F1080 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N THR F1088 " --> pdb=" O CYS F1084 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N CYS F1089 " --> pdb=" O ILE F1085 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER F1090 " --> pdb=" O TYR F1086 " (cutoff:3.500A) Processing helix chain 'F' and resid 1097 through 1114 removed outlier: 5.312A pdb=" N THR F1103 " --> pdb=" O CYS F1099 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ILE F1104 " --> pdb=" O PHE F1100 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA F1105 " --> pdb=" O CYS F1101 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N VAL F1110 " --> pdb=" O ALA F1106 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N HIS F1114 " --> pdb=" O VAL F1110 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 118 removed outlier: 3.923A pdb=" N GLY B 117 " --> pdb=" O ALA B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 191 removed outlier: 3.505A pdb=" N TRP B 191 " --> pdb=" O PHE B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 212 removed outlier: 3.758A pdb=" N ASN B 211 " --> pdb=" O SER B 208 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE B 212 " --> pdb=" O SER B 209 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 208 through 212' Processing helix chain 'B' and resid 216 through 221 removed outlier: 3.758A pdb=" N LEU B 221 " --> pdb=" O MET B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 231 removed outlier: 4.279A pdb=" N CYS B 225 " --> pdb=" O LEU B 221 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N LEU B 228 " --> pdb=" O GLN B 224 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N LYS B 229 " --> pdb=" O CYS B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 235 Processing helix chain 'B' and resid 243 through 251 removed outlier: 3.585A pdb=" N GLU B 251 " --> pdb=" O VAL B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 263 removed outlier: 3.881A pdb=" N CYS B 263 " --> pdb=" O GLY B 260 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 260 through 263' Processing helix chain 'B' and resid 264 through 278 removed outlier: 3.710A pdb=" N TYR B 271 " --> pdb=" O ALA B 267 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ARG B 273 " --> pdb=" O LEU B 269 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLU B 278 " --> pdb=" O THR B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 348 Processing helix chain 'B' and resid 514 through 517 Processing helix chain 'B' and resid 545 through 550 removed outlier: 3.506A pdb=" N PHE B 549 " --> pdb=" O ARG B 545 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 554 removed outlier: 3.782A pdb=" N LYS B 554 " --> pdb=" O ASN B 551 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 551 through 554' Processing helix chain 'B' and resid 568 through 572 Processing helix chain 'B' and resid 573 through 574 No H-bonds generated for 'chain 'B' and resid 573 through 574' Processing helix chain 'B' and resid 575 through 584 removed outlier: 4.825A pdb=" N PHE B 579 " --> pdb=" O ARG B 575 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLU B 581 " --> pdb=" O THR B 577 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N CYS B 584 " --> pdb=" O SER B 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 589 through 596 removed outlier: 4.903A pdb=" N ALA B 594 " --> pdb=" O THR B 591 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N HIS B 596 " --> pdb=" O GLU B 593 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 613 removed outlier: 3.820A pdb=" N CYS B 608 " --> pdb=" O TYR B 604 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG B 609 " --> pdb=" O LEU B 605 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N TYR B 610 " --> pdb=" O ARG B 606 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ASP B 611 " --> pdb=" O ASN B 607 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N CYS B 613 " --> pdb=" O ARG B 609 " (cutoff:3.500A) Processing helix chain 'B' and resid 617 through 623 removed outlier: 3.721A pdb=" N CYS B 621 " --> pdb=" O ASP B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 635 removed outlier: 3.655A pdb=" N ALA B 632 " --> pdb=" O SER B 628 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 674 removed outlier: 4.234A pdb=" N LEU B 672 " --> pdb=" O THR B 668 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N SER B 673 " --> pdb=" O CYS B 669 " (cutoff:3.500A) Processing helix chain 'H' and resid 1017 through 1023 removed outlier: 3.545A pdb=" N PHE H1021 " --> pdb=" O ASP H1017 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ASN H1023 " --> pdb=" O VAL H1019 " (cutoff:3.500A) Processing helix chain 'H' and resid 1049 through 1060 removed outlier: 3.548A pdb=" N MET H1055 " --> pdb=" O MET H1051 " (cutoff:3.500A) Processing helix chain 'H' and resid 1061 through 1065 Processing helix chain 'H' and resid 1068 through 1075 removed outlier: 3.869A pdb=" N LYS H1073 " --> pdb=" O GLN H1069 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LEU H1074 " --> pdb=" O ASP H1070 " (cutoff:3.500A) Processing helix chain 'H' and resid 1077 through 1091 removed outlier: 3.626A pdb=" N VAL H1083 " --> pdb=" O PRO H1079 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N CYS H1084 " --> pdb=" O TYR H1080 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR H1088 " --> pdb=" O CYS H1084 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N CYS H1089 " --> pdb=" O ILE H1085 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER H1090 " --> pdb=" O TYR H1086 " (cutoff:3.500A) Processing helix chain 'H' and resid 1097 through 1114 removed outlier: 5.312A pdb=" N THR H1103 " --> pdb=" O CYS H1099 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ILE H1104 " --> pdb=" O PHE H1100 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA H1105 " --> pdb=" O CYS H1101 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N VAL H1110 " --> pdb=" O ALA H1106 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N HIS H1114 " --> pdb=" O VAL H1110 " (cutoff:3.500A) Processing helix chain 'E' and resid 114 through 118 removed outlier: 3.923A pdb=" N GLY E 117 " --> pdb=" O ALA E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 185 through 191 removed outlier: 3.505A pdb=" N TRP E 191 " --> pdb=" O PHE E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 208 through 212 removed outlier: 3.759A pdb=" N ASN E 211 " --> pdb=" O SER E 208 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE E 212 " --> pdb=" O SER E 209 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 208 through 212' Processing helix chain 'E' and resid 216 through 221 removed outlier: 3.757A pdb=" N LEU E 221 " --> pdb=" O MET E 217 " (cutoff:3.500A) Processing helix chain 'E' and resid 221 through 231 removed outlier: 4.278A pdb=" N CYS E 225 " --> pdb=" O LEU E 221 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N LEU E 228 " --> pdb=" O GLN E 224 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N LYS E 229 " --> pdb=" O CYS E 225 " (cutoff:3.500A) Processing helix chain 'E' and resid 232 through 235 Processing helix chain 'E' and resid 243 through 251 removed outlier: 3.585A pdb=" N GLU E 251 " --> pdb=" O VAL E 247 " (cutoff:3.500A) Processing helix chain 'E' and resid 260 through 263 removed outlier: 3.881A pdb=" N CYS E 263 " --> pdb=" O GLY E 260 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 260 through 263' Processing helix chain 'E' and resid 264 through 278 removed outlier: 3.710A pdb=" N TYR E 271 " --> pdb=" O ALA E 267 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ARG E 273 " --> pdb=" O LEU E 269 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLU E 278 " --> pdb=" O THR E 274 " (cutoff:3.500A) Processing helix chain 'E' and resid 344 through 348 Processing helix chain 'E' and resid 514 through 517 Processing helix chain 'E' and resid 545 through 550 removed outlier: 3.506A pdb=" N PHE E 549 " --> pdb=" O ARG E 545 " (cutoff:3.500A) Processing helix chain 'E' and resid 551 through 554 removed outlier: 3.782A pdb=" N LYS E 554 " --> pdb=" O ASN E 551 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 551 through 554' Processing helix chain 'E' and resid 568 through 572 Processing helix chain 'E' and resid 573 through 574 No H-bonds generated for 'chain 'E' and resid 573 through 574' Processing helix chain 'E' and resid 575 through 584 removed outlier: 4.826A pdb=" N PHE E 579 " --> pdb=" O ARG E 575 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLU E 581 " --> pdb=" O THR E 577 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N CYS E 584 " --> pdb=" O SER E 580 " (cutoff:3.500A) Processing helix chain 'E' and resid 589 through 596 removed outlier: 4.902A pdb=" N ALA E 594 " --> pdb=" O THR E 591 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N HIS E 596 " --> pdb=" O GLU E 593 " (cutoff:3.500A) Processing helix chain 'E' and resid 601 through 613 removed outlier: 3.819A pdb=" N CYS E 608 " --> pdb=" O TYR E 604 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG E 609 " --> pdb=" O LEU E 605 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N TYR E 610 " --> pdb=" O ARG E 606 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASP E 611 " --> pdb=" O ASN E 607 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N CYS E 613 " --> pdb=" O ARG E 609 " (cutoff:3.500A) Processing helix chain 'E' and resid 617 through 623 removed outlier: 3.721A pdb=" N CYS E 621 " --> pdb=" O ASP E 617 " (cutoff:3.500A) Processing helix chain 'E' and resid 625 through 635 removed outlier: 3.656A pdb=" N ALA E 632 " --> pdb=" O SER E 628 " (cutoff:3.500A) Processing helix chain 'E' and resid 668 through 674 removed outlier: 4.233A pdb=" N LEU E 672 " --> pdb=" O THR E 668 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N SER E 673 " --> pdb=" O CYS E 669 " (cutoff:3.500A) Processing helix chain 'G' and resid 114 through 118 removed outlier: 3.923A pdb=" N GLY G 117 " --> pdb=" O ALA G 114 " (cutoff:3.500A) Processing helix chain 'G' and resid 185 through 191 removed outlier: 3.504A pdb=" N TRP G 191 " --> pdb=" O PHE G 187 " (cutoff:3.500A) Processing helix chain 'G' and resid 208 through 212 removed outlier: 3.758A pdb=" N ASN G 211 " --> pdb=" O SER G 208 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE G 212 " --> pdb=" O SER G 209 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 208 through 212' Processing helix chain 'G' and resid 216 through 221 removed outlier: 3.759A pdb=" N LEU G 221 " --> pdb=" O MET G 217 " (cutoff:3.500A) Processing helix chain 'G' and resid 221 through 231 removed outlier: 4.278A pdb=" N CYS G 225 " --> pdb=" O LEU G 221 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N LEU G 228 " --> pdb=" O GLN G 224 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N LYS G 229 " --> pdb=" O CYS G 225 " (cutoff:3.500A) Processing helix chain 'G' and resid 232 through 235 Processing helix chain 'G' and resid 243 through 251 removed outlier: 3.586A pdb=" N GLU G 251 " --> pdb=" O VAL G 247 " (cutoff:3.500A) Processing helix chain 'G' and resid 260 through 263 removed outlier: 3.881A pdb=" N CYS G 263 " --> pdb=" O GLY G 260 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 260 through 263' Processing helix chain 'G' and resid 264 through 278 removed outlier: 3.710A pdb=" N TYR G 271 " --> pdb=" O ALA G 267 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ARG G 273 " --> pdb=" O LEU G 269 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLU G 278 " --> pdb=" O THR G 274 " (cutoff:3.500A) Processing helix chain 'G' and resid 344 through 348 Processing helix chain 'G' and resid 514 through 517 Processing helix chain 'G' and resid 545 through 550 removed outlier: 3.505A pdb=" N PHE G 549 " --> pdb=" O ARG G 545 " (cutoff:3.500A) Processing helix chain 'G' and resid 551 through 554 removed outlier: 3.783A pdb=" N LYS G 554 " --> pdb=" O ASN G 551 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 551 through 554' Processing helix chain 'G' and resid 568 through 572 Processing helix chain 'G' and resid 573 through 574 No H-bonds generated for 'chain 'G' and resid 573 through 574' Processing helix chain 'G' and resid 575 through 584 removed outlier: 4.827A pdb=" N PHE G 579 " --> pdb=" O ARG G 575 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLU G 581 " --> pdb=" O THR G 577 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N CYS G 584 " --> pdb=" O SER G 580 " (cutoff:3.500A) Processing helix chain 'G' and resid 589 through 596 removed outlier: 4.902A pdb=" N ALA G 594 " --> pdb=" O THR G 591 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N HIS G 596 " --> pdb=" O GLU G 593 " (cutoff:3.500A) Processing helix chain 'G' and resid 601 through 613 removed outlier: 3.819A pdb=" N CYS G 608 " --> pdb=" O TYR G 604 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG G 609 " --> pdb=" O LEU G 605 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N TYR G 610 " --> pdb=" O ARG G 606 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASP G 611 " --> pdb=" O ASN G 607 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N CYS G 613 " --> pdb=" O ARG G 609 " (cutoff:3.500A) Processing helix chain 'G' and resid 617 through 623 removed outlier: 3.721A pdb=" N CYS G 621 " --> pdb=" O ASP G 617 " (cutoff:3.500A) Processing helix chain 'G' and resid 625 through 635 removed outlier: 3.655A pdb=" N ALA G 632 " --> pdb=" O SER G 628 " (cutoff:3.500A) Processing helix chain 'G' and resid 668 through 674 removed outlier: 4.233A pdb=" N LEU G 672 " --> pdb=" O THR G 668 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N SER G 673 " --> pdb=" O CYS G 669 " (cutoff:3.500A) Processing helix chain 'C' and resid 1017 through 1023 removed outlier: 3.545A pdb=" N PHE C1021 " --> pdb=" O ASP C1017 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ASN C1023 " --> pdb=" O VAL C1019 " (cutoff:3.500A) Processing helix chain 'C' and resid 1049 through 1060 removed outlier: 3.548A pdb=" N MET C1055 " --> pdb=" O MET C1051 " (cutoff:3.500A) Processing helix chain 'C' and resid 1061 through 1065 Processing helix chain 'C' and resid 1068 through 1075 removed outlier: 3.868A pdb=" N LYS C1073 " --> pdb=" O GLN C1069 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N LEU C1074 " --> pdb=" O ASP C1070 " (cutoff:3.500A) Processing helix chain 'C' and resid 1077 through 1091 removed outlier: 3.626A pdb=" N VAL C1083 " --> pdb=" O PRO C1079 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N CYS C1084 " --> pdb=" O TYR C1080 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N THR C1088 " --> pdb=" O CYS C1084 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N CYS C1089 " --> pdb=" O ILE C1085 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER C1090 " --> pdb=" O TYR C1086 " (cutoff:3.500A) Processing helix chain 'C' and resid 1097 through 1114 removed outlier: 5.312A pdb=" N THR C1103 " --> pdb=" O CYS C1099 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ILE C1104 " --> pdb=" O PHE C1100 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA C1105 " --> pdb=" O CYS C1101 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N VAL C1110 " --> pdb=" O ALA C1106 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N HIS C1114 " --> pdb=" O VAL C1110 " (cutoff:3.500A) Processing helix chain 'D' and resid 1017 through 1023 removed outlier: 3.545A pdb=" N PHE D1021 " --> pdb=" O ASP D1017 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ASN D1023 " --> pdb=" O VAL D1019 " (cutoff:3.500A) Processing helix chain 'D' and resid 1049 through 1060 removed outlier: 3.548A pdb=" N MET D1055 " --> pdb=" O MET D1051 " (cutoff:3.500A) Processing helix chain 'D' and resid 1061 through 1065 Processing helix chain 'D' and resid 1068 through 1075 removed outlier: 3.869A pdb=" N LYS D1073 " --> pdb=" O GLN D1069 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N LEU D1074 " --> pdb=" O ASP D1070 " (cutoff:3.500A) Processing helix chain 'D' and resid 1077 through 1091 removed outlier: 3.626A pdb=" N VAL D1083 " --> pdb=" O PRO D1079 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N CYS D1084 " --> pdb=" O TYR D1080 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N THR D1088 " --> pdb=" O CYS D1084 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N CYS D1089 " --> pdb=" O ILE D1085 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER D1090 " --> pdb=" O TYR D1086 " (cutoff:3.500A) Processing helix chain 'D' and resid 1097 through 1114 removed outlier: 5.311A pdb=" N THR D1103 " --> pdb=" O CYS D1099 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ILE D1104 " --> pdb=" O PHE D1100 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA D1105 " --> pdb=" O CYS D1101 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N VAL D1110 " --> pdb=" O ALA D1106 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N HIS D1114 " --> pdb=" O VAL D1110 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 37 Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 44 removed outlier: 3.767A pdb=" N TYR A 51 " --> pdb=" O VAL A 43 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 58 through 62 removed outlier: 6.909A pdb=" N ILE A 72 " --> pdb=" O LEU A 61 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 350 through 352 Processing sheet with id=AA5, first strand: chain 'A' and resid 362 through 364 Processing sheet with id=AA6, first strand: chain 'A' and resid 389 through 391 removed outlier: 3.512A pdb=" N PHE A 404 " --> pdb=" O PHE A 396 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 411 through 416 removed outlier: 5.472A pdb=" N GLN A 411 " --> pdb=" O THR A 429 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N THR A 429 " --> pdb=" O GLN A 411 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N LEU A 413 " --> pdb=" O ILE A 427 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N ILE A 427 " --> pdb=" O LEU A 413 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA A 415 " --> pdb=" O ILE A 425 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N SER A 443 " --> pdb=" O GLU A 428 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N VAL A 430 " --> pdb=" O THR A 441 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N THR A 441 " --> pdb=" O VAL A 430 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LEU A 448 " --> pdb=" O SER A 454 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER A 454 " --> pdb=" O LEU A 448 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 481 through 484 Processing sheet with id=AA9, first strand: chain 'A' and resid 498 through 499 removed outlier: 3.572A pdb=" N LYS A 511 " --> pdb=" O GLN A 499 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 536 through 537 removed outlier: 4.122A pdb=" N LEU A 541 " --> pdb=" O THR A 537 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 657 through 662 removed outlier: 3.893A pdb=" N CYS A 661 " --> pdb=" O LEU A 684 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N LEU A 684 " --> pdb=" O CYS A 661 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 694 through 695 Processing sheet with id=AB4, first strand: chain 'A' and resid 709 through 711 Processing sheet with id=AB5, first strand: chain 'A' and resid 720 through 722 removed outlier: 4.225A pdb=" N ASP A 720 " --> pdb=" O CYS A 731 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N CYS A 731 " --> pdb=" O ASP A 720 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N MET A 728 " --> pdb=" O THR A 739 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 772 through 773 Processing sheet with id=AB7, first strand: chain 'F' and resid 841 through 844 removed outlier: 3.596A pdb=" N VAL F 850 " --> pdb=" O ASN F 857 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 875 through 876 Processing sheet with id=AB9, first strand: chain 'F' and resid 890 through 891 Processing sheet with id=AC1, first strand: chain 'F' and resid 894 through 895 Processing sheet with id=AC2, first strand: chain 'F' and resid 925 through 927 removed outlier: 3.606A pdb=" N ILE F 934 " --> pdb=" O ILE F 927 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N GLU F 933 " --> pdb=" O LYS F 944 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLU F 940 " --> pdb=" O PHE F 937 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 954 through 956 removed outlier: 3.788A pdb=" N GLU F 954 " --> pdb=" O LEU F 965 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU F 966 " --> pdb=" O LEU F 970 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N LEU F 970 " --> pdb=" O LEU F 966 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 1144 through 1146 Processing sheet with id=AC5, first strand: chain 'F' and resid 1150 through 1151 Processing sheet with id=AC6, first strand: chain 'F' and resid 1182 through 1183 Processing sheet with id=AC7, first strand: chain 'B' and resid 35 through 37 Processing sheet with id=AC8, first strand: chain 'B' and resid 42 through 44 removed outlier: 3.767A pdb=" N TYR B 51 " --> pdb=" O VAL B 43 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 58 through 62 removed outlier: 6.909A pdb=" N ILE B 72 " --> pdb=" O LEU B 61 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 103 through 104 Processing sheet with id=AD2, first strand: chain 'B' and resid 350 through 352 Processing sheet with id=AD3, first strand: chain 'B' and resid 362 through 364 Processing sheet with id=AD4, first strand: chain 'B' and resid 389 through 391 removed outlier: 3.514A pdb=" N PHE B 404 " --> pdb=" O PHE B 396 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 411 through 416 removed outlier: 5.473A pdb=" N GLN B 411 " --> pdb=" O THR B 429 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N THR B 429 " --> pdb=" O GLN B 411 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N LEU B 413 " --> pdb=" O ILE B 427 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N ILE B 427 " --> pdb=" O LEU B 413 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA B 415 " --> pdb=" O ILE B 425 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N SER B 443 " --> pdb=" O GLU B 428 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N VAL B 430 " --> pdb=" O THR B 441 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N THR B 441 " --> pdb=" O VAL B 430 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LEU B 448 " --> pdb=" O SER B 454 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER B 454 " --> pdb=" O LEU B 448 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 481 through 484 Processing sheet with id=AD7, first strand: chain 'B' and resid 498 through 499 removed outlier: 3.571A pdb=" N LYS B 511 " --> pdb=" O GLN B 499 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 536 through 537 removed outlier: 4.123A pdb=" N LEU B 541 " --> pdb=" O THR B 537 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 657 through 662 removed outlier: 3.893A pdb=" N CYS B 661 " --> pdb=" O LEU B 684 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N LEU B 684 " --> pdb=" O CYS B 661 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 694 through 695 Processing sheet with id=AE2, first strand: chain 'B' and resid 709 through 711 Processing sheet with id=AE3, first strand: chain 'B' and resid 720 through 722 removed outlier: 4.226A pdb=" N ASP B 720 " --> pdb=" O CYS B 731 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N CYS B 731 " --> pdb=" O ASP B 720 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N MET B 728 " --> pdb=" O THR B 739 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 772 through 773 Processing sheet with id=AE5, first strand: chain 'H' and resid 841 through 844 Processing sheet with id=AE6, first strand: chain 'H' and resid 875 through 876 Processing sheet with id=AE7, first strand: chain 'H' and resid 890 through 891 Processing sheet with id=AE8, first strand: chain 'H' and resid 894 through 895 Processing sheet with id=AE9, first strand: chain 'H' and resid 925 through 927 removed outlier: 3.606A pdb=" N ILE H 934 " --> pdb=" O ILE H 927 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N GLU H 933 " --> pdb=" O LYS H 944 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLU H 940 " --> pdb=" O PHE H 937 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'H' and resid 954 through 956 removed outlier: 3.788A pdb=" N GLU H 954 " --> pdb=" O LEU H 965 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU H 966 " --> pdb=" O LEU H 970 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N LEU H 970 " --> pdb=" O LEU H 966 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'H' and resid 1144 through 1146 Processing sheet with id=AF3, first strand: chain 'H' and resid 1150 through 1151 Processing sheet with id=AF4, first strand: chain 'H' and resid 1182 through 1183 Processing sheet with id=AF5, first strand: chain 'E' and resid 35 through 37 removed outlier: 3.500A pdb=" N TYR E 119 " --> pdb=" O SER E 130 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'E' and resid 42 through 44 removed outlier: 3.766A pdb=" N TYR E 51 " --> pdb=" O VAL E 43 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'E' and resid 58 through 62 removed outlier: 6.909A pdb=" N ILE E 72 " --> pdb=" O LEU E 61 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'E' and resid 350 through 352 Processing sheet with id=AF9, first strand: chain 'E' and resid 362 through 364 Processing sheet with id=AG1, first strand: chain 'E' and resid 389 through 391 removed outlier: 3.514A pdb=" N PHE E 404 " --> pdb=" O PHE E 396 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'E' and resid 411 through 416 removed outlier: 5.472A pdb=" N GLN E 411 " --> pdb=" O THR E 429 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N THR E 429 " --> pdb=" O GLN E 411 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N LEU E 413 " --> pdb=" O ILE E 427 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N ILE E 427 " --> pdb=" O LEU E 413 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA E 415 " --> pdb=" O ILE E 425 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N SER E 443 " --> pdb=" O GLU E 428 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N VAL E 430 " --> pdb=" O THR E 441 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N THR E 441 " --> pdb=" O VAL E 430 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LEU E 448 " --> pdb=" O SER E 454 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER E 454 " --> pdb=" O LEU E 448 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'E' and resid 481 through 484 Processing sheet with id=AG4, first strand: chain 'E' and resid 498 through 499 removed outlier: 3.571A pdb=" N LYS E 511 " --> pdb=" O GLN E 499 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'E' and resid 536 through 537 removed outlier: 4.122A pdb=" N LEU E 541 " --> pdb=" O THR E 537 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'E' and resid 657 through 662 removed outlier: 3.893A pdb=" N CYS E 661 " --> pdb=" O LEU E 684 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N LEU E 684 " --> pdb=" O CYS E 661 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'E' and resid 694 through 695 Processing sheet with id=AG8, first strand: chain 'E' and resid 709 through 711 Processing sheet with id=AG9, first strand: chain 'E' and resid 720 through 722 removed outlier: 4.226A pdb=" N ASP E 720 " --> pdb=" O CYS E 731 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N CYS E 731 " --> pdb=" O ASP E 720 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N MET E 728 " --> pdb=" O THR E 739 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'G' and resid 35 through 37 Processing sheet with id=AH2, first strand: chain 'G' and resid 42 through 44 removed outlier: 3.767A pdb=" N TYR G 51 " --> pdb=" O VAL G 43 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'G' and resid 58 through 62 removed outlier: 6.908A pdb=" N ILE G 72 " --> pdb=" O LEU G 61 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'G' and resid 103 through 104 Processing sheet with id=AH5, first strand: chain 'G' and resid 350 through 352 Processing sheet with id=AH6, first strand: chain 'G' and resid 362 through 364 Processing sheet with id=AH7, first strand: chain 'G' and resid 389 through 391 removed outlier: 3.513A pdb=" N PHE G 404 " --> pdb=" O PHE G 396 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'G' and resid 411 through 416 removed outlier: 5.472A pdb=" N GLN G 411 " --> pdb=" O THR G 429 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N THR G 429 " --> pdb=" O GLN G 411 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N LEU G 413 " --> pdb=" O ILE G 427 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N ILE G 427 " --> pdb=" O LEU G 413 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA G 415 " --> pdb=" O ILE G 425 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N SER G 443 " --> pdb=" O GLU G 428 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N VAL G 430 " --> pdb=" O THR G 441 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N THR G 441 " --> pdb=" O VAL G 430 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LEU G 448 " --> pdb=" O SER G 454 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER G 454 " --> pdb=" O LEU G 448 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'G' and resid 481 through 484 Processing sheet with id=AI1, first strand: chain 'G' and resid 498 through 499 removed outlier: 3.571A pdb=" N LYS G 511 " --> pdb=" O GLN G 499 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'G' and resid 536 through 537 removed outlier: 4.122A pdb=" N LEU G 541 " --> pdb=" O THR G 537 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'G' and resid 657 through 662 removed outlier: 3.892A pdb=" N CYS G 661 " --> pdb=" O LEU G 684 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N LEU G 684 " --> pdb=" O CYS G 661 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'G' and resid 694 through 695 Processing sheet with id=AI5, first strand: chain 'G' and resid 709 through 711 Processing sheet with id=AI6, first strand: chain 'G' and resid 720 through 722 removed outlier: 4.226A pdb=" N ASP G 720 " --> pdb=" O CYS G 731 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N CYS G 731 " --> pdb=" O ASP G 720 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N MET G 728 " --> pdb=" O THR G 739 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'C' and resid 772 through 773 Processing sheet with id=AI8, first strand: chain 'C' and resid 841 through 844 removed outlier: 3.750A pdb=" N VAL C 850 " --> pdb=" O ASN C 857 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'C' and resid 875 through 876 Processing sheet with id=AJ1, first strand: chain 'C' and resid 890 through 891 Processing sheet with id=AJ2, first strand: chain 'C' and resid 894 through 895 Processing sheet with id=AJ3, first strand: chain 'C' and resid 925 through 927 removed outlier: 3.606A pdb=" N ILE C 934 " --> pdb=" O ILE C 927 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N GLU C 933 " --> pdb=" O LYS C 944 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLU C 940 " --> pdb=" O PHE C 937 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'C' and resid 954 through 956 removed outlier: 3.788A pdb=" N GLU C 954 " --> pdb=" O LEU C 965 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU C 966 " --> pdb=" O LEU C 970 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N LEU C 970 " --> pdb=" O LEU C 966 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'C' and resid 1144 through 1146 Processing sheet with id=AJ6, first strand: chain 'C' and resid 1150 through 1151 Processing sheet with id=AJ7, first strand: chain 'C' and resid 1182 through 1183 Processing sheet with id=AJ8, first strand: chain 'D' and resid 772 through 773 Processing sheet with id=AJ9, first strand: chain 'D' and resid 841 through 844 Processing sheet with id=AK1, first strand: chain 'D' and resid 875 through 876 Processing sheet with id=AK2, first strand: chain 'D' and resid 890 through 891 Processing sheet with id=AK3, first strand: chain 'D' and resid 894 through 895 Processing sheet with id=AK4, first strand: chain 'D' and resid 925 through 927 removed outlier: 3.606A pdb=" N ILE D 934 " --> pdb=" O ILE D 927 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N GLU D 933 " --> pdb=" O LYS D 944 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLU D 940 " --> pdb=" O PHE D 937 " (cutoff:3.500A) Processing sheet with id=AK5, first strand: chain 'D' and resid 954 through 956 removed outlier: 3.788A pdb=" N GLU D 954 " --> pdb=" O LEU D 965 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU D 966 " --> pdb=" O LEU D 970 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N LEU D 970 " --> pdb=" O LEU D 966 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'D' and resid 1144 through 1146 Processing sheet with id=AK7, first strand: chain 'D' and resid 1150 through 1151 Processing sheet with id=AK8, first strand: chain 'D' and resid 1182 through 1183 731 hydrogen bonds defined for protein. 1748 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.29 Time building geometry restraints manager: 4.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 12297 1.34 - 1.47: 8552 1.47 - 1.59: 15875 1.59 - 1.71: 0 1.71 - 1.84: 656 Bond restraints: 37380 Sorted by residual: bond pdb=" N VAL E 98 " pdb=" CA VAL E 98 " ideal model delta sigma weight residual 1.457 1.493 -0.037 1.07e-02 8.73e+03 1.18e+01 bond pdb=" C SER H1217 " pdb=" N ASP H1218 " ideal model delta sigma weight residual 1.331 1.384 -0.053 1.63e-02 3.76e+03 1.06e+01 bond pdb=" C SER F1217 " pdb=" N ASP F1218 " ideal model delta sigma weight residual 1.331 1.384 -0.052 1.63e-02 3.76e+03 1.03e+01 bond pdb=" N VAL D1155 " pdb=" CA VAL D1155 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.15e-02 7.56e+03 1.02e+01 bond pdb=" C SER C1217 " pdb=" N ASP C1218 " ideal model delta sigma weight residual 1.331 1.383 -0.052 1.63e-02 3.76e+03 1.02e+01 ... (remaining 37375 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.16: 50157 4.16 - 8.33: 513 8.33 - 12.49: 34 12.49 - 16.66: 16 16.66 - 20.82: 4 Bond angle restraints: 50724 Sorted by residual: angle pdb=" C SER C1217 " pdb=" N ASP C1218 " pdb=" CA ASP C1218 " ideal model delta sigma weight residual 121.61 142.43 -20.82 1.39e+00 5.18e-01 2.24e+02 angle pdb=" C SER D1217 " pdb=" N ASP D1218 " pdb=" CA ASP D1218 " ideal model delta sigma weight residual 121.61 142.40 -20.79 1.39e+00 5.18e-01 2.24e+02 angle pdb=" C SER F1217 " pdb=" N ASP F1218 " pdb=" CA ASP F1218 " ideal model delta sigma weight residual 121.61 142.39 -20.78 1.39e+00 5.18e-01 2.24e+02 angle pdb=" C SER H1217 " pdb=" N ASP H1218 " pdb=" CA ASP H1218 " ideal model delta sigma weight residual 121.61 142.36 -20.75 1.39e+00 5.18e-01 2.23e+02 angle pdb=" C GLU C 784 " pdb=" N GLY C 785 " pdb=" CA GLY C 785 " ideal model delta sigma weight residual 121.41 137.98 -16.57 1.96e+00 2.60e-01 7.15e+01 ... (remaining 50719 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.18: 21823 17.18 - 34.36: 1174 34.36 - 51.53: 319 51.53 - 68.71: 80 68.71 - 85.89: 26 Dihedral angle restraints: 23422 sinusoidal: 9730 harmonic: 13692 Sorted by residual: dihedral pdb=" CB CYS A 312 " pdb=" SG CYS A 312 " pdb=" SG CYS A 348 " pdb=" CB CYS A 348 " ideal model delta sinusoidal sigma weight residual 93.00 174.00 -81.00 1 1.00e+01 1.00e-02 8.10e+01 dihedral pdb=" CB CYS E 312 " pdb=" SG CYS E 312 " pdb=" SG CYS E 348 " pdb=" CB CYS E 348 " ideal model delta sinusoidal sigma weight residual 93.00 173.98 -80.98 1 1.00e+01 1.00e-02 8.10e+01 dihedral pdb=" CB CYS G 312 " pdb=" SG CYS G 312 " pdb=" SG CYS G 348 " pdb=" CB CYS G 348 " ideal model delta sinusoidal sigma weight residual 93.00 173.97 -80.97 1 1.00e+01 1.00e-02 8.09e+01 ... (remaining 23419 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.308: 5490 0.308 - 0.616: 39 0.616 - 0.924: 18 0.924 - 1.232: 4 1.232 - 1.540: 1 Chirality restraints: 5552 Sorted by residual: chirality pdb=" C1 NAG E 804 " pdb=" ND2 ASN E 99 " pdb=" C2 NAG E 804 " pdb=" O5 NAG E 804 " both_signs ideal model delta sigma weight residual False -2.40 -0.86 -1.54 2.00e-01 2.50e+01 5.93e+01 chirality pdb=" CB VAL H 815 " pdb=" CA VAL H 815 " pdb=" CG1 VAL H 815 " pdb=" CG2 VAL H 815 " both_signs ideal model delta sigma weight residual False -2.63 -1.63 -1.00 2.00e-01 2.50e+01 2.50e+01 chirality pdb=" CB VAL F 815 " pdb=" CA VAL F 815 " pdb=" CG1 VAL F 815 " pdb=" CG2 VAL F 815 " both_signs ideal model delta sigma weight residual False -2.63 -1.63 -1.00 2.00e-01 2.50e+01 2.49e+01 ... (remaining 5549 not shown) Planarity restraints: 6748 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN G 99 " -0.136 2.00e-02 2.50e+03 1.87e-01 4.39e+02 pdb=" CG ASN G 99 " 0.057 2.00e-02 2.50e+03 pdb=" OD1 ASN G 99 " -0.058 2.00e-02 2.50e+03 pdb=" ND2 ASN G 99 " 0.334 2.00e-02 2.50e+03 pdb=" C1 NAG G 804 " -0.197 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 804 " 0.158 2.00e-02 2.50e+03 1.30e-01 2.12e+02 pdb=" C7 NAG B 804 " -0.042 2.00e-02 2.50e+03 pdb=" C8 NAG B 804 " 0.116 2.00e-02 2.50e+03 pdb=" N2 NAG B 804 " -0.210 2.00e-02 2.50e+03 pdb=" O7 NAG B 804 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG G 804 " -0.044 2.00e-02 2.50e+03 3.65e-02 1.66e+01 pdb=" C7 NAG G 804 " 0.012 2.00e-02 2.50e+03 pdb=" C8 NAG G 804 " -0.034 2.00e-02 2.50e+03 pdb=" N2 NAG G 804 " 0.058 2.00e-02 2.50e+03 pdb=" O7 NAG G 804 " 0.008 2.00e-02 2.50e+03 ... (remaining 6745 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 420 2.59 - 3.17: 33032 3.17 - 3.75: 53602 3.75 - 4.32: 74307 4.32 - 4.90: 121259 Nonbonded interactions: 282620 Sorted by model distance: nonbonded pdb=" O GLU H 888 " pdb=" OH TYR G 119 " model vdw 2.016 3.040 nonbonded pdb=" O SER C1093 " pdb=" OG SER D1093 " model vdw 2.031 3.040 nonbonded pdb=" OG SER H1009 " pdb=" OD1 ASN H1011 " model vdw 2.040 3.040 nonbonded pdb=" OG SER F1009 " pdb=" OD1 ASN F1011 " model vdw 2.041 3.040 nonbonded pdb=" OG SER D1009 " pdb=" OD1 ASN D1011 " model vdw 2.041 3.040 ... (remaining 282615 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'E' selection = chain 'G' } ncs_group { reference = (chain 'C' and (resid 764 through 1052 or resid 1054 through 1305)) selection = (chain 'D' and (resid 764 through 1052 or resid 1054 through 1305)) selection = (chain 'F' and (resid 764 through 1052 or resid 1054 through 1305)) selection = (chain 'H' and (resid 764 through 1052 or resid 1054 through 1305)) } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.050 Extract box with map and model: 0.690 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 38.090 Find NCS groups from input model: 0.830 Set up NCS constraints: 0.090 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:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6447 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 : 0.007 0.302 37630 Z= 0.345 Angle : 1.163 34.094 51244 Z= 0.624 Chirality : 0.089 1.540 5552 Planarity : 0.006 0.130 6728 Dihedral : 10.595 85.890 13964 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.17 % Allowed : 11.90 % Favored : 87.93 % Rotamer: Outliers : 0.44 % Allowed : 2.86 % Favored : 96.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -4.63 (0.10), residues: 4744 helix: -4.09 (0.13), residues: 480 sheet: -3.94 (0.14), residues: 832 loop : -2.88 (0.10), residues: 3432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 960 TYR 0.015 0.002 TYR C 988 PHE 0.022 0.002 PHE A 535 TRP 0.017 0.003 TRP F 974 HIS 0.010 0.002 HIS H1047 Details of bonding type rmsd covalent geometry : bond 0.00697 (37380) covalent geometry : angle 1.11262 (50724) SS BOND : bond 0.00620 ( 230) SS BOND : angle 1.67697 ( 460) hydrogen bonds : bond 0.28095 ( 731) hydrogen bonds : angle 10.36900 ( 1748) link_NAG-ASN : bond 0.07999 ( 20) link_NAG-ASN : angle 9.33204 ( 60) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9488 Ramachandran restraints generated. 4744 Oldfield, 0 Emsley, 4744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9488 Ramachandran restraints generated. 4744 Oldfield, 0 Emsley, 4744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1095 residues out of total 4112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 1081 time to evaluate : 1.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 TYR cc_start: 0.6769 (m-10) cc_final: 0.6468 (m-80) REVERT: A 222 TRP cc_start: 0.6387 (t60) cc_final: 0.6044 (t60) REVERT: A 320 MET cc_start: 0.4995 (ppp) cc_final: 0.4793 (tmm) REVERT: A 420 ASP cc_start: 0.7285 (p0) cc_final: 0.6974 (p0) REVERT: A 429 THR cc_start: 0.5798 (p) cc_final: 0.4539 (p) REVERT: A 553 TRP cc_start: 0.4951 (m100) cc_final: 0.4745 (m100) REVERT: A 736 MET cc_start: 0.6039 (tpt) cc_final: 0.5710 (tpt) REVERT: F 1142 CYS cc_start: 0.5380 (t) cc_final: 0.4482 (t) REVERT: F 1144 TRP cc_start: 0.6367 (m100) cc_final: 0.6042 (m100) REVERT: F 1210 LYS cc_start: 0.4023 (pttm) cc_final: 0.3668 (tttt) REVERT: B 299 MET cc_start: 0.6893 (mtm) cc_final: 0.6470 (ptp) REVERT: B 680 ASN cc_start: 0.7342 (m-40) cc_final: 0.7054 (p0) REVERT: H 814 MET cc_start: 0.6514 (ttm) cc_final: 0.6272 (ttm) REVERT: H 848 THR cc_start: 0.7383 (t) cc_final: 0.7137 (p) REVERT: H 1151 PRO cc_start: 0.6585 (Cg_exo) cc_final: 0.5659 (Cg_endo) REVERT: E 199 TRP cc_start: 0.5098 (m-90) cc_final: 0.4795 (m-90) REVERT: E 301 TYR cc_start: 0.7640 (t80) cc_final: 0.7359 (t80) REVERT: E 381 ASN cc_start: 0.7653 (p0) cc_final: 0.7227 (t0) REVERT: G 224 GLN cc_start: 0.7277 (mp10) cc_final: 0.6996 (mp10) REVERT: G 283 TYR cc_start: 0.6626 (m-80) cc_final: 0.6424 (m-10) REVERT: G 512 LEU cc_start: 0.6426 (mm) cc_final: 0.5922 (tt) REVERT: G 722 PHE cc_start: 0.5623 (t80) cc_final: 0.5168 (t80) REVERT: C 856 TRP cc_start: 0.5525 (m100) cc_final: 0.4786 (m100) REVERT: C 1146 TYR cc_start: 0.5788 (t80) cc_final: 0.3708 (t80) REVERT: D 830 PHE cc_start: 0.6814 (m-80) cc_final: 0.6182 (m-80) outliers start: 14 outliers final: 3 residues processed: 1089 average time/residue: 0.2474 time to fit residues: 418.3005 Evaluate side-chains 469 residues out of total 4112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 466 time to evaluate : 1.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 1231 ASN Chi-restraints excluded: chain B residue 97 PHE Chi-restraints excluded: chain H residue 1231 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 432 optimal weight: 6.9990 chunk 197 optimal weight: 20.0000 chunk 388 optimal weight: 2.9990 chunk 455 optimal weight: 5.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 0.1980 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 9.9990 chunk 470 optimal weight: 30.0000 overall best weight: 3.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 HIS A 226 GLN A 352 HIS A 566 HIS ** A 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 874 HIS F1013 GLN ** F1128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1221 HIS B 226 GLN B 313 GLN B 411 GLN B 421 HIS B 737 HIS H 852 GLN H1053 GLN B E 322 GLN E 499 GLN G 313 GLN G 401 ASN G 563 GLN ** C 874 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1013 GLN C1053 GLN B C1134 ASN C1174 HIS C1221 HIS D1013 GLN D1134 ASN ** D1174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1221 HIS Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4494 r_free = 0.4494 target = 0.149019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.120599 restraints weight = 109423.031| |-----------------------------------------------------------------------------| r_work (start): 0.4094 rms_B_bonded: 3.91 r_work: 0.3941 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.3941 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3939 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3939 r_free = 0.3939 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3939 r_free = 0.3939 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| r_final: 0.3939 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 moved from start: 0.4011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 37630 Z= 0.190 Angle : 0.854 14.297 51244 Z= 0.429 Chirality : 0.051 0.580 5552 Planarity : 0.006 0.055 6728 Dihedral : 6.441 51.140 5562 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.10 % Favored : 91.88 % Rotamer: Outliers : 2.22 % Allowed : 10.48 % Favored : 87.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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: -3.78 (0.11), residues: 4744 helix: -2.92 (0.17), residues: 580 sheet: -3.26 (0.17), residues: 760 loop : -2.40 (0.10), residues: 3404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C1133 TYR 0.026 0.002 TYR G 126 PHE 0.034 0.003 PHE B 406 TRP 0.027 0.002 TRP A 642 HIS 0.007 0.001 HIS A 95 Details of bonding type rmsd covalent geometry : bond 0.00426 (37380) covalent geometry : angle 0.83075 (50724) SS BOND : bond 0.00514 ( 230) SS BOND : angle 1.71208 ( 460) hydrogen bonds : bond 0.04505 ( 731) hydrogen bonds : angle 6.76286 ( 1748) link_NAG-ASN : bond 0.00614 ( 20) link_NAG-ASN : angle 4.19552 ( 60) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9488 Ramachandran restraints generated. 4744 Oldfield, 0 Emsley, 4744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9488 Ramachandran restraints generated. 4744 Oldfield, 0 Emsley, 4744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 606 residues out of total 4112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 519 time to evaluate : 1.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 ASP cc_start: 0.7283 (t0) cc_final: 0.7073 (t0) REVERT: A 222 TRP cc_start: 0.7514 (t60) cc_final: 0.7091 (t60) REVERT: A 339 GLU cc_start: 0.6990 (tm-30) cc_final: 0.6451 (pm20) REVERT: A 466 MET cc_start: 0.8037 (ptp) cc_final: 0.6703 (tpt) REVERT: A 494 TYR cc_start: 0.7197 (t80) cc_final: 0.6486 (t80) REVERT: A 553 TRP cc_start: 0.5511 (m100) cc_final: 0.5199 (m100) REVERT: A 581 GLU cc_start: 0.7429 (tm-30) cc_final: 0.7170 (tm-30) REVERT: A 722 PHE cc_start: 0.8206 (OUTLIER) cc_final: 0.7222 (m-80) REVERT: A 737 HIS cc_start: 0.4360 (m90) cc_final: 0.4008 (m90) REVERT: A 740 MET cc_start: 0.5177 (mmt) cc_final: 0.4752 (tpt) REVERT: F 935 GLU cc_start: 0.8244 (pp20) cc_final: 0.7996 (pp20) REVERT: F 1210 LYS cc_start: 0.4674 (pttm) cc_final: 0.3779 (tttp) REVERT: B 152 ASP cc_start: 0.7646 (p0) cc_final: 0.7057 (t0) REVERT: B 171 ASP cc_start: 0.6967 (p0) cc_final: 0.6747 (p0) REVERT: B 179 THR cc_start: 0.7681 (p) cc_final: 0.7241 (p) REVERT: B 268 LEU cc_start: 0.7470 (tt) cc_final: 0.7178 (mt) REVERT: B 299 MET cc_start: 0.7478 (mtm) cc_final: 0.6803 (ptp) REVERT: B 475 LEU cc_start: 0.8568 (tt) cc_final: 0.8260 (tt) REVERT: B 576 MET cc_start: 0.8559 (tpp) cc_final: 0.8329 (tpp) REVERT: B 680 ASN cc_start: 0.7554 (m-40) cc_final: 0.6930 (p0) REVERT: H 1211 LYS cc_start: 0.3075 (mptt) cc_final: 0.2709 (mmmt) REVERT: E 301 TYR cc_start: 0.7897 (t80) cc_final: 0.7300 (t80) REVERT: E 373 ARG cc_start: 0.7516 (mmp80) cc_final: 0.6716 (tpp80) REVERT: E 381 ASN cc_start: 0.7972 (p0) cc_final: 0.7618 (t0) REVERT: G 285 TRP cc_start: 0.7247 (p-90) cc_final: 0.6986 (p-90) REVERT: G 421 HIS cc_start: 0.6632 (m-70) cc_final: 0.6294 (m90) REVERT: G 526 ASN cc_start: 0.7770 (m-40) cc_final: 0.7552 (m110) REVERT: G 697 GLU cc_start: 0.6764 (mt-10) cc_final: 0.6374 (pm20) REVERT: C 1035 ARG cc_start: 0.7282 (tpp-160) cc_final: 0.6906 (mmt-90) REVERT: D 883 TYR cc_start: 0.8471 (p90) cc_final: 0.8102 (p90) REVERT: D 961 TYR cc_start: 0.8028 (m-10) cc_final: 0.7804 (m-10) REVERT: D 990 GLU cc_start: 0.7834 (tm-30) cc_final: 0.7558 (tt0) REVERT: D 1055 MET cc_start: 0.6604 (ptm) cc_final: 0.6051 (ptp) outliers start: 87 outliers final: 48 residues processed: 583 average time/residue: 0.2175 time to fit residues: 204.8768 Evaluate side-chains 412 residues out of total 4112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 363 time to evaluate : 1.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain A residue 722 PHE Chi-restraints excluded: chain F residue 789 THR Chi-restraints excluded: chain F residue 870 ILE Chi-restraints excluded: chain F residue 1019 VAL Chi-restraints excluded: chain F residue 1057 ASP Chi-restraints excluded: chain B residue 97 PHE Chi-restraints excluded: chain B residue 339 GLU Chi-restraints excluded: chain B residue 669 CYS Chi-restraints excluded: chain H residue 772 VAL Chi-restraints excluded: chain H residue 799 CYS Chi-restraints excluded: chain H residue 809 LEU Chi-restraints excluded: chain H residue 829 CYS Chi-restraints excluded: chain H residue 919 VAL Chi-restraints excluded: chain H residue 934 ILE Chi-restraints excluded: chain H residue 1029 SER Chi-restraints excluded: chain H residue 1055 MET Chi-restraints excluded: chain H residue 1167 VAL Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain E residue 289 SER Chi-restraints excluded: chain E residue 536 LEU Chi-restraints excluded: chain E residue 663 THR Chi-restraints excluded: chain E residue 668 THR Chi-restraints excluded: chain G residue 58 SER Chi-restraints excluded: chain G residue 94 ILE Chi-restraints excluded: chain G residue 129 LEU Chi-restraints excluded: chain G residue 158 THR Chi-restraints excluded: chain G residue 227 LEU Chi-restraints excluded: chain G residue 311 THR Chi-restraints excluded: chain G residue 315 LEU Chi-restraints excluded: chain G residue 345 SER Chi-restraints excluded: chain G residue 401 ASN Chi-restraints excluded: chain G residue 452 HIS Chi-restraints excluded: chain G residue 614 SER Chi-restraints excluded: chain G residue 715 ILE Chi-restraints excluded: chain G residue 740 MET Chi-restraints excluded: chain C residue 884 LEU Chi-restraints excluded: chain C residue 981 SER Chi-restraints excluded: chain C residue 1230 VAL Chi-restraints excluded: chain D residue 789 THR Chi-restraints excluded: chain D residue 934 ILE Chi-restraints excluded: chain D residue 941 VAL Chi-restraints excluded: chain D residue 956 VAL Chi-restraints excluded: chain D residue 1034 THR Chi-restraints excluded: chain D residue 1088 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 68 optimal weight: 7.9990 chunk 125 optimal weight: 5.9990 chunk 286 optimal weight: 0.0270 chunk 132 optimal weight: 2.9990 chunk 415 optimal weight: 0.3980 chunk 263 optimal weight: 30.0000 chunk 306 optimal weight: 9.9990 chunk 198 optimal weight: 5.9990 chunk 314 optimal weight: 0.3980 chunk 74 optimal weight: 9.9990 chunk 469 optimal weight: 7.9990 overall best weight: 1.9642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 368 ASN A 395 HIS A 526 ASN A 563 GLN ** A 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F1013 GLN ** F1128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 277 GLN H 977 HIS H1113 GLN C 861 HIS ** C1011 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1176 HIS D 852 GLN ** D1188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4478 r_free = 0.4478 target = 0.147595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.118742 restraints weight = 131968.783| |-----------------------------------------------------------------------------| r_work (start): 0.4055 rms_B_bonded: 4.96 r_work (final): 0.4055 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4055 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4055 r_free = 0.4055 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4055 r_free = 0.4055 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| r_final: 0.4055 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7157 moved from start: 0.4793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 37630 Z= 0.140 Angle : 0.739 12.796 51244 Z= 0.369 Chirality : 0.047 0.533 5552 Planarity : 0.005 0.045 6728 Dihedral : 5.858 50.604 5558 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.22 % Favored : 92.76 % Rotamer: Outliers : 2.20 % Allowed : 12.81 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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: -3.38 (0.11), residues: 4744 helix: -2.29 (0.18), residues: 632 sheet: -3.00 (0.17), residues: 780 loop : -2.16 (0.10), residues: 3332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 436 TYR 0.028 0.002 TYR G 126 PHE 0.034 0.002 PHE G 165 TRP 0.046 0.002 TRP G 553 HIS 0.007 0.001 HIS D1047 Details of bonding type rmsd covalent geometry : bond 0.00320 (37380) covalent geometry : angle 0.71687 (50724) SS BOND : bond 0.00395 ( 230) SS BOND : angle 1.50976 ( 460) hydrogen bonds : bond 0.03815 ( 731) hydrogen bonds : angle 6.25909 ( 1748) link_NAG-ASN : bond 0.00530 ( 20) link_NAG-ASN : angle 3.83984 ( 60) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9488 Ramachandran restraints generated. 4744 Oldfield, 0 Emsley, 4744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9488 Ramachandran restraints generated. 4744 Oldfield, 0 Emsley, 4744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 508 residues out of total 4112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 422 time to evaluate : 1.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 466 MET cc_start: 0.7844 (ptp) cc_final: 0.6621 (tpt) REVERT: A 494 TYR cc_start: 0.6844 (t80) cc_final: 0.6366 (t80) REVERT: A 553 TRP cc_start: 0.5367 (m100) cc_final: 0.5107 (m100) REVERT: A 740 MET cc_start: 0.4987 (mmt) cc_final: 0.4432 (tpt) REVERT: F 947 MET cc_start: 0.5522 (ptp) cc_final: 0.5019 (ptt) REVERT: F 1210 LYS cc_start: 0.4697 (pttm) cc_final: 0.3909 (tttt) REVERT: B 179 THR cc_start: 0.7630 (p) cc_final: 0.7370 (p) REVERT: B 299 MET cc_start: 0.7373 (mtm) cc_final: 0.6600 (ptp) REVERT: B 302 ARG cc_start: 0.6671 (mmt90) cc_final: 0.6205 (mmt180) REVERT: B 338 ASP cc_start: 0.7259 (t0) cc_final: 0.6674 (m-30) REVERT: B 576 MET cc_start: 0.8440 (tpp) cc_final: 0.8192 (tpp) REVERT: B 680 ASN cc_start: 0.7736 (m-40) cc_final: 0.6939 (p0) REVERT: B 723 SER cc_start: 0.8666 (p) cc_final: 0.8329 (m) REVERT: H 802 MET cc_start: 0.3807 (mmp) cc_final: 0.3531 (mmm) REVERT: H 1211 LYS cc_start: 0.2938 (mptt) cc_final: 0.2637 (mmmt) REVERT: E 301 TYR cc_start: 0.7704 (t80) cc_final: 0.7265 (t80) REVERT: E 315 LEU cc_start: 0.7874 (OUTLIER) cc_final: 0.7511 (mm) REVERT: E 381 ASN cc_start: 0.8028 (p0) cc_final: 0.7683 (t0) REVERT: E 475 LEU cc_start: 0.7756 (tt) cc_final: 0.7519 (tt) REVERT: G 271 TYR cc_start: 0.7617 (OUTLIER) cc_final: 0.6974 (t80) REVERT: G 285 TRP cc_start: 0.7167 (p-90) cc_final: 0.6794 (p-90) REVERT: G 302 ARG cc_start: 0.7452 (mmt180) cc_final: 0.7225 (mmt180) REVERT: G 376 GLN cc_start: 0.7451 (OUTLIER) cc_final: 0.6582 (mp10) REVERT: G 494 TYR cc_start: 0.6983 (t80) cc_final: 0.6742 (t80) REVERT: G 526 ASN cc_start: 0.7799 (m-40) cc_final: 0.7563 (m110) REVERT: C 800 MET cc_start: 0.7158 (ppp) cc_final: 0.6834 (ppp) REVERT: C 1035 ARG cc_start: 0.7136 (tpp-160) cc_final: 0.6694 (mmt-90) REVERT: D 800 MET cc_start: 0.3418 (mmt) cc_final: 0.3181 (mmt) REVERT: D 883 TYR cc_start: 0.8194 (p90) cc_final: 0.7744 (p90) REVERT: D 1055 MET cc_start: 0.5922 (ptm) cc_final: 0.5393 (ptp) outliers start: 86 outliers final: 51 residues processed: 490 average time/residue: 0.2110 time to fit residues: 171.0088 Evaluate side-chains 397 residues out of total 4112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 343 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 368 ASN Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain A residue 715 ILE Chi-restraints excluded: chain F residue 789 THR Chi-restraints excluded: chain F residue 870 ILE Chi-restraints excluded: chain F residue 1057 ASP Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 97 PHE Chi-restraints excluded: chain B residue 158 THR Chi-restraints excluded: chain B residue 312 CYS Chi-restraints excluded: chain B residue 339 GLU Chi-restraints excluded: chain B residue 501 ASP Chi-restraints excluded: chain B residue 638 VAL Chi-restraints excluded: chain B residue 669 CYS Chi-restraints excluded: chain H residue 799 CYS Chi-restraints excluded: chain H residue 809 LEU Chi-restraints excluded: chain H residue 829 CYS Chi-restraints excluded: chain H residue 1029 SER Chi-restraints excluded: chain H residue 1075 VAL Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain E residue 434 ASP Chi-restraints excluded: chain E residue 536 LEU Chi-restraints excluded: chain E residue 663 THR Chi-restraints excluded: chain E residue 668 THR Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain G residue 129 LEU Chi-restraints excluded: chain G residue 158 THR Chi-restraints excluded: chain G residue 227 LEU Chi-restraints excluded: chain G residue 271 TYR Chi-restraints excluded: chain G residue 311 THR Chi-restraints excluded: chain G residue 345 SER Chi-restraints excluded: chain G residue 376 GLN Chi-restraints excluded: chain G residue 412 TYR Chi-restraints excluded: chain G residue 490 VAL Chi-restraints excluded: chain G residue 512 LEU Chi-restraints excluded: chain G residue 614 SER Chi-restraints excluded: chain G residue 709 CYS Chi-restraints excluded: chain C residue 870 ILE Chi-restraints excluded: chain C residue 884 LEU Chi-restraints excluded: chain C residue 927 ILE Chi-restraints excluded: chain C residue 981 SER Chi-restraints excluded: chain D residue 789 THR Chi-restraints excluded: chain D residue 934 ILE Chi-restraints excluded: chain D residue 956 VAL Chi-restraints excluded: chain D residue 1034 THR Chi-restraints excluded: chain D residue 1088 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 253 optimal weight: 8.9990 chunk 366 optimal weight: 0.2980 chunk 97 optimal weight: 4.9990 chunk 257 optimal weight: 8.9990 chunk 457 optimal weight: 0.7980 chunk 131 optimal weight: 9.9990 chunk 172 optimal weight: 7.9990 chunk 75 optimal weight: 5.9990 chunk 357 optimal weight: 8.9990 chunk 266 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 GLN A 551 ASN A 726 HIS A 737 HIS ** F 832 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1128 GLN F1134 ASN B 107 GLN E 316 HIS G 189 ASN G 556 HIS C 819 ASN C 874 HIS ** C1011 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1013 GLN ** D1188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4446 r_free = 0.4446 target = 0.145066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.116427 restraints weight = 155738.897| |-----------------------------------------------------------------------------| r_work (start): 0.4017 rms_B_bonded: 5.51 r_work: 0.3832 rms_B_bonded: 5.14 restraints_weight: 2.0000 r_work (final): 0.3832 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3830 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3830 r_free = 0.3830 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3830 r_free = 0.3830 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3830 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.5442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 37630 Z= 0.140 Angle : 0.718 12.417 51244 Z= 0.358 Chirality : 0.047 0.516 5552 Planarity : 0.005 0.054 6728 Dihedral : 5.615 51.526 5558 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.45 % Favored : 92.53 % Rotamer: Outliers : 2.57 % Allowed : 13.73 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -3.07 (0.11), residues: 4744 helix: -1.87 (0.19), residues: 632 sheet: -2.72 (0.18), residues: 784 loop : -2.00 (0.10), residues: 3328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 436 TYR 0.020 0.002 TYR G 134 PHE 0.031 0.002 PHE H 953 TRP 0.046 0.002 TRP G 553 HIS 0.007 0.001 HIS E 316 Details of bonding type rmsd covalent geometry : bond 0.00318 (37380) covalent geometry : angle 0.69710 (50724) SS BOND : bond 0.00406 ( 230) SS BOND : angle 1.44166 ( 460) hydrogen bonds : bond 0.03415 ( 731) hydrogen bonds : angle 6.09615 ( 1748) link_NAG-ASN : bond 0.00552 ( 20) link_NAG-ASN : angle 3.69384 ( 60) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9488 Ramachandran restraints generated. 4744 Oldfield, 0 Emsley, 4744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9488 Ramachandran restraints generated. 4744 Oldfield, 0 Emsley, 4744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 4112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 380 time to evaluate : 1.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 TYR cc_start: 0.7288 (t80) cc_final: 0.7080 (t80) REVERT: A 356 ARG cc_start: 0.6277 (tmt170) cc_final: 0.5903 (mtt180) REVERT: A 406 PHE cc_start: 0.8075 (t80) cc_final: 0.7752 (t80) REVERT: A 436 ARG cc_start: 0.7572 (tpp80) cc_final: 0.7358 (ttm-80) REVERT: A 466 MET cc_start: 0.8170 (ptp) cc_final: 0.6727 (tpt) REVERT: A 469 GLN cc_start: 0.7063 (mp10) cc_final: 0.6850 (mp10) REVERT: A 494 TYR cc_start: 0.7391 (t80) cc_final: 0.6905 (t80) REVERT: A 696 ASP cc_start: 0.7109 (t0) cc_final: 0.6892 (t70) REVERT: A 740 MET cc_start: 0.5499 (mmt) cc_final: 0.5287 (tpt) REVERT: F 1210 LYS cc_start: 0.4981 (pttm) cc_final: 0.4049 (tttt) REVERT: B 111 MET cc_start: 0.8654 (ttt) cc_final: 0.8449 (ttm) REVERT: B 171 ASP cc_start: 0.6614 (p0) cc_final: 0.6396 (p0) REVERT: B 299 MET cc_start: 0.7527 (mtm) cc_final: 0.6694 (ptp) REVERT: B 338 ASP cc_start: 0.7069 (t0) cc_final: 0.6419 (m-30) REVERT: B 507 ARG cc_start: 0.8127 (OUTLIER) cc_final: 0.7773 (tpt90) REVERT: B 576 MET cc_start: 0.8764 (tpp) cc_final: 0.8515 (tpp) REVERT: B 680 ASN cc_start: 0.7694 (m-40) cc_final: 0.6864 (p0) REVERT: B 693 LEU cc_start: 0.8461 (mm) cc_final: 0.8169 (mp) REVERT: B 723 SER cc_start: 0.8937 (p) cc_final: 0.8635 (m) REVERT: H 1211 LYS cc_start: 0.3442 (mptt) cc_final: 0.3012 (mmmt) REVERT: E 315 LEU cc_start: 0.7801 (OUTLIER) cc_final: 0.7422 (mm) REVERT: E 381 ASN cc_start: 0.8124 (p0) cc_final: 0.7866 (t0) REVERT: E 475 LEU cc_start: 0.8079 (tt) cc_final: 0.7867 (tt) REVERT: G 145 ASN cc_start: 0.7965 (m-40) cc_final: 0.7592 (m110) REVERT: G 271 TYR cc_start: 0.7748 (OUTLIER) cc_final: 0.7273 (t80) REVERT: G 285 TRP cc_start: 0.7342 (p-90) cc_final: 0.6975 (p-90) REVERT: G 299 MET cc_start: 0.6167 (ttp) cc_final: 0.5953 (ttp) REVERT: G 300 GLU cc_start: 0.7116 (mp0) cc_final: 0.6582 (mp0) REVERT: G 302 ARG cc_start: 0.7971 (mmt180) cc_final: 0.7569 (mmt180) REVERT: G 338 ASP cc_start: 0.7019 (m-30) cc_final: 0.6730 (m-30) REVERT: G 526 ASN cc_start: 0.8584 (m-40) cc_final: 0.8242 (m110) REVERT: G 553 TRP cc_start: 0.6053 (m100) cc_final: 0.5810 (m-10) REVERT: C 800 MET cc_start: 0.7257 (ppp) cc_final: 0.6929 (ppp) REVERT: C 1035 ARG cc_start: 0.7329 (tpp-160) cc_final: 0.6809 (mmt-90) REVERT: C 1051 MET cc_start: 0.6873 (tmm) cc_final: 0.6385 (tpt) REVERT: D 883 TYR cc_start: 0.8645 (p90) cc_final: 0.8216 (p90) outliers start: 101 outliers final: 65 residues processed: 456 average time/residue: 0.2125 time to fit residues: 160.7982 Evaluate side-chains 396 residues out of total 4112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 328 time to evaluate : 1.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain A residue 712 ASP Chi-restraints excluded: chain A residue 722 PHE Chi-restraints excluded: chain F residue 789 THR Chi-restraints excluded: chain F residue 870 ILE Chi-restraints excluded: chain F residue 1019 VAL Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 97 PHE Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 107 GLN Chi-restraints excluded: chain B residue 158 THR Chi-restraints excluded: chain B residue 323 GLU Chi-restraints excluded: chain B residue 501 ASP Chi-restraints excluded: chain B residue 507 ARG Chi-restraints excluded: chain B residue 638 VAL Chi-restraints excluded: chain B residue 707 CYS Chi-restraints excluded: chain H residue 799 CYS Chi-restraints excluded: chain H residue 809 LEU Chi-restraints excluded: chain H residue 829 CYS Chi-restraints excluded: chain H residue 870 ILE Chi-restraints excluded: chain H residue 934 ILE Chi-restraints excluded: chain H residue 1029 SER Chi-restraints excluded: chain H residue 1055 MET Chi-restraints excluded: chain H residue 1075 VAL Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain E residue 434 ASP Chi-restraints excluded: chain E residue 536 LEU Chi-restraints excluded: chain E residue 659 LEU Chi-restraints excluded: chain E residue 668 THR Chi-restraints excluded: chain G residue 58 SER Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain G residue 102 VAL Chi-restraints excluded: chain G residue 129 LEU Chi-restraints excluded: chain G residue 227 LEU Chi-restraints excluded: chain G residue 271 TYR Chi-restraints excluded: chain G residue 311 THR Chi-restraints excluded: chain G residue 326 VAL Chi-restraints excluded: chain G residue 345 SER Chi-restraints excluded: chain G residue 426 VAL Chi-restraints excluded: chain G residue 464 VAL Chi-restraints excluded: chain G residue 490 VAL Chi-restraints excluded: chain G residue 510 VAL Chi-restraints excluded: chain G residue 512 LEU Chi-restraints excluded: chain G residue 599 VAL Chi-restraints excluded: chain G residue 614 SER Chi-restraints excluded: chain G residue 707 CYS Chi-restraints excluded: chain G residue 709 CYS Chi-restraints excluded: chain C residue 771 MET Chi-restraints excluded: chain C residue 870 ILE Chi-restraints excluded: chain C residue 884 LEU Chi-restraints excluded: chain C residue 927 ILE Chi-restraints excluded: chain C residue 981 SER Chi-restraints excluded: chain D residue 789 THR Chi-restraints excluded: chain D residue 870 ILE Chi-restraints excluded: chain D residue 934 ILE Chi-restraints excluded: chain D residue 941 VAL Chi-restraints excluded: chain D residue 956 VAL Chi-restraints excluded: chain D residue 1088 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 424 optimal weight: 6.9990 chunk 129 optimal weight: 10.0000 chunk 23 optimal weight: 0.5980 chunk 174 optimal weight: 5.9990 chunk 90 optimal weight: 9.9990 chunk 231 optimal weight: 5.9990 chunk 441 optimal weight: 3.9990 chunk 215 optimal weight: 0.6980 chunk 134 optimal weight: 20.0000 chunk 155 optimal weight: 4.9990 chunk 326 optimal weight: 7.9990 overall best weight: 3.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 368 ASN A 737 HIS ** F 832 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 874 HIS F1003 GLN ** F1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 737 HIS H 916 HIS ** E 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 189 ASN C 819 ASN C 874 HIS C1011 ASN ** C1188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1003 GLN ** D1188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.140693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.110804 restraints weight = 131144.616| |-----------------------------------------------------------------------------| r_work (start): 0.3935 rms_B_bonded: 5.01 r_work: 0.3763 rms_B_bonded: 4.89 restraints_weight: 0.5000 r_work (final): 0.3763 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3763 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3763 r_free = 0.3763 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3763 r_free = 0.3763 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3763 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.6273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 37630 Z= 0.169 Angle : 0.732 17.276 51244 Z= 0.369 Chirality : 0.048 0.515 5552 Planarity : 0.005 0.051 6728 Dihedral : 5.738 50.452 5558 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.04 % Favored : 91.94 % Rotamer: Outliers : 2.91 % Allowed : 14.05 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -2.91 (0.11), residues: 4744 helix: -1.64 (0.20), residues: 628 sheet: -2.54 (0.18), residues: 772 loop : -1.94 (0.10), residues: 3344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 578 TYR 0.022 0.002 TYR G 126 PHE 0.025 0.002 PHE G 406 TRP 0.025 0.002 TRP G 553 HIS 0.010 0.001 HIS E 737 Details of bonding type rmsd covalent geometry : bond 0.00385 (37380) covalent geometry : angle 0.71199 (50724) SS BOND : bond 0.00449 ( 230) SS BOND : angle 1.48252 ( 460) hydrogen bonds : bond 0.03410 ( 731) hydrogen bonds : angle 6.08288 ( 1748) link_NAG-ASN : bond 0.00540 ( 20) link_NAG-ASN : angle 3.45719 ( 60) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9488 Ramachandran restraints generated. 4744 Oldfield, 0 Emsley, 4744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9488 Ramachandran restraints generated. 4744 Oldfield, 0 Emsley, 4744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 4112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 360 time to evaluate : 1.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 GLN cc_start: 0.7382 (mm-40) cc_final: 0.6898 (pt0) REVERT: A 338 ASP cc_start: 0.6609 (m-30) cc_final: 0.6319 (m-30) REVERT: A 406 PHE cc_start: 0.8172 (t80) cc_final: 0.7844 (t80) REVERT: A 466 MET cc_start: 0.8160 (ptp) cc_final: 0.6930 (tpt) REVERT: A 469 GLN cc_start: 0.6900 (mp10) cc_final: 0.6671 (mp10) REVERT: A 494 TYR cc_start: 0.7443 (t80) cc_final: 0.7186 (t80) REVERT: A 696 ASP cc_start: 0.7576 (t0) cc_final: 0.7324 (t0) REVERT: F 1210 LYS cc_start: 0.4892 (pttm) cc_final: 0.3941 (tptt) REVERT: B 101 THR cc_start: 0.6951 (p) cc_final: 0.6681 (p) REVERT: B 108 ARG cc_start: 0.7442 (OUTLIER) cc_final: 0.6809 (ttt180) REVERT: B 338 ASP cc_start: 0.7155 (t0) cc_final: 0.6511 (m-30) REVERT: B 507 ARG cc_start: 0.8114 (OUTLIER) cc_final: 0.7789 (tpt90) REVERT: B 576 MET cc_start: 0.8789 (tpp) cc_final: 0.8500 (tpp) REVERT: B 680 ASN cc_start: 0.7666 (m-40) cc_final: 0.6741 (p0) REVERT: B 693 LEU cc_start: 0.8440 (mm) cc_final: 0.8128 (mp) REVERT: B 723 SER cc_start: 0.9072 (p) cc_final: 0.8750 (m) REVERT: H 802 MET cc_start: 0.4287 (mmp) cc_final: 0.4007 (mmm) REVERT: H 1211 LYS cc_start: 0.3745 (mptt) cc_final: 0.3178 (mmmt) REVERT: G 107 GLN cc_start: 0.7371 (mp10) cc_final: 0.7165 (mp10) REVERT: G 111 MET cc_start: 0.8498 (ttt) cc_final: 0.8262 (mmm) REVERT: G 134 TYR cc_start: 0.7037 (m-10) cc_final: 0.6664 (m-10) REVERT: G 145 ASN cc_start: 0.8223 (m-40) cc_final: 0.7866 (m110) REVERT: G 271 TYR cc_start: 0.7777 (OUTLIER) cc_final: 0.6995 (t80) REVERT: G 285 TRP cc_start: 0.7616 (p-90) cc_final: 0.7325 (p-90) REVERT: G 526 ASN cc_start: 0.8945 (m-40) cc_final: 0.8508 (m110) REVERT: G 736 MET cc_start: 0.5429 (mmt) cc_final: 0.4672 (mmm) REVERT: C 800 MET cc_start: 0.7462 (ppp) cc_final: 0.6926 (ppp) REVERT: C 1051 MET cc_start: 0.6900 (tmm) cc_final: 0.6367 (tpt) REVERT: D 883 TYR cc_start: 0.8718 (p90) cc_final: 0.8362 (p90) outliers start: 115 outliers final: 76 residues processed: 450 average time/residue: 0.2125 time to fit residues: 158.5271 Evaluate side-chains 391 residues out of total 4112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 312 time to evaluate : 1.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 MET Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 368 ASN Chi-restraints excluded: chain A residue 420 ASP Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 526 ASN Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 687 CYS Chi-restraints excluded: chain A residue 722 PHE Chi-restraints excluded: chain F residue 789 THR Chi-restraints excluded: chain F residue 814 MET Chi-restraints excluded: chain F residue 870 ILE Chi-restraints excluded: chain F residue 1019 VAL Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 97 PHE Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 108 ARG Chi-restraints excluded: chain B residue 312 CYS Chi-restraints excluded: chain B residue 323 GLU Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 384 CYS Chi-restraints excluded: chain B residue 501 ASP Chi-restraints excluded: chain B residue 507 ARG Chi-restraints excluded: chain B residue 582 GLU Chi-restraints excluded: chain B residue 638 VAL Chi-restraints excluded: chain B residue 659 LEU Chi-restraints excluded: chain B residue 707 CYS Chi-restraints excluded: chain B residue 729 CYS Chi-restraints excluded: chain H residue 799 CYS Chi-restraints excluded: chain H residue 809 LEU Chi-restraints excluded: chain H residue 829 CYS Chi-restraints excluded: chain H residue 884 LEU Chi-restraints excluded: chain H residue 904 THR Chi-restraints excluded: chain H residue 934 ILE Chi-restraints excluded: chain H residue 1029 SER Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain E residue 434 ASP Chi-restraints excluded: chain E residue 536 LEU Chi-restraints excluded: chain E residue 659 LEU Chi-restraints excluded: chain E residue 668 THR Chi-restraints excluded: chain E residue 733 ASP Chi-restraints excluded: chain G residue 58 SER Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain G residue 97 PHE Chi-restraints excluded: chain G residue 271 TYR Chi-restraints excluded: chain G residue 280 MET Chi-restraints excluded: chain G residue 311 THR Chi-restraints excluded: chain G residue 426 VAL Chi-restraints excluded: chain G residue 428 GLU Chi-restraints excluded: chain G residue 510 VAL Chi-restraints excluded: chain G residue 512 LEU Chi-restraints excluded: chain G residue 599 VAL Chi-restraints excluded: chain G residue 608 CYS Chi-restraints excluded: chain G residue 614 SER Chi-restraints excluded: chain G residue 640 VAL Chi-restraints excluded: chain G residue 707 CYS Chi-restraints excluded: chain G residue 709 CYS Chi-restraints excluded: chain C residue 819 ASN Chi-restraints excluded: chain C residue 870 ILE Chi-restraints excluded: chain C residue 884 LEU Chi-restraints excluded: chain C residue 927 ILE Chi-restraints excluded: chain C residue 942 ASN Chi-restraints excluded: chain C residue 981 SER Chi-restraints excluded: chain C residue 1017 ASP Chi-restraints excluded: chain D residue 789 THR Chi-restraints excluded: chain D residue 870 ILE Chi-restraints excluded: chain D residue 916 HIS Chi-restraints excluded: chain D residue 934 ILE Chi-restraints excluded: chain D residue 941 VAL Chi-restraints excluded: chain D residue 956 VAL Chi-restraints excluded: chain D residue 1088 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 136 optimal weight: 20.0000 chunk 272 optimal weight: 9.9990 chunk 293 optimal weight: 4.9990 chunk 36 optimal weight: 10.0000 chunk 317 optimal weight: 10.0000 chunk 274 optimal weight: 3.9990 chunk 286 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 chunk 409 optimal weight: 9.9990 chunk 182 optimal weight: 9.9990 chunk 291 optimal weight: 0.8980 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 GLN A 368 ASN ** F 832 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 95 HIS B 107 GLN H 986 GLN H1013 GLN ** E 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 189 ASN G 368 ASN C 819 ASN ** C1188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 952 HIS ** D1188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.138539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.108944 restraints weight = 127530.915| |-----------------------------------------------------------------------------| r_work (start): 0.3909 rms_B_bonded: 4.83 r_work: 0.3728 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.3728 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3728 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3728 r_free = 0.3728 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3728 r_free = 0.3728 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3728 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.6819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 37630 Z= 0.172 Angle : 0.729 16.854 51244 Z= 0.367 Chirality : 0.048 0.519 5552 Planarity : 0.005 0.049 6728 Dihedral : 5.812 51.911 5558 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.00 % Favored : 91.98 % Rotamer: Outliers : 2.74 % Allowed : 15.18 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -2.80 (0.12), residues: 4744 helix: -1.54 (0.20), residues: 640 sheet: -2.48 (0.18), residues: 792 loop : -1.86 (0.10), residues: 3312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 436 TYR 0.031 0.002 TYR G 113 PHE 0.027 0.002 PHE F 937 TRP 0.029 0.002 TRP G 553 HIS 0.007 0.001 HIS D1047 Details of bonding type rmsd covalent geometry : bond 0.00388 (37380) covalent geometry : angle 0.70993 (50724) SS BOND : bond 0.00510 ( 230) SS BOND : angle 1.47106 ( 460) hydrogen bonds : bond 0.03438 ( 731) hydrogen bonds : angle 5.96015 ( 1748) link_NAG-ASN : bond 0.00509 ( 20) link_NAG-ASN : angle 3.38712 ( 60) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9488 Ramachandran restraints generated. 4744 Oldfield, 0 Emsley, 4744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9488 Ramachandran restraints generated. 4744 Oldfield, 0 Emsley, 4744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 4112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 340 time to evaluate : 1.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 GLN cc_start: 0.7458 (mm-40) cc_final: 0.7196 (pt0) REVERT: A 180 LEU cc_start: 0.7828 (tp) cc_final: 0.7623 (pp) REVERT: A 338 ASP cc_start: 0.6473 (m-30) cc_final: 0.6237 (m-30) REVERT: A 466 MET cc_start: 0.8304 (ptp) cc_final: 0.6987 (tpt) REVERT: A 469 GLN cc_start: 0.6906 (mp10) cc_final: 0.6660 (mp10) REVERT: A 494 TYR cc_start: 0.7586 (t80) cc_final: 0.7327 (t80) REVERT: B 101 THR cc_start: 0.7101 (p) cc_final: 0.6822 (p) REVERT: B 171 ASP cc_start: 0.6902 (p0) cc_final: 0.6685 (p0) REVERT: B 244 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.8219 (pm20) REVERT: B 282 LEU cc_start: 0.7626 (OUTLIER) cc_final: 0.7358 (pt) REVERT: B 338 ASP cc_start: 0.7160 (t0) cc_final: 0.6369 (m-30) REVERT: B 507 ARG cc_start: 0.8103 (OUTLIER) cc_final: 0.7799 (tpt90) REVERT: B 680 ASN cc_start: 0.7610 (m-40) cc_final: 0.6609 (p0) REVERT: H 802 MET cc_start: 0.4316 (mmp) cc_final: 0.3842 (mmm) REVERT: H 1036 LYS cc_start: 0.7141 (tptm) cc_final: 0.6907 (tttp) REVERT: H 1211 LYS cc_start: 0.4022 (mptt) cc_final: 0.3281 (mmmt) REVERT: E 736 MET cc_start: 0.8297 (mmm) cc_final: 0.8074 (mmm) REVERT: G 145 ASN cc_start: 0.8187 (m-40) cc_final: 0.7814 (m110) REVERT: G 179 THR cc_start: 0.8147 (OUTLIER) cc_final: 0.7512 (m) REVERT: G 271 TYR cc_start: 0.7887 (OUTLIER) cc_final: 0.7207 (t80) REVERT: G 285 TRP cc_start: 0.7668 (p-90) cc_final: 0.7402 (p-90) REVERT: G 300 GLU cc_start: 0.7840 (mp0) cc_final: 0.7409 (mp0) REVERT: G 302 ARG cc_start: 0.7958 (mmt180) cc_final: 0.7651 (mmt180) REVERT: G 526 ASN cc_start: 0.9036 (m-40) cc_final: 0.8584 (m110) REVERT: G 715 ILE cc_start: 0.5453 (OUTLIER) cc_final: 0.5108 (tt) REVERT: G 736 MET cc_start: 0.5905 (mmt) cc_final: 0.4289 (mtp) REVERT: C 800 MET cc_start: 0.7445 (ppp) cc_final: 0.7092 (ppp) REVERT: C 1051 MET cc_start: 0.7003 (tmm) cc_final: 0.6574 (tpt) REVERT: C 1055 MET cc_start: 0.7682 (mtp) cc_final: 0.7397 (mtm) REVERT: D 883 TYR cc_start: 0.8721 (p90) cc_final: 0.8369 (p90) outliers start: 108 outliers final: 73 residues processed: 432 average time/residue: 0.2082 time to fit residues: 150.6030 Evaluate side-chains 366 residues out of total 4112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 287 time to evaluate : 1.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 MET Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 420 ASP Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain A residue 687 CYS Chi-restraints excluded: chain A residue 722 PHE Chi-restraints excluded: chain A residue 737 HIS Chi-restraints excluded: chain F residue 789 THR Chi-restraints excluded: chain F residue 814 MET Chi-restraints excluded: chain F residue 870 ILE Chi-restraints excluded: chain F residue 894 VAL Chi-restraints excluded: chain F residue 1019 VAL Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 97 PHE Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 107 GLN Chi-restraints excluded: chain B residue 244 GLU Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 312 CYS Chi-restraints excluded: chain B residue 323 GLU Chi-restraints excluded: chain B residue 501 ASP Chi-restraints excluded: chain B residue 507 ARG Chi-restraints excluded: chain B residue 638 VAL Chi-restraints excluded: chain B residue 659 LEU Chi-restraints excluded: chain B residue 707 CYS Chi-restraints excluded: chain B residue 729 CYS Chi-restraints excluded: chain H residue 799 CYS Chi-restraints excluded: chain H residue 809 LEU Chi-restraints excluded: chain H residue 829 CYS Chi-restraints excluded: chain H residue 904 THR Chi-restraints excluded: chain H residue 934 ILE Chi-restraints excluded: chain H residue 1029 SER Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain E residue 536 LEU Chi-restraints excluded: chain E residue 608 CYS Chi-restraints excluded: chain E residue 659 LEU Chi-restraints excluded: chain E residue 668 THR Chi-restraints excluded: chain E residue 733 ASP Chi-restraints excluded: chain G residue 58 SER Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain G residue 96 LEU Chi-restraints excluded: chain G residue 97 PHE Chi-restraints excluded: chain G residue 179 THR Chi-restraints excluded: chain G residue 189 ASN Chi-restraints excluded: chain G residue 271 TYR Chi-restraints excluded: chain G residue 280 MET Chi-restraints excluded: chain G residue 311 THR Chi-restraints excluded: chain G residue 368 ASN Chi-restraints excluded: chain G residue 426 VAL Chi-restraints excluded: chain G residue 464 VAL Chi-restraints excluded: chain G residue 490 VAL Chi-restraints excluded: chain G residue 508 LEU Chi-restraints excluded: chain G residue 512 LEU Chi-restraints excluded: chain G residue 599 VAL Chi-restraints excluded: chain G residue 608 CYS Chi-restraints excluded: chain G residue 614 SER Chi-restraints excluded: chain G residue 640 VAL Chi-restraints excluded: chain G residue 709 CYS Chi-restraints excluded: chain G residue 715 ILE Chi-restraints excluded: chain C residue 819 ASN Chi-restraints excluded: chain C residue 870 ILE Chi-restraints excluded: chain C residue 884 LEU Chi-restraints excluded: chain C residue 927 ILE Chi-restraints excluded: chain C residue 981 SER Chi-restraints excluded: chain C residue 1017 ASP Chi-restraints excluded: chain D residue 789 THR Chi-restraints excluded: chain D residue 870 ILE Chi-restraints excluded: chain D residue 916 HIS Chi-restraints excluded: chain D residue 934 ILE Chi-restraints excluded: chain D residue 941 VAL Chi-restraints excluded: chain D residue 956 VAL Chi-restraints excluded: chain D residue 992 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 167 optimal weight: 6.9990 chunk 355 optimal weight: 9.9990 chunk 211 optimal weight: 10.0000 chunk 35 optimal weight: 10.0000 chunk 172 optimal weight: 9.9990 chunk 151 optimal weight: 7.9990 chunk 184 optimal weight: 0.0060 chunk 226 optimal weight: 8.9990 chunk 462 optimal weight: 7.9990 chunk 450 optimal weight: 10.0000 chunk 49 optimal weight: 0.7980 overall best weight: 4.7602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 368 ASN ** F 832 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 952 HIS ** H1188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 189 ASN G 322 GLN G 717 GLN C 819 ASN C 861 HIS ** C1188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1154 GLN D1174 HIS ** D1188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.134633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.104372 restraints weight = 142815.646| |-----------------------------------------------------------------------------| r_work (start): 0.3831 rms_B_bonded: 5.19 r_work: 0.3650 rms_B_bonded: 5.03 restraints_weight: 2.0000 r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3649 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3649 r_free = 0.3649 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3649 r_free = 0.3649 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3649 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.7535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.097 37630 Z= 0.208 Angle : 0.771 17.046 51244 Z= 0.391 Chirality : 0.049 0.545 5552 Planarity : 0.005 0.051 6728 Dihedral : 6.218 57.372 5558 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.02 % Allowed : 9.28 % Favored : 90.70 % Rotamer: Outliers : 3.03 % Allowed : 16.03 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -2.82 (0.12), residues: 4744 helix: -1.62 (0.20), residues: 612 sheet: -2.50 (0.18), residues: 800 loop : -1.85 (0.10), residues: 3332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 108 TYR 0.045 0.002 TYR G 113 PHE 0.030 0.002 PHE G 406 TRP 0.036 0.002 TRP G 553 HIS 0.011 0.001 HIS C 817 Details of bonding type rmsd covalent geometry : bond 0.00477 (37380) covalent geometry : angle 0.75190 (50724) SS BOND : bond 0.00685 ( 230) SS BOND : angle 1.50777 ( 460) hydrogen bonds : bond 0.03930 ( 731) hydrogen bonds : angle 6.18876 ( 1748) link_NAG-ASN : bond 0.00580 ( 20) link_NAG-ASN : angle 3.48804 ( 60) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9488 Ramachandran restraints generated. 4744 Oldfield, 0 Emsley, 4744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9488 Ramachandran restraints generated. 4744 Oldfield, 0 Emsley, 4744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 4112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 329 time to evaluate : 1.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 GLN cc_start: 0.7874 (mm-40) cc_final: 0.7520 (pt0) REVERT: A 180 LEU cc_start: 0.7934 (tp) cc_final: 0.7660 (pp) REVERT: A 223 GLU cc_start: 0.7449 (pt0) cc_final: 0.7243 (pm20) REVERT: A 254 LEU cc_start: 0.4923 (OUTLIER) cc_final: 0.4462 (tp) REVERT: A 338 ASP cc_start: 0.6565 (OUTLIER) cc_final: 0.6308 (m-30) REVERT: A 466 MET cc_start: 0.8339 (ptp) cc_final: 0.7112 (tpt) REVERT: A 469 GLN cc_start: 0.6913 (mp10) cc_final: 0.6676 (mp10) REVERT: B 174 MET cc_start: 0.8154 (tpp) cc_final: 0.7872 (tpp) REVERT: B 282 LEU cc_start: 0.7609 (OUTLIER) cc_final: 0.7388 (pt) REVERT: B 299 MET cc_start: 0.6769 (ttp) cc_final: 0.6406 (ttp) REVERT: B 644 GLU cc_start: 0.8458 (mt-10) cc_final: 0.8243 (mp0) REVERT: B 680 ASN cc_start: 0.7750 (m-40) cc_final: 0.6685 (p0) REVERT: B 728 MET cc_start: 0.7452 (tmm) cc_final: 0.7218 (tmm) REVERT: B 740 MET cc_start: 0.6814 (tmm) cc_final: 0.6303 (tpt) REVERT: H 802 MET cc_start: 0.4243 (mmp) cc_final: 0.3891 (mmm) REVERT: H 986 GLN cc_start: 0.7375 (mt0) cc_final: 0.7138 (pp30) REVERT: G 107 GLN cc_start: 0.7472 (mp10) cc_final: 0.7272 (mp10) REVERT: G 111 MET cc_start: 0.8462 (mmm) cc_final: 0.8220 (mmm) REVERT: G 145 ASN cc_start: 0.8237 (m-40) cc_final: 0.7735 (m110) REVERT: G 179 THR cc_start: 0.8174 (OUTLIER) cc_final: 0.7451 (m) REVERT: G 271 TYR cc_start: 0.8074 (OUTLIER) cc_final: 0.7379 (t80) REVERT: G 285 TRP cc_start: 0.7781 (p-90) cc_final: 0.7581 (p-90) REVERT: G 302 ARG cc_start: 0.8276 (mmt180) cc_final: 0.7933 (mmt180) REVERT: G 695 MET cc_start: 0.6728 (mmm) cc_final: 0.5894 (mmm) REVERT: G 736 MET cc_start: 0.6233 (mmt) cc_final: 0.4709 (mmt) REVERT: C 800 MET cc_start: 0.7417 (ppp) cc_final: 0.6925 (ppp) REVERT: C 814 MET cc_start: 0.6166 (tpt) cc_final: 0.5815 (tpp) REVERT: C 1051 MET cc_start: 0.6921 (tmm) cc_final: 0.6439 (tpt) REVERT: D 872 MET cc_start: 0.8775 (mtp) cc_final: 0.8543 (mtp) REVERT: D 883 TYR cc_start: 0.8769 (p90) cc_final: 0.8476 (p90) outliers start: 120 outliers final: 80 residues processed: 432 average time/residue: 0.2068 time to fit residues: 149.7973 Evaluate side-chains 373 residues out of total 4112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 288 time to evaluate : 1.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 50 MET Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 323 GLU Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain A residue 368 ASN Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain A residue 687 CYS Chi-restraints excluded: chain A residue 737 HIS Chi-restraints excluded: chain F residue 772 VAL Chi-restraints excluded: chain F residue 789 THR Chi-restraints excluded: chain F residue 870 ILE Chi-restraints excluded: chain F residue 919 VAL Chi-restraints excluded: chain F residue 947 MET Chi-restraints excluded: chain F residue 1019 VAL Chi-restraints excluded: chain F residue 1132 GLU Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 97 PHE Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 312 CYS Chi-restraints excluded: chain B residue 323 GLU Chi-restraints excluded: chain B residue 501 ASP Chi-restraints excluded: chain B residue 638 VAL Chi-restraints excluded: chain B residue 707 CYS Chi-restraints excluded: chain B residue 723 SER Chi-restraints excluded: chain B residue 729 CYS Chi-restraints excluded: chain H residue 799 CYS Chi-restraints excluded: chain H residue 809 LEU Chi-restraints excluded: chain H residue 829 CYS Chi-restraints excluded: chain H residue 904 THR Chi-restraints excluded: chain H residue 919 VAL Chi-restraints excluded: chain H residue 934 ILE Chi-restraints excluded: chain H residue 1029 SER Chi-restraints excluded: chain H residue 1226 HIS Chi-restraints excluded: chain E residue 97 PHE Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain E residue 536 LEU Chi-restraints excluded: chain E residue 608 CYS Chi-restraints excluded: chain E residue 668 THR Chi-restraints excluded: chain E residue 673 SER Chi-restraints excluded: chain E residue 733 ASP Chi-restraints excluded: chain G residue 58 SER Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain G residue 96 LEU Chi-restraints excluded: chain G residue 97 PHE Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 179 THR Chi-restraints excluded: chain G residue 271 TYR Chi-restraints excluded: chain G residue 280 MET Chi-restraints excluded: chain G residue 311 THR Chi-restraints excluded: chain G residue 341 LEU Chi-restraints excluded: chain G residue 356 ARG Chi-restraints excluded: chain G residue 370 CYS Chi-restraints excluded: chain G residue 426 VAL Chi-restraints excluded: chain G residue 471 VAL Chi-restraints excluded: chain G residue 490 VAL Chi-restraints excluded: chain G residue 508 LEU Chi-restraints excluded: chain G residue 512 LEU Chi-restraints excluded: chain G residue 608 CYS Chi-restraints excluded: chain G residue 640 VAL Chi-restraints excluded: chain G residue 709 CYS Chi-restraints excluded: chain C residue 870 ILE Chi-restraints excluded: chain C residue 884 LEU Chi-restraints excluded: chain C residue 927 ILE Chi-restraints excluded: chain C residue 942 ASN Chi-restraints excluded: chain C residue 981 SER Chi-restraints excluded: chain D residue 789 THR Chi-restraints excluded: chain D residue 870 ILE Chi-restraints excluded: chain D residue 916 HIS Chi-restraints excluded: chain D residue 934 ILE Chi-restraints excluded: chain D residue 941 VAL Chi-restraints excluded: chain D residue 956 VAL Chi-restraints excluded: chain D residue 992 VAL Chi-restraints excluded: chain D residue 1048 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 240 optimal weight: 5.9990 chunk 177 optimal weight: 0.7980 chunk 103 optimal weight: 0.8980 chunk 279 optimal weight: 10.0000 chunk 195 optimal weight: 20.0000 chunk 392 optimal weight: 9.9990 chunk 436 optimal weight: 5.9990 chunk 371 optimal weight: 5.9990 chunk 178 optimal weight: 9.9990 chunk 410 optimal weight: 0.7980 chunk 323 optimal weight: 10.0000 overall best weight: 2.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 832 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1003 GLN ** F1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 986 GLN H1188 GLN ** H1215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 189 ASN C 819 ASN ** C1188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1176 HIS ** D1188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.135055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.105191 restraints weight = 133701.037| |-----------------------------------------------------------------------------| r_work (start): 0.3850 rms_B_bonded: 4.85 r_work: 0.3682 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3682 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3682 r_free = 0.3682 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3682 r_free = 0.3682 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3682 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.7770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.099 37630 Z= 0.150 Angle : 0.738 18.195 51244 Z= 0.369 Chirality : 0.047 0.495 5552 Planarity : 0.005 0.076 6728 Dihedral : 5.952 56.206 5558 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.53 % Favored : 92.45 % Rotamer: Outliers : 2.69 % Allowed : 16.30 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -2.70 (0.12), residues: 4744 helix: -1.50 (0.20), residues: 616 sheet: -2.40 (0.17), residues: 840 loop : -1.76 (0.11), residues: 3288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 578 TYR 0.037 0.002 TYR G 113 PHE 0.027 0.002 PHE F 937 TRP 0.025 0.001 TRP G 553 HIS 0.006 0.001 HIS D1047 Details of bonding type rmsd covalent geometry : bond 0.00351 (37380) covalent geometry : angle 0.71861 (50724) SS BOND : bond 0.00397 ( 230) SS BOND : angle 1.49477 ( 460) hydrogen bonds : bond 0.03411 ( 731) hydrogen bonds : angle 5.99199 ( 1748) link_NAG-ASN : bond 0.00467 ( 20) link_NAG-ASN : angle 3.33995 ( 60) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9488 Ramachandran restraints generated. 4744 Oldfield, 0 Emsley, 4744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9488 Ramachandran restraints generated. 4744 Oldfield, 0 Emsley, 4744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 4112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 310 time to evaluate : 1.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 GLN cc_start: 0.7876 (mm-40) cc_final: 0.7572 (pt0) REVERT: A 254 LEU cc_start: 0.5025 (OUTLIER) cc_final: 0.4755 (tp) REVERT: A 299 MET cc_start: 0.5909 (OUTLIER) cc_final: 0.5562 (tmm) REVERT: A 338 ASP cc_start: 0.6475 (OUTLIER) cc_final: 0.6237 (m-30) REVERT: A 466 MET cc_start: 0.8378 (ptp) cc_final: 0.7080 (tpt) REVERT: A 469 GLN cc_start: 0.6945 (mp10) cc_final: 0.6681 (mp10) REVERT: A 696 ASP cc_start: 0.7118 (OUTLIER) cc_final: 0.5784 (t0) REVERT: A 698 ARG cc_start: 0.8224 (mtm-85) cc_final: 0.7934 (mtm-85) REVERT: B 50 MET cc_start: 0.8282 (mmt) cc_final: 0.7715 (ttt) REVERT: B 299 MET cc_start: 0.6963 (ttp) cc_final: 0.6572 (ttp) REVERT: B 644 GLU cc_start: 0.8652 (mt-10) cc_final: 0.8238 (mp0) REVERT: B 680 ASN cc_start: 0.7682 (m-40) cc_final: 0.6567 (p0) REVERT: B 728 MET cc_start: 0.7385 (tmm) cc_final: 0.7142 (tmm) REVERT: B 740 MET cc_start: 0.6838 (tmm) cc_final: 0.6352 (tpt) REVERT: H 802 MET cc_start: 0.4206 (mmp) cc_final: 0.3883 (mmm) REVERT: H 986 GLN cc_start: 0.7327 (mt0) cc_final: 0.7061 (pp30) REVERT: E 476 LEU cc_start: 0.8246 (tp) cc_final: 0.7946 (mp) REVERT: G 90 GLU cc_start: 0.6838 (mm-30) cc_final: 0.6611 (mt-10) REVERT: G 111 MET cc_start: 0.8234 (mmm) cc_final: 0.7950 (mmm) REVERT: G 145 ASN cc_start: 0.8242 (m-40) cc_final: 0.7715 (m110) REVERT: G 179 THR cc_start: 0.8103 (OUTLIER) cc_final: 0.7432 (m) REVERT: G 242 ASP cc_start: 0.7412 (OUTLIER) cc_final: 0.7161 (t70) REVERT: G 271 TYR cc_start: 0.7975 (OUTLIER) cc_final: 0.7314 (t80) REVERT: G 300 GLU cc_start: 0.8096 (mp0) cc_final: 0.7218 (mp0) REVERT: G 302 ARG cc_start: 0.8135 (mmt180) cc_final: 0.7708 (mmt180) REVERT: G 695 MET cc_start: 0.6645 (mmm) cc_final: 0.5773 (mmm) REVERT: G 736 MET cc_start: 0.6208 (mmt) cc_final: 0.4708 (mmt) REVERT: C 800 MET cc_start: 0.7400 (ppp) cc_final: 0.6882 (ppp) REVERT: C 814 MET cc_start: 0.6130 (tpt) cc_final: 0.5814 (tpp) REVERT: C 1051 MET cc_start: 0.6877 (tmm) cc_final: 0.6456 (tpt) REVERT: D 872 MET cc_start: 0.8764 (mtp) cc_final: 0.8551 (mtp) REVERT: D 883 TYR cc_start: 0.8735 (p90) cc_final: 0.8442 (p90) REVERT: D 898 CYS cc_start: 0.5897 (t) cc_final: 0.5650 (t) outliers start: 106 outliers final: 87 residues processed: 403 average time/residue: 0.1983 time to fit residues: 134.9579 Evaluate side-chains 379 residues out of total 4112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 285 time to evaluate : 1.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 50 MET Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 299 MET Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 323 GLU Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 687 CYS Chi-restraints excluded: chain A residue 696 ASP Chi-restraints excluded: chain A residue 737 HIS Chi-restraints excluded: chain F residue 772 VAL Chi-restraints excluded: chain F residue 789 THR Chi-restraints excluded: chain F residue 814 MET Chi-restraints excluded: chain F residue 870 ILE Chi-restraints excluded: chain F residue 894 VAL Chi-restraints excluded: chain F residue 919 VAL Chi-restraints excluded: chain F residue 1019 VAL Chi-restraints excluded: chain F residue 1132 GLU Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 97 PHE Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 312 CYS Chi-restraints excluded: chain B residue 323 GLU Chi-restraints excluded: chain B residue 329 CYS Chi-restraints excluded: chain B residue 501 ASP Chi-restraints excluded: chain B residue 638 VAL Chi-restraints excluded: chain B residue 707 CYS Chi-restraints excluded: chain B residue 723 SER Chi-restraints excluded: chain B residue 729 CYS Chi-restraints excluded: chain H residue 799 CYS Chi-restraints excluded: chain H residue 809 LEU Chi-restraints excluded: chain H residue 829 CYS Chi-restraints excluded: chain H residue 870 ILE Chi-restraints excluded: chain H residue 904 THR Chi-restraints excluded: chain H residue 919 VAL Chi-restraints excluded: chain H residue 934 ILE Chi-restraints excluded: chain H residue 1029 SER Chi-restraints excluded: chain H residue 1188 GLN Chi-restraints excluded: chain H residue 1226 HIS Chi-restraints excluded: chain E residue 97 PHE Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain E residue 152 ASP Chi-restraints excluded: chain E residue 536 LEU Chi-restraints excluded: chain E residue 608 CYS Chi-restraints excluded: chain E residue 668 THR Chi-restraints excluded: chain E residue 673 SER Chi-restraints excluded: chain E residue 733 ASP Chi-restraints excluded: chain G residue 58 SER Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain G residue 97 PHE Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 179 THR Chi-restraints excluded: chain G residue 242 ASP Chi-restraints excluded: chain G residue 271 TYR Chi-restraints excluded: chain G residue 280 MET Chi-restraints excluded: chain G residue 311 THR Chi-restraints excluded: chain G residue 341 LEU Chi-restraints excluded: chain G residue 345 SER Chi-restraints excluded: chain G residue 356 ARG Chi-restraints excluded: chain G residue 426 VAL Chi-restraints excluded: chain G residue 471 VAL Chi-restraints excluded: chain G residue 490 VAL Chi-restraints excluded: chain G residue 508 LEU Chi-restraints excluded: chain G residue 510 VAL Chi-restraints excluded: chain G residue 512 LEU Chi-restraints excluded: chain G residue 640 VAL Chi-restraints excluded: chain G residue 704 LYS Chi-restraints excluded: chain G residue 709 CYS Chi-restraints excluded: chain C residue 771 MET Chi-restraints excluded: chain C residue 870 ILE Chi-restraints excluded: chain C residue 884 LEU Chi-restraints excluded: chain C residue 927 ILE Chi-restraints excluded: chain C residue 981 SER Chi-restraints excluded: chain C residue 1094 ILE Chi-restraints excluded: chain D residue 789 THR Chi-restraints excluded: chain D residue 870 ILE Chi-restraints excluded: chain D residue 916 HIS Chi-restraints excluded: chain D residue 934 ILE Chi-restraints excluded: chain D residue 941 VAL Chi-restraints excluded: chain D residue 956 VAL Chi-restraints excluded: chain D residue 992 VAL Chi-restraints excluded: chain D residue 1048 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 152 optimal weight: 10.0000 chunk 449 optimal weight: 0.0370 chunk 215 optimal weight: 0.6980 chunk 130 optimal weight: 0.3980 chunk 359 optimal weight: 9.9990 chunk 33 optimal weight: 6.9990 chunk 316 optimal weight: 10.0000 chunk 306 optimal weight: 9.9990 chunk 239 optimal weight: 1.9990 chunk 25 optimal weight: 20.0000 chunk 192 optimal weight: 10.0000 overall best weight: 2.0262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 368 ASN ** F 832 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1188 GLN ** 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 = 0.4313 r_free = 0.4313 target = 0.134640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.105727 restraints weight = 119639.612| |-----------------------------------------------------------------------------| r_work (start): 0.3873 rms_B_bonded: 4.26 r_work: 0.3709 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.3709 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3709 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3709 r_free = 0.3709 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3709 r_free = 0.3709 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3709 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.7947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.092 37630 Z= 0.133 Angle : 0.725 19.876 51244 Z= 0.360 Chirality : 0.046 0.451 5552 Planarity : 0.005 0.073 6728 Dihedral : 5.681 51.993 5558 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.85 % Favored : 92.13 % Rotamer: Outliers : 2.39 % Allowed : 17.01 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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: -2.58 (0.12), residues: 4744 helix: -1.43 (0.20), residues: 616 sheet: -2.26 (0.18), residues: 840 loop : -1.69 (0.11), residues: 3288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 698 TYR 0.017 0.001 TYR A 527 PHE 0.027 0.001 PHE F 937 TRP 0.053 0.002 TRP F1144 HIS 0.005 0.001 HIS D1047 Details of bonding type rmsd covalent geometry : bond 0.00310 (37380) covalent geometry : angle 0.70817 (50724) SS BOND : bond 0.00361 ( 230) SS BOND : angle 1.39524 ( 460) hydrogen bonds : bond 0.03444 ( 731) hydrogen bonds : angle 5.83249 ( 1748) link_NAG-ASN : bond 0.00460 ( 20) link_NAG-ASN : angle 3.16991 ( 60) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9488 Ramachandran restraints generated. 4744 Oldfield, 0 Emsley, 4744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9488 Ramachandran restraints generated. 4744 Oldfield, 0 Emsley, 4744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 4112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 308 time to evaluate : 1.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 GLN cc_start: 0.7828 (mm-40) cc_final: 0.7616 (pt0) REVERT: A 254 LEU cc_start: 0.5058 (OUTLIER) cc_final: 0.4806 (tp) REVERT: A 299 MET cc_start: 0.5961 (OUTLIER) cc_final: 0.5603 (tmm) REVERT: A 338 ASP cc_start: 0.6378 (OUTLIER) cc_final: 0.6143 (m-30) REVERT: A 455 LEU cc_start: 0.7908 (mt) cc_final: 0.7550 (tp) REVERT: B 50 MET cc_start: 0.8179 (mmt) cc_final: 0.7739 (ttt) REVERT: B 299 MET cc_start: 0.7015 (ttp) cc_final: 0.6611 (ttp) REVERT: B 644 GLU cc_start: 0.8619 (mt-10) cc_final: 0.8232 (mp0) REVERT: B 680 ASN cc_start: 0.7632 (m-40) cc_final: 0.6505 (p0) REVERT: B 728 MET cc_start: 0.7338 (tmm) cc_final: 0.7106 (tmm) REVERT: B 740 MET cc_start: 0.6687 (tmm) cc_final: 0.6345 (tpt) REVERT: H 793 GLN cc_start: 0.7511 (mm110) cc_final: 0.6993 (tt0) REVERT: H 986 GLN cc_start: 0.7225 (mt0) cc_final: 0.6968 (pp30) REVERT: E 347 GLU cc_start: 0.8129 (tp30) cc_final: 0.7388 (tm-30) REVERT: E 476 LEU cc_start: 0.8199 (tp) cc_final: 0.7938 (mp) REVERT: G 111 MET cc_start: 0.8080 (mmm) cc_final: 0.7806 (mmm) REVERT: G 145 ASN cc_start: 0.8179 (m-40) cc_final: 0.7659 (m110) REVERT: G 179 THR cc_start: 0.8022 (OUTLIER) cc_final: 0.7808 (p) REVERT: G 242 ASP cc_start: 0.7335 (OUTLIER) cc_final: 0.7050 (t70) REVERT: G 271 TYR cc_start: 0.7951 (OUTLIER) cc_final: 0.7314 (t80) REVERT: G 299 MET cc_start: 0.5861 (tpp) cc_final: 0.4278 (tpp) REVERT: G 302 ARG cc_start: 0.8158 (mmt180) cc_final: 0.7827 (mmt180) REVERT: G 695 MET cc_start: 0.6722 (mmm) cc_final: 0.5783 (mmm) REVERT: G 736 MET cc_start: 0.6219 (mmt) cc_final: 0.4770 (mmt) REVERT: C 800 MET cc_start: 0.7504 (ppp) cc_final: 0.7105 (ppp) REVERT: C 814 MET cc_start: 0.6000 (tpt) cc_final: 0.5619 (tpp) REVERT: C 1051 MET cc_start: 0.6912 (tmm) cc_final: 0.6509 (tpt) REVERT: D 872 MET cc_start: 0.8683 (mtp) cc_final: 0.8449 (mtp) REVERT: D 883 TYR cc_start: 0.8691 (p90) cc_final: 0.8343 (p90) REVERT: D 898 CYS cc_start: 0.5940 (t) cc_final: 0.5736 (t) outliers start: 94 outliers final: 74 residues processed: 386 average time/residue: 0.2111 time to fit residues: 136.6613 Evaluate side-chains 366 residues out of total 4112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 286 time to evaluate : 1.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 MET Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 299 MET Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 323 GLU Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain A residue 368 ASN Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain A residue 687 CYS Chi-restraints excluded: chain A residue 737 HIS Chi-restraints excluded: chain F residue 789 THR Chi-restraints excluded: chain F residue 814 MET Chi-restraints excluded: chain F residue 870 ILE Chi-restraints excluded: chain F residue 919 VAL Chi-restraints excluded: chain F residue 1019 VAL Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 97 PHE Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 312 CYS Chi-restraints excluded: chain B residue 323 GLU Chi-restraints excluded: chain B residue 329 CYS Chi-restraints excluded: chain B residue 501 ASP Chi-restraints excluded: chain B residue 638 VAL Chi-restraints excluded: chain B residue 707 CYS Chi-restraints excluded: chain B residue 729 CYS Chi-restraints excluded: chain H residue 799 CYS Chi-restraints excluded: chain H residue 809 LEU Chi-restraints excluded: chain H residue 829 CYS Chi-restraints excluded: chain H residue 870 ILE Chi-restraints excluded: chain H residue 904 THR Chi-restraints excluded: chain H residue 934 ILE Chi-restraints excluded: chain H residue 1029 SER Chi-restraints excluded: chain H residue 1226 HIS Chi-restraints excluded: chain E residue 97 PHE Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain E residue 536 LEU Chi-restraints excluded: chain E residue 608 CYS Chi-restraints excluded: chain E residue 668 THR Chi-restraints excluded: chain E residue 673 SER Chi-restraints excluded: chain E residue 733 ASP Chi-restraints excluded: chain G residue 58 SER Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain G residue 96 LEU Chi-restraints excluded: chain G residue 97 PHE Chi-restraints excluded: chain G residue 102 VAL Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 179 THR Chi-restraints excluded: chain G residue 242 ASP Chi-restraints excluded: chain G residue 271 TYR Chi-restraints excluded: chain G residue 280 MET Chi-restraints excluded: chain G residue 311 THR Chi-restraints excluded: chain G residue 341 LEU Chi-restraints excluded: chain G residue 345 SER Chi-restraints excluded: chain G residue 356 ARG Chi-restraints excluded: chain G residue 426 VAL Chi-restraints excluded: chain G residue 471 VAL Chi-restraints excluded: chain G residue 508 LEU Chi-restraints excluded: chain G residue 510 VAL Chi-restraints excluded: chain G residue 512 LEU Chi-restraints excluded: chain G residue 614 SER Chi-restraints excluded: chain G residue 640 VAL Chi-restraints excluded: chain G residue 704 LYS Chi-restraints excluded: chain G residue 709 CYS Chi-restraints excluded: chain C residue 870 ILE Chi-restraints excluded: chain C residue 884 LEU Chi-restraints excluded: chain C residue 981 SER Chi-restraints excluded: chain D residue 789 THR Chi-restraints excluded: chain D residue 870 ILE Chi-restraints excluded: chain D residue 916 HIS Chi-restraints excluded: chain D residue 934 ILE Chi-restraints excluded: chain D residue 941 VAL Chi-restraints excluded: chain D residue 992 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 161 optimal weight: 9.9990 chunk 417 optimal weight: 3.9990 chunk 287 optimal weight: 0.9980 chunk 297 optimal weight: 5.9990 chunk 250 optimal weight: 8.9990 chunk 324 optimal weight: 9.9990 chunk 143 optimal weight: 0.0670 chunk 376 optimal weight: 10.0000 chunk 129 optimal weight: 0.9980 chunk 122 optimal weight: 10.0000 chunk 21 optimal weight: 0.0670 overall best weight: 1.2258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 GLN A 368 ASN ** F 832 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 288 HIS ** C1188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1188 GLN ** 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 = 0.4325 r_free = 0.4325 target = 0.136041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.107553 restraints weight = 144510.498| |-----------------------------------------------------------------------------| r_work (start): 0.3888 rms_B_bonded: 5.14 r_work: 0.3705 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3704 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3704 r_free = 0.3704 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3704 r_free = 0.3704 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3704 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.8024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 37630 Z= 0.119 Angle : 0.709 16.040 51244 Z= 0.351 Chirality : 0.046 0.413 5552 Planarity : 0.005 0.073 6728 Dihedral : 5.478 51.836 5558 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.90 % Favored : 93.08 % Rotamer: Outliers : 2.15 % Allowed : 17.38 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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: -2.48 (0.12), residues: 4744 helix: -1.29 (0.20), residues: 644 sheet: -2.09 (0.19), residues: 760 loop : -1.69 (0.10), residues: 3340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 578 TYR 0.021 0.001 TYR F 897 PHE 0.028 0.001 PHE F 937 TRP 0.085 0.002 TRP F1144 HIS 0.006 0.001 HIS A 395 Details of bonding type rmsd covalent geometry : bond 0.00274 (37380) covalent geometry : angle 0.69086 (50724) SS BOND : bond 0.00337 ( 230) SS BOND : angle 1.47056 ( 460) hydrogen bonds : bond 0.03073 ( 731) hydrogen bonds : angle 5.71523 ( 1748) link_NAG-ASN : bond 0.00441 ( 20) link_NAG-ASN : angle 3.05923 ( 60) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9488 Ramachandran restraints generated. 4744 Oldfield, 0 Emsley, 4744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9488 Ramachandran restraints generated. 4744 Oldfield, 0 Emsley, 4744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 4112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 308 time to evaluate : 1.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 ASP cc_start: 0.7919 (m-30) cc_final: 0.7370 (m-30) REVERT: A 107 GLN cc_start: 0.7876 (mm-40) cc_final: 0.7674 (pt0) REVERT: A 254 LEU cc_start: 0.5065 (OUTLIER) cc_final: 0.4760 (tp) REVERT: A 338 ASP cc_start: 0.6379 (OUTLIER) cc_final: 0.6123 (m-30) REVERT: A 455 LEU cc_start: 0.8014 (mt) cc_final: 0.7663 (tp) REVERT: B 50 MET cc_start: 0.8151 (mmt) cc_final: 0.7720 (ttt) REVERT: B 75 ASP cc_start: 0.5800 (t0) cc_final: 0.5268 (t70) REVERT: B 644 GLU cc_start: 0.8643 (mt-10) cc_final: 0.8219 (mp0) REVERT: B 680 ASN cc_start: 0.7618 (m-40) cc_final: 0.6490 (p0) REVERT: B 728 MET cc_start: 0.7360 (tmm) cc_final: 0.7130 (tmm) REVERT: B 740 MET cc_start: 0.6750 (tmm) cc_final: 0.6357 (tpt) REVERT: H 814 MET cc_start: 0.7023 (mtt) cc_final: 0.6723 (mtp) REVERT: H 852 GLN cc_start: 0.7476 (tp-100) cc_final: 0.7185 (tp-100) REVERT: H 986 GLN cc_start: 0.7233 (mt0) cc_final: 0.6920 (pp30) REVERT: E 299 MET cc_start: 0.7617 (mtm) cc_final: 0.7251 (mmm) REVERT: E 347 GLU cc_start: 0.8121 (tp30) cc_final: 0.7346 (tm-30) REVERT: E 476 LEU cc_start: 0.8209 (tp) cc_final: 0.7956 (mp) REVERT: G 111 MET cc_start: 0.8096 (mmm) cc_final: 0.7791 (mmm) REVERT: G 145 ASN cc_start: 0.8192 (m-40) cc_final: 0.7666 (m110) REVERT: G 179 THR cc_start: 0.7953 (OUTLIER) cc_final: 0.7712 (p) REVERT: G 242 ASP cc_start: 0.7353 (OUTLIER) cc_final: 0.7077 (t70) REVERT: G 271 TYR cc_start: 0.7924 (OUTLIER) cc_final: 0.7331 (t80) REVERT: G 299 MET cc_start: 0.5753 (tpp) cc_final: 0.3994 (tpp) REVERT: G 302 ARG cc_start: 0.8215 (mmt180) cc_final: 0.7925 (mmt180) REVERT: G 695 MET cc_start: 0.6674 (mmm) cc_final: 0.5776 (mmm) REVERT: G 736 MET cc_start: 0.6367 (mmt) cc_final: 0.4875 (mmt) REVERT: C 1035 ARG cc_start: 0.7489 (tpp-160) cc_final: 0.7129 (mmt-90) REVERT: C 1051 MET cc_start: 0.6905 (tmm) cc_final: 0.6582 (tpt) REVERT: D 872 MET cc_start: 0.8668 (mtp) cc_final: 0.8461 (mtp) REVERT: D 883 TYR cc_start: 0.8666 (p90) cc_final: 0.8320 (p90) REVERT: D 898 CYS cc_start: 0.6134 (t) cc_final: 0.5882 (t) outliers start: 84 outliers final: 68 residues processed: 379 average time/residue: 0.2013 time to fit residues: 128.7004 Evaluate side-chains 364 residues out of total 4112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 291 time to evaluate : 1.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 MET Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 323 GLU Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain A residue 368 ASN Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain A residue 687 CYS Chi-restraints excluded: chain A residue 737 HIS Chi-restraints excluded: chain F residue 789 THR Chi-restraints excluded: chain F residue 814 MET Chi-restraints excluded: chain F residue 870 ILE Chi-restraints excluded: chain F residue 919 VAL Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 97 PHE Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 312 CYS Chi-restraints excluded: chain B residue 323 GLU Chi-restraints excluded: chain B residue 501 ASP Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 638 VAL Chi-restraints excluded: chain B residue 659 LEU Chi-restraints excluded: chain B residue 707 CYS Chi-restraints excluded: chain B residue 729 CYS Chi-restraints excluded: chain H residue 799 CYS Chi-restraints excluded: chain H residue 809 LEU Chi-restraints excluded: chain H residue 858 CYS Chi-restraints excluded: chain H residue 870 ILE Chi-restraints excluded: chain H residue 934 ILE Chi-restraints excluded: chain H residue 1029 SER Chi-restraints excluded: chain E residue 97 PHE Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain E residue 536 LEU Chi-restraints excluded: chain E residue 608 CYS Chi-restraints excluded: chain E residue 668 THR Chi-restraints excluded: chain E residue 733 ASP Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain G residue 96 LEU Chi-restraints excluded: chain G residue 97 PHE Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 179 THR Chi-restraints excluded: chain G residue 242 ASP Chi-restraints excluded: chain G residue 271 TYR Chi-restraints excluded: chain G residue 280 MET Chi-restraints excluded: chain G residue 311 THR Chi-restraints excluded: chain G residue 341 LEU Chi-restraints excluded: chain G residue 345 SER Chi-restraints excluded: chain G residue 426 VAL Chi-restraints excluded: chain G residue 471 VAL Chi-restraints excluded: chain G residue 508 LEU Chi-restraints excluded: chain G residue 510 VAL Chi-restraints excluded: chain G residue 512 LEU Chi-restraints excluded: chain G residue 614 SER Chi-restraints excluded: chain G residue 640 VAL Chi-restraints excluded: chain G residue 709 CYS Chi-restraints excluded: chain C residue 870 ILE Chi-restraints excluded: chain C residue 884 LEU Chi-restraints excluded: chain C residue 981 SER Chi-restraints excluded: chain D residue 789 THR Chi-restraints excluded: chain D residue 870 ILE Chi-restraints excluded: chain D residue 916 HIS Chi-restraints excluded: chain D residue 934 ILE Chi-restraints excluded: chain D residue 941 VAL Chi-restraints excluded: chain D residue 992 VAL Chi-restraints excluded: chain D residue 1048 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 402 optimal weight: 0.0010 chunk 274 optimal weight: 5.9990 chunk 145 optimal weight: 8.9990 chunk 217 optimal weight: 0.1980 chunk 444 optimal weight: 9.9990 chunk 391 optimal weight: 0.9980 chunk 341 optimal weight: 9.9990 chunk 31 optimal weight: 8.9990 chunk 269 optimal weight: 0.0010 chunk 297 optimal weight: 0.4980 chunk 240 optimal weight: 0.0970 overall best weight: 0.1590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 368 ASN ** F 832 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 737 HIS H 861 HIS ** E 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 421 HIS G 288 HIS ** C1188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.137970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.109537 restraints weight = 153084.625| |-----------------------------------------------------------------------------| r_work (start): 0.3913 rms_B_bonded: 5.55 r_work: 0.3729 rms_B_bonded: 5.03 restraints_weight: 2.0000 r_work (final): 0.3729 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3728 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3728 r_free = 0.3728 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3728 r_free = 0.3728 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3728 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.8092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 37630 Z= 0.115 Angle : 0.698 15.473 51244 Z= 0.344 Chirality : 0.045 0.376 5552 Planarity : 0.005 0.072 6728 Dihedral : 5.126 51.829 5558 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.77 % Favored : 93.21 % Rotamer: Outliers : 1.71 % Allowed : 17.96 % Favored : 80.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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: -2.36 (0.12), residues: 4744 helix: -1.20 (0.20), residues: 644 sheet: -1.94 (0.18), residues: 796 loop : -1.61 (0.11), residues: 3304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 365 TYR 0.017 0.001 TYR G 711 PHE 0.032 0.001 PHE F 937 TRP 0.058 0.002 TRP F1144 HIS 0.004 0.000 HIS D1047 Details of bonding type rmsd covalent geometry : bond 0.00254 (37380) covalent geometry : angle 0.68239 (50724) SS BOND : bond 0.00292 ( 230) SS BOND : angle 1.34149 ( 460) hydrogen bonds : bond 0.02953 ( 731) hydrogen bonds : angle 5.50709 ( 1748) link_NAG-ASN : bond 0.00459 ( 20) link_NAG-ASN : angle 2.88510 ( 60) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11705.57 seconds wall clock time: 199 minutes 39.76 seconds (11979.76 seconds total)