Starting phenix.real_space_refine on Sat Mar 7 00:59:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wpq_32688/03_2026/7wpq_32688_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wpq_32688/03_2026/7wpq_32688.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.267 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7wpq_32688/03_2026/7wpq_32688_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wpq_32688/03_2026/7wpq_32688_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7wpq_32688/03_2026/7wpq_32688.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wpq_32688/03_2026/7wpq_32688.map" } resolution = 3.267 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= 0.005 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 552 5.16 5 C 22560 2.51 5 N 6260 2.21 5 O 7188 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 45 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: 36576 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: "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: "C" Number of atoms: 3649 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 478, 3643 Classifications: {'peptide': 478} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 28, 'TRANS': 449} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Conformer: "B" Number of residues, atoms: 478, 3643 Classifications: {'peptide': 478} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 28, 'TRANS': 449} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 3712 Chain: "D" Number of atoms: 3649 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 478, 3643 Classifications: {'peptide': 478} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 28, 'TRANS': 449} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Conformer: "B" Number of residues, atoms: 478, 3643 Classifications: {'peptide': 478} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 28, 'TRANS': 449} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 3712 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: "F" Number of atoms: 3649 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 478, 3643 Classifications: {'peptide': 478} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 28, 'TRANS': 449} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Conformer: "B" Number of residues, atoms: 478, 3643 Classifications: {'peptide': 478} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 28, 'TRANS': 449} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 3712 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: "H" Number of atoms: 3649 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 478, 3643 Classifications: {'peptide': 478} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 28, 'TRANS': 449} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Conformer: "B" Number of residues, atoms: 478, 3643 Classifications: {'peptide': 478} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 28, 'TRANS': 449} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 3712 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: "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: "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 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: "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: "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: "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 Time building chain proxies: 10.69, per 1000 atoms: 0.29 Number of scatterers: 36576 At special positions: 0 Unit cell: (161.02, 248.32, 177.51, 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 552 16.00 O 7188 8.00 N 6260 7.00 C 22560 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=232, 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=2.03 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=2.03 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=2.03 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=2.03 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=2.04 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=2.03 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=2.02 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 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=2.03 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=2.03 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 C 767 " - pdb=" SG CYS C 808 " distance=2.03 Simple disulfide: pdb=" SG CYS C 776 " - pdb=" SG CYS C 804 " distance=2.02 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=2.02 Simple disulfide: pdb=" SG CYS C1101 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C1130 " - pdb=" SG CYS C1173 " distance=2.03 Simple disulfide: pdb=" SG CYS C1142 " - pdb=" SG CYS D1142 " distance=2.04 Simple disulfide: pdb=" SG CYS C1149 " - pdb=" SG CYS C1169 " distance=2.03 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=2.02 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=2.02 Simple disulfide: pdb=" SG CYS D1091 " - pdb=" SG CYS D1099 " distance=2.03 Simple disulfide: pdb=" SG CYS D1101 " - pdb=" SG CYS D1126 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS D1225 " - pdb=" SG CYS D1234 " 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=2.03 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS E 304 " - pdb=" SG CYS E 325 " distance=2.04 Simple disulfide: pdb=" SG CYS E 308 " - pdb=" SG CYS E 321 " distance=2.03 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=2.04 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 F 767 " - pdb=" SG CYS F 808 " distance=2.03 Simple disulfide: pdb=" SG CYS F 776 " - pdb=" SG CYS F 804 " distance=2.02 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS F1071 " - pdb=" SG CYS F1111 " distance=2.02 Simple disulfide: pdb=" SG CYS F1091 " - pdb=" SG CYS F1099 " distance=2.03 Simple disulfide: pdb=" SG CYS F1097 " - pdb=" SG CYS H1097 " distance=2.03 Simple disulfide: pdb=" SG CYS F1101 " - pdb=" SG CYS F1126 " distance=2.03 Simple disulfide: pdb=" SG CYS F1130 " - pdb=" SG CYS F1173 " distance=2.03 Simple disulfide: pdb=" SG CYS F1142 " - pdb=" SG CYS H1142 " 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 G 35 " - pdb=" SG CYS G 162 " distance=2.03 Simple disulfide: pdb=" SG CYS G 57 " - pdb=" SG CYS G 200 " distance=2.03 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=2.03 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=2.03 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=2.03 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=2.04 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 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=2.04 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS H1071 " - pdb=" SG CYS H1111 " distance=2.02 Simple disulfide: pdb=" SG CYS H1091 " - pdb=" SG CYS H1099 " distance=2.03 Simple disulfide: pdb=" SG CYS H1101 " - pdb=" SG CYS H1126 " distance=2.03 Simple disulfide: pdb=" SG CYS H1130 " - pdb=" SG CYS H1173 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS H1225 " - pdb=" SG CYS H1234 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 801 " - " ASN A 156 " " NAG A 802 " - " ASN A 99 " " NAG B 801 " - " ASN B 156 " " NAG B 802 " - " ASN B 99 " " NAG C1301 " - " ASN C1231 " " NAG C1302 " - " ASN C 857 " " NAG C1303 " - " ASN C1147 " " NAG D1301 " - " ASN D1231 " " NAG D1302 " - " ASN D 857 " " NAG D1303 " - " ASN D1147 " " NAG E 801 " - " ASN E 156 " " NAG E 802 " - " ASN E 99 " " NAG F1301 " - " ASN F1231 " " NAG F1302 " - " ASN F 857 " " NAG F1303 " - " ASN F1147 " " NAG G 801 " - " ASN G 156 " " NAG G 802 " - " ASN G 99 " " NAG H1301 " - " ASN H1231 " " NAG H1302 " - " ASN H 857 " " NAG H1303 " - " ASN H1147 " Time building additional restraints: 2.87 Conformation dependent library (CDL) restraints added in 2.0 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: 112 helices and 97 sheets defined 17.6% alpha, 14.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.41 Creating SS restraints... Processing helix chain 'A' and resid 114 through 118 removed outlier: 3.844A pdb=" N GLY A 117 " --> pdb=" O ALA A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 155 Processing helix chain 'A' and resid 208 through 212 removed outlier: 3.870A pdb=" N ASN A 211 " --> pdb=" O SER A 208 " (cutoff:3.500A) removed outlier: 3.551A 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 214 through 219 removed outlier: 4.227A pdb=" N GLN A 218 " --> pdb=" O GLY A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 231 removed outlier: 4.309A pdb=" N CYS A 225 " --> pdb=" O LEU A 221 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N LEU A 228 " --> pdb=" O GLN A 224 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N LYS A 229 " --> pdb=" O CYS A 225 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR A 231 " --> pdb=" O LEU A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 235 Processing helix chain 'A' and resid 243 through 251 removed outlier: 3.559A pdb=" N GLU A 251 " --> pdb=" O VAL A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 263 No H-bonds generated for 'chain 'A' and resid 261 through 263' Processing helix chain 'A' and resid 264 through 277 removed outlier: 3.755A pdb=" N TYR A 271 " --> pdb=" O ALA A 267 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG A 273 " --> pdb=" O LEU A 269 " (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 Processing helix chain 'A' and resid 551 through 553 No H-bonds generated for 'chain 'A' and resid 551 through 553' Processing helix chain 'A' and resid 575 through 584 removed outlier: 4.722A pdb=" N PHE A 579 " --> pdb=" O ARG A 575 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU A 581 " --> pdb=" O THR A 577 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N CYS A 584 " --> pdb=" O SER A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 588 Processing helix chain 'A' and resid 589 through 596 removed outlier: 5.126A pdb=" N ALA A 594 " --> pdb=" O THR A 591 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N HIS A 596 " --> pdb=" O GLU A 593 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 613 removed outlier: 3.538A pdb=" N CYS A 608 " --> pdb=" O TYR A 604 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG A 609 " --> pdb=" O LEU A 605 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N TYR A 610 " --> pdb=" O ARG A 606 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N CYS A 613 " --> pdb=" O ARG A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 617 through 624 removed outlier: 3.593A pdb=" N CYS A 621 " --> pdb=" O ASP A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 634 removed outlier: 3.561A pdb=" N TYR A 629 " --> pdb=" O ALA A 625 " (cutoff:3.500A) removed outlier: 3.718A 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: 3.798A pdb=" N SER A 673 " --> pdb=" O CYS A 669 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 118 removed outlier: 3.843A pdb=" N GLY B 117 " --> pdb=" O ALA B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 155 Processing helix chain 'B' and resid 208 through 212 removed outlier: 3.869A pdb=" N ASN B 211 " --> pdb=" O SER B 208 " (cutoff:3.500A) removed outlier: 3.549A 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 214 through 219 removed outlier: 4.229A pdb=" N GLN B 218 " --> pdb=" O GLY B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 231 removed outlier: 4.309A pdb=" N CYS B 225 " --> pdb=" O LEU B 221 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N LEU B 228 " --> pdb=" O GLN B 224 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N LYS B 229 " --> pdb=" O CYS B 225 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR B 231 " --> pdb=" O LEU B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 235 Processing helix chain 'B' and resid 243 through 251 removed outlier: 3.558A pdb=" N GLU B 251 " --> pdb=" O VAL B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 263 No H-bonds generated for 'chain 'B' and resid 261 through 263' Processing helix chain 'B' and resid 264 through 277 removed outlier: 3.755A pdb=" N TYR B 271 " --> pdb=" O ALA B 267 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG B 273 " --> pdb=" O LEU B 269 " (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 Processing helix chain 'B' and resid 551 through 553 No H-bonds generated for 'chain 'B' and resid 551 through 553' Processing helix chain 'B' and resid 575 through 584 removed outlier: 4.722A pdb=" N PHE B 579 " --> pdb=" O ARG B 575 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU B 581 " --> pdb=" O THR B 577 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N CYS B 584 " --> pdb=" O SER B 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 585 through 588 Processing helix chain 'B' and resid 589 through 596 removed outlier: 5.125A pdb=" N ALA B 594 " --> pdb=" O THR B 591 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N HIS B 596 " --> pdb=" O GLU B 593 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 613 removed outlier: 3.538A pdb=" N CYS B 608 " --> pdb=" O TYR B 604 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG B 609 " --> pdb=" O LEU B 605 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N TYR B 610 " --> pdb=" O ARG B 606 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N CYS B 613 " --> pdb=" O ARG B 609 " (cutoff:3.500A) Processing helix chain 'B' and resid 617 through 624 removed outlier: 3.593A pdb=" N CYS B 621 " --> pdb=" O ASP B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 634 removed outlier: 3.561A pdb=" N TYR B 629 " --> pdb=" O ALA B 625 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA B 632 " --> pdb=" O SER B 628 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 674 removed outlier: 4.235A pdb=" N LEU B 672 " --> pdb=" O THR B 668 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N SER B 673 " --> pdb=" O CYS B 669 " (cutoff:3.500A) Processing helix chain 'C' and resid 1017 through 1022 Processing helix chain 'C' and resid 1023 through 1026 removed outlier: 3.905A pdb=" N LYS C1026 " --> pdb=" O ASN C1023 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1023 through 1026' Processing helix chain 'C' and resid 1049 through 1060 removed outlier: 3.525A pdb=" N THR C1054 " --> pdb=" O ILE C1050 " (cutoff:3.500A) Processing helix chain 'C' and resid 1061 through 1064 Processing helix chain 'C' and resid 1068 through 1073 removed outlier: 3.875A pdb=" N LYS C1073 " --> pdb=" O GLN C1069 " (cutoff:3.500A) Processing helix chain 'C' and resid 1077 through 1091 removed outlier: 3.527A pdb=" N VAL C1083 " --> pdb=" O PRO C1079 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N CYS C1084 " --> pdb=" O TYR C1080 " (cutoff:3.500A) Processing helix chain 'C' and resid 1097 through 1114 removed outlier: 5.001A pdb=" N THR C1103 " --> pdb=" O CYS C1099 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ILE C1104 " --> pdb=" O PHE C1100 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA C1105 " --> pdb=" O CYS C1101 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N TYR C1107 " --> pdb=" O THR C1103 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL C1110 " --> pdb=" O ALA C1106 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N HIS C1114 " --> pdb=" O VAL C1110 " (cutoff:3.500A) Processing helix chain 'C' and resid 1192 through 1196 Processing helix chain 'D' and resid 1017 through 1022 Processing helix chain 'D' and resid 1023 through 1026 removed outlier: 3.905A pdb=" N LYS D1026 " --> pdb=" O ASN D1023 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1023 through 1026' Processing helix chain 'D' and resid 1049 through 1060 removed outlier: 3.524A pdb=" N THR D1054 " --> pdb=" O ILE D1050 " (cutoff:3.500A) Processing helix chain 'D' and resid 1061 through 1064 Processing helix chain 'D' and resid 1068 through 1073 removed outlier: 3.876A pdb=" N LYS D1073 " --> pdb=" O GLN D1069 " (cutoff:3.500A) Processing helix chain 'D' and resid 1077 through 1091 removed outlier: 3.528A pdb=" N VAL D1083 " --> pdb=" O PRO D1079 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N CYS D1084 " --> pdb=" O TYR D1080 " (cutoff:3.500A) Processing helix chain 'D' and resid 1097 through 1114 removed outlier: 5.002A pdb=" N THR D1103 " --> pdb=" O CYS D1099 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ILE D1104 " --> pdb=" O PHE D1100 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA D1105 " --> pdb=" O CYS D1101 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TYR D1107 " --> pdb=" O THR D1103 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL D1110 " --> pdb=" O ALA D1106 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N HIS D1114 " --> pdb=" O VAL D1110 " (cutoff:3.500A) Processing helix chain 'D' and resid 1192 through 1196 Processing helix chain 'E' and resid 114 through 118 removed outlier: 3.843A pdb=" N GLY E 117 " --> pdb=" O ALA E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 152 through 155 Processing helix chain 'E' and resid 208 through 212 removed outlier: 3.870A pdb=" N ASN E 211 " --> pdb=" O SER E 208 " (cutoff:3.500A) removed outlier: 3.549A 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 214 through 219 removed outlier: 4.228A pdb=" N GLN E 218 " --> pdb=" O GLY E 215 " (cutoff:3.500A) Processing helix chain 'E' and resid 221 through 231 removed outlier: 4.309A pdb=" N CYS E 225 " --> pdb=" O LEU E 221 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N LEU E 228 " --> pdb=" O GLN E 224 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N LYS E 229 " --> pdb=" O CYS E 225 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR E 231 " --> pdb=" O LEU E 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 232 through 235 Processing helix chain 'E' and resid 243 through 251 removed outlier: 3.559A pdb=" N GLU E 251 " --> pdb=" O VAL E 247 " (cutoff:3.500A) Processing helix chain 'E' and resid 261 through 263 No H-bonds generated for 'chain 'E' and resid 261 through 263' Processing helix chain 'E' and resid 264 through 277 removed outlier: 3.754A pdb=" N TYR E 271 " --> pdb=" O ALA E 267 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ARG E 273 " --> pdb=" O LEU E 269 " (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 Processing helix chain 'E' and resid 551 through 553 No H-bonds generated for 'chain 'E' and resid 551 through 553' Processing helix chain 'E' and resid 575 through 584 removed outlier: 4.722A pdb=" N PHE E 579 " --> pdb=" O ARG E 575 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLU E 581 " --> pdb=" O THR E 577 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N CYS E 584 " --> pdb=" O SER E 580 " (cutoff:3.500A) Processing helix chain 'E' and resid 585 through 588 Processing helix chain 'E' and resid 589 through 596 removed outlier: 5.126A pdb=" N ALA E 594 " --> pdb=" O THR E 591 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N HIS E 596 " --> pdb=" O GLU E 593 " (cutoff:3.500A) Processing helix chain 'E' and resid 601 through 613 removed outlier: 3.537A pdb=" N CYS E 608 " --> pdb=" O TYR E 604 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG E 609 " --> pdb=" O LEU E 605 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N TYR E 610 " --> pdb=" O ARG E 606 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N CYS E 613 " --> pdb=" O ARG E 609 " (cutoff:3.500A) Processing helix chain 'E' and resid 617 through 624 removed outlier: 3.594A pdb=" N CYS E 621 " --> pdb=" O ASP E 617 " (cutoff:3.500A) Processing helix chain 'E' and resid 625 through 634 removed outlier: 3.563A pdb=" N TYR E 629 " --> pdb=" O ALA E 625 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA E 632 " --> pdb=" O SER E 628 " (cutoff:3.500A) Processing helix chain 'E' and resid 668 through 674 removed outlier: 4.235A pdb=" N LEU E 672 " --> pdb=" O THR E 668 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N SER E 673 " --> pdb=" O CYS E 669 " (cutoff:3.500A) Processing helix chain 'F' and resid 1017 through 1022 Processing helix chain 'F' and resid 1023 through 1026 removed outlier: 3.906A pdb=" N LYS F1026 " --> pdb=" O ASN F1023 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 1023 through 1026' Processing helix chain 'F' and resid 1049 through 1060 removed outlier: 3.525A pdb=" N THR F1054 " --> pdb=" O ILE F1050 " (cutoff:3.500A) Processing helix chain 'F' and resid 1061 through 1064 Processing helix chain 'F' and resid 1068 through 1073 removed outlier: 3.877A pdb=" N LYS F1073 " --> pdb=" O GLN F1069 " (cutoff:3.500A) Processing helix chain 'F' and resid 1077 through 1091 removed outlier: 3.528A pdb=" N VAL F1083 " --> pdb=" O PRO F1079 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N CYS F1084 " --> pdb=" O TYR F1080 " (cutoff:3.500A) Processing helix chain 'F' and resid 1097 through 1114 removed outlier: 5.003A pdb=" N THR F1103 " --> pdb=" O CYS F1099 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ILE F1104 " --> pdb=" O PHE F1100 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA F1105 " --> pdb=" O CYS F1101 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TYR F1107 " --> pdb=" O THR F1103 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL F1110 " --> pdb=" O ALA F1106 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N HIS F1114 " --> pdb=" O VAL F1110 " (cutoff:3.500A) Processing helix chain 'F' and resid 1192 through 1196 Processing helix chain 'G' and resid 114 through 118 removed outlier: 3.844A pdb=" N GLY G 117 " --> pdb=" O ALA G 114 " (cutoff:3.500A) Processing helix chain 'G' and resid 152 through 155 Processing helix chain 'G' and resid 208 through 212 removed outlier: 3.868A pdb=" N ASN G 211 " --> pdb=" O SER G 208 " (cutoff:3.500A) removed outlier: 3.549A 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 214 through 219 removed outlier: 4.228A pdb=" N GLN G 218 " --> pdb=" O GLY G 215 " (cutoff:3.500A) Processing helix chain 'G' and resid 221 through 231 removed outlier: 4.310A pdb=" N CYS G 225 " --> pdb=" O LEU G 221 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N LEU G 228 " --> pdb=" O GLN G 224 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N LYS G 229 " --> pdb=" O CYS G 225 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR G 231 " --> pdb=" O LEU G 227 " (cutoff:3.500A) Processing helix chain 'G' and resid 232 through 235 Processing helix chain 'G' and resid 243 through 251 removed outlier: 3.558A pdb=" N GLU G 251 " --> pdb=" O VAL G 247 " (cutoff:3.500A) Processing helix chain 'G' and resid 261 through 263 No H-bonds generated for 'chain 'G' and resid 261 through 263' Processing helix chain 'G' and resid 264 through 277 removed outlier: 3.754A pdb=" N TYR G 271 " --> pdb=" O ALA G 267 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG G 273 " --> pdb=" O LEU G 269 " (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 Processing helix chain 'G' and resid 551 through 553 No H-bonds generated for 'chain 'G' and resid 551 through 553' Processing helix chain 'G' and resid 575 through 584 removed outlier: 4.723A pdb=" N PHE G 579 " --> pdb=" O ARG G 575 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLU G 581 " --> pdb=" O THR G 577 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N CYS G 584 " --> pdb=" O SER G 580 " (cutoff:3.500A) Processing helix chain 'G' and resid 585 through 588 Processing helix chain 'G' and resid 589 through 596 removed outlier: 5.126A pdb=" N ALA G 594 " --> pdb=" O THR G 591 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N HIS G 596 " --> pdb=" O GLU G 593 " (cutoff:3.500A) Processing helix chain 'G' and resid 601 through 613 removed outlier: 3.538A pdb=" N CYS G 608 " --> pdb=" O TYR G 604 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG G 609 " --> pdb=" O LEU G 605 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N TYR G 610 " --> pdb=" O ARG G 606 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N CYS G 613 " --> pdb=" O ARG G 609 " (cutoff:3.500A) Processing helix chain 'G' and resid 617 through 624 removed outlier: 3.594A pdb=" N CYS G 621 " --> pdb=" O ASP G 617 " (cutoff:3.500A) Processing helix chain 'G' and resid 625 through 634 removed outlier: 3.561A pdb=" N TYR G 629 " --> pdb=" O ALA G 625 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA G 632 " --> pdb=" O SER G 628 " (cutoff:3.500A) Processing helix chain 'G' and resid 668 through 674 removed outlier: 4.236A pdb=" N LEU G 672 " --> pdb=" O THR G 668 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N SER G 673 " --> pdb=" O CYS G 669 " (cutoff:3.500A) Processing helix chain 'H' and resid 1017 through 1022 Processing helix chain 'H' and resid 1023 through 1026 removed outlier: 3.906A pdb=" N LYS H1026 " --> pdb=" O ASN H1023 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 1023 through 1026' Processing helix chain 'H' and resid 1049 through 1060 removed outlier: 3.524A pdb=" N THR H1054 " --> pdb=" O ILE H1050 " (cutoff:3.500A) Processing helix chain 'H' and resid 1061 through 1064 Processing helix chain 'H' and resid 1068 through 1073 removed outlier: 3.877A pdb=" N LYS H1073 " --> pdb=" O GLN H1069 " (cutoff:3.500A) Processing helix chain 'H' and resid 1077 through 1091 removed outlier: 3.527A pdb=" N VAL H1083 " --> pdb=" O PRO H1079 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N CYS H1084 " --> pdb=" O TYR H1080 " (cutoff:3.500A) Processing helix chain 'H' and resid 1097 through 1114 removed outlier: 5.001A pdb=" N THR H1103 " --> pdb=" O CYS H1099 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ILE H1104 " --> pdb=" O PHE H1100 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA H1105 " --> pdb=" O CYS H1101 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TYR H1107 " --> pdb=" O THR H1103 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL H1110 " --> pdb=" O ALA H1106 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N HIS H1114 " --> pdb=" O VAL H1110 " (cutoff:3.500A) Processing helix chain 'H' and resid 1192 through 1196 Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 37 removed outlier: 3.520A pdb=" N PHE A 146 " --> pdb=" O LEU A 37 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 44 removed outlier: 3.537A 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 63 removed outlier: 6.835A pdb=" N ILE A 72 " --> pdb=" O LEU A 61 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 102 through 104 removed outlier: 4.650A pdb=" N VAL A 102 " --> pdb=" O VAL A 109 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 300 through 301 removed outlier: 3.769A pdb=" N GLU A 300 " --> pdb=" O SER A 330 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 350 through 352 Processing sheet with id=AA7, first strand: chain 'A' and resid 362 through 364 Processing sheet with id=AA8, first strand: chain 'A' and resid 389 through 391 Processing sheet with id=AA9, first strand: chain 'A' and resid 411 through 416 removed outlier: 5.615A pdb=" N GLN A 411 " --> pdb=" O THR A 429 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N THR A 429 " --> pdb=" O GLN A 411 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N LEU A 413 " --> pdb=" O ILE A 427 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N ILE A 427 " --> pdb=" O LEU A 413 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA A 415 " --> pdb=" O ILE A 425 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N SER A 443 " --> pdb=" O GLU A 428 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N VAL A 430 " --> pdb=" O THR A 441 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N THR A 441 " --> pdb=" O VAL A 430 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 465 through 466 Processing sheet with id=AB2, first strand: chain 'A' and resid 480 through 484 Processing sheet with id=AB3, first strand: chain 'A' and resid 498 through 499 removed outlier: 3.544A pdb=" N LYS A 511 " --> pdb=" O GLN A 499 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 536 through 537 removed outlier: 3.525A pdb=" N THR A 537 " --> pdb=" O LEU A 541 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N LEU A 541 " --> pdb=" O THR A 537 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 657 through 662 removed outlier: 3.834A pdb=" N CYS A 661 " --> pdb=" O LEU A 684 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N LEU A 684 " --> pdb=" O CYS A 661 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 694 through 695 Processing sheet with id=AB7, first strand: chain 'A' and resid 709 through 711 Processing sheet with id=AB8, first strand: chain 'A' and resid 728 through 731 removed outlier: 3.736A pdb=" N MET A 728 " --> pdb=" O THR A 739 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 35 through 37 removed outlier: 3.520A pdb=" N PHE B 146 " --> pdb=" O LEU B 37 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 42 through 44 removed outlier: 3.536A pdb=" N TYR B 51 " --> pdb=" O VAL B 43 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.834A pdb=" N ILE B 72 " --> pdb=" O LEU B 61 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 103 through 104 Processing sheet with id=AC4, first strand: chain 'B' and resid 300 through 301 removed outlier: 3.769A pdb=" N GLU B 300 " --> pdb=" O SER B 330 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 350 through 352 Processing sheet with id=AC6, first strand: chain 'B' and resid 362 through 364 Processing sheet with id=AC7, first strand: chain 'B' and resid 389 through 391 Processing sheet with id=AC8, first strand: chain 'B' and resid 411 through 416 removed outlier: 5.615A pdb=" N GLN B 411 " --> pdb=" O THR B 429 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N THR B 429 " --> pdb=" O GLN B 411 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N LEU B 413 " --> pdb=" O ILE B 427 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N ILE B 427 " --> pdb=" O LEU B 413 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA B 415 " --> pdb=" O ILE B 425 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N SER B 443 " --> pdb=" O GLU B 428 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N VAL B 430 " --> pdb=" O THR B 441 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N THR B 441 " --> pdb=" O VAL B 430 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 465 through 466 Processing sheet with id=AD1, first strand: chain 'B' and resid 480 through 484 Processing sheet with id=AD2, first strand: chain 'B' and resid 498 through 499 removed outlier: 3.544A pdb=" N LYS B 511 " --> pdb=" O GLN B 499 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 536 through 537 removed outlier: 3.525A pdb=" N THR B 537 " --> pdb=" O LEU B 541 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N LEU B 541 " --> pdb=" O THR B 537 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'B' and resid 657 through 662 removed outlier: 3.835A pdb=" N CYS B 661 " --> pdb=" O LEU B 684 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N LEU B 684 " --> pdb=" O CYS B 661 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 694 through 695 Processing sheet with id=AD6, first strand: chain 'B' and resid 709 through 711 Processing sheet with id=AD7, first strand: chain 'B' and resid 728 through 731 removed outlier: 3.736A pdb=" N MET B 728 " --> pdb=" O THR B 739 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 772 through 773 Processing sheet with id=AD9, first strand: chain 'C' and resid 841 through 844 Processing sheet with id=AE1, first strand: chain 'C' and resid 865 through 866 removed outlier: 6.147A pdb=" N LEU C 970 " --> pdb=" O LEU C 966 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 875 through 876 Processing sheet with id=AE3, first strand: chain 'C' and resid 890 through 895 removed outlier: 3.731A pdb=" N LEU C 893 " --> pdb=" O ILE C 907 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N ILE C 907 " --> pdb=" O LEU C 893 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N THR C 926 " --> pdb=" O LEU C 908 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LYS C 912 " --> pdb=" O LYS C 922 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N LYS C 922 " --> pdb=" O LYS C 912 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N GLU C 933 " --> pdb=" O LYS C 944 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLU C 940 " --> pdb=" O PHE C 937 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 1144 through 1151 removed outlier: 3.626A pdb=" N GLY C1172 " --> pdb=" O ASN C1147 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N CYS C1149 " --> pdb=" O VAL C1170 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N VAL C1170 " --> pdb=" O CYS C1149 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 1182 through 1183 Processing sheet with id=AE6, first strand: chain 'D' and resid 772 through 773 Processing sheet with id=AE7, first strand: chain 'D' and resid 841 through 844 Processing sheet with id=AE8, first strand: chain 'D' and resid 865 through 866 removed outlier: 6.148A pdb=" N LEU D 970 " --> pdb=" O LEU D 966 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 875 through 876 Processing sheet with id=AF1, first strand: chain 'D' and resid 890 through 895 removed outlier: 3.731A pdb=" N LEU D 893 " --> pdb=" O ILE D 907 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N ILE D 907 " --> pdb=" O LEU D 893 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N THR D 926 " --> pdb=" O LEU D 908 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LYS D 912 " --> pdb=" O LYS D 922 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N LYS D 922 " --> pdb=" O LYS D 912 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N GLU D 933 " --> pdb=" O LYS D 944 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLU D 940 " --> pdb=" O PHE D 937 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 1144 through 1146 Processing sheet with id=AF3, first strand: chain 'D' and resid 1150 through 1151 Processing sheet with id=AF4, first strand: chain 'D' and resid 1182 through 1183 Processing sheet with id=AF5, first strand: chain 'E' and resid 35 through 37 removed outlier: 3.520A pdb=" N PHE E 146 " --> pdb=" O LEU E 37 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'E' and resid 42 through 44 removed outlier: 3.536A 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 63 removed outlier: 6.834A pdb=" N ILE E 72 " --> pdb=" O LEU E 61 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'E' and resid 103 through 104 Processing sheet with id=AF9, first strand: chain 'E' and resid 300 through 301 removed outlier: 3.769A pdb=" N GLU E 300 " --> pdb=" O SER E 330 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'E' and resid 350 through 352 Processing sheet with id=AG2, first strand: chain 'E' and resid 362 through 364 Processing sheet with id=AG3, first strand: chain 'E' and resid 389 through 391 Processing sheet with id=AG4, first strand: chain 'E' and resid 411 through 416 removed outlier: 5.615A pdb=" N GLN E 411 " --> pdb=" O THR E 429 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N THR E 429 " --> pdb=" O GLN E 411 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N LEU E 413 " --> pdb=" O ILE E 427 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N ILE E 427 " --> pdb=" O LEU E 413 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA E 415 " --> pdb=" O ILE E 425 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N SER E 443 " --> pdb=" O GLU E 428 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N VAL E 430 " --> pdb=" O THR E 441 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N THR E 441 " --> pdb=" O VAL E 430 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'E' and resid 465 through 466 Processing sheet with id=AG6, first strand: chain 'E' and resid 480 through 484 Processing sheet with id=AG7, first strand: chain 'E' and resid 498 through 499 removed outlier: 3.545A pdb=" N LYS E 511 " --> pdb=" O GLN E 499 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'E' and resid 536 through 537 removed outlier: 3.525A pdb=" N THR E 537 " --> pdb=" O LEU E 541 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N LEU E 541 " --> pdb=" O THR E 537 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG8 Processing sheet with id=AG9, first strand: chain 'E' and resid 657 through 662 removed outlier: 3.834A pdb=" N CYS E 661 " --> pdb=" O LEU E 684 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N LEU E 684 " --> pdb=" O CYS E 661 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'E' and resid 694 through 695 Processing sheet with id=AH2, first strand: chain 'E' and resid 709 through 711 Processing sheet with id=AH3, first strand: chain 'E' and resid 728 through 731 removed outlier: 3.736A pdb=" N MET E 728 " --> pdb=" O THR E 739 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'F' and resid 772 through 773 Processing sheet with id=AH5, first strand: chain 'F' and resid 841 through 844 Processing sheet with id=AH6, first strand: chain 'F' and resid 865 through 866 removed outlier: 6.147A pdb=" N LEU F 970 " --> pdb=" O LEU F 966 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'F' and resid 875 through 876 Processing sheet with id=AH8, first strand: chain 'F' and resid 890 through 895 removed outlier: 3.731A pdb=" N LEU F 893 " --> pdb=" O ILE F 907 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N ILE F 907 " --> pdb=" O LEU F 893 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N THR F 926 " --> pdb=" O LEU F 908 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LYS F 912 " --> pdb=" O LYS F 922 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N LYS F 922 " --> pdb=" O LYS F 912 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N GLU F 933 " --> pdb=" O LYS F 944 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLU F 940 " --> pdb=" O PHE F 937 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'F' and resid 1144 through 1151 removed outlier: 3.523A pdb=" N GLY F1172 " --> pdb=" O ASN F1147 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N CYS F1149 " --> pdb=" O VAL F1170 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N VAL F1170 " --> pdb=" O CYS F1149 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'F' and resid 1182 through 1183 Processing sheet with id=AI2, first strand: chain 'G' and resid 35 through 37 removed outlier: 3.521A pdb=" N PHE G 146 " --> pdb=" O LEU G 37 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'G' and resid 42 through 44 removed outlier: 3.536A pdb=" N TYR G 51 " --> pdb=" O VAL G 43 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'G' and resid 58 through 63 removed outlier: 6.834A pdb=" N ILE G 72 " --> pdb=" O LEU G 61 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'G' and resid 103 through 104 Processing sheet with id=AI6, first strand: chain 'G' and resid 300 through 301 removed outlier: 3.769A pdb=" N GLU G 300 " --> pdb=" O SER G 330 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'G' and resid 350 through 352 Processing sheet with id=AI8, first strand: chain 'G' and resid 362 through 364 Processing sheet with id=AI9, first strand: chain 'G' and resid 389 through 391 Processing sheet with id=AJ1, first strand: chain 'G' and resid 411 through 416 removed outlier: 5.615A pdb=" N GLN G 411 " --> pdb=" O THR G 429 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N THR G 429 " --> pdb=" O GLN G 411 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N LEU G 413 " --> pdb=" O ILE G 427 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N ILE G 427 " --> pdb=" O LEU G 413 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA G 415 " --> pdb=" O ILE G 425 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N SER G 443 " --> pdb=" O GLU G 428 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N VAL G 430 " --> pdb=" O THR G 441 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N THR G 441 " --> pdb=" O VAL G 430 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'G' and resid 465 through 466 Processing sheet with id=AJ3, first strand: chain 'G' and resid 480 through 484 Processing sheet with id=AJ4, first strand: chain 'G' and resid 498 through 499 removed outlier: 3.546A pdb=" N LYS G 511 " --> pdb=" O GLN G 499 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'G' and resid 536 through 537 removed outlier: 3.525A pdb=" N THR G 537 " --> pdb=" O LEU G 541 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N LEU G 541 " --> pdb=" O THR G 537 " (cutoff:3.500A) No H-bonds generated for sheet with id=AJ5 Processing sheet with id=AJ6, first strand: chain 'G' and resid 657 through 662 removed outlier: 3.835A pdb=" N CYS G 661 " --> pdb=" O LEU G 684 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N LEU G 684 " --> pdb=" O CYS G 661 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'G' and resid 694 through 695 Processing sheet with id=AJ8, first strand: chain 'G' and resid 709 through 711 Processing sheet with id=AJ9, first strand: chain 'G' and resid 728 through 731 removed outlier: 3.737A pdb=" N MET G 728 " --> pdb=" O THR G 739 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'H' and resid 772 through 773 Processing sheet with id=AK2, first strand: chain 'H' and resid 841 through 844 Processing sheet with id=AK3, first strand: chain 'H' and resid 865 through 866 removed outlier: 6.148A pdb=" N LEU H 970 " --> pdb=" O LEU H 966 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'H' and resid 875 through 876 Processing sheet with id=AK5, first strand: chain 'H' and resid 890 through 895 removed outlier: 3.731A pdb=" N LEU H 893 " --> pdb=" O ILE H 907 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N ILE H 907 " --> pdb=" O LEU H 893 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N THR H 926 " --> pdb=" O LEU H 908 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LYS H 912 " --> pdb=" O LYS H 922 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N LYS H 922 " --> pdb=" O LYS H 912 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N GLU H 933 " --> pdb=" O LYS H 944 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLU H 940 " --> pdb=" O PHE H 937 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'H' and resid 1144 through 1151 removed outlier: 3.605A pdb=" N GLY H1172 " --> pdb=" O ASN H1147 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N CYS H1149 " --> pdb=" O VAL H1170 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N VAL H1170 " --> pdb=" O CYS H1149 " (cutoff:3.500A) Processing sheet with id=AK7, first strand: chain 'H' and resid 1182 through 1183 744 hydrogen bonds defined for protein. 1766 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: 9.44 Time building geometry restraints manager: 3.95 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: 12331 1.34 - 1.47: 8708 1.47 - 1.59: 15693 1.59 - 1.71: 0 1.71 - 1.84: 640 Bond restraints: 37372 Sorted by residual: bond pdb=" N ASN B 156 " pdb=" CA ASN B 156 " ideal model delta sigma weight residual 1.457 1.499 -0.042 1.29e-02 6.01e+03 1.04e+01 bond pdb=" N ASN A 156 " pdb=" CA ASN A 156 " ideal model delta sigma weight residual 1.457 1.497 -0.039 1.29e-02 6.01e+03 9.25e+00 bond pdb=" N PHE A 155 " pdb=" CA PHE A 155 " ideal model delta sigma weight residual 1.454 1.493 -0.040 1.34e-02 5.57e+03 8.77e+00 bond pdb=" N CYS D 858 " pdb=" CA CYS D 858 " ideal model delta sigma weight residual 1.452 1.488 -0.036 1.22e-02 6.72e+03 8.63e+00 bond pdb=" N THR D 859 " pdb=" CA THR D 859 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.19e-02 7.06e+03 8.25e+00 ... (remaining 37367 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 48243 1.92 - 3.84: 2045 3.84 - 5.77: 363 5.77 - 7.69: 61 7.69 - 9.61: 8 Bond angle restraints: 50720 Sorted by residual: angle pdb=" N ASN B 156 " pdb=" CA ASN B 156 " pdb=" CB ASN B 156 " ideal model delta sigma weight residual 110.49 116.86 -6.37 1.69e+00 3.50e-01 1.42e+01 angle pdb=" CA THR B 101 " pdb=" C THR B 101 " pdb=" O THR B 101 " ideal model delta sigma weight residual 122.64 118.15 4.49 1.25e+00 6.40e-01 1.29e+01 angle pdb=" CA LYS H 920 " pdb=" CB LYS H 920 " pdb=" CG LYS H 920 " ideal model delta sigma weight residual 114.10 121.19 -7.09 2.00e+00 2.50e-01 1.26e+01 angle pdb=" CA LYS C 920 " pdb=" CB LYS C 920 " pdb=" CG LYS C 920 " ideal model delta sigma weight residual 114.10 121.18 -7.08 2.00e+00 2.50e-01 1.25e+01 angle pdb=" CA LYS D 920 " pdb=" CB LYS D 920 " pdb=" CG LYS D 920 " ideal model delta sigma weight residual 114.10 121.18 -7.08 2.00e+00 2.50e-01 1.25e+01 ... (remaining 50715 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 21888 17.83 - 35.66: 1152 35.66 - 53.48: 290 53.48 - 71.31: 68 71.31 - 89.14: 18 Dihedral angle restraints: 23416 sinusoidal: 9724 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 93.00 173.76 -80.76 1 1.00e+01 1.00e-02 8.06e+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 93.00 173.76 -80.76 1 1.00e+01 1.00e-02 8.06e+01 dihedral pdb=" CB CYS B 312 " pdb=" SG CYS B 312 " pdb=" SG CYS B 348 " pdb=" CB CYS B 348 " ideal model delta sinusoidal sigma weight residual 93.00 173.74 -80.74 1 1.00e+01 1.00e-02 8.06e+01 ... (remaining 23413 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.115: 5349 0.115 - 0.230: 196 0.230 - 0.346: 2 0.346 - 0.461: 1 0.461 - 0.576: 4 Chirality restraints: 5552 Sorted by residual: chirality pdb=" C1 NAG E 802 " pdb=" ND2 ASN E 99 " pdb=" C2 NAG E 802 " pdb=" O5 NAG E 802 " both_signs ideal model delta sigma weight residual False -2.40 -1.82 -0.58 2.00e-01 2.50e+01 8.29e+00 chirality pdb=" C1 NAG B 801 " pdb=" ND2 ASN B 156 " pdb=" C2 NAG B 801 " pdb=" O5 NAG B 801 " both_signs ideal model delta sigma weight residual False -2.40 -2.96 0.56 2.00e-01 2.50e+01 7.89e+00 chirality pdb=" C1 NAG D1302 " pdb=" ND2 ASN D 857 " pdb=" C2 NAG D1302 " pdb=" O5 NAG D1302 " both_signs ideal model delta sigma weight residual False -2.40 -1.87 -0.53 2.00e-01 2.50e+01 6.98e+00 ... (remaining 5549 not shown) Planarity restraints: 6752 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 802 " -0.290 2.00e-02 2.50e+03 2.44e-01 7.43e+02 pdb=" C7 NAG E 802 " 0.075 2.00e-02 2.50e+03 pdb=" C8 NAG E 802 " -0.185 2.00e-02 2.50e+03 pdb=" N2 NAG E 802 " 0.416 2.00e-02 2.50e+03 pdb=" O7 NAG E 802 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D1302 " -0.277 2.00e-02 2.50e+03 2.34e-01 6.83e+02 pdb=" C7 NAG D1302 " 0.072 2.00e-02 2.50e+03 pdb=" C8 NAG D1302 " -0.179 2.00e-02 2.50e+03 pdb=" N2 NAG D1302 " 0.399 2.00e-02 2.50e+03 pdb=" O7 NAG D1302 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 802 " -0.239 2.00e-02 2.50e+03 2.02e-01 5.12e+02 pdb=" C7 NAG A 802 " 0.053 2.00e-02 2.50e+03 pdb=" C8 NAG A 802 " 0.039 2.00e-02 2.50e+03 pdb=" N2 NAG A 802 " 0.331 2.00e-02 2.50e+03 pdb=" O7 NAG A 802 " -0.184 2.00e-02 2.50e+03 ... (remaining 6749 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 376 2.60 - 3.17: 32626 3.17 - 3.75: 52843 3.75 - 4.32: 73889 4.32 - 4.90: 120978 Nonbonded interactions: 280712 Sorted by model distance: nonbonded pdb=" OG SER D1009 " pdb=" OD1 ASN D1011 " model vdw 2.022 3.040 nonbonded pdb=" OG SER H1009 " pdb=" OD1 ASN H1011 " model vdw 2.022 3.040 nonbonded pdb=" OG SER F1009 " pdb=" OD1 ASN F1011 " model vdw 2.023 3.040 nonbonded pdb=" OG SER C1009 " pdb=" OD1 ASN C1011 " model vdw 2.023 3.040 nonbonded pdb=" O PRO F1197 " pdb=" OG SER F1208 " model vdw 2.128 3.040 ... (remaining 280707 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: 0.07 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: 0.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.630 Check model and map are aligned: 0.110 Set scattering table: 0.100 Process input model: 38.170 Find NCS groups from input model: 0.860 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7193 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 0.132 37624 Z= 0.314 Angle : 0.973 23.572 51244 Z= 0.496 Chirality : 0.055 0.576 5552 Planarity : 0.008 0.244 6732 Dihedral : 10.509 89.139 13952 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.25 % Allowed : 10.00 % Favored : 89.75 % Rotamer: Outliers : 0.29 % Allowed : 2.59 % Favored : 97.11 % 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: -4.59 (0.10), residues: 4744 helix: -4.22 (0.11), residues: 616 sheet: -3.76 (0.16), residues: 764 loop : -2.81 (0.09), residues: 3364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 273 TYR 0.018 0.002 TYR A 527 PHE 0.027 0.003 PHE G 535 TRP 0.017 0.002 TRP H 974 HIS 0.009 0.002 HIS C1109 Details of bonding type rmsd covalent geometry : bond 0.00740 (37372) covalent geometry : angle 0.92914 (50720) SS BOND : bond 0.00364 ( 232) SS BOND : angle 1.72676 ( 464) hydrogen bonds : bond 0.29902 ( 744) hydrogen bonds : angle 10.04950 ( 1766) link_NAG-ASN : bond 0.03279 ( 20) link_NAG-ASN : angle 7.43195 ( 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 1063 residues out of total 4112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 1055 time to evaluate : 1.289 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: A 730 TYR cc_start: 0.6264 (p90) cc_final: 0.5912 (p90) REVERT: B 106 ASP cc_start: 0.7402 (p0) cc_final: 0.6918 (p0) REVERT: B 199 TRP cc_start: 0.7396 (m-90) cc_final: 0.6813 (m-90) REVERT: B 547 GLU cc_start: 0.7139 (mp0) cc_final: 0.6601 (mp0) REVERT: B 560 GLN cc_start: 0.7500 (mt0) cc_final: 0.7279 (mt0) REVERT: B 683 CYS cc_start: 0.6344 (t) cc_final: 0.6100 (p) REVERT: B 693 LEU cc_start: 0.8391 (mm) cc_final: 0.8040 (mt) REVERT: D 951 THR cc_start: 0.7293 (p) cc_final: 0.6908 (t) REVERT: E 526 ASN cc_start: 0.8738 (m-40) cc_final: 0.8496 (m-40) REVERT: E 560 GLN cc_start: 0.7401 (mt0) cc_final: 0.7094 (mt0) REVERT: F 868 SER cc_start: 0.8490 (t) cc_final: 0.8290 (m) REVERT: F 952 HIS cc_start: 0.6728 (m90) cc_final: 0.6448 (m-70) REVERT: G 736 MET cc_start: 0.6096 (tpt) cc_final: 0.5839 (tpt) REVERT: G 740 MET cc_start: 0.3567 (mmm) cc_final: 0.3249 (tmm) REVERT: H 771 MET cc_start: 0.5896 (pmt) cc_final: 0.5685 (pmm) REVERT: H 936 LEU cc_start: 0.7650 (pp) cc_final: 0.7285 (pp) outliers start: 8 outliers final: 3 residues processed: 1061 average time/residue: 0.2432 time to fit residues: 401.9919 Evaluate side-chains 428 residues out of total 4112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 425 time to evaluate : 1.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 PHE Chi-restraints excluded: chain B residue 97 PHE Chi-restraints excluded: chain H residue 850 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 432 optimal weight: 7.9990 chunk 197 optimal weight: 6.9990 chunk 388 optimal weight: 5.9990 chunk 455 optimal weight: 0.6980 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 20.0000 chunk 470 optimal weight: 50.0000 overall best weight: 4.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 GLN A 452 HIS A 565 GLN ** B 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 419 GLN B 452 HIS C 794 ASN C 852 GLN C1003 GLN C1109 HIS C1113 GLN C1168 GLN ** C1174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 901 ASN D1159 HIS ** D1174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1221 HIS E 147 GLN E 452 HIS ** E 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 556 HIS F 977 HIS F1113 GLN ** F1174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F1221 HIS G 107 GLN G 198 GLN ** G 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 393 GLN G 419 GLN G 421 HIS H 986 GLN H1047 HIS H1168 GLN ** H1174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H1221 HIS Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.165276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.134965 restraints weight = 73679.152| |-----------------------------------------------------------------------------| r_work (start): 0.3692 rms_B_bonded: 4.30 r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3715 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3715 r_free = 0.3715 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3715 r_free = 0.3715 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3715 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.3750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 37624 Z= 0.238 Angle : 0.848 13.692 51244 Z= 0.426 Chirality : 0.052 0.338 5552 Planarity : 0.006 0.054 6732 Dihedral : 6.575 57.490 5561 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.54 % Favored : 91.43 % Rotamer: Outliers : 2.69 % Allowed : 9.59 % Favored : 87.72 % 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: -3.65 (0.11), residues: 4744 helix: -2.89 (0.16), residues: 644 sheet: -3.07 (0.16), residues: 864 loop : -2.24 (0.10), residues: 3236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 273 TYR 0.028 0.002 TYR G 527 PHE 0.027 0.003 PHE D 999 TRP 0.027 0.002 TRP H1144 HIS 0.015 0.002 HIS B 452 Details of bonding type rmsd covalent geometry : bond 0.00572 (37372) covalent geometry : angle 0.81708 (50720) SS BOND : bond 0.00500 ( 232) SS BOND : angle 1.90934 ( 464) hydrogen bonds : bond 0.04454 ( 744) hydrogen bonds : angle 6.30882 ( 1766) link_NAG-ASN : bond 0.00661 ( 20) link_NAG-ASN : angle 4.60043 ( 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 570 residues out of total 4112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 464 time to evaluate : 1.083 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 PHE cc_start: 0.8111 (m-80) cc_final: 0.7907 (m-80) REVERT: A 226 GLN cc_start: 0.6469 (OUTLIER) cc_final: 0.5581 (mp10) REVERT: A 435 ASP cc_start: 0.7206 (m-30) cc_final: 0.6749 (m-30) REVERT: B 199 TRP cc_start: 0.7539 (m-90) cc_final: 0.7061 (m-90) REVERT: B 693 LEU cc_start: 0.8782 (mm) cc_final: 0.8440 (mt) REVERT: B 740 MET cc_start: 0.7995 (mmm) cc_final: 0.7410 (mmm) REVERT: C 814 MET cc_start: 0.5274 (ptp) cc_final: 0.4794 (mtp) REVERT: F 771 MET cc_start: 0.6532 (pmm) cc_final: 0.6285 (ptt) REVERT: F 826 ARG cc_start: 0.5932 (mtm110) cc_final: 0.5449 (ptm160) REVERT: G 282 LEU cc_start: 0.6754 (pt) cc_final: 0.6037 (mt) REVERT: G 320 MET cc_start: 0.6175 (OUTLIER) cc_final: 0.5846 (mtp) REVERT: G 451 LEU cc_start: 0.7645 (mp) cc_final: 0.7435 (pt) REVERT: G 500 MET cc_start: 0.8666 (mmm) cc_final: 0.8187 (mtp) REVERT: G 511 LYS cc_start: 0.8405 (mppt) cc_final: 0.8096 (mppt) REVERT: G 636 ARG cc_start: 0.7575 (mmt90) cc_final: 0.7353 (mmm-85) REVERT: G 740 MET cc_start: 0.4581 (mmm) cc_final: 0.3924 (tmm) REVERT: H 850 VAL cc_start: 0.7537 (OUTLIER) cc_final: 0.7207 (p) REVERT: H 954 GLU cc_start: 0.6923 (tp30) cc_final: 0.6554 (mt-10) outliers start: 106 outliers final: 52 residues processed: 533 average time/residue: 0.2101 time to fit residues: 186.2012 Evaluate side-chains 374 residues out of total 4112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 319 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 PHE Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 226 GLN Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 526 ASN Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 661 CYS Chi-restraints excluded: chain A residue 669 CYS Chi-restraints excluded: chain B residue 327 ASP Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 526 ASN Chi-restraints excluded: chain B residue 602 LEU Chi-restraints excluded: chain B residue 669 CYS Chi-restraints excluded: chain C residue 841 THR Chi-restraints excluded: chain C residue 870 ILE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 938 ASP Chi-restraints excluded: chain C residue 1081 LEU Chi-restraints excluded: chain C residue 1093 SER Chi-restraints excluded: chain D residue 862 VAL Chi-restraints excluded: chain D residue 870 ILE Chi-restraints excluded: chain D residue 911 ASN Chi-restraints excluded: chain E residue 69 SER Chi-restraints excluded: chain E residue 107 GLN Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 159 CYS Chi-restraints excluded: chain E residue 326 VAL Chi-restraints excluded: chain E residue 394 SER Chi-restraints excluded: chain E residue 537 THR Chi-restraints excluded: chain E residue 669 CYS Chi-restraints excluded: chain F residue 862 VAL Chi-restraints excluded: chain F residue 870 ILE Chi-restraints excluded: chain F residue 935 GLU Chi-restraints excluded: chain F residue 937 PHE Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 158 THR Chi-restraints excluded: chain G residue 198 GLN Chi-restraints excluded: chain G residue 265 CYS Chi-restraints excluded: chain G residue 294 VAL Chi-restraints excluded: chain G residue 320 MET Chi-restraints excluded: chain G residue 348 CYS Chi-restraints excluded: chain G residue 394 SER Chi-restraints excluded: chain G residue 668 THR Chi-restraints excluded: chain G residue 669 CYS Chi-restraints excluded: chain G residue 695 MET Chi-restraints excluded: chain G residue 709 CYS Chi-restraints excluded: chain H residue 850 VAL Chi-restraints excluded: chain H residue 862 VAL Chi-restraints excluded: chain H residue 870 ILE Chi-restraints excluded: chain H residue 934 ILE Chi-restraints excluded: chain H residue 938 ASP Chi-restraints excluded: chain H residue 1019 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 441 optimal weight: 1.9990 chunk 276 optimal weight: 7.9990 chunk 287 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 322 optimal weight: 0.0270 chunk 54 optimal weight: 10.0000 chunk 456 optimal weight: 2.9990 chunk 460 optimal weight: 4.9990 chunk 162 optimal weight: 8.9990 chunk 236 optimal weight: 10.0000 chunk 68 optimal weight: 7.9990 overall best weight: 2.4046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 ASN ** A 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 313 GLN A 737 HIS ** B 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 313 GLN B 393 GLN B 452 HIS C 794 ASN ** C1134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 989 GLN D1159 HIS ** D1174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 78 ASN E 452 HIS ** E 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 660 GLN F 989 GLN ** F1174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 107 GLN G 189 ASN G 313 GLN G 374 ASN H 989 GLN ** H1174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.165274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.135824 restraints weight = 75873.476| |-----------------------------------------------------------------------------| r_work (start): 0.3712 rms_B_bonded: 4.29 r_work (final): 0.3712 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3711 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3711 r_free = 0.3711 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3711 r_free = 0.3711 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3711 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.4359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.095 37624 Z= 0.159 Angle : 0.730 22.569 51244 Z= 0.362 Chirality : 0.048 0.534 5552 Planarity : 0.005 0.055 6732 Dihedral : 6.050 59.982 5559 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 2.52 % Allowed : 11.35 % Favored : 86.13 % 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: -3.21 (0.11), residues: 4744 helix: -2.27 (0.18), residues: 648 sheet: -2.72 (0.16), residues: 912 loop : -1.99 (0.10), residues: 3184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 647 TYR 0.025 0.002 TYR A 87 PHE 0.018 0.002 PHE D 878 TRP 0.017 0.001 TRP G 222 HIS 0.016 0.001 HIS B 452 Details of bonding type rmsd covalent geometry : bond 0.00380 (37372) covalent geometry : angle 0.69744 (50720) SS BOND : bond 0.00366 ( 232) SS BOND : angle 1.51975 ( 464) hydrogen bonds : bond 0.03909 ( 744) hydrogen bonds : angle 5.67873 ( 1766) link_NAG-ASN : bond 0.00664 ( 20) link_NAG-ASN : angle 5.08389 ( 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 482 residues out of total 4112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 383 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: A 67 LYS cc_start: 0.8401 (pmmt) cc_final: 0.8185 (pttm) REVERT: B 77 GLN cc_start: 0.6891 (tp40) cc_final: 0.6682 (tt0) REVERT: B 199 TRP cc_start: 0.7475 (m-90) cc_final: 0.7195 (m-90) REVERT: B 217 MET cc_start: 0.3687 (tpt) cc_final: 0.3159 (ttm) REVERT: B 483 GLN cc_start: 0.8000 (OUTLIER) cc_final: 0.7476 (pt0) REVERT: B 499 GLN cc_start: 0.7964 (OUTLIER) cc_final: 0.7670 (tt0) REVERT: B 659 LEU cc_start: 0.8938 (OUTLIER) cc_final: 0.8449 (mp) REVERT: B 681 GLU cc_start: 0.6645 (OUTLIER) cc_final: 0.6306 (mt-10) REVERT: B 740 MET cc_start: 0.7808 (mmm) cc_final: 0.7292 (mmm) REVERT: C 814 MET cc_start: 0.4846 (ptp) cc_final: 0.4487 (mtp) REVERT: C 847 ASN cc_start: 0.7686 (OUTLIER) cc_final: 0.7475 (t0) REVERT: C 854 ARG cc_start: 0.5481 (OUTLIER) cc_final: 0.4934 (ttm110) REVERT: C 954 GLU cc_start: 0.7516 (tm-30) cc_final: 0.7312 (mt-10) REVERT: F 826 ARG cc_start: 0.5754 (mtm110) cc_final: 0.4937 (ptm160) REVERT: F 868 SER cc_start: 0.8653 (t) cc_final: 0.8349 (m) REVERT: F 927 ILE cc_start: 0.8505 (OUTLIER) cc_final: 0.8254 (mp) REVERT: G 282 LEU cc_start: 0.6675 (pt) cc_final: 0.6021 (mt) REVERT: G 636 ARG cc_start: 0.7495 (mmt90) cc_final: 0.7197 (mmm-85) REVERT: G 736 MET cc_start: 0.5972 (tpt) cc_final: 0.5639 (tpt) REVERT: G 740 MET cc_start: 0.5196 (mmm) cc_final: 0.4185 (tmm) REVERT: H 795 TYR cc_start: 0.6947 (t80) cc_final: 0.6717 (t80) outliers start: 99 outliers final: 62 residues processed: 457 average time/residue: 0.2082 time to fit residues: 158.4741 Evaluate side-chains 368 residues out of total 4112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 299 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 CYS Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 189 ASN Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 709 CYS Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 353 SER Chi-restraints excluded: chain B residue 417 ASP Chi-restraints excluded: chain B residue 480 LEU Chi-restraints excluded: chain B residue 483 GLN Chi-restraints excluded: chain B residue 499 GLN Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 526 ASN Chi-restraints excluded: chain B residue 602 LEU Chi-restraints excluded: chain B residue 659 LEU Chi-restraints excluded: chain B residue 669 CYS Chi-restraints excluded: chain B residue 681 GLU Chi-restraints excluded: chain C residue 847 ASN Chi-restraints excluded: chain C residue 854 ARG Chi-restraints excluded: chain C residue 870 ILE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 937 PHE Chi-restraints excluded: chain C residue 938 ASP Chi-restraints excluded: chain C residue 1081 LEU Chi-restraints excluded: chain C residue 1122 THR Chi-restraints excluded: chain D residue 862 VAL Chi-restraints excluded: chain D residue 870 ILE Chi-restraints excluded: chain D residue 911 ASN Chi-restraints excluded: chain D residue 927 ILE Chi-restraints excluded: chain D residue 934 ILE Chi-restraints excluded: chain D residue 1122 THR Chi-restraints excluded: chain E residue 69 SER Chi-restraints excluded: chain E residue 107 GLN Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 159 CYS Chi-restraints excluded: chain E residue 311 THR Chi-restraints excluded: chain E residue 326 VAL Chi-restraints excluded: chain E residue 394 SER Chi-restraints excluded: chain E residue 470 ASP Chi-restraints excluded: chain E residue 480 LEU Chi-restraints excluded: chain E residue 537 THR Chi-restraints excluded: chain E residue 725 HIS Chi-restraints excluded: chain F residue 862 VAL Chi-restraints excluded: chain F residue 870 ILE Chi-restraints excluded: chain F residue 927 ILE Chi-restraints excluded: chain F residue 934 ILE Chi-restraints excluded: chain F residue 935 GLU Chi-restraints excluded: chain F residue 936 LEU Chi-restraints excluded: chain F residue 1055 MET Chi-restraints excluded: chain G residue 65 CYS Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 158 THR Chi-restraints excluded: chain G residue 189 ASN Chi-restraints excluded: chain G residue 265 CYS Chi-restraints excluded: chain G residue 348 CYS Chi-restraints excluded: chain G residue 394 SER Chi-restraints excluded: chain G residue 669 CYS Chi-restraints excluded: chain G residue 695 MET Chi-restraints excluded: chain H residue 850 VAL Chi-restraints excluded: chain H residue 870 ILE Chi-restraints excluded: chain H residue 934 ILE Chi-restraints excluded: chain H residue 938 ASP Chi-restraints excluded: chain H residue 1019 VAL Chi-restraints excluded: chain H residue 1093 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 259 optimal weight: 9.9990 chunk 234 optimal weight: 4.9990 chunk 13 optimal weight: 6.9990 chunk 333 optimal weight: 0.8980 chunk 301 optimal weight: 8.9990 chunk 257 optimal weight: 9.9990 chunk 50 optimal weight: 7.9990 chunk 448 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 426 optimal weight: 5.9990 chunk 146 optimal weight: 7.9990 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 HIS A 189 ASN ** A 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 737 HIS B 95 HIS ** B 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 452 HIS C 794 ASN ** C1174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1072 ASN D1159 HIS ** D1174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 95 HIS E 313 GLN E 322 GLN E 452 HIS ** E 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 95 HIS G 189 ASN H1013 GLN H1113 GLN ** H1174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.159759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.133312 restraints weight = 71030.825| |-----------------------------------------------------------------------------| r_work (start): 0.3681 rms_B_bonded: 3.66 r_work: 0.3164 rms_B_bonded: 4.87 restraints_weight: 0.5000 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3174 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3174 r_free = 0.3174 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3174 r_free = 0.3174 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3174 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.5016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 37624 Z= 0.259 Angle : 0.802 18.607 51244 Z= 0.400 Chirality : 0.051 0.575 5552 Planarity : 0.005 0.060 6732 Dihedral : 6.297 59.781 5557 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.60 % Favored : 90.40 % Rotamer: Outliers : 3.52 % Allowed : 12.06 % Favored : 84.42 % 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: -3.17 (0.11), residues: 4744 helix: -2.28 (0.18), residues: 652 sheet: -2.69 (0.16), residues: 940 loop : -1.94 (0.10), residues: 3152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 643 TYR 0.044 0.002 TYR A 87 PHE 0.035 0.003 PHE D 999 TRP 0.016 0.002 TRP G 222 HIS 0.016 0.002 HIS B 452 Details of bonding type rmsd covalent geometry : bond 0.00630 (37372) covalent geometry : angle 0.77322 (50720) SS BOND : bond 0.00517 ( 232) SS BOND : angle 1.69323 ( 464) hydrogen bonds : bond 0.04094 ( 744) hydrogen bonds : angle 5.61671 ( 1766) link_NAG-ASN : bond 0.00684 ( 20) link_NAG-ASN : angle 4.71750 ( 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 458 residues out of total 4112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 318 time to evaluate : 1.440 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 65 CYS cc_start: 0.6740 (OUTLIER) cc_final: 0.6348 (m) REVERT: A 185 TYR cc_start: 0.8629 (OUTLIER) cc_final: 0.7530 (t80) REVERT: A 268 LEU cc_start: 0.8165 (OUTLIER) cc_final: 0.7901 (mm) REVERT: A 619 ARG cc_start: 0.7408 (mmm160) cc_final: 0.6474 (mpp80) REVERT: B 77 GLN cc_start: 0.7340 (tp40) cc_final: 0.6877 (tt0) REVERT: B 81 ARG cc_start: 0.8531 (ptp90) cc_final: 0.8163 (mtm-85) REVERT: B 199 TRP cc_start: 0.7821 (m-90) cc_final: 0.7167 (m-90) REVERT: B 483 GLN cc_start: 0.8344 (OUTLIER) cc_final: 0.7939 (pt0) REVERT: B 659 LEU cc_start: 0.9192 (OUTLIER) cc_final: 0.8732 (mp) REVERT: B 681 GLU cc_start: 0.6950 (OUTLIER) cc_final: 0.6710 (mt-10) REVERT: B 740 MET cc_start: 0.8515 (mmm) cc_final: 0.8209 (mmm) REVERT: C 771 MET cc_start: 0.5478 (ptp) cc_final: 0.4924 (mtt) REVERT: C 814 MET cc_start: 0.6002 (ptp) cc_final: 0.5272 (mtp) REVERT: C 847 ASN cc_start: 0.7904 (OUTLIER) cc_final: 0.7629 (t0) REVERT: E 159 CYS cc_start: 0.7332 (OUTLIER) cc_final: 0.7092 (m) REVERT: E 384 CYS cc_start: 0.8018 (OUTLIER) cc_final: 0.7544 (m) REVERT: E 500 MET cc_start: 0.8551 (mmt) cc_final: 0.8273 (mtt) REVERT: E 722 PHE cc_start: 0.8233 (OUTLIER) cc_final: 0.7725 (t80) REVERT: F 826 ARG cc_start: 0.6355 (mtm110) cc_final: 0.5662 (ptm160) REVERT: G 282 LEU cc_start: 0.7336 (pt) cc_final: 0.6600 (mt) REVERT: G 475 LEU cc_start: 0.8639 (tt) cc_final: 0.8436 (tt) REVERT: G 740 MET cc_start: 0.5587 (mmm) cc_final: 0.4235 (tmm) REVERT: H 802 MET cc_start: 0.4801 (mmp) cc_final: 0.4492 (mmt) REVERT: H 954 GLU cc_start: 0.7358 (tp30) cc_final: 0.7118 (mt-10) outliers start: 140 outliers final: 91 residues processed: 433 average time/residue: 0.2059 time to fit residues: 149.7731 Evaluate side-chains 391 residues out of total 4112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 290 time to evaluate : 1.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 CYS Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 185 TYR Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 526 ASN Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 684 LEU Chi-restraints excluded: chain A residue 709 CYS Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 327 ASP Chi-restraints excluded: chain B residue 353 SER Chi-restraints excluded: chain B residue 384 CYS Chi-restraints excluded: chain B residue 480 LEU Chi-restraints excluded: chain B residue 483 GLN Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 526 ASN Chi-restraints excluded: chain B residue 602 LEU Chi-restraints excluded: chain B residue 638 VAL Chi-restraints excluded: chain B residue 659 LEU Chi-restraints excluded: chain B residue 669 CYS Chi-restraints excluded: chain B residue 681 GLU Chi-restraints excluded: chain B residue 684 LEU Chi-restraints excluded: chain B residue 722 PHE Chi-restraints excluded: chain C residue 841 THR Chi-restraints excluded: chain C residue 847 ASN Chi-restraints excluded: chain C residue 862 VAL Chi-restraints excluded: chain C residue 870 ILE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 937 PHE Chi-restraints excluded: chain C residue 938 ASP Chi-restraints excluded: chain C residue 1055 MET Chi-restraints excluded: chain C residue 1081 LEU Chi-restraints excluded: chain C residue 1093 SER Chi-restraints excluded: chain C residue 1122 THR Chi-restraints excluded: chain D residue 862 VAL Chi-restraints excluded: chain D residue 870 ILE Chi-restraints excluded: chain D residue 911 ASN Chi-restraints excluded: chain D residue 915 SER Chi-restraints excluded: chain D residue 927 ILE Chi-restraints excluded: chain D residue 934 ILE Chi-restraints excluded: chain D residue 937 PHE Chi-restraints excluded: chain D residue 1122 THR Chi-restraints excluded: chain E residue 69 SER Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain E residue 107 GLN Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 159 CYS Chi-restraints excluded: chain E residue 222 TRP Chi-restraints excluded: chain E residue 318 ASN Chi-restraints excluded: chain E residue 326 VAL Chi-restraints excluded: chain E residue 338 ASP Chi-restraints excluded: chain E residue 384 CYS Chi-restraints excluded: chain E residue 394 SER Chi-restraints excluded: chain E residue 470 ASP Chi-restraints excluded: chain E residue 480 LEU Chi-restraints excluded: chain E residue 509 LEU Chi-restraints excluded: chain E residue 537 THR Chi-restraints excluded: chain E residue 584 CYS Chi-restraints excluded: chain E residue 677 GLU Chi-restraints excluded: chain E residue 722 PHE Chi-restraints excluded: chain F residue 862 VAL Chi-restraints excluded: chain F residue 870 ILE Chi-restraints excluded: chain F residue 915 SER Chi-restraints excluded: chain F residue 927 ILE Chi-restraints excluded: chain F residue 934 ILE Chi-restraints excluded: chain F residue 936 LEU Chi-restraints excluded: chain F residue 1055 MET Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain G residue 158 THR Chi-restraints excluded: chain G residue 179 THR Chi-restraints excluded: chain G residue 189 ASN Chi-restraints excluded: chain G residue 265 CYS Chi-restraints excluded: chain G residue 294 VAL Chi-restraints excluded: chain G residue 348 CYS Chi-restraints excluded: chain G residue 394 SER Chi-restraints excluded: chain G residue 471 VAL Chi-restraints excluded: chain G residue 669 CYS Chi-restraints excluded: chain G residue 695 MET Chi-restraints excluded: chain G residue 710 TYR Chi-restraints excluded: chain H residue 850 VAL Chi-restraints excluded: chain H residue 862 VAL Chi-restraints excluded: chain H residue 870 ILE Chi-restraints excluded: chain H residue 934 ILE Chi-restraints excluded: chain H residue 938 ASP Chi-restraints excluded: chain H residue 1019 VAL Chi-restraints excluded: chain H residue 1093 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 331 optimal weight: 9.9990 chunk 377 optimal weight: 5.9990 chunk 48 optimal weight: 5.9990 chunk 153 optimal weight: 0.2980 chunk 194 optimal weight: 8.9990 chunk 451 optimal weight: 0.9980 chunk 469 optimal weight: 20.0000 chunk 62 optimal weight: 7.9990 chunk 438 optimal weight: 4.9990 chunk 396 optimal weight: 10.0000 chunk 274 optimal weight: 0.7980 overall best weight: 2.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 ASN ** A 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 374 ASN B 452 HIS C 794 ASN ** C1174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1159 HIS ** D1174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 78 ASN E 452 HIS ** E 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 189 ASN ** H1174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.162179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.130488 restraints weight = 62669.760| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 3.96 r_work: 0.3226 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3235 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3235 r_free = 0.3235 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3235 r_free = 0.3235 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3235 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.5187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 37624 Z= 0.158 Angle : 0.693 16.847 51244 Z= 0.344 Chirality : 0.047 0.525 5552 Planarity : 0.005 0.059 6732 Dihedral : 5.796 58.594 5557 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.57 % Favored : 92.43 % Rotamer: Outliers : 3.08 % Allowed : 13.36 % Favored : 83.56 % 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: -2.96 (0.11), residues: 4744 helix: -2.15 (0.18), residues: 692 sheet: -2.55 (0.16), residues: 880 loop : -1.81 (0.11), residues: 3172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 302 TYR 0.023 0.002 TYR H 897 PHE 0.020 0.002 PHE A 76 TRP 0.021 0.001 TRP G 502 HIS 0.019 0.001 HIS B 452 Details of bonding type rmsd covalent geometry : bond 0.00381 (37372) covalent geometry : angle 0.66857 (50720) SS BOND : bond 0.00367 ( 232) SS BOND : angle 1.35368 ( 464) hydrogen bonds : bond 0.03373 ( 744) hydrogen bonds : angle 5.32638 ( 1766) link_NAG-ASN : bond 0.00692 ( 20) link_NAG-ASN : angle 4.24809 ( 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 432 residues out of total 4112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 310 time to evaluate : 1.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 LYS cc_start: 0.8740 (OUTLIER) cc_final: 0.8408 (pttm) REVERT: A 172 ASP cc_start: 0.8357 (p0) cc_final: 0.7943 (p0) REVERT: A 185 TYR cc_start: 0.8594 (OUTLIER) cc_final: 0.7701 (t80) REVERT: A 735 PHE cc_start: 0.6640 (t80) cc_final: 0.6329 (t80) REVERT: A 737 HIS cc_start: 0.4346 (OUTLIER) cc_final: 0.3965 (m90) REVERT: B 77 GLN cc_start: 0.7356 (tp40) cc_final: 0.6905 (tt0) REVERT: B 81 ARG cc_start: 0.8457 (ptp90) cc_final: 0.8102 (mtm-85) REVERT: B 197 GLU cc_start: 0.7458 (OUTLIER) cc_final: 0.7049 (pm20) REVERT: B 199 TRP cc_start: 0.7752 (m-90) cc_final: 0.7537 (m-90) REVERT: B 483 GLN cc_start: 0.8275 (OUTLIER) cc_final: 0.7841 (pt0) REVERT: B 659 LEU cc_start: 0.9181 (OUTLIER) cc_final: 0.8820 (mp) REVERT: B 681 GLU cc_start: 0.6903 (OUTLIER) cc_final: 0.6654 (mt-10) REVERT: B 740 MET cc_start: 0.8449 (mmm) cc_final: 0.8175 (mmm) REVERT: C 771 MET cc_start: 0.5450 (ptp) cc_final: 0.4722 (mtt) REVERT: C 814 MET cc_start: 0.5947 (ptp) cc_final: 0.5199 (mtp) REVERT: C 847 ASN cc_start: 0.7827 (OUTLIER) cc_final: 0.7611 (t0) REVERT: E 313 GLN cc_start: 0.6901 (mt0) cc_final: 0.6304 (mp10) REVERT: E 347 GLU cc_start: 0.7881 (tm-30) cc_final: 0.7515 (tm-30) REVERT: E 384 CYS cc_start: 0.7987 (OUTLIER) cc_final: 0.7406 (m) REVERT: F 826 ARG cc_start: 0.6374 (mtm110) cc_final: 0.5604 (ptm160) REVERT: F 927 ILE cc_start: 0.8710 (OUTLIER) cc_final: 0.8407 (mt) REVERT: G 185 TYR cc_start: 0.8536 (OUTLIER) cc_final: 0.8101 (t80) REVERT: G 282 LEU cc_start: 0.7216 (pt) cc_final: 0.6465 (mt) REVERT: G 740 MET cc_start: 0.5772 (mmm) cc_final: 0.4360 (tmm) outliers start: 122 outliers final: 83 residues processed: 405 average time/residue: 0.2079 time to fit residues: 141.8594 Evaluate side-chains 372 residues out of total 4112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 278 time to evaluate : 1.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LYS Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 185 TYR Chi-restraints excluded: chain A residue 189 ASN Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 684 LEU Chi-restraints excluded: chain A residue 709 CYS Chi-restraints excluded: chain A residue 737 HIS Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 353 SER Chi-restraints excluded: chain B residue 384 CYS Chi-restraints excluded: chain B residue 480 LEU Chi-restraints excluded: chain B residue 483 GLN Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 526 ASN Chi-restraints excluded: chain B residue 584 CYS Chi-restraints excluded: chain B residue 638 VAL Chi-restraints excluded: chain B residue 659 LEU Chi-restraints excluded: chain B residue 669 CYS Chi-restraints excluded: chain B residue 681 GLU Chi-restraints excluded: chain B residue 684 LEU Chi-restraints excluded: chain C residue 794 ASN Chi-restraints excluded: chain C residue 847 ASN Chi-restraints excluded: chain C residue 862 VAL Chi-restraints excluded: chain C residue 870 ILE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 937 PHE Chi-restraints excluded: chain C residue 938 ASP Chi-restraints excluded: chain C residue 1055 MET Chi-restraints excluded: chain C residue 1081 LEU Chi-restraints excluded: chain C residue 1093 SER Chi-restraints excluded: chain C residue 1122 THR Chi-restraints excluded: chain C residue 1135 LEU Chi-restraints excluded: chain C residue 1165 CYS Chi-restraints excluded: chain D residue 862 VAL Chi-restraints excluded: chain D residue 870 ILE Chi-restraints excluded: chain D residue 911 ASN Chi-restraints excluded: chain D residue 915 SER Chi-restraints excluded: chain D residue 927 ILE Chi-restraints excluded: chain D residue 934 ILE Chi-restraints excluded: chain D residue 1055 MET Chi-restraints excluded: chain D residue 1122 THR Chi-restraints excluded: chain E residue 69 SER Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain E residue 107 GLN Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 159 CYS Chi-restraints excluded: chain E residue 222 TRP Chi-restraints excluded: chain E residue 326 VAL Chi-restraints excluded: chain E residue 338 ASP Chi-restraints excluded: chain E residue 384 CYS Chi-restraints excluded: chain E residue 394 SER Chi-restraints excluded: chain E residue 470 ASP Chi-restraints excluded: chain E residue 480 LEU Chi-restraints excluded: chain E residue 537 THR Chi-restraints excluded: chain E residue 582 GLU Chi-restraints excluded: chain F residue 853 ASP Chi-restraints excluded: chain F residue 862 VAL Chi-restraints excluded: chain F residue 870 ILE Chi-restraints excluded: chain F residue 915 SER Chi-restraints excluded: chain F residue 927 ILE Chi-restraints excluded: chain F residue 934 ILE Chi-restraints excluded: chain F residue 936 LEU Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain G residue 179 THR Chi-restraints excluded: chain G residue 185 TYR Chi-restraints excluded: chain G residue 187 PHE Chi-restraints excluded: chain G residue 189 ASN Chi-restraints excluded: chain G residue 265 CYS Chi-restraints excluded: chain G residue 348 CYS Chi-restraints excluded: chain G residue 394 SER Chi-restraints excluded: chain G residue 669 CYS Chi-restraints excluded: chain G residue 695 MET Chi-restraints excluded: chain H residue 850 VAL Chi-restraints excluded: chain H residue 870 ILE Chi-restraints excluded: chain H residue 934 ILE Chi-restraints excluded: chain H residue 938 ASP Chi-restraints excluded: chain H residue 1093 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 420 optimal weight: 1.9990 chunk 145 optimal weight: 10.0000 chunk 83 optimal weight: 5.9990 chunk 173 optimal weight: 0.7980 chunk 375 optimal weight: 5.9990 chunk 97 optimal weight: 9.9990 chunk 470 optimal weight: 30.0000 chunk 191 optimal weight: 5.9990 chunk 195 optimal weight: 0.0060 chunk 321 optimal weight: 6.9990 chunk 77 optimal weight: 6.9990 overall best weight: 2.9602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 ASN A 224 GLN A 374 ASN ** B 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 288 HIS B 452 HIS C 794 ASN C 911 ASN ** C1174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 78 ASN E 452 HIS ** E 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 189 ASN H1047 HIS ** H1174 HIS ** 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 = 0.4033 r_free = 0.4033 target = 0.161080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.130789 restraints weight = 62582.033| |-----------------------------------------------------------------------------| r_work (start): 0.3657 rms_B_bonded: 3.70 r_work: 0.3215 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3220 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3220 r_free = 0.3220 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3220 r_free = 0.3220 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3220 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.5376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 37624 Z= 0.171 Angle : 0.696 15.571 51244 Z= 0.345 Chirality : 0.047 0.526 5552 Planarity : 0.005 0.061 6732 Dihedral : 5.696 57.973 5557 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.71 % Favored : 91.27 % Rotamer: Outliers : 3.18 % Allowed : 14.26 % Favored : 82.56 % 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: -2.85 (0.11), residues: 4744 helix: -2.01 (0.18), residues: 688 sheet: -2.46 (0.16), residues: 880 loop : -1.75 (0.11), residues: 3176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 619 TYR 0.020 0.002 TYR A 87 PHE 0.020 0.002 PHE D 999 TRP 0.015 0.001 TRP B 222 HIS 0.020 0.001 HIS B 452 Details of bonding type rmsd covalent geometry : bond 0.00415 (37372) covalent geometry : angle 0.67253 (50720) SS BOND : bond 0.00391 ( 232) SS BOND : angle 1.41501 ( 464) hydrogen bonds : bond 0.03369 ( 744) hydrogen bonds : angle 5.24004 ( 1766) link_NAG-ASN : bond 0.00678 ( 20) link_NAG-ASN : angle 4.04502 ( 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 428 residues out of total 4112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 302 time to evaluate : 1.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 LYS cc_start: 0.8730 (OUTLIER) cc_final: 0.8371 (pttm) REVERT: A 172 ASP cc_start: 0.8567 (p0) cc_final: 0.8062 (p0) REVERT: A 185 TYR cc_start: 0.8643 (OUTLIER) cc_final: 0.7787 (t80) REVERT: A 472 GLN cc_start: 0.8166 (OUTLIER) cc_final: 0.7715 (tm-30) REVERT: A 511 LYS cc_start: 0.8571 (mmmm) cc_final: 0.8357 (mmtp) REVERT: B 77 GLN cc_start: 0.7372 (tp40) cc_final: 0.6927 (tt0) REVERT: B 254 LEU cc_start: 0.6241 (OUTLIER) cc_final: 0.5888 (tt) REVERT: B 302 ARG cc_start: 0.8016 (mpt180) cc_final: 0.7541 (mpt180) REVERT: B 483 GLN cc_start: 0.8273 (OUTLIER) cc_final: 0.7836 (pt0) REVERT: B 659 LEU cc_start: 0.9192 (OUTLIER) cc_final: 0.8832 (mp) REVERT: B 681 GLU cc_start: 0.7015 (OUTLIER) cc_final: 0.6741 (mt-10) REVERT: B 740 MET cc_start: 0.8460 (mmm) cc_final: 0.8220 (mmm) REVERT: C 771 MET cc_start: 0.5551 (ptp) cc_final: 0.4818 (mtt) REVERT: C 795 TYR cc_start: 0.7380 (t80) cc_final: 0.7170 (t80) REVERT: C 814 MET cc_start: 0.5866 (ptp) cc_final: 0.5156 (mtp) REVERT: C 830 PHE cc_start: 0.7984 (m-80) cc_final: 0.7592 (m-10) REVERT: E 347 GLU cc_start: 0.7955 (tm-30) cc_final: 0.7541 (tm-30) REVERT: E 384 CYS cc_start: 0.7879 (OUTLIER) cc_final: 0.7430 (m) REVERT: E 500 MET cc_start: 0.8275 (mtt) cc_final: 0.7871 (mtt) REVERT: E 722 PHE cc_start: 0.8108 (OUTLIER) cc_final: 0.7614 (t80) REVERT: F 826 ARG cc_start: 0.6295 (mtm110) cc_final: 0.5559 (ptm160) REVERT: F 927 ILE cc_start: 0.8711 (OUTLIER) cc_final: 0.8405 (mt) REVERT: G 185 TYR cc_start: 0.8563 (OUTLIER) cc_final: 0.8131 (t80) REVERT: G 282 LEU cc_start: 0.7238 (pt) cc_final: 0.6417 (mt) REVERT: H 911 ASN cc_start: 0.8639 (OUTLIER) cc_final: 0.8378 (p0) outliers start: 126 outliers final: 90 residues processed: 400 average time/residue: 0.2109 time to fit residues: 140.4036 Evaluate side-chains 385 residues out of total 4112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 283 time to evaluate : 1.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LYS Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 185 TYR Chi-restraints excluded: chain A residue 189 ASN Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 472 GLN Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 684 LEU Chi-restraints excluded: chain A residue 709 CYS Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 262 GLU Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 353 SER Chi-restraints excluded: chain B residue 384 CYS Chi-restraints excluded: chain B residue 480 LEU Chi-restraints excluded: chain B residue 483 GLN Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 526 ASN Chi-restraints excluded: chain B residue 584 CYS Chi-restraints excluded: chain B residue 638 VAL Chi-restraints excluded: chain B residue 659 LEU Chi-restraints excluded: chain B residue 669 CYS Chi-restraints excluded: chain B residue 681 GLU Chi-restraints excluded: chain B residue 684 LEU Chi-restraints excluded: chain C residue 841 THR Chi-restraints excluded: chain C residue 862 VAL Chi-restraints excluded: chain C residue 870 ILE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 937 PHE Chi-restraints excluded: chain C residue 938 ASP Chi-restraints excluded: chain C residue 1055 MET Chi-restraints excluded: chain C residue 1081 LEU Chi-restraints excluded: chain C residue 1093 SER Chi-restraints excluded: chain C residue 1122 THR Chi-restraints excluded: chain C residue 1135 LEU Chi-restraints excluded: chain C residue 1165 CYS Chi-restraints excluded: chain D residue 862 VAL Chi-restraints excluded: chain D residue 870 ILE Chi-restraints excluded: chain D residue 911 ASN Chi-restraints excluded: chain D residue 915 SER Chi-restraints excluded: chain D residue 927 ILE Chi-restraints excluded: chain D residue 934 ILE Chi-restraints excluded: chain D residue 1055 MET Chi-restraints excluded: chain D residue 1122 THR Chi-restraints excluded: chain E residue 69 SER Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain E residue 107 GLN Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 159 CYS Chi-restraints excluded: chain E residue 222 TRP Chi-restraints excluded: chain E residue 326 VAL Chi-restraints excluded: chain E residue 338 ASP Chi-restraints excluded: chain E residue 384 CYS Chi-restraints excluded: chain E residue 394 SER Chi-restraints excluded: chain E residue 470 ASP Chi-restraints excluded: chain E residue 480 LEU Chi-restraints excluded: chain E residue 537 THR Chi-restraints excluded: chain E residue 567 SER Chi-restraints excluded: chain E residue 582 GLU Chi-restraints excluded: chain E residue 677 GLU Chi-restraints excluded: chain E residue 722 PHE Chi-restraints excluded: chain F residue 853 ASP Chi-restraints excluded: chain F residue 862 VAL Chi-restraints excluded: chain F residue 870 ILE Chi-restraints excluded: chain F residue 915 SER Chi-restraints excluded: chain F residue 927 ILE Chi-restraints excluded: chain F residue 934 ILE Chi-restraints excluded: chain F residue 936 LEU Chi-restraints excluded: chain G residue 179 THR Chi-restraints excluded: chain G residue 185 TYR Chi-restraints excluded: chain G residue 187 PHE Chi-restraints excluded: chain G residue 189 ASN Chi-restraints excluded: chain G residue 265 CYS Chi-restraints excluded: chain G residue 329 CYS Chi-restraints excluded: chain G residue 348 CYS Chi-restraints excluded: chain G residue 394 SER Chi-restraints excluded: chain G residue 501 ASP Chi-restraints excluded: chain G residue 669 CYS Chi-restraints excluded: chain G residue 695 MET Chi-restraints excluded: chain H residue 850 VAL Chi-restraints excluded: chain H residue 870 ILE Chi-restraints excluded: chain H residue 911 ASN Chi-restraints excluded: chain H residue 934 ILE Chi-restraints excluded: chain H residue 938 ASP Chi-restraints excluded: chain H residue 1019 VAL Chi-restraints excluded: chain H residue 1093 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 423 optimal weight: 5.9990 chunk 255 optimal weight: 8.9990 chunk 284 optimal weight: 2.9990 chunk 435 optimal weight: 2.9990 chunk 131 optimal weight: 9.9990 chunk 437 optimal weight: 0.9990 chunk 67 optimal weight: 0.9980 chunk 352 optimal weight: 0.9990 chunk 89 optimal weight: 6.9990 chunk 218 optimal weight: 0.9980 chunk 290 optimal weight: 0.8980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 ASN A 484 HIS A 737 HIS C 794 ASN C 911 ASN ** C1134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1174 HIS E 78 ASN E 147 GLN E 452 HIS ** E 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F1174 HIS G 189 ASN ** H1174 HIS ** 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 = 0.4077 r_free = 0.4077 target = 0.165017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.129233 restraints weight = 77149.071| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 2.92 r_work: 0.3349 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3371 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3371 r_free = 0.3371 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3371 r_free = 0.3371 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3371 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.5500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 37624 Z= 0.109 Angle : 0.630 13.932 51244 Z= 0.312 Chirality : 0.045 0.470 5552 Planarity : 0.005 0.055 6732 Dihedral : 5.220 55.786 5557 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.43 % Favored : 93.54 % Rotamer: Outliers : 2.47 % Allowed : 15.02 % Favored : 82.51 % 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: -2.52 (0.12), residues: 4744 helix: -1.67 (0.19), residues: 668 sheet: -2.23 (0.18), residues: 772 loop : -1.60 (0.10), residues: 3304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 302 TYR 0.021 0.001 TYR H 897 PHE 0.017 0.001 PHE A 76 TRP 0.014 0.001 TRP A 222 HIS 0.010 0.001 HIS E 452 Details of bonding type rmsd covalent geometry : bond 0.00252 (37372) covalent geometry : angle 0.60950 (50720) SS BOND : bond 0.00284 ( 232) SS BOND : angle 1.20112 ( 464) hydrogen bonds : bond 0.02844 ( 744) hydrogen bonds : angle 5.01727 ( 1766) link_NAG-ASN : bond 0.00666 ( 20) link_NAG-ASN : angle 3.69597 ( 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 422 residues out of total 4112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 325 time to evaluate : 1.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 LYS cc_start: 0.8476 (OUTLIER) cc_final: 0.8163 (pttm) REVERT: A 172 ASP cc_start: 0.7987 (p0) cc_final: 0.7741 (p0) REVERT: A 185 TYR cc_start: 0.8491 (OUTLIER) cc_final: 0.7714 (t80) REVERT: A 341 LEU cc_start: 0.7938 (pp) cc_final: 0.7678 (pt) REVERT: A 475 LEU cc_start: 0.8238 (tt) cc_final: 0.7999 (tt) REVERT: A 735 PHE cc_start: 0.5603 (t80) cc_final: 0.5342 (t80) REVERT: B 77 GLN cc_start: 0.7249 (tp40) cc_final: 0.6834 (tt0) REVERT: B 197 GLU cc_start: 0.7427 (OUTLIER) cc_final: 0.7220 (pm20) REVERT: B 261 LEU cc_start: 0.6641 (OUTLIER) cc_final: 0.6424 (mp) REVERT: B 302 ARG cc_start: 0.7772 (mpt180) cc_final: 0.7224 (mpt180) REVERT: B 659 LEU cc_start: 0.9101 (OUTLIER) cc_final: 0.8809 (mp) REVERT: B 681 GLU cc_start: 0.6997 (OUTLIER) cc_final: 0.6718 (mt-10) REVERT: B 740 MET cc_start: 0.8255 (mmm) cc_final: 0.7999 (mmm) REVERT: C 771 MET cc_start: 0.5222 (ptp) cc_final: 0.4744 (mtt) REVERT: C 795 TYR cc_start: 0.7452 (t80) cc_final: 0.7155 (t80) REVERT: C 814 MET cc_start: 0.5868 (ptp) cc_final: 0.5347 (mtp) REVERT: E 320 MET cc_start: 0.7110 (mmt) cc_final: 0.6816 (mmt) REVERT: E 347 GLU cc_start: 0.7788 (tm-30) cc_final: 0.7407 (tm-30) REVERT: E 384 CYS cc_start: 0.7435 (OUTLIER) cc_final: 0.7093 (m) REVERT: E 500 MET cc_start: 0.8093 (mtt) cc_final: 0.7632 (mtt) REVERT: F 826 ARG cc_start: 0.5986 (mtm110) cc_final: 0.5383 (ptm160) REVERT: F 1074 LEU cc_start: 0.8273 (mm) cc_final: 0.7962 (tp) REVERT: G 282 LEU cc_start: 0.6936 (pt) cc_final: 0.5968 (mt) REVERT: G 347 GLU cc_start: 0.7610 (tm-30) cc_final: 0.7152 (tm-30) REVERT: G 736 MET cc_start: 0.5597 (tpt) cc_final: 0.5038 (tpt) REVERT: H 911 ASN cc_start: 0.8469 (OUTLIER) cc_final: 0.8229 (p0) outliers start: 97 outliers final: 65 residues processed: 405 average time/residue: 0.2133 time to fit residues: 143.7866 Evaluate side-chains 357 residues out of total 4112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 284 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LYS Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 185 TYR Chi-restraints excluded: chain A residue 189 ASN Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 684 LEU Chi-restraints excluded: chain A residue 709 CYS Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 384 CYS Chi-restraints excluded: chain B residue 418 CYS Chi-restraints excluded: chain B residue 480 LEU Chi-restraints excluded: chain B residue 584 CYS Chi-restraints excluded: chain B residue 659 LEU Chi-restraints excluded: chain B residue 669 CYS Chi-restraints excluded: chain B residue 681 GLU Chi-restraints excluded: chain C residue 870 ILE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 938 ASP Chi-restraints excluded: chain C residue 1081 LEU Chi-restraints excluded: chain C residue 1093 SER Chi-restraints excluded: chain C residue 1135 LEU Chi-restraints excluded: chain C residue 1165 CYS Chi-restraints excluded: chain D residue 862 VAL Chi-restraints excluded: chain D residue 870 ILE Chi-restraints excluded: chain D residue 911 ASN Chi-restraints excluded: chain D residue 915 SER Chi-restraints excluded: chain D residue 934 ILE Chi-restraints excluded: chain E residue 69 SER Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 107 GLN Chi-restraints excluded: chain E residue 159 CYS Chi-restraints excluded: chain E residue 326 VAL Chi-restraints excluded: chain E residue 338 ASP Chi-restraints excluded: chain E residue 384 CYS Chi-restraints excluded: chain E residue 394 SER Chi-restraints excluded: chain E residue 470 ASP Chi-restraints excluded: chain E residue 537 THR Chi-restraints excluded: chain E residue 567 SER Chi-restraints excluded: chain E residue 582 GLU Chi-restraints excluded: chain F residue 814 MET Chi-restraints excluded: chain F residue 862 VAL Chi-restraints excluded: chain F residue 870 ILE Chi-restraints excluded: chain F residue 915 SER Chi-restraints excluded: chain F residue 934 ILE Chi-restraints excluded: chain F residue 936 LEU Chi-restraints excluded: chain F residue 1135 LEU Chi-restraints excluded: chain G residue 179 THR Chi-restraints excluded: chain G residue 187 PHE Chi-restraints excluded: chain G residue 265 CYS Chi-restraints excluded: chain G residue 329 CYS Chi-restraints excluded: chain G residue 348 CYS Chi-restraints excluded: chain G residue 394 SER Chi-restraints excluded: chain G residue 669 CYS Chi-restraints excluded: chain G residue 695 MET Chi-restraints excluded: chain H residue 870 ILE Chi-restraints excluded: chain H residue 911 ASN Chi-restraints excluded: chain H residue 934 ILE Chi-restraints excluded: chain H residue 938 ASP Chi-restraints excluded: chain H residue 947 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 380 optimal weight: 8.9990 chunk 102 optimal weight: 10.0000 chunk 264 optimal weight: 20.0000 chunk 45 optimal weight: 6.9990 chunk 130 optimal weight: 6.9990 chunk 184 optimal weight: 20.0000 chunk 346 optimal weight: 10.0000 chunk 433 optimal weight: 2.9990 chunk 328 optimal weight: 0.1980 chunk 83 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 overall best weight: 3.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 ASN B 452 HIS C 911 ASN C1072 ASN ** D1174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 78 ASN E 452 HIS ** E 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 189 ASN H 952 HIS ** H1174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.159757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.129484 restraints weight = 79958.932| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 2.65 r_work: 0.3269 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3282 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3282 r_free = 0.3282 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3282 r_free = 0.3282 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3282 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.5663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 37624 Z= 0.197 Angle : 0.711 13.845 51244 Z= 0.352 Chirality : 0.048 0.510 5552 Planarity : 0.005 0.052 6732 Dihedral : 5.564 59.563 5556 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.38 % Favored : 91.58 % Rotamer: Outliers : 3.06 % Allowed : 14.97 % Favored : 81.97 % 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: -2.55 (0.12), residues: 4744 helix: -1.67 (0.19), residues: 660 sheet: -2.11 (0.17), residues: 816 loop : -1.65 (0.11), residues: 3268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 619 TYR 0.021 0.002 TYR B 710 PHE 0.023 0.002 PHE F 937 TRP 0.022 0.001 TRP A 222 HIS 0.018 0.001 HIS B 452 Details of bonding type rmsd covalent geometry : bond 0.00481 (37372) covalent geometry : angle 0.68884 (50720) SS BOND : bond 0.00409 ( 232) SS BOND : angle 1.47311 ( 464) hydrogen bonds : bond 0.03405 ( 744) hydrogen bonds : angle 5.12704 ( 1766) link_NAG-ASN : bond 0.00654 ( 20) link_NAG-ASN : angle 3.77963 ( 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 407 residues out of total 4112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 286 time to evaluate : 1.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 LYS cc_start: 0.8509 (OUTLIER) cc_final: 0.8175 (pttm) REVERT: A 185 TYR cc_start: 0.8631 (OUTLIER) cc_final: 0.7704 (t80) REVERT: A 341 LEU cc_start: 0.8186 (pp) cc_final: 0.7945 (pt) REVERT: A 472 GLN cc_start: 0.8077 (OUTLIER) cc_final: 0.7732 (tm-30) REVERT: A 475 LEU cc_start: 0.8202 (tt) cc_final: 0.7995 (tt) REVERT: A 735 PHE cc_start: 0.6276 (t80) cc_final: 0.5947 (t80) REVERT: B 77 GLN cc_start: 0.7276 (tp40) cc_final: 0.6866 (tt0) REVERT: B 197 GLU cc_start: 0.7373 (OUTLIER) cc_final: 0.6904 (pm20) REVERT: B 254 LEU cc_start: 0.6404 (OUTLIER) cc_final: 0.5869 (tt) REVERT: B 261 LEU cc_start: 0.6673 (OUTLIER) cc_final: 0.6471 (mp) REVERT: B 483 GLN cc_start: 0.8151 (OUTLIER) cc_final: 0.7738 (pt0) REVERT: B 659 LEU cc_start: 0.9191 (OUTLIER) cc_final: 0.8833 (mp) REVERT: B 681 GLU cc_start: 0.7051 (OUTLIER) cc_final: 0.6785 (mt-10) REVERT: B 740 MET cc_start: 0.8375 (mmm) cc_final: 0.8142 (mmm) REVERT: C 771 MET cc_start: 0.5654 (ptp) cc_final: 0.5156 (mtp) REVERT: C 795 TYR cc_start: 0.7467 (t80) cc_final: 0.7124 (t80) REVERT: C 814 MET cc_start: 0.5836 (ptp) cc_final: 0.5254 (mtp) REVERT: E 159 CYS cc_start: 0.6807 (OUTLIER) cc_final: 0.6591 (m) REVERT: E 347 GLU cc_start: 0.7908 (tm-30) cc_final: 0.7512 (tm-30) REVERT: E 384 CYS cc_start: 0.7662 (OUTLIER) cc_final: 0.7355 (m) REVERT: E 500 MET cc_start: 0.8251 (mtt) cc_final: 0.7859 (mtt) REVERT: E 722 PHE cc_start: 0.8008 (OUTLIER) cc_final: 0.7427 (t80) REVERT: F 826 ARG cc_start: 0.6063 (mtm110) cc_final: 0.5475 (ptm160) REVERT: F 897 TYR cc_start: 0.7340 (t80) cc_final: 0.7139 (t80) REVERT: F 1186 LEU cc_start: 0.7764 (OUTLIER) cc_final: 0.7482 (mt) REVERT: G 198 GLN cc_start: 0.8733 (OUTLIER) cc_final: 0.8335 (pp30) REVERT: G 282 LEU cc_start: 0.7159 (pt) cc_final: 0.6286 (mt) REVERT: G 347 GLU cc_start: 0.7612 (tm-30) cc_final: 0.7229 (tm-30) REVERT: G 736 MET cc_start: 0.5439 (tpt) cc_final: 0.4951 (tpt) outliers start: 121 outliers final: 89 residues processed: 388 average time/residue: 0.2014 time to fit residues: 132.5458 Evaluate side-chains 368 residues out of total 4112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 265 time to evaluate : 1.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LYS Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 185 TYR Chi-restraints excluded: chain A residue 189 ASN Chi-restraints excluded: chain A residue 265 CYS Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 472 GLN Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 709 CYS Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 262 GLU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 353 SER Chi-restraints excluded: chain B residue 384 CYS Chi-restraints excluded: chain B residue 418 CYS Chi-restraints excluded: chain B residue 480 LEU Chi-restraints excluded: chain B residue 483 GLN Chi-restraints excluded: chain B residue 526 ASN Chi-restraints excluded: chain B residue 584 CYS Chi-restraints excluded: chain B residue 638 VAL Chi-restraints excluded: chain B residue 659 LEU Chi-restraints excluded: chain B residue 669 CYS Chi-restraints excluded: chain B residue 681 GLU Chi-restraints excluded: chain C residue 862 VAL Chi-restraints excluded: chain C residue 870 ILE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 937 PHE Chi-restraints excluded: chain C residue 938 ASP Chi-restraints excluded: chain C residue 1081 LEU Chi-restraints excluded: chain C residue 1093 SER Chi-restraints excluded: chain C residue 1122 THR Chi-restraints excluded: chain C residue 1135 LEU Chi-restraints excluded: chain D residue 862 VAL Chi-restraints excluded: chain D residue 870 ILE Chi-restraints excluded: chain D residue 911 ASN Chi-restraints excluded: chain D residue 915 SER Chi-restraints excluded: chain D residue 1055 MET Chi-restraints excluded: chain D residue 1122 THR Chi-restraints excluded: chain E residue 69 SER Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain E residue 107 GLN Chi-restraints excluded: chain E residue 159 CYS Chi-restraints excluded: chain E residue 222 TRP Chi-restraints excluded: chain E residue 338 ASP Chi-restraints excluded: chain E residue 384 CYS Chi-restraints excluded: chain E residue 394 SER Chi-restraints excluded: chain E residue 470 ASP Chi-restraints excluded: chain E residue 480 LEU Chi-restraints excluded: chain E residue 537 THR Chi-restraints excluded: chain E residue 567 SER Chi-restraints excluded: chain E residue 582 GLU Chi-restraints excluded: chain E residue 584 CYS Chi-restraints excluded: chain E residue 677 GLU Chi-restraints excluded: chain E residue 681 GLU Chi-restraints excluded: chain E residue 722 PHE Chi-restraints excluded: chain F residue 853 ASP Chi-restraints excluded: chain F residue 862 VAL Chi-restraints excluded: chain F residue 870 ILE Chi-restraints excluded: chain F residue 915 SER Chi-restraints excluded: chain F residue 936 LEU Chi-restraints excluded: chain F residue 937 PHE Chi-restraints excluded: chain F residue 1135 LEU Chi-restraints excluded: chain F residue 1186 LEU Chi-restraints excluded: chain G residue 158 THR Chi-restraints excluded: chain G residue 179 THR Chi-restraints excluded: chain G residue 185 TYR Chi-restraints excluded: chain G residue 187 PHE Chi-restraints excluded: chain G residue 198 GLN Chi-restraints excluded: chain G residue 265 CYS Chi-restraints excluded: chain G residue 329 CYS Chi-restraints excluded: chain G residue 348 CYS Chi-restraints excluded: chain G residue 394 SER Chi-restraints excluded: chain G residue 493 SER Chi-restraints excluded: chain G residue 501 ASP Chi-restraints excluded: chain G residue 669 CYS Chi-restraints excluded: chain G residue 695 MET Chi-restraints excluded: chain H residue 850 VAL Chi-restraints excluded: chain H residue 862 VAL Chi-restraints excluded: chain H residue 870 ILE Chi-restraints excluded: chain H residue 934 ILE Chi-restraints excluded: chain H residue 935 GLU Chi-restraints excluded: chain H residue 938 ASP Chi-restraints excluded: chain H residue 947 MET Chi-restraints excluded: chain H residue 1019 VAL Chi-restraints excluded: chain H residue 1059 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 245 optimal weight: 0.4980 chunk 315 optimal weight: 7.9990 chunk 228 optimal weight: 20.0000 chunk 128 optimal weight: 0.0970 chunk 165 optimal weight: 3.9990 chunk 68 optimal weight: 0.0670 chunk 227 optimal weight: 8.9990 chunk 439 optimal weight: 5.9990 chunk 454 optimal weight: 0.9980 chunk 149 optimal weight: 2.9990 chunk 421 optimal weight: 0.9990 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 ASN ** B 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 911 ASN C1072 ASN ** C1134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1072 ASN E 78 ASN E 145 ASN E 393 GLN E 452 HIS ** E 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H1174 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.165936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.136963 restraints weight = 70331.298| |-----------------------------------------------------------------------------| r_work (start): 0.3724 rms_B_bonded: 3.88 r_work: 0.3276 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3290 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3290 r_free = 0.3290 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3290 r_free = 0.3290 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3290 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.5757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 37624 Z= 0.105 Angle : 0.631 12.680 51244 Z= 0.312 Chirality : 0.045 0.453 5552 Planarity : 0.005 0.059 6732 Dihedral : 5.030 56.593 5556 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.27 % Favored : 93.71 % Rotamer: Outliers : 1.88 % Allowed : 16.39 % Favored : 81.73 % 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: -2.29 (0.12), residues: 4744 helix: -1.54 (0.20), residues: 668 sheet: -1.95 (0.18), residues: 772 loop : -1.46 (0.11), residues: 3304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 698 TYR 0.022 0.001 TYR H 897 PHE 0.017 0.001 PHE F 937 TRP 0.033 0.001 TRP G 502 HIS 0.012 0.001 HIS E 452 Details of bonding type rmsd covalent geometry : bond 0.00234 (37372) covalent geometry : angle 0.61320 (50720) SS BOND : bond 0.00279 ( 232) SS BOND : angle 1.17271 ( 464) hydrogen bonds : bond 0.02712 ( 744) hydrogen bonds : angle 4.88794 ( 1766) link_NAG-ASN : bond 0.00671 ( 20) link_NAG-ASN : angle 3.41825 ( 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 381 residues out of total 4112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 308 time to evaluate : 1.278 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 67 LYS cc_start: 0.8472 (OUTLIER) cc_final: 0.8188 (pttm) REVERT: A 185 TYR cc_start: 0.8487 (OUTLIER) cc_final: 0.7741 (t80) REVERT: A 341 LEU cc_start: 0.8017 (pp) cc_final: 0.7752 (pt) REVERT: A 475 LEU cc_start: 0.8225 (tt) cc_final: 0.7998 (tt) REVERT: A 735 PHE cc_start: 0.6179 (t80) cc_final: 0.5692 (t80) REVERT: B 77 GLN cc_start: 0.7360 (tp40) cc_final: 0.6950 (tt0) REVERT: B 254 LEU cc_start: 0.6399 (OUTLIER) cc_final: 0.5949 (tt) REVERT: B 261 LEU cc_start: 0.6684 (OUTLIER) cc_final: 0.6470 (mp) REVERT: B 681 GLU cc_start: 0.7202 (OUTLIER) cc_final: 0.6789 (mp0) REVERT: B 740 MET cc_start: 0.8467 (mmm) cc_final: 0.8251 (mmm) REVERT: C 771 MET cc_start: 0.5374 (ptp) cc_final: 0.4813 (mtt) REVERT: C 795 TYR cc_start: 0.7470 (t80) cc_final: 0.7115 (t80) REVERT: E 347 GLU cc_start: 0.7927 (tm-30) cc_final: 0.7527 (tm-30) REVERT: E 384 CYS cc_start: 0.7980 (OUTLIER) cc_final: 0.7560 (m) REVERT: F 826 ARG cc_start: 0.6180 (mtm110) cc_final: 0.5580 (ptm160) REVERT: F 1186 LEU cc_start: 0.7827 (OUTLIER) cc_final: 0.7543 (mt) REVERT: G 282 LEU cc_start: 0.6992 (pt) cc_final: 0.5857 (mt) REVERT: G 347 GLU cc_start: 0.7851 (tm-30) cc_final: 0.7328 (tm-30) REVERT: G 693 LEU cc_start: 0.6447 (mt) cc_final: 0.6170 (mt) REVERT: G 736 MET cc_start: 0.5479 (tpt) cc_final: 0.5119 (tpt) outliers start: 73 outliers final: 52 residues processed: 370 average time/residue: 0.1998 time to fit residues: 125.4875 Evaluate side-chains 336 residues out of total 4112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 277 time to evaluate : 1.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LYS Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 185 TYR Chi-restraints excluded: chain A residue 189 ASN Chi-restraints excluded: chain A residue 265 CYS Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 684 LEU Chi-restraints excluded: chain A residue 709 CYS Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 384 CYS Chi-restraints excluded: chain B residue 418 CYS Chi-restraints excluded: chain B residue 480 LEU Chi-restraints excluded: chain B residue 669 CYS Chi-restraints excluded: chain B residue 681 GLU Chi-restraints excluded: chain C residue 870 ILE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 938 ASP Chi-restraints excluded: chain C residue 1081 LEU Chi-restraints excluded: chain C residue 1093 SER Chi-restraints excluded: chain D residue 862 VAL Chi-restraints excluded: chain D residue 870 ILE Chi-restraints excluded: chain D residue 911 ASN Chi-restraints excluded: chain D residue 915 SER Chi-restraints excluded: chain E residue 69 SER Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 159 CYS Chi-restraints excluded: chain E residue 338 ASP Chi-restraints excluded: chain E residue 384 CYS Chi-restraints excluded: chain E residue 394 SER Chi-restraints excluded: chain E residue 537 THR Chi-restraints excluded: chain E residue 582 GLU Chi-restraints excluded: chain F residue 862 VAL Chi-restraints excluded: chain F residue 870 ILE Chi-restraints excluded: chain F residue 915 SER Chi-restraints excluded: chain F residue 1135 LEU Chi-restraints excluded: chain F residue 1186 LEU Chi-restraints excluded: chain G residue 179 THR Chi-restraints excluded: chain G residue 265 CYS Chi-restraints excluded: chain G residue 348 CYS Chi-restraints excluded: chain G residue 394 SER Chi-restraints excluded: chain G residue 669 CYS Chi-restraints excluded: chain G residue 695 MET Chi-restraints excluded: chain H residue 870 ILE Chi-restraints excluded: chain H residue 935 GLU Chi-restraints excluded: chain H residue 938 ASP Chi-restraints excluded: chain H residue 941 VAL Chi-restraints excluded: chain H residue 947 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 66 optimal weight: 0.9980 chunk 454 optimal weight: 3.9990 chunk 319 optimal weight: 0.0470 chunk 412 optimal weight: 8.9990 chunk 420 optimal weight: 0.4980 chunk 263 optimal weight: 5.9990 chunk 200 optimal weight: 7.9990 chunk 439 optimal weight: 0.0870 chunk 325 optimal weight: 8.9990 chunk 68 optimal weight: 9.9990 chunk 360 optimal weight: 0.7980 overall best weight: 0.4856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 ASN ** B 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 911 ASN ** C1134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 78 ASN E 452 HIS ** E 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 107 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.166416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.136594 restraints weight = 79019.556| |-----------------------------------------------------------------------------| r_work (start): 0.3723 rms_B_bonded: 2.71 r_work: 0.3359 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3383 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3383 r_free = 0.3383 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3383 r_free = 0.3383 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3383 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.5827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 37624 Z= 0.105 Angle : 0.632 12.378 51244 Z= 0.311 Chirality : 0.044 0.453 5552 Planarity : 0.005 0.051 6732 Dihedral : 4.909 55.592 5556 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.33 % Favored : 93.65 % Rotamer: Outliers : 1.81 % Allowed : 16.63 % Favored : 81.56 % 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: -2.16 (0.12), residues: 4744 helix: -1.30 (0.20), residues: 664 sheet: -1.76 (0.19), residues: 756 loop : -1.44 (0.11), residues: 3324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 826 TYR 0.021 0.001 TYR H 897 PHE 0.019 0.001 PHE F 937 TRP 0.039 0.001 TRP A 222 HIS 0.013 0.001 HIS E 452 Details of bonding type rmsd covalent geometry : bond 0.00237 (37372) covalent geometry : angle 0.61449 (50720) SS BOND : bond 0.00262 ( 232) SS BOND : angle 1.18982 ( 464) hydrogen bonds : bond 0.02675 ( 744) hydrogen bonds : angle 4.79557 ( 1766) link_NAG-ASN : bond 0.00640 ( 20) link_NAG-ASN : angle 3.27953 ( 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 362 residues out of total 4112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 292 time to evaluate : 1.766 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: A 67 LYS cc_start: 0.8512 (OUTLIER) cc_final: 0.8170 (pttm) REVERT: A 185 TYR cc_start: 0.8525 (OUTLIER) cc_final: 0.7823 (t80) REVERT: A 341 LEU cc_start: 0.7988 (pp) cc_final: 0.7744 (pt) REVERT: A 475 LEU cc_start: 0.8036 (tt) cc_final: 0.7607 (tt) REVERT: A 735 PHE cc_start: 0.6246 (t80) cc_final: 0.5832 (t80) REVERT: B 77 GLN cc_start: 0.7203 (tp40) cc_final: 0.6879 (tt0) REVERT: B 373 ARG cc_start: 0.7146 (mtt90) cc_final: 0.6848 (mmt90) REVERT: B 681 GLU cc_start: 0.7176 (OUTLIER) cc_final: 0.6900 (mp0) REVERT: B 740 MET cc_start: 0.8278 (mmm) cc_final: 0.8046 (mmm) REVERT: C 771 MET cc_start: 0.5574 (ptp) cc_final: 0.5237 (mtp) REVERT: C 795 TYR cc_start: 0.7502 (t80) cc_final: 0.7115 (t80) REVERT: C 1185 GLU cc_start: 0.6348 (mp0) cc_final: 0.6135 (mp0) REVERT: E 347 GLU cc_start: 0.7873 (tm-30) cc_final: 0.7527 (tm-30) REVERT: E 384 CYS cc_start: 0.7630 (OUTLIER) cc_final: 0.7385 (m) REVERT: E 500 MET cc_start: 0.8089 (mtt) cc_final: 0.7605 (mtt) REVERT: F 826 ARG cc_start: 0.6017 (mtm110) cc_final: 0.5501 (ptm160) REVERT: F 1186 LEU cc_start: 0.7685 (OUTLIER) cc_final: 0.7447 (mt) REVERT: G 185 TYR cc_start: 0.8442 (OUTLIER) cc_final: 0.7988 (t80) REVERT: G 282 LEU cc_start: 0.6800 (pt) cc_final: 0.5715 (mt) REVERT: G 347 GLU cc_start: 0.7742 (tm-30) cc_final: 0.7231 (tm-30) REVERT: G 693 LEU cc_start: 0.6446 (mt) cc_final: 0.6128 (mt) REVERT: G 736 MET cc_start: 0.5550 (tpt) cc_final: 0.5172 (tpt) outliers start: 70 outliers final: 51 residues processed: 351 average time/residue: 0.2095 time to fit residues: 123.2870 Evaluate side-chains 325 residues out of total 4112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 268 time to evaluate : 1.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LYS Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 185 TYR Chi-restraints excluded: chain A residue 265 CYS Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 709 CYS Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 384 CYS Chi-restraints excluded: chain B residue 418 CYS Chi-restraints excluded: chain B residue 480 LEU Chi-restraints excluded: chain B residue 584 CYS Chi-restraints excluded: chain B residue 669 CYS Chi-restraints excluded: chain B residue 681 GLU Chi-restraints excluded: chain C residue 870 ILE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1093 SER Chi-restraints excluded: chain C residue 1135 LEU Chi-restraints excluded: chain D residue 862 VAL Chi-restraints excluded: chain D residue 870 ILE Chi-restraints excluded: chain D residue 911 ASN Chi-restraints excluded: chain D residue 915 SER Chi-restraints excluded: chain E residue 69 SER Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 107 GLN Chi-restraints excluded: chain E residue 159 CYS Chi-restraints excluded: chain E residue 338 ASP Chi-restraints excluded: chain E residue 384 CYS Chi-restraints excluded: chain E residue 394 SER Chi-restraints excluded: chain E residue 537 THR Chi-restraints excluded: chain E residue 582 GLU Chi-restraints excluded: chain E residue 584 CYS Chi-restraints excluded: chain F residue 814 MET Chi-restraints excluded: chain F residue 862 VAL Chi-restraints excluded: chain F residue 870 ILE Chi-restraints excluded: chain F residue 915 SER Chi-restraints excluded: chain F residue 936 LEU Chi-restraints excluded: chain F residue 1135 LEU Chi-restraints excluded: chain F residue 1186 LEU Chi-restraints excluded: chain G residue 179 THR Chi-restraints excluded: chain G residue 185 TYR Chi-restraints excluded: chain G residue 265 CYS Chi-restraints excluded: chain G residue 348 CYS Chi-restraints excluded: chain G residue 394 SER Chi-restraints excluded: chain G residue 669 CYS Chi-restraints excluded: chain G residue 695 MET Chi-restraints excluded: chain H residue 870 ILE Chi-restraints excluded: chain H residue 935 GLU Chi-restraints excluded: chain H residue 938 ASP Chi-restraints excluded: chain H residue 941 VAL Chi-restraints excluded: chain H residue 947 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 253 optimal weight: 40.0000 chunk 321 optimal weight: 4.9990 chunk 124 optimal weight: 0.9980 chunk 200 optimal weight: 7.9990 chunk 314 optimal weight: 0.0170 chunk 428 optimal weight: 9.9990 chunk 203 optimal weight: 10.0000 chunk 285 optimal weight: 4.9990 chunk 350 optimal weight: 0.3980 chunk 4 optimal weight: 0.2980 chunk 193 optimal weight: 0.2980 overall best weight: 0.4018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 ASN B 224 GLN B 419 GLN C 911 ASN C1109 HIS ** C1134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1113 GLN E 78 ASN E 452 HIS ** E 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.167844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.138967 restraints weight = 85727.482| |-----------------------------------------------------------------------------| r_work (start): 0.3770 rms_B_bonded: 2.80 r_work: 0.3394 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3398 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3398 r_free = 0.3398 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3398 r_free = 0.3398 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3398 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.5909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 37624 Z= 0.102 Angle : 0.618 12.045 51244 Z= 0.305 Chirality : 0.044 0.446 5552 Planarity : 0.005 0.055 6732 Dihedral : 4.767 55.763 5556 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.03 % Favored : 93.95 % Rotamer: Outliers : 1.86 % Allowed : 16.73 % Favored : 81.41 % 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: -2.10 (0.12), residues: 4744 helix: -1.55 (0.19), residues: 716 sheet: -1.63 (0.20), residues: 708 loop : -1.35 (0.11), residues: 3320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 826 TYR 0.021 0.001 TYR H 897 PHE 0.017 0.001 PHE F 937 TRP 0.046 0.001 TRP A 222 HIS 0.013 0.000 HIS E 452 Details of bonding type rmsd covalent geometry : bond 0.00230 (37372) covalent geometry : angle 0.60345 (50720) SS BOND : bond 0.00238 ( 232) SS BOND : angle 1.06909 ( 464) hydrogen bonds : bond 0.02632 ( 744) hydrogen bonds : angle 4.71735 ( 1766) link_NAG-ASN : bond 0.00627 ( 20) link_NAG-ASN : angle 3.16723 ( 60) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9051.01 seconds wall clock time: 155 minutes 6.65 seconds (9306.65 seconds total)