Starting phenix.real_space_refine on Tue Apr 16 00:18:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wn6_32622/04_2024/7wn6_32622_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wn6_32622/04_2024/7wn6_32622.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wn6_32622/04_2024/7wn6_32622.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wn6_32622/04_2024/7wn6_32622.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wn6_32622/04_2024/7wn6_32622_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wn6_32622/04_2024/7wn6_32622_neut.pdb" } resolution = 3.29 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 16 9.91 5 S 560 5.16 5 C 22568 2.51 5 N 6260 2.21 5 O 7180 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 34": "NH1" <-> "NH2" Residue "A PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 81": "NH1" <-> "NH2" Residue "A PHE 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 302": "NH1" <-> "NH2" Residue "F ARG 854": "NH1" <-> "NH2" Residue "F ARG 924": "NH1" <-> "NH2" Residue "F ARG 1035": "NH1" <-> "NH2" Residue "F ARG 1061": "NH1" <-> "NH2" Residue "F ARG 1121": "NH1" <-> "NH2" Residue "F GLU 1141": "OE1" <-> "OE2" Residue "F PHE 1206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 34": "NH1" <-> "NH2" Residue "B PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 81": "NH1" <-> "NH2" Residue "B PHE 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 302": "NH1" <-> "NH2" Residue "H ARG 854": "NH1" <-> "NH2" Residue "H ARG 924": "NH1" <-> "NH2" Residue "H ARG 1035": "NH1" <-> "NH2" Residue "H ARG 1061": "NH1" <-> "NH2" Residue "H ARG 1121": "NH1" <-> "NH2" Residue "H TYR 1146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 1206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 34": "NH1" <-> "NH2" Residue "E PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 81": "NH1" <-> "NH2" Residue "E PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 302": "NH1" <-> "NH2" Residue "G ARG 34": "NH1" <-> "NH2" Residue "G PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 81": "NH1" <-> "NH2" Residue "G PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 302": "NH1" <-> "NH2" Residue "C ARG 854": "NH1" <-> "NH2" Residue "C ARG 924": "NH1" <-> "NH2" Residue "C ARG 1035": "NH1" <-> "NH2" Residue "C ARG 1061": "NH1" <-> "NH2" Residue "C ARG 1121": "NH1" <-> "NH2" Residue "C PHE 1206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 854": "NH1" <-> "NH2" Residue "D ARG 924": "NH1" <-> "NH2" Residue "D ARG 1035": "NH1" <-> "NH2" Residue "D ARG 1061": "NH1" <-> "NH2" Residue "D ARG 1121": "NH1" <-> "NH2" Residue "D PHE 1206": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 36584 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 5421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 711, 5421 Classifications: {'peptide': 711} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 2, 'PTRANS': 33, 'TRANS': 675} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "F" Number of atoms: 3651 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 478, 3645 Classifications: {'peptide': 478} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 28, 'TRANS': 449} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 478, 3645 Classifications: {'peptide': 478} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 28, 'TRANS': 449} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 3714 Chain: "B" Number of atoms: 5421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 711, 5421 Classifications: {'peptide': 711} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 2, 'PTRANS': 33, 'TRANS': 675} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "H" Number of atoms: 3651 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 478, 3645 Classifications: {'peptide': 478} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 28, 'TRANS': 449} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 478, 3645 Classifications: {'peptide': 478} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 28, 'TRANS': 449} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 3714 Chain: "E" Number of atoms: 5421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 711, 5421 Classifications: {'peptide': 711} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 2, 'PTRANS': 33, 'TRANS': 675} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "G" Number of atoms: 5421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 711, 5421 Classifications: {'peptide': 711} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 2, 'PTRANS': 33, 'TRANS': 675} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "C" Number of atoms: 3651 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 478, 3645 Classifications: {'peptide': 478} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 28, 'TRANS': 449} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 478, 3645 Classifications: {'peptide': 478} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 28, 'TRANS': 449} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 3714 Chain: "D" Number of atoms: 3651 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 478, 3645 Classifications: {'peptide': 478} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 28, 'TRANS': 449} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 478, 3645 Classifications: {'peptide': 478} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 28, 'TRANS': 449} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 3714 Chain: "A" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 30 Unusual residues: {' CA': 2, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 44 Unusual residues: {' CA': 2, 'NAG': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 30 Unusual residues: {' CA': 2, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 44 Unusual residues: {' CA': 2, 'NAG': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 30 Unusual residues: {' CA': 2, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 30 Unusual residues: {' CA': 2, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 44 Unusual residues: {' CA': 2, 'NAG': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 44 Unusual residues: {' CA': 2, 'NAG': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 24.50, per 1000 atoms: 0.67 Number of scatterers: 36584 At special positions: 0 Unit cell: (161.02, 246.38, 176.54, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 16 19.99 S 560 16.00 O 7180 8.00 N 6260 7.00 C 22568 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=230, symmetry=0 Simple disulfide: pdb=" SG CYS A 35 " - pdb=" SG CYS A 162 " distance=2.03 Simple disulfide: pdb=" SG CYS A 57 " - pdb=" SG CYS A 200 " distance=2.03 Simple disulfide: pdb=" SG CYS A 65 " - pdb=" SG CYS A 159 " distance=2.02 Simple disulfide: pdb=" SG CYS A 210 " - pdb=" SG CYS A 255 " distance=2.03 Simple disulfide: pdb=" SG CYS A 225 " - pdb=" SG CYS A 250 " distance=2.02 Simple disulfide: pdb=" SG CYS A 237 " - pdb=" SG CYS A 275 " distance=2.03 Simple disulfide: pdb=" SG CYS A 257 " - pdb=" SG CYS A 263 " distance=2.03 Simple disulfide: pdb=" SG CYS A 265 " - pdb=" SG CYS A 291 " distance=2.03 Simple disulfide: pdb=" SG CYS A 295 " - pdb=" SG CYS A 329 " distance=2.02 Simple disulfide: pdb=" SG CYS A 304 " - pdb=" SG CYS A 325 " distance=2.03 Simple disulfide: pdb=" SG CYS A 308 " - pdb=" SG CYS A 321 " distance=2.02 Simple disulfide: pdb=" SG CYS A 312 " - pdb=" SG CYS A 348 " distance=2.03 Simple disulfide: pdb=" SG CYS A 331 " - pdb=" SG CYS A 342 " distance=2.03 Simple disulfide: pdb=" SG CYS A 350 " - pdb=" SG CYS A 372 " distance=2.03 Simple disulfide: pdb=" SG CYS A 367 " - pdb=" SG CYS A 384 " distance=2.03 Simple disulfide: pdb=" SG CYS A 370 " - pdb=" SG CYS A 379 " distance=2.03 Simple disulfide: pdb=" SG CYS A 388 " - pdb=" SG CYS A 524 " distance=2.03 Simple disulfide: pdb=" SG CYS A 410 " - pdb=" SG CYS A 559 " distance=2.03 Simple disulfide: pdb=" SG CYS A 418 " - pdb=" SG CYS A 521 " distance=2.03 Simple disulfide: pdb=" SG CYS A 432 " - pdb=" SG CYS A 440 " distance=2.03 Simple disulfide: pdb=" SG CYS A 570 " - pdb=" SG CYS A 613 " distance=2.03 Simple disulfide: pdb=" SG CYS A 584 " - pdb=" SG CYS A 608 " distance=2.02 Simple disulfide: pdb=" SG CYS A 595 " - pdb=" SG CYS A 633 " distance=2.04 Simple disulfide: pdb=" SG CYS A 615 " - pdb=" SG CYS A 621 " distance=2.03 Simple disulfide: pdb=" SG CYS A 623 " - pdb=" SG CYS A 648 " distance=2.02 Simple disulfide: pdb=" SG CYS A 652 " - pdb=" SG CYS A 687 " distance=2.03 Simple disulfide: pdb=" SG CYS A 661 " - pdb=" SG CYS A 683 " distance=2.03 Simple disulfide: pdb=" SG CYS A 665 " - pdb=" SG CYS A 679 " distance=2.03 Simple disulfide: pdb=" SG CYS A 669 " - pdb=" SG CYS A 707 " distance=2.03 Simple disulfide: pdb=" SG CYS A 689 " - pdb=" SG CYS A 701 " distance=2.04 Simple disulfide: pdb=" SG CYS A 709 " - pdb=" SG CYS A 731 " distance=2.03 Simple disulfide: pdb=" SG CYS A 729 " - pdb=" SG CYS A 738 " distance=2.03 Simple disulfide: pdb=" SG CYS F 767 " - pdb=" SG CYS F 808 " distance=2.03 Simple disulfide: pdb=" SG CYS F 776 " - pdb=" SG CYS F 804 " distance=2.03 Simple disulfide: pdb=" SG CYS F 788 " - pdb=" SG CYS F 799 " distance=2.03 Simple disulfide: pdb=" SG CYS F 792 " - pdb=" SG CYS F 827 " distance=2.03 Simple disulfide: pdb=" SG CYS F 810 " - pdb=" SG CYS F 821 " distance=2.03 Simple disulfide: pdb=" SG CYS F 829 " - pdb=" SG CYS F 851 " distance=2.03 Simple disulfide: pdb=" SG CYS F 846 " - pdb=" SG CYS F 863 " distance=2.03 Simple disulfide: pdb=" SG CYS F 849 " - pdb=" SG CYS F 858 " distance=2.03 Simple disulfide: pdb=" SG CYS F 867 " - pdb=" SG CYS F 996 " distance=2.03 Simple disulfide: pdb=" SG CYS F 889 " - pdb=" SG CYS F1031 " distance=2.02 Simple disulfide: pdb=" SG CYS F 898 " - pdb=" SG CYS F 993 " distance=2.03 Simple disulfide: pdb=" SG CYS F 914 " - pdb=" SG CYS F 921 " distance=2.03 Simple disulfide: pdb=" SG CYS F1046 " - pdb=" SG CYS F1089 " distance=2.03 Simple disulfide: pdb=" SG CYS F1060 " - pdb=" SG CYS F1084 " distance=2.04 Simple disulfide: pdb=" SG CYS F1071 " - pdb=" SG CYS F1111 " distance=2.03 Simple disulfide: pdb=" SG CYS F1091 " - pdb=" SG CYS F1099 " distance=2.03 Simple disulfide: pdb=" SG CYS F1097 " - pdb=" SG CYS H1097 " distance=1.99 Simple disulfide: pdb=" SG CYS F1101 " - pdb=" SG CYS F1126 " distance=2.02 Simple disulfide: pdb=" SG CYS F1130 " - pdb=" SG CYS F1173 " distance=2.02 Simple disulfide: pdb=" SG CYS F1149 " - pdb=" SG CYS F1169 " distance=2.03 Simple disulfide: pdb=" SG CYS F1153 " - pdb=" SG CYS F1165 " distance=2.03 Simple disulfide: pdb=" SG CYS F1157 " - pdb=" SG CYS F1196 " distance=2.03 Simple disulfide: pdb=" SG CYS F1177 " - pdb=" SG CYS F1190 " distance=2.03 Simple disulfide: pdb=" SG CYS F1199 " - pdb=" SG CYS F1227 " distance=2.03 Simple disulfide: pdb=" SG CYS F1222 " - pdb=" SG CYS F1237 " distance=2.03 Simple disulfide: pdb=" SG CYS F1225 " - pdb=" SG CYS F1234 " distance=2.03 Simple disulfide: pdb=" SG CYS B 35 " - pdb=" SG CYS B 162 " distance=2.03 Simple disulfide: pdb=" SG CYS B 57 " - pdb=" SG CYS B 200 " distance=2.03 Simple disulfide: pdb=" SG CYS B 65 " - pdb=" SG CYS B 159 " distance=2.03 Simple disulfide: pdb=" SG CYS B 210 " - pdb=" SG CYS B 255 " distance=2.03 Simple disulfide: pdb=" SG CYS B 225 " - pdb=" SG CYS B 250 " distance=2.02 Simple disulfide: pdb=" SG CYS B 237 " - pdb=" SG CYS B 275 " distance=2.03 Simple disulfide: pdb=" SG CYS B 257 " - pdb=" SG CYS B 263 " distance=2.03 Simple disulfide: pdb=" SG CYS B 265 " - pdb=" SG CYS B 291 " distance=2.03 Simple disulfide: pdb=" SG CYS B 295 " - pdb=" SG CYS B 329 " distance=2.02 Simple disulfide: pdb=" SG CYS B 304 " - pdb=" SG CYS B 325 " distance=2.03 Simple disulfide: pdb=" SG CYS B 308 " - pdb=" SG CYS B 321 " distance=2.02 Simple disulfide: pdb=" SG CYS B 312 " - pdb=" SG CYS B 348 " distance=2.03 Simple disulfide: pdb=" SG CYS B 331 " - pdb=" SG CYS B 342 " distance=2.03 Simple disulfide: pdb=" SG CYS B 350 " - pdb=" SG CYS B 372 " distance=2.03 Simple disulfide: pdb=" SG CYS B 367 " - pdb=" SG CYS B 384 " distance=2.03 Simple disulfide: pdb=" SG CYS B 370 " - pdb=" SG CYS B 379 " distance=2.03 Simple disulfide: pdb=" SG CYS B 388 " - pdb=" SG CYS B 524 " distance=2.03 Simple disulfide: pdb=" SG CYS B 410 " - pdb=" SG CYS B 559 " distance=2.03 Simple disulfide: pdb=" SG CYS B 418 " - pdb=" SG CYS B 521 " distance=2.03 Simple disulfide: pdb=" SG CYS B 432 " - pdb=" SG CYS B 440 " distance=2.03 Simple disulfide: pdb=" SG CYS B 570 " - pdb=" SG CYS B 613 " distance=2.03 Simple disulfide: pdb=" SG CYS B 584 " - pdb=" SG CYS B 608 " distance=2.02 Simple disulfide: pdb=" SG CYS B 595 " - pdb=" SG CYS B 633 " distance=2.03 Simple disulfide: pdb=" SG CYS B 615 " - pdb=" SG CYS B 621 " distance=2.03 Simple disulfide: pdb=" SG CYS B 623 " - pdb=" SG CYS B 648 " distance=2.02 Simple disulfide: pdb=" SG CYS B 652 " - pdb=" SG CYS B 687 " distance=2.03 Simple disulfide: pdb=" SG CYS B 661 " - pdb=" SG CYS B 683 " distance=2.03 Simple disulfide: pdb=" SG CYS B 665 " - pdb=" SG CYS B 679 " distance=2.03 Simple disulfide: pdb=" SG CYS B 669 " - pdb=" SG CYS B 707 " distance=2.03 Simple disulfide: pdb=" SG CYS B 689 " - pdb=" SG CYS B 701 " distance=2.04 Simple disulfide: pdb=" SG CYS B 709 " - pdb=" SG CYS B 731 " distance=2.03 Simple disulfide: pdb=" SG CYS B 729 " - pdb=" SG CYS B 738 " distance=2.03 Simple disulfide: pdb=" SG CYS H 767 " - pdb=" SG CYS H 808 " distance=2.03 Simple disulfide: pdb=" SG CYS H 776 " - pdb=" SG CYS H 804 " distance=2.03 Simple disulfide: pdb=" SG CYS H 788 " - pdb=" SG CYS H 799 " distance=2.03 Simple disulfide: pdb=" SG CYS H 792 " - pdb=" SG CYS H 827 " distance=2.03 Simple disulfide: pdb=" SG CYS H 810 " - pdb=" SG CYS H 821 " distance=2.03 Simple disulfide: pdb=" SG CYS H 829 " - pdb=" SG CYS H 851 " distance=2.03 Simple disulfide: pdb=" SG CYS H 846 " - pdb=" SG CYS H 863 " distance=2.03 Simple disulfide: pdb=" SG CYS H 849 " - pdb=" SG CYS H 858 " distance=2.04 Simple disulfide: pdb=" SG CYS H 867 " - pdb=" SG CYS H 996 " distance=2.03 Simple disulfide: pdb=" SG CYS H 889 " - pdb=" SG CYS H1031 " distance=2.03 Simple disulfide: pdb=" SG CYS H 898 " - pdb=" SG CYS H 993 " distance=2.03 Simple disulfide: pdb=" SG CYS H 914 " - pdb=" SG CYS H 921 " distance=2.03 Simple disulfide: pdb=" SG CYS H1046 " - pdb=" SG CYS H1089 " distance=2.03 Simple disulfide: pdb=" SG CYS H1060 " - pdb=" SG CYS H1084 " distance=2.04 Simple disulfide: pdb=" SG CYS H1071 " - pdb=" SG CYS H1111 " distance=2.03 Simple disulfide: pdb=" SG CYS H1091 " - pdb=" SG CYS H1099 " distance=2.03 Simple disulfide: pdb=" SG CYS H1101 " - pdb=" SG CYS H1126 " distance=2.02 Simple disulfide: pdb=" SG CYS H1130 " - pdb=" SG CYS H1173 " distance=2.02 Simple disulfide: pdb=" SG CYS H1149 " - pdb=" SG CYS H1169 " distance=2.03 Simple disulfide: pdb=" SG CYS H1153 " - pdb=" SG CYS H1165 " distance=2.03 Simple disulfide: pdb=" SG CYS H1157 " - pdb=" SG CYS H1196 " distance=2.03 Simple disulfide: pdb=" SG CYS H1177 " - pdb=" SG CYS H1190 " distance=2.03 Simple disulfide: pdb=" SG CYS H1199 " - pdb=" SG CYS H1227 " distance=2.03 Simple disulfide: pdb=" SG CYS H1222 " - pdb=" SG CYS H1237 " distance=2.04 Simple disulfide: pdb=" SG CYS H1225 " - pdb=" SG CYS H1234 " distance=2.03 Simple disulfide: pdb=" SG CYS E 35 " - pdb=" SG CYS E 162 " distance=2.03 Simple disulfide: pdb=" SG CYS E 57 " - pdb=" SG CYS E 200 " distance=2.03 Simple disulfide: pdb=" SG CYS E 65 " - pdb=" SG CYS E 159 " distance=2.02 Simple disulfide: pdb=" SG CYS E 210 " - pdb=" SG CYS E 255 " distance=2.03 Simple disulfide: pdb=" SG CYS E 225 " - pdb=" SG CYS E 250 " distance=2.02 Simple disulfide: pdb=" SG CYS E 237 " - pdb=" SG CYS E 275 " distance=2.03 Simple disulfide: pdb=" SG CYS E 257 " - pdb=" SG CYS E 263 " distance=2.03 Simple disulfide: pdb=" SG CYS E 265 " - pdb=" SG CYS E 291 " distance=2.03 Simple disulfide: pdb=" SG CYS E 295 " - pdb=" SG CYS E 329 " distance=2.02 Simple disulfide: pdb=" SG CYS E 304 " - pdb=" SG CYS E 325 " distance=2.03 Simple disulfide: pdb=" SG CYS E 308 " - pdb=" SG CYS E 321 " distance=2.02 Simple disulfide: pdb=" SG CYS E 312 " - pdb=" SG CYS E 348 " distance=2.03 Simple disulfide: pdb=" SG CYS E 331 " - pdb=" SG CYS E 342 " distance=2.03 Simple disulfide: pdb=" SG CYS E 350 " - pdb=" SG CYS E 372 " distance=2.03 Simple disulfide: pdb=" SG CYS E 367 " - pdb=" SG CYS E 384 " distance=2.03 Simple disulfide: pdb=" SG CYS E 370 " - pdb=" SG CYS E 379 " distance=2.03 Simple disulfide: pdb=" SG CYS E 388 " - pdb=" SG CYS E 524 " distance=2.03 Simple disulfide: pdb=" SG CYS E 410 " - pdb=" SG CYS E 559 " distance=2.03 Simple disulfide: pdb=" SG CYS E 418 " - pdb=" SG CYS E 521 " distance=2.03 Simple disulfide: pdb=" SG CYS E 432 " - pdb=" SG CYS E 440 " distance=2.03 Simple disulfide: pdb=" SG CYS E 570 " - pdb=" SG CYS E 613 " distance=2.03 Simple disulfide: pdb=" SG CYS E 584 " - pdb=" SG CYS E 608 " distance=2.02 Simple disulfide: pdb=" SG CYS E 595 " - pdb=" SG CYS E 633 " distance=2.03 Simple disulfide: pdb=" SG CYS E 615 " - pdb=" SG CYS E 621 " distance=2.03 Simple disulfide: pdb=" SG CYS E 623 " - pdb=" SG CYS E 648 " distance=2.02 Simple disulfide: pdb=" SG CYS E 652 " - pdb=" SG CYS E 687 " distance=2.03 Simple disulfide: pdb=" SG CYS E 661 " - pdb=" SG CYS E 683 " distance=2.03 Simple disulfide: pdb=" SG CYS E 665 " - pdb=" SG CYS E 679 " distance=2.03 Simple disulfide: pdb=" SG CYS E 669 " - pdb=" SG CYS E 707 " distance=2.03 Simple disulfide: pdb=" SG CYS E 689 " - pdb=" SG CYS E 701 " distance=2.04 Simple disulfide: pdb=" SG CYS E 709 " - pdb=" SG CYS E 731 " distance=2.03 Simple disulfide: pdb=" SG CYS E 729 " - pdb=" SG CYS E 738 " distance=2.03 Simple disulfide: pdb=" SG CYS G 35 " - pdb=" SG CYS G 162 " distance=2.04 Simple disulfide: pdb=" SG CYS G 57 " - pdb=" SG CYS G 200 " distance=2.04 Simple disulfide: pdb=" SG CYS G 65 " - pdb=" SG CYS G 159 " distance=2.03 Simple disulfide: pdb=" SG CYS G 210 " - pdb=" SG CYS G 255 " distance=2.03 Simple disulfide: pdb=" SG CYS G 225 " - pdb=" SG CYS G 250 " distance=2.02 Simple disulfide: pdb=" SG CYS G 237 " - pdb=" SG CYS G 275 " distance=2.03 Simple disulfide: pdb=" SG CYS G 257 " - pdb=" SG CYS G 263 " distance=2.03 Simple disulfide: pdb=" SG CYS G 265 " - pdb=" SG CYS G 291 " distance=2.03 Simple disulfide: pdb=" SG CYS G 295 " - pdb=" SG CYS G 329 " distance=2.02 Simple disulfide: pdb=" SG CYS G 304 " - pdb=" SG CYS G 325 " distance=2.03 Simple disulfide: pdb=" SG CYS G 308 " - pdb=" SG CYS G 321 " distance=2.02 Simple disulfide: pdb=" SG CYS G 312 " - pdb=" SG CYS G 348 " distance=2.03 Simple disulfide: pdb=" SG CYS G 331 " - pdb=" SG CYS G 342 " distance=2.03 Simple disulfide: pdb=" SG CYS G 350 " - pdb=" SG CYS G 372 " distance=2.03 Simple disulfide: pdb=" SG CYS G 367 " - pdb=" SG CYS G 384 " distance=2.03 Simple disulfide: pdb=" SG CYS G 370 " - pdb=" SG CYS G 379 " distance=2.03 Simple disulfide: pdb=" SG CYS G 388 " - pdb=" SG CYS G 524 " distance=2.03 Simple disulfide: pdb=" SG CYS G 410 " - pdb=" SG CYS G 559 " distance=2.03 Simple disulfide: pdb=" SG CYS G 418 " - pdb=" SG CYS G 521 " distance=2.03 Simple disulfide: pdb=" SG CYS G 432 " - pdb=" SG CYS G 440 " distance=2.03 Simple disulfide: pdb=" SG CYS G 570 " - pdb=" SG CYS G 613 " distance=2.03 Simple disulfide: pdb=" SG CYS G 584 " - pdb=" SG CYS G 608 " distance=2.02 Simple disulfide: pdb=" SG CYS G 595 " - pdb=" SG CYS G 633 " distance=2.03 Simple disulfide: pdb=" SG CYS G 615 " - pdb=" SG CYS G 621 " distance=2.03 Simple disulfide: pdb=" SG CYS G 623 " - pdb=" SG CYS G 648 " distance=2.02 Simple disulfide: pdb=" SG CYS G 652 " - pdb=" SG CYS G 687 " distance=2.03 Simple disulfide: pdb=" SG CYS G 661 " - pdb=" SG CYS G 683 " distance=2.03 Simple disulfide: pdb=" SG CYS G 665 " - pdb=" SG CYS G 679 " distance=2.03 Simple disulfide: pdb=" SG CYS G 669 " - pdb=" SG CYS G 707 " distance=2.03 Simple disulfide: pdb=" SG CYS G 689 " - pdb=" SG CYS G 701 " distance=2.04 Simple disulfide: pdb=" SG CYS G 709 " - pdb=" SG CYS G 731 " distance=2.03 Simple disulfide: pdb=" SG CYS G 729 " - pdb=" SG CYS G 738 " distance=2.03 Simple disulfide: pdb=" SG CYS C 767 " - pdb=" SG CYS C 808 " distance=2.03 Simple disulfide: pdb=" SG CYS C 776 " - pdb=" SG CYS C 804 " distance=2.03 Simple disulfide: pdb=" SG CYS C 788 " - pdb=" SG CYS C 799 " distance=2.03 Simple disulfide: pdb=" SG CYS C 792 " - pdb=" SG CYS C 827 " distance=2.03 Simple disulfide: pdb=" SG CYS C 810 " - pdb=" SG CYS C 821 " distance=2.03 Simple disulfide: pdb=" SG CYS C 829 " - pdb=" SG CYS C 851 " distance=2.03 Simple disulfide: pdb=" SG CYS C 846 " - pdb=" SG CYS C 863 " distance=2.03 Simple disulfide: pdb=" SG CYS C 849 " - pdb=" SG CYS C 858 " distance=2.03 Simple disulfide: pdb=" SG CYS C 867 " - pdb=" SG CYS C 996 " distance=2.03 Simple disulfide: pdb=" SG CYS C 889 " - pdb=" SG CYS C1031 " distance=2.03 Simple disulfide: pdb=" SG CYS C 898 " - pdb=" SG CYS C 993 " distance=2.03 Simple disulfide: pdb=" SG CYS C 914 " - pdb=" SG CYS C 921 " distance=2.03 Simple disulfide: pdb=" SG CYS C1046 " - pdb=" SG CYS C1089 " distance=2.03 Simple disulfide: pdb=" SG CYS C1060 " - pdb=" SG CYS C1084 " distance=2.04 Simple disulfide: pdb=" SG CYS C1071 " - pdb=" SG CYS C1111 " distance=2.02 Simple disulfide: pdb=" SG CYS C1091 " - pdb=" SG CYS C1099 " distance=2.03 Simple disulfide: pdb=" SG CYS C1097 " - pdb=" SG CYS D1097 " distance=2.08 Simple disulfide: pdb=" SG CYS C1101 " - pdb=" SG CYS C1126 " distance=2.02 Simple disulfide: pdb=" SG CYS C1130 " - pdb=" SG CYS C1173 " distance=2.02 Simple disulfide: pdb=" SG CYS C1149 " - pdb=" SG CYS C1169 " distance=2.04 Simple disulfide: pdb=" SG CYS C1153 " - pdb=" SG CYS C1165 " distance=2.03 Simple disulfide: pdb=" SG CYS C1157 " - pdb=" SG CYS C1196 " distance=2.03 Simple disulfide: pdb=" SG CYS C1177 " - pdb=" SG CYS C1190 " distance=2.03 Simple disulfide: pdb=" SG CYS C1199 " - pdb=" SG CYS C1227 " distance=2.03 Simple disulfide: pdb=" SG CYS C1222 " - pdb=" SG CYS C1237 " distance=2.03 Simple disulfide: pdb=" SG CYS C1225 " - pdb=" SG CYS C1234 " distance=2.03 Simple disulfide: pdb=" SG CYS D 767 " - pdb=" SG CYS D 808 " distance=2.03 Simple disulfide: pdb=" SG CYS D 776 " - pdb=" SG CYS D 804 " distance=2.03 Simple disulfide: pdb=" SG CYS D 788 " - pdb=" SG CYS D 799 " distance=2.03 Simple disulfide: pdb=" SG CYS D 792 " - pdb=" SG CYS D 827 " distance=2.03 Simple disulfide: pdb=" SG CYS D 810 " - pdb=" SG CYS D 821 " distance=2.03 Simple disulfide: pdb=" SG CYS D 829 " - pdb=" SG CYS D 851 " distance=2.03 Simple disulfide: pdb=" SG CYS D 846 " - pdb=" SG CYS D 863 " distance=2.03 Simple disulfide: pdb=" SG CYS D 849 " - pdb=" SG CYS D 858 " distance=2.03 Simple disulfide: pdb=" SG CYS D 867 " - pdb=" SG CYS D 996 " distance=2.03 Simple disulfide: pdb=" SG CYS D 889 " - pdb=" SG CYS D1031 " distance=2.03 Simple disulfide: pdb=" SG CYS D 898 " - pdb=" SG CYS D 993 " distance=2.03 Simple disulfide: pdb=" SG CYS D 914 " - pdb=" SG CYS D 921 " distance=2.03 Simple disulfide: pdb=" SG CYS D1046 " - pdb=" SG CYS D1089 " distance=2.03 Simple disulfide: pdb=" SG CYS D1060 " - pdb=" SG CYS D1084 " distance=2.04 Simple disulfide: pdb=" SG CYS D1071 " - pdb=" SG CYS D1111 " distance=2.03 Simple disulfide: pdb=" SG CYS D1091 " - pdb=" SG CYS D1099 " distance=2.03 Simple disulfide: pdb=" SG CYS D1101 " - pdb=" SG CYS D1126 " distance=2.02 Simple disulfide: pdb=" SG CYS D1130 " - pdb=" SG CYS D1173 " distance=2.03 Simple disulfide: pdb=" SG CYS D1149 " - pdb=" SG CYS D1169 " distance=2.03 Simple disulfide: pdb=" SG CYS D1153 " - pdb=" SG CYS D1165 " distance=2.03 Simple disulfide: pdb=" SG CYS D1157 " - pdb=" SG CYS D1196 " distance=2.03 Simple disulfide: pdb=" SG CYS D1177 " - pdb=" SG CYS D1190 " distance=2.03 Simple disulfide: pdb=" SG CYS D1199 " - pdb=" SG CYS D1227 " distance=2.03 Simple disulfide: pdb=" SG CYS D1222 " - pdb=" SG CYS D1237 " distance=2.04 Simple disulfide: pdb=" SG CYS D1225 " - pdb=" SG CYS D1234 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "HETATM36582 O5 NAG D1305 .*. O " rejected from bonding due to valence issues. Atom "HETATM36434 O5 NAG H1305 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 803 " - " ASN A 156 " " NAG A 804 " - " ASN A 99 " " NAG B 803 " - " ASN B 156 " " NAG B 804 " - " ASN B 99 " " NAG C1301 " - " ASN C1231 " " NAG C1304 " - " ASN C 857 " " NAG C1305 " - " ASN C1147 " " NAG D1301 " - " ASN D1231 " " NAG D1304 " - " ASN D 857 " " NAG D1305 " - " ASN D1147 " " NAG E 803 " - " ASN E 156 " " NAG E 804 " - " ASN E 99 " " NAG F1301 " - " ASN F1231 " " NAG F1304 " - " ASN F 857 " " NAG F1305 " - " ASN F1147 " " NAG G 803 " - " ASN G 156 " " NAG G 804 " - " ASN G 99 " " NAG H1301 " - " ASN H1231 " " NAG H1304 " - " ASN H 857 " " NAG H1305 " - " ASN H1147 " Time building additional restraints: 13.29 Conformation dependent library (CDL) restraints added in 9.4 seconds 9488 Ramachandran restraints generated. 4744 Oldfield, 0 Emsley, 4744 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8768 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 98 sheets defined 17.9% alpha, 13.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.15 Creating SS restraints... Processing helix chain 'A' and resid 114 through 118 removed outlier: 3.923A pdb=" N GLY A 117 " --> pdb=" O ALA A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 191 removed outlier: 3.504A pdb=" N TRP A 191 " --> pdb=" O PHE A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 212 removed outlier: 3.758A pdb=" N ASN A 211 " --> pdb=" O SER A 208 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE A 212 " --> pdb=" O SER A 209 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 208 through 212' Processing helix chain 'A' and resid 216 through 221 removed outlier: 3.757A pdb=" N LEU A 221 " --> pdb=" O MET A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 231 removed outlier: 4.279A pdb=" N CYS A 225 " --> pdb=" O LEU A 221 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N LEU A 228 " --> pdb=" O GLN A 224 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N LYS A 229 " --> pdb=" O CYS A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 235 Processing helix chain 'A' and resid 243 through 251 removed outlier: 3.585A pdb=" N GLU A 251 " --> pdb=" O VAL A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 263 removed outlier: 3.881A pdb=" N CYS A 263 " --> pdb=" O GLY A 260 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 260 through 263' Processing helix chain 'A' and resid 264 through 278 removed outlier: 3.710A pdb=" N TYR A 271 " --> pdb=" O ALA A 267 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ARG A 273 " --> pdb=" O LEU A 269 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLU A 278 " --> pdb=" O THR A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 348 Processing helix chain 'A' and resid 514 through 517 Processing helix chain 'A' and resid 545 through 550 removed outlier: 3.505A pdb=" N PHE A 549 " --> pdb=" O ARG A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 554 removed outlier: 3.783A pdb=" N LYS A 554 " --> pdb=" O ASN A 551 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 551 through 554' Processing helix chain 'A' and resid 568 through 572 Processing helix chain 'A' and resid 573 through 574 No H-bonds generated for 'chain 'A' and resid 573 through 574' Processing helix chain 'A' and resid 575 through 584 removed outlier: 4.825A pdb=" N PHE A 579 " --> pdb=" O ARG A 575 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLU A 581 " --> pdb=" O THR A 577 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N CYS A 584 " --> pdb=" O SER A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 589 through 596 removed outlier: 4.902A pdb=" N ALA A 594 " --> pdb=" O THR A 591 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N HIS A 596 " --> pdb=" O GLU A 593 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 613 removed outlier: 3.819A pdb=" N CYS A 608 " --> pdb=" O TYR A 604 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG A 609 " --> pdb=" O LEU A 605 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N TYR A 610 " --> pdb=" O ARG A 606 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ASP A 611 " --> pdb=" O ASN A 607 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N CYS A 613 " --> pdb=" O ARG A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 617 through 623 removed outlier: 3.720A pdb=" N CYS A 621 " --> pdb=" O ASP A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 635 removed outlier: 3.657A pdb=" N ALA A 632 " --> pdb=" O SER A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 668 through 674 removed outlier: 4.235A pdb=" N LEU A 672 " --> pdb=" O THR A 668 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N SER A 673 " --> pdb=" O CYS A 669 " (cutoff:3.500A) Processing helix chain 'F' and resid 1017 through 1023 removed outlier: 3.544A pdb=" N PHE F1021 " --> pdb=" O ASP F1017 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ASN F1023 " --> pdb=" O VAL F1019 " (cutoff:3.500A) Processing helix chain 'F' and resid 1049 through 1060 removed outlier: 3.549A pdb=" N MET F1055 " --> pdb=" O MET F1051 " (cutoff:3.500A) Processing helix chain 'F' and resid 1061 through 1065 Processing helix chain 'F' and resid 1068 through 1075 removed outlier: 3.869A pdb=" N LYS F1073 " --> pdb=" O GLN F1069 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LEU F1074 " --> pdb=" O ASP F1070 " (cutoff:3.500A) Processing helix chain 'F' and resid 1077 through 1091 removed outlier: 3.625A pdb=" N VAL F1083 " --> pdb=" O PRO F1079 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N CYS F1084 " --> pdb=" O TYR F1080 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N THR F1088 " --> pdb=" O CYS F1084 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N CYS F1089 " --> pdb=" O ILE F1085 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER F1090 " --> pdb=" O TYR F1086 " (cutoff:3.500A) Processing helix chain 'F' and resid 1097 through 1114 removed outlier: 5.312A pdb=" N THR F1103 " --> pdb=" O CYS F1099 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ILE F1104 " --> pdb=" O PHE F1100 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA F1105 " --> pdb=" O CYS F1101 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N VAL F1110 " --> pdb=" O ALA F1106 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N HIS F1114 " --> pdb=" O VAL F1110 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 118 removed outlier: 3.923A pdb=" N GLY B 117 " --> pdb=" O ALA B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 191 removed outlier: 3.505A pdb=" N TRP B 191 " --> pdb=" O PHE B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 212 removed outlier: 3.758A pdb=" N ASN B 211 " --> pdb=" O SER B 208 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE B 212 " --> pdb=" O SER B 209 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 208 through 212' Processing helix chain 'B' and resid 216 through 221 removed outlier: 3.758A pdb=" N LEU B 221 " --> pdb=" O MET B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 231 removed outlier: 4.279A pdb=" N CYS B 225 " --> pdb=" O LEU B 221 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N LEU B 228 " --> pdb=" O GLN B 224 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N LYS B 229 " --> pdb=" O CYS B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 235 Processing helix chain 'B' and resid 243 through 251 removed outlier: 3.585A pdb=" N GLU B 251 " --> pdb=" O VAL B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 263 removed outlier: 3.881A pdb=" N CYS B 263 " --> pdb=" O GLY B 260 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 260 through 263' Processing helix chain 'B' and resid 264 through 278 removed outlier: 3.710A pdb=" N TYR B 271 " --> pdb=" O ALA B 267 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ARG B 273 " --> pdb=" O LEU B 269 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLU B 278 " --> pdb=" O THR B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 348 Processing helix chain 'B' and resid 514 through 517 Processing helix chain 'B' and resid 545 through 550 removed outlier: 3.506A pdb=" N PHE B 549 " --> pdb=" O ARG B 545 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 554 removed outlier: 3.782A pdb=" N LYS B 554 " --> pdb=" O ASN B 551 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 551 through 554' Processing helix chain 'B' and resid 568 through 572 Processing helix chain 'B' and resid 573 through 574 No H-bonds generated for 'chain 'B' and resid 573 through 574' Processing helix chain 'B' and resid 575 through 584 removed outlier: 4.825A pdb=" N PHE B 579 " --> pdb=" O ARG B 575 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLU B 581 " --> pdb=" O THR B 577 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N CYS B 584 " --> pdb=" O SER B 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 589 through 596 removed outlier: 4.903A pdb=" N ALA B 594 " --> pdb=" O THR B 591 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N HIS B 596 " --> pdb=" O GLU B 593 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 613 removed outlier: 3.820A pdb=" N CYS B 608 " --> pdb=" O TYR B 604 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG B 609 " --> pdb=" O LEU B 605 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N TYR B 610 " --> pdb=" O ARG B 606 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ASP B 611 " --> pdb=" O ASN B 607 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N CYS B 613 " --> pdb=" O ARG B 609 " (cutoff:3.500A) Processing helix chain 'B' and resid 617 through 623 removed outlier: 3.721A pdb=" N CYS B 621 " --> pdb=" O ASP B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 635 removed outlier: 3.655A pdb=" N ALA B 632 " --> pdb=" O SER B 628 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 674 removed outlier: 4.234A pdb=" N LEU B 672 " --> pdb=" O THR B 668 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N SER B 673 " --> pdb=" O CYS B 669 " (cutoff:3.500A) Processing helix chain 'H' and resid 1017 through 1023 removed outlier: 3.545A pdb=" N PHE H1021 " --> pdb=" O ASP H1017 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ASN H1023 " --> pdb=" O VAL H1019 " (cutoff:3.500A) Processing helix chain 'H' and resid 1049 through 1060 removed outlier: 3.548A pdb=" N MET H1055 " --> pdb=" O MET H1051 " (cutoff:3.500A) Processing helix chain 'H' and resid 1061 through 1065 Processing helix chain 'H' and resid 1068 through 1075 removed outlier: 3.869A pdb=" N LYS H1073 " --> pdb=" O GLN H1069 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LEU H1074 " --> pdb=" O ASP H1070 " (cutoff:3.500A) Processing helix chain 'H' and resid 1077 through 1091 removed outlier: 3.626A pdb=" N VAL H1083 " --> pdb=" O PRO H1079 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N CYS H1084 " --> pdb=" O TYR H1080 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR H1088 " --> pdb=" O CYS H1084 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N CYS H1089 " --> pdb=" O ILE H1085 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER H1090 " --> pdb=" O TYR H1086 " (cutoff:3.500A) Processing helix chain 'H' and resid 1097 through 1114 removed outlier: 5.312A pdb=" N THR H1103 " --> pdb=" O CYS H1099 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ILE H1104 " --> pdb=" O PHE H1100 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA H1105 " --> pdb=" O CYS H1101 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N VAL H1110 " --> pdb=" O ALA H1106 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N HIS H1114 " --> pdb=" O VAL H1110 " (cutoff:3.500A) Processing helix chain 'E' and resid 114 through 118 removed outlier: 3.923A pdb=" N GLY E 117 " --> pdb=" O ALA E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 185 through 191 removed outlier: 3.505A pdb=" N TRP E 191 " --> pdb=" O PHE E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 208 through 212 removed outlier: 3.759A pdb=" N ASN E 211 " --> pdb=" O SER E 208 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE E 212 " --> pdb=" O SER E 209 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 208 through 212' Processing helix chain 'E' and resid 216 through 221 removed outlier: 3.757A pdb=" N LEU E 221 " --> pdb=" O MET E 217 " (cutoff:3.500A) Processing helix chain 'E' and resid 221 through 231 removed outlier: 4.278A pdb=" N CYS E 225 " --> pdb=" O LEU E 221 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N LEU E 228 " --> pdb=" O GLN E 224 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N LYS E 229 " --> pdb=" O CYS E 225 " (cutoff:3.500A) Processing helix chain 'E' and resid 232 through 235 Processing helix chain 'E' and resid 243 through 251 removed outlier: 3.585A pdb=" N GLU E 251 " --> pdb=" O VAL E 247 " (cutoff:3.500A) Processing helix chain 'E' and resid 260 through 263 removed outlier: 3.881A pdb=" N CYS E 263 " --> pdb=" O GLY E 260 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 260 through 263' Processing helix chain 'E' and resid 264 through 278 removed outlier: 3.710A pdb=" N TYR E 271 " --> pdb=" O ALA E 267 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ARG E 273 " --> pdb=" O LEU E 269 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLU E 278 " --> pdb=" O THR E 274 " (cutoff:3.500A) Processing helix chain 'E' and resid 344 through 348 Processing helix chain 'E' and resid 514 through 517 Processing helix chain 'E' and resid 545 through 550 removed outlier: 3.506A pdb=" N PHE E 549 " --> pdb=" O ARG E 545 " (cutoff:3.500A) Processing helix chain 'E' and resid 551 through 554 removed outlier: 3.782A pdb=" N LYS E 554 " --> pdb=" O ASN E 551 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 551 through 554' Processing helix chain 'E' and resid 568 through 572 Processing helix chain 'E' and resid 573 through 574 No H-bonds generated for 'chain 'E' and resid 573 through 574' Processing helix chain 'E' and resid 575 through 584 removed outlier: 4.826A pdb=" N PHE E 579 " --> pdb=" O ARG E 575 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLU E 581 " --> pdb=" O THR E 577 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N CYS E 584 " --> pdb=" O SER E 580 " (cutoff:3.500A) Processing helix chain 'E' and resid 589 through 596 removed outlier: 4.902A pdb=" N ALA E 594 " --> pdb=" O THR E 591 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N HIS E 596 " --> pdb=" O GLU E 593 " (cutoff:3.500A) Processing helix chain 'E' and resid 601 through 613 removed outlier: 3.819A pdb=" N CYS E 608 " --> pdb=" O TYR E 604 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG E 609 " --> pdb=" O LEU E 605 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N TYR E 610 " --> pdb=" O ARG E 606 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASP E 611 " --> pdb=" O ASN E 607 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N CYS E 613 " --> pdb=" O ARG E 609 " (cutoff:3.500A) Processing helix chain 'E' and resid 617 through 623 removed outlier: 3.721A pdb=" N CYS E 621 " --> pdb=" O ASP E 617 " (cutoff:3.500A) Processing helix chain 'E' and resid 625 through 635 removed outlier: 3.656A pdb=" N ALA E 632 " --> pdb=" O SER E 628 " (cutoff:3.500A) Processing helix chain 'E' and resid 668 through 674 removed outlier: 4.233A pdb=" N LEU E 672 " --> pdb=" O THR E 668 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N SER E 673 " --> pdb=" O CYS E 669 " (cutoff:3.500A) Processing helix chain 'G' and resid 114 through 118 removed outlier: 3.923A pdb=" N GLY G 117 " --> pdb=" O ALA G 114 " (cutoff:3.500A) Processing helix chain 'G' and resid 185 through 191 removed outlier: 3.504A pdb=" N TRP G 191 " --> pdb=" O PHE G 187 " (cutoff:3.500A) Processing helix chain 'G' and resid 208 through 212 removed outlier: 3.758A pdb=" N ASN G 211 " --> pdb=" O SER G 208 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE G 212 " --> pdb=" O SER G 209 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 208 through 212' Processing helix chain 'G' and resid 216 through 221 removed outlier: 3.759A pdb=" N LEU G 221 " --> pdb=" O MET G 217 " (cutoff:3.500A) Processing helix chain 'G' and resid 221 through 231 removed outlier: 4.278A pdb=" N CYS G 225 " --> pdb=" O LEU G 221 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N LEU G 228 " --> pdb=" O GLN G 224 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N LYS G 229 " --> pdb=" O CYS G 225 " (cutoff:3.500A) Processing helix chain 'G' and resid 232 through 235 Processing helix chain 'G' and resid 243 through 251 removed outlier: 3.586A pdb=" N GLU G 251 " --> pdb=" O VAL G 247 " (cutoff:3.500A) Processing helix chain 'G' and resid 260 through 263 removed outlier: 3.881A pdb=" N CYS G 263 " --> pdb=" O GLY G 260 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 260 through 263' Processing helix chain 'G' and resid 264 through 278 removed outlier: 3.710A pdb=" N TYR G 271 " --> pdb=" O ALA G 267 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ARG G 273 " --> pdb=" O LEU G 269 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLU G 278 " --> pdb=" O THR G 274 " (cutoff:3.500A) Processing helix chain 'G' and resid 344 through 348 Processing helix chain 'G' and resid 514 through 517 Processing helix chain 'G' and resid 545 through 550 removed outlier: 3.505A pdb=" N PHE G 549 " --> pdb=" O ARG G 545 " (cutoff:3.500A) Processing helix chain 'G' and resid 551 through 554 removed outlier: 3.783A pdb=" N LYS G 554 " --> pdb=" O ASN G 551 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 551 through 554' Processing helix chain 'G' and resid 568 through 572 Processing helix chain 'G' and resid 573 through 574 No H-bonds generated for 'chain 'G' and resid 573 through 574' Processing helix chain 'G' and resid 575 through 584 removed outlier: 4.827A pdb=" N PHE G 579 " --> pdb=" O ARG G 575 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLU G 581 " --> pdb=" O THR G 577 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N CYS G 584 " --> pdb=" O SER G 580 " (cutoff:3.500A) Processing helix chain 'G' and resid 589 through 596 removed outlier: 4.902A pdb=" N ALA G 594 " --> pdb=" O THR G 591 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N HIS G 596 " --> pdb=" O GLU G 593 " (cutoff:3.500A) Processing helix chain 'G' and resid 601 through 613 removed outlier: 3.819A pdb=" N CYS G 608 " --> pdb=" O TYR G 604 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG G 609 " --> pdb=" O LEU G 605 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N TYR G 610 " --> pdb=" O ARG G 606 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASP G 611 " --> pdb=" O ASN G 607 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N CYS G 613 " --> pdb=" O ARG G 609 " (cutoff:3.500A) Processing helix chain 'G' and resid 617 through 623 removed outlier: 3.721A pdb=" N CYS G 621 " --> pdb=" O ASP G 617 " (cutoff:3.500A) Processing helix chain 'G' and resid 625 through 635 removed outlier: 3.655A pdb=" N ALA G 632 " --> pdb=" O SER G 628 " (cutoff:3.500A) Processing helix chain 'G' and resid 668 through 674 removed outlier: 4.233A pdb=" N LEU G 672 " --> pdb=" O THR G 668 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N SER G 673 " --> pdb=" O CYS G 669 " (cutoff:3.500A) Processing helix chain 'C' and resid 1017 through 1023 removed outlier: 3.545A pdb=" N PHE C1021 " --> pdb=" O ASP C1017 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ASN C1023 " --> pdb=" O VAL C1019 " (cutoff:3.500A) Processing helix chain 'C' and resid 1049 through 1060 removed outlier: 3.548A pdb=" N MET C1055 " --> pdb=" O MET C1051 " (cutoff:3.500A) Processing helix chain 'C' and resid 1061 through 1065 Processing helix chain 'C' and resid 1068 through 1075 removed outlier: 3.868A pdb=" N LYS C1073 " --> pdb=" O GLN C1069 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N LEU C1074 " --> pdb=" O ASP C1070 " (cutoff:3.500A) Processing helix chain 'C' and resid 1077 through 1091 removed outlier: 3.626A pdb=" N VAL C1083 " --> pdb=" O PRO C1079 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N CYS C1084 " --> pdb=" O TYR C1080 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N THR C1088 " --> pdb=" O CYS C1084 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N CYS C1089 " --> pdb=" O ILE C1085 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER C1090 " --> pdb=" O TYR C1086 " (cutoff:3.500A) Processing helix chain 'C' and resid 1097 through 1114 removed outlier: 5.312A pdb=" N THR C1103 " --> pdb=" O CYS C1099 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ILE C1104 " --> pdb=" O PHE C1100 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA C1105 " --> pdb=" O CYS C1101 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N VAL C1110 " --> pdb=" O ALA C1106 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N HIS C1114 " --> pdb=" O VAL C1110 " (cutoff:3.500A) Processing helix chain 'D' and resid 1017 through 1023 removed outlier: 3.545A pdb=" N PHE D1021 " --> pdb=" O ASP D1017 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ASN D1023 " --> pdb=" O VAL D1019 " (cutoff:3.500A) Processing helix chain 'D' and resid 1049 through 1060 removed outlier: 3.548A pdb=" N MET D1055 " --> pdb=" O MET D1051 " (cutoff:3.500A) Processing helix chain 'D' and resid 1061 through 1065 Processing helix chain 'D' and resid 1068 through 1075 removed outlier: 3.869A pdb=" N LYS D1073 " --> pdb=" O GLN D1069 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N LEU D1074 " --> pdb=" O ASP D1070 " (cutoff:3.500A) Processing helix chain 'D' and resid 1077 through 1091 removed outlier: 3.626A pdb=" N VAL D1083 " --> pdb=" O PRO D1079 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N CYS D1084 " --> pdb=" O TYR D1080 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N THR D1088 " --> pdb=" O CYS D1084 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N CYS D1089 " --> pdb=" O ILE D1085 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER D1090 " --> pdb=" O TYR D1086 " (cutoff:3.500A) Processing helix chain 'D' and resid 1097 through 1114 removed outlier: 5.311A pdb=" N THR D1103 " --> pdb=" O CYS D1099 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ILE D1104 " --> pdb=" O PHE D1100 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA D1105 " --> pdb=" O CYS D1101 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N VAL D1110 " --> pdb=" O ALA D1106 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N HIS D1114 " --> pdb=" O VAL D1110 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 37 Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 44 removed outlier: 3.767A pdb=" N TYR A 51 " --> pdb=" O VAL A 43 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 58 through 62 removed outlier: 6.909A pdb=" N ILE A 72 " --> pdb=" O LEU A 61 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 350 through 352 Processing sheet with id=AA5, first strand: chain 'A' and resid 362 through 364 Processing sheet with id=AA6, first strand: chain 'A' and resid 389 through 391 removed outlier: 3.512A pdb=" N PHE A 404 " --> pdb=" O PHE A 396 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 411 through 416 removed outlier: 5.472A pdb=" N GLN A 411 " --> pdb=" O THR A 429 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N THR A 429 " --> pdb=" O GLN A 411 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N LEU A 413 " --> pdb=" O ILE A 427 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N ILE A 427 " --> pdb=" O LEU A 413 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA A 415 " --> pdb=" O ILE A 425 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N SER A 443 " --> pdb=" O GLU A 428 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N VAL A 430 " --> pdb=" O THR A 441 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N THR A 441 " --> pdb=" O VAL A 430 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LEU A 448 " --> pdb=" O SER A 454 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER A 454 " --> pdb=" O LEU A 448 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 481 through 484 Processing sheet with id=AA9, first strand: chain 'A' and resid 498 through 499 removed outlier: 3.572A pdb=" N LYS A 511 " --> pdb=" O GLN A 499 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 536 through 537 removed outlier: 4.122A pdb=" N LEU A 541 " --> pdb=" O THR A 537 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 657 through 662 removed outlier: 3.893A pdb=" N CYS A 661 " --> pdb=" O LEU A 684 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N LEU A 684 " --> pdb=" O CYS A 661 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 694 through 695 Processing sheet with id=AB4, first strand: chain 'A' and resid 709 through 711 Processing sheet with id=AB5, first strand: chain 'A' and resid 720 through 722 removed outlier: 4.225A pdb=" N ASP A 720 " --> pdb=" O CYS A 731 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N CYS A 731 " --> pdb=" O ASP A 720 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N MET A 728 " --> pdb=" O THR A 739 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 772 through 773 Processing sheet with id=AB7, first strand: chain 'F' and resid 841 through 844 removed outlier: 3.596A pdb=" N VAL F 850 " --> pdb=" O ASN F 857 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 875 through 876 Processing sheet with id=AB9, first strand: chain 'F' and resid 890 through 891 Processing sheet with id=AC1, first strand: chain 'F' and resid 894 through 895 Processing sheet with id=AC2, first strand: chain 'F' and resid 925 through 927 removed outlier: 3.606A pdb=" N ILE F 934 " --> pdb=" O ILE F 927 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N GLU F 933 " --> pdb=" O LYS F 944 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLU F 940 " --> pdb=" O PHE F 937 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 954 through 956 removed outlier: 3.788A pdb=" N GLU F 954 " --> pdb=" O LEU F 965 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU F 966 " --> pdb=" O LEU F 970 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N LEU F 970 " --> pdb=" O LEU F 966 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 1144 through 1146 Processing sheet with id=AC5, first strand: chain 'F' and resid 1150 through 1151 Processing sheet with id=AC6, first strand: chain 'F' and resid 1182 through 1183 Processing sheet with id=AC7, first strand: chain 'B' and resid 35 through 37 Processing sheet with id=AC8, first strand: chain 'B' and resid 42 through 44 removed outlier: 3.767A pdb=" N TYR B 51 " --> pdb=" O VAL B 43 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 58 through 62 removed outlier: 6.909A pdb=" N ILE B 72 " --> pdb=" O LEU B 61 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 103 through 104 Processing sheet with id=AD2, first strand: chain 'B' and resid 350 through 352 Processing sheet with id=AD3, first strand: chain 'B' and resid 362 through 364 Processing sheet with id=AD4, first strand: chain 'B' and resid 389 through 391 removed outlier: 3.514A pdb=" N PHE B 404 " --> pdb=" O PHE B 396 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 411 through 416 removed outlier: 5.473A pdb=" N GLN B 411 " --> pdb=" O THR B 429 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N THR B 429 " --> pdb=" O GLN B 411 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N LEU B 413 " --> pdb=" O ILE B 427 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N ILE B 427 " --> pdb=" O LEU B 413 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA B 415 " --> pdb=" O ILE B 425 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N SER B 443 " --> pdb=" O GLU B 428 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N VAL B 430 " --> pdb=" O THR B 441 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N THR B 441 " --> pdb=" O VAL B 430 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LEU B 448 " --> pdb=" O SER B 454 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER B 454 " --> pdb=" O LEU B 448 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 481 through 484 Processing sheet with id=AD7, first strand: chain 'B' and resid 498 through 499 removed outlier: 3.571A pdb=" N LYS B 511 " --> pdb=" O GLN B 499 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 536 through 537 removed outlier: 4.123A pdb=" N LEU B 541 " --> pdb=" O THR B 537 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 657 through 662 removed outlier: 3.893A pdb=" N CYS B 661 " --> pdb=" O LEU B 684 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N LEU B 684 " --> pdb=" O CYS B 661 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 694 through 695 Processing sheet with id=AE2, first strand: chain 'B' and resid 709 through 711 Processing sheet with id=AE3, first strand: chain 'B' and resid 720 through 722 removed outlier: 4.226A pdb=" N ASP B 720 " --> pdb=" O CYS B 731 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N CYS B 731 " --> pdb=" O ASP B 720 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N MET B 728 " --> pdb=" O THR B 739 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 772 through 773 Processing sheet with id=AE5, first strand: chain 'H' and resid 841 through 844 Processing sheet with id=AE6, first strand: chain 'H' and resid 875 through 876 Processing sheet with id=AE7, first strand: chain 'H' and resid 890 through 891 Processing sheet with id=AE8, first strand: chain 'H' and resid 894 through 895 Processing sheet with id=AE9, first strand: chain 'H' and resid 925 through 927 removed outlier: 3.606A pdb=" N ILE H 934 " --> pdb=" O ILE H 927 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N GLU H 933 " --> pdb=" O LYS H 944 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLU H 940 " --> pdb=" O PHE H 937 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'H' and resid 954 through 956 removed outlier: 3.788A pdb=" N GLU H 954 " --> pdb=" O LEU H 965 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU H 966 " --> pdb=" O LEU H 970 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N LEU H 970 " --> pdb=" O LEU H 966 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'H' and resid 1144 through 1146 Processing sheet with id=AF3, first strand: chain 'H' and resid 1150 through 1151 Processing sheet with id=AF4, first strand: chain 'H' and resid 1182 through 1183 Processing sheet with id=AF5, first strand: chain 'E' and resid 35 through 37 removed outlier: 3.500A pdb=" N TYR E 119 " --> pdb=" O SER E 130 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'E' and resid 42 through 44 removed outlier: 3.766A pdb=" N TYR E 51 " --> pdb=" O VAL E 43 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'E' and resid 58 through 62 removed outlier: 6.909A pdb=" N ILE E 72 " --> pdb=" O LEU E 61 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'E' and resid 350 through 352 Processing sheet with id=AF9, first strand: chain 'E' and resid 362 through 364 Processing sheet with id=AG1, first strand: chain 'E' and resid 389 through 391 removed outlier: 3.514A pdb=" N PHE E 404 " --> pdb=" O PHE E 396 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'E' and resid 411 through 416 removed outlier: 5.472A pdb=" N GLN E 411 " --> pdb=" O THR E 429 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N THR E 429 " --> pdb=" O GLN E 411 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N LEU E 413 " --> pdb=" O ILE E 427 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N ILE E 427 " --> pdb=" O LEU E 413 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA E 415 " --> pdb=" O ILE E 425 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N SER E 443 " --> pdb=" O GLU E 428 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N VAL E 430 " --> pdb=" O THR E 441 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N THR E 441 " --> pdb=" O VAL E 430 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LEU E 448 " --> pdb=" O SER E 454 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER E 454 " --> pdb=" O LEU E 448 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'E' and resid 481 through 484 Processing sheet with id=AG4, first strand: chain 'E' and resid 498 through 499 removed outlier: 3.571A pdb=" N LYS E 511 " --> pdb=" O GLN E 499 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'E' and resid 536 through 537 removed outlier: 4.122A pdb=" N LEU E 541 " --> pdb=" O THR E 537 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'E' and resid 657 through 662 removed outlier: 3.893A pdb=" N CYS E 661 " --> pdb=" O LEU E 684 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N LEU E 684 " --> pdb=" O CYS E 661 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'E' and resid 694 through 695 Processing sheet with id=AG8, first strand: chain 'E' and resid 709 through 711 Processing sheet with id=AG9, first strand: chain 'E' and resid 720 through 722 removed outlier: 4.226A pdb=" N ASP E 720 " --> pdb=" O CYS E 731 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N CYS E 731 " --> pdb=" O ASP E 720 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N MET E 728 " --> pdb=" O THR E 739 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'G' and resid 35 through 37 Processing sheet with id=AH2, first strand: chain 'G' and resid 42 through 44 removed outlier: 3.767A pdb=" N TYR G 51 " --> pdb=" O VAL G 43 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'G' and resid 58 through 62 removed outlier: 6.908A pdb=" N ILE G 72 " --> pdb=" O LEU G 61 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'G' and resid 103 through 104 Processing sheet with id=AH5, first strand: chain 'G' and resid 350 through 352 Processing sheet with id=AH6, first strand: chain 'G' and resid 362 through 364 Processing sheet with id=AH7, first strand: chain 'G' and resid 389 through 391 removed outlier: 3.513A pdb=" N PHE G 404 " --> pdb=" O PHE G 396 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'G' and resid 411 through 416 removed outlier: 5.472A pdb=" N GLN G 411 " --> pdb=" O THR G 429 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N THR G 429 " --> pdb=" O GLN G 411 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N LEU G 413 " --> pdb=" O ILE G 427 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N ILE G 427 " --> pdb=" O LEU G 413 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA G 415 " --> pdb=" O ILE G 425 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N SER G 443 " --> pdb=" O GLU G 428 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N VAL G 430 " --> pdb=" O THR G 441 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N THR G 441 " --> pdb=" O VAL G 430 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LEU G 448 " --> pdb=" O SER G 454 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER G 454 " --> pdb=" O LEU G 448 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'G' and resid 481 through 484 Processing sheet with id=AI1, first strand: chain 'G' and resid 498 through 499 removed outlier: 3.571A pdb=" N LYS G 511 " --> pdb=" O GLN G 499 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'G' and resid 536 through 537 removed outlier: 4.122A pdb=" N LEU G 541 " --> pdb=" O THR G 537 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'G' and resid 657 through 662 removed outlier: 3.892A pdb=" N CYS G 661 " --> pdb=" O LEU G 684 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N LEU G 684 " --> pdb=" O CYS G 661 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'G' and resid 694 through 695 Processing sheet with id=AI5, first strand: chain 'G' and resid 709 through 711 Processing sheet with id=AI6, first strand: chain 'G' and resid 720 through 722 removed outlier: 4.226A pdb=" N ASP G 720 " --> pdb=" O CYS G 731 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N CYS G 731 " --> pdb=" O ASP G 720 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N MET G 728 " --> pdb=" O THR G 739 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'C' and resid 772 through 773 Processing sheet with id=AI8, first strand: chain 'C' and resid 841 through 844 removed outlier: 3.750A pdb=" N VAL C 850 " --> pdb=" O ASN C 857 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'C' and resid 875 through 876 Processing sheet with id=AJ1, first strand: chain 'C' and resid 890 through 891 Processing sheet with id=AJ2, first strand: chain 'C' and resid 894 through 895 Processing sheet with id=AJ3, first strand: chain 'C' and resid 925 through 927 removed outlier: 3.606A pdb=" N ILE C 934 " --> pdb=" O ILE C 927 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N GLU C 933 " --> pdb=" O LYS C 944 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLU C 940 " --> pdb=" O PHE C 937 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'C' and resid 954 through 956 removed outlier: 3.788A pdb=" N GLU C 954 " --> pdb=" O LEU C 965 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU C 966 " --> pdb=" O LEU C 970 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N LEU C 970 " --> pdb=" O LEU C 966 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'C' and resid 1144 through 1146 Processing sheet with id=AJ6, first strand: chain 'C' and resid 1150 through 1151 Processing sheet with id=AJ7, first strand: chain 'C' and resid 1182 through 1183 Processing sheet with id=AJ8, first strand: chain 'D' and resid 772 through 773 Processing sheet with id=AJ9, first strand: chain 'D' and resid 841 through 844 Processing sheet with id=AK1, first strand: chain 'D' and resid 875 through 876 Processing sheet with id=AK2, first strand: chain 'D' and resid 890 through 891 Processing sheet with id=AK3, first strand: chain 'D' and resid 894 through 895 Processing sheet with id=AK4, first strand: chain 'D' and resid 925 through 927 removed outlier: 3.606A pdb=" N ILE D 934 " --> pdb=" O ILE D 927 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N GLU D 933 " --> pdb=" O LYS D 944 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLU D 940 " --> pdb=" O PHE D 937 " (cutoff:3.500A) Processing sheet with id=AK5, first strand: chain 'D' and resid 954 through 956 removed outlier: 3.788A pdb=" N GLU D 954 " --> pdb=" O LEU D 965 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU D 966 " --> pdb=" O LEU D 970 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N LEU D 970 " --> pdb=" O LEU D 966 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'D' and resid 1144 through 1146 Processing sheet with id=AK7, first strand: chain 'D' and resid 1150 through 1151 Processing sheet with id=AK8, first strand: chain 'D' and resid 1182 through 1183 731 hydrogen bonds defined for protein. 1748 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 14.96 Time building geometry restraints manager: 14.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 12297 1.34 - 1.47: 8552 1.47 - 1.59: 15875 1.59 - 1.71: 0 1.71 - 1.84: 656 Bond restraints: 37380 Sorted by residual: bond pdb=" N VAL E 98 " pdb=" CA VAL E 98 " ideal model delta sigma weight residual 1.457 1.493 -0.037 1.07e-02 8.73e+03 1.18e+01 bond pdb=" C SER H1217 " pdb=" N ASP H1218 " ideal model delta sigma weight residual 1.331 1.384 -0.053 1.63e-02 3.76e+03 1.06e+01 bond pdb=" C SER F1217 " pdb=" N ASP F1218 " ideal model delta sigma weight residual 1.331 1.384 -0.052 1.63e-02 3.76e+03 1.03e+01 bond pdb=" N VAL D1155 " pdb=" CA VAL D1155 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.15e-02 7.56e+03 1.02e+01 bond pdb=" C SER C1217 " pdb=" N ASP C1218 " ideal model delta sigma weight residual 1.331 1.383 -0.052 1.63e-02 3.76e+03 1.02e+01 ... (remaining 37375 not shown) Histogram of bond angle deviations from ideal: 99.06 - 107.73: 1939 107.73 - 116.41: 23664 116.41 - 125.08: 24216 125.08 - 133.76: 841 133.76 - 142.43: 64 Bond angle restraints: 50724 Sorted by residual: angle pdb=" C SER C1217 " pdb=" N ASP C1218 " pdb=" CA ASP C1218 " ideal model delta sigma weight residual 121.61 142.43 -20.82 1.39e+00 5.18e-01 2.24e+02 angle pdb=" C SER D1217 " pdb=" N ASP D1218 " pdb=" CA ASP D1218 " ideal model delta sigma weight residual 121.61 142.40 -20.79 1.39e+00 5.18e-01 2.24e+02 angle pdb=" C SER F1217 " pdb=" N ASP F1218 " pdb=" CA ASP F1218 " ideal model delta sigma weight residual 121.61 142.39 -20.78 1.39e+00 5.18e-01 2.24e+02 angle pdb=" C SER H1217 " pdb=" N ASP H1218 " pdb=" CA ASP H1218 " ideal model delta sigma weight residual 121.61 142.36 -20.75 1.39e+00 5.18e-01 2.23e+02 angle pdb=" C GLU C 784 " pdb=" N GLY C 785 " pdb=" CA GLY C 785 " ideal model delta sigma weight residual 121.41 137.98 -16.57 1.96e+00 2.60e-01 7.15e+01 ... (remaining 50719 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.18: 21823 17.18 - 34.36: 1174 34.36 - 51.53: 319 51.53 - 68.71: 80 68.71 - 85.89: 26 Dihedral angle restraints: 23422 sinusoidal: 9730 harmonic: 13692 Sorted by residual: dihedral pdb=" CB CYS A 312 " pdb=" SG CYS A 312 " pdb=" SG CYS A 348 " pdb=" CB CYS A 348 " ideal model delta sinusoidal sigma weight residual 93.00 174.00 -81.00 1 1.00e+01 1.00e-02 8.10e+01 dihedral pdb=" CB CYS E 312 " pdb=" SG CYS E 312 " pdb=" SG CYS E 348 " pdb=" CB CYS E 348 " ideal model delta sinusoidal sigma weight residual 93.00 173.98 -80.98 1 1.00e+01 1.00e-02 8.10e+01 dihedral pdb=" CB CYS G 312 " pdb=" SG CYS G 312 " pdb=" SG CYS G 348 " pdb=" CB CYS G 348 " ideal model delta sinusoidal sigma weight residual 93.00 173.97 -80.97 1 1.00e+01 1.00e-02 8.09e+01 ... (remaining 23419 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.308: 5490 0.308 - 0.616: 39 0.616 - 0.924: 18 0.924 - 1.232: 4 1.232 - 1.540: 1 Chirality restraints: 5552 Sorted by residual: chirality pdb=" C1 NAG E 804 " pdb=" ND2 ASN E 99 " pdb=" C2 NAG E 804 " pdb=" O5 NAG E 804 " both_signs ideal model delta sigma weight residual False -2.40 -0.86 -1.54 2.00e-01 2.50e+01 5.93e+01 chirality pdb=" CB VAL H 815 " pdb=" CA VAL H 815 " pdb=" CG1 VAL H 815 " pdb=" CG2 VAL H 815 " both_signs ideal model delta sigma weight residual False -2.63 -1.63 -1.00 2.00e-01 2.50e+01 2.50e+01 chirality pdb=" CB VAL F 815 " pdb=" CA VAL F 815 " pdb=" CG1 VAL F 815 " pdb=" CG2 VAL F 815 " both_signs ideal model delta sigma weight residual False -2.63 -1.63 -1.00 2.00e-01 2.50e+01 2.49e+01 ... (remaining 5549 not shown) Planarity restraints: 6748 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN G 99 " -0.136 2.00e-02 2.50e+03 1.87e-01 4.39e+02 pdb=" CG ASN G 99 " 0.057 2.00e-02 2.50e+03 pdb=" OD1 ASN G 99 " -0.058 2.00e-02 2.50e+03 pdb=" ND2 ASN G 99 " 0.334 2.00e-02 2.50e+03 pdb=" C1 NAG G 804 " -0.197 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 804 " 0.158 2.00e-02 2.50e+03 1.30e-01 2.12e+02 pdb=" C7 NAG B 804 " -0.042 2.00e-02 2.50e+03 pdb=" C8 NAG B 804 " 0.116 2.00e-02 2.50e+03 pdb=" N2 NAG B 804 " -0.210 2.00e-02 2.50e+03 pdb=" O7 NAG B 804 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG G 804 " -0.044 2.00e-02 2.50e+03 3.65e-02 1.66e+01 pdb=" C7 NAG G 804 " 0.012 2.00e-02 2.50e+03 pdb=" C8 NAG G 804 " -0.034 2.00e-02 2.50e+03 pdb=" N2 NAG G 804 " 0.058 2.00e-02 2.50e+03 pdb=" O7 NAG G 804 " 0.008 2.00e-02 2.50e+03 ... (remaining 6745 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 420 2.59 - 3.17: 33032 3.17 - 3.75: 53602 3.75 - 4.32: 74307 4.32 - 4.90: 121259 Nonbonded interactions: 282620 Sorted by model distance: nonbonded pdb=" O GLU H 888 " pdb=" OH TYR G 119 " model vdw 2.016 2.440 nonbonded pdb=" O SER C1093 " pdb=" OG SER D1093 " model vdw 2.031 2.440 nonbonded pdb=" OG SER H1009 " pdb=" OD1 ASN H1011 " model vdw 2.040 2.440 nonbonded pdb=" OG SER F1009 " pdb=" OD1 ASN F1011 " model vdw 2.041 2.440 nonbonded pdb=" OG SER D1009 " pdb=" OD1 ASN D1011 " model vdw 2.041 2.440 ... (remaining 282615 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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 1241 or resid 1301 \ through 1305)) selection = (chain 'D' and (resid 764 through 1052 or resid 1054 through 1241 or resid 1301 \ through 1305)) selection = (chain 'F' and (resid 764 through 1052 or resid 1054 through 1241 or resid 1301 \ through 1305)) selection = (chain 'H' and (resid 764 through 1052 or resid 1054 through 1241 or resid 1301 \ 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: 0.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 4.780 Check model and map are aligned: 0.540 Set scattering table: 0.290 Process input model: 102.840 Find NCS groups from input model: 2.420 Set up NCS constraints: 0.330 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 114.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6447 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 37380 Z= 0.464 Angle : 1.113 20.819 50724 Z= 0.613 Chirality : 0.089 1.540 5552 Planarity : 0.006 0.130 6728 Dihedral : 10.595 85.890 13964 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.17 % Allowed : 11.90 % Favored : 87.93 % Rotamer: Outliers : 0.44 % Allowed : 2.86 % Favored : 96.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.63 (0.10), residues: 4744 helix: -4.09 (0.13), residues: 480 sheet: -3.94 (0.14), residues: 832 loop : -2.88 (0.10), residues: 3432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP F 974 HIS 0.010 0.002 HIS H1047 PHE 0.022 0.002 PHE A 535 TYR 0.015 0.002 TYR C 988 ARG 0.013 0.001 ARG D 960 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9488 Ramachandran restraints generated. 4744 Oldfield, 0 Emsley, 4744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9488 Ramachandran restraints generated. 4744 Oldfield, 0 Emsley, 4744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1095 residues out of total 4112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 1081 time to evaluate : 4.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 TYR cc_start: 0.6769 (m-10) cc_final: 0.6468 (m-80) REVERT: A 222 TRP cc_start: 0.6387 (t60) cc_final: 0.6044 (t60) REVERT: A 320 MET cc_start: 0.4995 (ppp) cc_final: 0.4792 (tmm) REVERT: A 420 ASP cc_start: 0.7285 (p0) cc_final: 0.6974 (p0) REVERT: A 429 THR cc_start: 0.5798 (p) cc_final: 0.4539 (p) REVERT: A 553 TRP cc_start: 0.4951 (m100) cc_final: 0.4745 (m100) REVERT: A 736 MET cc_start: 0.6039 (tpt) cc_final: 0.5711 (tpt) REVERT: F 1142 CYS cc_start: 0.5380 (t) cc_final: 0.4482 (t) REVERT: F 1144 TRP cc_start: 0.6367 (m100) cc_final: 0.6042 (m100) REVERT: F 1210 LYS cc_start: 0.4023 (pttm) cc_final: 0.3668 (tttt) REVERT: B 299 MET cc_start: 0.6893 (mtm) cc_final: 0.6472 (ptp) REVERT: B 680 ASN cc_start: 0.7342 (m-40) cc_final: 0.7054 (p0) REVERT: H 814 MET cc_start: 0.6514 (ttm) cc_final: 0.6272 (ttm) REVERT: H 848 THR cc_start: 0.7383 (t) cc_final: 0.7137 (p) REVERT: H 1151 PRO cc_start: 0.6585 (Cg_exo) cc_final: 0.5660 (Cg_endo) REVERT: E 199 TRP cc_start: 0.5098 (m-90) cc_final: 0.4795 (m-90) REVERT: E 301 TYR cc_start: 0.7640 (t80) cc_final: 0.7359 (t80) REVERT: E 381 ASN cc_start: 0.7653 (p0) cc_final: 0.7227 (t0) REVERT: G 224 GLN cc_start: 0.7277 (mp10) cc_final: 0.6996 (mp10) REVERT: G 283 TYR cc_start: 0.6626 (m-80) cc_final: 0.6424 (m-10) REVERT: G 512 LEU cc_start: 0.6426 (mm) cc_final: 0.5921 (tt) REVERT: G 722 PHE cc_start: 0.5623 (t80) cc_final: 0.5168 (t80) REVERT: C 856 TRP cc_start: 0.5525 (m100) cc_final: 0.4786 (m100) REVERT: C 1146 TYR cc_start: 0.5788 (t80) cc_final: 0.3708 (t80) REVERT: D 830 PHE cc_start: 0.6814 (m-80) cc_final: 0.6182 (m-80) outliers start: 14 outliers final: 3 residues processed: 1089 average time/residue: 0.5773 time to fit residues: 978.4328 Evaluate side-chains 471 residues out of total 4112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 468 time to evaluate : 4.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 1231 ASN Chi-restraints excluded: chain B residue 97 PHE Chi-restraints excluded: chain H residue 1231 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 398 optimal weight: 1.9990 chunk 357 optimal weight: 3.9990 chunk 198 optimal weight: 5.9990 chunk 122 optimal weight: 0.7980 chunk 241 optimal weight: 3.9990 chunk 191 optimal weight: 0.6980 chunk 369 optimal weight: 0.9980 chunk 143 optimal weight: 0.0970 chunk 224 optimal weight: 5.9990 chunk 275 optimal weight: 5.9990 chunk 428 optimal weight: 5.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 566 HIS ** A 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F1013 GLN F1053 GLN A ** F1128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 GLN B 313 GLN B 411 GLN B 737 HIS H 819 ASN H 852 GLN H 977 HIS H1053 GLN A H1053 GLN B H1113 GLN E 421 HIS E 499 GLN G 313 GLN G 401 ASN G 499 GLN C 793 GLN ** C1013 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1053 GLN B C1134 ASN C1174 HIS D1134 ASN ** D1174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6677 moved from start: 0.3426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.095 37380 Z= 0.210 Angle : 0.766 10.730 50724 Z= 0.385 Chirality : 0.049 0.559 5552 Planarity : 0.005 0.054 6728 Dihedral : 6.375 52.856 5562 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.59 % Favored : 92.38 % Rotamer: Outliers : 2.15 % Allowed : 10.17 % Favored : 87.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.93 (0.11), residues: 4744 helix: -3.08 (0.16), residues: 616 sheet: -3.42 (0.16), residues: 800 loop : -2.44 (0.10), residues: 3328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP G 553 HIS 0.005 0.001 HIS A 95 PHE 0.025 0.002 PHE G 165 TYR 0.024 0.002 TYR G 126 ARG 0.008 0.001 ARG C1133 *********************** 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 613 residues out of total 4112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 529 time to evaluate : 4.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 TRP cc_start: 0.6541 (t60) cc_final: 0.6236 (t60) REVERT: A 339 GLU cc_start: 0.6664 (tm-30) cc_final: 0.6374 (pm20) REVERT: A 466 MET cc_start: 0.7526 (ptp) cc_final: 0.6593 (tpt) REVERT: A 494 TYR cc_start: 0.6733 (t80) cc_final: 0.6133 (t80) REVERT: A 581 GLU cc_start: 0.6974 (tm-30) cc_final: 0.6768 (tm-30) REVERT: A 722 PHE cc_start: 0.7756 (OUTLIER) cc_final: 0.7155 (m-80) REVERT: A 740 MET cc_start: 0.4901 (mmt) cc_final: 0.4688 (tpt) REVERT: F 1210 LYS cc_start: 0.3999 (pttm) cc_final: 0.3644 (tttt) REVERT: B 179 THR cc_start: 0.7246 (p) cc_final: 0.6657 (p) REVERT: B 299 MET cc_start: 0.7004 (mtm) cc_final: 0.6539 (ptp) REVERT: B 475 LEU cc_start: 0.8243 (tt) cc_final: 0.7907 (tt) REVERT: H 777 PRO cc_start: 0.6437 (Cg_endo) cc_final: 0.6142 (Cg_exo) REVERT: E 381 ASN cc_start: 0.7477 (p0) cc_final: 0.7208 (t0) REVERT: G 174 MET cc_start: 0.6586 (tpp) cc_final: 0.6317 (mmt) REVERT: G 224 GLN cc_start: 0.7442 (mp10) cc_final: 0.7165 (mp10) REVERT: D 800 MET cc_start: 0.3343 (mmt) cc_final: 0.3032 (mmt) REVERT: D 811 PRO cc_start: 0.7154 (Cg_endo) cc_final: 0.6940 (Cg_exo) REVERT: D 883 TYR cc_start: 0.8065 (p90) cc_final: 0.7745 (p90) REVERT: D 1055 MET cc_start: 0.5936 (ptm) cc_final: 0.5438 (ptp) outliers start: 84 outliers final: 44 residues processed: 590 average time/residue: 0.5095 time to fit residues: 483.2152 Evaluate side-chains 403 residues out of total 4112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 358 time to evaluate : 4.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 722 PHE Chi-restraints excluded: chain F residue 789 THR Chi-restraints excluded: chain F residue 870 ILE Chi-restraints excluded: chain F residue 1057 ASP Chi-restraints excluded: chain B residue 97 PHE Chi-restraints excluded: chain B residue 320 MET Chi-restraints excluded: chain B residue 339 GLU Chi-restraints excluded: chain H residue 799 CYS Chi-restraints excluded: chain H residue 809 LEU Chi-restraints excluded: chain H residue 829 CYS Chi-restraints excluded: chain H residue 1029 SER Chi-restraints excluded: chain H residue 1055 MET Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain E residue 434 ASP Chi-restraints excluded: chain E residue 511 LYS Chi-restraints excluded: chain E residue 536 LEU Chi-restraints excluded: chain E residue 663 THR Chi-restraints excluded: chain G residue 58 SER Chi-restraints excluded: chain G residue 76 PHE Chi-restraints excluded: chain G residue 94 ILE Chi-restraints excluded: chain G residue 129 LEU Chi-restraints excluded: chain G residue 158 THR Chi-restraints excluded: chain G residue 227 LEU Chi-restraints excluded: chain G residue 311 THR Chi-restraints excluded: chain G residue 345 SER Chi-restraints excluded: chain G residue 368 ASN Chi-restraints excluded: chain G residue 401 ASN Chi-restraints excluded: chain G residue 434 ASP Chi-restraints excluded: chain G residue 452 HIS Chi-restraints excluded: chain G residue 614 SER Chi-restraints excluded: chain G residue 740 MET Chi-restraints excluded: chain C residue 884 LEU Chi-restraints excluded: chain C residue 981 SER Chi-restraints excluded: chain C residue 1230 VAL Chi-restraints excluded: chain D residue 864 ASP Chi-restraints excluded: chain D residue 934 ILE Chi-restraints excluded: chain D residue 941 VAL Chi-restraints excluded: chain D residue 956 VAL Chi-restraints excluded: chain D residue 1029 SER Chi-restraints excluded: chain D residue 1034 THR Chi-restraints excluded: chain D residue 1088 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 238 optimal weight: 10.0000 chunk 133 optimal weight: 6.9990 chunk 356 optimal weight: 0.1980 chunk 291 optimal weight: 4.9990 chunk 118 optimal weight: 30.0000 chunk 429 optimal weight: 5.9990 chunk 463 optimal weight: 20.0000 chunk 382 optimal weight: 40.0000 chunk 425 optimal weight: 0.9990 chunk 146 optimal weight: 6.9990 chunk 344 optimal weight: 2.9990 overall best weight: 3.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 HIS A 352 HIS ** A 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 526 ASN ** A 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 737 HIS ** F1003 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1013 GLN ** F1128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1221 HIS ** B 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 277 GLN H 986 GLN E 322 GLN ** C 874 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1013 GLN C1176 HIS ** D1188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1221 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6972 moved from start: 0.4903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 37380 Z= 0.257 Angle : 0.744 10.872 50724 Z= 0.377 Chirality : 0.049 0.545 5552 Planarity : 0.005 0.046 6728 Dihedral : 5.909 51.361 5558 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.27 % Favored : 91.71 % Rotamer: Outliers : 3.03 % Allowed : 12.59 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.37 (0.11), residues: 4744 helix: -2.15 (0.19), residues: 604 sheet: -3.03 (0.17), residues: 824 loop : -2.15 (0.10), residues: 3316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP G 553 HIS 0.007 0.001 HIS A 737 PHE 0.024 0.002 PHE G 165 TYR 0.027 0.002 TYR E 730 ARG 0.014 0.001 ARG C 826 *********************** 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 538 residues out of total 4112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 418 time to evaluate : 4.195 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 222 TRP cc_start: 0.6686 (t60) cc_final: 0.5955 (t60) REVERT: A 339 GLU cc_start: 0.6806 (tm-30) cc_final: 0.6393 (pm20) REVERT: A 356 ARG cc_start: 0.6178 (tmt170) cc_final: 0.5918 (mtp85) REVERT: A 466 MET cc_start: 0.7536 (ptp) cc_final: 0.6707 (tpt) REVERT: A 494 TYR cc_start: 0.7028 (t80) cc_final: 0.6364 (t80) REVERT: A 553 TRP cc_start: 0.5508 (m100) cc_final: 0.5258 (m100) REVERT: F 1210 LYS cc_start: 0.4459 (pttm) cc_final: 0.3607 (tttp) REVERT: B 179 THR cc_start: 0.7296 (p) cc_final: 0.6994 (p) REVERT: B 299 MET cc_start: 0.7060 (mtm) cc_final: 0.6276 (ptp) REVERT: B 313 GLN cc_start: 0.6672 (OUTLIER) cc_final: 0.6464 (mp10) REVERT: B 338 ASP cc_start: 0.7226 (t0) cc_final: 0.6982 (m-30) REVERT: B 475 LEU cc_start: 0.8427 (tt) cc_final: 0.8082 (tt) REVERT: B 476 LEU cc_start: 0.7729 (tt) cc_final: 0.7377 (mm) REVERT: H 1211 LYS cc_start: 0.2910 (mptt) cc_final: 0.2666 (mmmt) REVERT: E 313 GLN cc_start: 0.5900 (mp10) cc_final: 0.5583 (mp10) REVERT: E 315 LEU cc_start: 0.7611 (OUTLIER) cc_final: 0.7317 (mm) REVERT: E 374 ASN cc_start: 0.6828 (OUTLIER) cc_final: 0.6315 (p0) REVERT: E 381 ASN cc_start: 0.7553 (p0) cc_final: 0.7316 (t0) REVERT: E 740 MET cc_start: 0.6776 (tpt) cc_final: 0.6120 (tpt) REVERT: G 271 TYR cc_start: 0.7708 (OUTLIER) cc_final: 0.7439 (t80) REVERT: G 376 GLN cc_start: 0.7628 (OUTLIER) cc_final: 0.6763 (mp10) REVERT: G 494 TYR cc_start: 0.6900 (t80) cc_final: 0.6686 (t80) REVERT: G 736 MET cc_start: 0.6081 (mmt) cc_final: 0.5495 (mmt) REVERT: C 800 MET cc_start: 0.7333 (ppp) cc_final: 0.7034 (ppp) REVERT: D 883 TYR cc_start: 0.8361 (p90) cc_final: 0.7854 (p90) REVERT: D 1055 MET cc_start: 0.5785 (ptm) cc_final: 0.5272 (ptp) outliers start: 120 outliers final: 77 residues processed: 507 average time/residue: 0.4889 time to fit residues: 408.8027 Evaluate side-chains 416 residues out of total 4112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 334 time to evaluate : 4.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 MET Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 299 MET Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 420 ASP Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 501 ASP Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain A residue 687 CYS Chi-restraints excluded: chain F residue 789 THR Chi-restraints excluded: chain F residue 870 ILE Chi-restraints excluded: chain F residue 981 SER Chi-restraints excluded: chain F residue 1019 VAL Chi-restraints excluded: chain F residue 1057 ASP Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 97 PHE Chi-restraints excluded: chain B residue 158 THR Chi-restraints excluded: chain B residue 312 CYS Chi-restraints excluded: chain B residue 313 GLN Chi-restraints excluded: chain B residue 339 GLU Chi-restraints excluded: chain B residue 501 ASP Chi-restraints excluded: chain B residue 638 VAL Chi-restraints excluded: chain B residue 707 CYS Chi-restraints excluded: chain H residue 797 LEU Chi-restraints excluded: chain H residue 799 CYS Chi-restraints excluded: chain H residue 809 LEU Chi-restraints excluded: chain H residue 829 CYS Chi-restraints excluded: chain H residue 852 GLN Chi-restraints excluded: chain H residue 904 THR Chi-restraints excluded: chain H residue 934 ILE Chi-restraints excluded: chain H residue 986 GLN Chi-restraints excluded: chain H residue 1029 SER Chi-restraints excluded: chain H residue 1055 MET Chi-restraints excluded: chain H residue 1075 VAL Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain E residue 289 SER Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain E residue 374 ASN Chi-restraints excluded: chain E residue 434 ASP Chi-restraints excluded: chain E residue 501 ASP Chi-restraints excluded: chain E residue 536 LEU Chi-restraints excluded: chain E residue 663 THR Chi-restraints excluded: chain E residue 668 THR Chi-restraints excluded: chain G residue 58 SER Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain G residue 94 ILE Chi-restraints excluded: chain G residue 109 VAL Chi-restraints excluded: chain G residue 129 LEU Chi-restraints excluded: chain G residue 158 THR Chi-restraints excluded: chain G residue 227 LEU Chi-restraints excluded: chain G residue 271 TYR Chi-restraints excluded: chain G residue 280 MET Chi-restraints excluded: chain G residue 311 THR Chi-restraints excluded: chain G residue 326 VAL Chi-restraints excluded: chain G residue 345 SER Chi-restraints excluded: chain G residue 368 ASN Chi-restraints excluded: chain G residue 376 GLN Chi-restraints excluded: chain G residue 426 VAL Chi-restraints excluded: chain G residue 434 ASP Chi-restraints excluded: chain G residue 464 VAL Chi-restraints excluded: chain G residue 490 VAL Chi-restraints excluded: chain G residue 614 SER Chi-restraints excluded: chain G residue 709 CYS Chi-restraints excluded: chain C residue 870 ILE Chi-restraints excluded: chain C residue 884 LEU Chi-restraints excluded: chain C residue 927 ILE Chi-restraints excluded: chain C residue 942 ASN Chi-restraints excluded: chain C residue 981 SER Chi-restraints excluded: chain D residue 789 THR Chi-restraints excluded: chain D residue 864 ASP Chi-restraints excluded: chain D residue 916 HIS Chi-restraints excluded: chain D residue 934 ILE Chi-restraints excluded: chain D residue 941 VAL Chi-restraints excluded: chain D residue 956 VAL Chi-restraints excluded: chain D residue 1034 THR Chi-restraints excluded: chain D residue 1088 THR Chi-restraints excluded: chain D residue 1124 THR Chi-restraints excluded: chain D residue 1231 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 424 optimal weight: 0.1980 chunk 322 optimal weight: 0.0000 chunk 222 optimal weight: 5.9990 chunk 47 optimal weight: 8.9990 chunk 204 optimal weight: 7.9990 chunk 288 optimal weight: 8.9990 chunk 430 optimal weight: 5.9990 chunk 456 optimal weight: 9.9990 chunk 225 optimal weight: 10.0000 chunk 408 optimal weight: 6.9990 chunk 122 optimal weight: 0.6980 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 551 ASN A 563 GLN ** A 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 726 HIS ** F 832 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1128 GLN ** B 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 874 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 986 GLN ** H1013 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 316 HIS G 556 HIS ** D1188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7041 moved from start: 0.5555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 37380 Z= 0.222 Angle : 0.697 14.787 50724 Z= 0.351 Chirality : 0.047 0.517 5552 Planarity : 0.005 0.043 6728 Dihedral : 5.607 51.355 5558 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.94 % Favored : 93.04 % Rotamer: Outliers : 2.91 % Allowed : 14.27 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.98 (0.12), residues: 4744 helix: -1.62 (0.21), residues: 600 sheet: -2.90 (0.17), residues: 784 loop : -1.91 (0.10), residues: 3360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP G 553 HIS 0.007 0.001 HIS E 316 PHE 0.033 0.002 PHE H 953 TYR 0.025 0.002 TYR F 897 ARG 0.008 0.001 ARG G 578 *********************** 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 487 residues out of total 4112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 372 time to evaluate : 4.015 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 339 GLU cc_start: 0.6779 (tm-30) cc_final: 0.6412 (pm20) REVERT: A 406 PHE cc_start: 0.7865 (t80) cc_final: 0.7458 (t80) REVERT: A 466 MET cc_start: 0.7713 (ptp) cc_final: 0.6580 (tpt) REVERT: A 494 TYR cc_start: 0.7120 (t80) cc_final: 0.6529 (t80) REVERT: F 860 ASP cc_start: 0.6574 (t0) cc_final: 0.6118 (t70) REVERT: F 894 VAL cc_start: 0.7919 (OUTLIER) cc_final: 0.7684 (p) REVERT: F 1210 LYS cc_start: 0.4607 (pttm) cc_final: 0.3836 (tttt) REVERT: B 299 MET cc_start: 0.6540 (mtm) cc_final: 0.6151 (ptp) REVERT: B 338 ASP cc_start: 0.7253 (t0) cc_final: 0.6797 (m-30) REVERT: B 507 ARG cc_start: 0.7465 (OUTLIER) cc_final: 0.7139 (tpt90) REVERT: B 693 LEU cc_start: 0.8366 (mm) cc_final: 0.8021 (mp) REVERT: H 1211 LYS cc_start: 0.3218 (mptt) cc_final: 0.2891 (mmmt) REVERT: E 374 ASN cc_start: 0.6667 (OUTLIER) cc_final: 0.6353 (p0) REVERT: E 381 ASN cc_start: 0.7560 (p0) cc_final: 0.7300 (t0) REVERT: G 302 ARG cc_start: 0.7626 (mmt180) cc_final: 0.7413 (mmt180) REVERT: G 696 ASP cc_start: 0.7159 (m-30) cc_final: 0.6603 (p0) REVERT: C 800 MET cc_start: 0.7453 (ppp) cc_final: 0.7209 (ppp) REVERT: C 1051 MET cc_start: 0.6732 (tmm) cc_final: 0.6235 (tpt) REVERT: D 883 TYR cc_start: 0.8415 (p90) cc_final: 0.7954 (p90) REVERT: D 1055 MET cc_start: 0.5759 (ptm) cc_final: 0.5294 (ptp) outliers start: 115 outliers final: 76 residues processed: 464 average time/residue: 0.4866 time to fit residues: 375.5457 Evaluate side-chains 392 residues out of total 4112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 313 time to evaluate : 3.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 MET Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 299 MET Chi-restraints excluded: chain A residue 420 ASP Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 501 ASP Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain A residue 652 CYS Chi-restraints excluded: chain A residue 687 CYS Chi-restraints excluded: chain A residue 712 ASP Chi-restraints excluded: chain A residue 737 HIS Chi-restraints excluded: chain F residue 789 THR Chi-restraints excluded: chain F residue 870 ILE Chi-restraints excluded: chain F residue 894 VAL Chi-restraints excluded: chain F residue 981 SER Chi-restraints excluded: chain F residue 1198 VAL Chi-restraints excluded: chain B residue 97 PHE Chi-restraints excluded: chain B residue 223 GLU Chi-restraints excluded: chain B residue 280 MET Chi-restraints excluded: chain B residue 312 CYS Chi-restraints excluded: chain B residue 339 GLU Chi-restraints excluded: chain B residue 501 ASP Chi-restraints excluded: chain B residue 507 ARG Chi-restraints excluded: chain B residue 638 VAL Chi-restraints excluded: chain B residue 707 CYS Chi-restraints excluded: chain B residue 723 SER Chi-restraints excluded: chain B residue 729 CYS Chi-restraints excluded: chain H residue 797 LEU Chi-restraints excluded: chain H residue 799 CYS Chi-restraints excluded: chain H residue 809 LEU Chi-restraints excluded: chain H residue 829 CYS Chi-restraints excluded: chain H residue 870 ILE Chi-restraints excluded: chain H residue 874 HIS Chi-restraints excluded: chain H residue 934 ILE Chi-restraints excluded: chain H residue 1029 SER Chi-restraints excluded: chain H residue 1075 VAL Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain E residue 311 THR Chi-restraints excluded: chain E residue 374 ASN Chi-restraints excluded: chain E residue 434 ASP Chi-restraints excluded: chain E residue 476 LEU Chi-restraints excluded: chain E residue 501 ASP Chi-restraints excluded: chain E residue 511 LYS Chi-restraints excluded: chain E residue 536 LEU Chi-restraints excluded: chain G residue 58 SER Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain G residue 109 VAL Chi-restraints excluded: chain G residue 129 LEU Chi-restraints excluded: chain G residue 158 THR Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 227 LEU Chi-restraints excluded: chain G residue 280 MET Chi-restraints excluded: chain G residue 311 THR Chi-restraints excluded: chain G residue 326 VAL Chi-restraints excluded: chain G residue 345 SER Chi-restraints excluded: chain G residue 426 VAL Chi-restraints excluded: chain G residue 428 GLU Chi-restraints excluded: chain G residue 434 ASP Chi-restraints excluded: chain G residue 464 VAL Chi-restraints excluded: chain G residue 475 LEU Chi-restraints excluded: chain G residue 490 VAL Chi-restraints excluded: chain G residue 614 SER Chi-restraints excluded: chain G residue 707 CYS Chi-restraints excluded: chain G residue 709 CYS Chi-restraints excluded: chain C residue 819 ASN Chi-restraints excluded: chain C residue 870 ILE Chi-restraints excluded: chain C residue 884 LEU Chi-restraints excluded: chain C residue 942 ASN Chi-restraints excluded: chain C residue 981 SER Chi-restraints excluded: chain D residue 864 ASP Chi-restraints excluded: chain D residue 870 ILE Chi-restraints excluded: chain D residue 898 CYS Chi-restraints excluded: chain D residue 934 ILE Chi-restraints excluded: chain D residue 941 VAL Chi-restraints excluded: chain D residue 1034 THR Chi-restraints excluded: chain D residue 1088 THR Chi-restraints excluded: chain D residue 1124 THR Chi-restraints excluded: chain D residue 1231 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 379 optimal weight: 9.9990 chunk 258 optimal weight: 7.9990 chunk 6 optimal weight: 10.0000 chunk 339 optimal weight: 0.0070 chunk 188 optimal weight: 5.9990 chunk 389 optimal weight: 0.9980 chunk 315 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 232 optimal weight: 20.0000 chunk 409 optimal weight: 0.8980 chunk 115 optimal weight: 0.0970 overall best weight: 1.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 832 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1128 GLN ** H 874 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1013 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1011 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1003 GLN D1047 HIS ** D1188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7050 moved from start: 0.5914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 37380 Z= 0.178 Angle : 0.651 14.071 50724 Z= 0.325 Chirality : 0.045 0.475 5552 Planarity : 0.004 0.043 6728 Dihedral : 5.424 52.604 5558 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.11 % Favored : 92.87 % Rotamer: Outliers : 2.96 % Allowed : 14.83 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.84 (0.12), residues: 4744 helix: -1.40 (0.21), residues: 632 sheet: -2.62 (0.17), residues: 808 loop : -1.88 (0.10), residues: 3304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP G 553 HIS 0.007 0.001 HIS D1047 PHE 0.025 0.001 PHE G 406 TYR 0.049 0.001 TYR H 897 ARG 0.007 0.000 ARG G 578 *********************** 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 470 residues out of total 4112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 353 time to evaluate : 4.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 339 GLU cc_start: 0.6767 (tm-30) cc_final: 0.6446 (pm20) REVERT: A 406 PHE cc_start: 0.7895 (t80) cc_final: 0.7466 (t80) REVERT: A 466 MET cc_start: 0.7904 (ptp) cc_final: 0.6747 (tpt) REVERT: A 494 TYR cc_start: 0.7227 (t80) cc_final: 0.6680 (t80) REVERT: F 1128 GLN cc_start: 0.8925 (OUTLIER) cc_final: 0.8213 (tp-100) REVERT: F 1210 LYS cc_start: 0.4712 (pttm) cc_final: 0.3901 (tptt) REVERT: B 97 PHE cc_start: 0.5992 (OUTLIER) cc_final: 0.5558 (p90) REVERT: B 167 ILE cc_start: 0.7691 (pp) cc_final: 0.7482 (mm) REVERT: B 299 MET cc_start: 0.6660 (mtm) cc_final: 0.6400 (ptp) REVERT: B 338 ASP cc_start: 0.7254 (t0) cc_final: 0.6860 (m-30) REVERT: B 507 ARG cc_start: 0.7347 (OUTLIER) cc_final: 0.7084 (tpt90) REVERT: H 1211 LYS cc_start: 0.3305 (mptt) cc_final: 0.2956 (mmmt) REVERT: E 374 ASN cc_start: 0.6689 (OUTLIER) cc_final: 0.6418 (p0) REVERT: E 381 ASN cc_start: 0.7652 (p0) cc_final: 0.7418 (t0) REVERT: G 302 ARG cc_start: 0.7579 (mmt180) cc_final: 0.7360 (mmt180) REVERT: G 736 MET cc_start: 0.6078 (mmt) cc_final: 0.5460 (mmt) REVERT: C 800 MET cc_start: 0.7243 (ppp) cc_final: 0.6997 (ppp) REVERT: C 1051 MET cc_start: 0.6676 (tmm) cc_final: 0.6147 (tpt) REVERT: D 883 TYR cc_start: 0.8380 (p90) cc_final: 0.7956 (p90) REVERT: D 1055 MET cc_start: 0.5907 (ptm) cc_final: 0.5414 (ptp) outliers start: 117 outliers final: 84 residues processed: 449 average time/residue: 0.4726 time to fit residues: 358.1742 Evaluate side-chains 393 residues out of total 4112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 305 time to evaluate : 4.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 MET Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 299 MET Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 501 ASP Chi-restraints excluded: chain A residue 580 SER Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain A residue 687 CYS Chi-restraints excluded: chain A residue 712 ASP Chi-restraints excluded: chain A residue 737 HIS Chi-restraints excluded: chain F residue 789 THR Chi-restraints excluded: chain F residue 870 ILE Chi-restraints excluded: chain F residue 981 SER Chi-restraints excluded: chain F residue 1012 LEU Chi-restraints excluded: chain F residue 1128 GLN Chi-restraints excluded: chain F residue 1198 VAL Chi-restraints excluded: chain B residue 97 PHE Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 280 MET Chi-restraints excluded: chain B residue 312 CYS Chi-restraints excluded: chain B residue 323 GLU Chi-restraints excluded: chain B residue 384 CYS Chi-restraints excluded: chain B residue 476 LEU Chi-restraints excluded: chain B residue 501 ASP Chi-restraints excluded: chain B residue 507 ARG Chi-restraints excluded: chain B residue 638 VAL Chi-restraints excluded: chain B residue 659 LEU Chi-restraints excluded: chain B residue 707 CYS Chi-restraints excluded: chain B residue 723 SER Chi-restraints excluded: chain B residue 729 CYS Chi-restraints excluded: chain H residue 797 LEU Chi-restraints excluded: chain H residue 799 CYS Chi-restraints excluded: chain H residue 809 LEU Chi-restraints excluded: chain H residue 829 CYS Chi-restraints excluded: chain H residue 870 ILE Chi-restraints excluded: chain H residue 904 THR Chi-restraints excluded: chain H residue 934 ILE Chi-restraints excluded: chain H residue 1029 SER Chi-restraints excluded: chain H residue 1075 VAL Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain E residue 311 THR Chi-restraints excluded: chain E residue 374 ASN Chi-restraints excluded: chain E residue 434 ASP Chi-restraints excluded: chain E residue 501 ASP Chi-restraints excluded: chain E residue 511 LYS Chi-restraints excluded: chain E residue 536 LEU Chi-restraints excluded: chain E residue 659 LEU Chi-restraints excluded: chain E residue 733 ASP Chi-restraints excluded: chain G residue 58 SER Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain G residue 109 VAL Chi-restraints excluded: chain G residue 129 LEU Chi-restraints excluded: chain G residue 158 THR Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 227 LEU Chi-restraints excluded: chain G residue 280 MET Chi-restraints excluded: chain G residue 326 VAL Chi-restraints excluded: chain G residue 345 SER Chi-restraints excluded: chain G residue 368 ASN Chi-restraints excluded: chain G residue 426 VAL Chi-restraints excluded: chain G residue 434 ASP Chi-restraints excluded: chain G residue 441 THR Chi-restraints excluded: chain G residue 451 LEU Chi-restraints excluded: chain G residue 471 VAL Chi-restraints excluded: chain G residue 475 LEU Chi-restraints excluded: chain G residue 490 VAL Chi-restraints excluded: chain G residue 614 SER Chi-restraints excluded: chain G residue 622 LEU Chi-restraints excluded: chain G residue 640 VAL Chi-restraints excluded: chain G residue 709 CYS Chi-restraints excluded: chain G residue 715 ILE Chi-restraints excluded: chain C residue 819 ASN Chi-restraints excluded: chain C residue 870 ILE Chi-restraints excluded: chain C residue 927 ILE Chi-restraints excluded: chain C residue 981 SER Chi-restraints excluded: chain D residue 864 ASP Chi-restraints excluded: chain D residue 870 ILE Chi-restraints excluded: chain D residue 897 TYR Chi-restraints excluded: chain D residue 898 CYS Chi-restraints excluded: chain D residue 934 ILE Chi-restraints excluded: chain D residue 941 VAL Chi-restraints excluded: chain D residue 956 VAL Chi-restraints excluded: chain D residue 1088 THR Chi-restraints excluded: chain D residue 1124 THR Chi-restraints excluded: chain D residue 1231 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 153 optimal weight: 6.9990 chunk 410 optimal weight: 2.9990 chunk 90 optimal weight: 6.9990 chunk 267 optimal weight: 20.0000 chunk 112 optimal weight: 10.0000 chunk 456 optimal weight: 0.4980 chunk 379 optimal weight: 2.9990 chunk 211 optimal weight: 3.9990 chunk 37 optimal weight: 9.9990 chunk 151 optimal weight: 7.9990 chunk 239 optimal weight: 10.0000 overall best weight: 3.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 531 GLN ** F 832 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 737 HIS ** H 874 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 986 GLN ** H1013 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 95 HIS ** E 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 952 HIS D1069 GLN D1154 GLN D1174 HIS D1176 HIS ** D1188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7196 moved from start: 0.6717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 37380 Z= 0.261 Angle : 0.715 16.135 50724 Z= 0.362 Chirality : 0.048 0.507 5552 Planarity : 0.005 0.047 6728 Dihedral : 5.811 58.620 5558 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.86 % Favored : 91.12 % Rotamer: Outliers : 3.30 % Allowed : 15.32 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.74 (0.12), residues: 4744 helix: -1.40 (0.20), residues: 628 sheet: -2.52 (0.17), residues: 832 loop : -1.79 (0.11), residues: 3284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP G 553 HIS 0.007 0.001 HIS D 861 PHE 0.025 0.002 PHE F 937 TYR 0.050 0.002 TYR H 897 ARG 0.009 0.001 ARG H 826 *********************** 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 470 residues out of total 4112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 339 time to evaluate : 4.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 466 MET cc_start: 0.7979 (ptp) cc_final: 0.6759 (tpt) REVERT: A 494 TYR cc_start: 0.7240 (t80) cc_final: 0.6976 (t80) REVERT: A 740 MET cc_start: 0.5484 (mmt) cc_final: 0.5237 (tpt) REVERT: F 860 ASP cc_start: 0.7157 (t0) cc_final: 0.6501 (t70) REVERT: B 179 THR cc_start: 0.7471 (p) cc_final: 0.7209 (p) REVERT: B 338 ASP cc_start: 0.7267 (t0) cc_final: 0.6717 (m-30) REVERT: B 507 ARG cc_start: 0.7526 (OUTLIER) cc_final: 0.7228 (tpt90) REVERT: H 852 GLN cc_start: 0.7997 (tm-30) cc_final: 0.7157 (tp-100) REVERT: H 1211 LYS cc_start: 0.3796 (mptt) cc_final: 0.3259 (mmmt) REVERT: E 222 TRP cc_start: 0.6906 (t60) cc_final: 0.6703 (t60) REVERT: E 374 ASN cc_start: 0.6661 (OUTLIER) cc_final: 0.6298 (p0) REVERT: E 498 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.7929 (tt) REVERT: E 740 MET cc_start: 0.7402 (tpt) cc_final: 0.7088 (tpt) REVERT: G 41 ASP cc_start: 0.7332 (OUTLIER) cc_final: 0.7064 (m-30) REVERT: G 302 ARG cc_start: 0.7795 (mmt180) cc_final: 0.7581 (mmt180) REVERT: G 553 TRP cc_start: 0.6879 (m-10) cc_final: 0.6480 (m-10) REVERT: C 814 MET cc_start: 0.7113 (tpp) cc_final: 0.6893 (tpp) REVERT: C 1051 MET cc_start: 0.6833 (tmm) cc_final: 0.6382 (tpt) REVERT: D 856 TRP cc_start: 0.7075 (OUTLIER) cc_final: 0.6480 (m-10) REVERT: D 883 TYR cc_start: 0.8500 (p90) cc_final: 0.8049 (p90) outliers start: 131 outliers final: 89 residues processed: 449 average time/residue: 0.5329 time to fit residues: 397.7374 Evaluate side-chains 383 residues out of total 4112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 289 time to evaluate : 3.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 299 MET Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 323 GLU Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 501 ASP Chi-restraints excluded: chain A residue 580 SER Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain A residue 651 ASN Chi-restraints excluded: chain A residue 687 CYS Chi-restraints excluded: chain A residue 737 HIS Chi-restraints excluded: chain F residue 789 THR Chi-restraints excluded: chain F residue 870 ILE Chi-restraints excluded: chain F residue 981 SER Chi-restraints excluded: chain F residue 1019 VAL Chi-restraints excluded: chain F residue 1198 VAL Chi-restraints excluded: chain B residue 78 ASN Chi-restraints excluded: chain B residue 97 PHE Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 280 MET Chi-restraints excluded: chain B residue 323 GLU Chi-restraints excluded: chain B residue 339 GLU Chi-restraints excluded: chain B residue 384 CYS Chi-restraints excluded: chain B residue 501 ASP Chi-restraints excluded: chain B residue 507 ARG Chi-restraints excluded: chain B residue 638 VAL Chi-restraints excluded: chain B residue 659 LEU Chi-restraints excluded: chain B residue 669 CYS Chi-restraints excluded: chain B residue 707 CYS Chi-restraints excluded: chain B residue 723 SER Chi-restraints excluded: chain B residue 729 CYS Chi-restraints excluded: chain H residue 797 LEU Chi-restraints excluded: chain H residue 799 CYS Chi-restraints excluded: chain H residue 809 LEU Chi-restraints excluded: chain H residue 829 CYS Chi-restraints excluded: chain H residue 870 ILE Chi-restraints excluded: chain H residue 874 HIS Chi-restraints excluded: chain H residue 904 THR Chi-restraints excluded: chain H residue 934 ILE Chi-restraints excluded: chain H residue 1029 SER Chi-restraints excluded: chain H residue 1159 HIS Chi-restraints excluded: chain H residue 1171 GLU Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain E residue 311 THR Chi-restraints excluded: chain E residue 374 ASN Chi-restraints excluded: chain E residue 476 LEU Chi-restraints excluded: chain E residue 498 LEU Chi-restraints excluded: chain E residue 501 ASP Chi-restraints excluded: chain E residue 511 LYS Chi-restraints excluded: chain E residue 536 LEU Chi-restraints excluded: chain E residue 608 CYS Chi-restraints excluded: chain E residue 659 LEU Chi-restraints excluded: chain E residue 668 THR Chi-restraints excluded: chain E residue 733 ASP Chi-restraints excluded: chain G residue 41 ASP Chi-restraints excluded: chain G residue 58 SER Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain G residue 97 PHE Chi-restraints excluded: chain G residue 109 VAL Chi-restraints excluded: chain G residue 158 THR Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 280 MET Chi-restraints excluded: chain G residue 368 ASN Chi-restraints excluded: chain G residue 370 CYS Chi-restraints excluded: chain G residue 426 VAL Chi-restraints excluded: chain G residue 434 ASP Chi-restraints excluded: chain G residue 451 LEU Chi-restraints excluded: chain G residue 471 VAL Chi-restraints excluded: chain G residue 475 LEU Chi-restraints excluded: chain G residue 562 LEU Chi-restraints excluded: chain G residue 599 VAL Chi-restraints excluded: chain G residue 614 SER Chi-restraints excluded: chain G residue 640 VAL Chi-restraints excluded: chain G residue 709 CYS Chi-restraints excluded: chain G residue 715 ILE Chi-restraints excluded: chain C residue 870 ILE Chi-restraints excluded: chain C residue 884 LEU Chi-restraints excluded: chain C residue 927 ILE Chi-restraints excluded: chain C residue 942 ASN Chi-restraints excluded: chain C residue 981 SER Chi-restraints excluded: chain D residue 789 THR Chi-restraints excluded: chain D residue 856 TRP Chi-restraints excluded: chain D residue 864 ASP Chi-restraints excluded: chain D residue 870 ILE Chi-restraints excluded: chain D residue 897 TYR Chi-restraints excluded: chain D residue 898 CYS Chi-restraints excluded: chain D residue 916 HIS Chi-restraints excluded: chain D residue 934 ILE Chi-restraints excluded: chain D residue 941 VAL Chi-restraints excluded: chain D residue 1124 THR Chi-restraints excluded: chain D residue 1231 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 440 optimal weight: 9.9990 chunk 51 optimal weight: 7.9990 chunk 260 optimal weight: 9.9990 chunk 333 optimal weight: 0.0040 chunk 258 optimal weight: 4.9990 chunk 384 optimal weight: 0.3980 chunk 255 optimal weight: 5.9990 chunk 454 optimal weight: 0.9990 chunk 284 optimal weight: 5.9990 chunk 277 optimal weight: 1.9990 chunk 210 optimal weight: 0.9980 overall best weight: 0.8796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 GLN A 352 HIS A 531 GLN ** A 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 832 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 874 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1013 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 189 ASN ** G 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1011 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7127 moved from start: 0.6910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 37380 Z= 0.159 Angle : 0.674 25.801 50724 Z= 0.332 Chirality : 0.045 0.414 5552 Planarity : 0.004 0.050 6728 Dihedral : 5.323 52.907 5558 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.52 % Favored : 93.46 % Rotamer: Outliers : 2.44 % Allowed : 16.45 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.57 (0.12), residues: 4744 helix: -1.13 (0.21), residues: 628 sheet: -2.40 (0.18), residues: 804 loop : -1.72 (0.10), residues: 3312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP G 553 HIS 0.004 0.001 HIS H 874 PHE 0.037 0.001 PHE E 722 TYR 0.045 0.001 TYR H 897 ARG 0.008 0.000 ARG G 578 *********************** 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 429 residues out of total 4112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 333 time to evaluate : 4.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 466 MET cc_start: 0.7908 (ptp) cc_final: 0.6854 (tpt) REVERT: A 494 TYR cc_start: 0.7322 (t80) cc_final: 0.7072 (t80) REVERT: B 97 PHE cc_start: 0.6184 (OUTLIER) cc_final: 0.5910 (p90) REVERT: B 174 MET cc_start: 0.7663 (tpp) cc_final: 0.7347 (tpp) REVERT: H 1036 LYS cc_start: 0.6697 (tptm) cc_final: 0.6489 (tttp) REVERT: H 1211 LYS cc_start: 0.3967 (mptt) cc_final: 0.3474 (mmmt) REVERT: E 497 ASP cc_start: 0.6482 (m-30) cc_final: 0.6056 (m-30) REVERT: G 227 LEU cc_start: 0.7620 (mt) cc_final: 0.7398 (mt) REVERT: G 302 ARG cc_start: 0.7658 (mmt180) cc_final: 0.7443 (mmt180) REVERT: G 466 MET cc_start: 0.6812 (mtm) cc_final: 0.6459 (mtm) REVERT: G 500 MET cc_start: 0.6062 (mmm) cc_final: 0.5811 (mmm) REVERT: G 695 MET cc_start: 0.6016 (mmm) cc_final: 0.5333 (mmm) REVERT: C 814 MET cc_start: 0.6944 (tpp) cc_final: 0.6631 (tpp) REVERT: C 1051 MET cc_start: 0.6626 (tmm) cc_final: 0.6234 (tpt) REVERT: D 883 TYR cc_start: 0.8419 (p90) cc_final: 0.8039 (p90) outliers start: 96 outliers final: 70 residues processed: 409 average time/residue: 0.4713 time to fit residues: 322.8710 Evaluate side-chains 368 residues out of total 4112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 297 time to evaluate : 4.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ASP Chi-restraints excluded: chain A residue 50 MET Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 299 MET Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 501 ASP Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 652 CYS Chi-restraints excluded: chain A residue 737 HIS Chi-restraints excluded: chain F residue 789 THR Chi-restraints excluded: chain F residue 870 ILE Chi-restraints excluded: chain F residue 981 SER Chi-restraints excluded: chain F residue 1198 VAL Chi-restraints excluded: chain B residue 78 ASN Chi-restraints excluded: chain B residue 97 PHE Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 280 MET Chi-restraints excluded: chain B residue 323 GLU Chi-restraints excluded: chain B residue 501 ASP Chi-restraints excluded: chain B residue 638 VAL Chi-restraints excluded: chain B residue 659 LEU Chi-restraints excluded: chain B residue 707 CYS Chi-restraints excluded: chain B residue 729 CYS Chi-restraints excluded: chain H residue 797 LEU Chi-restraints excluded: chain H residue 799 CYS Chi-restraints excluded: chain H residue 809 LEU Chi-restraints excluded: chain H residue 829 CYS Chi-restraints excluded: chain H residue 870 ILE Chi-restraints excluded: chain H residue 874 HIS Chi-restraints excluded: chain H residue 934 ILE Chi-restraints excluded: chain H residue 1226 HIS Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain E residue 476 LEU Chi-restraints excluded: chain E residue 501 ASP Chi-restraints excluded: chain E residue 511 LYS Chi-restraints excluded: chain E residue 536 LEU Chi-restraints excluded: chain E residue 608 CYS Chi-restraints excluded: chain E residue 659 LEU Chi-restraints excluded: chain E residue 733 ASP Chi-restraints excluded: chain G residue 58 SER Chi-restraints excluded: chain G residue 96 LEU Chi-restraints excluded: chain G residue 97 PHE Chi-restraints excluded: chain G residue 109 VAL Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 189 ASN Chi-restraints excluded: chain G residue 280 MET Chi-restraints excluded: chain G residue 370 CYS Chi-restraints excluded: chain G residue 426 VAL Chi-restraints excluded: chain G residue 475 LEU Chi-restraints excluded: chain G residue 490 VAL Chi-restraints excluded: chain G residue 562 LEU Chi-restraints excluded: chain G residue 599 VAL Chi-restraints excluded: chain G residue 614 SER Chi-restraints excluded: chain G residue 622 LEU Chi-restraints excluded: chain G residue 640 VAL Chi-restraints excluded: chain G residue 709 CYS Chi-restraints excluded: chain G residue 715 ILE Chi-restraints excluded: chain C residue 870 ILE Chi-restraints excluded: chain C residue 927 ILE Chi-restraints excluded: chain C residue 981 SER Chi-restraints excluded: chain D residue 864 ASP Chi-restraints excluded: chain D residue 870 ILE Chi-restraints excluded: chain D residue 897 TYR Chi-restraints excluded: chain D residue 898 CYS Chi-restraints excluded: chain D residue 916 HIS Chi-restraints excluded: chain D residue 934 ILE Chi-restraints excluded: chain D residue 941 VAL Chi-restraints excluded: chain D residue 1048 ASN Chi-restraints excluded: chain D residue 1124 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 281 optimal weight: 10.0000 chunk 181 optimal weight: 10.0000 chunk 271 optimal weight: 9.9990 chunk 137 optimal weight: 4.9990 chunk 89 optimal weight: 20.0000 chunk 88 optimal weight: 7.9990 chunk 289 optimal weight: 1.9990 chunk 309 optimal weight: 7.9990 chunk 224 optimal weight: 0.9980 chunk 42 optimal weight: 20.0000 chunk 357 optimal weight: 10.0000 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 531 GLN ** F 832 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1003 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 874 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 952 HIS ** H1013 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H1188 GLN ** E 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 737 HIS G 189 ASN ** G 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 499 GLN ** C 986 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1188 GLN ** D1188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 moved from start: 0.7601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.112 37380 Z= 0.323 Angle : 0.781 22.713 50724 Z= 0.395 Chirality : 0.049 0.512 5552 Planarity : 0.005 0.052 6728 Dihedral : 5.980 54.202 5558 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.02 % Allowed : 9.94 % Favored : 90.04 % Rotamer: Outliers : 2.88 % Allowed : 16.42 % Favored : 80.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.76 (0.12), residues: 4744 helix: -1.41 (0.20), residues: 636 sheet: -2.53 (0.17), residues: 836 loop : -1.80 (0.10), residues: 3272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP G 553 HIS 0.007 0.001 HIS G 484 PHE 0.028 0.002 PHE D 905 TYR 0.065 0.002 TYR H 897 ARG 0.009 0.001 ARG A 578 *********************** 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 438 residues out of total 4112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 324 time to evaluate : 4.097 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 ASP cc_start: 0.7864 (OUTLIER) cc_final: 0.7321 (m-30) REVERT: A 254 LEU cc_start: 0.4046 (OUTLIER) cc_final: 0.3543 (tp) REVERT: A 466 MET cc_start: 0.7957 (ptp) cc_final: 0.6844 (tpt) REVERT: F 860 ASP cc_start: 0.7332 (t0) cc_final: 0.6774 (t70) REVERT: B 174 MET cc_start: 0.7637 (tpp) cc_final: 0.7358 (tpt) REVERT: B 356 ARG cc_start: 0.7624 (tpp-160) cc_final: 0.7003 (ttm-80) REVERT: B 608 CYS cc_start: 0.7456 (OUTLIER) cc_final: 0.7208 (t) REVERT: B 722 PHE cc_start: 0.7530 (OUTLIER) cc_final: 0.7010 (t80) REVERT: B 740 MET cc_start: 0.6503 (tmm) cc_final: 0.6132 (tpt) REVERT: H 814 MET cc_start: 0.6265 (mtp) cc_final: 0.5917 (mtt) REVERT: H 852 GLN cc_start: 0.7973 (tm-30) cc_final: 0.7268 (tp-100) REVERT: H 1055 MET cc_start: 0.6781 (mtp) cc_final: 0.6548 (mtt) REVERT: E 498 LEU cc_start: 0.8278 (OUTLIER) cc_final: 0.7983 (tt) REVERT: G 300 GLU cc_start: 0.7640 (mp0) cc_final: 0.6752 (mp0) REVERT: G 302 ARG cc_start: 0.7904 (mmt180) cc_final: 0.7530 (mmt180) REVERT: G 710 TYR cc_start: 0.6379 (m-10) cc_final: 0.5918 (m-80) REVERT: G 736 MET cc_start: 0.6232 (mmt) cc_final: 0.5376 (mmt) REVERT: C 1051 MET cc_start: 0.6698 (tmm) cc_final: 0.6329 (tpt) REVERT: D 883 TYR cc_start: 0.8583 (p90) cc_final: 0.8179 (p90) outliers start: 114 outliers final: 82 residues processed: 412 average time/residue: 0.4701 time to fit residues: 326.0144 Evaluate side-chains 380 residues out of total 4112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 293 time to evaluate : 4.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ASP Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 299 MET Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 323 GLU Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 501 ASP Chi-restraints excluded: chain A residue 526 ASN Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 651 ASN Chi-restraints excluded: chain A residue 652 CYS Chi-restraints excluded: chain A residue 737 HIS Chi-restraints excluded: chain F residue 789 THR Chi-restraints excluded: chain F residue 870 ILE Chi-restraints excluded: chain F residue 947 MET Chi-restraints excluded: chain F residue 981 SER Chi-restraints excluded: chain F residue 1019 VAL Chi-restraints excluded: chain F residue 1198 VAL Chi-restraints excluded: chain B residue 78 ASN Chi-restraints excluded: chain B residue 97 PHE Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 280 MET Chi-restraints excluded: chain B residue 323 GLU Chi-restraints excluded: chain B residue 501 ASP Chi-restraints excluded: chain B residue 608 CYS Chi-restraints excluded: chain B residue 638 VAL Chi-restraints excluded: chain B residue 707 CYS Chi-restraints excluded: chain B residue 722 PHE Chi-restraints excluded: chain B residue 723 SER Chi-restraints excluded: chain H residue 797 LEU Chi-restraints excluded: chain H residue 799 CYS Chi-restraints excluded: chain H residue 809 LEU Chi-restraints excluded: chain H residue 829 CYS Chi-restraints excluded: chain H residue 904 THR Chi-restraints excluded: chain H residue 934 ILE Chi-restraints excluded: chain H residue 1029 SER Chi-restraints excluded: chain H residue 1188 GLN Chi-restraints excluded: chain H residue 1226 HIS Chi-restraints excluded: chain E residue 97 PHE Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain E residue 152 ASP Chi-restraints excluded: chain E residue 464 VAL Chi-restraints excluded: chain E residue 476 LEU Chi-restraints excluded: chain E residue 498 LEU Chi-restraints excluded: chain E residue 501 ASP Chi-restraints excluded: chain E residue 511 LYS Chi-restraints excluded: chain E residue 536 LEU Chi-restraints excluded: chain E residue 608 CYS Chi-restraints excluded: chain G residue 58 SER Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain G residue 96 LEU Chi-restraints excluded: chain G residue 97 PHE Chi-restraints excluded: chain G residue 109 VAL Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 280 MET Chi-restraints excluded: chain G residue 345 SER Chi-restraints excluded: chain G residue 368 ASN Chi-restraints excluded: chain G residue 370 CYS Chi-restraints excluded: chain G residue 426 VAL Chi-restraints excluded: chain G residue 451 LEU Chi-restraints excluded: chain G residue 508 LEU Chi-restraints excluded: chain G residue 562 LEU Chi-restraints excluded: chain G residue 614 SER Chi-restraints excluded: chain G residue 640 VAL Chi-restraints excluded: chain G residue 709 CYS Chi-restraints excluded: chain G residue 715 ILE Chi-restraints excluded: chain C residue 870 ILE Chi-restraints excluded: chain C residue 884 LEU Chi-restraints excluded: chain C residue 927 ILE Chi-restraints excluded: chain C residue 981 SER Chi-restraints excluded: chain C residue 1230 VAL Chi-restraints excluded: chain D residue 864 ASP Chi-restraints excluded: chain D residue 897 TYR Chi-restraints excluded: chain D residue 898 CYS Chi-restraints excluded: chain D residue 916 HIS Chi-restraints excluded: chain D residue 934 ILE Chi-restraints excluded: chain D residue 941 VAL Chi-restraints excluded: chain D residue 1048 ASN Chi-restraints excluded: chain D residue 1124 THR Chi-restraints excluded: chain D residue 1231 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 413 optimal weight: 8.9990 chunk 435 optimal weight: 4.9990 chunk 397 optimal weight: 7.9990 chunk 423 optimal weight: 1.9990 chunk 255 optimal weight: 5.9990 chunk 184 optimal weight: 0.0370 chunk 332 optimal weight: 10.0000 chunk 130 optimal weight: 3.9990 chunk 383 optimal weight: 5.9990 chunk 400 optimal weight: 1.9990 chunk 422 optimal weight: 0.8980 overall best weight: 1.7864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 832 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 874 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1013 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 189 ASN ** G 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 717 GLN C1109 HIS ** D1188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7241 moved from start: 0.7719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 37380 Z= 0.196 Angle : 0.700 21.624 50724 Z= 0.346 Chirality : 0.046 0.443 5552 Planarity : 0.005 0.075 6728 Dihedral : 5.580 51.027 5558 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.09 % Favored : 92.89 % Rotamer: Outliers : 2.54 % Allowed : 16.98 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.51 (0.12), residues: 4744 helix: -1.13 (0.21), residues: 628 sheet: -2.28 (0.18), residues: 784 loop : -1.70 (0.10), residues: 3332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP G 553 HIS 0.004 0.001 HIS C1174 PHE 0.028 0.001 PHE G 406 TYR 0.046 0.001 TYR H 897 ARG 0.008 0.001 ARG A 481 *********************** 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 418 residues out of total 4112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 318 time to evaluate : 4.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 ASP cc_start: 0.7797 (OUTLIER) cc_final: 0.7201 (m-30) REVERT: A 466 MET cc_start: 0.7921 (ptp) cc_final: 0.6946 (tpt) REVERT: A 695 MET cc_start: 0.6590 (tpp) cc_final: 0.6374 (tpt) REVERT: A 736 MET cc_start: 0.5810 (mmm) cc_final: 0.4713 (tmm) REVERT: F 1144 TRP cc_start: 0.7418 (m100) cc_final: 0.7113 (m-10) REVERT: B 174 MET cc_start: 0.7550 (tpp) cc_final: 0.7253 (tpt) REVERT: B 217 MET cc_start: 0.4720 (mtp) cc_final: 0.4188 (mpp) REVERT: B 356 ARG cc_start: 0.7608 (tpp-160) cc_final: 0.7053 (ttm-80) REVERT: B 695 MET cc_start: 0.7623 (tpp) cc_final: 0.7350 (tpt) REVERT: H 800 MET cc_start: 0.5924 (mmt) cc_final: 0.5672 (tmm) REVERT: H 814 MET cc_start: 0.6239 (mtp) cc_final: 0.6001 (mtt) REVERT: H 852 GLN cc_start: 0.7848 (tm-30) cc_final: 0.7269 (tp-100) REVERT: H 1055 MET cc_start: 0.6617 (mtp) cc_final: 0.6417 (mtt) REVERT: E 497 ASP cc_start: 0.6533 (m-30) cc_final: 0.6056 (m-30) REVERT: E 498 LEU cc_start: 0.8242 (OUTLIER) cc_final: 0.7873 (tt) REVERT: E 678 GLU cc_start: 0.6757 (mm-30) cc_final: 0.6409 (mm-30) REVERT: G 244 GLU cc_start: 0.5914 (OUTLIER) cc_final: 0.5686 (tm-30) REVERT: G 300 GLU cc_start: 0.7620 (mp0) cc_final: 0.6702 (mp0) REVERT: G 302 ARG cc_start: 0.7784 (mmt180) cc_final: 0.7330 (mmt180) REVERT: G 466 MET cc_start: 0.7241 (mtm) cc_final: 0.6975 (mtm) REVERT: G 695 MET cc_start: 0.6170 (mmm) cc_final: 0.5235 (mmm) REVERT: C 1051 MET cc_start: 0.6607 (tmm) cc_final: 0.6315 (tpt) REVERT: D 883 TYR cc_start: 0.8456 (p90) cc_final: 0.8130 (p90) outliers start: 100 outliers final: 88 residues processed: 399 average time/residue: 0.4774 time to fit residues: 320.6585 Evaluate side-chains 385 residues out of total 4112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 294 time to evaluate : 3.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ASP Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 107 GLN Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 299 MET Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 323 GLU Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 501 ASP Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 652 CYS Chi-restraints excluded: chain A residue 737 HIS Chi-restraints excluded: chain F residue 789 THR Chi-restraints excluded: chain F residue 870 ILE Chi-restraints excluded: chain F residue 947 MET Chi-restraints excluded: chain F residue 981 SER Chi-restraints excluded: chain F residue 1019 VAL Chi-restraints excluded: chain F residue 1198 VAL Chi-restraints excluded: chain B residue 78 ASN Chi-restraints excluded: chain B residue 97 PHE Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 280 MET Chi-restraints excluded: chain B residue 312 CYS Chi-restraints excluded: chain B residue 323 GLU Chi-restraints excluded: chain B residue 501 ASP Chi-restraints excluded: chain B residue 638 VAL Chi-restraints excluded: chain B residue 659 LEU Chi-restraints excluded: chain B residue 707 CYS Chi-restraints excluded: chain H residue 797 LEU Chi-restraints excluded: chain H residue 799 CYS Chi-restraints excluded: chain H residue 829 CYS Chi-restraints excluded: chain H residue 858 CYS Chi-restraints excluded: chain H residue 870 ILE Chi-restraints excluded: chain H residue 874 HIS Chi-restraints excluded: chain H residue 904 THR Chi-restraints excluded: chain H residue 934 ILE Chi-restraints excluded: chain H residue 1029 SER Chi-restraints excluded: chain H residue 1226 HIS Chi-restraints excluded: chain E residue 97 PHE Chi-restraints excluded: chain E residue 152 ASP Chi-restraints excluded: chain E residue 311 THR Chi-restraints excluded: chain E residue 476 LEU Chi-restraints excluded: chain E residue 498 LEU Chi-restraints excluded: chain E residue 501 ASP Chi-restraints excluded: chain E residue 511 LYS Chi-restraints excluded: chain E residue 536 LEU Chi-restraints excluded: chain E residue 608 CYS Chi-restraints excluded: chain E residue 668 THR Chi-restraints excluded: chain G residue 58 SER Chi-restraints excluded: chain G residue 96 LEU Chi-restraints excluded: chain G residue 97 PHE Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 244 GLU Chi-restraints excluded: chain G residue 280 MET Chi-restraints excluded: chain G residue 341 LEU Chi-restraints excluded: chain G residue 345 SER Chi-restraints excluded: chain G residue 368 ASN Chi-restraints excluded: chain G residue 370 CYS Chi-restraints excluded: chain G residue 426 VAL Chi-restraints excluded: chain G residue 451 LEU Chi-restraints excluded: chain G residue 508 LEU Chi-restraints excluded: chain G residue 562 LEU Chi-restraints excluded: chain G residue 608 CYS Chi-restraints excluded: chain G residue 614 SER Chi-restraints excluded: chain G residue 640 VAL Chi-restraints excluded: chain G residue 709 CYS Chi-restraints excluded: chain G residue 715 ILE Chi-restraints excluded: chain C residue 870 ILE Chi-restraints excluded: chain C residue 884 LEU Chi-restraints excluded: chain C residue 927 ILE Chi-restraints excluded: chain C residue 981 SER Chi-restraints excluded: chain C residue 1084 CYS Chi-restraints excluded: chain C residue 1230 VAL Chi-restraints excluded: chain D residue 864 ASP Chi-restraints excluded: chain D residue 870 ILE Chi-restraints excluded: chain D residue 897 TYR Chi-restraints excluded: chain D residue 898 CYS Chi-restraints excluded: chain D residue 916 HIS Chi-restraints excluded: chain D residue 934 ILE Chi-restraints excluded: chain D residue 941 VAL Chi-restraints excluded: chain D residue 956 VAL Chi-restraints excluded: chain D residue 1048 ASN Chi-restraints excluded: chain D residue 1124 THR Chi-restraints excluded: chain D residue 1143 MET Chi-restraints excluded: chain D residue 1231 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 278 optimal weight: 3.9990 chunk 448 optimal weight: 3.9990 chunk 273 optimal weight: 7.9990 chunk 212 optimal weight: 5.9990 chunk 311 optimal weight: 9.9990 chunk 470 optimal weight: 0.0870 chunk 432 optimal weight: 0.4980 chunk 374 optimal weight: 9.9990 chunk 38 optimal weight: 2.9990 chunk 289 optimal weight: 7.9990 chunk 229 optimal weight: 9.9990 overall best weight: 2.3164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 368 ASN A 531 GLN ** A 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 832 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 421 HIS ** H 874 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1013 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 189 ASN ** G 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1188 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7256 moved from start: 0.7904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 37380 Z= 0.207 Angle : 0.709 21.672 50724 Z= 0.352 Chirality : 0.047 0.446 5552 Planarity : 0.005 0.066 6728 Dihedral : 5.542 52.182 5558 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.95 % Favored : 92.03 % Rotamer: Outliers : 2.52 % Allowed : 17.38 % Favored : 80.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.47 (0.12), residues: 4744 helix: -1.07 (0.21), residues: 628 sheet: -2.22 (0.18), residues: 784 loop : -1.69 (0.10), residues: 3332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP G 553 HIS 0.004 0.001 HIS C1174 PHE 0.027 0.002 PHE F 937 TYR 0.049 0.002 TYR H 897 ARG 0.009 0.001 ARG A 481 ********************** 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 409 residues out of total 4112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 310 time to evaluate : 4.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 ASP cc_start: 0.7819 (OUTLIER) cc_final: 0.7224 (m-30) REVERT: A 455 LEU cc_start: 0.7784 (mt) cc_final: 0.7576 (tp) REVERT: F 1144 TRP cc_start: 0.7434 (m100) cc_final: 0.7186 (m-10) REVERT: B 174 MET cc_start: 0.7429 (tpp) cc_final: 0.7085 (mmm) REVERT: B 217 MET cc_start: 0.4597 (mtp) cc_final: 0.4026 (mpp) REVERT: B 356 ARG cc_start: 0.7634 (tpp-160) cc_final: 0.7076 (ttm-80) REVERT: B 722 PHE cc_start: 0.7408 (OUTLIER) cc_final: 0.6719 (t80) REVERT: H 814 MET cc_start: 0.6229 (mtp) cc_final: 0.5961 (mtt) REVERT: H 852 GLN cc_start: 0.7939 (tm-30) cc_final: 0.7375 (tp-100) REVERT: H 1055 MET cc_start: 0.6649 (mtp) cc_final: 0.6447 (mtt) REVERT: E 498 LEU cc_start: 0.8258 (OUTLIER) cc_final: 0.7889 (tt) REVERT: G 244 GLU cc_start: 0.5958 (OUTLIER) cc_final: 0.5722 (tm-30) REVERT: G 299 MET cc_start: 0.5982 (tpp) cc_final: 0.4477 (tpp) REVERT: G 300 GLU cc_start: 0.7566 (mp0) cc_final: 0.6868 (mp0) REVERT: G 302 ARG cc_start: 0.7757 (mmt180) cc_final: 0.7426 (mmt180) REVERT: G 466 MET cc_start: 0.7309 (mtm) cc_final: 0.7088 (mtm) REVERT: G 695 MET cc_start: 0.6008 (mmm) cc_final: 0.5010 (mmm) REVERT: G 736 MET cc_start: 0.6085 (mmt) cc_final: 0.5512 (mmt) REVERT: C 1051 MET cc_start: 0.6688 (tmm) cc_final: 0.6402 (tpt) REVERT: D 883 TYR cc_start: 0.8494 (p90) cc_final: 0.8121 (p90) outliers start: 99 outliers final: 88 residues processed: 389 average time/residue: 0.4678 time to fit residues: 306.5803 Evaluate side-chains 383 residues out of total 4112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 291 time to evaluate : 4.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ASP Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 107 GLN Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 299 MET Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 323 GLU Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 368 ASN Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 501 ASP Chi-restraints excluded: chain A residue 526 ASN Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 580 SER Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain A residue 652 CYS Chi-restraints excluded: chain A residue 737 HIS Chi-restraints excluded: chain F residue 789 THR Chi-restraints excluded: chain F residue 870 ILE Chi-restraints excluded: chain F residue 947 MET Chi-restraints excluded: chain F residue 981 SER Chi-restraints excluded: chain F residue 1019 VAL Chi-restraints excluded: chain F residue 1198 VAL Chi-restraints excluded: chain B residue 78 ASN Chi-restraints excluded: chain B residue 97 PHE Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 280 MET Chi-restraints excluded: chain B residue 312 CYS Chi-restraints excluded: chain B residue 323 GLU Chi-restraints excluded: chain B residue 501 ASP Chi-restraints excluded: chain B residue 638 VAL Chi-restraints excluded: chain B residue 659 LEU Chi-restraints excluded: chain B residue 707 CYS Chi-restraints excluded: chain B residue 722 PHE Chi-restraints excluded: chain B residue 723 SER Chi-restraints excluded: chain H residue 797 LEU Chi-restraints excluded: chain H residue 799 CYS Chi-restraints excluded: chain H residue 829 CYS Chi-restraints excluded: chain H residue 858 CYS Chi-restraints excluded: chain H residue 870 ILE Chi-restraints excluded: chain H residue 904 THR Chi-restraints excluded: chain H residue 934 ILE Chi-restraints excluded: chain H residue 1029 SER Chi-restraints excluded: chain E residue 97 PHE Chi-restraints excluded: chain E residue 311 THR Chi-restraints excluded: chain E residue 476 LEU Chi-restraints excluded: chain E residue 498 LEU Chi-restraints excluded: chain E residue 501 ASP Chi-restraints excluded: chain E residue 511 LYS Chi-restraints excluded: chain E residue 536 LEU Chi-restraints excluded: chain E residue 608 CYS Chi-restraints excluded: chain E residue 668 THR Chi-restraints excluded: chain G residue 58 SER Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain G residue 96 LEU Chi-restraints excluded: chain G residue 97 PHE Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 189 ASN Chi-restraints excluded: chain G residue 244 GLU Chi-restraints excluded: chain G residue 280 MET Chi-restraints excluded: chain G residue 341 LEU Chi-restraints excluded: chain G residue 345 SER Chi-restraints excluded: chain G residue 368 ASN Chi-restraints excluded: chain G residue 370 CYS Chi-restraints excluded: chain G residue 426 VAL Chi-restraints excluded: chain G residue 451 LEU Chi-restraints excluded: chain G residue 508 LEU Chi-restraints excluded: chain G residue 562 LEU Chi-restraints excluded: chain G residue 608 CYS Chi-restraints excluded: chain G residue 614 SER Chi-restraints excluded: chain G residue 640 VAL Chi-restraints excluded: chain G residue 709 CYS Chi-restraints excluded: chain C residue 870 ILE Chi-restraints excluded: chain C residue 884 LEU Chi-restraints excluded: chain C residue 927 ILE Chi-restraints excluded: chain C residue 981 SER Chi-restraints excluded: chain C residue 1084 CYS Chi-restraints excluded: chain C residue 1230 VAL Chi-restraints excluded: chain D residue 864 ASP Chi-restraints excluded: chain D residue 870 ILE Chi-restraints excluded: chain D residue 897 TYR Chi-restraints excluded: chain D residue 898 CYS Chi-restraints excluded: chain D residue 916 HIS Chi-restraints excluded: chain D residue 934 ILE Chi-restraints excluded: chain D residue 941 VAL Chi-restraints excluded: chain D residue 956 VAL Chi-restraints excluded: chain D residue 1048 ASN Chi-restraints excluded: chain D residue 1124 THR Chi-restraints excluded: chain D residue 1231 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 297 optimal weight: 4.9990 chunk 398 optimal weight: 10.0000 chunk 114 optimal weight: 7.9990 chunk 345 optimal weight: 5.9990 chunk 55 optimal weight: 0.9980 chunk 104 optimal weight: 6.9990 chunk 375 optimal weight: 5.9990 chunk 156 optimal weight: 3.9990 chunk 385 optimal weight: 7.9990 chunk 47 optimal weight: 5.9990 chunk 69 optimal weight: 1.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 531 GLN ** A 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 832 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 874 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1013 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 78 ASN ** G 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.135060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.107038 restraints weight = 152502.318| |-----------------------------------------------------------------------------| r_work (start): 0.3883 rms_B_bonded: 5.29 r_work: 0.3707 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.3707 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3706 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3706 r_free = 0.3706 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3706 r_free = 0.3706 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3706 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.7910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.415 37380 Z= 0.345 Angle : 0.900 59.195 50724 Z= 0.489 Chirality : 0.048 0.515 5552 Planarity : 0.005 0.073 6728 Dihedral : 5.546 52.181 5558 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.08 % Favored : 91.90 % Rotamer: Outliers : 2.57 % Allowed : 17.30 % Favored : 80.13 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.47 (0.12), residues: 4744 helix: -1.08 (0.21), residues: 628 sheet: -2.21 (0.18), residues: 784 loop : -1.68 (0.10), residues: 3332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP G 553 HIS 0.004 0.001 HIS C1174 PHE 0.027 0.001 PHE F 937 TYR 0.044 0.001 TYR H 897 ARG 0.007 0.000 ARG A 481 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9297.47 seconds wall clock time: 169 minutes 13.56 seconds (10153.56 seconds total)