Starting phenix.real_space_refine on Tue Apr 16 02:49:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wpq_32688/04_2024/7wpq_32688_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wpq_32688/04_2024/7wpq_32688.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.267 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wpq_32688/04_2024/7wpq_32688.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wpq_32688/04_2024/7wpq_32688.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wpq_32688/04_2024/7wpq_32688_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wpq_32688/04_2024/7wpq_32688_neut.pdb" } resolution = 3.267 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= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 16 9.91 5 S 552 5.16 5 C 22560 2.51 5 N 6260 2.21 5 O 7188 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 34": "NH1" <-> "NH2" Residue "A PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 81": "NH1" <-> "NH2" Residue "A ARG 302": "NH1" <-> "NH2" Residue "B ARG 34": "NH1" <-> "NH2" Residue "B PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 81": "NH1" <-> "NH2" Residue "B ARG 302": "NH1" <-> "NH2" Residue "C TYR 883": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 "D TYR 883": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 "E ARG 34": "NH1" <-> "NH2" Residue "E PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 81": "NH1" <-> "NH2" Residue "E ARG 302": "NH1" <-> "NH2" Residue "F TYR 883": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 "G ARG 34": "NH1" <-> "NH2" Residue "G PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 81": "NH1" <-> "NH2" Residue "G PHE 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 302": "NH1" <-> "NH2" Residue "H TYR 883": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 924": "NH1" <-> "NH2" Residue "H ARG 1035": "NH1" <-> "NH2" Residue "H ARG 1061": "NH1" <-> "NH2" Residue "H ARG 1121": "NH1" <-> "NH2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 36576 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 5421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 711, 5421 Classifications: {'peptide': 711} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 2, 'PTRANS': 33, 'TRANS': 675} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 5421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 711, 5421 Classifications: {'peptide': 711} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 2, 'PTRANS': 33, 'TRANS': 675} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "C" Number of atoms: 3649 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 478, 3643 Classifications: {'peptide': 478} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 28, 'TRANS': 449} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Conformer: "B" Number of residues, atoms: 478, 3643 Classifications: {'peptide': 478} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 28, 'TRANS': 449} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 3712 Chain: "D" Number of atoms: 3649 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 478, 3643 Classifications: {'peptide': 478} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 28, 'TRANS': 449} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Conformer: "B" Number of residues, atoms: 478, 3643 Classifications: {'peptide': 478} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 28, 'TRANS': 449} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 3712 Chain: "E" Number of atoms: 5421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 711, 5421 Classifications: {'peptide': 711} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 2, 'PTRANS': 33, 'TRANS': 675} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "F" Number of atoms: 3649 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 478, 3643 Classifications: {'peptide': 478} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 28, 'TRANS': 449} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Conformer: "B" Number of residues, atoms: 478, 3643 Classifications: {'peptide': 478} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 28, 'TRANS': 449} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 3712 Chain: "G" Number of atoms: 5421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 711, 5421 Classifications: {'peptide': 711} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 2, 'PTRANS': 33, 'TRANS': 675} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "H" Number of atoms: 3649 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 478, 3643 Classifications: {'peptide': 478} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 28, 'TRANS': 449} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Conformer: "B" Number of residues, atoms: 478, 3643 Classifications: {'peptide': 478} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 28, 'TRANS': 449} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 3712 Chain: "A" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 30 Unusual residues: {' CA': 2, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 30 Unusual residues: {' CA': 2, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 44 Unusual residues: {' CA': 2, 'NAG': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 44 Unusual residues: {' CA': 2, 'NAG': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 30 Unusual residues: {' CA': 2, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 44 Unusual residues: {' CA': 2, 'NAG': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 30 Unusual residues: {' CA': 2, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 44 Unusual residues: {' CA': 2, 'NAG': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 26.47, per 1000 atoms: 0.72 Number of scatterers: 36576 At special positions: 0 Unit cell: (161.02, 248.32, 177.51, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 16 19.99 S 552 16.00 O 7188 8.00 N 6260 7.00 C 22560 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=232, symmetry=0 Simple disulfide: pdb=" SG CYS A 35 " - pdb=" SG CYS A 162 " distance=2.03 Simple disulfide: pdb=" SG CYS A 57 " - pdb=" SG CYS A 200 " distance=2.03 Simple disulfide: pdb=" SG CYS A 65 " - pdb=" SG CYS A 159 " distance=2.03 Simple disulfide: pdb=" SG CYS A 210 " - pdb=" SG CYS A 255 " distance=2.03 Simple disulfide: pdb=" SG CYS A 225 " - pdb=" SG CYS A 250 " distance=2.03 Simple disulfide: pdb=" SG CYS A 237 " - pdb=" SG CYS A 275 " distance=2.03 Simple disulfide: pdb=" SG CYS A 257 " - pdb=" SG CYS A 263 " distance=2.03 Simple disulfide: pdb=" SG CYS A 265 " - pdb=" SG CYS A 291 " distance=2.03 Simple disulfide: pdb=" SG CYS A 295 " - pdb=" SG CYS A 329 " distance=2.03 Simple disulfide: pdb=" SG CYS A 304 " - pdb=" SG CYS A 325 " distance=2.03 Simple disulfide: pdb=" SG CYS A 308 " - pdb=" SG CYS A 321 " distance=2.03 Simple disulfide: pdb=" SG CYS A 312 " - pdb=" SG CYS A 348 " distance=2.03 Simple disulfide: pdb=" SG CYS A 331 " - pdb=" SG CYS A 342 " distance=2.03 Simple disulfide: pdb=" SG CYS A 350 " - pdb=" SG CYS A 372 " distance=2.03 Simple disulfide: pdb=" SG CYS A 367 " - pdb=" SG CYS A 384 " distance=2.03 Simple disulfide: pdb=" SG CYS A 370 " - pdb=" SG CYS A 379 " distance=2.03 Simple disulfide: pdb=" SG CYS A 388 " - pdb=" SG CYS A 524 " distance=2.03 Simple disulfide: pdb=" SG CYS A 410 " - pdb=" SG CYS A 559 " distance=2.03 Simple disulfide: pdb=" SG CYS A 418 " - pdb=" SG CYS A 521 " distance=2.03 Simple disulfide: pdb=" SG CYS A 432 " - pdb=" SG CYS A 440 " distance=2.04 Simple disulfide: pdb=" SG CYS A 570 " - pdb=" SG CYS A 613 " distance=2.03 Simple disulfide: pdb=" SG CYS A 584 " - pdb=" SG CYS A 608 " distance=2.02 Simple disulfide: pdb=" SG CYS A 595 " - pdb=" SG CYS A 633 " distance=2.03 Simple disulfide: pdb=" SG CYS A 615 " - pdb=" SG CYS A 621 " distance=2.03 Simple disulfide: pdb=" SG CYS A 623 " - pdb=" SG CYS A 648 " distance=2.02 Simple disulfide: pdb=" SG CYS A 652 " - pdb=" SG CYS A 687 " distance=2.03 Simple disulfide: pdb=" SG CYS A 661 " - pdb=" SG CYS A 683 " distance=2.03 Simple disulfide: pdb=" SG CYS A 665 " - pdb=" SG CYS A 679 " distance=2.03 Simple disulfide: pdb=" SG CYS A 669 " - pdb=" SG CYS A 707 " distance=2.02 Simple disulfide: pdb=" SG CYS A 689 " - pdb=" SG CYS A 701 " distance=2.04 Simple disulfide: pdb=" SG CYS A 709 " - pdb=" SG CYS A 731 " distance=2.03 Simple disulfide: pdb=" SG CYS A 729 " - pdb=" SG CYS A 738 " distance=2.03 Simple disulfide: pdb=" SG CYS B 35 " - pdb=" SG CYS B 162 " distance=2.03 Simple disulfide: pdb=" SG CYS B 57 " - pdb=" SG CYS B 200 " distance=2.03 Simple disulfide: pdb=" SG CYS B 65 " - pdb=" SG CYS B 159 " distance=2.03 Simple disulfide: pdb=" SG CYS B 210 " - pdb=" SG CYS B 255 " distance=2.03 Simple disulfide: pdb=" SG CYS B 225 " - pdb=" SG CYS B 250 " distance=2.03 Simple disulfide: pdb=" SG CYS B 237 " - pdb=" SG CYS B 275 " distance=2.03 Simple disulfide: pdb=" SG CYS B 257 " - pdb=" SG CYS B 263 " distance=2.03 Simple disulfide: pdb=" SG CYS B 265 " - pdb=" SG CYS B 291 " distance=2.03 Simple disulfide: pdb=" SG CYS B 295 " - pdb=" SG CYS B 329 " distance=2.03 Simple disulfide: pdb=" SG CYS B 304 " - pdb=" SG CYS B 325 " distance=2.03 Simple disulfide: pdb=" SG CYS B 308 " - pdb=" SG CYS B 321 " distance=2.02 Simple disulfide: pdb=" SG CYS B 312 " - pdb=" SG CYS B 348 " distance=2.03 Simple disulfide: pdb=" SG CYS B 331 " - pdb=" SG CYS B 342 " distance=2.03 Simple disulfide: pdb=" SG CYS B 350 " - pdb=" SG CYS B 372 " distance=2.03 Simple disulfide: pdb=" SG CYS B 367 " - pdb=" SG CYS B 384 " distance=2.03 Simple disulfide: pdb=" SG CYS B 370 " - pdb=" SG CYS B 379 " distance=2.03 Simple disulfide: pdb=" SG CYS B 388 " - pdb=" SG CYS B 524 " distance=2.03 Simple disulfide: pdb=" SG CYS B 410 " - pdb=" SG CYS B 559 " distance=2.03 Simple disulfide: pdb=" SG CYS B 418 " - pdb=" SG CYS B 521 " distance=2.03 Simple disulfide: pdb=" SG CYS B 432 " - pdb=" SG CYS B 440 " distance=2.03 Simple disulfide: pdb=" SG CYS B 570 " - pdb=" SG CYS B 613 " distance=2.03 Simple disulfide: pdb=" SG CYS B 584 " - pdb=" SG CYS B 608 " distance=2.02 Simple disulfide: pdb=" SG CYS B 595 " - pdb=" SG CYS B 633 " distance=2.03 Simple disulfide: pdb=" SG CYS B 615 " - pdb=" SG CYS B 621 " distance=2.03 Simple disulfide: pdb=" SG CYS B 623 " - pdb=" SG CYS B 648 " distance=2.02 Simple disulfide: pdb=" SG CYS B 652 " - pdb=" SG CYS B 687 " distance=2.03 Simple disulfide: pdb=" SG CYS B 661 " - pdb=" SG CYS B 683 " distance=2.03 Simple disulfide: pdb=" SG CYS B 665 " - pdb=" SG CYS B 679 " distance=2.03 Simple disulfide: pdb=" SG CYS B 669 " - pdb=" SG CYS B 707 " distance=2.03 Simple disulfide: pdb=" SG CYS B 689 " - pdb=" SG CYS B 701 " distance=2.04 Simple disulfide: pdb=" SG CYS B 709 " - pdb=" SG CYS B 731 " distance=2.03 Simple disulfide: pdb=" SG CYS B 729 " - pdb=" SG CYS B 738 " distance=2.03 Simple disulfide: pdb=" SG CYS C 767 " - pdb=" SG CYS C 808 " distance=2.03 Simple disulfide: pdb=" SG CYS C 776 " - pdb=" SG CYS C 804 " distance=2.02 Simple disulfide: pdb=" SG CYS C 788 " - pdb=" SG CYS C 799 " distance=2.03 Simple disulfide: pdb=" SG CYS C 792 " - pdb=" SG CYS C 827 " distance=2.03 Simple disulfide: pdb=" SG CYS C 810 " - pdb=" SG CYS C 821 " distance=2.03 Simple disulfide: pdb=" SG CYS C 829 " - pdb=" SG CYS C 851 " distance=2.03 Simple disulfide: pdb=" SG CYS C 846 " - pdb=" SG CYS C 863 " distance=2.03 Simple disulfide: pdb=" SG CYS C 849 " - pdb=" SG CYS C 858 " distance=2.03 Simple disulfide: pdb=" SG CYS C 867 " - pdb=" SG CYS C 996 " distance=2.03 Simple disulfide: pdb=" SG CYS C 889 " - pdb=" SG CYS C1031 " distance=2.03 Simple disulfide: pdb=" SG CYS C 898 " - pdb=" SG CYS C 993 " distance=2.03 Simple disulfide: pdb=" SG CYS C 914 " - pdb=" SG CYS C 921 " distance=2.03 Simple disulfide: pdb=" SG CYS C1046 " - pdb=" SG CYS C1089 " distance=2.03 Simple disulfide: pdb=" SG CYS C1060 " - pdb=" SG CYS C1084 " distance=2.04 Simple disulfide: pdb=" SG CYS C1071 " - pdb=" SG CYS C1111 " distance=2.02 Simple disulfide: pdb=" SG CYS C1091 " - pdb=" SG CYS C1099 " distance=2.03 Simple disulfide: pdb=" SG CYS C1097 " - pdb=" SG CYS D1097 " distance=2.02 Simple disulfide: pdb=" SG CYS C1101 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C1130 " - pdb=" SG CYS C1173 " distance=2.03 Simple disulfide: pdb=" SG CYS C1142 " - pdb=" SG CYS D1142 " distance=2.04 Simple disulfide: pdb=" SG CYS C1149 " - pdb=" SG CYS C1169 " distance=2.03 Simple disulfide: pdb=" SG CYS C1153 " - pdb=" SG CYS C1165 " distance=2.03 Simple disulfide: pdb=" SG CYS C1157 " - pdb=" SG CYS C1196 " distance=2.03 Simple disulfide: pdb=" SG CYS C1177 " - pdb=" SG CYS C1190 " distance=2.03 Simple disulfide: pdb=" SG CYS C1199 " - pdb=" SG CYS C1227 " distance=2.03 Simple disulfide: pdb=" SG CYS C1222 " - pdb=" SG CYS C1237 " distance=2.03 Simple disulfide: pdb=" SG CYS C1225 " - pdb=" SG CYS C1234 " distance=2.03 Simple disulfide: pdb=" SG CYS D 767 " - pdb=" SG CYS D 808 " distance=2.03 Simple disulfide: pdb=" SG CYS D 776 " - pdb=" SG CYS D 804 " distance=2.02 Simple disulfide: pdb=" SG CYS D 788 " - pdb=" SG CYS D 799 " distance=2.03 Simple disulfide: pdb=" SG CYS D 792 " - pdb=" SG CYS D 827 " distance=2.03 Simple disulfide: pdb=" SG CYS D 810 " - pdb=" SG CYS D 821 " distance=2.03 Simple disulfide: pdb=" SG CYS D 829 " - pdb=" SG CYS D 851 " distance=2.03 Simple disulfide: pdb=" SG CYS D 846 " - pdb=" SG CYS D 863 " distance=2.03 Simple disulfide: pdb=" SG CYS D 849 " - pdb=" SG CYS D 858 " distance=2.03 Simple disulfide: pdb=" SG CYS D 867 " - pdb=" SG CYS D 996 " distance=2.03 Simple disulfide: pdb=" SG CYS D 889 " - pdb=" SG CYS D1031 " distance=2.03 Simple disulfide: pdb=" SG CYS D 898 " - pdb=" SG CYS D 993 " distance=2.03 Simple disulfide: pdb=" SG CYS D 914 " - pdb=" SG CYS D 921 " distance=2.03 Simple disulfide: pdb=" SG CYS D1046 " - pdb=" SG CYS D1089 " distance=2.03 Simple disulfide: pdb=" SG CYS D1060 " - pdb=" SG CYS D1084 " distance=2.04 Simple disulfide: pdb=" SG CYS D1071 " - pdb=" SG CYS D1111 " distance=2.02 Simple disulfide: pdb=" SG CYS D1091 " - pdb=" SG CYS D1099 " distance=2.03 Simple disulfide: pdb=" SG CYS D1101 " - pdb=" SG CYS D1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D1130 " - pdb=" SG CYS D1173 " distance=2.03 Simple disulfide: pdb=" SG CYS D1149 " - pdb=" SG CYS D1169 " distance=2.03 Simple disulfide: pdb=" SG CYS D1153 " - pdb=" SG CYS D1165 " distance=2.03 Simple disulfide: pdb=" SG CYS D1157 " - pdb=" SG CYS D1196 " distance=2.03 Simple disulfide: pdb=" SG CYS D1177 " - pdb=" SG CYS D1190 " distance=2.03 Simple disulfide: pdb=" SG CYS D1199 " - pdb=" SG CYS D1227 " distance=2.03 Simple disulfide: pdb=" SG CYS D1222 " - pdb=" SG CYS D1237 " distance=2.03 Simple disulfide: pdb=" SG CYS D1225 " - pdb=" SG CYS D1234 " distance=2.03 Simple disulfide: pdb=" SG CYS E 35 " - pdb=" SG CYS E 162 " distance=2.03 Simple disulfide: pdb=" SG CYS E 57 " - pdb=" SG CYS E 200 " distance=2.03 Simple disulfide: pdb=" SG CYS E 65 " - pdb=" SG CYS E 159 " distance=2.03 Simple disulfide: pdb=" SG CYS E 210 " - pdb=" SG CYS E 255 " distance=2.03 Simple disulfide: pdb=" SG CYS E 225 " - pdb=" SG CYS E 250 " distance=2.03 Simple disulfide: pdb=" SG CYS E 237 " - pdb=" SG CYS E 275 " distance=2.03 Simple disulfide: pdb=" SG CYS E 257 " - pdb=" SG CYS E 263 " distance=2.03 Simple disulfide: pdb=" SG CYS E 265 " - pdb=" SG CYS E 291 " distance=2.03 Simple disulfide: pdb=" SG CYS E 295 " - pdb=" SG CYS E 329 " distance=2.03 Simple disulfide: pdb=" SG CYS E 304 " - pdb=" SG CYS E 325 " distance=2.04 Simple disulfide: pdb=" SG CYS E 308 " - pdb=" SG CYS E 321 " distance=2.03 Simple disulfide: pdb=" SG CYS E 312 " - pdb=" SG CYS E 348 " distance=2.03 Simple disulfide: pdb=" SG CYS E 331 " - pdb=" SG CYS E 342 " distance=2.03 Simple disulfide: pdb=" SG CYS E 350 " - pdb=" SG CYS E 372 " distance=2.03 Simple disulfide: pdb=" SG CYS E 367 " - pdb=" SG CYS E 384 " distance=2.03 Simple disulfide: pdb=" SG CYS E 370 " - pdb=" SG CYS E 379 " distance=2.03 Simple disulfide: pdb=" SG CYS E 388 " - pdb=" SG CYS E 524 " distance=2.03 Simple disulfide: pdb=" SG CYS E 410 " - pdb=" SG CYS E 559 " distance=2.03 Simple disulfide: pdb=" SG CYS E 418 " - pdb=" SG CYS E 521 " distance=2.03 Simple disulfide: pdb=" SG CYS E 432 " - pdb=" SG CYS E 440 " distance=2.04 Simple disulfide: pdb=" SG CYS E 570 " - pdb=" SG CYS E 613 " distance=2.03 Simple disulfide: pdb=" SG CYS E 584 " - pdb=" SG CYS E 608 " distance=2.02 Simple disulfide: pdb=" SG CYS E 595 " - pdb=" SG CYS E 633 " distance=2.03 Simple disulfide: pdb=" SG CYS E 615 " - pdb=" SG CYS E 621 " distance=2.03 Simple disulfide: pdb=" SG CYS E 623 " - pdb=" SG CYS E 648 " distance=2.02 Simple disulfide: pdb=" SG CYS E 652 " - pdb=" SG CYS E 687 " distance=2.03 Simple disulfide: pdb=" SG CYS E 661 " - pdb=" SG CYS E 683 " distance=2.03 Simple disulfide: pdb=" SG CYS E 665 " - pdb=" SG CYS E 679 " distance=2.03 Simple disulfide: pdb=" SG CYS E 669 " - pdb=" SG CYS E 707 " distance=2.03 Simple disulfide: pdb=" SG CYS E 689 " - pdb=" SG CYS E 701 " distance=2.04 Simple disulfide: pdb=" SG CYS E 709 " - pdb=" SG CYS E 731 " distance=2.03 Simple disulfide: pdb=" SG CYS E 729 " - pdb=" SG CYS E 738 " distance=2.03 Simple disulfide: pdb=" SG CYS F 767 " - pdb=" SG CYS F 808 " distance=2.03 Simple disulfide: pdb=" SG CYS F 776 " - pdb=" SG CYS F 804 " distance=2.02 Simple disulfide: pdb=" SG CYS F 788 " - pdb=" SG CYS F 799 " distance=2.03 Simple disulfide: pdb=" SG CYS F 792 " - pdb=" SG CYS F 827 " distance=2.03 Simple disulfide: pdb=" SG CYS F 810 " - pdb=" SG CYS F 821 " distance=2.03 Simple disulfide: pdb=" SG CYS F 829 " - pdb=" SG CYS F 851 " distance=2.03 Simple disulfide: pdb=" SG CYS F 846 " - pdb=" SG CYS F 863 " distance=2.03 Simple disulfide: pdb=" SG CYS F 849 " - pdb=" SG CYS F 858 " distance=2.03 Simple disulfide: pdb=" SG CYS F 867 " - pdb=" SG CYS F 996 " distance=2.03 Simple disulfide: pdb=" SG CYS F 889 " - pdb=" SG CYS F1031 " distance=2.03 Simple disulfide: pdb=" SG CYS F 898 " - pdb=" SG CYS F 993 " distance=2.03 Simple disulfide: pdb=" SG CYS F 914 " - pdb=" SG CYS F 921 " distance=2.03 Simple disulfide: pdb=" SG CYS F1046 " - pdb=" SG CYS F1089 " distance=2.03 Simple disulfide: pdb=" SG CYS F1060 " - pdb=" SG CYS F1084 " distance=2.03 Simple disulfide: pdb=" SG CYS F1071 " - pdb=" SG CYS F1111 " distance=2.02 Simple disulfide: pdb=" SG CYS F1091 " - pdb=" SG CYS F1099 " distance=2.03 Simple disulfide: pdb=" SG CYS F1097 " - pdb=" SG CYS H1097 " distance=2.03 Simple disulfide: pdb=" SG CYS F1101 " - pdb=" SG CYS F1126 " distance=2.03 Simple disulfide: pdb=" SG CYS F1130 " - pdb=" SG CYS F1173 " distance=2.03 Simple disulfide: pdb=" SG CYS F1142 " - pdb=" SG CYS H1142 " distance=2.02 Simple disulfide: pdb=" SG CYS F1149 " - pdb=" SG CYS F1169 " distance=2.03 Simple disulfide: pdb=" SG CYS F1153 " - pdb=" SG CYS F1165 " distance=2.03 Simple disulfide: pdb=" SG CYS F1157 " - pdb=" SG CYS F1196 " distance=2.03 Simple disulfide: pdb=" SG CYS F1177 " - pdb=" SG CYS F1190 " distance=2.03 Simple disulfide: pdb=" SG CYS F1199 " - pdb=" SG CYS F1227 " distance=2.03 Simple disulfide: pdb=" SG CYS F1222 " - pdb=" SG CYS F1237 " distance=2.03 Simple disulfide: pdb=" SG CYS F1225 " - pdb=" SG CYS F1234 " distance=2.03 Simple disulfide: pdb=" SG CYS G 35 " - pdb=" SG CYS G 162 " distance=2.03 Simple disulfide: pdb=" SG CYS G 57 " - pdb=" SG CYS G 200 " distance=2.03 Simple disulfide: pdb=" SG CYS G 65 " - pdb=" SG CYS G 159 " distance=2.03 Simple disulfide: pdb=" SG CYS G 210 " - pdb=" SG CYS G 255 " distance=2.03 Simple disulfide: pdb=" SG CYS G 225 " - pdb=" SG CYS G 250 " distance=2.03 Simple disulfide: pdb=" SG CYS G 237 " - pdb=" SG CYS G 275 " distance=2.03 Simple disulfide: pdb=" SG CYS G 257 " - pdb=" SG CYS G 263 " distance=2.03 Simple disulfide: pdb=" SG CYS G 265 " - pdb=" SG CYS G 291 " distance=2.03 Simple disulfide: pdb=" SG CYS G 295 " - pdb=" SG CYS G 329 " distance=2.03 Simple disulfide: pdb=" SG CYS G 304 " - pdb=" SG CYS G 325 " distance=2.03 Simple disulfide: pdb=" SG CYS G 308 " - pdb=" SG CYS G 321 " distance=2.03 Simple disulfide: pdb=" SG CYS G 312 " - pdb=" SG CYS G 348 " distance=2.03 Simple disulfide: pdb=" SG CYS G 331 " - pdb=" SG CYS G 342 " distance=2.03 Simple disulfide: pdb=" SG CYS G 350 " - pdb=" SG CYS G 372 " distance=2.03 Simple disulfide: pdb=" SG CYS G 367 " - pdb=" SG CYS G 384 " distance=2.03 Simple disulfide: pdb=" SG CYS G 370 " - pdb=" SG CYS G 379 " distance=2.03 Simple disulfide: pdb=" SG CYS G 388 " - pdb=" SG CYS G 524 " distance=2.03 Simple disulfide: pdb=" SG CYS G 410 " - pdb=" SG CYS G 559 " distance=2.03 Simple disulfide: pdb=" SG CYS G 418 " - pdb=" SG CYS G 521 " distance=2.03 Simple disulfide: pdb=" SG CYS G 432 " - pdb=" SG CYS G 440 " distance=2.04 Simple disulfide: pdb=" SG CYS G 570 " - pdb=" SG CYS G 613 " distance=2.03 Simple disulfide: pdb=" SG CYS G 584 " - pdb=" SG CYS G 608 " distance=2.02 Simple disulfide: pdb=" SG CYS G 595 " - pdb=" SG CYS G 633 " distance=2.03 Simple disulfide: pdb=" SG CYS G 615 " - pdb=" SG CYS G 621 " distance=2.03 Simple disulfide: pdb=" SG CYS G 623 " - pdb=" SG CYS G 648 " distance=2.02 Simple disulfide: pdb=" SG CYS G 652 " - pdb=" SG CYS G 687 " distance=2.03 Simple disulfide: pdb=" SG CYS G 661 " - pdb=" SG CYS G 683 " distance=2.03 Simple disulfide: pdb=" SG CYS G 665 " - pdb=" SG CYS G 679 " distance=2.03 Simple disulfide: pdb=" SG CYS G 669 " - pdb=" SG CYS G 707 " distance=2.03 Simple disulfide: pdb=" SG CYS G 689 " - pdb=" SG CYS G 701 " distance=2.04 Simple disulfide: pdb=" SG CYS G 709 " - pdb=" SG CYS G 731 " distance=2.03 Simple disulfide: pdb=" SG CYS G 729 " - pdb=" SG CYS G 738 " distance=2.03 Simple disulfide: pdb=" SG CYS H 767 " - pdb=" SG CYS H 808 " distance=2.03 Simple disulfide: pdb=" SG CYS H 776 " - pdb=" SG CYS H 804 " distance=2.03 Simple disulfide: pdb=" SG CYS H 788 " - pdb=" SG CYS H 799 " distance=2.03 Simple disulfide: pdb=" SG CYS H 792 " - pdb=" SG CYS H 827 " distance=2.03 Simple disulfide: pdb=" SG CYS H 810 " - pdb=" SG CYS H 821 " distance=2.04 Simple disulfide: pdb=" SG CYS H 829 " - pdb=" SG CYS H 851 " distance=2.03 Simple disulfide: pdb=" SG CYS H 846 " - pdb=" SG CYS H 863 " distance=2.03 Simple disulfide: pdb=" SG CYS H 849 " - pdb=" SG CYS H 858 " distance=2.03 Simple disulfide: pdb=" SG CYS H 867 " - pdb=" SG CYS H 996 " distance=2.03 Simple disulfide: pdb=" SG CYS H 889 " - pdb=" SG CYS H1031 " distance=2.03 Simple disulfide: pdb=" SG CYS H 898 " - pdb=" SG CYS H 993 " distance=2.03 Simple disulfide: pdb=" SG CYS H 914 " - pdb=" SG CYS H 921 " distance=2.03 Simple disulfide: pdb=" SG CYS H1046 " - pdb=" SG CYS H1089 " distance=2.03 Simple disulfide: pdb=" SG CYS H1060 " - pdb=" SG CYS H1084 " distance=2.03 Simple disulfide: pdb=" SG CYS H1071 " - pdb=" SG CYS H1111 " distance=2.02 Simple disulfide: pdb=" SG CYS H1091 " - pdb=" SG CYS H1099 " distance=2.03 Simple disulfide: pdb=" SG CYS H1101 " - pdb=" SG CYS H1126 " distance=2.03 Simple disulfide: pdb=" SG CYS H1130 " - pdb=" SG CYS H1173 " distance=2.03 Simple disulfide: pdb=" SG CYS H1149 " - pdb=" SG CYS H1169 " distance=2.03 Simple disulfide: pdb=" SG CYS H1153 " - pdb=" SG CYS H1165 " distance=2.03 Simple disulfide: pdb=" SG CYS H1157 " - pdb=" SG CYS H1196 " distance=2.03 Simple disulfide: pdb=" SG CYS H1177 " - pdb=" SG CYS H1190 " distance=2.03 Simple disulfide: pdb=" SG CYS H1199 " - pdb=" SG CYS H1227 " distance=2.03 Simple disulfide: pdb=" SG CYS H1222 " - pdb=" SG CYS H1237 " distance=2.03 Simple disulfide: pdb=" SG CYS H1225 " - pdb=" SG CYS H1234 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 801 " - " ASN A 156 " " NAG A 802 " - " ASN A 99 " " NAG B 801 " - " ASN B 156 " " NAG B 802 " - " ASN B 99 " " NAG C1301 " - " ASN C1231 " " NAG C1302 " - " ASN C 857 " " NAG C1303 " - " ASN C1147 " " NAG D1301 " - " ASN D1231 " " NAG D1302 " - " ASN D 857 " " NAG D1303 " - " ASN D1147 " " NAG E 801 " - " ASN E 156 " " NAG E 802 " - " ASN E 99 " " NAG F1301 " - " ASN F1231 " " NAG F1302 " - " ASN F 857 " " NAG F1303 " - " ASN F1147 " " NAG G 801 " - " ASN G 156 " " NAG G 802 " - " ASN G 99 " " NAG H1301 " - " ASN H1231 " " NAG H1302 " - " ASN H 857 " " NAG H1303 " - " ASN H1147 " Time building additional restraints: 15.78 Conformation dependent library (CDL) restraints added in 9.9 seconds 9488 Ramachandran restraints generated. 4744 Oldfield, 0 Emsley, 4744 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8768 Finding SS restraints... Secondary structure from input PDB file: 112 helices and 97 sheets defined 17.6% alpha, 14.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.51 Creating SS restraints... Processing helix chain 'A' and resid 114 through 118 removed outlier: 3.844A pdb=" N GLY A 117 " --> pdb=" O ALA A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 155 Processing helix chain 'A' and resid 208 through 212 removed outlier: 3.870A pdb=" N ASN A 211 " --> pdb=" O SER A 208 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE A 212 " --> pdb=" O SER A 209 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 208 through 212' Processing helix chain 'A' and resid 214 through 219 removed outlier: 4.227A pdb=" N GLN A 218 " --> pdb=" O GLY A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 231 removed outlier: 4.309A pdb=" N CYS A 225 " --> pdb=" O LEU A 221 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N LEU A 228 " --> pdb=" O GLN A 224 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N LYS A 229 " --> pdb=" O CYS A 225 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR A 231 " --> pdb=" O LEU A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 235 Processing helix chain 'A' and resid 243 through 251 removed outlier: 3.559A pdb=" N GLU A 251 " --> pdb=" O VAL A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 263 No H-bonds generated for 'chain 'A' and resid 261 through 263' Processing helix chain 'A' and resid 264 through 277 removed outlier: 3.755A pdb=" N TYR A 271 " --> pdb=" O ALA A 267 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG A 273 " --> pdb=" O LEU A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 348 Processing helix chain 'A' and resid 514 through 517 Processing helix chain 'A' and resid 545 through 550 Processing helix chain 'A' and resid 551 through 553 No H-bonds generated for 'chain 'A' and resid 551 through 553' Processing helix chain 'A' and resid 575 through 584 removed outlier: 4.722A pdb=" N PHE A 579 " --> pdb=" O ARG A 575 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU A 581 " --> pdb=" O THR A 577 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N CYS A 584 " --> pdb=" O SER A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 588 Processing helix chain 'A' and resid 589 through 596 removed outlier: 5.126A pdb=" N ALA A 594 " --> pdb=" O THR A 591 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N HIS A 596 " --> pdb=" O GLU A 593 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 613 removed outlier: 3.538A pdb=" N CYS A 608 " --> pdb=" O TYR A 604 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG A 609 " --> pdb=" O LEU A 605 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N TYR A 610 " --> pdb=" O ARG A 606 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N CYS A 613 " --> pdb=" O ARG A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 617 through 624 removed outlier: 3.593A pdb=" N CYS A 621 " --> pdb=" O ASP A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 634 removed outlier: 3.561A pdb=" N TYR A 629 " --> pdb=" O ALA A 625 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA A 632 " --> pdb=" O SER A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 668 through 674 removed outlier: 4.235A pdb=" N LEU A 672 " --> pdb=" O THR A 668 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N SER A 673 " --> pdb=" O CYS A 669 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 118 removed outlier: 3.843A pdb=" N GLY B 117 " --> pdb=" O ALA B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 155 Processing helix chain 'B' and resid 208 through 212 removed outlier: 3.869A pdb=" N ASN B 211 " --> pdb=" O SER B 208 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE B 212 " --> pdb=" O SER B 209 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 208 through 212' Processing helix chain 'B' and resid 214 through 219 removed outlier: 4.229A pdb=" N GLN B 218 " --> pdb=" O GLY B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 231 removed outlier: 4.309A pdb=" N CYS B 225 " --> pdb=" O LEU B 221 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N LEU B 228 " --> pdb=" O GLN B 224 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N LYS B 229 " --> pdb=" O CYS B 225 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR B 231 " --> pdb=" O LEU B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 235 Processing helix chain 'B' and resid 243 through 251 removed outlier: 3.558A pdb=" N GLU B 251 " --> pdb=" O VAL B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 263 No H-bonds generated for 'chain 'B' and resid 261 through 263' Processing helix chain 'B' and resid 264 through 277 removed outlier: 3.755A pdb=" N TYR B 271 " --> pdb=" O ALA B 267 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG B 273 " --> pdb=" O LEU B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 348 Processing helix chain 'B' and resid 514 through 517 Processing helix chain 'B' and resid 545 through 550 Processing helix chain 'B' and resid 551 through 553 No H-bonds generated for 'chain 'B' and resid 551 through 553' Processing helix chain 'B' and resid 575 through 584 removed outlier: 4.722A pdb=" N PHE B 579 " --> pdb=" O ARG B 575 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU B 581 " --> pdb=" O THR B 577 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N CYS B 584 " --> pdb=" O SER B 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 585 through 588 Processing helix chain 'B' and resid 589 through 596 removed outlier: 5.125A pdb=" N ALA B 594 " --> pdb=" O THR B 591 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N HIS B 596 " --> pdb=" O GLU B 593 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 613 removed outlier: 3.538A pdb=" N CYS B 608 " --> pdb=" O TYR B 604 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG B 609 " --> pdb=" O LEU B 605 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N TYR B 610 " --> pdb=" O ARG B 606 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N CYS B 613 " --> pdb=" O ARG B 609 " (cutoff:3.500A) Processing helix chain 'B' and resid 617 through 624 removed outlier: 3.593A pdb=" N CYS B 621 " --> pdb=" O ASP B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 634 removed outlier: 3.561A pdb=" N TYR B 629 " --> pdb=" O ALA B 625 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA B 632 " --> pdb=" O SER B 628 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 674 removed outlier: 4.235A pdb=" N LEU B 672 " --> pdb=" O THR B 668 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N SER B 673 " --> pdb=" O CYS B 669 " (cutoff:3.500A) Processing helix chain 'C' and resid 1017 through 1022 Processing helix chain 'C' and resid 1023 through 1026 removed outlier: 3.905A pdb=" N LYS C1026 " --> pdb=" O ASN C1023 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1023 through 1026' Processing helix chain 'C' and resid 1049 through 1060 removed outlier: 3.525A pdb=" N THR C1054 " --> pdb=" O ILE C1050 " (cutoff:3.500A) Processing helix chain 'C' and resid 1061 through 1064 Processing helix chain 'C' and resid 1068 through 1073 removed outlier: 3.875A pdb=" N LYS C1073 " --> pdb=" O GLN C1069 " (cutoff:3.500A) Processing helix chain 'C' and resid 1077 through 1091 removed outlier: 3.527A pdb=" N VAL C1083 " --> pdb=" O PRO C1079 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N CYS C1084 " --> pdb=" O TYR C1080 " (cutoff:3.500A) Processing helix chain 'C' and resid 1097 through 1114 removed outlier: 5.001A pdb=" N THR C1103 " --> pdb=" O CYS C1099 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ILE C1104 " --> pdb=" O PHE C1100 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA C1105 " --> pdb=" O CYS C1101 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N TYR C1107 " --> pdb=" O THR C1103 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL C1110 " --> pdb=" O ALA C1106 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N HIS C1114 " --> pdb=" O VAL C1110 " (cutoff:3.500A) Processing helix chain 'C' and resid 1192 through 1196 Processing helix chain 'D' and resid 1017 through 1022 Processing helix chain 'D' and resid 1023 through 1026 removed outlier: 3.905A pdb=" N LYS D1026 " --> pdb=" O ASN D1023 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1023 through 1026' Processing helix chain 'D' and resid 1049 through 1060 removed outlier: 3.524A pdb=" N THR D1054 " --> pdb=" O ILE D1050 " (cutoff:3.500A) Processing helix chain 'D' and resid 1061 through 1064 Processing helix chain 'D' and resid 1068 through 1073 removed outlier: 3.876A pdb=" N LYS D1073 " --> pdb=" O GLN D1069 " (cutoff:3.500A) Processing helix chain 'D' and resid 1077 through 1091 removed outlier: 3.528A pdb=" N VAL D1083 " --> pdb=" O PRO D1079 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N CYS D1084 " --> pdb=" O TYR D1080 " (cutoff:3.500A) Processing helix chain 'D' and resid 1097 through 1114 removed outlier: 5.002A pdb=" N THR D1103 " --> pdb=" O CYS D1099 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ILE D1104 " --> pdb=" O PHE D1100 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA D1105 " --> pdb=" O CYS D1101 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TYR D1107 " --> pdb=" O THR D1103 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL D1110 " --> pdb=" O ALA D1106 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N HIS D1114 " --> pdb=" O VAL D1110 " (cutoff:3.500A) Processing helix chain 'D' and resid 1192 through 1196 Processing helix chain 'E' and resid 114 through 118 removed outlier: 3.843A pdb=" N GLY E 117 " --> pdb=" O ALA E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 152 through 155 Processing helix chain 'E' and resid 208 through 212 removed outlier: 3.870A pdb=" N ASN E 211 " --> pdb=" O SER E 208 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE E 212 " --> pdb=" O SER E 209 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 208 through 212' Processing helix chain 'E' and resid 214 through 219 removed outlier: 4.228A pdb=" N GLN E 218 " --> pdb=" O GLY E 215 " (cutoff:3.500A) Processing helix chain 'E' and resid 221 through 231 removed outlier: 4.309A pdb=" N CYS E 225 " --> pdb=" O LEU E 221 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N LEU E 228 " --> pdb=" O GLN E 224 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N LYS E 229 " --> pdb=" O CYS E 225 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR E 231 " --> pdb=" O LEU E 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 232 through 235 Processing helix chain 'E' and resid 243 through 251 removed outlier: 3.559A pdb=" N GLU E 251 " --> pdb=" O VAL E 247 " (cutoff:3.500A) Processing helix chain 'E' and resid 261 through 263 No H-bonds generated for 'chain 'E' and resid 261 through 263' Processing helix chain 'E' and resid 264 through 277 removed outlier: 3.754A pdb=" N TYR E 271 " --> pdb=" O ALA E 267 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ARG E 273 " --> pdb=" O LEU E 269 " (cutoff:3.500A) Processing helix chain 'E' and resid 344 through 348 Processing helix chain 'E' and resid 514 through 517 Processing helix chain 'E' and resid 545 through 550 Processing helix chain 'E' and resid 551 through 553 No H-bonds generated for 'chain 'E' and resid 551 through 553' Processing helix chain 'E' and resid 575 through 584 removed outlier: 4.722A pdb=" N PHE E 579 " --> pdb=" O ARG E 575 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLU E 581 " --> pdb=" O THR E 577 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N CYS E 584 " --> pdb=" O SER E 580 " (cutoff:3.500A) Processing helix chain 'E' and resid 585 through 588 Processing helix chain 'E' and resid 589 through 596 removed outlier: 5.126A pdb=" N ALA E 594 " --> pdb=" O THR E 591 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N HIS E 596 " --> pdb=" O GLU E 593 " (cutoff:3.500A) Processing helix chain 'E' and resid 601 through 613 removed outlier: 3.537A pdb=" N CYS E 608 " --> pdb=" O TYR E 604 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG E 609 " --> pdb=" O LEU E 605 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N TYR E 610 " --> pdb=" O ARG E 606 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N CYS E 613 " --> pdb=" O ARG E 609 " (cutoff:3.500A) Processing helix chain 'E' and resid 617 through 624 removed outlier: 3.594A pdb=" N CYS E 621 " --> pdb=" O ASP E 617 " (cutoff:3.500A) Processing helix chain 'E' and resid 625 through 634 removed outlier: 3.563A pdb=" N TYR E 629 " --> pdb=" O ALA E 625 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA E 632 " --> pdb=" O SER E 628 " (cutoff:3.500A) Processing helix chain 'E' and resid 668 through 674 removed outlier: 4.235A pdb=" N LEU E 672 " --> pdb=" O THR E 668 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N SER E 673 " --> pdb=" O CYS E 669 " (cutoff:3.500A) Processing helix chain 'F' and resid 1017 through 1022 Processing helix chain 'F' and resid 1023 through 1026 removed outlier: 3.906A pdb=" N LYS F1026 " --> pdb=" O ASN F1023 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 1023 through 1026' Processing helix chain 'F' and resid 1049 through 1060 removed outlier: 3.525A pdb=" N THR F1054 " --> pdb=" O ILE F1050 " (cutoff:3.500A) Processing helix chain 'F' and resid 1061 through 1064 Processing helix chain 'F' and resid 1068 through 1073 removed outlier: 3.877A pdb=" N LYS F1073 " --> pdb=" O GLN F1069 " (cutoff:3.500A) Processing helix chain 'F' and resid 1077 through 1091 removed outlier: 3.528A pdb=" N VAL F1083 " --> pdb=" O PRO F1079 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N CYS F1084 " --> pdb=" O TYR F1080 " (cutoff:3.500A) Processing helix chain 'F' and resid 1097 through 1114 removed outlier: 5.003A pdb=" N THR F1103 " --> pdb=" O CYS F1099 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ILE F1104 " --> pdb=" O PHE F1100 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA F1105 " --> pdb=" O CYS F1101 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TYR F1107 " --> pdb=" O THR F1103 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL F1110 " --> pdb=" O ALA F1106 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N HIS F1114 " --> pdb=" O VAL F1110 " (cutoff:3.500A) Processing helix chain 'F' and resid 1192 through 1196 Processing helix chain 'G' and resid 114 through 118 removed outlier: 3.844A pdb=" N GLY G 117 " --> pdb=" O ALA G 114 " (cutoff:3.500A) Processing helix chain 'G' and resid 152 through 155 Processing helix chain 'G' and resid 208 through 212 removed outlier: 3.868A pdb=" N ASN G 211 " --> pdb=" O SER G 208 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE G 212 " --> pdb=" O SER G 209 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 208 through 212' Processing helix chain 'G' and resid 214 through 219 removed outlier: 4.228A pdb=" N GLN G 218 " --> pdb=" O GLY G 215 " (cutoff:3.500A) Processing helix chain 'G' and resid 221 through 231 removed outlier: 4.310A pdb=" N CYS G 225 " --> pdb=" O LEU G 221 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N LEU G 228 " --> pdb=" O GLN G 224 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N LYS G 229 " --> pdb=" O CYS G 225 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR G 231 " --> pdb=" O LEU G 227 " (cutoff:3.500A) Processing helix chain 'G' and resid 232 through 235 Processing helix chain 'G' and resid 243 through 251 removed outlier: 3.558A pdb=" N GLU G 251 " --> pdb=" O VAL G 247 " (cutoff:3.500A) Processing helix chain 'G' and resid 261 through 263 No H-bonds generated for 'chain 'G' and resid 261 through 263' Processing helix chain 'G' and resid 264 through 277 removed outlier: 3.754A pdb=" N TYR G 271 " --> pdb=" O ALA G 267 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG G 273 " --> pdb=" O LEU G 269 " (cutoff:3.500A) Processing helix chain 'G' and resid 344 through 348 Processing helix chain 'G' and resid 514 through 517 Processing helix chain 'G' and resid 545 through 550 Processing helix chain 'G' and resid 551 through 553 No H-bonds generated for 'chain 'G' and resid 551 through 553' Processing helix chain 'G' and resid 575 through 584 removed outlier: 4.723A pdb=" N PHE G 579 " --> pdb=" O ARG G 575 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLU G 581 " --> pdb=" O THR G 577 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N CYS G 584 " --> pdb=" O SER G 580 " (cutoff:3.500A) Processing helix chain 'G' and resid 585 through 588 Processing helix chain 'G' and resid 589 through 596 removed outlier: 5.126A pdb=" N ALA G 594 " --> pdb=" O THR G 591 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N HIS G 596 " --> pdb=" O GLU G 593 " (cutoff:3.500A) Processing helix chain 'G' and resid 601 through 613 removed outlier: 3.538A pdb=" N CYS G 608 " --> pdb=" O TYR G 604 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG G 609 " --> pdb=" O LEU G 605 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N TYR G 610 " --> pdb=" O ARG G 606 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N CYS G 613 " --> pdb=" O ARG G 609 " (cutoff:3.500A) Processing helix chain 'G' and resid 617 through 624 removed outlier: 3.594A pdb=" N CYS G 621 " --> pdb=" O ASP G 617 " (cutoff:3.500A) Processing helix chain 'G' and resid 625 through 634 removed outlier: 3.561A pdb=" N TYR G 629 " --> pdb=" O ALA G 625 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA G 632 " --> pdb=" O SER G 628 " (cutoff:3.500A) Processing helix chain 'G' and resid 668 through 674 removed outlier: 4.236A pdb=" N LEU G 672 " --> pdb=" O THR G 668 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N SER G 673 " --> pdb=" O CYS G 669 " (cutoff:3.500A) Processing helix chain 'H' and resid 1017 through 1022 Processing helix chain 'H' and resid 1023 through 1026 removed outlier: 3.906A pdb=" N LYS H1026 " --> pdb=" O ASN H1023 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 1023 through 1026' Processing helix chain 'H' and resid 1049 through 1060 removed outlier: 3.524A pdb=" N THR H1054 " --> pdb=" O ILE H1050 " (cutoff:3.500A) Processing helix chain 'H' and resid 1061 through 1064 Processing helix chain 'H' and resid 1068 through 1073 removed outlier: 3.877A pdb=" N LYS H1073 " --> pdb=" O GLN H1069 " (cutoff:3.500A) Processing helix chain 'H' and resid 1077 through 1091 removed outlier: 3.527A pdb=" N VAL H1083 " --> pdb=" O PRO H1079 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N CYS H1084 " --> pdb=" O TYR H1080 " (cutoff:3.500A) Processing helix chain 'H' and resid 1097 through 1114 removed outlier: 5.001A pdb=" N THR H1103 " --> pdb=" O CYS H1099 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ILE H1104 " --> pdb=" O PHE H1100 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA H1105 " --> pdb=" O CYS H1101 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TYR H1107 " --> pdb=" O THR H1103 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL H1110 " --> pdb=" O ALA H1106 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N HIS H1114 " --> pdb=" O VAL H1110 " (cutoff:3.500A) Processing helix chain 'H' and resid 1192 through 1196 Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 37 removed outlier: 3.520A pdb=" N PHE A 146 " --> pdb=" O LEU A 37 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 44 removed outlier: 3.537A pdb=" N TYR A 51 " --> pdb=" O VAL A 43 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 58 through 63 removed outlier: 6.835A pdb=" N ILE A 72 " --> pdb=" O LEU A 61 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 102 through 104 removed outlier: 4.650A pdb=" N VAL A 102 " --> pdb=" O VAL A 109 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 300 through 301 removed outlier: 3.769A pdb=" N GLU A 300 " --> pdb=" O SER A 330 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 350 through 352 Processing sheet with id=AA7, first strand: chain 'A' and resid 362 through 364 Processing sheet with id=AA8, first strand: chain 'A' and resid 389 through 391 Processing sheet with id=AA9, first strand: chain 'A' and resid 411 through 416 removed outlier: 5.615A pdb=" N GLN A 411 " --> pdb=" O THR A 429 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N THR A 429 " --> pdb=" O GLN A 411 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N LEU A 413 " --> pdb=" O ILE A 427 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N ILE A 427 " --> pdb=" O LEU A 413 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA A 415 " --> pdb=" O ILE A 425 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N SER A 443 " --> pdb=" O GLU A 428 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N VAL A 430 " --> pdb=" O THR A 441 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N THR A 441 " --> pdb=" O VAL A 430 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 465 through 466 Processing sheet with id=AB2, first strand: chain 'A' and resid 480 through 484 Processing sheet with id=AB3, first strand: chain 'A' and resid 498 through 499 removed outlier: 3.544A pdb=" N LYS A 511 " --> pdb=" O GLN A 499 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 536 through 537 removed outlier: 3.525A pdb=" N THR A 537 " --> pdb=" O LEU A 541 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N LEU A 541 " --> pdb=" O THR A 537 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 657 through 662 removed outlier: 3.834A pdb=" N CYS A 661 " --> pdb=" O LEU A 684 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N LEU A 684 " --> pdb=" O CYS A 661 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 694 through 695 Processing sheet with id=AB7, first strand: chain 'A' and resid 709 through 711 Processing sheet with id=AB8, first strand: chain 'A' and resid 728 through 731 removed outlier: 3.736A pdb=" N MET A 728 " --> pdb=" O THR A 739 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 35 through 37 removed outlier: 3.520A pdb=" N PHE B 146 " --> pdb=" O LEU B 37 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 42 through 44 removed outlier: 3.536A pdb=" N TYR B 51 " --> pdb=" O VAL B 43 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.834A pdb=" N ILE B 72 " --> pdb=" O LEU B 61 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 103 through 104 Processing sheet with id=AC4, first strand: chain 'B' and resid 300 through 301 removed outlier: 3.769A pdb=" N GLU B 300 " --> pdb=" O SER B 330 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 350 through 352 Processing sheet with id=AC6, first strand: chain 'B' and resid 362 through 364 Processing sheet with id=AC7, first strand: chain 'B' and resid 389 through 391 Processing sheet with id=AC8, first strand: chain 'B' and resid 411 through 416 removed outlier: 5.615A pdb=" N GLN B 411 " --> pdb=" O THR B 429 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N THR B 429 " --> pdb=" O GLN B 411 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N LEU B 413 " --> pdb=" O ILE B 427 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N ILE B 427 " --> pdb=" O LEU B 413 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA B 415 " --> pdb=" O ILE B 425 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N SER B 443 " --> pdb=" O GLU B 428 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N VAL B 430 " --> pdb=" O THR B 441 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N THR B 441 " --> pdb=" O VAL B 430 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 465 through 466 Processing sheet with id=AD1, first strand: chain 'B' and resid 480 through 484 Processing sheet with id=AD2, first strand: chain 'B' and resid 498 through 499 removed outlier: 3.544A pdb=" N LYS B 511 " --> pdb=" O GLN B 499 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 536 through 537 removed outlier: 3.525A pdb=" N THR B 537 " --> pdb=" O LEU B 541 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N LEU B 541 " --> pdb=" O THR B 537 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'B' and resid 657 through 662 removed outlier: 3.835A pdb=" N CYS B 661 " --> pdb=" O LEU B 684 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N LEU B 684 " --> pdb=" O CYS B 661 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 694 through 695 Processing sheet with id=AD6, first strand: chain 'B' and resid 709 through 711 Processing sheet with id=AD7, first strand: chain 'B' and resid 728 through 731 removed outlier: 3.736A pdb=" N MET B 728 " --> pdb=" O THR B 739 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 772 through 773 Processing sheet with id=AD9, first strand: chain 'C' and resid 841 through 844 Processing sheet with id=AE1, first strand: chain 'C' and resid 865 through 866 removed outlier: 6.147A pdb=" N LEU C 970 " --> pdb=" O LEU C 966 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 875 through 876 Processing sheet with id=AE3, first strand: chain 'C' and resid 890 through 895 removed outlier: 3.731A pdb=" N LEU C 893 " --> pdb=" O ILE C 907 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N ILE C 907 " --> pdb=" O LEU C 893 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N THR C 926 " --> pdb=" O LEU C 908 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LYS C 912 " --> pdb=" O LYS C 922 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N LYS C 922 " --> pdb=" O LYS C 912 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N GLU C 933 " --> pdb=" O LYS C 944 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLU C 940 " --> pdb=" O PHE C 937 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 1144 through 1151 removed outlier: 3.626A pdb=" N GLY C1172 " --> pdb=" O ASN C1147 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N CYS C1149 " --> pdb=" O VAL C1170 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N VAL C1170 " --> pdb=" O CYS C1149 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 1182 through 1183 Processing sheet with id=AE6, first strand: chain 'D' and resid 772 through 773 Processing sheet with id=AE7, first strand: chain 'D' and resid 841 through 844 Processing sheet with id=AE8, first strand: chain 'D' and resid 865 through 866 removed outlier: 6.148A pdb=" N LEU D 970 " --> pdb=" O LEU D 966 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 875 through 876 Processing sheet with id=AF1, first strand: chain 'D' and resid 890 through 895 removed outlier: 3.731A pdb=" N LEU D 893 " --> pdb=" O ILE D 907 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N ILE D 907 " --> pdb=" O LEU D 893 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N THR D 926 " --> pdb=" O LEU D 908 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LYS D 912 " --> pdb=" O LYS D 922 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N LYS D 922 " --> pdb=" O LYS D 912 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N GLU D 933 " --> pdb=" O LYS D 944 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLU D 940 " --> pdb=" O PHE D 937 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 1144 through 1146 Processing sheet with id=AF3, first strand: chain 'D' and resid 1150 through 1151 Processing sheet with id=AF4, first strand: chain 'D' and resid 1182 through 1183 Processing sheet with id=AF5, first strand: chain 'E' and resid 35 through 37 removed outlier: 3.520A pdb=" N PHE E 146 " --> pdb=" O LEU E 37 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'E' and resid 42 through 44 removed outlier: 3.536A pdb=" N TYR E 51 " --> pdb=" O VAL E 43 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'E' and resid 58 through 63 removed outlier: 6.834A pdb=" N ILE E 72 " --> pdb=" O LEU E 61 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'E' and resid 103 through 104 Processing sheet with id=AF9, first strand: chain 'E' and resid 300 through 301 removed outlier: 3.769A pdb=" N GLU E 300 " --> pdb=" O SER E 330 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'E' and resid 350 through 352 Processing sheet with id=AG2, first strand: chain 'E' and resid 362 through 364 Processing sheet with id=AG3, first strand: chain 'E' and resid 389 through 391 Processing sheet with id=AG4, first strand: chain 'E' and resid 411 through 416 removed outlier: 5.615A pdb=" N GLN E 411 " --> pdb=" O THR E 429 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N THR E 429 " --> pdb=" O GLN E 411 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N LEU E 413 " --> pdb=" O ILE E 427 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N ILE E 427 " --> pdb=" O LEU E 413 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA E 415 " --> pdb=" O ILE E 425 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N SER E 443 " --> pdb=" O GLU E 428 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N VAL E 430 " --> pdb=" O THR E 441 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N THR E 441 " --> pdb=" O VAL E 430 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'E' and resid 465 through 466 Processing sheet with id=AG6, first strand: chain 'E' and resid 480 through 484 Processing sheet with id=AG7, first strand: chain 'E' and resid 498 through 499 removed outlier: 3.545A pdb=" N LYS E 511 " --> pdb=" O GLN E 499 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'E' and resid 536 through 537 removed outlier: 3.525A pdb=" N THR E 537 " --> pdb=" O LEU E 541 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N LEU E 541 " --> pdb=" O THR E 537 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG8 Processing sheet with id=AG9, first strand: chain 'E' and resid 657 through 662 removed outlier: 3.834A pdb=" N CYS E 661 " --> pdb=" O LEU E 684 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N LEU E 684 " --> pdb=" O CYS E 661 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'E' and resid 694 through 695 Processing sheet with id=AH2, first strand: chain 'E' and resid 709 through 711 Processing sheet with id=AH3, first strand: chain 'E' and resid 728 through 731 removed outlier: 3.736A pdb=" N MET E 728 " --> pdb=" O THR E 739 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'F' and resid 772 through 773 Processing sheet with id=AH5, first strand: chain 'F' and resid 841 through 844 Processing sheet with id=AH6, first strand: chain 'F' and resid 865 through 866 removed outlier: 6.147A pdb=" N LEU F 970 " --> pdb=" O LEU F 966 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'F' and resid 875 through 876 Processing sheet with id=AH8, first strand: chain 'F' and resid 890 through 895 removed outlier: 3.731A pdb=" N LEU F 893 " --> pdb=" O ILE F 907 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N ILE F 907 " --> pdb=" O LEU F 893 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N THR F 926 " --> pdb=" O LEU F 908 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LYS F 912 " --> pdb=" O LYS F 922 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N LYS F 922 " --> pdb=" O LYS F 912 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N GLU F 933 " --> pdb=" O LYS F 944 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLU F 940 " --> pdb=" O PHE F 937 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'F' and resid 1144 through 1151 removed outlier: 3.523A pdb=" N GLY F1172 " --> pdb=" O ASN F1147 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N CYS F1149 " --> pdb=" O VAL F1170 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N VAL F1170 " --> pdb=" O CYS F1149 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'F' and resid 1182 through 1183 Processing sheet with id=AI2, first strand: chain 'G' and resid 35 through 37 removed outlier: 3.521A pdb=" N PHE G 146 " --> pdb=" O LEU G 37 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'G' and resid 42 through 44 removed outlier: 3.536A pdb=" N TYR G 51 " --> pdb=" O VAL G 43 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'G' and resid 58 through 63 removed outlier: 6.834A pdb=" N ILE G 72 " --> pdb=" O LEU G 61 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'G' and resid 103 through 104 Processing sheet with id=AI6, first strand: chain 'G' and resid 300 through 301 removed outlier: 3.769A pdb=" N GLU G 300 " --> pdb=" O SER G 330 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'G' and resid 350 through 352 Processing sheet with id=AI8, first strand: chain 'G' and resid 362 through 364 Processing sheet with id=AI9, first strand: chain 'G' and resid 389 through 391 Processing sheet with id=AJ1, first strand: chain 'G' and resid 411 through 416 removed outlier: 5.615A pdb=" N GLN G 411 " --> pdb=" O THR G 429 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N THR G 429 " --> pdb=" O GLN G 411 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N LEU G 413 " --> pdb=" O ILE G 427 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N ILE G 427 " --> pdb=" O LEU G 413 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA G 415 " --> pdb=" O ILE G 425 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N SER G 443 " --> pdb=" O GLU G 428 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N VAL G 430 " --> pdb=" O THR G 441 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N THR G 441 " --> pdb=" O VAL G 430 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'G' and resid 465 through 466 Processing sheet with id=AJ3, first strand: chain 'G' and resid 480 through 484 Processing sheet with id=AJ4, first strand: chain 'G' and resid 498 through 499 removed outlier: 3.546A pdb=" N LYS G 511 " --> pdb=" O GLN G 499 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'G' and resid 536 through 537 removed outlier: 3.525A pdb=" N THR G 537 " --> pdb=" O LEU G 541 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N LEU G 541 " --> pdb=" O THR G 537 " (cutoff:3.500A) No H-bonds generated for sheet with id=AJ5 Processing sheet with id=AJ6, first strand: chain 'G' and resid 657 through 662 removed outlier: 3.835A pdb=" N CYS G 661 " --> pdb=" O LEU G 684 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N LEU G 684 " --> pdb=" O CYS G 661 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'G' and resid 694 through 695 Processing sheet with id=AJ8, first strand: chain 'G' and resid 709 through 711 Processing sheet with id=AJ9, first strand: chain 'G' and resid 728 through 731 removed outlier: 3.737A pdb=" N MET G 728 " --> pdb=" O THR G 739 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'H' and resid 772 through 773 Processing sheet with id=AK2, first strand: chain 'H' and resid 841 through 844 Processing sheet with id=AK3, first strand: chain 'H' and resid 865 through 866 removed outlier: 6.148A pdb=" N LEU H 970 " --> pdb=" O LEU H 966 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'H' and resid 875 through 876 Processing sheet with id=AK5, first strand: chain 'H' and resid 890 through 895 removed outlier: 3.731A pdb=" N LEU H 893 " --> pdb=" O ILE H 907 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N ILE H 907 " --> pdb=" O LEU H 893 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N THR H 926 " --> pdb=" O LEU H 908 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LYS H 912 " --> pdb=" O LYS H 922 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N LYS H 922 " --> pdb=" O LYS H 912 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N GLU H 933 " --> pdb=" O LYS H 944 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLU H 940 " --> pdb=" O PHE H 937 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'H' and resid 1144 through 1151 removed outlier: 3.605A pdb=" N GLY H1172 " --> pdb=" O ASN H1147 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N CYS H1149 " --> pdb=" O VAL H1170 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N VAL H1170 " --> pdb=" O CYS H1149 " (cutoff:3.500A) Processing sheet with id=AK7, first strand: chain 'H' and resid 1182 through 1183 744 hydrogen bonds defined for protein. 1766 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 16.96 Time building geometry restraints manager: 16.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 12331 1.34 - 1.47: 8708 1.47 - 1.59: 15693 1.59 - 1.71: 0 1.71 - 1.84: 640 Bond restraints: 37372 Sorted by residual: bond pdb=" N ASN B 156 " pdb=" CA ASN B 156 " ideal model delta sigma weight residual 1.457 1.499 -0.042 1.29e-02 6.01e+03 1.04e+01 bond pdb=" N ASN A 156 " pdb=" CA ASN A 156 " ideal model delta sigma weight residual 1.457 1.497 -0.039 1.29e-02 6.01e+03 9.25e+00 bond pdb=" N PHE A 155 " pdb=" CA PHE A 155 " ideal model delta sigma weight residual 1.454 1.493 -0.040 1.34e-02 5.57e+03 8.77e+00 bond pdb=" N CYS D 858 " pdb=" CA CYS D 858 " ideal model delta sigma weight residual 1.452 1.488 -0.036 1.22e-02 6.72e+03 8.63e+00 bond pdb=" N THR D 859 " pdb=" CA THR D 859 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.19e-02 7.06e+03 8.25e+00 ... (remaining 37367 not shown) Histogram of bond angle deviations from ideal: 98.35 - 105.52: 912 105.52 - 112.70: 18319 112.70 - 119.87: 13769 119.87 - 127.04: 17234 127.04 - 134.21: 486 Bond angle restraints: 50720 Sorted by residual: angle pdb=" N ASN B 156 " pdb=" CA ASN B 156 " pdb=" CB ASN B 156 " ideal model delta sigma weight residual 110.49 116.86 -6.37 1.69e+00 3.50e-01 1.42e+01 angle pdb=" CA THR B 101 " pdb=" C THR B 101 " pdb=" O THR B 101 " ideal model delta sigma weight residual 122.64 118.15 4.49 1.25e+00 6.40e-01 1.29e+01 angle pdb=" CA LYS H 920 " pdb=" CB LYS H 920 " pdb=" CG LYS H 920 " ideal model delta sigma weight residual 114.10 121.19 -7.09 2.00e+00 2.50e-01 1.26e+01 angle pdb=" CA LYS C 920 " pdb=" CB LYS C 920 " pdb=" CG LYS C 920 " ideal model delta sigma weight residual 114.10 121.18 -7.08 2.00e+00 2.50e-01 1.25e+01 angle pdb=" CA LYS D 920 " pdb=" CB LYS D 920 " pdb=" CG LYS D 920 " ideal model delta sigma weight residual 114.10 121.18 -7.08 2.00e+00 2.50e-01 1.25e+01 ... (remaining 50715 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 21888 17.83 - 35.66: 1152 35.66 - 53.48: 290 53.48 - 71.31: 68 71.31 - 89.14: 18 Dihedral angle restraints: 23416 sinusoidal: 9724 harmonic: 13692 Sorted by residual: dihedral pdb=" CB CYS A 312 " pdb=" SG CYS A 312 " pdb=" SG CYS A 348 " pdb=" CB CYS A 348 " ideal model delta sinusoidal sigma weight residual 93.00 173.76 -80.76 1 1.00e+01 1.00e-02 8.06e+01 dihedral pdb=" CB CYS G 312 " pdb=" SG CYS G 312 " pdb=" SG CYS G 348 " pdb=" CB CYS G 348 " ideal model delta sinusoidal sigma weight residual 93.00 173.76 -80.76 1 1.00e+01 1.00e-02 8.06e+01 dihedral pdb=" CB CYS B 312 " pdb=" SG CYS B 312 " pdb=" SG CYS B 348 " pdb=" CB CYS B 348 " ideal model delta sinusoidal sigma weight residual 93.00 173.74 -80.74 1 1.00e+01 1.00e-02 8.06e+01 ... (remaining 23413 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.115: 5349 0.115 - 0.230: 196 0.230 - 0.346: 2 0.346 - 0.461: 1 0.461 - 0.576: 4 Chirality restraints: 5552 Sorted by residual: chirality pdb=" C1 NAG E 802 " pdb=" ND2 ASN E 99 " pdb=" C2 NAG E 802 " pdb=" O5 NAG E 802 " both_signs ideal model delta sigma weight residual False -2.40 -1.82 -0.58 2.00e-01 2.50e+01 8.29e+00 chirality pdb=" C1 NAG B 801 " pdb=" ND2 ASN B 156 " pdb=" C2 NAG B 801 " pdb=" O5 NAG B 801 " both_signs ideal model delta sigma weight residual False -2.40 -2.96 0.56 2.00e-01 2.50e+01 7.89e+00 chirality pdb=" C1 NAG D1302 " pdb=" ND2 ASN D 857 " pdb=" C2 NAG D1302 " pdb=" O5 NAG D1302 " both_signs ideal model delta sigma weight residual False -2.40 -1.87 -0.53 2.00e-01 2.50e+01 6.98e+00 ... (remaining 5549 not shown) Planarity restraints: 6752 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 802 " -0.290 2.00e-02 2.50e+03 2.44e-01 7.43e+02 pdb=" C7 NAG E 802 " 0.075 2.00e-02 2.50e+03 pdb=" C8 NAG E 802 " -0.185 2.00e-02 2.50e+03 pdb=" N2 NAG E 802 " 0.416 2.00e-02 2.50e+03 pdb=" O7 NAG E 802 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D1302 " -0.277 2.00e-02 2.50e+03 2.34e-01 6.83e+02 pdb=" C7 NAG D1302 " 0.072 2.00e-02 2.50e+03 pdb=" C8 NAG D1302 " -0.179 2.00e-02 2.50e+03 pdb=" N2 NAG D1302 " 0.399 2.00e-02 2.50e+03 pdb=" O7 NAG D1302 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 802 " -0.239 2.00e-02 2.50e+03 2.02e-01 5.12e+02 pdb=" C7 NAG A 802 " 0.053 2.00e-02 2.50e+03 pdb=" C8 NAG A 802 " 0.039 2.00e-02 2.50e+03 pdb=" N2 NAG A 802 " 0.331 2.00e-02 2.50e+03 pdb=" O7 NAG A 802 " -0.184 2.00e-02 2.50e+03 ... (remaining 6749 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 376 2.60 - 3.17: 32626 3.17 - 3.75: 52843 3.75 - 4.32: 73889 4.32 - 4.90: 120978 Nonbonded interactions: 280712 Sorted by model distance: nonbonded pdb=" OG SER D1009 " pdb=" OD1 ASN D1011 " model vdw 2.022 2.440 nonbonded pdb=" OG SER H1009 " pdb=" OD1 ASN H1011 " model vdw 2.022 2.440 nonbonded pdb=" OG SER F1009 " pdb=" OD1 ASN F1011 " model vdw 2.023 2.440 nonbonded pdb=" OG SER C1009 " pdb=" OD1 ASN C1011 " model vdw 2.023 2.440 nonbonded pdb=" O PRO F1197 " pdb=" OG SER F1208 " model vdw 2.128 2.440 ... (remaining 280707 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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: 0.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.060 Extract box with map and model: 5.130 Check model and map are aligned: 0.570 Set scattering table: 0.370 Process input model: 111.230 Find NCS groups from input model: 2.650 Set up NCS constraints: 0.410 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:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 123.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7193 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 37372 Z= 0.493 Angle : 0.929 9.609 50720 Z= 0.484 Chirality : 0.055 0.576 5552 Planarity : 0.008 0.244 6732 Dihedral : 10.509 89.139 13952 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.25 % Allowed : 10.00 % Favored : 89.75 % Rotamer: Outliers : 0.29 % Allowed : 2.59 % Favored : 97.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -4.59 (0.10), residues: 4744 helix: -4.22 (0.11), residues: 616 sheet: -3.76 (0.16), residues: 764 loop : -2.81 (0.09), residues: 3364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP H 974 HIS 0.009 0.002 HIS C1109 PHE 0.027 0.003 PHE G 535 TYR 0.018 0.002 TYR A 527 ARG 0.010 0.001 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9488 Ramachandran restraints generated. 4744 Oldfield, 0 Emsley, 4744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9488 Ramachandran restraints generated. 4744 Oldfield, 0 Emsley, 4744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1063 residues out of total 4112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 1055 time to evaluate : 4.147 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 730 TYR cc_start: 0.6264 (p90) cc_final: 0.5912 (p90) REVERT: B 106 ASP cc_start: 0.7402 (p0) cc_final: 0.6918 (p0) REVERT: B 199 TRP cc_start: 0.7396 (m-90) cc_final: 0.6813 (m-90) REVERT: B 547 GLU cc_start: 0.7139 (mp0) cc_final: 0.6601 (mp0) REVERT: B 560 GLN cc_start: 0.7500 (mt0) cc_final: 0.7279 (mt0) REVERT: B 683 CYS cc_start: 0.6344 (t) cc_final: 0.6100 (p) REVERT: B 693 LEU cc_start: 0.8391 (mm) cc_final: 0.8040 (mt) REVERT: D 951 THR cc_start: 0.7293 (p) cc_final: 0.6908 (t) REVERT: E 526 ASN cc_start: 0.8738 (m-40) cc_final: 0.8496 (m-40) REVERT: E 560 GLN cc_start: 0.7401 (mt0) cc_final: 0.7094 (mt0) REVERT: F 868 SER cc_start: 0.8490 (t) cc_final: 0.8290 (m) REVERT: F 952 HIS cc_start: 0.6728 (m90) cc_final: 0.6448 (m-70) REVERT: G 736 MET cc_start: 0.6097 (tpt) cc_final: 0.5840 (tpt) REVERT: G 740 MET cc_start: 0.3567 (mmm) cc_final: 0.3249 (tmm) REVERT: H 771 MET cc_start: 0.5896 (pmt) cc_final: 0.5685 (pmm) REVERT: H 936 LEU cc_start: 0.7650 (pp) cc_final: 0.7285 (pp) outliers start: 8 outliers final: 3 residues processed: 1061 average time/residue: 0.5925 time to fit residues: 988.0900 Evaluate side-chains 428 residues out of total 4112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 425 time to evaluate : 4.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 PHE Chi-restraints excluded: chain B residue 97 PHE Chi-restraints excluded: chain H residue 850 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 398 optimal weight: 4.9990 chunk 357 optimal weight: 0.1980 chunk 198 optimal weight: 10.0000 chunk 122 optimal weight: 0.5980 chunk 241 optimal weight: 4.9990 chunk 191 optimal weight: 9.9990 chunk 369 optimal weight: 5.9990 chunk 143 optimal weight: 30.0000 chunk 224 optimal weight: 2.9990 chunk 275 optimal weight: 0.7980 chunk 428 optimal weight: 7.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 452 HIS A 565 GLN ** B 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 419 GLN B 452 HIS C 794 ASN ** C 852 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 977 HIS C1003 GLN ** C1134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1168 GLN C1188 GLN D 901 ASN D1159 HIS E 147 GLN E 452 HIS ** E 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 556 HIS E 660 GLN F 977 HIS F1053 GLN A F1113 GLN ** F1174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 107 GLN ** G 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 419 GLN G 421 HIS H 977 HIS H 986 GLN H1047 HIS H1134 ASN H1168 GLN ** H1174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.3321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 37372 Z= 0.239 Angle : 0.724 9.264 50720 Z= 0.366 Chirality : 0.048 0.268 5552 Planarity : 0.005 0.052 6732 Dihedral : 6.398 59.936 5561 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.92 % Favored : 93.06 % Rotamer: Outliers : 2.59 % Allowed : 9.12 % Favored : 88.28 % 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: -3.64 (0.11), residues: 4744 helix: -2.94 (0.17), residues: 640 sheet: -3.01 (0.16), residues: 884 loop : -2.23 (0.10), residues: 3220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP H1144 HIS 0.015 0.001 HIS B 452 PHE 0.021 0.002 PHE H 878 TYR 0.027 0.002 TYR H 897 ARG 0.005 0.001 ARG A 481 *********************** 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 592 residues out of total 4112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 490 time to evaluate : 4.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 PHE cc_start: 0.8199 (m-80) cc_final: 0.7978 (m-80) REVERT: A 226 GLN cc_start: 0.6536 (OUTLIER) cc_final: 0.5646 (mp10) REVERT: A 280 MET cc_start: 0.7529 (tmm) cc_final: 0.7314 (tmm) REVERT: A 735 PHE cc_start: 0.7264 (t80) cc_final: 0.7014 (t80) REVERT: A 740 MET cc_start: 0.2968 (mmm) cc_final: 0.2547 (mpp) REVERT: B 77 GLN cc_start: 0.6963 (tp40) cc_final: 0.6572 (tt0) REVERT: B 199 TRP cc_start: 0.7357 (m-90) cc_final: 0.6991 (m-90) REVERT: B 217 MET cc_start: 0.3900 (tpp) cc_final: 0.2268 (mpp) REVERT: B 497 ASP cc_start: 0.7582 (m-30) cc_final: 0.7361 (m-30) REVERT: B 681 GLU cc_start: 0.7295 (mm-30) cc_final: 0.7086 (mp0) REVERT: B 693 LEU cc_start: 0.8527 (mm) cc_final: 0.8169 (mt) REVERT: C 814 MET cc_start: 0.5601 (ptp) cc_final: 0.4937 (mtp) REVERT: E 479 ASP cc_start: 0.7327 (OUTLIER) cc_final: 0.7081 (t0) REVERT: E 537 THR cc_start: 0.7798 (t) cc_final: 0.7416 (p) REVERT: E 541 LEU cc_start: 0.9021 (tp) cc_final: 0.8775 (tp) REVERT: E 740 MET cc_start: 0.6839 (mmt) cc_final: 0.6543 (mmt) REVERT: F 826 ARG cc_start: 0.5933 (mtm110) cc_final: 0.5082 (ptm160) REVERT: F 952 HIS cc_start: 0.6733 (m90) cc_final: 0.6404 (m-70) REVERT: G 500 MET cc_start: 0.8618 (mmm) cc_final: 0.8027 (mtp) REVERT: G 636 ARG cc_start: 0.7698 (mmt90) cc_final: 0.7466 (mmm-85) REVERT: G 740 MET cc_start: 0.4298 (mmm) cc_final: 0.3431 (tmm) outliers start: 102 outliers final: 52 residues processed: 558 average time/residue: 0.4835 time to fit residues: 443.1446 Evaluate side-chains 392 residues out of total 4112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 338 time to evaluate : 4.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 PHE Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 226 GLN Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain A residue 435 ASP Chi-restraints excluded: chain A residue 526 ASN Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 661 CYS Chi-restraints excluded: chain A residue 669 CYS Chi-restraints excluded: chain B residue 97 PHE Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 526 ASN Chi-restraints excluded: chain B residue 602 LEU Chi-restraints excluded: chain C residue 870 ILE Chi-restraints excluded: chain C residue 911 ASN Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 938 ASP Chi-restraints excluded: chain C residue 1081 LEU Chi-restraints excluded: chain D residue 862 VAL Chi-restraints excluded: chain D residue 870 ILE Chi-restraints excluded: chain D residue 901 ASN Chi-restraints excluded: chain D residue 911 ASN Chi-restraints excluded: chain E residue 69 SER Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 159 CYS Chi-restraints excluded: chain E residue 394 SER Chi-restraints excluded: chain E residue 479 ASP Chi-restraints excluded: chain F residue 841 THR Chi-restraints excluded: chain F residue 842 VAL Chi-restraints excluded: chain F residue 862 VAL Chi-restraints excluded: chain F residue 870 ILE Chi-restraints excluded: chain F residue 937 PHE Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 158 THR Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 265 CYS Chi-restraints excluded: chain G residue 348 CYS Chi-restraints excluded: chain G residue 394 SER Chi-restraints excluded: chain G residue 526 ASN Chi-restraints excluded: chain G residue 668 THR Chi-restraints excluded: chain G residue 669 CYS Chi-restraints excluded: chain G residue 695 MET Chi-restraints excluded: chain G residue 709 CYS Chi-restraints excluded: chain H residue 796 ASP Chi-restraints excluded: chain H residue 850 VAL Chi-restraints excluded: chain H residue 862 VAL Chi-restraints excluded: chain H residue 870 ILE Chi-restraints excluded: chain H residue 934 ILE Chi-restraints excluded: chain H residue 938 ASP Chi-restraints excluded: chain H residue 1019 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 238 optimal weight: 9.9990 chunk 133 optimal weight: 8.9990 chunk 356 optimal weight: 10.0000 chunk 291 optimal weight: 7.9990 chunk 118 optimal weight: 5.9990 chunk 429 optimal weight: 50.0000 chunk 463 optimal weight: 6.9990 chunk 382 optimal weight: 4.9990 chunk 425 optimal weight: 8.9990 chunk 146 optimal weight: 50.0000 chunk 344 optimal weight: 10.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 ASN ** A 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 313 GLN A 393 GLN A 419 GLN A 737 HIS B 95 HIS B 147 GLN B 393 GLN B 452 HIS C 794 ASN C 852 GLN C1072 ASN C1113 GLN ** C1174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1053 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** D1069 GLN D1072 ASN D1159 HIS ** D1174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1221 HIS E 78 ASN E 226 GLN E 322 GLN E 352 HIS E 452 HIS ** E 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F1013 GLN ** F1174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 107 GLN ** G 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 313 GLN ** G 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 393 GLN H1072 ASN H1113 GLN ** H1134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.4985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.083 37372 Z= 0.558 Angle : 0.897 14.817 50720 Z= 0.455 Chirality : 0.056 0.304 5552 Planarity : 0.006 0.063 6732 Dihedral : 6.996 59.420 5561 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.02 % Allowed : 10.72 % Favored : 89.26 % Rotamer: Outliers : 3.38 % Allowed : 11.99 % Favored : 84.64 % 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: -3.51 (0.11), residues: 4744 helix: -2.64 (0.17), residues: 676 sheet: -2.91 (0.16), residues: 876 loop : -2.18 (0.10), residues: 3192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D 974 HIS 0.015 0.002 HIS B 452 PHE 0.043 0.004 PHE F 999 TYR 0.061 0.003 TYR B 710 ARG 0.009 0.001 ARG E 643 *********************** 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 501 residues out of total 4112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 367 time to evaluate : 4.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ASN cc_start: 0.5861 (OUTLIER) cc_final: 0.5602 (m-40) REVERT: A 185 TYR cc_start: 0.8512 (OUTLIER) cc_final: 0.7338 (t80) REVERT: A 320 MET cc_start: 0.5993 (tpt) cc_final: 0.5539 (tpt) REVERT: A 619 ARG cc_start: 0.6881 (mmm160) cc_final: 0.6558 (mpp80) REVERT: A 728 MET cc_start: 0.5785 (tpp) cc_final: 0.5438 (tpp) REVERT: B 199 TRP cc_start: 0.7619 (m-90) cc_final: 0.7155 (m-90) REVERT: B 483 GLN cc_start: 0.8182 (OUTLIER) cc_final: 0.7661 (pt0) REVERT: B 497 ASP cc_start: 0.7650 (m-30) cc_final: 0.7436 (m-30) REVERT: B 499 GLN cc_start: 0.7980 (OUTLIER) cc_final: 0.7748 (tt0) REVERT: B 500 MET cc_start: 0.8859 (mmt) cc_final: 0.8589 (mtt) REVERT: C 771 MET cc_start: 0.5416 (ptp) cc_final: 0.4872 (mtt) REVERT: C 814 MET cc_start: 0.5354 (ptp) cc_final: 0.4683 (mtp) REVERT: C 847 ASN cc_start: 0.7787 (OUTLIER) cc_final: 0.7456 (t0) REVERT: C 854 ARG cc_start: 0.5501 (OUTLIER) cc_final: 0.5051 (ttm110) REVERT: C 911 ASN cc_start: 0.8736 (OUTLIER) cc_final: 0.8503 (p0) REVERT: D 814 MET cc_start: 0.6526 (ptm) cc_final: 0.6058 (ptm) REVERT: E 185 TYR cc_start: 0.8590 (OUTLIER) cc_final: 0.8147 (t80) REVERT: E 384 CYS cc_start: 0.6999 (OUTLIER) cc_final: 0.6722 (m) REVERT: E 479 ASP cc_start: 0.7346 (OUTLIER) cc_final: 0.7121 (t0) REVERT: E 500 MET cc_start: 0.8742 (mmt) cc_final: 0.8358 (mtt) REVERT: E 722 PHE cc_start: 0.8002 (OUTLIER) cc_final: 0.7378 (t80) REVERT: F 826 ARG cc_start: 0.6236 (mtm110) cc_final: 0.5602 (ptm160) REVERT: G 282 LEU cc_start: 0.7057 (pt) cc_final: 0.6599 (mt) REVERT: G 740 MET cc_start: 0.5458 (mmm) cc_final: 0.4252 (tmm) outliers start: 134 outliers final: 89 residues processed: 472 average time/residue: 0.4805 time to fit residues: 375.5732 Evaluate side-chains 391 residues out of total 4112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 291 time to evaluate : 4.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 185 TYR Chi-restraints excluded: chain A residue 189 ASN Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 327 ASP Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain A residue 403 TYR Chi-restraints excluded: chain A residue 435 ASP Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 526 ASN Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 709 CYS Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 327 ASP Chi-restraints excluded: chain B residue 353 SER Chi-restraints excluded: chain B residue 384 CYS Chi-restraints excluded: chain B residue 480 LEU Chi-restraints excluded: chain B residue 483 GLN Chi-restraints excluded: chain B residue 499 GLN Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 526 ASN Chi-restraints excluded: chain B residue 602 LEU Chi-restraints excluded: chain B residue 669 CYS Chi-restraints excluded: chain B residue 722 PHE Chi-restraints excluded: chain C residue 841 THR Chi-restraints excluded: chain C residue 847 ASN Chi-restraints excluded: chain C residue 854 ARG Chi-restraints excluded: chain C residue 864 ASP Chi-restraints excluded: chain C residue 870 ILE Chi-restraints excluded: chain C residue 911 ASN Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 937 PHE Chi-restraints excluded: chain C residue 938 ASP Chi-restraints excluded: chain C residue 1081 LEU Chi-restraints excluded: chain C residue 1093 SER Chi-restraints excluded: chain C residue 1122 THR Chi-restraints excluded: chain D residue 862 VAL Chi-restraints excluded: chain D residue 870 ILE Chi-restraints excluded: chain D residue 911 ASN Chi-restraints excluded: chain D residue 915 SER Chi-restraints excluded: chain D residue 934 ILE Chi-restraints excluded: chain D residue 1122 THR Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 185 TYR Chi-restraints excluded: chain E residue 222 TRP Chi-restraints excluded: chain E residue 311 THR Chi-restraints excluded: chain E residue 326 VAL Chi-restraints excluded: chain E residue 338 ASP Chi-restraints excluded: chain E residue 384 CYS Chi-restraints excluded: chain E residue 394 SER Chi-restraints excluded: chain E residue 479 ASP Chi-restraints excluded: chain E residue 480 LEU Chi-restraints excluded: chain E residue 509 LEU Chi-restraints excluded: chain E residue 526 ASN Chi-restraints excluded: chain E residue 537 THR Chi-restraints excluded: chain E residue 558 ASP Chi-restraints excluded: chain E residue 616 SER Chi-restraints excluded: chain E residue 677 GLU Chi-restraints excluded: chain E residue 722 PHE Chi-restraints excluded: chain F residue 841 THR Chi-restraints excluded: chain F residue 853 ASP Chi-restraints excluded: chain F residue 862 VAL Chi-restraints excluded: chain F residue 870 ILE Chi-restraints excluded: chain F residue 915 SER Chi-restraints excluded: chain F residue 927 ILE Chi-restraints excluded: chain F residue 934 ILE Chi-restraints excluded: chain F residue 935 GLU Chi-restraints excluded: chain F residue 936 LEU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 106 ASP Chi-restraints excluded: chain G residue 158 THR Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 189 ASN Chi-restraints excluded: chain G residue 265 CYS Chi-restraints excluded: chain G residue 294 VAL Chi-restraints excluded: chain G residue 348 CYS Chi-restraints excluded: chain G residue 394 SER Chi-restraints excluded: chain G residue 526 ASN Chi-restraints excluded: chain G residue 669 CYS Chi-restraints excluded: chain G residue 710 TYR Chi-restraints excluded: chain H residue 796 ASP Chi-restraints excluded: chain H residue 850 VAL Chi-restraints excluded: chain H residue 861 HIS Chi-restraints excluded: chain H residue 862 VAL Chi-restraints excluded: chain H residue 866 THR Chi-restraints excluded: chain H residue 870 ILE Chi-restraints excluded: chain H residue 934 ILE Chi-restraints excluded: chain H residue 938 ASP Chi-restraints excluded: chain H residue 1019 VAL Chi-restraints excluded: chain H residue 1093 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 424 optimal weight: 20.0000 chunk 322 optimal weight: 0.8980 chunk 222 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 chunk 204 optimal weight: 10.0000 chunk 288 optimal weight: 1.9990 chunk 430 optimal weight: 20.0000 chunk 456 optimal weight: 1.9990 chunk 225 optimal weight: 4.9990 chunk 408 optimal weight: 1.9990 chunk 122 optimal weight: 0.9980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 GLN A 189 ASN B 77 GLN B 78 ASN B 313 GLN B 452 HIS C 794 ASN C1072 ASN ** C1174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1053 GLN A D1159 HIS ** D1174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 313 GLN E 452 HIS ** E 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 989 GLN ** F1174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 95 HIS G 107 GLN ** G 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 989 GLN ** H1174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.5087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 37372 Z= 0.198 Angle : 0.652 11.455 50720 Z= 0.329 Chirality : 0.046 0.239 5552 Planarity : 0.005 0.057 6732 Dihedral : 5.993 59.997 5557 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 2.89 % Allowed : 13.70 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (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: -3.06 (0.11), residues: 4744 helix: -2.14 (0.18), residues: 688 sheet: -2.43 (0.16), residues: 868 loop : -1.97 (0.10), residues: 3188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 502 HIS 0.016 0.001 HIS B 452 PHE 0.018 0.002 PHE A 76 TYR 0.019 0.001 TYR G 711 ARG 0.007 0.001 ARG G 505 *********************** 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 439 residues out of total 4112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 325 time to evaluate : 4.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 ASP cc_start: 0.8069 (p0) cc_final: 0.7777 (p0) REVERT: A 619 ARG cc_start: 0.6820 (mmm160) cc_final: 0.6447 (mpp80) REVERT: B 199 TRP cc_start: 0.7529 (m-90) cc_final: 0.7186 (m-90) REVERT: B 217 MET cc_start: 0.4949 (tpt) cc_final: 0.4175 (ttm) REVERT: B 420 ASP cc_start: 0.7617 (OUTLIER) cc_final: 0.7358 (p0) REVERT: B 499 GLN cc_start: 0.7958 (OUTLIER) cc_final: 0.7699 (tt0) REVERT: B 602 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8649 (mt) REVERT: C 771 MET cc_start: 0.5494 (ptp) cc_final: 0.5111 (mtt) REVERT: C 814 MET cc_start: 0.5325 (ptp) cc_final: 0.4639 (mtp) REVERT: C 847 ASN cc_start: 0.7649 (OUTLIER) cc_final: 0.7390 (t0) REVERT: D 998 ASN cc_start: 0.8801 (OUTLIER) cc_final: 0.8569 (p0) REVERT: E 313 GLN cc_start: 0.6150 (mt0) cc_final: 0.5846 (mp10) REVERT: F 826 ARG cc_start: 0.6056 (mtm110) cc_final: 0.5466 (ptm160) REVERT: F 927 ILE cc_start: 0.8332 (OUTLIER) cc_final: 0.8017 (mt) REVERT: F 952 HIS cc_start: 0.7010 (m-70) cc_final: 0.6780 (m-70) REVERT: G 282 LEU cc_start: 0.6645 (pt) cc_final: 0.6052 (mt) REVERT: G 320 MET cc_start: 0.6065 (mtp) cc_final: 0.5816 (ttm) REVERT: G 740 MET cc_start: 0.5616 (mmm) cc_final: 0.4485 (tmm) REVERT: H 790 LYS cc_start: 0.8043 (mmtt) cc_final: 0.7795 (mttm) REVERT: H 802 MET cc_start: 0.4476 (mmp) cc_final: 0.4108 (mmt) outliers start: 114 outliers final: 61 residues processed: 415 average time/residue: 0.4674 time to fit residues: 328.0754 Evaluate side-chains 347 residues out of total 4112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 280 time to evaluate : 4.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 ASN Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 435 ASP Chi-restraints excluded: chain A residue 526 ASN Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 684 LEU Chi-restraints excluded: chain A residue 709 CYS Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 420 ASP Chi-restraints excluded: chain B residue 480 LEU Chi-restraints excluded: chain B residue 499 GLN Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 526 ASN Chi-restraints excluded: chain B residue 584 CYS Chi-restraints excluded: chain B residue 602 LEU Chi-restraints excluded: chain B residue 651 ASN Chi-restraints excluded: chain B residue 669 CYS Chi-restraints excluded: chain C residue 794 ASN Chi-restraints excluded: chain C residue 841 THR Chi-restraints excluded: chain C residue 847 ASN Chi-restraints excluded: chain C residue 864 ASP Chi-restraints excluded: chain C residue 870 ILE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 937 PHE Chi-restraints excluded: chain C residue 938 ASP Chi-restraints excluded: chain C residue 1081 LEU Chi-restraints excluded: chain D residue 862 VAL Chi-restraints excluded: chain D residue 870 ILE Chi-restraints excluded: chain D residue 911 ASN Chi-restraints excluded: chain D residue 998 ASN Chi-restraints excluded: chain E residue 69 SER Chi-restraints excluded: chain E residue 75 ASP Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 107 GLN Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 222 TRP Chi-restraints excluded: chain E residue 394 SER Chi-restraints excluded: chain E residue 526 ASN Chi-restraints excluded: chain E residue 537 THR Chi-restraints excluded: chain F residue 841 THR Chi-restraints excluded: chain F residue 862 VAL Chi-restraints excluded: chain F residue 870 ILE Chi-restraints excluded: chain F residue 927 ILE Chi-restraints excluded: chain G residue 41 ASP Chi-restraints excluded: chain G residue 106 ASP Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 179 THR Chi-restraints excluded: chain G residue 265 CYS Chi-restraints excluded: chain G residue 348 CYS Chi-restraints excluded: chain G residue 394 SER Chi-restraints excluded: chain G residue 695 MET Chi-restraints excluded: chain G residue 731 CYS Chi-restraints excluded: chain H residue 796 ASP Chi-restraints excluded: chain H residue 850 VAL Chi-restraints excluded: chain H residue 866 THR Chi-restraints excluded: chain H residue 870 ILE Chi-restraints excluded: chain H residue 934 ILE Chi-restraints excluded: chain H residue 938 ASP Chi-restraints excluded: chain H residue 1019 VAL Chi-restraints excluded: chain H residue 1093 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 379 optimal weight: 9.9990 chunk 258 optimal weight: 20.0000 chunk 6 optimal weight: 6.9990 chunk 339 optimal weight: 0.9980 chunk 188 optimal weight: 10.0000 chunk 389 optimal weight: 7.9990 chunk 315 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 232 optimal weight: 8.9990 chunk 409 optimal weight: 9.9990 chunk 115 optimal weight: 6.9990 overall best weight: 5.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 HIS A 198 GLN A 484 HIS B 288 HIS ** B 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 452 HIS C 794 ASN C1072 ASN ** C1174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1113 GLN ** D1174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 95 HIS E 452 HIS ** E 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 725 HIS F1072 ASN ** F1174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 107 GLN G 189 ASN ** G 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H1047 HIS ** H1134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.5484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 37372 Z= 0.464 Angle : 0.781 15.454 50720 Z= 0.395 Chirality : 0.052 0.260 5552 Planarity : 0.005 0.064 6732 Dihedral : 6.421 59.900 5557 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.63 % Favored : 89.37 % Rotamer: Outliers : 3.99 % Allowed : 14.19 % Favored : 81.82 % 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: -3.09 (0.11), residues: 4744 helix: -2.21 (0.18), residues: 676 sheet: -2.54 (0.16), residues: 880 loop : -1.95 (0.10), residues: 3188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 502 HIS 0.012 0.002 HIS B 452 PHE 0.031 0.003 PHE C 999 TYR 0.034 0.003 TYR B 87 ARG 0.009 0.001 ARG E 643 *********************** 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 451 residues out of total 4112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 292 time to evaluate : 4.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 TYR cc_start: 0.8603 (OUTLIER) cc_final: 0.7639 (t80) REVERT: B 199 TRP cc_start: 0.7570 (m-90) cc_final: 0.7288 (m-90) REVERT: B 217 MET cc_start: 0.4724 (tpt) cc_final: 0.3997 (ttm) REVERT: B 420 ASP cc_start: 0.7802 (OUTLIER) cc_final: 0.7541 (p0) REVERT: B 483 GLN cc_start: 0.8202 (OUTLIER) cc_final: 0.7661 (pt0) REVERT: B 499 GLN cc_start: 0.8053 (OUTLIER) cc_final: 0.7815 (tt0) REVERT: C 771 MET cc_start: 0.5731 (ptp) cc_final: 0.4985 (mtt) REVERT: C 814 MET cc_start: 0.5307 (ptp) cc_final: 0.4607 (mtp) REVERT: C 847 ASN cc_start: 0.7601 (OUTLIER) cc_final: 0.7288 (t0) REVERT: E 132 GLU cc_start: 0.7701 (OUTLIER) cc_final: 0.7322 (mm-30) REVERT: E 384 CYS cc_start: 0.6937 (OUTLIER) cc_final: 0.6702 (m) REVERT: E 722 PHE cc_start: 0.7911 (OUTLIER) cc_final: 0.7236 (t80) REVERT: F 826 ARG cc_start: 0.6381 (mtm110) cc_final: 0.5667 (ptm160) REVERT: F 927 ILE cc_start: 0.8412 (OUTLIER) cc_final: 0.8068 (mp) REVERT: G 282 LEU cc_start: 0.6922 (pt) cc_final: 0.6624 (mt) outliers start: 159 outliers final: 115 residues processed: 423 average time/residue: 0.4667 time to fit residues: 331.0394 Evaluate side-chains 393 residues out of total 4112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 269 time to evaluate : 4.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 185 TYR Chi-restraints excluded: chain A residue 198 GLN Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 329 CYS Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain A residue 403 TYR Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 435 ASP Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 526 ASN Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 684 LEU Chi-restraints excluded: chain A residue 709 CYS Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 204 SER Chi-restraints excluded: chain B residue 262 GLU Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 384 CYS Chi-restraints excluded: chain B residue 420 ASP Chi-restraints excluded: chain B residue 480 LEU Chi-restraints excluded: chain B residue 483 GLN Chi-restraints excluded: chain B residue 499 GLN Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 526 ASN Chi-restraints excluded: chain B residue 584 CYS Chi-restraints excluded: chain B residue 602 LEU Chi-restraints excluded: chain B residue 638 VAL Chi-restraints excluded: chain B residue 651 ASN Chi-restraints excluded: chain B residue 659 LEU Chi-restraints excluded: chain B residue 669 CYS Chi-restraints excluded: chain B residue 684 LEU Chi-restraints excluded: chain C residue 794 ASN Chi-restraints excluded: chain C residue 841 THR Chi-restraints excluded: chain C residue 847 ASN Chi-restraints excluded: chain C residue 862 VAL Chi-restraints excluded: chain C residue 864 ASP Chi-restraints excluded: chain C residue 870 ILE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 937 PHE Chi-restraints excluded: chain C residue 938 ASP Chi-restraints excluded: chain C residue 1011 ASN Chi-restraints excluded: chain C residue 1039 LEU Chi-restraints excluded: chain C residue 1081 LEU Chi-restraints excluded: chain C residue 1093 SER Chi-restraints excluded: chain C residue 1122 THR Chi-restraints excluded: chain C residue 1135 LEU Chi-restraints excluded: chain D residue 862 VAL Chi-restraints excluded: chain D residue 870 ILE Chi-restraints excluded: chain D residue 911 ASN Chi-restraints excluded: chain D residue 915 SER Chi-restraints excluded: chain D residue 927 ILE Chi-restraints excluded: chain D residue 934 ILE Chi-restraints excluded: chain D residue 1016 GLU Chi-restraints excluded: chain D residue 1055 MET Chi-restraints excluded: chain D residue 1122 THR Chi-restraints excluded: chain E residue 69 SER Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain E residue 107 GLN Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 132 GLU Chi-restraints excluded: chain E residue 222 TRP Chi-restraints excluded: chain E residue 318 ASN Chi-restraints excluded: chain E residue 326 VAL Chi-restraints excluded: chain E residue 338 ASP Chi-restraints excluded: chain E residue 384 CYS Chi-restraints excluded: chain E residue 394 SER Chi-restraints excluded: chain E residue 480 LEU Chi-restraints excluded: chain E residue 526 ASN Chi-restraints excluded: chain E residue 537 THR Chi-restraints excluded: chain E residue 567 SER Chi-restraints excluded: chain E residue 616 SER Chi-restraints excluded: chain E residue 681 GLU Chi-restraints excluded: chain E residue 722 PHE Chi-restraints excluded: chain F residue 841 THR Chi-restraints excluded: chain F residue 853 ASP Chi-restraints excluded: chain F residue 862 VAL Chi-restraints excluded: chain F residue 870 ILE Chi-restraints excluded: chain F residue 915 SER Chi-restraints excluded: chain F residue 927 ILE Chi-restraints excluded: chain F residue 934 ILE Chi-restraints excluded: chain F residue 935 GLU Chi-restraints excluded: chain F residue 936 LEU Chi-restraints excluded: chain F residue 937 PHE Chi-restraints excluded: chain F residue 1055 MET Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 106 ASP Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 179 THR Chi-restraints excluded: chain G residue 189 ASN Chi-restraints excluded: chain G residue 265 CYS Chi-restraints excluded: chain G residue 294 VAL Chi-restraints excluded: chain G residue 329 CYS Chi-restraints excluded: chain G residue 348 CYS Chi-restraints excluded: chain G residue 394 SER Chi-restraints excluded: chain G residue 471 VAL Chi-restraints excluded: chain G residue 501 ASP Chi-restraints excluded: chain G residue 668 THR Chi-restraints excluded: chain G residue 669 CYS Chi-restraints excluded: chain G residue 695 MET Chi-restraints excluded: chain G residue 731 CYS Chi-restraints excluded: chain H residue 796 ASP Chi-restraints excluded: chain H residue 850 VAL Chi-restraints excluded: chain H residue 866 THR Chi-restraints excluded: chain H residue 870 ILE Chi-restraints excluded: chain H residue 911 ASN Chi-restraints excluded: chain H residue 934 ILE Chi-restraints excluded: chain H residue 938 ASP Chi-restraints excluded: chain H residue 1019 VAL Chi-restraints excluded: chain H residue 1059 SER Chi-restraints excluded: chain H residue 1070 ASP Chi-restraints excluded: chain H residue 1093 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 153 optimal weight: 0.5980 chunk 410 optimal weight: 10.0000 chunk 90 optimal weight: 10.0000 chunk 267 optimal weight: 20.0000 chunk 112 optimal weight: 0.8980 chunk 456 optimal weight: 1.9990 chunk 379 optimal weight: 6.9990 chunk 211 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 chunk 151 optimal weight: 0.3980 chunk 239 optimal weight: 2.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 ASN A 198 GLN B 452 HIS ** B 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 794 ASN C1072 ASN C1174 HIS ** D1174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 393 GLN E 452 HIS ** E 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F1072 ASN ** F1174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 189 ASN G 374 ASN ** H1174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.5549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 37372 Z= 0.182 Angle : 0.625 11.557 50720 Z= 0.314 Chirality : 0.045 0.213 5552 Planarity : 0.005 0.060 6732 Dihedral : 5.632 58.069 5557 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 3.03 % Allowed : 15.53 % Favored : 81.43 % 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: -2.81 (0.12), residues: 4744 helix: -1.83 (0.19), residues: 692 sheet: -2.34 (0.16), residues: 896 loop : -1.79 (0.11), residues: 3156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP B 502 HIS 0.014 0.001 HIS B 452 PHE 0.017 0.001 PHE A 76 TYR 0.024 0.001 TYR C 795 ARG 0.009 0.000 ARG A 619 *********************** 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 419 residues out of total 4112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 299 time to evaluate : 4.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 ASP cc_start: 0.8100 (p0) cc_final: 0.7710 (p0) REVERT: A 185 TYR cc_start: 0.8573 (OUTLIER) cc_final: 0.7732 (t80) REVERT: A 472 GLN cc_start: 0.7928 (OUTLIER) cc_final: 0.7546 (tm-30) REVERT: A 475 LEU cc_start: 0.8034 (tt) cc_final: 0.7737 (tt) REVERT: A 619 ARG cc_start: 0.7271 (mmp80) cc_final: 0.6582 (mpp80) REVERT: B 373 ARG cc_start: 0.6781 (mtt-85) cc_final: 0.6482 (mpt180) REVERT: C 771 MET cc_start: 0.5744 (ptp) cc_final: 0.5077 (mtt) REVERT: C 814 MET cc_start: 0.5260 (ptp) cc_final: 0.4565 (mtp) REVERT: E 313 GLN cc_start: 0.6069 (mt0) cc_final: 0.5759 (mp10) REVERT: F 826 ARG cc_start: 0.5962 (mtm110) cc_final: 0.5385 (ptm160) REVERT: G 189 ASN cc_start: 0.8708 (OUTLIER) cc_final: 0.8401 (t160) REVERT: G 282 LEU cc_start: 0.6823 (pt) cc_final: 0.6122 (mt) REVERT: H 802 MET cc_start: 0.4116 (mmp) cc_final: 0.3718 (mmt) outliers start: 120 outliers final: 78 residues processed: 397 average time/residue: 0.4916 time to fit residues: 325.5428 Evaluate side-chains 340 residues out of total 4112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 259 time to evaluate : 4.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 185 TYR Chi-restraints excluded: chain A residue 189 ASN Chi-restraints excluded: chain A residue 198 GLN Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 435 ASP Chi-restraints excluded: chain A residue 472 GLN Chi-restraints excluded: chain A residue 526 ASN Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 684 LEU Chi-restraints excluded: chain A residue 709 CYS Chi-restraints excluded: chain A residue 736 MET Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 204 SER Chi-restraints excluded: chain B residue 262 GLU Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 420 ASP Chi-restraints excluded: chain B residue 480 LEU Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 526 ASN Chi-restraints excluded: chain B residue 584 CYS Chi-restraints excluded: chain B residue 651 ASN Chi-restraints excluded: chain B residue 669 CYS Chi-restraints excluded: chain C residue 794 ASN Chi-restraints excluded: chain C residue 841 THR Chi-restraints excluded: chain C residue 862 VAL Chi-restraints excluded: chain C residue 864 ASP Chi-restraints excluded: chain C residue 870 ILE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 938 ASP Chi-restraints excluded: chain C residue 1011 ASN Chi-restraints excluded: chain C residue 1081 LEU Chi-restraints excluded: chain C residue 1135 LEU Chi-restraints excluded: chain D residue 862 VAL Chi-restraints excluded: chain D residue 870 ILE Chi-restraints excluded: chain D residue 911 ASN Chi-restraints excluded: chain D residue 927 ILE Chi-restraints excluded: chain D residue 934 ILE Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 107 GLN Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 222 TRP Chi-restraints excluded: chain E residue 318 ASN Chi-restraints excluded: chain E residue 326 VAL Chi-restraints excluded: chain E residue 394 SER Chi-restraints excluded: chain E residue 526 ASN Chi-restraints excluded: chain E residue 537 THR Chi-restraints excluded: chain E residue 616 SER Chi-restraints excluded: chain F residue 841 THR Chi-restraints excluded: chain F residue 862 VAL Chi-restraints excluded: chain F residue 870 ILE Chi-restraints excluded: chain F residue 934 ILE Chi-restraints excluded: chain G residue 106 ASP Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 179 THR Chi-restraints excluded: chain G residue 189 ASN Chi-restraints excluded: chain G residue 265 CYS Chi-restraints excluded: chain G residue 329 CYS Chi-restraints excluded: chain G residue 348 CYS Chi-restraints excluded: chain G residue 394 SER Chi-restraints excluded: chain G residue 471 VAL Chi-restraints excluded: chain G residue 526 ASN Chi-restraints excluded: chain G residue 695 MET Chi-restraints excluded: chain H residue 850 VAL Chi-restraints excluded: chain H residue 866 THR Chi-restraints excluded: chain H residue 870 ILE Chi-restraints excluded: chain H residue 938 ASP Chi-restraints excluded: chain H residue 1059 SER Chi-restraints excluded: chain H residue 1070 ASP Chi-restraints excluded: chain H residue 1074 LEU Chi-restraints excluded: chain H residue 1093 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 440 optimal weight: 0.9990 chunk 51 optimal weight: 10.0000 chunk 260 optimal weight: 10.0000 chunk 333 optimal weight: 5.9990 chunk 258 optimal weight: 7.9990 chunk 384 optimal weight: 0.0670 chunk 255 optimal weight: 5.9990 chunk 454 optimal weight: 5.9990 chunk 284 optimal weight: 0.1980 chunk 277 optimal weight: 0.9980 chunk 210 optimal weight: 0.4980 overall best weight: 0.5520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 ASN A 198 GLN B 452 HIS B 499 GLN ** B 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 794 ASN ** C 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1072 ASN E 145 ASN E 147 GLN E 452 HIS E 551 ASN E 725 HIS F1174 HIS H 890 GLN H1174 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.5662 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: