Starting phenix.real_space_refine (version: 1.21rc1) on Wed May 17 07:29:12 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jmc_22391/05_2023/7jmc_22391_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jmc_22391/05_2023/7jmc_22391.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jmc_22391/05_2023/7jmc_22391.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jmc_22391/05_2023/7jmc_22391.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jmc_22391/05_2023/7jmc_22391_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jmc_22391/05_2023/7jmc_22391_trim_updated.pdb" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.000 sd= 0.012 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: 6 Type Number sf(0) Gaussians P 12 5.49 5 S 120 5.16 5 C 14532 2.51 5 N 3084 2.21 5 O 3504 1.98 5 H 18576 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 106": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 106": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 106": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 106": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ARG 106": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ARG 106": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ARG 106": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ARG 106": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I ARG 106": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J ARG 106": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K ARG 106": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L ARG 106": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/chem_data/mon_lib" Total number of atoms: 39828 Number of models: 1 Model: "" Number of chains: 36 Chain: "A" Number of atoms: 3113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 3113 Classifications: {'peptide': 192} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 184} Chain breaks: 1 Chain: "B" Number of atoms: 3113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 3113 Classifications: {'peptide': 192} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 184} Chain breaks: 1 Chain: "C" Number of atoms: 3113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 3113 Classifications: {'peptide': 192} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 184} Chain breaks: 1 Chain: "D" Number of atoms: 3113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 3113 Classifications: {'peptide': 192} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 184} Chain breaks: 1 Chain: "E" Number of atoms: 3113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 3113 Classifications: {'peptide': 192} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 184} Chain breaks: 1 Chain: "F" Number of atoms: 3113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 3113 Classifications: {'peptide': 192} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 184} Chain breaks: 1 Chain: "G" Number of atoms: 3113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 3113 Classifications: {'peptide': 192} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 184} Chain breaks: 1 Chain: "H" Number of atoms: 3113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 3113 Classifications: {'peptide': 192} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 184} Chain breaks: 1 Chain: "I" Number of atoms: 3113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 3113 Classifications: {'peptide': 192} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 184} Chain breaks: 1 Chain: "J" Number of atoms: 3113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 3113 Classifications: {'peptide': 192} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 184} Chain breaks: 1 Chain: "K" Number of atoms: 3113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 3113 Classifications: {'peptide': 192} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 184} Chain breaks: 1 Chain: "L" Number of atoms: 3113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 3113 Classifications: {'peptide': 192} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 184} Chain breaks: 1 Chain: "A" Number of atoms: 192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 192 Unusual residues: {'MC3': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 360 Unresolved non-hydrogen angles: 457 Unresolved non-hydrogen dihedrals: 211 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'MC3:plan-2': 10, 'MC3:plan-1': 10} Unresolved non-hydrogen planarities: 75 Chain: "B" Number of atoms: 192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 192 Unusual residues: {'MC3': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 360 Unresolved non-hydrogen angles: 457 Unresolved non-hydrogen dihedrals: 211 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'MC3:plan-2': 10, 'MC3:plan-1': 10} Unresolved non-hydrogen planarities: 75 Chain: "C" Number of atoms: 192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 192 Unusual residues: {'MC3': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 360 Unresolved non-hydrogen angles: 457 Unresolved non-hydrogen dihedrals: 211 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'MC3:plan-2': 10, 'MC3:plan-1': 10} Unresolved non-hydrogen planarities: 75 Chain: "D" Number of atoms: 192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 192 Unusual residues: {'MC3': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 360 Unresolved non-hydrogen angles: 457 Unresolved non-hydrogen dihedrals: 211 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'MC3:plan-2': 10, 'MC3:plan-1': 10} Unresolved non-hydrogen planarities: 75 Chain: "E" Number of atoms: 192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 192 Unusual residues: {'MC3': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 360 Unresolved non-hydrogen angles: 457 Unresolved non-hydrogen dihedrals: 211 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'MC3:plan-2': 10, 'MC3:plan-1': 10} Unresolved non-hydrogen planarities: 75 Chain: "F" Number of atoms: 192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 192 Unusual residues: {'MC3': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 360 Unresolved non-hydrogen angles: 457 Unresolved non-hydrogen dihedrals: 211 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'MC3:plan-2': 10, 'MC3:plan-1': 10} Unresolved non-hydrogen planarities: 75 Chain: "G" Number of atoms: 192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 192 Unusual residues: {'MC3': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 360 Unresolved non-hydrogen angles: 457 Unresolved non-hydrogen dihedrals: 211 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'MC3:plan-2': 10, 'MC3:plan-1': 10} Unresolved non-hydrogen planarities: 75 Chain: "H" Number of atoms: 192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 192 Unusual residues: {'MC3': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 360 Unresolved non-hydrogen angles: 457 Unresolved non-hydrogen dihedrals: 211 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'MC3:plan-2': 10, 'MC3:plan-1': 10} Unresolved non-hydrogen planarities: 75 Chain: "I" Number of atoms: 192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 192 Unusual residues: {'MC3': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 360 Unresolved non-hydrogen angles: 457 Unresolved non-hydrogen dihedrals: 211 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'MC3:plan-2': 10, 'MC3:plan-1': 10} Unresolved non-hydrogen planarities: 75 Chain: "J" Number of atoms: 192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 192 Unusual residues: {'MC3': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 360 Unresolved non-hydrogen angles: 457 Unresolved non-hydrogen dihedrals: 211 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'MC3:plan-2': 10, 'MC3:plan-1': 10} Unresolved non-hydrogen planarities: 75 Chain: "K" Number of atoms: 192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 192 Unusual residues: {'MC3': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 360 Unresolved non-hydrogen angles: 457 Unresolved non-hydrogen dihedrals: 211 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'MC3:plan-2': 10, 'MC3:plan-1': 10} Unresolved non-hydrogen planarities: 75 Chain: "L" Number of atoms: 192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 192 Unusual residues: {'MC3': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 360 Unresolved non-hydrogen angles: 457 Unresolved non-hydrogen dihedrals: 211 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'MC3:plan-2': 10, 'MC3:plan-1': 10} Unresolved non-hydrogen planarities: 75 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "G" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "H" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "I" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "J" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "K" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "L" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Time building chain proxies: 16.13, per 1000 atoms: 0.40 Number of scatterers: 39828 At special positions: 0 Unit cell: (95.403, 96.701, 161.601, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 120 16.00 P 12 15.00 O 3504 8.00 N 3084 7.00 C 14532 6.00 H 18576 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 201 " distance=2.03 Simple disulfide: pdb=" SG CYS A 61 " - pdb=" SG CYS A 195 " distance=2.03 Simple disulfide: pdb=" SG CYS A 65 " - pdb=" SG CYS A 190 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 201 " distance=2.03 Simple disulfide: pdb=" SG CYS B 61 " - pdb=" SG CYS B 195 " distance=2.03 Simple disulfide: pdb=" SG CYS B 65 " - pdb=" SG CYS B 190 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 201 " distance=2.03 Simple disulfide: pdb=" SG CYS C 61 " - pdb=" SG CYS C 195 " distance=2.03 Simple disulfide: pdb=" SG CYS C 65 " - pdb=" SG CYS C 190 " distance=2.03 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 201 " distance=2.03 Simple disulfide: pdb=" SG CYS D 61 " - pdb=" SG CYS D 195 " distance=2.03 Simple disulfide: pdb=" SG CYS D 65 " - pdb=" SG CYS D 190 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 201 " distance=2.03 Simple disulfide: pdb=" SG CYS E 61 " - pdb=" SG CYS E 195 " distance=2.03 Simple disulfide: pdb=" SG CYS E 65 " - pdb=" SG CYS E 190 " distance=2.03 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 201 " distance=2.03 Simple disulfide: pdb=" SG CYS F 61 " - pdb=" SG CYS F 195 " distance=2.03 Simple disulfide: pdb=" SG CYS F 65 " - pdb=" SG CYS F 190 " distance=2.03 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 201 " distance=2.03 Simple disulfide: pdb=" SG CYS G 61 " - pdb=" SG CYS G 195 " distance=2.03 Simple disulfide: pdb=" SG CYS G 65 " - pdb=" SG CYS G 190 " distance=2.03 Simple disulfide: pdb=" SG CYS H 54 " - pdb=" SG CYS H 201 " distance=2.03 Simple disulfide: pdb=" SG CYS H 61 " - pdb=" SG CYS H 195 " distance=2.03 Simple disulfide: pdb=" SG CYS H 65 " - pdb=" SG CYS H 190 " distance=2.03 Simple disulfide: pdb=" SG CYS I 54 " - pdb=" SG CYS I 201 " distance=2.03 Simple disulfide: pdb=" SG CYS I 61 " - pdb=" SG CYS I 195 " distance=2.03 Simple disulfide: pdb=" SG CYS I 65 " - pdb=" SG CYS I 190 " distance=2.03 Simple disulfide: pdb=" SG CYS J 54 " - pdb=" SG CYS J 201 " distance=2.03 Simple disulfide: pdb=" SG CYS J 61 " - pdb=" SG CYS J 195 " distance=2.03 Simple disulfide: pdb=" SG CYS J 65 " - pdb=" SG CYS J 190 " distance=2.03 Simple disulfide: pdb=" SG CYS K 54 " - pdb=" SG CYS K 201 " distance=2.03 Simple disulfide: pdb=" SG CYS K 61 " - pdb=" SG CYS K 195 " distance=2.03 Simple disulfide: pdb=" SG CYS K 65 " - pdb=" SG CYS K 190 " distance=2.04 Simple disulfide: pdb=" SG CYS L 54 " - pdb=" SG CYS L 201 " distance=2.03 Simple disulfide: pdb=" SG CYS L 61 " - pdb=" SG CYS L 195 " distance=2.03 Simple disulfide: pdb=" SG CYS L 65 " - pdb=" SG CYS L 190 " 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 Time building additional restraints: 31.17 Conformation dependent library (CDL) restraints added in 3.2 seconds 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4320 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 108 helices and 12 sheets defined 71.4% alpha, 3.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.44 Creating SS restraints... Processing helix chain 'A' and resid 5 through 15 Processing helix chain 'A' and resid 20 through 32 Processing helix chain 'A' and resid 34 through 39 Processing helix chain 'A' and resid 41 through 44 No H-bonds generated for 'chain 'A' and resid 41 through 44' Processing helix chain 'A' and resid 48 through 51 No H-bonds generated for 'chain 'A' and resid 48 through 51' Processing helix chain 'A' and resid 61 through 69 Processing helix chain 'A' and resid 74 through 105 Proline residue: A 88 - end of helix Processing helix chain 'A' and resid 153 through 180 Processing helix chain 'A' and resid 206 through 235 Processing helix chain 'B' and resid 5 through 15 Processing helix chain 'B' and resid 20 through 32 Processing helix chain 'B' and resid 34 through 39 Processing helix chain 'B' and resid 41 through 44 No H-bonds generated for 'chain 'B' and resid 41 through 44' Processing helix chain 'B' and resid 48 through 51 No H-bonds generated for 'chain 'B' and resid 48 through 51' Processing helix chain 'B' and resid 61 through 69 Processing helix chain 'B' and resid 74 through 105 Proline residue: B 88 - end of helix Processing helix chain 'B' and resid 153 through 180 Processing helix chain 'B' and resid 206 through 235 Processing helix chain 'C' and resid 5 through 15 Processing helix chain 'C' and resid 20 through 32 Processing helix chain 'C' and resid 34 through 39 Processing helix chain 'C' and resid 41 through 44 No H-bonds generated for 'chain 'C' and resid 41 through 44' Processing helix chain 'C' and resid 48 through 51 No H-bonds generated for 'chain 'C' and resid 48 through 51' Processing helix chain 'C' and resid 61 through 69 Processing helix chain 'C' and resid 74 through 105 Proline residue: C 88 - end of helix Processing helix chain 'C' and resid 153 through 180 Processing helix chain 'C' and resid 206 through 235 Processing helix chain 'D' and resid 5 through 15 Processing helix chain 'D' and resid 20 through 32 Processing helix chain 'D' and resid 34 through 39 Processing helix chain 'D' and resid 41 through 44 No H-bonds generated for 'chain 'D' and resid 41 through 44' Processing helix chain 'D' and resid 48 through 51 No H-bonds generated for 'chain 'D' and resid 48 through 51' Processing helix chain 'D' and resid 61 through 69 Processing helix chain 'D' and resid 74 through 105 Proline residue: D 88 - end of helix Processing helix chain 'D' and resid 153 through 180 Processing helix chain 'D' and resid 206 through 235 Processing helix chain 'E' and resid 5 through 15 Processing helix chain 'E' and resid 20 through 32 Processing helix chain 'E' and resid 34 through 39 Processing helix chain 'E' and resid 41 through 44 No H-bonds generated for 'chain 'E' and resid 41 through 44' Processing helix chain 'E' and resid 48 through 51 No H-bonds generated for 'chain 'E' and resid 48 through 51' Processing helix chain 'E' and resid 61 through 69 Processing helix chain 'E' and resid 74 through 105 Proline residue: E 88 - end of helix Processing helix chain 'E' and resid 153 through 180 Processing helix chain 'E' and resid 206 through 235 Processing helix chain 'F' and resid 5 through 15 Processing helix chain 'F' and resid 20 through 32 Processing helix chain 'F' and resid 34 through 39 Processing helix chain 'F' and resid 41 through 44 No H-bonds generated for 'chain 'F' and resid 41 through 44' Processing helix chain 'F' and resid 48 through 51 No H-bonds generated for 'chain 'F' and resid 48 through 51' Processing helix chain 'F' and resid 61 through 69 Processing helix chain 'F' and resid 74 through 105 Proline residue: F 88 - end of helix Processing helix chain 'F' and resid 153 through 180 Processing helix chain 'F' and resid 206 through 235 Processing helix chain 'G' and resid 5 through 15 Processing helix chain 'G' and resid 20 through 32 Processing helix chain 'G' and resid 34 through 39 Processing helix chain 'G' and resid 41 through 44 No H-bonds generated for 'chain 'G' and resid 41 through 44' Processing helix chain 'G' and resid 48 through 51 No H-bonds generated for 'chain 'G' and resid 48 through 51' Processing helix chain 'G' and resid 61 through 69 Processing helix chain 'G' and resid 74 through 105 Proline residue: G 88 - end of helix Processing helix chain 'G' and resid 153 through 180 Processing helix chain 'G' and resid 206 through 235 Processing helix chain 'H' and resid 5 through 15 Processing helix chain 'H' and resid 20 through 32 Processing helix chain 'H' and resid 34 through 39 Processing helix chain 'H' and resid 41 through 44 No H-bonds generated for 'chain 'H' and resid 41 through 44' Processing helix chain 'H' and resid 48 through 51 No H-bonds generated for 'chain 'H' and resid 48 through 51' Processing helix chain 'H' and resid 61 through 69 Processing helix chain 'H' and resid 74 through 105 Proline residue: H 88 - end of helix Processing helix chain 'H' and resid 153 through 180 Processing helix chain 'H' and resid 206 through 235 Processing helix chain 'I' and resid 5 through 15 Processing helix chain 'I' and resid 20 through 32 Processing helix chain 'I' and resid 34 through 39 Processing helix chain 'I' and resid 41 through 44 No H-bonds generated for 'chain 'I' and resid 41 through 44' Processing helix chain 'I' and resid 48 through 51 No H-bonds generated for 'chain 'I' and resid 48 through 51' Processing helix chain 'I' and resid 61 through 69 Processing helix chain 'I' and resid 74 through 105 Proline residue: I 88 - end of helix Processing helix chain 'I' and resid 153 through 180 Processing helix chain 'I' and resid 206 through 235 Processing helix chain 'J' and resid 5 through 15 Processing helix chain 'J' and resid 20 through 32 Processing helix chain 'J' and resid 34 through 39 Processing helix chain 'J' and resid 41 through 44 No H-bonds generated for 'chain 'J' and resid 41 through 44' Processing helix chain 'J' and resid 48 through 51 No H-bonds generated for 'chain 'J' and resid 48 through 51' Processing helix chain 'J' and resid 61 through 69 Processing helix chain 'J' and resid 74 through 105 Proline residue: J 88 - end of helix Processing helix chain 'J' and resid 153 through 180 Processing helix chain 'J' and resid 206 through 235 Processing helix chain 'K' and resid 5 through 15 Processing helix chain 'K' and resid 20 through 32 Processing helix chain 'K' and resid 34 through 39 Processing helix chain 'K' and resid 41 through 44 No H-bonds generated for 'chain 'K' and resid 41 through 44' Processing helix chain 'K' and resid 48 through 51 No H-bonds generated for 'chain 'K' and resid 48 through 51' Processing helix chain 'K' and resid 61 through 69 Processing helix chain 'K' and resid 74 through 105 Proline residue: K 88 - end of helix Processing helix chain 'K' and resid 153 through 180 Processing helix chain 'K' and resid 206 through 235 Processing helix chain 'L' and resid 5 through 15 Processing helix chain 'L' and resid 20 through 32 Processing helix chain 'L' and resid 34 through 39 Processing helix chain 'L' and resid 41 through 44 No H-bonds generated for 'chain 'L' and resid 41 through 44' Processing helix chain 'L' and resid 48 through 51 No H-bonds generated for 'chain 'L' and resid 48 through 51' Processing helix chain 'L' and resid 61 through 69 Processing helix chain 'L' and resid 74 through 105 Proline residue: L 88 - end of helix Processing helix chain 'L' and resid 153 through 180 Processing helix chain 'L' and resid 206 through 235 Processing sheet with id= A, first strand: chain 'A' and resid 187 through 190 Processing sheet with id= B, first strand: chain 'B' and resid 187 through 190 Processing sheet with id= C, first strand: chain 'C' and resid 187 through 190 Processing sheet with id= D, first strand: chain 'D' and resid 187 through 190 Processing sheet with id= E, first strand: chain 'E' and resid 187 through 190 Processing sheet with id= F, first strand: chain 'F' and resid 187 through 190 Processing sheet with id= G, first strand: chain 'G' and resid 187 through 190 Processing sheet with id= H, first strand: chain 'H' and resid 187 through 190 Processing sheet with id= I, first strand: chain 'I' and resid 187 through 190 Processing sheet with id= J, first strand: chain 'J' and resid 187 through 190 Processing sheet with id= K, first strand: chain 'K' and resid 187 through 190 Processing sheet with id= L, first strand: chain 'L' and resid 187 through 190 1224 hydrogen bonds defined for protein. 3636 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 14.51 Time building geometry restraints manager: 32.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 18564 1.03 - 1.22: 72 1.22 - 1.42: 8535 1.42 - 1.61: 12705 1.61 - 1.80: 180 Bond restraints: 40056 Sorted by residual: bond pdb=" C11 MC3 A 506 " pdb=" O3 MC3 A 506 " ideal model delta sigma weight residual 1.327 1.399 -0.072 2.00e-02 2.50e+03 1.31e+01 bond pdb=" C31 MC3 E 508 " pdb=" O2 MC3 E 508 " ideal model delta sigma weight residual 1.328 1.400 -0.072 2.00e-02 2.50e+03 1.30e+01 bond pdb=" C11 MC3 H 501 " pdb=" O3 MC3 H 501 " ideal model delta sigma weight residual 1.327 1.399 -0.072 2.00e-02 2.50e+03 1.30e+01 bond pdb=" C11 MC3 K 501 " pdb=" O3 MC3 K 501 " ideal model delta sigma weight residual 1.327 1.399 -0.072 2.00e-02 2.50e+03 1.30e+01 bond pdb=" C11 MC3 B 501 " pdb=" O3 MC3 B 501 " ideal model delta sigma weight residual 1.327 1.399 -0.072 2.00e-02 2.50e+03 1.30e+01 ... (remaining 40051 not shown) Histogram of bond angle deviations from ideal: 99.07 - 106.09: 446 106.09 - 113.11: 44963 113.11 - 120.14: 12620 120.14 - 127.16: 12147 127.16 - 134.18: 300 Bond angle restraints: 70476 Sorted by residual: angle pdb=" O3P MC3 L 508 " pdb=" P MC3 L 508 " pdb=" O4P MC3 L 508 " ideal model delta sigma weight residual 93.26 109.95 -16.69 3.00e+00 1.11e-01 3.09e+01 angle pdb=" O3P MC3 C 508 " pdb=" P MC3 C 508 " pdb=" O4P MC3 C 508 " ideal model delta sigma weight residual 93.26 109.95 -16.69 3.00e+00 1.11e-01 3.09e+01 angle pdb=" O3P MC3 J 508 " pdb=" P MC3 J 508 " pdb=" O4P MC3 J 508 " ideal model delta sigma weight residual 93.26 109.94 -16.68 3.00e+00 1.11e-01 3.09e+01 angle pdb=" O3P MC3 D 508 " pdb=" P MC3 D 508 " pdb=" O4P MC3 D 508 " ideal model delta sigma weight residual 93.26 109.94 -16.68 3.00e+00 1.11e-01 3.09e+01 angle pdb=" O3P MC3 G 501 " pdb=" P MC3 G 501 " pdb=" O4P MC3 G 501 " ideal model delta sigma weight residual 93.26 109.94 -16.68 3.00e+00 1.11e-01 3.09e+01 ... (remaining 70471 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.38: 16812 35.38 - 70.75: 204 70.75 - 106.13: 36 106.13 - 141.50: 0 141.50 - 176.88: 24 Dihedral angle restraints: 17076 sinusoidal: 8508 harmonic: 8568 Sorted by residual: dihedral pdb=" C33 MC3 E 501 " pdb=" C31 MC3 E 501 " pdb=" C32 MC3 E 501 " pdb=" O2 MC3 E 501 " ideal model delta sinusoidal sigma weight residual 175.52 -1.36 176.88 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C33 MC3 K 501 " pdb=" C31 MC3 K 501 " pdb=" C32 MC3 K 501 " pdb=" O2 MC3 K 501 " ideal model delta sinusoidal sigma weight residual 175.52 -1.36 176.88 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C33 MC3 B 501 " pdb=" C31 MC3 B 501 " pdb=" C32 MC3 B 501 " pdb=" O2 MC3 B 501 " ideal model delta sinusoidal sigma weight residual 175.52 -1.36 176.88 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 17073 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 2112 0.053 - 0.106: 735 0.106 - 0.159: 129 0.159 - 0.213: 12 0.213 - 0.266: 24 Chirality restraints: 3012 Sorted by residual: chirality pdb=" CA ASN I 197 " pdb=" N ASN I 197 " pdb=" C ASN I 197 " pdb=" CB ASN I 197 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" CA ASN F 197 " pdb=" N ASN F 197 " pdb=" C ASN F 197 " pdb=" CB ASN F 197 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" CA ASN A 197 " pdb=" N ASN A 197 " pdb=" C ASN A 197 " pdb=" CB ASN A 197 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.74e+00 ... (remaining 3009 not shown) Planarity restraints: 5484 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN E 197 " 0.216 2.00e-02 2.50e+03 2.80e-01 1.18e+03 pdb=" CG ASN E 197 " -0.022 2.00e-02 2.50e+03 pdb=" OD1 ASN E 197 " -0.212 2.00e-02 2.50e+03 pdb=" ND2 ASN E 197 " 0.014 2.00e-02 2.50e+03 pdb="HD21 ASN E 197 " 0.437 2.00e-02 2.50e+03 pdb="HD22 ASN E 197 " -0.434 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 197 " -0.217 2.00e-02 2.50e+03 2.80e-01 1.18e+03 pdb=" CG ASN C 197 " 0.022 2.00e-02 2.50e+03 pdb=" OD1 ASN C 197 " 0.212 2.00e-02 2.50e+03 pdb=" ND2 ASN C 197 " -0.014 2.00e-02 2.50e+03 pdb="HD21 ASN C 197 " -0.437 2.00e-02 2.50e+03 pdb="HD22 ASN C 197 " 0.433 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN L 197 " -0.217 2.00e-02 2.50e+03 2.80e-01 1.18e+03 pdb=" CG ASN L 197 " 0.022 2.00e-02 2.50e+03 pdb=" OD1 ASN L 197 " 0.212 2.00e-02 2.50e+03 pdb=" ND2 ASN L 197 " -0.014 2.00e-02 2.50e+03 pdb="HD21 ASN L 197 " -0.437 2.00e-02 2.50e+03 pdb="HD22 ASN L 197 " 0.433 2.00e-02 2.50e+03 ... (remaining 5481 not shown) Histogram of nonbonded interaction distances: 1.65 - 2.24: 3889 2.24 - 2.83: 84937 2.83 - 3.42: 101444 3.42 - 4.01: 143537 4.01 - 4.60: 227583 Nonbonded interactions: 561390 Sorted by model distance: nonbonded pdb=" O TYR H 158 " pdb=" HD1 HIS H 161 " model vdw 1.650 1.850 nonbonded pdb=" O TYR I 158 " pdb=" HD1 HIS I 161 " model vdw 1.650 1.850 nonbonded pdb=" O TYR F 158 " pdb=" HD1 HIS F 161 " model vdw 1.650 1.850 nonbonded pdb=" O TYR E 158 " pdb=" HD1 HIS E 161 " model vdw 1.651 1.850 nonbonded pdb=" O TYR K 158 " pdb=" HD1 HIS K 161 " model vdw 1.651 1.850 ... (remaining 561385 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' and (resid 2 through 236 or (resid 501 and (name C11 or name C12 or n \ ame C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name C19 \ or name C2 or name C20 or name C21 or name C22 or name C3 or name C31 or name C3 \ 2 or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or nam \ e C39 or name C40 or name C41 or name C42 or name C43 or name O11 or name O2 or \ name O3 or name O31)) or resid 502 through 504 or (resid 505 through 506 and (na \ me C15 or name C16 or name C17 or name C18 or name C19 or name C20 or name C21 o \ r name C22 or name C23 or name C24)) or (resid 507 and (name C13 or name C14 or \ name C15 or name C16 or name C17 or name C18 or name C19 or name C20 or name C21 \ or name C22 or name C23 or name C24)) or (resid 508 and (name C12 or name C13 o \ r name C14 or name C15 or name C16 or name C17 or name C18 or name C19 or name C \ 20 or name C21 or name C22)) or resid 509 through 510 or (resid 511 and (name C1 \ 6 or name C17 or name C18 or name C19 or name C20 or name C21 or name C22 or nam \ e C23 or name C24)) or (resid 512 and (name C14 or name C15 or name C16 or name \ C17 or name C18 or name C19 or name C20 or name C21 or name C22 or name C23 or n \ ame C24)))) selection = (chain 'B' and (resid 2 through 236 or (resid 501 and (name C11 or name C12 or n \ ame C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name C19 \ or name C2 or name C20 or name C21 or name C22 or name C3 or name C31 or name C3 \ 2 or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or nam \ e C39 or name C40 or name C41 or name C42 or name C43 or name O11 or name O2 or \ name O3 or name O31)) or (resid 502 through 503 and (name C12 or name C13 or nam \ e C14 or name C15 or name C16 or name C17 or name C18 or name C19 or name C20 or \ name C21 or name C22 or name C23 or name C24)) or (resid 504 and (name C16 or n \ ame C17 or name C18 or name C19 or name C20 or name C21 or name C22 or name C23 \ or name C24)) or resid 505 through 507 or (resid 508 and (name C12 or name C13 o \ r name C14 or name C15 or name C16 or name C17 or name C18 or name C19 or name C \ 20 or name C21 or name C22)) or (resid 509 through 510 and (name C15 or name C16 \ or name C17 or name C18 or name C19 or name C20 or name C21 or name C22 or name \ C23 or name C24)) or resid 511 through 512)) selection = (chain 'C' and (resid 2 through 236 or (resid 501 and (name C11 or name C12 or n \ ame C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name C19 \ or name C2 or name C20 or name C21 or name C22 or name C3 or name C31 or name C3 \ 2 or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or nam \ e C39 or name C40 or name C41 or name C42 or name C43 or name O11 or name O2 or \ name O3 or name O31)) or (resid 502 through 503 and (name C12 or name C13 or nam \ e C14 or name C15 or name C16 or name C17 or name C18 or name C19 or name C20 or \ name C21 or name C22 or name C23 or name C24)) or (resid 504 and (name C16 or n \ ame C17 or name C18 or name C19 or name C20 or name C21 or name C22 or name C23 \ or name C24)) or resid 505 through 507 or (resid 508 and (name C12 or name C13 o \ r name C14 or name C15 or name C16 or name C17 or name C18 or name C19 or name C \ 20 or name C21 or name C22)) or (resid 509 through 510 and (name C15 or name C16 \ or name C17 or name C18 or name C19 or name C20 or name C21 or name C22 or name \ C23 or name C24)) or resid 511 through 512)) selection = (chain 'D' and (resid 2 through 236 or (resid 501 and (name C11 or name C12 or n \ ame C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name C19 \ or name C2 or name C20 or name C21 or name C22 or name C3 or name C31 or name C3 \ 2 or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or nam \ e C39 or name C40 or name C41 or name C42 or name C43 or name O11 or name O2 or \ name O3 or name O31)) or (resid 502 through 503 and (name C12 or name C13 or nam \ e C14 or name C15 or name C16 or name C17 or name C18 or name C19 or name C20 or \ name C21 or name C22 or name C23 or name C24)) or (resid 504 and (name C16 or n \ ame C17 or name C18 or name C19 or name C20 or name C21 or name C22 or name C23 \ or name C24)) or resid 505 through 507 or (resid 508 and (name C12 or name C13 o \ r name C14 or name C15 or name C16 or name C17 or name C18 or name C19 or name C \ 20 or name C21 or name C22)) or (resid 509 through 510 and (name C15 or name C16 \ or name C17 or name C18 or name C19 or name C20 or name C21 or name C22 or name \ C23 or name C24)) or resid 511 through 512)) selection = (chain 'E' and (resid 2 through 236 or (resid 501 and (name C11 or name C12 or n \ ame C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name C19 \ or name C2 or name C20 or name C21 or name C22 or name C3 or name C31 or name C3 \ 2 or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or nam \ e C39 or name C40 or name C41 or name C42 or name C43 or name O11 or name O2 or \ name O3 or name O31)) or (resid 502 through 503 and (name C12 or name C13 or nam \ e C14 or name C15 or name C16 or name C17 or name C18 or name C19 or name C20 or \ name C21 or name C22 or name C23 or name C24)) or (resid 504 and (name C16 or n \ ame C17 or name C18 or name C19 or name C20 or name C21 or name C22 or name C23 \ or name C24)) or resid 505 through 507 or (resid 508 and (name C12 or name C13 o \ r name C14 or name C15 or name C16 or name C17 or name C18 or name C19 or name C \ 20 or name C21 or name C22)) or (resid 509 through 510 and (name C15 or name C16 \ or name C17 or name C18 or name C19 or name C20 or name C21 or name C22 or name \ C23 or name C24)) or resid 511 through 512)) selection = (chain 'F' and (resid 2 through 236 or (resid 501 and (name C11 or name C12 or n \ ame C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name C19 \ or name C2 or name C20 or name C21 or name C22 or name C3 or name C31 or name C3 \ 2 or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or nam \ e C39 or name C40 or name C41 or name C42 or name C43 or name O11 or name O2 or \ name O3 or name O31)) or (resid 502 through 503 and (name C12 or name C13 or nam \ e C14 or name C15 or name C16 or name C17 or name C18 or name C19 or name C20 or \ name C21 or name C22 or name C23 or name C24)) or (resid 504 and (name C16 or n \ ame C17 or name C18 or name C19 or name C20 or name C21 or name C22 or name C23 \ or name C24)) or resid 505 through 507 or (resid 508 and (name C12 or name C13 o \ r name C14 or name C15 or name C16 or name C17 or name C18 or name C19 or name C \ 20 or name C21 or name C22)) or (resid 509 through 510 and (name C15 or name C16 \ or name C17 or name C18 or name C19 or name C20 or name C21 or name C22 or name \ C23 or name C24)) or resid 511 through 512)) selection = (chain 'G' and (resid 2 through 236 or (resid 501 and (name C11 or name C12 or n \ ame C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name C19 \ or name C2 or name C20 or name C21 or name C22 or name C3 or name C31 or name C3 \ 2 or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or nam \ e C39 or name C40 or name C41 or name C42 or name C43 or name O11 or name O2 or \ name O3 or name O31)) or resid 502 through 504 or (resid 505 through 506 and (na \ me C15 or name C16 or name C17 or name C18 or name C19 or name C20 or name C21 o \ r name C22 or name C23 or name C24)) or (resid 507 and (name C13 or name C14 or \ name C15 or name C16 or name C17 or name C18 or name C19 or name C20 or name C21 \ or name C22 or name C23 or name C24)) or (resid 508 and (name C12 or name C13 o \ r name C14 or name C15 or name C16 or name C17 or name C18 or name C19 or name C \ 20 or name C21 or name C22)) or resid 509 through 510 or (resid 511 and (name C1 \ 6 or name C17 or name C18 or name C19 or name C20 or name C21 or name C22 or nam \ e C23 or name C24)) or (resid 512 and (name C14 or name C15 or name C16 or name \ C17 or name C18 or name C19 or name C20 or name C21 or name C22 or name C23 or n \ ame C24)))) selection = (chain 'H' and (resid 2 through 236 or (resid 501 and (name C11 or name C12 or n \ ame C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name C19 \ or name C2 or name C20 or name C21 or name C22 or name C3 or name C31 or name C3 \ 2 or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or nam \ e C39 or name C40 or name C41 or name C42 or name C43 or name O11 or name O2 or \ name O3 or name O31)) or (resid 502 through 503 and (name C12 or name C13 or nam \ e C14 or name C15 or name C16 or name C17 or name C18 or name C19 or name C20 or \ name C21 or name C22 or name C23 or name C24)) or (resid 504 and (name C16 or n \ ame C17 or name C18 or name C19 or name C20 or name C21 or name C22 or name C23 \ or name C24)) or resid 505 through 507 or (resid 508 and (name C12 or name C13 o \ r name C14 or name C15 or name C16 or name C17 or name C18 or name C19 or name C \ 20 or name C21 or name C22)) or (resid 509 through 510 and (name C15 or name C16 \ or name C17 or name C18 or name C19 or name C20 or name C21 or name C22 or name \ C23 or name C24)) or resid 511 through 512)) selection = (chain 'I' and (resid 2 through 236 or (resid 501 and (name C11 or name C12 or n \ ame C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name C19 \ or name C2 or name C20 or name C21 or name C22 or name C3 or name C31 or name C3 \ 2 or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or nam \ e C39 or name C40 or name C41 or name C42 or name C43 or name O11 or name O2 or \ name O3 or name O31)) or (resid 502 through 503 and (name C12 or name C13 or nam \ e C14 or name C15 or name C16 or name C17 or name C18 or name C19 or name C20 or \ name C21 or name C22 or name C23 or name C24)) or (resid 504 and (name C16 or n \ ame C17 or name C18 or name C19 or name C20 or name C21 or name C22 or name C23 \ or name C24)) or resid 505 through 507 or (resid 508 and (name C12 or name C13 o \ r name C14 or name C15 or name C16 or name C17 or name C18 or name C19 or name C \ 20 or name C21 or name C22)) or (resid 509 through 510 and (name C15 or name C16 \ or name C17 or name C18 or name C19 or name C20 or name C21 or name C22 or name \ C23 or name C24)) or resid 511 through 512)) selection = (chain 'J' and (resid 2 through 236 or (resid 501 and (name C11 or name C12 or n \ ame C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name C19 \ or name C2 or name C20 or name C21 or name C22 or name C3 or name C31 or name C3 \ 2 or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or nam \ e C39 or name C40 or name C41 or name C42 or name C43 or name O11 or name O2 or \ name O3 or name O31)) or (resid 502 through 503 and (name C12 or name C13 or nam \ e C14 or name C15 or name C16 or name C17 or name C18 or name C19 or name C20 or \ name C21 or name C22 or name C23 or name C24)) or (resid 504 and (name C16 or n \ ame C17 or name C18 or name C19 or name C20 or name C21 or name C22 or name C23 \ or name C24)) or resid 505 through 507 or (resid 508 and (name C12 or name C13 o \ r name C14 or name C15 or name C16 or name C17 or name C18 or name C19 or name C \ 20 or name C21 or name C22)) or (resid 509 through 510 and (name C15 or name C16 \ or name C17 or name C18 or name C19 or name C20 or name C21 or name C22 or name \ C23 or name C24)) or resid 511 through 512)) selection = (chain 'K' and (resid 2 through 236 or (resid 501 and (name C11 or name C12 or n \ ame C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name C19 \ or name C2 or name C20 or name C21 or name C22 or name C3 or name C31 or name C3 \ 2 or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or nam \ e C39 or name C40 or name C41 or name C42 or name C43 or name O11 or name O2 or \ name O3 or name O31)) or (resid 502 through 503 and (name C12 or name C13 or nam \ e C14 or name C15 or name C16 or name C17 or name C18 or name C19 or name C20 or \ name C21 or name C22 or name C23 or name C24)) or (resid 504 and (name C16 or n \ ame C17 or name C18 or name C19 or name C20 or name C21 or name C22 or name C23 \ or name C24)) or resid 505 through 507 or (resid 508 and (name C12 or name C13 o \ r name C14 or name C15 or name C16 or name C17 or name C18 or name C19 or name C \ 20 or name C21 or name C22)) or (resid 509 through 510 and (name C15 or name C16 \ or name C17 or name C18 or name C19 or name C20 or name C21 or name C22 or name \ C23 or name C24)) or resid 511 through 512)) selection = (chain 'L' and (resid 2 through 236 or (resid 501 and (name C11 or name C12 or n \ ame C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name C19 \ or name C2 or name C20 or name C21 or name C22 or name C3 or name C31 or name C3 \ 2 or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or nam \ e C39 or name C40 or name C41 or name C42 or name C43 or name O11 or name O2 or \ name O3 or name O31)) or (resid 502 through 503 and (name C12 or name C13 or nam \ e C14 or name C15 or name C16 or name C17 or name C18 or name C19 or name C20 or \ name C21 or name C22 or name C23 or name C24)) or (resid 504 and (name C16 or n \ ame C17 or name C18 or name C19 or name C20 or name C21 or name C22 or name C23 \ or name C24)) or resid 505 through 507 or (resid 508 and (name C12 or name C13 o \ r name C14 or name C15 or name C16 or name C17 or name C18 or name C19 or name C \ 20 or name C21 or name C22)) or (resid 509 through 510 and (name C15 or name C16 \ or name C17 or name C18 or name C19 or name C20 or name C21 or name C22 or name \ C23 or name C24)) or resid 511 through 512)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.580 Extract box with map and model: 17.040 Check model and map are aligned: 0.520 Set scattering table: 0.290 Process input model: 114.860 Find NCS groups from input model: 2.000 Set up NCS constraints: 0.240 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:12.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 154.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 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 : 0.010 0.072 21480 Z= 0.636 Angle : 1.287 16.685 28440 Z= 0.530 Chirality : 0.057 0.266 3012 Planarity : 0.006 0.055 3288 Dihedral : 13.903 176.875 8352 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer Outliers : 0.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 3.40 (0.16), residues: 2256 helix: 3.16 (0.10), residues: 1704 sheet: 0.10 (0.46), residues: 132 loop : -1.18 (0.28), residues: 420 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 251 time to evaluate : 2.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 outliers start: 12 outliers final: 12 residues processed: 263 average time/residue: 2.0791 time to fit residues: 647.7190 Evaluate side-chains 223 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 211 time to evaluate : 3.051 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 12 residues processed: 0 time to fit residues: 3.8637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 192 optimal weight: 2.9990 chunk 172 optimal weight: 6.9990 chunk 95 optimal weight: 0.5980 chunk 59 optimal weight: 0.9990 chunk 116 optimal weight: 0.7980 chunk 92 optimal weight: 0.9980 chunk 178 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 chunk 108 optimal weight: 0.7980 chunk 133 optimal weight: 3.9990 chunk 207 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 15 ASN E 15 ASN K 15 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.0903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.022 21480 Z= 0.185 Angle : 0.510 4.905 28440 Z= 0.256 Chirality : 0.039 0.118 3012 Planarity : 0.004 0.041 3288 Dihedral : 12.742 170.803 4116 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Rotamer Outliers : 1.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.93 (0.17), residues: 2256 helix: 3.54 (0.11), residues: 1704 sheet: 0.55 (0.45), residues: 132 loop : -1.08 (0.27), residues: 420 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 236 time to evaluate : 3.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 outliers start: 30 outliers final: 29 residues processed: 248 average time/residue: 2.2104 time to fit residues: 648.8683 Evaluate side-chains 252 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 223 time to evaluate : 2.997 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 13 residues processed: 17 average time/residue: 0.4907 time to fit residues: 18.3181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 115 optimal weight: 6.9990 chunk 64 optimal weight: 2.9990 chunk 172 optimal weight: 6.9990 chunk 140 optimal weight: 2.9990 chunk 57 optimal weight: 5.9990 chunk 207 optimal weight: 3.9990 chunk 224 optimal weight: 0.5980 chunk 184 optimal weight: 4.9990 chunk 205 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 166 optimal weight: 2.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.1570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.031 21480 Z= 0.290 Angle : 0.527 5.960 28440 Z= 0.269 Chirality : 0.040 0.125 3012 Planarity : 0.004 0.046 3288 Dihedral : 11.878 151.818 4116 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Rotamer Outliers : 2.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 3.36 (0.17), residues: 2256 helix: 3.18 (0.12), residues: 1728 sheet: -0.87 (0.31), residues: 204 loop : -1.35 (0.30), residues: 324 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 243 time to evaluate : 3.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 47 outliers final: 36 residues processed: 262 average time/residue: 2.1426 time to fit residues: 666.4783 Evaluate side-chains 266 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 230 time to evaluate : 2.972 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 13 residues processed: 24 average time/residue: 0.5458 time to fit residues: 25.6051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 204 optimal weight: 1.9990 chunk 155 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 139 optimal weight: 1.9990 chunk 208 optimal weight: 2.9990 chunk 220 optimal weight: 2.9990 chunk 108 optimal weight: 0.8980 chunk 197 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 HIS B 176 HIS C 176 HIS D 176 HIS E 176 HIS F 176 HIS H 176 HIS I 176 HIS J 176 HIS L 176 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.1926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.024 21480 Z= 0.240 Angle : 0.485 4.484 28440 Z= 0.248 Chirality : 0.038 0.117 3012 Planarity : 0.004 0.039 3288 Dihedral : 9.654 123.858 4116 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer Outliers : 2.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 3.34 (0.17), residues: 2256 helix: 3.10 (0.12), residues: 1728 sheet: -0.54 (0.37), residues: 132 loop : -1.09 (0.27), residues: 396 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 241 time to evaluate : 3.238 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 outliers start: 47 outliers final: 36 residues processed: 261 average time/residue: 2.1599 time to fit residues: 663.0168 Evaluate side-chains 266 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 230 time to evaluate : 2.767 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 12 residues processed: 24 average time/residue: 0.6493 time to fit residues: 29.6238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 183 optimal weight: 0.9980 chunk 125 optimal weight: 5.9990 chunk 3 optimal weight: 2.9990 chunk 164 optimal weight: 2.9990 chunk 90 optimal weight: 0.0980 chunk 188 optimal weight: 2.9990 chunk 152 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 112 optimal weight: 3.9990 chunk 197 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 176 HIS C 176 HIS D 9 ASN D 176 HIS E 176 HIS F 176 HIS G 176 HIS H 176 HIS I 176 HIS K 176 HIS L 176 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.2141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.024 21480 Z= 0.257 Angle : 0.481 4.387 28440 Z= 0.247 Chirality : 0.039 0.118 3012 Planarity : 0.003 0.034 3288 Dihedral : 8.583 102.771 4116 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer Outliers : 2.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 3.29 (0.17), residues: 2256 helix: 3.06 (0.12), residues: 1728 sheet: -0.77 (0.37), residues: 132 loop : -1.04 (0.27), residues: 396 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 239 time to evaluate : 3.257 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 outliers start: 55 outliers final: 40 residues processed: 267 average time/residue: 2.1468 time to fit residues: 667.9035 Evaluate side-chains 275 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 235 time to evaluate : 2.291 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 16 residues processed: 24 average time/residue: 0.4475 time to fit residues: 20.7773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 74 optimal weight: 3.9990 chunk 198 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 129 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 220 optimal weight: 5.9990 chunk 183 optimal weight: 0.6980 chunk 102 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 72 optimal weight: 0.4980 chunk 115 optimal weight: 6.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: