Starting phenix.real_space_refine (version: 1.21rc1) on Tue May 16 06:56:22 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fwj_29506/05_2023/8fwj_29506_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fwj_29506/05_2023/8fwj_29506.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fwj_29506/05_2023/8fwj_29506.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fwj_29506/05_2023/8fwj_29506.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fwj_29506/05_2023/8fwj_29506_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fwj_29506/05_2023/8fwj_29506_trim_updated.pdb" } resolution = 2.7 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= 0.003 sd= 0.030 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 35292 atoms to isotropic. 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: 7 Type Number sf(0) Gaussians P 60 5.49 5 Mg 24 5.21 5 S 216 5.16 5 C 37512 2.51 5 N 10872 2.21 5 O 11496 1.98 5 H 24 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 105": "OD1" <-> "OD2" Residue "A PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 116": "OE1" <-> "OE2" Residue "A PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 225": "OD1" <-> "OD2" Residue "A PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 310": "NH1" <-> "NH2" Residue "A TYR 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 441": "NH1" <-> "NH2" Residue "A ARG 508": "NH1" <-> "NH2" Residue "A ARG 510": "NH1" <-> "NH2" Residue "A GLU 519": "OE1" <-> "OE2" Residue "B ASP 105": "OD1" <-> "OD2" Residue "B PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 116": "OE1" <-> "OE2" Residue "B PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 225": "OD1" <-> "OD2" Residue "B PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 310": "NH1" <-> "NH2" Residue "B TYR 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 441": "NH1" <-> "NH2" Residue "B ARG 508": "NH1" <-> "NH2" Residue "B ARG 510": "NH1" <-> "NH2" Residue "B GLU 519": "OE1" <-> "OE2" Residue "C ASP 105": "OD1" <-> "OD2" Residue "C PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 116": "OE1" <-> "OE2" Residue "C PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 225": "OD1" <-> "OD2" Residue "C PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 310": "NH1" <-> "NH2" Residue "C TYR 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 441": "NH1" <-> "NH2" Residue "C ARG 508": "NH1" <-> "NH2" Residue "C ARG 510": "NH1" <-> "NH2" Residue "C GLU 519": "OE1" <-> "OE2" Residue "D ASP 105": "OD1" <-> "OD2" Residue "D PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 116": "OE1" <-> "OE2" Residue "D PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 225": "OD1" <-> "OD2" Residue "D PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 310": "NH1" <-> "NH2" Residue "D TYR 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 441": "NH1" <-> "NH2" Residue "D ARG 508": "NH1" <-> "NH2" Residue "D ARG 510": "NH1" <-> "NH2" Residue "D GLU 519": "OE1" <-> "OE2" Residue "E ASP 105": "OD1" <-> "OD2" Residue "E PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 116": "OE1" <-> "OE2" Residue "E PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 225": "OD1" <-> "OD2" Residue "E PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 310": "NH1" <-> "NH2" Residue "E TYR 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 441": "NH1" <-> "NH2" Residue "E ARG 508": "NH1" <-> "NH2" Residue "E ARG 510": "NH1" <-> "NH2" Residue "E GLU 519": "OE1" <-> "OE2" Residue "F ASP 105": "OD1" <-> "OD2" Residue "F PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 116": "OE1" <-> "OE2" Residue "F PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 225": "OD1" <-> "OD2" Residue "F PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 310": "NH1" <-> "NH2" Residue "F TYR 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 441": "NH1" <-> "NH2" Residue "F ARG 508": "NH1" <-> "NH2" Residue "F ARG 510": "NH1" <-> "NH2" Residue "F GLU 519": "OE1" <-> "OE2" Residue "G ASP 105": "OD1" <-> "OD2" Residue "G PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 116": "OE1" <-> "OE2" Residue "G PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 225": "OD1" <-> "OD2" Residue "G PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 310": "NH1" <-> "NH2" Residue "G TYR 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 441": "NH1" <-> "NH2" Residue "G ARG 508": "NH1" <-> "NH2" Residue "G ARG 510": "NH1" <-> "NH2" Residue "G GLU 519": "OE1" <-> "OE2" Residue "H ASP 105": "OD1" <-> "OD2" Residue "H PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 116": "OE1" <-> "OE2" Residue "H PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 225": "OD1" <-> "OD2" Residue "H PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 310": "NH1" <-> "NH2" Residue "H TYR 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 441": "NH1" <-> "NH2" Residue "H ARG 508": "NH1" <-> "NH2" Residue "H ARG 510": "NH1" <-> "NH2" Residue "H GLU 519": "OE1" <-> "OE2" Residue "I ASP 105": "OD1" <-> "OD2" Residue "I PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 116": "OE1" <-> "OE2" Residue "I PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 225": "OD1" <-> "OD2" Residue "I PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 310": "NH1" <-> "NH2" Residue "I TYR 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 441": "NH1" <-> "NH2" Residue "I ARG 508": "NH1" <-> "NH2" Residue "I ARG 510": "NH1" <-> "NH2" Residue "I GLU 519": "OE1" <-> "OE2" Residue "J ASP 105": "OD1" <-> "OD2" Residue "J PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 116": "OE1" <-> "OE2" Residue "J PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 225": "OD1" <-> "OD2" Residue "J PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 310": "NH1" <-> "NH2" Residue "J TYR 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 441": "NH1" <-> "NH2" Residue "J ARG 508": "NH1" <-> "NH2" Residue "J ARG 510": "NH1" <-> "NH2" Residue "J GLU 519": "OE1" <-> "OE2" Residue "K ASP 105": "OD1" <-> "OD2" Residue "K PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 116": "OE1" <-> "OE2" Residue "K PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 225": "OD1" <-> "OD2" Residue "K PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 310": "NH1" <-> "NH2" Residue "K TYR 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 441": "NH1" <-> "NH2" Residue "K ARG 508": "NH1" <-> "NH2" Residue "K ARG 510": "NH1" <-> "NH2" Residue "K GLU 519": "OE1" <-> "OE2" Residue "L ASP 105": "OD1" <-> "OD2" Residue "L PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 116": "OE1" <-> "OE2" Residue "L PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 225": "OD1" <-> "OD2" Residue "L PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 310": "NH1" <-> "NH2" Residue "L TYR 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 441": "NH1" <-> "NH2" Residue "L ARG 508": "NH1" <-> "NH2" Residue "L ARG 510": "NH1" <-> "NH2" Residue "L GLU 519": "OE1" <-> "OE2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/chem_data/mon_lib" Total number of atoms: 60204 Number of models: 1 Model: "" Number of chains: 48 Chain: "A" Number of atoms: 4283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 552, 4283 Classifications: {'peptide': 552} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 536} Chain breaks: 1 Chain: "B" Number of atoms: 4283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 552, 4283 Classifications: {'peptide': 552} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 536} Chain breaks: 1 Chain: "C" Number of atoms: 4283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 552, 4283 Classifications: {'peptide': 552} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 536} Chain breaks: 1 Chain: "D" Number of atoms: 4283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 552, 4283 Classifications: {'peptide': 552} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 536} Chain breaks: 1 Chain: "E" Number of atoms: 4283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 552, 4283 Classifications: {'peptide': 552} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 536} Chain breaks: 1 Chain: "F" Number of atoms: 4283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 552, 4283 Classifications: {'peptide': 552} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 536} Chain breaks: 1 Chain: "G" Number of atoms: 4283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 552, 4283 Classifications: {'peptide': 552} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 536} Chain breaks: 1 Chain: "H" Number of atoms: 4283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 552, 4283 Classifications: {'peptide': 552} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 536} Chain breaks: 1 Chain: "I" Number of atoms: 4283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 552, 4283 Classifications: {'peptide': 552} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 536} Chain breaks: 1 Chain: "J" Number of atoms: 4283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 552, 4283 Classifications: {'peptide': 552} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 536} Chain breaks: 1 Chain: "K" Number of atoms: 4283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 552, 4283 Classifications: {'peptide': 552} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 536} Chain breaks: 1 Chain: "L" Number of atoms: 4283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 552, 4283 Classifications: {'peptide': 552} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 536} Chain breaks: 1 Chain: "M" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 670 Classifications: {'peptide': 85} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 78} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "N" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 670 Classifications: {'peptide': 85} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 78} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "O" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 670 Classifications: {'peptide': 85} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 78} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "P" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 670 Classifications: {'peptide': 85} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 78} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "Q" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 670 Classifications: {'peptide': 85} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 78} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "R" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 670 Classifications: {'peptide': 85} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 78} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "S" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 670 Classifications: {'peptide': 85} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 78} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "T" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 670 Classifications: {'peptide': 85} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 78} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "U" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 670 Classifications: {'peptide': 85} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 78} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "V" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 670 Classifications: {'peptide': 85} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 78} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "W" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 670 Classifications: {'peptide': 85} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 78} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "X" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 670 Classifications: {'peptide': 85} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 78} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {' MG': 3, 'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 60 Unusual residues: {' MG': 2, 'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 60 Unusual residues: {' MG': 2, 'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 60 Unusual residues: {' MG': 2, 'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 60 Unusual residues: {' MG': 2, 'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "F" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 59 Unusual residues: {' MG': 1, 'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 60 Unusual residues: {' MG': 2, 'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "H" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 60 Unusual residues: {' MG': 2, 'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "I" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 60 Unusual residues: {' MG': 2, 'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "J" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 60 Unusual residues: {' MG': 2, 'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "K" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 60 Unusual residues: {' MG': 2, 'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "L" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 60 Unusual residues: {' MG': 2, 'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "F" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "G" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "H" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "I" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "J" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "K" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "L" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Time building chain proxies: 22.43, per 1000 atoms: 0.37 Number of scatterers: 60204 At special positions: 0 Unit cell: (113, 121, 367, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 216 16.00 P 60 15.00 Mg 24 11.99 O 11496 8.00 N 10872 7.00 C 37512 6.00 H 24 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 18.65 Conformation dependent library (CDL) restraints added in 6.4 seconds 15144 Ramachandran restraints generated. 7572 Oldfield, 0 Emsley, 7572 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13992 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 228 helices and 48 sheets defined 41.4% alpha, 16.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.96 Creating SS restraints... Processing helix chain 'A' and resid 11 through 17 Processing helix chain 'A' and resid 37 through 51 Processing helix chain 'A' and resid 65 through 75 removed outlier: 3.845A pdb=" N VAL A 72 " --> pdb=" O ILE A 68 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N SER A 74 " --> pdb=" O ASN A 70 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N LEU A 75 " --> pdb=" O ASN A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 84 Processing helix chain 'A' and resid 109 through 122 Processing helix chain 'A' and resid 133 through 138 Processing helix chain 'A' and resid 142 through 159 Processing helix chain 'A' and resid 251 through 256 Processing helix chain 'A' and resid 278 through 292 removed outlier: 3.552A pdb=" N ARG A 292 " --> pdb=" O ALA A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 315 removed outlier: 3.929A pdb=" N SER A 314 " --> pdb=" O ARG A 310 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LEU A 315 " --> pdb=" O ASN A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 325 Processing helix chain 'A' and resid 340 through 354 Processing helix chain 'A' and resid 364 through 367 removed outlier: 3.849A pdb=" N PHE A 367 " --> pdb=" O ILE A 364 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 364 through 367' Processing helix chain 'A' and resid 373 through 390 Processing helix chain 'A' and resid 413 through 415 No H-bonds generated for 'chain 'A' and resid 413 through 415' Processing helix chain 'A' and resid 474 through 551 removed outlier: 3.685A pdb=" N SER A 533 " --> pdb=" O LEU A 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 17 Processing helix chain 'B' and resid 37 through 51 Processing helix chain 'B' and resid 65 through 75 removed outlier: 3.845A pdb=" N VAL B 72 " --> pdb=" O ILE B 68 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N SER B 74 " --> pdb=" O ASN B 70 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N LEU B 75 " --> pdb=" O ASN B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 84 Processing helix chain 'B' and resid 109 through 122 Processing helix chain 'B' and resid 133 through 138 Processing helix chain 'B' and resid 142 through 159 Processing helix chain 'B' and resid 251 through 256 Processing helix chain 'B' and resid 278 through 292 removed outlier: 3.553A pdb=" N ARG B 292 " --> pdb=" O ALA B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 315 removed outlier: 3.929A pdb=" N SER B 314 " --> pdb=" O ARG B 310 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LEU B 315 " --> pdb=" O ASN B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 325 Processing helix chain 'B' and resid 340 through 354 Processing helix chain 'B' and resid 364 through 367 removed outlier: 3.849A pdb=" N PHE B 367 " --> pdb=" O ILE B 364 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 364 through 367' Processing helix chain 'B' and resid 373 through 390 Processing helix chain 'B' and resid 413 through 415 No H-bonds generated for 'chain 'B' and resid 413 through 415' Processing helix chain 'B' and resid 474 through 551 removed outlier: 3.685A pdb=" N SER B 533 " --> pdb=" O LEU B 530 " (cutoff:3.500A) Processing helix chain 'C' and resid 11 through 17 Processing helix chain 'C' and resid 37 through 51 Processing helix chain 'C' and resid 65 through 75 removed outlier: 3.845A pdb=" N VAL C 72 " --> pdb=" O ILE C 68 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N SER C 74 " --> pdb=" O ASN C 70 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N LEU C 75 " --> pdb=" O ASN C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 84 Processing helix chain 'C' and resid 109 through 122 Processing helix chain 'C' and resid 133 through 138 Processing helix chain 'C' and resid 142 through 159 Processing helix chain 'C' and resid 251 through 256 Processing helix chain 'C' and resid 278 through 292 removed outlier: 3.554A pdb=" N ARG C 292 " --> pdb=" O ALA C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 315 removed outlier: 3.929A pdb=" N SER C 314 " --> pdb=" O ARG C 310 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LEU C 315 " --> pdb=" O ASN C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 325 Processing helix chain 'C' and resid 340 through 354 Processing helix chain 'C' and resid 364 through 367 removed outlier: 3.850A pdb=" N PHE C 367 " --> pdb=" O ILE C 364 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 364 through 367' Processing helix chain 'C' and resid 373 through 390 Processing helix chain 'C' and resid 413 through 415 No H-bonds generated for 'chain 'C' and resid 413 through 415' Processing helix chain 'C' and resid 474 through 551 removed outlier: 3.685A pdb=" N SER C 533 " --> pdb=" O LEU C 530 " (cutoff:3.500A) Processing helix chain 'D' and resid 11 through 17 Processing helix chain 'D' and resid 37 through 51 Processing helix chain 'D' and resid 65 through 75 removed outlier: 3.845A pdb=" N VAL D 72 " --> pdb=" O ILE D 68 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N SER D 74 " --> pdb=" O ASN D 70 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N LEU D 75 " --> pdb=" O ASN D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 84 Processing helix chain 'D' and resid 109 through 122 Processing helix chain 'D' and resid 133 through 138 Processing helix chain 'D' and resid 142 through 159 Processing helix chain 'D' and resid 251 through 256 Processing helix chain 'D' and resid 278 through 292 removed outlier: 3.553A pdb=" N ARG D 292 " --> pdb=" O ALA D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 315 removed outlier: 3.930A pdb=" N SER D 314 " --> pdb=" O ARG D 310 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LEU D 315 " --> pdb=" O ASN D 311 " (cutoff:3.500A) Processing helix chain 'D' and resid 319 through 325 Processing helix chain 'D' and resid 340 through 354 Processing helix chain 'D' and resid 364 through 367 removed outlier: 3.850A pdb=" N PHE D 367 " --> pdb=" O ILE D 364 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 364 through 367' Processing helix chain 'D' and resid 373 through 390 Processing helix chain 'D' and resid 413 through 415 No H-bonds generated for 'chain 'D' and resid 413 through 415' Processing helix chain 'D' and resid 474 through 551 removed outlier: 3.685A pdb=" N SER D 533 " --> pdb=" O LEU D 530 " (cutoff:3.500A) Processing helix chain 'E' and resid 11 through 17 Processing helix chain 'E' and resid 37 through 51 Processing helix chain 'E' and resid 65 through 75 removed outlier: 3.846A pdb=" N VAL E 72 " --> pdb=" O ILE E 68 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N SER E 74 " --> pdb=" O ASN E 70 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N LEU E 75 " --> pdb=" O ASN E 71 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 84 Processing helix chain 'E' and resid 109 through 122 Processing helix chain 'E' and resid 133 through 138 Processing helix chain 'E' and resid 142 through 159 Processing helix chain 'E' and resid 251 through 256 Processing helix chain 'E' and resid 278 through 292 removed outlier: 3.553A pdb=" N ARG E 292 " --> pdb=" O ALA E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 305 through 315 removed outlier: 3.929A pdb=" N SER E 314 " --> pdb=" O ARG E 310 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LEU E 315 " --> pdb=" O ASN E 311 " (cutoff:3.500A) Processing helix chain 'E' and resid 319 through 325 Processing helix chain 'E' and resid 340 through 354 Processing helix chain 'E' and resid 364 through 367 removed outlier: 3.849A pdb=" N PHE E 367 " --> pdb=" O ILE E 364 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 364 through 367' Processing helix chain 'E' and resid 373 through 390 Processing helix chain 'E' and resid 413 through 415 No H-bonds generated for 'chain 'E' and resid 413 through 415' Processing helix chain 'E' and resid 474 through 551 removed outlier: 3.686A pdb=" N SER E 533 " --> pdb=" O LEU E 530 " (cutoff:3.500A) Processing helix chain 'F' and resid 11 through 17 Processing helix chain 'F' and resid 37 through 51 Processing helix chain 'F' and resid 65 through 75 removed outlier: 3.845A pdb=" N VAL F 72 " --> pdb=" O ILE F 68 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N SER F 74 " --> pdb=" O ASN F 70 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N LEU F 75 " --> pdb=" O ASN F 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 79 through 84 Processing helix chain 'F' and resid 109 through 122 Processing helix chain 'F' and resid 133 through 138 Processing helix chain 'F' and resid 142 through 159 Processing helix chain 'F' and resid 251 through 256 Processing helix chain 'F' and resid 278 through 292 removed outlier: 3.553A pdb=" N ARG F 292 " --> pdb=" O ALA F 288 " (cutoff:3.500A) Processing helix chain 'F' and resid 305 through 315 removed outlier: 3.929A pdb=" N SER F 314 " --> pdb=" O ARG F 310 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LEU F 315 " --> pdb=" O ASN F 311 " (cutoff:3.500A) Processing helix chain 'F' and resid 319 through 325 Processing helix chain 'F' and resid 340 through 354 Processing helix chain 'F' and resid 364 through 367 removed outlier: 3.849A pdb=" N PHE F 367 " --> pdb=" O ILE F 364 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 364 through 367' Processing helix chain 'F' and resid 373 through 390 Processing helix chain 'F' and resid 413 through 415 No H-bonds generated for 'chain 'F' and resid 413 through 415' Processing helix chain 'F' and resid 474 through 551 removed outlier: 3.684A pdb=" N SER F 533 " --> pdb=" O LEU F 530 " (cutoff:3.500A) Processing helix chain 'G' and resid 11 through 17 Processing helix chain 'G' and resid 37 through 51 Processing helix chain 'G' and resid 65 through 75 removed outlier: 3.845A pdb=" N VAL G 72 " --> pdb=" O ILE G 68 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N SER G 74 " --> pdb=" O ASN G 70 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N LEU G 75 " --> pdb=" O ASN G 71 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 84 Processing helix chain 'G' and resid 109 through 122 Processing helix chain 'G' and resid 133 through 138 Processing helix chain 'G' and resid 142 through 159 Processing helix chain 'G' and resid 251 through 256 Processing helix chain 'G' and resid 278 through 292 removed outlier: 3.554A pdb=" N ARG G 292 " --> pdb=" O ALA G 288 " (cutoff:3.500A) Processing helix chain 'G' and resid 305 through 315 removed outlier: 3.929A pdb=" N SER G 314 " --> pdb=" O ARG G 310 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LEU G 315 " --> pdb=" O ASN G 311 " (cutoff:3.500A) Processing helix chain 'G' and resid 319 through 325 Processing helix chain 'G' and resid 340 through 354 Processing helix chain 'G' and resid 364 through 367 removed outlier: 3.850A pdb=" N PHE G 367 " --> pdb=" O ILE G 364 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 364 through 367' Processing helix chain 'G' and resid 373 through 390 Processing helix chain 'G' and resid 413 through 415 No H-bonds generated for 'chain 'G' and resid 413 through 415' Processing helix chain 'G' and resid 474 through 551 removed outlier: 3.685A pdb=" N SER G 533 " --> pdb=" O LEU G 530 " (cutoff:3.500A) Processing helix chain 'H' and resid 11 through 17 Processing helix chain 'H' and resid 37 through 51 Processing helix chain 'H' and resid 65 through 75 removed outlier: 3.845A pdb=" N VAL H 72 " --> pdb=" O ILE H 68 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N SER H 74 " --> pdb=" O ASN H 70 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N LEU H 75 " --> pdb=" O ASN H 71 " (cutoff:3.500A) Processing helix chain 'H' and resid 79 through 84 Processing helix chain 'H' and resid 109 through 122 Processing helix chain 'H' and resid 133 through 138 Processing helix chain 'H' and resid 142 through 159 Processing helix chain 'H' and resid 251 through 256 Processing helix chain 'H' and resid 278 through 292 removed outlier: 3.553A pdb=" N ARG H 292 " --> pdb=" O ALA H 288 " (cutoff:3.500A) Processing helix chain 'H' and resid 305 through 315 removed outlier: 3.928A pdb=" N SER H 314 " --> pdb=" O ARG H 310 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LEU H 315 " --> pdb=" O ASN H 311 " (cutoff:3.500A) Processing helix chain 'H' and resid 319 through 325 Processing helix chain 'H' and resid 340 through 354 Processing helix chain 'H' and resid 364 through 367 removed outlier: 3.850A pdb=" N PHE H 367 " --> pdb=" O ILE H 364 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 364 through 367' Processing helix chain 'H' and resid 373 through 390 Processing helix chain 'H' and resid 413 through 415 No H-bonds generated for 'chain 'H' and resid 413 through 415' Processing helix chain 'H' and resid 474 through 551 removed outlier: 3.686A pdb=" N SER H 533 " --> pdb=" O LEU H 530 " (cutoff:3.500A) Processing helix chain 'I' and resid 11 through 17 Processing helix chain 'I' and resid 37 through 51 Processing helix chain 'I' and resid 65 through 75 removed outlier: 3.846A pdb=" N VAL I 72 " --> pdb=" O ILE I 68 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N SER I 74 " --> pdb=" O ASN I 70 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N LEU I 75 " --> pdb=" O ASN I 71 " (cutoff:3.500A) Processing helix chain 'I' and resid 79 through 84 Processing helix chain 'I' and resid 109 through 122 Processing helix chain 'I' and resid 133 through 138 Processing helix chain 'I' and resid 142 through 159 Processing helix chain 'I' and resid 251 through 256 Processing helix chain 'I' and resid 278 through 292 removed outlier: 3.553A pdb=" N ARG I 292 " --> pdb=" O ALA I 288 " (cutoff:3.500A) Processing helix chain 'I' and resid 305 through 315 removed outlier: 3.929A pdb=" N SER I 314 " --> pdb=" O ARG I 310 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LEU I 315 " --> pdb=" O ASN I 311 " (cutoff:3.500A) Processing helix chain 'I' and resid 319 through 325 Processing helix chain 'I' and resid 340 through 354 Processing helix chain 'I' and resid 364 through 367 removed outlier: 3.850A pdb=" N PHE I 367 " --> pdb=" O ILE I 364 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 364 through 367' Processing helix chain 'I' and resid 373 through 390 Processing helix chain 'I' and resid 413 through 415 No H-bonds generated for 'chain 'I' and resid 413 through 415' Processing helix chain 'I' and resid 474 through 551 removed outlier: 3.686A pdb=" N SER I 533 " --> pdb=" O LEU I 530 " (cutoff:3.500A) Processing helix chain 'J' and resid 11 through 17 Processing helix chain 'J' and resid 37 through 51 Processing helix chain 'J' and resid 65 through 75 removed outlier: 3.846A pdb=" N VAL J 72 " --> pdb=" O ILE J 68 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N SER J 74 " --> pdb=" O ASN J 70 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N LEU J 75 " --> pdb=" O ASN J 71 " (cutoff:3.500A) Processing helix chain 'J' and resid 79 through 84 Processing helix chain 'J' and resid 109 through 122 Processing helix chain 'J' and resid 133 through 138 Processing helix chain 'J' and resid 142 through 159 Processing helix chain 'J' and resid 251 through 256 Processing helix chain 'J' and resid 278 through 292 removed outlier: 3.554A pdb=" N ARG J 292 " --> pdb=" O ALA J 288 " (cutoff:3.500A) Processing helix chain 'J' and resid 305 through 315 removed outlier: 3.930A pdb=" N SER J 314 " --> pdb=" O ARG J 310 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LEU J 315 " --> pdb=" O ASN J 311 " (cutoff:3.500A) Processing helix chain 'J' and resid 319 through 325 Processing helix chain 'J' and resid 340 through 354 Processing helix chain 'J' and resid 364 through 367 removed outlier: 3.850A pdb=" N PHE J 367 " --> pdb=" O ILE J 364 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 364 through 367' Processing helix chain 'J' and resid 373 through 390 Processing helix chain 'J' and resid 413 through 415 No H-bonds generated for 'chain 'J' and resid 413 through 415' Processing helix chain 'J' and resid 474 through 551 removed outlier: 3.685A pdb=" N SER J 533 " --> pdb=" O LEU J 530 " (cutoff:3.500A) Processing helix chain 'K' and resid 11 through 17 Processing helix chain 'K' and resid 37 through 51 Processing helix chain 'K' and resid 65 through 75 removed outlier: 3.845A pdb=" N VAL K 72 " --> pdb=" O ILE K 68 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N SER K 74 " --> pdb=" O ASN K 70 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N LEU K 75 " --> pdb=" O ASN K 71 " (cutoff:3.500A) Processing helix chain 'K' and resid 79 through 84 Processing helix chain 'K' and resid 109 through 122 Processing helix chain 'K' and resid 133 through 138 Processing helix chain 'K' and resid 142 through 159 Processing helix chain 'K' and resid 251 through 256 Processing helix chain 'K' and resid 278 through 292 removed outlier: 3.553A pdb=" N ARG K 292 " --> pdb=" O ALA K 288 " (cutoff:3.500A) Processing helix chain 'K' and resid 305 through 315 removed outlier: 3.929A pdb=" N SER K 314 " --> pdb=" O ARG K 310 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LEU K 315 " --> pdb=" O ASN K 311 " (cutoff:3.500A) Processing helix chain 'K' and resid 319 through 325 Processing helix chain 'K' and resid 340 through 354 Processing helix chain 'K' and resid 364 through 367 removed outlier: 3.850A pdb=" N PHE K 367 " --> pdb=" O ILE K 364 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 364 through 367' Processing helix chain 'K' and resid 373 through 390 Processing helix chain 'K' and resid 413 through 415 No H-bonds generated for 'chain 'K' and resid 413 through 415' Processing helix chain 'K' and resid 474 through 551 removed outlier: 3.685A pdb=" N SER K 533 " --> pdb=" O LEU K 530 " (cutoff:3.500A) Processing helix chain 'L' and resid 11 through 17 Processing helix chain 'L' and resid 37 through 51 Processing helix chain 'L' and resid 65 through 75 removed outlier: 3.845A pdb=" N VAL L 72 " --> pdb=" O ILE L 68 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N SER L 74 " --> pdb=" O ASN L 70 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N LEU L 75 " --> pdb=" O ASN L 71 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 84 Processing helix chain 'L' and resid 109 through 122 Processing helix chain 'L' and resid 133 through 138 Processing helix chain 'L' and resid 142 through 159 Processing helix chain 'L' and resid 251 through 256 Processing helix chain 'L' and resid 278 through 292 removed outlier: 3.554A pdb=" N ARG L 292 " --> pdb=" O ALA L 288 " (cutoff:3.500A) Processing helix chain 'L' and resid 305 through 315 removed outlier: 3.929A pdb=" N SER L 314 " --> pdb=" O ARG L 310 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LEU L 315 " --> pdb=" O ASN L 311 " (cutoff:3.500A) Processing helix chain 'L' and resid 319 through 325 Processing helix chain 'L' and resid 340 through 354 Processing helix chain 'L' and resid 364 through 367 removed outlier: 3.850A pdb=" N PHE L 367 " --> pdb=" O ILE L 364 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 364 through 367' Processing helix chain 'L' and resid 373 through 390 Processing helix chain 'L' and resid 413 through 415 No H-bonds generated for 'chain 'L' and resid 413 through 415' Processing helix chain 'L' and resid 474 through 551 removed outlier: 3.684A pdb=" N SER L 533 " --> pdb=" O LEU L 530 " (cutoff:3.500A) Processing helix chain 'M' and resid 14 through 29 Processing helix chain 'M' and resid 46 through 52 Processing helix chain 'M' and resid 78 through 84 Processing helix chain 'N' and resid 14 through 29 Processing helix chain 'N' and resid 46 through 52 Processing helix chain 'N' and resid 78 through 84 Processing helix chain 'O' and resid 14 through 29 Processing helix chain 'O' and resid 46 through 52 Processing helix chain 'O' and resid 78 through 84 Processing helix chain 'P' and resid 14 through 29 Processing helix chain 'P' and resid 46 through 52 Processing helix chain 'P' and resid 78 through 84 Processing helix chain 'Q' and resid 14 through 29 Processing helix chain 'Q' and resid 46 through 52 Processing helix chain 'Q' and resid 78 through 84 Processing helix chain 'R' and resid 14 through 29 Processing helix chain 'R' and resid 46 through 52 Processing helix chain 'R' and resid 78 through 84 Processing helix chain 'S' and resid 14 through 29 Processing helix chain 'S' and resid 46 through 52 Processing helix chain 'S' and resid 78 through 84 Processing helix chain 'T' and resid 14 through 29 Processing helix chain 'T' and resid 46 through 52 Processing helix chain 'T' and resid 78 through 84 Processing helix chain 'U' and resid 14 through 29 Processing helix chain 'U' and resid 46 through 52 Processing helix chain 'U' and resid 78 through 84 Processing helix chain 'V' and resid 14 through 29 Processing helix chain 'V' and resid 46 through 52 Processing helix chain 'V' and resid 78 through 84 Processing helix chain 'W' and resid 14 through 29 Processing helix chain 'W' and resid 46 through 52 Processing helix chain 'W' and resid 78 through 84 Processing helix chain 'X' and resid 14 through 29 Processing helix chain 'X' and resid 46 through 52 Processing helix chain 'X' and resid 78 through 84 Processing sheet with id= A, first strand: chain 'A' and resid 218 through 220 removed outlier: 4.537A pdb=" N ARG A 201 " --> pdb=" O PHE A 220 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N VAL A 187 " --> pdb=" O VAL A 206 " (cutoff:3.500A) removed outlier: 8.658A pdb=" N ILE A 188 " --> pdb=" O PRO A 26 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N LEU A 28 " --> pdb=" O ILE A 188 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N LEU A 190 " --> pdb=" O LEU A 28 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N CYS A 30 " --> pdb=" O LEU A 190 " (cutoff:3.500A) removed outlier: 8.429A pdb=" N HIS A 192 " --> pdb=" O CYS A 30 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N THR A 163 " --> pdb=" O SER A 27 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N VAL A 29 " --> pdb=" O THR A 163 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ILE A 165 " --> pdb=" O VAL A 29 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N VAL A 127 " --> pdb=" O PRO A 55 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N VAL A 57 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N LEU A 129 " --> pdb=" O VAL A 57 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N VAL A 59 " --> pdb=" O LEU A 129 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 431 through 440 removed outlier: 6.505A pdb=" N TRP A 419 " --> pdb=" O LEU A 438 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N GLY A 394 " --> pdb=" O ILE A 268 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N VAL A 270 " --> pdb=" O GLY A 394 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N PHE A 396 " --> pdb=" O VAL A 270 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N GLY A 272 " --> pdb=" O PHE A 396 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N HIS A 398 " --> pdb=" O GLY A 272 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 452 through 455 removed outlier: 3.644A pdb=" N SER A 460 " --> pdb=" O LEU A 453 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 198 through 208 removed outlier: 6.711A pdb=" N VAL B 187 " --> pdb=" O VAL B 206 " (cutoff:3.500A) removed outlier: 8.659A pdb=" N ILE B 188 " --> pdb=" O PRO B 26 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N LEU B 28 " --> pdb=" O ILE B 188 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N LEU B 190 " --> pdb=" O LEU B 28 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N CYS B 30 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 8.429A pdb=" N HIS B 192 " --> pdb=" O CYS B 30 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N THR B 163 " --> pdb=" O SER B 27 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N VAL B 29 " --> pdb=" O THR B 163 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ILE B 165 " --> pdb=" O VAL B 29 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N VAL B 127 " --> pdb=" O PRO B 55 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N VAL B 57 " --> pdb=" O VAL B 127 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N LEU B 129 " --> pdb=" O VAL B 57 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N VAL B 59 " --> pdb=" O LEU B 129 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 431 through 440 removed outlier: 6.504A pdb=" N TRP B 419 " --> pdb=" O LEU B 438 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N GLY B 394 " --> pdb=" O ILE B 268 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N VAL B 270 " --> pdb=" O GLY B 394 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N PHE B 396 " --> pdb=" O VAL B 270 " (cutoff:3.500A) removed outlier: 8.203A pdb=" N GLY B 272 " --> pdb=" O PHE B 396 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N HIS B 398 " --> pdb=" O GLY B 272 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 452 through 455 removed outlier: 3.642A pdb=" N SER B 460 " --> pdb=" O LEU B 453 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 198 through 208 removed outlier: 6.712A pdb=" N VAL C 187 " --> pdb=" O VAL C 206 " (cutoff:3.500A) removed outlier: 8.658A pdb=" N ILE C 188 " --> pdb=" O PRO C 26 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N LEU C 28 " --> pdb=" O ILE C 188 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N LEU C 190 " --> pdb=" O LEU C 28 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N CYS C 30 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 8.428A pdb=" N HIS C 192 " --> pdb=" O CYS C 30 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N THR C 163 " --> pdb=" O SER C 27 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N VAL C 29 " --> pdb=" O THR C 163 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ILE C 165 " --> pdb=" O VAL C 29 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N VAL C 127 " --> pdb=" O PRO C 55 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N VAL C 57 " --> pdb=" O VAL C 127 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N LEU C 129 " --> pdb=" O VAL C 57 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N VAL C 59 " --> pdb=" O LEU C 129 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 431 through 440 removed outlier: 6.505A pdb=" N TRP C 419 " --> pdb=" O LEU C 438 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N GLY C 394 " --> pdb=" O ILE C 268 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N VAL C 270 " --> pdb=" O GLY C 394 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N PHE C 396 " --> pdb=" O VAL C 270 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N GLY C 272 " --> pdb=" O PHE C 396 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N HIS C 398 " --> pdb=" O GLY C 272 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 452 through 455 removed outlier: 3.643A pdb=" N SER C 460 " --> pdb=" O LEU C 453 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 218 through 220 removed outlier: 4.536A pdb=" N ARG D 201 " --> pdb=" O PHE D 220 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N VAL D 187 " --> pdb=" O VAL D 206 " (cutoff:3.500A) removed outlier: 8.658A pdb=" N ILE D 188 " --> pdb=" O PRO D 26 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N LEU D 28 " --> pdb=" O ILE D 188 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N LEU D 190 " --> pdb=" O LEU D 28 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N CYS D 30 " --> pdb=" O LEU D 190 " (cutoff:3.500A) removed outlier: 8.429A pdb=" N HIS D 192 " --> pdb=" O CYS D 30 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N THR D 163 " --> pdb=" O SER D 27 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N VAL D 29 " --> pdb=" O THR D 163 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ILE D 165 " --> pdb=" O VAL D 29 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N VAL D 127 " --> pdb=" O PRO D 55 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N VAL D 57 " --> pdb=" O VAL D 127 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N LEU D 129 " --> pdb=" O VAL D 57 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N VAL D 59 " --> pdb=" O LEU D 129 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 431 through 440 removed outlier: 6.505A pdb=" N TRP D 419 " --> pdb=" O LEU D 438 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N GLY D 394 " --> pdb=" O ILE D 268 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N VAL D 270 " --> pdb=" O GLY D 394 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N PHE D 396 " --> pdb=" O VAL D 270 " (cutoff:3.500A) removed outlier: 8.203A pdb=" N GLY D 272 " --> pdb=" O PHE D 396 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N HIS D 398 " --> pdb=" O GLY D 272 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 452 through 455 removed outlier: 3.643A pdb=" N SER D 460 " --> pdb=" O LEU D 453 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'E' and resid 198 through 208 removed outlier: 6.712A pdb=" N VAL E 187 " --> pdb=" O VAL E 206 " (cutoff:3.500A) removed outlier: 8.658A pdb=" N ILE E 188 " --> pdb=" O PRO E 26 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N LEU E 28 " --> pdb=" O ILE E 188 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N LEU E 190 " --> pdb=" O LEU E 28 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N CYS E 30 " --> pdb=" O LEU E 190 " (cutoff:3.500A) removed outlier: 8.429A pdb=" N HIS E 192 " --> pdb=" O CYS E 30 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N THR E 163 " --> pdb=" O SER E 27 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N VAL E 29 " --> pdb=" O THR E 163 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ILE E 165 " --> pdb=" O VAL E 29 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N VAL E 127 " --> pdb=" O PRO E 55 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N VAL E 57 " --> pdb=" O VAL E 127 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N LEU E 129 " --> pdb=" O VAL E 57 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N VAL E 59 " --> pdb=" O LEU E 129 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'E' and resid 431 through 440 removed outlier: 6.506A pdb=" N TRP E 419 " --> pdb=" O LEU E 438 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N GLY E 394 " --> pdb=" O ILE E 268 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N VAL E 270 " --> pdb=" O GLY E 394 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N PHE E 396 " --> pdb=" O VAL E 270 " (cutoff:3.500A) removed outlier: 8.203A pdb=" N GLY E 272 " --> pdb=" O PHE E 396 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N HIS E 398 " --> pdb=" O GLY E 272 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'E' and resid 452 through 455 removed outlier: 3.643A pdb=" N SER E 460 " --> pdb=" O LEU E 453 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'F' and resid 218 through 220 removed outlier: 4.537A pdb=" N ARG F 201 " --> pdb=" O PHE F 220 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N VAL F 187 " --> pdb=" O VAL F 206 " (cutoff:3.500A) removed outlier: 8.658A pdb=" N ILE F 188 " --> pdb=" O PRO F 26 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N LEU F 28 " --> pdb=" O ILE F 188 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N LEU F 190 " --> pdb=" O LEU F 28 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N CYS F 30 " --> pdb=" O LEU F 190 " (cutoff:3.500A) removed outlier: 8.428A pdb=" N HIS F 192 " --> pdb=" O CYS F 30 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N THR F 163 " --> pdb=" O SER F 27 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N VAL F 29 " --> pdb=" O THR F 163 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ILE F 165 " --> pdb=" O VAL F 29 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N VAL F 127 " --> pdb=" O PRO F 55 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N VAL F 57 " --> pdb=" O VAL F 127 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N LEU F 129 " --> pdb=" O VAL F 57 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N VAL F 59 " --> pdb=" O LEU F 129 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'F' and resid 431 through 440 removed outlier: 6.506A pdb=" N TRP F 419 " --> pdb=" O LEU F 438 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N GLY F 394 " --> pdb=" O ILE F 268 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N VAL F 270 " --> pdb=" O GLY F 394 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N PHE F 396 " --> pdb=" O VAL F 270 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N GLY F 272 " --> pdb=" O PHE F 396 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N HIS F 398 " --> pdb=" O GLY F 272 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'F' and resid 452 through 455 removed outlier: 3.642A pdb=" N SER F 460 " --> pdb=" O LEU F 453 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'G' and resid 218 through 220 removed outlier: 4.537A pdb=" N ARG G 201 " --> pdb=" O PHE G 220 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N VAL G 187 " --> pdb=" O VAL G 206 " (cutoff:3.500A) removed outlier: 8.657A pdb=" N ILE G 188 " --> pdb=" O PRO G 26 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N LEU G 28 " --> pdb=" O ILE G 188 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N LEU G 190 " --> pdb=" O LEU G 28 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N CYS G 30 " --> pdb=" O LEU G 190 " (cutoff:3.500A) removed outlier: 8.429A pdb=" N HIS G 192 " --> pdb=" O CYS G 30 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N THR G 163 " --> pdb=" O SER G 27 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N VAL G 29 " --> pdb=" O THR G 163 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ILE G 165 " --> pdb=" O VAL G 29 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N VAL G 127 " --> pdb=" O PRO G 55 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N VAL G 57 " --> pdb=" O VAL G 127 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N LEU G 129 " --> pdb=" O VAL G 57 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N VAL G 59 " --> pdb=" O LEU G 129 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'G' and resid 431 through 440 removed outlier: 6.506A pdb=" N TRP G 419 " --> pdb=" O LEU G 438 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N GLY G 394 " --> pdb=" O ILE G 268 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N VAL G 270 " --> pdb=" O GLY G 394 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N PHE G 396 " --> pdb=" O VAL G 270 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N GLY G 272 " --> pdb=" O PHE G 396 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N HIS G 398 " --> pdb=" O GLY G 272 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'G' and resid 452 through 455 removed outlier: 3.643A pdb=" N SER G 460 " --> pdb=" O LEU G 453 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'H' and resid 198 through 208 removed outlier: 6.711A pdb=" N VAL H 187 " --> pdb=" O VAL H 206 " (cutoff:3.500A) removed outlier: 8.657A pdb=" N ILE H 188 " --> pdb=" O PRO H 26 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N LEU H 28 " --> pdb=" O ILE H 188 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N LEU H 190 " --> pdb=" O LEU H 28 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N CYS H 30 " --> pdb=" O LEU H 190 " (cutoff:3.500A) removed outlier: 8.429A pdb=" N HIS H 192 " --> pdb=" O CYS H 30 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N THR H 163 " --> pdb=" O SER H 27 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N VAL H 29 " --> pdb=" O THR H 163 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ILE H 165 " --> pdb=" O VAL H 29 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N VAL H 127 " --> pdb=" O PRO H 55 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N VAL H 57 " --> pdb=" O VAL H 127 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N LEU H 129 " --> pdb=" O VAL H 57 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N VAL H 59 " --> pdb=" O LEU H 129 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'H' and resid 431 through 440 removed outlier: 6.505A pdb=" N TRP H 419 " --> pdb=" O LEU H 438 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N GLY H 394 " --> pdb=" O ILE H 268 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N VAL H 270 " --> pdb=" O GLY H 394 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N PHE H 396 " --> pdb=" O VAL H 270 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N GLY H 272 " --> pdb=" O PHE H 396 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N HIS H 398 " --> pdb=" O GLY H 272 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'H' and resid 452 through 455 removed outlier: 3.643A pdb=" N SER H 460 " --> pdb=" O LEU H 453 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'I' and resid 218 through 220 removed outlier: 4.537A pdb=" N ARG I 201 " --> pdb=" O PHE I 220 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N VAL I 187 " --> pdb=" O VAL I 206 " (cutoff:3.500A) removed outlier: 8.657A pdb=" N ILE I 188 " --> pdb=" O PRO I 26 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N LEU I 28 " --> pdb=" O ILE I 188 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N LEU I 190 " --> pdb=" O LEU I 28 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N CYS I 30 " --> pdb=" O LEU I 190 " (cutoff:3.500A) removed outlier: 8.429A pdb=" N HIS I 192 " --> pdb=" O CYS I 30 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N THR I 163 " --> pdb=" O SER I 27 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N VAL I 29 " --> pdb=" O THR I 163 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ILE I 165 " --> pdb=" O VAL I 29 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N VAL I 127 " --> pdb=" O PRO I 55 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N VAL I 57 " --> pdb=" O VAL I 127 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N LEU I 129 " --> pdb=" O VAL I 57 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N VAL I 59 " --> pdb=" O LEU I 129 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'I' and resid 431 through 440 removed outlier: 6.506A pdb=" N TRP I 419 " --> pdb=" O LEU I 438 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N GLY I 394 " --> pdb=" O ILE I 268 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N VAL I 270 " --> pdb=" O GLY I 394 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N PHE I 396 " --> pdb=" O VAL I 270 " (cutoff:3.500A) removed outlier: 8.203A pdb=" N GLY I 272 " --> pdb=" O PHE I 396 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N HIS I 398 " --> pdb=" O GLY I 272 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'I' and resid 452 through 455 removed outlier: 3.643A pdb=" N SER I 460 " --> pdb=" O LEU I 453 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'J' and resid 218 through 220 removed outlier: 4.537A pdb=" N ARG J 201 " --> pdb=" O PHE J 220 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N VAL J 187 " --> pdb=" O VAL J 206 " (cutoff:3.500A) removed outlier: 8.658A pdb=" N ILE J 188 " --> pdb=" O PRO J 26 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N LEU J 28 " --> pdb=" O ILE J 188 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N LEU J 190 " --> pdb=" O LEU J 28 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N CYS J 30 " --> pdb=" O LEU J 190 " (cutoff:3.500A) removed outlier: 8.428A pdb=" N HIS J 192 " --> pdb=" O CYS J 30 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N THR J 163 " --> pdb=" O SER J 27 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N VAL J 29 " --> pdb=" O THR J 163 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ILE J 165 " --> pdb=" O VAL J 29 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N VAL J 127 " --> pdb=" O PRO J 55 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N VAL J 57 " --> pdb=" O VAL J 127 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N LEU J 129 " --> pdb=" O VAL J 57 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N VAL J 59 " --> pdb=" O LEU J 129 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'J' and resid 431 through 440 removed outlier: 6.506A pdb=" N TRP J 419 " --> pdb=" O LEU J 438 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N GLY J 394 " --> pdb=" O ILE J 268 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N VAL J 270 " --> pdb=" O GLY J 394 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N PHE J 396 " --> pdb=" O VAL J 270 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N GLY J 272 " --> pdb=" O PHE J 396 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N HIS J 398 " --> pdb=" O GLY J 272 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'J' and resid 452 through 455 removed outlier: 3.643A pdb=" N SER J 460 " --> pdb=" O LEU J 453 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'K' and resid 198 through 208 removed outlier: 6.712A pdb=" N VAL K 187 " --> pdb=" O VAL K 206 " (cutoff:3.500A) removed outlier: 8.658A pdb=" N ILE K 188 " --> pdb=" O PRO K 26 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N LEU K 28 " --> pdb=" O ILE K 188 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N LEU K 190 " --> pdb=" O LEU K 28 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N CYS K 30 " --> pdb=" O LEU K 190 " (cutoff:3.500A) removed outlier: 8.428A pdb=" N HIS K 192 " --> pdb=" O CYS K 30 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N THR K 163 " --> pdb=" O SER K 27 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N VAL K 29 " --> pdb=" O THR K 163 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ILE K 165 " --> pdb=" O VAL K 29 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N VAL K 127 " --> pdb=" O PRO K 55 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N VAL K 57 " --> pdb=" O VAL K 127 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N LEU K 129 " --> pdb=" O VAL K 57 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N VAL K 59 " --> pdb=" O LEU K 129 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'K' and resid 431 through 440 removed outlier: 6.506A pdb=" N TRP K 419 " --> pdb=" O LEU K 438 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N GLY K 394 " --> pdb=" O ILE K 268 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N VAL K 270 " --> pdb=" O GLY K 394 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N PHE K 396 " --> pdb=" O VAL K 270 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N GLY K 272 " --> pdb=" O PHE K 396 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N HIS K 398 " --> pdb=" O GLY K 272 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'K' and resid 452 through 455 removed outlier: 3.644A pdb=" N SER K 460 " --> pdb=" O LEU K 453 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'L' and resid 218 through 220 removed outlier: 4.537A pdb=" N ARG L 201 " --> pdb=" O PHE L 220 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N VAL L 187 " --> pdb=" O VAL L 206 " (cutoff:3.500A) removed outlier: 8.658A pdb=" N ILE L 188 " --> pdb=" O PRO L 26 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N LEU L 28 " --> pdb=" O ILE L 188 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N LEU L 190 " --> pdb=" O LEU L 28 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N CYS L 30 " --> pdb=" O LEU L 190 " (cutoff:3.500A) removed outlier: 8.429A pdb=" N HIS L 192 " --> pdb=" O CYS L 30 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N THR L 163 " --> pdb=" O SER L 27 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N VAL L 29 " --> pdb=" O THR L 163 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ILE L 165 " --> pdb=" O VAL L 29 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N VAL L 127 " --> pdb=" O PRO L 55 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N VAL L 57 " --> pdb=" O VAL L 127 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N LEU L 129 " --> pdb=" O VAL L 57 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N VAL L 59 " --> pdb=" O LEU L 129 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'L' and resid 431 through 440 removed outlier: 6.504A pdb=" N TRP L 419 " --> pdb=" O LEU L 438 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N GLY L 394 " --> pdb=" O ILE L 268 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N VAL L 270 " --> pdb=" O GLY L 394 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N PHE L 396 " --> pdb=" O VAL L 270 " (cutoff:3.500A) removed outlier: 8.203A pdb=" N GLY L 272 " --> pdb=" O PHE L 396 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N HIS L 398 " --> pdb=" O GLY L 272 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'L' and resid 452 through 455 removed outlier: 3.643A pdb=" N SER L 460 " --> pdb=" O LEU L 453 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'M' and resid 36 through 41 Processing sheet with id= AL, first strand: chain 'N' and resid 36 through 41 Processing sheet with id= AM, first strand: chain 'O' and resid 36 through 41 Processing sheet with id= AN, first strand: chain 'P' and resid 36 through 41 Processing sheet with id= AO, first strand: chain 'Q' and resid 36 through 41 Processing sheet with id= AP, first strand: chain 'R' and resid 36 through 41 Processing sheet with id= AQ, first strand: chain 'S' and resid 36 through 41 Processing sheet with id= AR, first strand: chain 'T' and resid 36 through 41 Processing sheet with id= AS, first strand: chain 'U' and resid 36 through 41 Processing sheet with id= AT, first strand: chain 'V' and resid 36 through 41 Processing sheet with id= AU, first strand: chain 'W' and resid 36 through 41 Processing sheet with id= AV, first strand: chain 'X' and resid 36 through 41 2901 hydrogen bonds defined for protein. 5838 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: 19.87 Time building geometry restraints manager: 20.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.86 - 1.05: 24 1.05 - 1.24: 6860 1.24 - 1.43: 18072 1.43 - 1.62: 35728 1.62 - 1.81: 372 Bond restraints: 61056 Sorted by residual: bond pdb=" CZ ARG B 310 " pdb=" NH2 ARG B 310 " ideal model delta sigma weight residual 1.330 1.354 -0.024 1.30e-02 5.92e+03 3.32e+00 bond pdb=" CZ ARG C 310 " pdb=" NH2 ARG C 310 " ideal model delta sigma weight residual 1.330 1.354 -0.024 1.30e-02 5.92e+03 3.30e+00 bond pdb=" CZ ARG D 310 " pdb=" NH2 ARG D 310 " ideal model delta sigma weight residual 1.330 1.354 -0.024 1.30e-02 5.92e+03 3.29e+00 bond pdb=" CZ ARG I 310 " pdb=" NH2 ARG I 310 " ideal model delta sigma weight residual 1.330 1.353 -0.023 1.30e-02 5.92e+03 3.26e+00 bond pdb=" CZ ARG L 310 " pdb=" NH2 ARG L 310 " ideal model delta sigma weight residual 1.330 1.353 -0.023 1.30e-02 5.92e+03 3.23e+00 ... (remaining 61051 not shown) Histogram of bond angle deviations from ideal: 100.18 - 108.12: 2465 108.12 - 116.06: 38060 116.06 - 124.00: 40608 124.00 - 131.94: 1331 131.94 - 139.88: 96 Bond angle restraints: 82560 Sorted by residual: angle pdb=" CB ARG H 310 " pdb=" CG ARG H 310 " pdb=" CD ARG H 310 " ideal model delta sigma weight residual 111.30 122.37 -11.07 2.30e+00 1.89e-01 2.31e+01 angle pdb=" CB ARG E 310 " pdb=" CG ARG E 310 " pdb=" CD ARG E 310 " ideal model delta sigma weight residual 111.30 122.35 -11.05 2.30e+00 1.89e-01 2.31e+01 angle pdb=" CB ARG A 310 " pdb=" CG ARG A 310 " pdb=" CD ARG A 310 " ideal model delta sigma weight residual 111.30 122.35 -11.05 2.30e+00 1.89e-01 2.31e+01 angle pdb=" CB ARG J 310 " pdb=" CG ARG J 310 " pdb=" CD ARG J 310 " ideal model delta sigma weight residual 111.30 122.34 -11.04 2.30e+00 1.89e-01 2.30e+01 angle pdb=" CB ARG L 310 " pdb=" CG ARG L 310 " pdb=" CD ARG L 310 " ideal model delta sigma weight residual 111.30 122.33 -11.03 2.30e+00 1.89e-01 2.30e+01 ... (remaining 82555 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.89: 35359 27.89 - 55.79: 1337 55.79 - 83.68: 186 83.68 - 111.58: 18 111.58 - 139.47: 12 Dihedral angle restraints: 36912 sinusoidal: 15204 harmonic: 21708 Sorted by residual: dihedral pdb=" C5' ADP J 602 " pdb=" O5' ADP J 602 " pdb=" PA ADP J 602 " pdb=" O2A ADP J 602 " ideal model delta sinusoidal sigma weight residual -60.00 79.47 -139.47 1 2.00e+01 2.50e-03 4.22e+01 dihedral pdb=" C5' ADP K 602 " pdb=" O5' ADP K 602 " pdb=" PA ADP K 602 " pdb=" O2A ADP K 602 " ideal model delta sinusoidal sigma weight residual -60.00 79.44 -139.44 1 2.00e+01 2.50e-03 4.22e+01 dihedral pdb=" C5' ADP I 602 " pdb=" O5' ADP I 602 " pdb=" PA ADP I 602 " pdb=" O2A ADP I 602 " ideal model delta sinusoidal sigma weight residual -60.00 79.42 -139.42 1 2.00e+01 2.50e-03 4.22e+01 ... (remaining 36909 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 8132 0.060 - 0.119: 1145 0.119 - 0.179: 59 0.179 - 0.239: 0 0.239 - 0.298: 36 Chirality restraints: 9372 Sorted by residual: chirality pdb=" C2' ATP B 601 " pdb=" C1' ATP B 601 " pdb=" C3' ATP B 601 " pdb=" O2' ATP B 601 " both_signs ideal model delta sigma weight residual False -2.68 -2.98 0.30 2.00e-01 2.50e+01 2.23e+00 chirality pdb=" C2' ATP I 601 " pdb=" C1' ATP I 601 " pdb=" C3' ATP I 601 " pdb=" O2' ATP I 601 " both_signs ideal model delta sigma weight residual False -2.68 -2.98 0.30 2.00e-01 2.50e+01 2.19e+00 chirality pdb=" C2' ATP K 601 " pdb=" C1' ATP K 601 " pdb=" C3' ATP K 601 " pdb=" O2' ATP K 601 " both_signs ideal model delta sigma weight residual False -2.68 -2.97 0.29 2.00e-01 2.50e+01 2.16e+00 ... (remaining 9369 not shown) Planarity restraints: 10752 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 550 " -0.465 9.50e-02 1.11e+02 2.08e-01 2.70e+01 pdb=" NE ARG B 550 " 0.032 2.00e-02 2.50e+03 pdb=" CZ ARG B 550 " -0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG B 550 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG B 550 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 550 " -0.464 9.50e-02 1.11e+02 2.08e-01 2.69e+01 pdb=" NE ARG C 550 " 0.032 2.00e-02 2.50e+03 pdb=" CZ ARG C 550 " -0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG C 550 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG C 550 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 550 " 0.464 9.50e-02 1.11e+02 2.08e-01 2.69e+01 pdb=" NE ARG D 550 " -0.032 2.00e-02 2.50e+03 pdb=" CZ ARG D 550 " 0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG D 550 " -0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG D 550 " 0.012 2.00e-02 2.50e+03 ... (remaining 10749 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.50: 510 2.50 - 3.03: 38458 3.03 - 3.55: 69697 3.55 - 4.08: 101394 4.08 - 4.60: 153223 Nonbonded interactions: 363282 Sorted by model distance: nonbonded pdb=" OG SER H 279 " pdb="MG MG H 603 " model vdw 1.976 2.050 nonbonded pdb=" OG SER F 279 " pdb="MG MG F 603 " model vdw 1.976 2.050 nonbonded pdb=" OG SER C 279 " pdb="MG MG C 603 " model vdw 1.976 2.050 nonbonded pdb=" OG SER E 279 " pdb="MG MG E 603 " model vdw 1.977 2.050 nonbonded pdb=" OG SER G 279 " pdb="MG MG G 603 " model vdw 1.977 2.050 ... (remaining 363277 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 558 or resid 601 through 603)) selection = (chain 'B' and (resid 2 through 558 or resid 601 through 603)) selection = (chain 'C' and (resid 2 through 558 or resid 601 through 603)) selection = (chain 'D' and (resid 2 through 558 or resid 601 through 603)) selection = (chain 'E' and (resid 2 through 558 or resid 601 through 603)) selection = chain 'F' selection = (chain 'G' and (resid 2 through 558 or resid 601 through 603)) selection = (chain 'H' and (resid 2 through 558 or resid 601 through 603)) selection = (chain 'I' and (resid 2 through 558 or resid 601 through 603)) selection = (chain 'J' and (resid 2 through 558 or resid 601 through 603)) selection = (chain 'K' and (resid 2 through 558 or resid 601 through 603)) selection = (chain 'L' and (resid 2 through 558 or resid 601 through 603)) } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' } 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: 8.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.440 Construct map_model_manager: 1.150 Extract box with map and model: 30.310 Check model and map are aligned: 0.660 Set scattering table: 0.390 Process input model: 111.650 Find NCS groups from input model: 3.860 Set up NCS constraints: 0.580 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:11.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 169.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6769 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 : 0.003 0.045 61032 Z= 0.199 Angle : 0.722 11.066 82500 Z= 0.397 Chirality : 0.044 0.298 9372 Planarity : 0.009 0.208 10740 Dihedral : 14.772 139.469 22920 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 31.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer Outliers : 3.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: 0.43 (0.10), residues: 7572 helix: 1.64 (0.09), residues: 3360 sheet: -0.69 (0.12), residues: 1728 loop : -0.76 (0.13), residues: 2484 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15144 Ramachandran restraints generated. 7572 Oldfield, 0 Emsley, 7572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15144 Ramachandran restraints generated. 7572 Oldfield, 0 Emsley, 7572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2214 residues out of total 6264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 216 poor density : 1998 time to evaluate : 5.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 216 outliers final: 23 residues processed: 2110 average time/residue: 1.4513 time to fit residues: 3880.8466 Evaluate side-chains 1133 residues out of total 6264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 1110 time to evaluate : 5.249 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 11 residues processed: 13 average time/residue: 0.7147 time to fit residues: 21.3297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 756 random chunks: chunk 638 optimal weight: 7.9990 chunk 573 optimal weight: 10.0000 chunk 317 optimal weight: 0.0980 chunk 195 optimal weight: 2.9990 chunk 386 optimal weight: 3.9990 chunk 306 optimal weight: 5.9990 chunk 592 optimal weight: 8.9990 chunk 229 optimal weight: 0.0030 chunk 360 optimal weight: 8.9990 chunk 441 optimal weight: 3.9990 chunk 686 optimal weight: 7.9990 overall best weight: 2.2196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 196 ASN A 239 HIS A 432 ASN A 540 GLN ** B 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 540 GLN ** C 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 389 ASN ** C 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 540 GLN ** D 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 239 HIS D 307 GLN ** D 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 432 ASN ** D 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 540 GLN ** E 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 177 GLN E 377 GLN E 540 GLN ** F 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 177 GLN F 389 ASN ** F 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 540 GLN ** G 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 192 HIS ** G 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 432 ASN G 540 GLN ** H 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 540 GLN ** I 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 192 HIS I 307 GLN I 377 GLN I 432 ASN I 540 GLN ** J 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 239 HIS J 389 ASN ** J 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 540 GLN ** K 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 197 GLN K 240 GLN K 389 ASN K 540 GLN ** L 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 196 ASN L 377 GLN L 389 ASN L 432 ASN L 540 GLN M 22 ASN N 22 ASN O 52 HIS U 22 ASN V 22 ASN X 22 ASN Total number of N/Q/H flips: 44 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7271 moved from start: 0.4305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.061 61032 Z= 0.304 Angle : 0.674 7.761 82500 Z= 0.350 Chirality : 0.043 0.199 9372 Planarity : 0.007 0.050 10740 Dihedral : 6.574 100.421 8580 Min Nonbonded Distance : 1.619 Molprobity Statistics. All-atom Clashscore : 22.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer Outliers : 5.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: -0.40 (0.09), residues: 7572 helix: 0.34 (0.09), residues: 3456 sheet: -0.51 (0.13), residues: 1728 loop : -0.73 (0.13), residues: 2388 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15144 Ramachandran restraints generated. 7572 Oldfield, 0 Emsley, 7572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15144 Ramachandran restraints generated. 7572 Oldfield, 0 Emsley, 7572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1373 residues out of total 6264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 323 poor density : 1050 time to evaluate : 5.321 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 323 outliers final: 97 residues processed: 1272 average time/residue: 1.4272 time to fit residues: 2326.0531 Evaluate side-chains 982 residues out of total 6264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 885 time to evaluate : 5.201 Switching outliers to nearest non-outliers outliers start: 97 outliers final: 76 residues processed: 22 average time/residue: 0.5829 time to fit residues: 28.5470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 756 random chunks: chunk 381 optimal weight: 0.9980 chunk 213 optimal weight: 1.9990 chunk 571 optimal weight: 0.9980 chunk 467 optimal weight: 4.9990 chunk 189 optimal weight: 7.9990 chunk 687 optimal weight: 4.9990 chunk 742 optimal weight: 2.9990 chunk 612 optimal weight: 0.0670 chunk 682 optimal weight: 7.9990 chunk 234 optimal weight: 0.6980 chunk 551 optimal weight: 0.9990 overall best weight: 0.7520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 ASN A 192 HIS A 239 HIS ** B 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 177 GLN B 192 HIS B 377 GLN ** C 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 177 GLN C 192 HIS C 389 ASN ** C 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 141 ASN D 177 GLN D 192 HIS D 239 HIS D 432 ASN ** D 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 192 HIS ** F 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 192 HIS ** F 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 177 GLN G 377 GLN ** G 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 432 ASN ** H 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 177 GLN H 192 HIS ** I 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 177 GLN I 377 GLN ** J 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 177 GLN J 192 HIS J 239 HIS J 377 GLN ** K 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 192 HIS K 239 HIS ** L 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 177 GLN L 192 HIS L 239 HIS L 377 GLN M 52 HIS O 22 ASN O 52 HIS P 52 HIS R 22 ASN R 52 HIS T 22 ASN T 52 HIS U 22 ASN U 52 HIS V 52 HIS W 52 HIS ** X 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 52 HIS Total number of N/Q/H flips: 46 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7268 moved from start: 0.4642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.022 61032 Z= 0.136 Angle : 0.465 6.338 82500 Z= 0.244 Chirality : 0.037 0.133 9372 Planarity : 0.005 0.043 10740 Dihedral : 6.002 100.310 8580 Min Nonbonded Distance : 1.789 Molprobity Statistics. All-atom Clashscore : 23.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer Outliers : 4.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: -0.28 (0.10), residues: 7572 helix: 0.25 (0.09), residues: 3432 sheet: -0.33 (0.13), residues: 1764 loop : -0.43 (0.13), residues: 2376 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15144 Ramachandran restraints generated. 7572 Oldfield, 0 Emsley, 7572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15144 Ramachandran restraints generated. 7572 Oldfield, 0 Emsley, 7572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1221 residues out of total 6264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 260 poor density : 961 time to evaluate : 5.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 260 outliers final: 115 residues processed: 1159 average time/residue: 1.3910 time to fit residues: 2079.6833 Evaluate side-chains 1001 residues out of total 6264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 886 time to evaluate : 5.341 Switching outliers to nearest non-outliers outliers start: 115 outliers final: 99 residues processed: 16 average time/residue: 0.9131 time to fit residues: 28.2161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 756 random chunks: chunk 679 optimal weight: 0.6980 chunk 517 optimal weight: 8.9990 chunk 356 optimal weight: 8.9990 chunk 76 optimal weight: 0.0470 chunk 328 optimal weight: 0.9990 chunk 461 optimal weight: 2.9990 chunk 690 optimal weight: 10.0000 chunk 730 optimal weight: 3.9990 chunk 360 optimal weight: 0.8980 chunk 654 optimal weight: 1.9990 chunk 196 optimal weight: 6.9990 overall best weight: 0.9282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 GLN A 239 HIS A 377 GLN ** A 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 377 GLN ** B 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 HIS C 377 GLN ** C 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 377 GLN ** F 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 377 GLN ** G 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 377 GLN ** J 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 377 GLN ** J 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 239 HIS L 377 GLN M 52 HIS N 52 HIS O 52 HIS P 52 HIS R 22 ASN R 52 HIS S 22 ASN S 52 HIS T 52 HIS U 52 HIS V 22 ASN V 52 HIS W 52 HIS X 52 HIS Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 moved from start: 0.5097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 61032 Z= 0.152 Angle : 0.469 7.274 82500 Z= 0.242 Chirality : 0.037 0.133 9372 Planarity : 0.004 0.045 10740 Dihedral : 5.732 94.064 8580 Min Nonbonded Distance : 1.769 Molprobity Statistics. All-atom Clashscore : 22.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer Outliers : 4.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: -0.19 (0.10), residues: 7572 helix: 0.15 (0.09), residues: 3456 sheet: -0.13 (0.13), residues: 1716 loop : -0.22 (0.13), residues: 2400 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15144 Ramachandran restraints generated. 7572 Oldfield, 0 Emsley, 7572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15144 Ramachandran restraints generated. 7572 Oldfield, 0 Emsley, 7572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1269 residues out of total 6264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 296 poor density : 973 time to evaluate : 7.985 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 296 outliers final: 140 residues processed: 1176 average time/residue: 1.4153 time to fit residues: 2185.7349 Evaluate side-chains 1041 residues out of total 6264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 901 time to evaluate : 5.204 Switching outliers to nearest non-outliers outliers start: 140 outliers final: 120 residues processed: 21 average time/residue: 0.6982 time to fit residues: 30.7661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 756 random chunks: chunk 608 optimal weight: 0.0970 chunk 414 optimal weight: 8.9990 chunk 10 optimal weight: 8.9990 chunk 544 optimal weight: 9.9990 chunk 301 optimal weight: 7.9990 chunk 623 optimal weight: 3.9990 chunk 505 optimal weight: 0.3980 chunk 0 optimal weight: 7.9990 chunk 373 optimal weight: 9.9990 chunk 655 optimal weight: 10.0000 chunk 184 optimal weight: 5.9990 overall best weight: 3.6984 ------------------------------------------------------------------------------- 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: