Starting phenix.real_space_refine on Fri Mar 22 20:10:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lxz_23580/03_2024/7lxz_23580.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lxz_23580/03_2024/7lxz_23580.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lxz_23580/03_2024/7lxz_23580.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lxz_23580/03_2024/7lxz_23580.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lxz_23580/03_2024/7lxz_23580.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lxz_23580/03_2024/7lxz_23580.pdb" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.120 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 153 5.16 5 C 21732 2.51 5 N 5739 2.21 5 O 6729 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 156": "OE1" <-> "OE2" Residue "A PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 298": "OE1" <-> "OE2" Residue "A GLU 340": "OE1" <-> "OE2" Residue "A ARG 646": "NH1" <-> "NH2" Residue "A GLU 773": "OE1" <-> "OE2" Residue "A ARG 815": "NH1" <-> "NH2" Residue "A GLU 988": "OE1" <-> "OE2" Residue "A GLU 990": "OE1" <-> "OE2" Residue "A PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 98": "NH1" <-> "NH2" Residue "H TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 156": "OE1" <-> "OE2" Residue "B PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 298": "OE1" <-> "OE2" Residue "B GLU 340": "OE1" <-> "OE2" Residue "B ARG 646": "NH1" <-> "NH2" Residue "B GLU 773": "OE1" <-> "OE2" Residue "B ARG 815": "NH1" <-> "NH2" Residue "B GLU 988": "OE1" <-> "OE2" Residue "B GLU 990": "OE1" <-> "OE2" Residue "B PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 98": "NH1" <-> "NH2" Residue "G TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 156": "OE1" <-> "OE2" Residue "K PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 298": "OE1" <-> "OE2" Residue "K GLU 340": "OE1" <-> "OE2" Residue "K ARG 646": "NH1" <-> "NH2" Residue "K GLU 773": "OE1" <-> "OE2" Residue "K ARG 815": "NH1" <-> "NH2" Residue "K GLU 988": "OE1" <-> "OE2" Residue "K GLU 990": "OE1" <-> "OE2" Residue "K PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 98": "NH1" <-> "NH2" Residue "N TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 34353 Number of models: 1 Model: "" Number of chains: 33 Chain: "A" Number of atoms: 8197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1060, 8197 Classifications: {'peptide': 1060} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 58, 'TRANS': 1001} Chain breaks: 5 Unresolved non-hydrogen bonds: 106 Unresolved non-hydrogen angles: 131 Unresolved non-hydrogen dihedrals: 87 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 1, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 3, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 58 Chain: "D" Number of atoms: 770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 770 Classifications: {'peptide': 104} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 97} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "E" Number of atoms: 954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 954 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 117} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "H" Number of atoms: 643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 643 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 97} Link IDs: {'PTRANS': 2, 'TRANS': 123} Unresolved non-hydrogen bonds: 351 Unresolved non-hydrogen angles: 456 Unresolved non-hydrogen dihedrals: 298 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'TYR:plan': 7, 'ASN:plan1': 7, 'TRP:plan': 3, 'ASP:plan': 6, 'PHE:plan': 4, 'GLU:plan': 5, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 215 Chain: "J" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 534 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 82} Link IDs: {'PTRANS': 6, 'TRANS': 100} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 266 Unresolved non-hydrogen angles: 347 Unresolved non-hydrogen dihedrals: 227 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLN:plan1': 5, 'ARG:plan': 2, 'TYR:plan': 7, 'ASN:plan1': 4, 'TRP:plan': 2, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 2, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 149 Chain: "B" Number of atoms: 8197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1060, 8197 Classifications: {'peptide': 1060} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 58, 'TRANS': 1001} Chain breaks: 5 Unresolved non-hydrogen bonds: 106 Unresolved non-hydrogen angles: 131 Unresolved non-hydrogen dihedrals: 87 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 1, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 3, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 58 Chain: "C" Number of atoms: 770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 770 Classifications: {'peptide': 104} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 97} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "F" Number of atoms: 954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 954 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 117} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "G" Number of atoms: 643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 643 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 97} Link IDs: {'PTRANS': 2, 'TRANS': 123} Unresolved non-hydrogen bonds: 351 Unresolved non-hydrogen angles: 456 Unresolved non-hydrogen dihedrals: 298 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'TYR:plan': 7, 'ASN:plan1': 7, 'TRP:plan': 3, 'ASP:plan': 6, 'PHE:plan': 4, 'GLU:plan': 5, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 215 Chain: "I" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 534 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 82} Link IDs: {'PTRANS': 6, 'TRANS': 100} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 266 Unresolved non-hydrogen angles: 347 Unresolved non-hydrogen dihedrals: 227 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLN:plan1': 5, 'ARG:plan': 2, 'TYR:plan': 7, 'ASN:plan1': 4, 'TRP:plan': 2, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 2, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 149 Chain: "K" Number of atoms: 8197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1060, 8197 Classifications: {'peptide': 1060} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 58, 'TRANS': 1001} Chain breaks: 5 Unresolved non-hydrogen bonds: 106 Unresolved non-hydrogen angles: 131 Unresolved non-hydrogen dihedrals: 87 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 1, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 3, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 58 Chain: "L" Number of atoms: 770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 770 Classifications: {'peptide': 104} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 97} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "M" Number of atoms: 954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 954 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 117} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "N" Number of atoms: 643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 643 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 97} Link IDs: {'PTRANS': 2, 'TRANS': 123} Unresolved non-hydrogen bonds: 351 Unresolved non-hydrogen angles: 456 Unresolved non-hydrogen dihedrals: 298 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'TYR:plan': 7, 'ASN:plan1': 7, 'TRP:plan': 3, 'ASP:plan': 6, 'PHE:plan': 4, 'GLU:plan': 5, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 215 Chain: "O" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 534 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 82} Link IDs: {'PTRANS': 6, 'TRANS': 100} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 266 Unresolved non-hydrogen angles: 347 Unresolved non-hydrogen dihedrals: 227 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLN:plan1': 5, 'ARG:plan': 2, 'TYR:plan': 7, 'ASN:plan1': 4, 'TRP:plan': 2, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 2, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 149 Chain: "P" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "U" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Z" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "B" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "K" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Time building chain proxies: 16.75, per 1000 atoms: 0.49 Number of scatterers: 34353 At special positions: 0 Unit cell: (194.25, 208.95, 191.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 153 16.00 O 6729 8.00 N 5739 7.00 C 21732 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=54, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.02 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.02 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.14 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.09 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.02 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.04 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.04 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.08 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.09 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.02 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 89 " distance=2.05 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 90 " distance=2.01 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.02 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.02 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.02 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.14 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.09 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.02 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.04 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.04 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.08 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.09 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.02 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 89 " distance=2.05 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 90 " distance=2.01 Simple disulfide: pdb=" SG CYS K 15 " - pdb=" SG CYS K 136 " distance=2.02 Simple disulfide: pdb=" SG CYS K 131 " - pdb=" SG CYS K 166 " distance=2.03 Simple disulfide: pdb=" SG CYS K 291 " - pdb=" SG CYS K 301 " distance=2.02 Simple disulfide: pdb=" SG CYS K 336 " - pdb=" SG CYS K 361 " distance=2.02 Simple disulfide: pdb=" SG CYS K 379 " - pdb=" SG CYS K 432 " distance=2.14 Simple disulfide: pdb=" SG CYS K 391 " - pdb=" SG CYS K 525 " distance=2.10 Simple disulfide: pdb=" SG CYS K 480 " - pdb=" SG CYS K 488 " distance=2.03 Simple disulfide: pdb=" SG CYS K 538 " - pdb=" SG CYS K 590 " distance=2.02 Simple disulfide: pdb=" SG CYS K 617 " - pdb=" SG CYS K 649 " distance=2.04 Simple disulfide: pdb=" SG CYS K 662 " - pdb=" SG CYS K 671 " distance=2.04 Simple disulfide: pdb=" SG CYS K 738 " - pdb=" SG CYS K 760 " distance=2.08 Simple disulfide: pdb=" SG CYS K 743 " - pdb=" SG CYS K 749 " distance=2.09 Simple disulfide: pdb=" SG CYS K1032 " - pdb=" SG CYS K1043 " distance=2.02 Simple disulfide: pdb=" SG CYS K1082 " - pdb=" SG CYS K1126 " distance=2.02 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 89 " distance=2.05 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 90 " distance=2.01 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " BETA1-6 " NAG P 1 " - " FUC P 4 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG T 1 " - " FUC T 3 " " NAG U 1 " - " FUC U 4 " " NAG Y 1 " - " FUC Y 3 " " NAG Z 1 " - " FUC Z 4 " " NAG d 1 " - " FUC d 3 " NAG-ASN " NAG A1301 " - " ASN A 331 " " NAG A1302 " - " ASN A 603 " " NAG A1303 " - " ASN A 616 " " NAG A1304 " - " ASN A 657 " " NAG A1305 " - " ASN A 709 " " NAG A1306 " - " ASN A1074 " " NAG A1307 " - " ASN A1098 " " NAG A1308 " - " ASN A1134 " " NAG A1309 " - " ASN A 122 " " NAG A1310 " - " ASN A 282 " " NAG A1311 " - " ASN A 234 " " NAG A1312 " - " ASN A 165 " " NAG A1313 " - " ASN A 61 " " NAG B1301 " - " ASN B 331 " " NAG B1302 " - " ASN B 603 " " NAG B1303 " - " ASN B 616 " " NAG B1304 " - " ASN B 657 " " NAG B1305 " - " ASN B 709 " " NAG B1306 " - " ASN B1074 " " NAG B1307 " - " ASN B1098 " " NAG B1308 " - " ASN B1134 " " NAG B1309 " - " ASN B 122 " " NAG B1310 " - " ASN B 282 " " NAG B1311 " - " ASN B 234 " " NAG B1312 " - " ASN B 165 " " NAG B1313 " - " ASN B 61 " " NAG K1301 " - " ASN K 331 " " NAG K1302 " - " ASN K 603 " " NAG K1303 " - " ASN K 616 " " NAG K1304 " - " ASN K 657 " " NAG K1305 " - " ASN K 709 " " NAG K1306 " - " ASN K1074 " " NAG K1307 " - " ASN K1098 " " NAG K1308 " - " ASN K1134 " " NAG K1309 " - " ASN K 122 " " NAG K1310 " - " ASN K 282 " " NAG K1311 " - " ASN K 234 " " NAG K1312 " - " ASN K 165 " " NAG K1313 " - " ASN K 61 " " NAG P 1 " - " ASN A 343 " " NAG Q 1 " - " ASN A 717 " " NAG R 1 " - " ASN A 801 " " NAG S 1 " - " ASN A 149 " " NAG T 1 " - " ASN A 17 " " NAG U 1 " - " ASN B 343 " " NAG V 1 " - " ASN B 717 " " NAG W 1 " - " ASN B 801 " " NAG X 1 " - " ASN B 149 " " NAG Y 1 " - " ASN B 17 " " NAG Z 1 " - " ASN K 343 " " NAG a 1 " - " ASN K 717 " " NAG b 1 " - " ASN K 801 " " NAG c 1 " - " ASN K 149 " " NAG d 1 " - " ASN K 17 " Time building additional restraints: 15.13 Conformation dependent library (CDL) restraints added in 5.9 seconds 8994 Ramachandran restraints generated. 4497 Oldfield, 0 Emsley, 4497 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8424 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 84 sheets defined 19.1% alpha, 41.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.23 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.811A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 386 through 389 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.148A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.727A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.083A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 940 Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.925A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.782A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 32 No H-bonds generated for 'chain 'D' and resid 30 through 32' Processing helix chain 'D' and resid 80 through 84 removed outlier: 3.565A pdb=" N PHE D 84 " --> pdb=" O PRO D 81 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 32 removed outlier: 3.566A pdb=" N TYR E 32 " --> pdb=" O PHE E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 74 through 76 No H-bonds generated for 'chain 'E' and resid 74 through 76' Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'J' and resid 81 through 85 Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.810A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 386 through 389 Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.148A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.727A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.084A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 940 Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.925A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.782A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 32 No H-bonds generated for 'chain 'C' and resid 30 through 32' Processing helix chain 'C' and resid 80 through 84 removed outlier: 3.565A pdb=" N PHE C 84 " --> pdb=" O PRO C 81 " (cutoff:3.500A) Processing helix chain 'F' and resid 28 through 32 removed outlier: 3.566A pdb=" N TYR F 32 " --> pdb=" O PHE F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 74 through 76 No H-bonds generated for 'chain 'F' and resid 74 through 76' Processing helix chain 'F' and resid 87 through 91 Processing helix chain 'G' and resid 28 through 32 Processing helix chain 'G' and resid 87 through 91 Processing helix chain 'I' and resid 81 through 85 Processing helix chain 'K' and resid 294 through 303 Processing helix chain 'K' and resid 338 through 343 Processing helix chain 'K' and resid 349 through 353 removed outlier: 3.811A pdb=" N TRP K 353 " --> pdb=" O VAL K 350 " (cutoff:3.500A) Processing helix chain 'K' and resid 365 through 370 Processing helix chain 'K' and resid 386 through 389 Processing helix chain 'K' and resid 405 through 410 removed outlier: 4.148A pdb=" N ARG K 408 " --> pdb=" O ASP K 405 " (cutoff:3.500A) Processing helix chain 'K' and resid 416 through 422 Processing helix chain 'K' and resid 502 through 505 Processing helix chain 'K' and resid 737 through 744 Processing helix chain 'K' and resid 746 through 754 Processing helix chain 'K' and resid 755 through 757 No H-bonds generated for 'chain 'K' and resid 755 through 757' Processing helix chain 'K' and resid 758 through 783 removed outlier: 3.727A pdb=" N ASP K 775 " --> pdb=" O ALA K 771 " (cutoff:3.500A) Processing helix chain 'K' and resid 816 through 826 Processing helix chain 'K' and resid 866 through 885 Processing helix chain 'K' and resid 886 through 890 Processing helix chain 'K' and resid 897 through 908 Processing helix chain 'K' and resid 912 through 919 removed outlier: 4.083A pdb=" N LEU K 916 " --> pdb=" O THR K 912 " (cutoff:3.500A) Processing helix chain 'K' and resid 919 through 940 Processing helix chain 'K' and resid 945 through 965 removed outlier: 3.925A pdb=" N VAL K 951 " --> pdb=" O LYS K 947 " (cutoff:3.500A) Processing helix chain 'K' and resid 966 through 968 No H-bonds generated for 'chain 'K' and resid 966 through 968' Processing helix chain 'K' and resid 976 through 984 Processing helix chain 'K' and resid 985 through 1033 removed outlier: 4.782A pdb=" N VAL K 991 " --> pdb=" O PRO K 987 " (cutoff:3.500A) Processing helix chain 'L' and resid 30 through 32 No H-bonds generated for 'chain 'L' and resid 30 through 32' Processing helix chain 'L' and resid 80 through 84 removed outlier: 3.565A pdb=" N PHE L 84 " --> pdb=" O PRO L 81 " (cutoff:3.500A) Processing helix chain 'M' and resid 28 through 32 removed outlier: 3.567A pdb=" N TYR M 32 " --> pdb=" O PHE M 29 " (cutoff:3.500A) Processing helix chain 'M' and resid 74 through 76 No H-bonds generated for 'chain 'M' and resid 74 through 76' Processing helix chain 'M' and resid 87 through 91 Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 87 through 91 Processing helix chain 'O' and resid 81 through 85 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 8.057A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLU A 224 " --> pdb=" O SER A 205 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.733A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 8.248A pdb=" N ASN B 542 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 7.389A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 83 through 85 removed outlier: 3.502A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N VAL A 126 " --> pdb=" O VAL A 171 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N VAL A 171 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ILE A 128 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N GLU A 169 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N VAL A 130 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N GLU A 132 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N ASN A 165 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N GLN A 134 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ALA A 163 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 8.613A pdb=" N CYS A 136 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N SER A 161 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ASP A 138 " --> pdb=" O VAL A 159 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N VAL A 159 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N PHE A 140 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N PHE A 157 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N GLY A 142 " --> pdb=" O SER A 155 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 83 through 85 removed outlier: 12.798A pdb=" N PHE A 238 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 12.254A pdb=" N ASN A 137 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 9.961A pdb=" N THR A 240 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N LEU A 242 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N VAL A 126 " --> pdb=" O VAL A 171 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N VAL A 171 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ILE A 128 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N GLU A 169 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N VAL A 130 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N GLU A 132 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N ASN A 165 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N GLN A 134 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ALA A 163 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 8.613A pdb=" N CYS A 136 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N SER A 161 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ASP A 138 " --> pdb=" O VAL A 159 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N VAL A 159 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N PHE A 140 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N PHE A 157 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N GLY A 142 " --> pdb=" O SER A 155 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.271A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 324 through 328 removed outlier: 6.259A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 8.248A pdb=" N ASN A 542 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N PHE A 565 " --> pdb=" O PHE K 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.885A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.552A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.549A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.659A pdb=" N ALA A 701 " --> pdb=" O ILE K 788 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N LYS K 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N ASN A 703 " --> pdb=" O LYS K 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.681A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.681A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.414A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 787 through 790 removed outlier: 3.513A pdb=" N LYS A 790 " --> pdb=" O ASN B 703 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.834A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 4 through 7 removed outlier: 5.544A pdb=" N THR D 70 " --> pdb=" O ALA D 25 " (cutoff:3.500A) removed outlier: 9.609A pdb=" N GLN D 27 " --> pdb=" O SER D 68 " (cutoff:3.500A) removed outlier: 9.687A pdb=" N SER D 68 " --> pdb=" O GLN D 27 " (cutoff:3.500A) removed outlier: 11.201A pdb=" N VAL D 29 " --> pdb=" O SER D 66 " (cutoff:3.500A) removed outlier: 11.299A pdb=" N SER D 66 " --> pdb=" O VAL D 29 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 54 through 55 removed outlier: 6.488A pdb=" N TRP D 36 " --> pdb=" O LEU D 48 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N TYR D 50 " --> pdb=" O LEU D 34 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N LEU D 34 " --> pdb=" O TYR D 50 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 54 through 55 removed outlier: 6.488A pdb=" N TRP D 36 " --> pdb=" O LEU D 48 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N TYR D 50 " --> pdb=" O LEU D 34 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N LEU D 34 " --> pdb=" O TYR D 50 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 3 through 6 Processing sheet with id=AC5, first strand: chain 'E' and resid 10 through 11 removed outlier: 6.760A pdb=" N GLU E 10 " --> pdb=" O THR E 122 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N MET E 34 " --> pdb=" O TRP E 50 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N TRP E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N TRP E 36 " --> pdb=" O MET E 48 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 10 through 11 removed outlier: 6.760A pdb=" N GLU E 10 " --> pdb=" O THR E 122 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N TYR E 114 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AC8, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.919A pdb=" N ILE H 34 " --> pdb=" O SER H 50 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N SER H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.692A pdb=" N TYR H 115 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'J' and resid 9 through 11 removed outlier: 6.511A pdb=" N TRP J 37 " --> pdb=" O MET J 49 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'J' and resid 9 through 11 Processing sheet with id=AD3, first strand: chain 'J' and resid 18 through 23 Processing sheet with id=AD4, first strand: chain 'B' and resid 27 through 30 removed outlier: 8.057A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLU B 224 " --> pdb=" O SER B 205 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 42 through 43 removed outlier: 3.734A pdb=" N ALA K 575 " --> pdb=" O GLY K 566 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N ASP K 574 " --> pdb=" O ILE K 587 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N GLU K 324 " --> pdb=" O ASN K 540 " (cutoff:3.500A) removed outlier: 8.248A pdb=" N ASN K 542 " --> pdb=" O GLU K 324 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ILE K 326 " --> pdb=" O ASN K 542 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 47 through 55 removed outlier: 7.388A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 83 through 85 removed outlier: 3.501A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N VAL B 126 " --> pdb=" O VAL B 171 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N VAL B 171 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ILE B 128 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N GLU B 169 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N VAL B 130 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N GLU B 132 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N ASN B 165 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N GLN B 134 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ALA B 163 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 8.613A pdb=" N CYS B 136 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N SER B 161 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ASP B 138 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N VAL B 159 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N PHE B 140 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N PHE B 157 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N GLY B 142 " --> pdb=" O SER B 155 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 83 through 85 removed outlier: 12.799A pdb=" N PHE B 238 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 12.254A pdb=" N ASN B 137 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 9.961A pdb=" N THR B 240 " --> pdb=" O ASN B 137 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N LEU B 242 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N VAL B 126 " --> pdb=" O VAL B 171 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N VAL B 171 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ILE B 128 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N GLU B 169 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N VAL B 130 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N GLU B 132 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N ASN B 165 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N GLN B 134 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ALA B 163 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 8.613A pdb=" N CYS B 136 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N SER B 161 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ASP B 138 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N VAL B 159 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N PHE B 140 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N PHE B 157 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N GLY B 142 " --> pdb=" O SER B 155 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.271A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.885A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.552A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AE4, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AE5, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.550A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.681A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.681A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.414A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'B' and resid 787 through 790 removed outlier: 3.513A pdb=" N LYS B 790 " --> pdb=" O ASN K 703 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.833A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 4 through 7 removed outlier: 5.544A pdb=" N THR C 70 " --> pdb=" O ALA C 25 " (cutoff:3.500A) removed outlier: 9.609A pdb=" N GLN C 27 " --> pdb=" O SER C 68 " (cutoff:3.500A) removed outlier: 9.688A pdb=" N SER C 68 " --> pdb=" O GLN C 27 " (cutoff:3.500A) removed outlier: 11.202A pdb=" N VAL C 29 " --> pdb=" O SER C 66 " (cutoff:3.500A) removed outlier: 11.299A pdb=" N SER C 66 " --> pdb=" O VAL C 29 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 54 through 55 removed outlier: 6.488A pdb=" N TRP C 36 " --> pdb=" O LEU C 48 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N TYR C 50 " --> pdb=" O LEU C 34 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N LEU C 34 " --> pdb=" O TYR C 50 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 54 through 55 removed outlier: 6.488A pdb=" N TRP C 36 " --> pdb=" O LEU C 48 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N TYR C 50 " --> pdb=" O LEU C 34 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N LEU C 34 " --> pdb=" O TYR C 50 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'F' and resid 3 through 6 Processing sheet with id=AF6, first strand: chain 'F' and resid 10 through 11 removed outlier: 6.759A pdb=" N GLU F 10 " --> pdb=" O THR F 122 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N MET F 34 " --> pdb=" O TRP F 50 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N TRP F 50 " --> pdb=" O MET F 34 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N TRP F 36 " --> pdb=" O MET F 48 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'F' and resid 10 through 11 removed outlier: 6.759A pdb=" N GLU F 10 " --> pdb=" O THR F 122 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N TYR F 114 " --> pdb=" O ARG F 98 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'G' and resid 3 through 7 Processing sheet with id=AF9, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.919A pdb=" N ILE G 34 " --> pdb=" O SER G 50 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N SER G 50 " --> pdb=" O ILE G 34 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N TRP G 36 " --> pdb=" O VAL G 48 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'G' and resid 10 through 12 removed outlier: 3.692A pdb=" N TYR G 115 " --> pdb=" O ARG G 98 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'I' and resid 9 through 11 removed outlier: 6.512A pdb=" N TRP I 37 " --> pdb=" O MET I 49 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'I' and resid 9 through 11 Processing sheet with id=AG4, first strand: chain 'I' and resid 18 through 23 Processing sheet with id=AG5, first strand: chain 'K' and resid 27 through 30 removed outlier: 8.057A pdb=" N ASN K 61 " --> pdb=" O TYR K 269 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N TYR K 269 " --> pdb=" O ASN K 61 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N PHE K 201 " --> pdb=" O ASP K 228 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N ASP K 228 " --> pdb=" O PHE K 201 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ILE K 203 " --> pdb=" O LEU K 226 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLU K 224 " --> pdb=" O SER K 205 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'K' and resid 47 through 55 removed outlier: 7.389A pdb=" N THR K 274 " --> pdb=" O ASP K 290 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N ASP K 290 " --> pdb=" O THR K 274 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N LEU K 276 " --> pdb=" O ALA K 288 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ALA K 288 " --> pdb=" O LEU K 276 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N LYS K 278 " --> pdb=" O THR K 286 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'K' and resid 83 through 85 removed outlier: 3.502A pdb=" N GLY K 103 " --> pdb=" O LEU K 241 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ALA K 243 " --> pdb=" O ILE K 101 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N ILE K 101 " --> pdb=" O ALA K 243 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N ARG K 102 " --> pdb=" O ASN K 121 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N VAL K 126 " --> pdb=" O VAL K 171 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N VAL K 171 " --> pdb=" O VAL K 126 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ILE K 128 " --> pdb=" O GLU K 169 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N GLU K 169 " --> pdb=" O ILE K 128 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N VAL K 130 " --> pdb=" O THR K 167 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N GLU K 132 " --> pdb=" O ASN K 165 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N ASN K 165 " --> pdb=" O GLU K 132 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N GLN K 134 " --> pdb=" O ALA K 163 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ALA K 163 " --> pdb=" O GLN K 134 " (cutoff:3.500A) removed outlier: 8.613A pdb=" N CYS K 136 " --> pdb=" O SER K 161 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N SER K 161 " --> pdb=" O CYS K 136 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ASP K 138 " --> pdb=" O VAL K 159 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N VAL K 159 " --> pdb=" O ASP K 138 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N PHE K 140 " --> pdb=" O PHE K 157 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N PHE K 157 " --> pdb=" O PHE K 140 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N GLY K 142 " --> pdb=" O SER K 155 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'K' and resid 83 through 85 removed outlier: 12.799A pdb=" N PHE K 238 " --> pdb=" O PHE K 135 " (cutoff:3.500A) removed outlier: 12.254A pdb=" N ASN K 137 " --> pdb=" O PHE K 238 " (cutoff:3.500A) removed outlier: 9.961A pdb=" N THR K 240 " --> pdb=" O ASN K 137 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N LEU K 242 " --> pdb=" O PRO K 139 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N VAL K 126 " --> pdb=" O VAL K 171 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N VAL K 171 " --> pdb=" O VAL K 126 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ILE K 128 " --> pdb=" O GLU K 169 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N GLU K 169 " --> pdb=" O ILE K 128 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N VAL K 130 " --> pdb=" O THR K 167 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N GLU K 132 " --> pdb=" O ASN K 165 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N ASN K 165 " --> pdb=" O GLU K 132 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N GLN K 134 " --> pdb=" O ALA K 163 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ALA K 163 " --> pdb=" O GLN K 134 " (cutoff:3.500A) removed outlier: 8.613A pdb=" N CYS K 136 " --> pdb=" O SER K 161 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N SER K 161 " --> pdb=" O CYS K 136 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ASP K 138 " --> pdb=" O VAL K 159 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N VAL K 159 " --> pdb=" O ASP K 138 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N PHE K 140 " --> pdb=" O PHE K 157 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N PHE K 157 " --> pdb=" O PHE K 140 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N GLY K 142 " --> pdb=" O SER K 155 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'K' and resid 311 through 319 removed outlier: 5.271A pdb=" N ILE K 312 " --> pdb=" O THR K 599 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N THR K 599 " --> pdb=" O ILE K 312 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N GLN K 314 " --> pdb=" O VAL K 597 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N VAL K 597 " --> pdb=" O GLN K 314 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLY K 594 " --> pdb=" O GLN K 613 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'K' and resid 354 through 358 removed outlier: 3.884A pdb=" N ASN K 394 " --> pdb=" O GLU K 516 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'K' and resid 361 through 362 removed outlier: 6.552A pdb=" N CYS K 361 " --> pdb=" O CYS K 525 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'K' and resid 452 through 454 Processing sheet with id=AH4, first strand: chain 'K' and resid 473 through 474 Processing sheet with id=AH5, first strand: chain 'K' and resid 654 through 655 removed outlier: 6.550A pdb=" N ILE K 670 " --> pdb=" O ILE K 666 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'K' and resid 711 through 728 removed outlier: 6.681A pdb=" N SER K 711 " --> pdb=" O THR K1076 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N THR K1076 " --> pdb=" O SER K 711 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ALA K 713 " --> pdb=" O ASN K1074 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ASN K1074 " --> pdb=" O ALA K 713 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N GLU K1072 " --> pdb=" O PRO K 715 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N TYR K1067 " --> pdb=" O HIS K1048 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N HIS K1048 " --> pdb=" O TYR K1067 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'K' and resid 711 through 728 removed outlier: 6.681A pdb=" N SER K 711 " --> pdb=" O THR K1076 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N THR K1076 " --> pdb=" O SER K 711 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ALA K 713 " --> pdb=" O ASN K1074 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ASN K1074 " --> pdb=" O ALA K 713 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N GLU K1072 " --> pdb=" O PRO K 715 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N PHE K1095 " --> pdb=" O ALA K1078 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'K' and resid 733 through 736 removed outlier: 4.415A pdb=" N LYS K 733 " --> pdb=" O LEU K 861 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'K' and resid 1120 through 1125 removed outlier: 4.833A pdb=" N ALA K1087 " --> pdb=" O SER K1123 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'L' and resid 4 through 7 removed outlier: 5.544A pdb=" N THR L 70 " --> pdb=" O ALA L 25 " (cutoff:3.500A) removed outlier: 9.609A pdb=" N GLN L 27 " --> pdb=" O SER L 68 " (cutoff:3.500A) removed outlier: 9.687A pdb=" N SER L 68 " --> pdb=" O GLN L 27 " (cutoff:3.500A) removed outlier: 11.202A pdb=" N VAL L 29 " --> pdb=" O SER L 66 " (cutoff:3.500A) removed outlier: 11.299A pdb=" N SER L 66 " --> pdb=" O VAL L 29 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'L' and resid 54 through 55 removed outlier: 6.487A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N TYR L 50 " --> pdb=" O LEU L 34 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N LEU L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'L' and resid 54 through 55 removed outlier: 6.487A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N TYR L 50 " --> pdb=" O LEU L 34 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N LEU L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'M' and resid 3 through 6 Processing sheet with id=AI5, first strand: chain 'M' and resid 10 through 11 removed outlier: 6.760A pdb=" N GLU M 10 " --> pdb=" O THR M 122 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N MET M 34 " --> pdb=" O TRP M 50 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N TRP M 50 " --> pdb=" O MET M 34 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N TRP M 36 " --> pdb=" O MET M 48 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'M' and resid 10 through 11 removed outlier: 6.760A pdb=" N GLU M 10 " --> pdb=" O THR M 122 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N TYR M 114 " --> pdb=" O ARG M 98 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AI8, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.919A pdb=" N ILE N 34 " --> pdb=" O SER N 50 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N SER N 50 " --> pdb=" O ILE N 34 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'N' and resid 10 through 12 removed outlier: 3.692A pdb=" N TYR N 115 " --> pdb=" O ARG N 98 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'O' and resid 9 through 11 removed outlier: 6.511A pdb=" N TRP O 37 " --> pdb=" O MET O 49 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'O' and resid 9 through 11 Processing sheet with id=AJ3, first strand: chain 'O' and resid 18 through 23 1634 hydrogen bonds defined for protein. 4200 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: 19.84 Time building geometry restraints manager: 16.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 9280 1.33 - 1.45: 8169 1.45 - 1.58: 17461 1.58 - 1.71: 1 1.71 - 1.83: 198 Bond restraints: 35109 Sorted by residual: bond pdb=" C5 NAG B1309 " pdb=" O5 NAG B1309 " ideal model delta sigma weight residual 1.413 1.470 -0.057 2.00e-02 2.50e+03 7.99e+00 bond pdb=" C5 NAG A1309 " pdb=" O5 NAG A1309 " ideal model delta sigma weight residual 1.413 1.469 -0.056 2.00e-02 2.50e+03 7.98e+00 bond pdb=" C5 NAG K1309 " pdb=" O5 NAG K1309 " ideal model delta sigma weight residual 1.413 1.469 -0.056 2.00e-02 2.50e+03 7.94e+00 bond pdb=" CA PRO B 986 " pdb=" C PRO B 986 " ideal model delta sigma weight residual 1.517 1.542 -0.025 9.30e-03 1.16e+04 7.31e+00 bond pdb=" CA PRO A 986 " pdb=" C PRO A 986 " ideal model delta sigma weight residual 1.517 1.542 -0.025 9.30e-03 1.16e+04 7.29e+00 ... (remaining 35104 not shown) Histogram of bond angle deviations from ideal: 99.52 - 106.43: 1041 106.43 - 113.33: 19004 113.33 - 120.23: 11929 120.23 - 127.13: 15769 127.13 - 134.03: 197 Bond angle restraints: 47940 Sorted by residual: angle pdb=" C THR B 791 " pdb=" N PRO B 792 " pdb=" CA PRO B 792 " ideal model delta sigma weight residual 119.66 125.89 -6.23 7.20e-01 1.93e+00 7.48e+01 angle pdb=" C THR K 791 " pdb=" N PRO K 792 " pdb=" CA PRO K 792 " ideal model delta sigma weight residual 119.66 125.86 -6.20 7.20e-01 1.93e+00 7.42e+01 angle pdb=" C THR A 791 " pdb=" N PRO A 792 " pdb=" CA PRO A 792 " ideal model delta sigma weight residual 119.66 125.84 -6.18 7.20e-01 1.93e+00 7.37e+01 angle pdb=" C ASP B1139 " pdb=" N PRO B1140 " pdb=" CA PRO B1140 " ideal model delta sigma weight residual 119.56 127.24 -7.68 1.02e+00 9.61e-01 5.68e+01 angle pdb=" C PRO K 862 " pdb=" N PRO K 863 " pdb=" CA PRO K 863 " ideal model delta sigma weight residual 119.78 127.20 -7.42 1.03e+00 9.43e-01 5.19e+01 ... (remaining 47935 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.33: 20987 21.33 - 42.66: 538 42.66 - 63.98: 117 63.98 - 85.31: 51 85.31 - 106.64: 24 Dihedral angle restraints: 21717 sinusoidal: 8571 harmonic: 13146 Sorted by residual: dihedral pdb=" CB CYS C 23 " pdb=" SG CYS C 23 " pdb=" SG CYS C 89 " pdb=" CB CYS C 89 " ideal model delta sinusoidal sigma weight residual 93.00 53.88 39.12 1 1.00e+01 1.00e-02 2.15e+01 dihedral pdb=" CB CYS D 23 " pdb=" SG CYS D 23 " pdb=" SG CYS D 89 " pdb=" CB CYS D 89 " ideal model delta sinusoidal sigma weight residual 93.00 53.90 39.10 1 1.00e+01 1.00e-02 2.15e+01 dihedral pdb=" CB CYS L 23 " pdb=" SG CYS L 23 " pdb=" SG CYS L 89 " pdb=" CB CYS L 89 " ideal model delta sinusoidal sigma weight residual 93.00 53.91 39.09 1 1.00e+01 1.00e-02 2.15e+01 ... (remaining 21714 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 4261 0.070 - 0.140: 1062 0.140 - 0.210: 258 0.210 - 0.280: 41 0.280 - 0.350: 63 Chirality restraints: 5685 Sorted by residual: chirality pdb=" C1 NAG W 2 " pdb=" O4 NAG W 1 " pdb=" C2 NAG W 2 " pdb=" O5 NAG W 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.51 0.11 2.00e-02 2.50e+03 3.14e+01 chirality pdb=" C1 NAG b 2 " pdb=" O4 NAG b 1 " pdb=" C2 NAG b 2 " pdb=" O5 NAG b 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.51 0.11 2.00e-02 2.50e+03 3.09e+01 chirality pdb=" C1 NAG R 2 " pdb=" O4 NAG R 1 " pdb=" C2 NAG R 2 " pdb=" O5 NAG R 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.51 0.11 2.00e-02 2.50e+03 2.96e+01 ... (remaining 5682 not shown) Planarity restraints: 6231 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG T 1 " 0.344 2.00e-02 2.50e+03 2.98e-01 1.11e+03 pdb=" C7 NAG T 1 " -0.082 2.00e-02 2.50e+03 pdb=" C8 NAG T 1 " 0.101 2.00e-02 2.50e+03 pdb=" N2 NAG T 1 " -0.530 2.00e-02 2.50e+03 pdb=" O7 NAG T 1 " 0.167 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG Y 1 " 0.344 2.00e-02 2.50e+03 2.98e-01 1.11e+03 pdb=" C7 NAG Y 1 " -0.082 2.00e-02 2.50e+03 pdb=" C8 NAG Y 1 " 0.101 2.00e-02 2.50e+03 pdb=" N2 NAG Y 1 " -0.530 2.00e-02 2.50e+03 pdb=" O7 NAG Y 1 " 0.166 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG d 1 " -0.344 2.00e-02 2.50e+03 2.98e-01 1.11e+03 pdb=" C7 NAG d 1 " 0.081 2.00e-02 2.50e+03 pdb=" C8 NAG d 1 " -0.101 2.00e-02 2.50e+03 pdb=" N2 NAG d 1 " 0.530 2.00e-02 2.50e+03 pdb=" O7 NAG d 1 " -0.166 2.00e-02 2.50e+03 ... (remaining 6228 not shown) Histogram of nonbonded interaction distances: 2.43 - 2.93: 15361 2.93 - 3.42: 30851 3.42 - 3.91: 59462 3.91 - 4.41: 66934 4.41 - 4.90: 110168 Nonbonded interactions: 282776 Sorted by model distance: nonbonded pdb=" OE2 GLU A 96 " pdb=" NH2 ARG A 190 " model vdw 2.435 2.520 nonbonded pdb=" OE2 GLU K 96 " pdb=" NH2 ARG K 190 " model vdw 2.435 2.520 nonbonded pdb=" OE2 GLU B 96 " pdb=" NH2 ARG B 190 " model vdw 2.435 2.520 nonbonded pdb=" NE2 GLN A 913 " pdb=" O PRO B1090 " model vdw 2.559 2.520 nonbonded pdb=" O PRO A1090 " pdb=" NE2 GLN K 913 " model vdw 2.559 2.520 ... (remaining 282771 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'K' } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'L' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'M' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'N' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'O' } ncs_group { reference = chain 'P' selection = chain 'U' selection = chain 'Z' } ncs_group { reference = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'a' selection = chain 'b' selection = chain 'c' } ncs_group { reference = chain 'T' selection = chain 'Y' selection = chain 'd' } 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: 0.010 Normalize map: mean=0, sd=1: 6.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 15.000 Check model and map are aligned: 0.450 Set scattering table: 0.270 Process input model: 98.050 Find NCS groups from input model: 2.400 Set up NCS constraints: 0.510 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 134.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 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 : 0.011 0.057 35109 Z= 0.734 Angle : 1.224 8.142 47940 Z= 0.825 Chirality : 0.074 0.350 5685 Planarity : 0.009 0.298 6177 Dihedral : 11.321 106.638 13131 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 0.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % 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: 0.49 (0.12), residues: 4497 helix: 0.47 (0.19), residues: 669 sheet: 0.66 (0.14), residues: 1350 loop : 0.21 (0.12), residues: 2478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.005 TRP E 106 HIS 0.003 0.001 HIS B1048 PHE 0.023 0.003 PHE K 898 TYR 0.041 0.004 TYR L 92 ARG 0.004 0.001 ARG B 357 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8994 Ramachandran restraints generated. 4497 Oldfield, 0 Emsley, 4497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8994 Ramachandran restraints generated. 4497 Oldfield, 0 Emsley, 4497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 696 residues out of total 3924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 696 time to evaluate : 4.076 Fit side-chains revert: symmetry clash REVERT: A 697 MET cc_start: 0.7866 (ptm) cc_final: 0.7582 (ptm) REVERT: E 34 MET cc_start: 0.8208 (tpp) cc_final: 0.7988 (mmm) REVERT: E 48 MET cc_start: 0.7927 (mtp) cc_final: 0.7646 (mtp) REVERT: E 70 MET cc_start: 0.8002 (mtt) cc_final: 0.7449 (mtt) REVERT: C 7 SER cc_start: 0.7162 (t) cc_final: 0.6785 (p) REVERT: F 70 MET cc_start: 0.7964 (mtt) cc_final: 0.7356 (mtt) REVERT: M 70 MET cc_start: 0.8135 (mtt) cc_final: 0.7519 (mtt) outliers start: 0 outliers final: 0 residues processed: 696 average time/residue: 1.4055 time to fit residues: 1172.3514 Evaluate side-chains 425 residues out of total 3924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 425 time to evaluate : 3.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 379 optimal weight: 0.2980 chunk 341 optimal weight: 0.2980 chunk 189 optimal weight: 0.6980 chunk 116 optimal weight: 3.9990 chunk 230 optimal weight: 0.5980 chunk 182 optimal weight: 0.5980 chunk 352 optimal weight: 0.9990 chunk 136 optimal weight: 30.0000 chunk 214 optimal weight: 3.9990 chunk 262 optimal weight: 4.9990 chunk 408 optimal weight: 0.7980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 239 GLN A 354 ASN A 501 ASN A 532 ASN A1101 HIS A1113 GLN D 27 GLN D 38 GLN D 101 GLN E 3 GLN B 207 HIS B 354 ASN B 564 GLN B 580 GLN B1113 GLN C 38 GLN F 3 GLN K 30 ASN K 207 HIS K 394 ASN K 532 ASN K 644 GLN K 957 GLN K 969 ASN K1101 HIS L 27 GLN M 3 GLN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.1774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 35109 Z= 0.181 Angle : 0.542 7.335 47940 Z= 0.290 Chirality : 0.044 0.172 5685 Planarity : 0.004 0.030 6177 Dihedral : 6.301 68.084 6468 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 2.36 % Allowed : 8.78 % Favored : 88.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % 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: 1.04 (0.12), residues: 4497 helix: 2.16 (0.20), residues: 648 sheet: 0.85 (0.13), residues: 1362 loop : 0.30 (0.12), residues: 2487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 106 HIS 0.006 0.001 HIS K 207 PHE 0.015 0.001 PHE B 898 TYR 0.025 0.001 TYR A1138 ARG 0.005 0.000 ARG B 346 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8994 Ramachandran restraints generated. 4497 Oldfield, 0 Emsley, 4497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8994 Ramachandran restraints generated. 4497 Oldfield, 0 Emsley, 4497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 569 residues out of total 3924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 492 time to evaluate : 3.439 Fit side-chains REVERT: A 239 GLN cc_start: 0.7560 (OUTLIER) cc_final: 0.7331 (tt0) REVERT: A 298 GLU cc_start: 0.7872 (OUTLIER) cc_final: 0.7654 (tt0) REVERT: A 354 ASN cc_start: 0.8066 (OUTLIER) cc_final: 0.7602 (m110) REVERT: A 498 GLN cc_start: 0.7572 (OUTLIER) cc_final: 0.7193 (mt0) REVERT: A 697 MET cc_start: 0.7917 (ptm) cc_final: 0.7558 (ptm) REVERT: A 900 MET cc_start: 0.8327 (mtp) cc_final: 0.8108 (mtm) REVERT: A 988 GLU cc_start: 0.6675 (OUTLIER) cc_final: 0.6321 (mm-30) REVERT: A 1058 HIS cc_start: 0.8144 (m170) cc_final: 0.7885 (m-70) REVERT: E 48 MET cc_start: 0.8071 (mtp) cc_final: 0.7745 (mtp) REVERT: B 298 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.7692 (tt0) REVERT: B 314 GLN cc_start: 0.7801 (OUTLIER) cc_final: 0.7278 (tt0) REVERT: B 324 GLU cc_start: 0.7256 (OUTLIER) cc_final: 0.6750 (tt0) REVERT: B 354 ASN cc_start: 0.8132 (OUTLIER) cc_final: 0.7775 (m110) REVERT: B 583 GLU cc_start: 0.6808 (OUTLIER) cc_final: 0.6486 (tp30) REVERT: B 740 MET cc_start: 0.7353 (OUTLIER) cc_final: 0.7066 (ttt) REVERT: B 987 PRO cc_start: 0.7517 (Cg_exo) cc_final: 0.7284 (Cg_endo) REVERT: B 988 GLU cc_start: 0.6404 (OUTLIER) cc_final: 0.6088 (mm-30) REVERT: C 4 MET cc_start: 0.6613 (mmp) cc_final: 0.6343 (mmp) REVERT: F 81 MET cc_start: 0.7553 (OUTLIER) cc_final: 0.7071 (ttp) REVERT: K 207 HIS cc_start: 0.6648 (t-90) cc_final: 0.6374 (m90) REVERT: K 900 MET cc_start: 0.8184 (ttm) cc_final: 0.7946 (ttm) REVERT: K 988 GLU cc_start: 0.6671 (OUTLIER) cc_final: 0.6274 (mm-30) REVERT: K 1019 ARG cc_start: 0.8423 (ttp-110) cc_final: 0.8154 (ttm110) REVERT: M 70 MET cc_start: 0.7938 (mtt) cc_final: 0.7462 (mtt) outliers start: 77 outliers final: 29 residues processed: 537 average time/residue: 1.3443 time to fit residues: 873.6184 Evaluate side-chains 461 residues out of total 3924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 418 time to evaluate : 3.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 498 GLN Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 698 SER Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain D residue 27 GLN Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 354 ASN Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 583 GLU Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain F residue 81 MET Chi-restraints excluded: chain K residue 29 THR Chi-restraints excluded: chain K residue 47 VAL Chi-restraints excluded: chain K residue 583 GLU Chi-restraints excluded: chain K residue 604 THR Chi-restraints excluded: chain K residue 659 SER Chi-restraints excluded: chain K residue 988 GLU Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 64 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 227 optimal weight: 1.9990 chunk 126 optimal weight: 0.9990 chunk 340 optimal weight: 2.9990 chunk 278 optimal weight: 50.0000 chunk 112 optimal weight: 7.9990 chunk 409 optimal weight: 3.9990 chunk 442 optimal weight: 50.0000 chunk 364 optimal weight: 4.9990 chunk 405 optimal weight: 6.9990 chunk 139 optimal weight: 30.0000 chunk 328 optimal weight: 0.8980 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 354 ASN A 394 ASN A 532 ASN A 804 GLN A 901 GLN A1101 HIS D 91 GLN D 101 GLN B 207 HIS B 394 ASN B 804 GLN B 901 GLN C 27 GLN ** K 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 394 ASN K 532 ASN K 644 GLN K 804 GLN K 901 GLN ** K1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K1113 GLN L 27 GLN M 3 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.108 35109 Z= 0.454 Angle : 0.675 8.895 47940 Z= 0.357 Chirality : 0.049 0.191 5685 Planarity : 0.005 0.051 6177 Dihedral : 6.081 51.579 6468 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 4.22 % Allowed : 9.95 % Favored : 85.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % 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: 0.76 (0.12), residues: 4497 helix: 2.00 (0.20), residues: 621 sheet: 0.71 (0.13), residues: 1446 loop : 0.05 (0.12), residues: 2430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP M 36 HIS 0.009 0.002 HIS K1048 PHE 0.030 0.003 PHE B 898 TYR 0.034 0.003 TYR L 92 ARG 0.006 0.001 ARG K 408 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8994 Ramachandran restraints generated. 4497 Oldfield, 0 Emsley, 4497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8994 Ramachandran restraints generated. 4497 Oldfield, 0 Emsley, 4497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 582 residues out of total 3924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 444 time to evaluate : 3.981 Fit side-chains revert: symmetry clash REVERT: A 81 ASN cc_start: 0.7621 (p0) cc_final: 0.7413 (p0) REVERT: A 224 GLU cc_start: 0.7894 (OUTLIER) cc_final: 0.7351 (mt-10) REVERT: A 239 GLN cc_start: 0.7603 (OUTLIER) cc_final: 0.7360 (tm-30) REVERT: A 314 GLN cc_start: 0.7890 (OUTLIER) cc_final: 0.7492 (tt0) REVERT: A 346 ARG cc_start: 0.7000 (OUTLIER) cc_final: 0.6704 (tmm160) REVERT: A 675 GLN cc_start: 0.7229 (OUTLIER) cc_final: 0.6973 (tm-30) REVERT: A 697 MET cc_start: 0.7971 (ptm) cc_final: 0.7582 (ptm) REVERT: A 731 MET cc_start: 0.8147 (OUTLIER) cc_final: 0.7785 (mtp) REVERT: E 38 ARG cc_start: 0.8248 (OUTLIER) cc_final: 0.7495 (ttm170) REVERT: E 48 MET cc_start: 0.8149 (mtp) cc_final: 0.7816 (mtp) REVERT: B 224 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.7352 (mt-10) REVERT: B 314 GLN cc_start: 0.7900 (OUTLIER) cc_final: 0.7355 (tt0) REVERT: B 324 GLU cc_start: 0.7373 (OUTLIER) cc_final: 0.6845 (tt0) REVERT: B 731 MET cc_start: 0.8120 (OUTLIER) cc_final: 0.7902 (mtm) REVERT: B 787 GLN cc_start: 0.8156 (mp10) cc_final: 0.7948 (mm-40) REVERT: B 814 LYS cc_start: 0.8011 (OUTLIER) cc_final: 0.7690 (mmtm) REVERT: B 1017 GLU cc_start: 0.7828 (OUTLIER) cc_final: 0.7528 (tp30) REVERT: B 1073 LYS cc_start: 0.8298 (OUTLIER) cc_final: 0.7951 (ptmt) REVERT: F 38 ARG cc_start: 0.8096 (OUTLIER) cc_final: 0.7169 (ttm170) REVERT: F 43 GLN cc_start: 0.7556 (tp40) cc_final: 0.7356 (tp40) REVERT: F 81 MET cc_start: 0.7636 (OUTLIER) cc_final: 0.7386 (ttp) REVERT: K 61 ASN cc_start: 0.7140 (t0) cc_final: 0.6888 (m-40) REVERT: K 207 HIS cc_start: 0.6651 (t-90) cc_final: 0.6431 (m90) REVERT: K 224 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.7289 (mt-10) REVERT: K 528 LYS cc_start: 0.8646 (OUTLIER) cc_final: 0.8173 (ttpp) REVERT: K 1019 ARG cc_start: 0.8495 (ttp-110) cc_final: 0.8205 (ttm110) REVERT: L 34 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8274 (tm) REVERT: L 64 SER cc_start: 0.8039 (OUTLIER) cc_final: 0.7816 (m) REVERT: M 70 MET cc_start: 0.7789 (mtt) cc_final: 0.7544 (mtt) outliers start: 138 outliers final: 60 residues processed: 523 average time/residue: 1.3970 time to fit residues: 879.3120 Evaluate side-chains 480 residues out of total 3924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 400 time to evaluate : 3.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain D residue 2 ILE Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain E residue 38 ARG Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 73 ASP Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 814 LYS Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain B residue 1073 LYS Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain F residue 38 ARG Chi-restraints excluded: chain F residue 73 ASP Chi-restraints excluded: chain F residue 76 ILE Chi-restraints excluded: chain F residue 81 MET Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 29 THR Chi-restraints excluded: chain K residue 47 VAL Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 224 GLU Chi-restraints excluded: chain K residue 359 SER Chi-restraints excluded: chain K residue 528 LYS Chi-restraints excluded: chain K residue 583 GLU Chi-restraints excluded: chain K residue 591 SER Chi-restraints excluded: chain K residue 604 THR Chi-restraints excluded: chain K residue 659 SER Chi-restraints excluded: chain K residue 702 GLU Chi-restraints excluded: chain K residue 754 LEU Chi-restraints excluded: chain K residue 963 VAL Chi-restraints excluded: chain K residue 988 GLU Chi-restraints excluded: chain K residue 1073 LYS Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain L residue 64 SER Chi-restraints excluded: chain L residue 103 THR Chi-restraints excluded: chain M residue 63 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 404 optimal weight: 0.7980 chunk 307 optimal weight: 4.9990 chunk 212 optimal weight: 0.0980 chunk 45 optimal weight: 0.4980 chunk 195 optimal weight: 0.3980 chunk 274 optimal weight: 6.9990 chunk 410 optimal weight: 1.9990 chunk 434 optimal weight: 30.0000 chunk 214 optimal weight: 3.9990 chunk 389 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN A 779 GLN A 926 GLN A 957 GLN A1101 HIS D 91 GLN D 101 GLN E 3 GLN B 207 HIS B 354 ASN B 957 GLN F 3 GLN ** K 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 394 ASN K 532 ASN K 613 GLN K 957 GLN K1101 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.2621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 35109 Z= 0.200 Angle : 0.526 7.944 47940 Z= 0.277 Chirality : 0.044 0.226 5685 Planarity : 0.004 0.037 6177 Dihedral : 5.037 53.278 6468 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 3.15 % Allowed : 11.60 % Favored : 85.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % 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: 0.91 (0.12), residues: 4497 helix: 2.39 (0.20), residues: 627 sheet: 0.75 (0.13), residues: 1386 loop : 0.12 (0.12), residues: 2484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 106 HIS 0.005 0.001 HIS B 207 PHE 0.020 0.001 PHE B 898 TYR 0.023 0.001 TYR A1138 ARG 0.004 0.000 ARG B 273 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8994 Ramachandran restraints generated. 4497 Oldfield, 0 Emsley, 4497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8994 Ramachandran restraints generated. 4497 Oldfield, 0 Emsley, 4497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 538 residues out of total 3924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 435 time to evaluate : 3.542 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 314 GLN cc_start: 0.7740 (OUTLIER) cc_final: 0.7271 (tt0) REVERT: A 697 MET cc_start: 0.7932 (ptm) cc_final: 0.7541 (ptm) REVERT: A 702 GLU cc_start: 0.7256 (OUTLIER) cc_final: 0.6598 (tt0) REVERT: A 740 MET cc_start: 0.7428 (OUTLIER) cc_final: 0.7170 (ttt) REVERT: A 747 THR cc_start: 0.8477 (m) cc_final: 0.8180 (p) REVERT: D 34 LEU cc_start: 0.8873 (OUTLIER) cc_final: 0.8576 (tm) REVERT: E 48 MET cc_start: 0.8137 (mtp) cc_final: 0.7837 (mtp) REVERT: B 324 GLU cc_start: 0.7349 (OUTLIER) cc_final: 0.6829 (tt0) REVERT: B 765 ARG cc_start: 0.8002 (ttp-110) cc_final: 0.7783 (ttp-110) REVERT: B 814 LYS cc_start: 0.7956 (OUTLIER) cc_final: 0.7628 (mmtm) REVERT: B 988 GLU cc_start: 0.6543 (OUTLIER) cc_final: 0.6129 (mm-30) REVERT: F 81 MET cc_start: 0.7633 (OUTLIER) cc_final: 0.7377 (ttp) REVERT: K 61 ASN cc_start: 0.7166 (t0) cc_final: 0.6945 (m-40) REVERT: K 498 GLN cc_start: 0.7894 (OUTLIER) cc_final: 0.7497 (mt0) REVERT: K 740 MET cc_start: 0.7309 (ttt) cc_final: 0.7095 (ttt) REVERT: K 1019 ARG cc_start: 0.8472 (ttp-110) cc_final: 0.8247 (ttm110) REVERT: L 34 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8317 (tm) REVERT: M 70 MET cc_start: 0.7777 (mtt) cc_final: 0.7467 (mtt) outliers start: 103 outliers final: 42 residues processed: 485 average time/residue: 1.3851 time to fit residues: 811.6204 Evaluate side-chains 450 residues out of total 3924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 398 time to evaluate : 3.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 73 ASP Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 814 LYS Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 73 ASP Chi-restraints excluded: chain F residue 76 ILE Chi-restraints excluded: chain F residue 81 MET Chi-restraints excluded: chain K residue 29 THR Chi-restraints excluded: chain K residue 54 LEU Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 84 LEU Chi-restraints excluded: chain K residue 427 ASP Chi-restraints excluded: chain K residue 498 GLN Chi-restraints excluded: chain K residue 583 GLU Chi-restraints excluded: chain K residue 604 THR Chi-restraints excluded: chain K residue 705 VAL Chi-restraints excluded: chain K residue 963 VAL Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain L residue 103 THR Chi-restraints excluded: chain M residue 63 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 362 optimal weight: 0.6980 chunk 246 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 323 optimal weight: 9.9990 chunk 179 optimal weight: 4.9990 chunk 371 optimal weight: 3.9990 chunk 300 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 222 optimal weight: 2.9990 chunk 390 optimal weight: 3.9990 chunk 109 optimal weight: 3.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 ASN A 926 GLN A 957 GLN A1101 HIS E 3 GLN B 207 HIS B 354 ASN B 394 ASN B 493 GLN B 564 GLN B 613 GLN B 957 GLN C 27 GLN F 3 GLN ** K 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 394 ASN K 926 GLN K1101 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.2936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.109 35109 Z= 0.442 Angle : 0.660 8.259 47940 Z= 0.346 Chirality : 0.048 0.248 5685 Planarity : 0.005 0.048 6177 Dihedral : 5.579 59.974 6468 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 4.32 % Allowed : 11.20 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % 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: 0.56 (0.12), residues: 4497 helix: 1.82 (0.20), residues: 624 sheet: 0.61 (0.13), residues: 1431 loop : -0.09 (0.12), residues: 2442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP M 36 HIS 0.008 0.002 HIS K1048 PHE 0.032 0.003 PHE B 898 TYR 0.034 0.003 TYR L 92 ARG 0.011 0.001 ARG K 346 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8994 Ramachandran restraints generated. 4497 Oldfield, 0 Emsley, 4497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8994 Ramachandran restraints generated. 4497 Oldfield, 0 Emsley, 4497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 539 residues out of total 3924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 398 time to evaluate : 3.803 Fit side-chains revert: symmetry clash REVERT: A 224 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.7333 (mt-10) REVERT: A 314 GLN cc_start: 0.7829 (OUTLIER) cc_final: 0.7484 (tt0) REVERT: A 697 MET cc_start: 0.7966 (ptm) cc_final: 0.7582 (ptm) REVERT: A 702 GLU cc_start: 0.7313 (OUTLIER) cc_final: 0.6824 (tt0) REVERT: A 731 MET cc_start: 0.8182 (OUTLIER) cc_final: 0.7583 (mtp) REVERT: E 48 MET cc_start: 0.8121 (mtp) cc_final: 0.7789 (mtp) REVERT: B 140 PHE cc_start: 0.7923 (p90) cc_final: 0.7695 (p90) REVERT: B 224 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.7342 (mt-10) REVERT: B 324 GLU cc_start: 0.7248 (OUTLIER) cc_final: 0.6745 (tt0) REVERT: B 354 ASN cc_start: 0.8475 (OUTLIER) cc_final: 0.8138 (m110) REVERT: B 564 GLN cc_start: 0.8338 (OUTLIER) cc_final: 0.8127 (mp-120) REVERT: B 592 PHE cc_start: 0.7678 (p90) cc_final: 0.7459 (p90) REVERT: B 702 GLU cc_start: 0.6900 (OUTLIER) cc_final: 0.6650 (tm-30) REVERT: B 814 LYS cc_start: 0.8011 (OUTLIER) cc_final: 0.7691 (mmtm) REVERT: B 988 GLU cc_start: 0.6802 (OUTLIER) cc_final: 0.6337 (mm-30) REVERT: B 1073 LYS cc_start: 0.8261 (OUTLIER) cc_final: 0.7907 (ptmt) REVERT: F 38 ARG cc_start: 0.8155 (OUTLIER) cc_final: 0.7219 (ttm170) REVERT: F 81 MET cc_start: 0.7724 (OUTLIER) cc_final: 0.7435 (ttp) REVERT: F 82 GLU cc_start: 0.7667 (tp30) cc_final: 0.7299 (mm-30) REVERT: K 61 ASN cc_start: 0.7107 (t0) cc_final: 0.6872 (t0) REVERT: K 224 GLU cc_start: 0.7796 (OUTLIER) cc_final: 0.7288 (mt-10) REVERT: K 287 ASP cc_start: 0.7620 (t0) cc_final: 0.7401 (t70) REVERT: K 346 ARG cc_start: 0.7526 (mmm160) cc_final: 0.7269 (mmm-85) REVERT: K 498 GLN cc_start: 0.7975 (OUTLIER) cc_final: 0.7582 (mt0) REVERT: K 528 LYS cc_start: 0.8675 (OUTLIER) cc_final: 0.8152 (ttpp) REVERT: K 1005 GLN cc_start: 0.8123 (OUTLIER) cc_final: 0.7894 (tt0) REVERT: K 1019 ARG cc_start: 0.8493 (ttp-110) cc_final: 0.8278 (ttm110) REVERT: M 38 ARG cc_start: 0.7966 (OUTLIER) cc_final: 0.6967 (ttp-170) outliers start: 141 outliers final: 70 residues processed: 482 average time/residue: 1.4411 time to fit residues: 834.1812 Evaluate side-chains 482 residues out of total 3924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 393 time to evaluate : 3.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 755 GLN Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain D residue 4 MET Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 73 ASP Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 256 SER Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 354 ASN Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 564 GLN Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 702 GLU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 814 LYS Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain B residue 1073 LYS Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain F residue 38 ARG Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 73 ASP Chi-restraints excluded: chain F residue 76 ILE Chi-restraints excluded: chain F residue 81 MET Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 29 THR Chi-restraints excluded: chain K residue 46 SER Chi-restraints excluded: chain K residue 47 VAL Chi-restraints excluded: chain K residue 54 LEU Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 205 SER Chi-restraints excluded: chain K residue 224 GLU Chi-restraints excluded: chain K residue 359 SER Chi-restraints excluded: chain K residue 427 ASP Chi-restraints excluded: chain K residue 483 VAL Chi-restraints excluded: chain K residue 498 GLN Chi-restraints excluded: chain K residue 528 LYS Chi-restraints excluded: chain K residue 583 GLU Chi-restraints excluded: chain K residue 604 THR Chi-restraints excluded: chain K residue 705 VAL Chi-restraints excluded: chain K residue 772 VAL Chi-restraints excluded: chain K residue 780 GLU Chi-restraints excluded: chain K residue 963 VAL Chi-restraints excluded: chain K residue 988 GLU Chi-restraints excluded: chain K residue 1001 LEU Chi-restraints excluded: chain K residue 1005 GLN Chi-restraints excluded: chain K residue 1073 LYS Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 103 THR Chi-restraints excluded: chain M residue 38 ARG Chi-restraints excluded: chain M residue 63 THR Chi-restraints excluded: chain M residue 119 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 146 optimal weight: 50.0000 chunk 391 optimal weight: 0.8980 chunk 85 optimal weight: 3.9990 chunk 255 optimal weight: 5.9990 chunk 107 optimal weight: 0.7980 chunk 435 optimal weight: 40.0000 chunk 361 optimal weight: 2.9990 chunk 201 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 144 optimal weight: 9.9990 chunk 228 optimal weight: 1.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 779 GLN A 926 GLN A 957 GLN A1101 HIS E 3 GLN B 207 HIS B 354 ASN B 394 ASN B 564 GLN B 957 GLN ** K 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 245 HIS K 394 ASN K 957 GLN K1101 HIS M 3 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.3017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 35109 Z= 0.336 Angle : 0.595 7.521 47940 Z= 0.313 Chirality : 0.046 0.173 5685 Planarity : 0.005 0.044 6177 Dihedral : 5.369 59.577 6468 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 3.83 % Allowed : 11.94 % Favored : 84.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % 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: 0.54 (0.12), residues: 4497 helix: 1.88 (0.20), residues: 630 sheet: 0.60 (0.13), residues: 1431 loop : -0.14 (0.12), residues: 2436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP M 106 HIS 0.007 0.001 HIS K 207 PHE 0.028 0.002 PHE B 898 TYR 0.031 0.002 TYR L 92 ARG 0.006 0.001 ARG K 346 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8994 Ramachandran restraints generated. 4497 Oldfield, 0 Emsley, 4497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8994 Ramachandran restraints generated. 4497 Oldfield, 0 Emsley, 4497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 523 residues out of total 3924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 398 time to evaluate : 3.650 Fit side-chains revert: symmetry clash REVERT: A 314 GLN cc_start: 0.7815 (OUTLIER) cc_final: 0.7417 (tt0) REVERT: A 697 MET cc_start: 0.7960 (ptm) cc_final: 0.7561 (ptm) REVERT: A 702 GLU cc_start: 0.7278 (OUTLIER) cc_final: 0.6788 (tt0) REVERT: A 747 THR cc_start: 0.8510 (m) cc_final: 0.8168 (p) REVERT: A 856 ASN cc_start: 0.7575 (OUTLIER) cc_final: 0.7268 (m110) REVERT: E 48 MET cc_start: 0.8156 (mtp) cc_final: 0.7864 (mtp) REVERT: B 140 PHE cc_start: 0.7921 (p90) cc_final: 0.7718 (p90) REVERT: B 207 HIS cc_start: 0.6947 (t70) cc_final: 0.6741 (m90) REVERT: B 224 GLU cc_start: 0.7772 (OUTLIER) cc_final: 0.7309 (mt-10) REVERT: B 324 GLU cc_start: 0.7213 (OUTLIER) cc_final: 0.6728 (tt0) REVERT: B 592 PHE cc_start: 0.7695 (p90) cc_final: 0.7483 (p90) REVERT: B 702 GLU cc_start: 0.6899 (OUTLIER) cc_final: 0.6635 (tm-30) REVERT: B 765 ARG cc_start: 0.8152 (ttp-110) cc_final: 0.7779 (ttp80) REVERT: B 814 LYS cc_start: 0.7945 (OUTLIER) cc_final: 0.7624 (mmtm) REVERT: B 988 GLU cc_start: 0.6784 (OUTLIER) cc_final: 0.6318 (mm-30) REVERT: B 1073 LYS cc_start: 0.8260 (OUTLIER) cc_final: 0.7929 (ptmt) REVERT: F 38 ARG cc_start: 0.8033 (OUTLIER) cc_final: 0.7231 (ttm170) REVERT: F 81 MET cc_start: 0.7644 (OUTLIER) cc_final: 0.7436 (ttp) REVERT: F 82 GLU cc_start: 0.7637 (tp30) cc_final: 0.7265 (mm-30) REVERT: K 61 ASN cc_start: 0.7036 (t0) cc_final: 0.6788 (t0) REVERT: K 224 GLU cc_start: 0.7781 (OUTLIER) cc_final: 0.7261 (mt-10) REVERT: K 287 ASP cc_start: 0.7574 (t0) cc_final: 0.7342 (t70) REVERT: K 528 LYS cc_start: 0.8667 (OUTLIER) cc_final: 0.8129 (ttpp) REVERT: K 856 ASN cc_start: 0.7606 (OUTLIER) cc_final: 0.7285 (m110) REVERT: K 957 GLN cc_start: 0.7848 (OUTLIER) cc_final: 0.7643 (tt0) REVERT: K 1019 ARG cc_start: 0.8500 (ttp-110) cc_final: 0.8276 (ttm110) REVERT: K 1092 GLU cc_start: 0.7154 (OUTLIER) cc_final: 0.6952 (pt0) REVERT: L 34 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8290 (tm) outliers start: 125 outliers final: 72 residues processed: 474 average time/residue: 1.3967 time to fit residues: 794.7145 Evaluate side-chains 479 residues out of total 3924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 390 time to evaluate : 3.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 755 GLN Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain D residue 4 MET Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 73 ASP Chi-restraints excluded: chain E residue 76 ILE Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 256 SER Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 702 GLU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 814 LYS Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain B residue 1055 SER Chi-restraints excluded: chain B residue 1073 LYS Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 22 SER Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain F residue 38 ARG Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 73 ASP Chi-restraints excluded: chain F residue 76 ILE Chi-restraints excluded: chain F residue 81 MET Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 29 THR Chi-restraints excluded: chain K residue 46 SER Chi-restraints excluded: chain K residue 47 VAL Chi-restraints excluded: chain K residue 54 LEU Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 224 GLU Chi-restraints excluded: chain K residue 359 SER Chi-restraints excluded: chain K residue 427 ASP Chi-restraints excluded: chain K residue 483 VAL Chi-restraints excluded: chain K residue 528 LYS Chi-restraints excluded: chain K residue 583 GLU Chi-restraints excluded: chain K residue 586 ASP Chi-restraints excluded: chain K residue 604 THR Chi-restraints excluded: chain K residue 705 VAL Chi-restraints excluded: chain K residue 772 VAL Chi-restraints excluded: chain K residue 780 GLU Chi-restraints excluded: chain K residue 856 ASN Chi-restraints excluded: chain K residue 957 GLN Chi-restraints excluded: chain K residue 963 VAL Chi-restraints excluded: chain K residue 988 GLU Chi-restraints excluded: chain K residue 1001 LEU Chi-restraints excluded: chain K residue 1073 LYS Chi-restraints excluded: chain K residue 1092 GLU Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain L residue 103 THR Chi-restraints excluded: chain M residue 43 GLN Chi-restraints excluded: chain M residue 63 THR Chi-restraints excluded: chain M residue 119 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 419 optimal weight: 2.9990 chunk 49 optimal weight: 0.0470 chunk 248 optimal weight: 0.9990 chunk 317 optimal weight: 4.9990 chunk 246 optimal weight: 0.9980 chunk 366 optimal weight: 0.6980 chunk 243 optimal weight: 0.9980 chunk 433 optimal weight: 10.0000 chunk 271 optimal weight: 0.0980 chunk 264 optimal weight: 1.9990 chunk 200 optimal weight: 0.6980 overall best weight: 0.5078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 779 GLN A 957 GLN A1101 HIS E 3 GLN B 354 ASN B 388 ASN B 957 GLN K 81 ASN K 239 GLN K 394 ASN K 926 GLN K1101 HIS M 3 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.3059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 35109 Z= 0.163 Angle : 0.509 6.861 47940 Z= 0.266 Chirality : 0.043 0.350 5685 Planarity : 0.004 0.075 6177 Dihedral : 4.790 54.912 6468 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 2.72 % Allowed : 13.44 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % 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: 0.71 (0.12), residues: 4497 helix: 2.13 (0.20), residues: 651 sheet: 0.64 (0.13), residues: 1425 loop : -0.03 (0.12), residues: 2421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP M 106 HIS 0.005 0.001 HIS K1048 PHE 0.019 0.001 PHE B 898 TYR 0.018 0.001 TYR A1067 ARG 0.018 0.000 ARG K 346 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8994 Ramachandran restraints generated. 4497 Oldfield, 0 Emsley, 4497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8994 Ramachandran restraints generated. 4497 Oldfield, 0 Emsley, 4497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 504 residues out of total 3924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 415 time to evaluate : 3.774 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 697 MET cc_start: 0.7876 (ptm) cc_final: 0.7509 (ptm) REVERT: A 740 MET cc_start: 0.7420 (OUTLIER) cc_final: 0.7156 (ttt) REVERT: A 747 THR cc_start: 0.8475 (m) cc_final: 0.8148 (p) REVERT: B 427 ASP cc_start: 0.7595 (OUTLIER) cc_final: 0.7053 (m-30) REVERT: B 814 LYS cc_start: 0.7867 (OUTLIER) cc_final: 0.7541 (mmtm) REVERT: B 988 GLU cc_start: 0.6584 (OUTLIER) cc_final: 0.6179 (mm-30) REVERT: K 207 HIS cc_start: 0.6308 (m-70) cc_final: 0.6015 (m-70) REVERT: K 740 MET cc_start: 0.7167 (OUTLIER) cc_final: 0.6957 (ttt) REVERT: K 988 GLU cc_start: 0.6598 (OUTLIER) cc_final: 0.5789 (tm-30) REVERT: K 1014 ARG cc_start: 0.8168 (OUTLIER) cc_final: 0.7902 (mtt90) REVERT: L 34 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8270 (tm) outliers start: 89 outliers final: 43 residues processed: 465 average time/residue: 1.3706 time to fit residues: 771.7997 Evaluate side-chains 441 residues out of total 3924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 390 time to evaluate : 3.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 814 LYS Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain B residue 1055 SER Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 22 SER Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain F residue 73 ASP Chi-restraints excluded: chain F residue 76 ILE Chi-restraints excluded: chain K residue 47 VAL Chi-restraints excluded: chain K residue 359 SER Chi-restraints excluded: chain K residue 427 ASP Chi-restraints excluded: chain K residue 583 GLU Chi-restraints excluded: chain K residue 604 THR Chi-restraints excluded: chain K residue 740 MET Chi-restraints excluded: chain K residue 754 LEU Chi-restraints excluded: chain K residue 963 VAL Chi-restraints excluded: chain K residue 988 GLU Chi-restraints excluded: chain K residue 1014 ARG Chi-restraints excluded: chain K residue 1073 LYS Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain L residue 103 THR Chi-restraints excluded: chain M residue 63 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 268 optimal weight: 1.9990 chunk 173 optimal weight: 9.9990 chunk 259 optimal weight: 4.9990 chunk 130 optimal weight: 30.0000 chunk 85 optimal weight: 5.9990 chunk 84 optimal weight: 0.9990 chunk 275 optimal weight: 4.9990 chunk 295 optimal weight: 20.0000 chunk 214 optimal weight: 4.9990 chunk 40 optimal weight: 0.9980 chunk 340 optimal weight: 0.9980 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 GLN A 957 GLN A1101 HIS B 207 HIS B 354 ASN B 388 ASN B 394 ASN B 564 GLN B 957 GLN K 394 ASN K 926 GLN K 957 GLN ** K1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.3183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.100 35109 Z= 0.419 Angle : 0.638 8.117 47940 Z= 0.333 Chirality : 0.049 0.729 5685 Planarity : 0.005 0.068 6177 Dihedral : 5.390 58.555 6468 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 3.40 % Allowed : 13.47 % Favored : 83.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % 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: 0.54 (0.12), residues: 4497 helix: 1.92 (0.20), residues: 624 sheet: 0.62 (0.13), residues: 1461 loop : -0.17 (0.12), residues: 2412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP E 106 HIS 0.008 0.002 HIS K1048 PHE 0.030 0.003 PHE B 898 TYR 0.035 0.003 TYR L 92 ARG 0.011 0.001 ARG B 346 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8994 Ramachandran restraints generated. 4497 Oldfield, 0 Emsley, 4497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8994 Ramachandran restraints generated. 4497 Oldfield, 0 Emsley, 4497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 504 residues out of total 3924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 393 time to evaluate : 3.653 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 224 GLU cc_start: 0.7843 (OUTLIER) cc_final: 0.7278 (mt-10) REVERT: A 697 MET cc_start: 0.7981 (ptm) cc_final: 0.7596 (ptm) REVERT: A 702 GLU cc_start: 0.7319 (OUTLIER) cc_final: 0.6740 (tt0) REVERT: E 38 ARG cc_start: 0.8224 (OUTLIER) cc_final: 0.7749 (ttm170) REVERT: B 207 HIS cc_start: 0.6879 (t70) cc_final: 0.6675 (m90) REVERT: B 224 GLU cc_start: 0.7752 (OUTLIER) cc_final: 0.7301 (mt-10) REVERT: B 324 GLU cc_start: 0.7252 (OUTLIER) cc_final: 0.6831 (tt0) REVERT: B 354 ASN cc_start: 0.8469 (OUTLIER) cc_final: 0.8129 (m110) REVERT: B 427 ASP cc_start: 0.7606 (OUTLIER) cc_final: 0.7269 (m-30) REVERT: B 564 GLN cc_start: 0.8308 (OUTLIER) cc_final: 0.7953 (mp-120) REVERT: B 765 ARG cc_start: 0.8147 (ttp-110) cc_final: 0.7774 (ttp-110) REVERT: B 814 LYS cc_start: 0.7901 (OUTLIER) cc_final: 0.7587 (mmtm) REVERT: B 988 GLU cc_start: 0.6887 (OUTLIER) cc_final: 0.6387 (mm-30) REVERT: B 1073 LYS cc_start: 0.8327 (OUTLIER) cc_final: 0.7862 (ptmt) REVERT: F 38 ARG cc_start: 0.8067 (OUTLIER) cc_final: 0.7191 (ttm170) REVERT: F 82 GLU cc_start: 0.7582 (tp30) cc_final: 0.7263 (mm-30) REVERT: K 207 HIS cc_start: 0.6362 (m-70) cc_final: 0.6115 (m90) REVERT: K 224 GLU cc_start: 0.7796 (OUTLIER) cc_final: 0.7281 (mt-10) REVERT: K 287 ASP cc_start: 0.7622 (t0) cc_final: 0.7391 (t70) REVERT: K 988 GLU cc_start: 0.6751 (OUTLIER) cc_final: 0.5910 (tm-30) REVERT: K 1014 ARG cc_start: 0.8255 (OUTLIER) cc_final: 0.7761 (mtt90) REVERT: K 1092 GLU cc_start: 0.7163 (OUTLIER) cc_final: 0.6952 (pt0) outliers start: 111 outliers final: 63 residues processed: 466 average time/residue: 1.4018 time to fit residues: 793.1728 Evaluate side-chains 462 residues out of total 3924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 383 time to evaluate : 3.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain E residue 38 ARG Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 73 ASP Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 256 SER Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 354 ASN Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 564 GLN Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 814 LYS Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain B residue 1055 SER Chi-restraints excluded: chain B residue 1073 LYS Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain F residue 38 ARG Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 73 ASP Chi-restraints excluded: chain F residue 76 ILE Chi-restraints excluded: chain K residue 47 VAL Chi-restraints excluded: chain K residue 54 LEU Chi-restraints excluded: chain K residue 205 SER Chi-restraints excluded: chain K residue 224 GLU Chi-restraints excluded: chain K residue 359 SER Chi-restraints excluded: chain K residue 427 ASP Chi-restraints excluded: chain K residue 483 VAL Chi-restraints excluded: chain K residue 583 GLU Chi-restraints excluded: chain K residue 586 ASP Chi-restraints excluded: chain K residue 604 THR Chi-restraints excluded: chain K residue 659 SER Chi-restraints excluded: chain K residue 705 VAL Chi-restraints excluded: chain K residue 963 VAL Chi-restraints excluded: chain K residue 988 GLU Chi-restraints excluded: chain K residue 1014 ARG Chi-restraints excluded: chain K residue 1073 LYS Chi-restraints excluded: chain K residue 1092 GLU Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 103 THR Chi-restraints excluded: chain M residue 63 THR Chi-restraints excluded: chain M residue 119 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 394 optimal weight: 0.5980 chunk 415 optimal weight: 0.0980 chunk 379 optimal weight: 0.5980 chunk 404 optimal weight: 1.9990 chunk 243 optimal weight: 0.8980 chunk 176 optimal weight: 5.9990 chunk 317 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 365 optimal weight: 0.7980 chunk 382 optimal weight: 0.5980 chunk 402 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 779 GLN A 957 GLN A1101 HIS B 354 ASN B 957 GLN F 3 GLN K 394 ASN K 957 GLN K1101 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.3201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 35109 Z= 0.165 Angle : 0.518 6.965 47940 Z= 0.271 Chirality : 0.044 0.591 5685 Planarity : 0.004 0.091 6177 Dihedral : 4.841 59.425 6468 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 2.17 % Allowed : 14.78 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % 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: 0.71 (0.12), residues: 4497 helix: 2.14 (0.20), residues: 651 sheet: 0.63 (0.13), residues: 1410 loop : -0.02 (0.12), residues: 2436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP M 106 HIS 0.005 0.001 HIS K1048 PHE 0.020 0.001 PHE B 562 TYR 0.018 0.001 TYR A1067 ARG 0.020 0.000 ARG K 346 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8994 Ramachandran restraints generated. 4497 Oldfield, 0 Emsley, 4497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8994 Ramachandran restraints generated. 4497 Oldfield, 0 Emsley, 4497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 3924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 397 time to evaluate : 3.710 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 307 THR cc_start: 0.8475 (t) cc_final: 0.8099 (m) REVERT: A 619 GLU cc_start: 0.7105 (mp0) cc_final: 0.6840 (mp0) REVERT: A 697 MET cc_start: 0.7920 (ptm) cc_final: 0.7521 (ptm) REVERT: A 702 GLU cc_start: 0.7266 (OUTLIER) cc_final: 0.6653 (tt0) REVERT: A 747 THR cc_start: 0.8482 (m) cc_final: 0.8157 (p) REVERT: B 177 MET cc_start: 0.4636 (mtt) cc_final: 0.4342 (mtm) REVERT: B 324 GLU cc_start: 0.7311 (OUTLIER) cc_final: 0.6894 (tt0) REVERT: B 814 LYS cc_start: 0.7865 (OUTLIER) cc_final: 0.7536 (mmtm) REVERT: B 988 GLU cc_start: 0.6661 (OUTLIER) cc_final: 0.6255 (mm-30) REVERT: B 1091 ARG cc_start: 0.7664 (mtt90) cc_final: 0.7285 (mtt-85) REVERT: F 82 GLU cc_start: 0.7456 (tp30) cc_final: 0.7213 (mm-30) REVERT: K 207 HIS cc_start: 0.6293 (m-70) cc_final: 0.6072 (m-70) REVERT: K 988 GLU cc_start: 0.6602 (OUTLIER) cc_final: 0.5769 (tm-30) REVERT: K 1014 ARG cc_start: 0.8182 (OUTLIER) cc_final: 0.7902 (mtt90) REVERT: L 34 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8204 (tm) outliers start: 71 outliers final: 37 residues processed: 443 average time/residue: 1.4419 time to fit residues: 776.8374 Evaluate side-chains 429 residues out of total 3924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 385 time to evaluate : 3.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 814 LYS Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain F residue 73 ASP Chi-restraints excluded: chain F residue 76 ILE Chi-restraints excluded: chain K residue 359 SER Chi-restraints excluded: chain K residue 427 ASP Chi-restraints excluded: chain K residue 583 GLU Chi-restraints excluded: chain K residue 586 ASP Chi-restraints excluded: chain K residue 604 THR Chi-restraints excluded: chain K residue 772 VAL Chi-restraints excluded: chain K residue 963 VAL Chi-restraints excluded: chain K residue 988 GLU Chi-restraints excluded: chain K residue 1014 ARG Chi-restraints excluded: chain K residue 1073 LYS Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain L residue 103 THR Chi-restraints excluded: chain M residue 63 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 265 optimal weight: 2.9990 chunk 427 optimal weight: 1.9990 chunk 260 optimal weight: 0.6980 chunk 202 optimal weight: 1.9990 chunk 297 optimal weight: 9.9990 chunk 448 optimal weight: 40.0000 chunk 412 optimal weight: 0.6980 chunk 356 optimal weight: 5.9990 chunk 37 optimal weight: 0.6980 chunk 275 optimal weight: 3.9990 chunk 218 optimal weight: 2.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 779 GLN A 957 GLN A1101 HIS B 354 ASN B 957 GLN B 969 ASN ** B1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 3 GLN K 394 ASN K 957 GLN K1058 HIS ** K1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.3240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 35109 Z= 0.280 Angle : 0.573 8.962 47940 Z= 0.299 Chirality : 0.046 0.734 5685 Planarity : 0.004 0.079 6177 Dihedral : 4.971 54.251 6468 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.11 % Allowed : 14.91 % Favored : 82.98 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 1.32 % 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: 0.67 (0.12), residues: 4497 helix: 2.00 (0.20), residues: 651 sheet: 0.68 (0.13), residues: 1455 loop : -0.08 (0.12), residues: 2391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP M 106 HIS 0.006 0.001 HIS K1048 PHE 0.025 0.002 PHE K 898 TYR 0.029 0.002 TYR L 92 ARG 0.016 0.001 ARG B 346 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8994 Ramachandran restraints generated. 4497 Oldfield, 0 Emsley, 4497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8994 Ramachandran restraints generated. 4497 Oldfield, 0 Emsley, 4497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 3924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 388 time to evaluate : 4.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 498 GLN cc_start: 0.7758 (OUTLIER) cc_final: 0.7376 (mt0) REVERT: A 697 MET cc_start: 0.7933 (ptm) cc_final: 0.7507 (ptm) REVERT: A 702 GLU cc_start: 0.7389 (OUTLIER) cc_final: 0.6772 (tt0) REVERT: A 747 THR cc_start: 0.8495 (m) cc_final: 0.8208 (p) REVERT: B 177 MET cc_start: 0.4872 (mtt) cc_final: 0.4578 (mtm) REVERT: B 324 GLU cc_start: 0.7252 (OUTLIER) cc_final: 0.6841 (tt0) REVERT: B 354 ASN cc_start: 0.8468 (OUTLIER) cc_final: 0.8128 (m110) REVERT: B 814 LYS cc_start: 0.7883 (OUTLIER) cc_final: 0.7556 (mmtm) REVERT: B 988 GLU cc_start: 0.6830 (OUTLIER) cc_final: 0.6346 (mm-30) REVERT: F 82 GLU cc_start: 0.7496 (tp30) cc_final: 0.7189 (mm-30) REVERT: K 207 HIS cc_start: 0.6273 (m-70) cc_final: 0.6050 (m90) REVERT: K 988 GLU cc_start: 0.6791 (OUTLIER) cc_final: 0.5888 (tm-30) REVERT: L 34 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.8251 (tm) outliers start: 69 outliers final: 45 residues processed: 429 average time/residue: 1.4137 time to fit residues: 731.0006 Evaluate side-chains 436 residues out of total 3924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 383 time to evaluate : 3.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 498 GLN Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 354 ASN Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 814 LYS Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain F residue 73 ASP Chi-restraints excluded: chain F residue 76 ILE Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 47 VAL Chi-restraints excluded: chain K residue 359 SER Chi-restraints excluded: chain K residue 427 ASP Chi-restraints excluded: chain K residue 583 GLU Chi-restraints excluded: chain K residue 586 ASP Chi-restraints excluded: chain K residue 604 THR Chi-restraints excluded: chain K residue 772 VAL Chi-restraints excluded: chain K residue 963 VAL Chi-restraints excluded: chain K residue 988 GLU Chi-restraints excluded: chain K residue 1073 LYS Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 103 THR Chi-restraints excluded: chain M residue 63 THR Chi-restraints excluded: chain M residue 119 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 50.1937 > 50: distance: 34 - 41: 5.670 distance: 41 - 42: 4.740 distance: 42 - 43: 6.868 distance: 42 - 45: 4.034 distance: 43 - 44: 6.831 distance: 43 - 49: 5.216 distance: 45 - 46: 6.070 distance: 46 - 47: 5.400 distance: 46 - 48: 7.954 distance: 48 - 272: 8.556 distance: 50 - 51: 5.074 distance: 50 - 53: 4.857 distance: 51 - 52: 4.967 distance: 51 - 60: 6.341 distance: 53 - 54: 11.811 distance: 54 - 55: 5.715 distance: 54 - 56: 8.956 distance: 55 - 57: 6.078 distance: 56 - 58: 6.336 distance: 57 - 59: 10.490 distance: 58 - 59: 10.189 distance: 60 - 61: 4.001 distance: 60 - 181: 8.334 distance: 61 - 62: 11.730 distance: 61 - 64: 3.491 distance: 62 - 63: 15.902 distance: 62 - 67: 6.089 distance: 63 - 178: 15.994 distance: 64 - 66: 8.456 distance: 67 - 68: 8.390 distance: 68 - 69: 13.128 distance: 68 - 71: 3.524 distance: 69 - 70: 17.928 distance: 69 - 74: 16.198 distance: 71 - 72: 9.429 distance: 71 - 73: 8.900 distance: 74 - 75: 12.297 distance: 74 - 163: 10.222 distance: 75 - 76: 11.497 distance: 75 - 78: 20.263 distance: 76 - 77: 24.567 distance: 76 - 79: 17.276 distance: 79 - 80: 5.636 distance: 79 - 85: 4.135 distance: 80 - 81: 14.770 distance: 80 - 83: 6.225 distance: 81 - 82: 14.313 distance: 81 - 86: 14.137 distance: 83 - 84: 11.058 distance: 84 - 85: 9.936 distance: 86 - 87: 4.878 distance: 87 - 90: 4.366 distance: 88 - 89: 7.555 distance: 88 - 91: 4.452 distance: 91 - 141: 6.327 distance: 92 - 93: 6.266 distance: 92 - 95: 12.460 distance: 93 - 94: 10.410 distance: 93 - 99: 3.918 distance: 94 - 138: 12.072 distance: 95 - 96: 12.334 distance: 95 - 97: 17.595 distance: 96 - 98: 5.251 distance: 99 - 100: 3.323 distance: 100 - 103: 4.443 distance: 101 - 102: 3.765 distance: 103 - 104: 8.792 distance: 104 - 207: 4.104 distance: 105 - 129: 6.367 distance: 106 - 109: 3.269 distance: 108 - 126: 4.531 distance: 109 - 110: 6.139 distance: 110 - 112: 4.258 distance: 111 - 113: 5.821 distance: 112 - 114: 4.099 distance: 113 - 114: 4.011