Starting phenix.real_space_refine on Wed Dec 13 22:04:37 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k8v_22732/12_2023/7k8v_22732_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k8v_22732/12_2023/7k8v_22732.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k8v_22732/12_2023/7k8v_22732.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k8v_22732/12_2023/7k8v_22732.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k8v_22732/12_2023/7k8v_22732_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k8v_22732/12_2023/7k8v_22732_neut.pdb" } resolution = 3.8 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= 0.002 sd= 0.015 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 114 5.16 5 C 16767 2.51 5 N 4319 2.21 5 O 5048 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 198": "OD1" <-> "OD2" Residue "A TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 389": "OD1" <-> "OD2" Residue "A PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 454": "NH1" <-> "NH2" Residue "A TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 904": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 994": "OD1" <-> "OD2" Residue "A GLU 1031": "OE1" <-> "OE2" Residue "A TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1095": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1107": "NH1" <-> "NH2" Residue "A ASP 1127": "OD1" <-> "OD2" Residue "A TYR 1138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 111": "OD1" <-> "OD2" Residue "B TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 228": "OD1" <-> "OD2" Residue "B TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 428": "OD1" <-> "OD2" Residue "B TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 454": "NH1" <-> "NH2" Residue "B PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 571": "OD1" <-> "OD2" Residue "B PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 614": "OD1" <-> "OD2" Residue "B TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 663": "OD1" <-> "OD2" Residue "B TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 702": "OE1" <-> "OE2" Residue "B PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 775": "OD1" <-> "OD2" Residue "B TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 819": "OE1" <-> "OE2" Residue "B PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 950": "OD1" <-> "OD2" Residue "B PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 994": "OD1" <-> "OD2" Residue "B GLU 1031": "OE1" <-> "OE2" Residue "B ASP 1041": "OD1" <-> "OD2" Residue "B PHE 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1072": "OE1" <-> "OE2" Residue "B PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1127": "OD1" <-> "OD2" Residue "B TYR 1138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 454": "NH1" <-> "NH2" Residue "C PHE 490": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 568": "OD1" <-> "OD2" Residue "C ASP 574": "OD1" <-> "OD2" Residue "C PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 873": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 936": "OD1" <-> "OD2" Residue "C PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 994": "OD1" <-> "OD2" Residue "C GLU 1017": "OE1" <-> "OE2" Residue "C ARG 1019": "NH1" <-> "NH2" Residue "C TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1095": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 10": "OE1" <-> "OE2" Residue "H TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 101": "OD1" <-> "OD2" Residue "L TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 81": "OD1" <-> "OD2" Residue "L TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 16": "OE1" <-> "OE2" Residue "M ASP 56": "OD1" <-> "OD2" Residue "M ASP 72": "OD1" <-> "OD2" Residue "M TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 101": "OD1" <-> "OD2" Residue "N TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.18s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 26248 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 7451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 978, 7451 Classifications: {'peptide': 978} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'PTRANS': 47, 'TRANS': 930} Chain breaks: 12 Unresolved non-hydrogen bonds: 215 Unresolved non-hydrogen angles: 271 Unresolved non-hydrogen dihedrals: 176 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 6, 'ASP:plan': 12, 'PHE:plan': 3, 'GLU:plan': 12, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 155 Chain: "B" Number of atoms: 7416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 973, 7416 Classifications: {'peptide': 973} Incomplete info: {'truncation_to_alanine': 58} Link IDs: {'PTRANS': 47, 'TRANS': 925} Chain breaks: 13 Unresolved non-hydrogen bonds: 215 Unresolved non-hydrogen angles: 271 Unresolved non-hydrogen dihedrals: 172 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 5, 'ARG:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 6, 'ASP:plan': 9, 'PHE:plan': 1, 'GLU:plan': 14, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 158 Chain: "C" Number of atoms: 7433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 977, 7433 Classifications: {'peptide': 977} Incomplete info: {'truncation_to_alanine': 64} Link IDs: {'PTRANS': 47, 'TRANS': 929} Chain breaks: 11 Unresolved non-hydrogen bonds: 224 Unresolved non-hydrogen angles: 282 Unresolved non-hydrogen dihedrals: 179 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 3, 'ASN:plan1': 6, 'ASP:plan': 13, 'PHE:plan': 1, 'GLU:plan': 15, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 161 Chain: "H" Number of atoms: 891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 891 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 6, 'TRANS': 119} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 87 Unresolved non-hydrogen angles: 104 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'PHE:plan': 2, 'ARG:plan': 4, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 49 Chain: "L" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 796 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 98} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 20 Chain: "M" Number of atoms: 891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 891 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 6, 'TRANS': 119} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 87 Unresolved non-hydrogen angles: 104 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'PHE:plan': 2, 'ARG:plan': 4, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 49 Chain: "N" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 796 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 98} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 20 Chain: "D" 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: "E" 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: "F" 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: "G" 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: "I" 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: "J" 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: "K" 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: "O" 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: "P" 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: "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: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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 Time building chain proxies: 13.83, per 1000 atoms: 0.53 Number of scatterers: 26248 At special positions: 0 Unit cell: (127.908, 139.612, 200.64, 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 114 16.00 O 5048 8.00 N 4319 7.00 C 16767 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=40, symmetry=0 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=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.02 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.02 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 343 " " NAG A1304 " - " ASN A 616 " " NAG A1305 " - " ASN A 657 " " NAG A1306 " - " ASN A 709 " " NAG A1307 " - " ASN A 801 " " NAG A1308 " - " ASN A1074 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 234 " " NAG B1304 " - " ASN B 343 " " NAG B1305 " - " ASN B 616 " " NAG B1306 " - " ASN B 657 " " NAG B1307 " - " ASN B 709 " " NAG B1308 " - " ASN B 717 " " NAG B1309 " - " ASN B1074 " " NAG B1310 " - " ASN B1098 " " NAG C1301 " - " ASN C 234 " " NAG C1302 " - " ASN C 709 " " NAG C1303 " - " ASN C1074 " " NAG D 1 " - " ASN A 234 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN A1098 " " NAG G 1 " - " ASN A1134 " " NAG I 1 " - " ASN B 801 " " NAG J 1 " - " ASN B1134 " " NAG K 1 " - " ASN C 717 " " NAG O 1 " - " ASN C 801 " " NAG P 1 " - " ASN C1098 " " NAG Q 1 " - " ASN C 343 " Time building additional restraints: 10.54 Conformation dependent library (CDL) restraints added in 5.2 seconds 6608 Ramachandran restraints generated. 3304 Oldfield, 0 Emsley, 3304 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6350 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 62 sheets defined 22.7% alpha, 24.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.68 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 364 through 371 removed outlier: 4.243A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 737 through 744 removed outlier: 3.629A pdb=" N GLY A 744 " --> pdb=" O MET A 740 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.537A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 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 891 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.166A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 968 removed outlier: 3.831A pdb=" N LEU A 966 " --> pdb=" O LEU A 962 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N SER A 967 " --> pdb=" O VAL A 963 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.907A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 3.757A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 337 through 341 Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 383 through 387 removed outlier: 3.840A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 407 removed outlier: 3.743A pdb=" N GLU B 406 " --> pdb=" O ARG B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 755 Processing helix chain 'B' and resid 758 through 783 Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.058A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 968 removed outlier: 3.829A pdb=" N LEU B 966 " --> pdb=" O LEU B 962 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 982 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.914A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 365 through 371 Processing helix chain 'C' and resid 406 through 410 Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 737 through 744 removed outlier: 3.594A pdb=" N GLY C 744 " --> pdb=" O MET C 740 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 782 Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 912 through 941 removed outlier: 3.975A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N LYS C 921 " --> pdb=" O TYR C 917 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N LEU C 922 " --> pdb=" O GLU C 918 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 967 removed outlier: 3.725A pdb=" N LEU C 966 " --> pdb=" O LEU C 962 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER C 967 " --> pdb=" O VAL C 963 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.693A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1147 Processing helix chain 'H' and resid 60 through 64 removed outlier: 3.794A pdb=" N GLN H 64 " --> pdb=" O PRO H 61 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.620A pdb=" N THR H 87 " --> pdb=" O ALA H 84 " (cutoff:3.500A) Processing helix chain 'M' and resid 60 through 64 removed outlier: 3.695A pdb=" N GLN M 64 " --> pdb=" O PRO M 61 " (cutoff:3.500A) Processing helix chain 'M' and resid 83 through 87 removed outlier: 3.728A pdb=" N THR M 87 " --> pdb=" O ALA M 84 " (cutoff:3.500A) Processing helix chain 'N' and resid 50 through 52 No H-bonds generated for 'chain 'N' and resid 50 through 52' Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.721A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.733A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N THR C 553 " --> pdb=" O ASP C 586 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N THR C 588 " --> pdb=" O VAL C 551 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLY C 548 " --> pdb=" O PHE C 541 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLY C 550 " --> pdb=" O VAL C 539 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL C 539 " --> pdb=" O GLY C 550 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 50 through 55 removed outlier: 3.529A pdb=" N LYS A 278 " --> pdb=" O ASP A 287 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.895A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 224 through 230 removed outlier: 7.178A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE A 203 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU A 229 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LYS A 202 " --> pdb=" O LYS A 195 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N TYR A 204 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N PHE A 194 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N VAL A 90 " --> pdb=" O PHE A 194 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N TYR A 91 " --> pdb=" O GLY A 268 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N GLY A 268 " --> pdb=" O TYR A 91 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 95 through 96 removed outlier: 3.964A pdb=" N GLU A 96 " --> pdb=" O ASN A 188 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ASN A 188 " --> pdb=" O GLU A 96 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 118 through 121 Processing sheet with id=AA8, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.360A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 324 through 328 removed outlier: 6.926A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 8.485A pdb=" N ASN A 542 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.644A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA A 397 " --> pdb=" O LYS A 356 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N PHE A 400 " --> pdb=" O VAL A 510 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL A 510 " --> pdb=" O PHE A 400 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE A 402 " --> pdb=" O TYR A 508 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ARG A 509 " --> pdb=" O TRP A 436 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N TRP A 436 " --> pdb=" O ARG A 509 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS A 378 " --> pdb=" O VAL A 433 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ALA A 435 " --> pdb=" O THR A 376 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.392A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB4, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.849A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.168A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 712 through 724 removed outlier: 3.916A pdb=" N ILE A 712 " --> pdb=" O PHE A1075 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS A1073 " --> pdb=" O ILE A 714 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 727 through 728 removed outlier: 3.525A pdb=" N VAL A1060 " --> pdb=" O LEU A 727 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL A1061 " --> pdb=" O GLN A1054 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1123 removed outlier: 3.547A pdb=" N ILE A1081 " --> pdb=" O HIS A1088 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC1, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.893A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 36 through 37 removed outlier: 7.450A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 10.156A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU B 226 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N LYS B 202 " --> pdb=" O LYS B 195 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N LYS B 195 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N THR B 208 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N PHE B 194 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL B 90 " --> pdb=" O PHE B 194 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 36 through 37 removed outlier: 7.450A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 10.156A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU B 226 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N LYS B 202 " --> pdb=" O LYS B 195 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N LYS B 195 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N THR B 208 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N SER B 94 " --> pdb=" O ARG B 190 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.505A pdb=" N PHE B 55 " --> pdb=" O GLN B 271 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 83 through 85 removed outlier: 3.868A pdb=" N ARG B 237 " --> pdb=" O GLY B 107 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N GLY B 107 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLN B 239 " --> pdb=" O ILE B 105 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ILE B 105 " --> pdb=" O GLN B 239 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 118 through 121 removed outlier: 3.547A pdb=" N LEU B 118 " --> pdb=" O LYS B 129 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LYS B 129 " --> pdb=" O LEU B 118 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.325A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N SER B 596 " --> pdb=" O LEU B 611 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N TYR B 612 " --> pdb=" O CYS B 649 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N CYS B 649 " --> pdb=" O TYR B 612 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 325 through 327 Processing sheet with id=AC9, first strand: chain 'B' and resid 355 through 356 removed outlier: 3.537A pdb=" N ASP B 398 " --> pdb=" O VAL B 512 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N VAL B 512 " --> pdb=" O ASP B 398 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 361 through 362 removed outlier: 5.479A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'B' and resid 565 through 566 removed outlier: 6.954A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'B' and resid 575 through 577 Processing sheet with id=AD4, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.493A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N SER B 673 " --> pdb=" O ILE B 693 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 717 through 728 removed outlier: 6.702A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER B 721 " --> pdb=" O THR B1066 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N TYR B1047 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 717 through 728 removed outlier: 6.702A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER B 721 " --> pdb=" O THR B1066 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD8, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 3.721A pdb=" N PHE B1089 " --> pdb=" O PHE B1121 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AE1, first strand: chain 'C' and resid 36 through 37 removed outlier: 6.970A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 10.480A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 9.951A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ILE C 203 " --> pdb=" O VAL C 227 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.687A pdb=" N ARG C 273 " --> pdb=" O ASP C 53 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.586A pdb=" N GLN C 239 " --> pdb=" O ILE C 105 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE C 105 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 118 through 121 removed outlier: 3.766A pdb=" N TYR C 170 " --> pdb=" O ILE C 128 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.773A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N GLN C 613 " --> pdb=" O GLY C 594 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.780A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N PHE C 400 " --> pdb=" O VAL C 510 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL C 510 " --> pdb=" O PHE C 400 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ILE C 402 " --> pdb=" O TYR C 508 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TYR C 508 " --> pdb=" O ILE C 402 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ARG C 509 " --> pdb=" O TRP C 436 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N CYS C 432 " --> pdb=" O LEU C 513 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS C 378 " --> pdb=" O VAL C 433 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA C 435 " --> pdb=" O THR C 376 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.712A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE9, first strand: chain 'C' and resid 654 through 660 removed outlier: 3.677A pdb=" N GLU C 654 " --> pdb=" O ILE C 692 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N THR C 696 " --> pdb=" O VAL C 656 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ASN C 658 " --> pdb=" O THR C 696 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA C 672 " --> pdb=" O ILE C 664 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ILE C 664 " --> pdb=" O ALA C 672 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 711 through 719 removed outlier: 3.613A pdb=" N ILE C 714 " --> pdb=" O LYS C1073 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS C1073 " --> pdb=" O ILE C 714 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA C1056 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 722 through 728 removed outlier: 3.749A pdb=" N THR C 723 " --> pdb=" O HIS C1064 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N HIS C1064 " --> pdb=" O THR C 723 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLU C 725 " --> pdb=" O PHE C1062 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AF4, first strand: chain 'C' and resid 1120 through 1123 removed outlier: 3.554A pdb=" N PHE C1089 " --> pdb=" O PHE C1121 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE C1081 " --> pdb=" O HIS C1088 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AF6, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AF7, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.267A pdb=" N GLU H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF7 Processing sheet with id=AF8, first strand: chain 'H' and resid 45 through 46 removed outlier: 3.922A pdb=" N VAL H 37 " --> pdb=" O TYR H 91 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N TYR H 91 " --> pdb=" O VAL H 37 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'H' and resid 50 through 52 removed outlier: 3.604A pdb=" N ILE H 50 " --> pdb=" O ARG H 58 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'L' and resid 5 through 7 removed outlier: 3.918A pdb=" N THR L 5 " --> pdb=" O ARG L 24 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG L 24 " --> pdb=" O THR L 5 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL L 19 " --> pdb=" O ILE L 75 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N SER L 63 " --> pdb=" O THR L 74 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'L' and resid 53 through 54 removed outlier: 6.416A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLN L 38 " --> pdb=" O THR L 85 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N THR L 85 " --> pdb=" O GLN L 38 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'M' and resid 3 through 6 removed outlier: 3.523A pdb=" N GLN M 3 " --> pdb=" O SER M 25 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'M' and resid 10 through 11 removed outlier: 6.006A pdb=" N GLU M 10 " --> pdb=" O THR M 110 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLN M 39 " --> pdb=" O MET M 89 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N TYR M 91 " --> pdb=" O VAL M 37 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N VAL M 37 " --> pdb=" O TYR M 91 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N TRP M 36 " --> pdb=" O MET M 48 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N MET M 48 " --> pdb=" O TRP M 36 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ILE M 50 " --> pdb=" O ARG M 58 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'M' and resid 71 through 72 Processing sheet with id=AG6, first strand: chain 'N' and resid 6 through 7 removed outlier: 3.832A pdb=" N THR N 22 " --> pdb=" O SER N 7 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'N' and resid 45 through 46 removed outlier: 3.670A pdb=" N ALA N 34 " --> pdb=" O GLN N 89 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLN N 89 " --> pdb=" O ALA N 34 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'N' and resid 48 through 49 928 hydrogen bonds defined for protein. 2556 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: 11.23 Time building geometry restraints manager: 11.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 8320 1.35 - 1.47: 6842 1.47 - 1.59: 11508 1.59 - 1.71: 0 1.71 - 1.83: 148 Bond restraints: 26818 Sorted by residual: bond pdb=" C1 NAG B1303 " pdb=" O5 NAG B1303 " ideal model delta sigma weight residual 1.406 1.487 -0.081 2.00e-02 2.50e+03 1.62e+01 bond pdb=" N THR C 29 " pdb=" CA THR C 29 " ideal model delta sigma weight residual 1.456 1.490 -0.035 1.23e-02 6.61e+03 7.88e+00 bond pdb=" N VAL C 62 " pdb=" CA VAL C 62 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 7.73e+00 bond pdb=" N TYR C 28 " pdb=" CA TYR C 28 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.34e-02 5.57e+03 6.48e+00 bond pdb=" N ASN C 30 " pdb=" CA ASN C 30 " ideal model delta sigma weight residual 1.454 1.487 -0.033 1.31e-02 5.83e+03 6.37e+00 ... (remaining 26813 not shown) Histogram of bond angle deviations from ideal: 99.65 - 106.53: 723 106.53 - 113.42: 14806 113.42 - 120.31: 9053 120.31 - 127.20: 11746 127.20 - 134.09: 222 Bond angle restraints: 36550 Sorted by residual: angle pdb=" N PRO H 100G" pdb=" CA PRO H 100G" pdb=" CB PRO H 100G" ideal model delta sigma weight residual 103.25 111.28 -8.03 1.05e+00 9.07e-01 5.85e+01 angle pdb=" N PRO M 100G" pdb=" CA PRO M 100G" pdb=" CB PRO M 100G" ideal model delta sigma weight residual 103.25 111.25 -8.00 1.05e+00 9.07e-01 5.80e+01 angle pdb=" N PRO M 100 " pdb=" CA PRO M 100 " pdb=" CB PRO M 100 " ideal model delta sigma weight residual 103.25 111.08 -7.83 1.05e+00 9.07e-01 5.56e+01 angle pdb=" N PRO H 100 " pdb=" CA PRO H 100 " pdb=" CB PRO H 100 " ideal model delta sigma weight residual 103.25 111.02 -7.77 1.05e+00 9.07e-01 5.48e+01 angle pdb=" N GLU A 169 " pdb=" CA GLU A 169 " pdb=" C GLU A 169 " ideal model delta sigma weight residual 112.97 108.93 4.04 1.06e+00 8.90e-01 1.45e+01 ... (remaining 36545 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.40: 15460 22.40 - 44.81: 773 44.81 - 67.21: 100 67.21 - 89.61: 48 89.61 - 112.01: 11 Dihedral angle restraints: 16392 sinusoidal: 6545 harmonic: 9847 Sorted by residual: dihedral pdb=" CB CYS C 291 " pdb=" SG CYS C 291 " pdb=" SG CYS C 301 " pdb=" CB CYS C 301 " ideal model delta sinusoidal sigma weight residual 93.00 5.63 87.37 1 1.00e+01 1.00e-02 9.16e+01 dihedral pdb=" CB CYS C1032 " pdb=" SG CYS C1032 " pdb=" SG CYS C1043 " pdb=" CB CYS C1043 " ideal model delta sinusoidal sigma weight residual 93.00 -179.85 -87.15 1 1.00e+01 1.00e-02 9.12e+01 dihedral pdb=" CB CYS A 738 " pdb=" SG CYS A 738 " pdb=" SG CYS A 760 " pdb=" CB CYS A 760 " ideal model delta sinusoidal sigma weight residual -86.00 -1.49 -84.51 1 1.00e+01 1.00e-02 8.68e+01 ... (remaining 16389 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.338: 4340 0.338 - 0.677: 4 0.677 - 1.015: 2 1.015 - 1.354: 2 1.354 - 1.692: 3 Chirality restraints: 4351 Sorted by residual: chirality pdb=" C1 NAG I 2 " pdb=" O4 NAG I 1 " pdb=" C2 NAG I 2 " pdb=" O5 NAG I 2 " both_signs ideal model delta sigma weight residual False -2.40 -0.71 -1.69 2.00e-02 2.50e+03 7.16e+03 chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -0.73 -1.67 2.00e-02 2.50e+03 6.95e+03 chirality pdb=" C1 NAG G 2 " pdb=" O4 NAG G 1 " pdb=" C2 NAG G 2 " pdb=" O5 NAG G 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.02 -1.38 2.00e-02 2.50e+03 4.77e+03 ... (remaining 4348 not shown) Planarity restraints: 4669 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN C1142 " 0.044 5.00e-02 4.00e+02 6.64e-02 7.06e+00 pdb=" N PRO C1143 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO C1143 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO C1143 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU C 916 " -0.008 2.00e-02 2.50e+03 1.53e-02 2.34e+00 pdb=" C LEU C 916 " 0.026 2.00e-02 2.50e+03 pdb=" O LEU C 916 " -0.010 2.00e-02 2.50e+03 pdb=" N TYR C 917 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS M 13 " -0.025 5.00e-02 4.00e+02 3.81e-02 2.33e+00 pdb=" N PRO M 14 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO M 14 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO M 14 " -0.021 5.00e-02 4.00e+02 ... (remaining 4666 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.58: 312 2.58 - 3.16: 22012 3.16 - 3.74: 40640 3.74 - 4.32: 55245 4.32 - 4.90: 89374 Nonbonded interactions: 207583 Sorted by model distance: nonbonded pdb=" CG1 VAL C 62 " pdb=" O VAL C 267 " model vdw 2.005 3.460 nonbonded pdb=" O LEU A 966 " pdb=" OG SER A 975 " model vdw 2.146 2.440 nonbonded pdb=" O LEU B 966 " pdb=" OG SER B 975 " model vdw 2.169 2.440 nonbonded pdb=" O LEU C 966 " pdb=" OG SER C 975 " model vdw 2.176 2.440 nonbonded pdb=" NE2 GLN B 644 " pdb=" O THR B 645 " model vdw 2.192 2.520 ... (remaining 207578 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 45 or (resid 46 and (name N or name CA or name \ C or name O or name CB )) or resid 47 through 52 or (resid 53 and (name N or nam \ e CA or name C or name O or name CB )) or resid 54 through 66 or resid 82 throug \ h 87 or (resid 88 and (name N or name CA or name C or name O or name CB )) or re \ sid 89 through 95 or (resid 96 through 97 and (name N or name CA or name C or na \ me O or name CB )) or resid 98 through 109 or (resid 110 through 113 and (name N \ or name CA or name C or name O or name CB )) or resid 116 through 124 or (resid \ 125 and (name N or name CA or name C or name O or name CB )) or resid 126 throu \ gh 131 or (resid 132 and (name N or name CA or name C or name O or name CB )) or \ resid 133 or (resid 134 through 138 and (name N or name CA or name C or name O \ or name CB )) or resid 139 through 140 or resid 166 through 168 or (resid 169 an \ d (name N or name CA or name C or name O or name CB )) or resid 170 through 171 \ or (resid 172 and (name N or name CA or name C or name O or name CB )) or resid \ 186 through 190 or (resid 191 and (name N or name CA or name C or name O or name \ CB )) or resid 192 through 196 or resid 200 through 210 or (resid 211 and (name \ N or name CA or name C or name O or name CB )) or (resid 215 and (name N or nam \ e CA or name C or name O or name CB )) or resid 216 through 217 or (resid 218 an \ d (name N or name CA or name C or name O or name CB )) or resid 219 through 223 \ or (resid 224 and (name N or name CA or name C or name O or name CB )) or resid \ 225 through 238 or (resid 239 and (name N or name CA or name C or name O or name \ CB )) or resid 240 through 263 or resid 265 through 308 or (resid 309 and (name \ N or name CA or name C or name O or name CB )) or resid 310 through 323 or (res \ id 324 and (name N or name CA or name C or name O or name CB )) or resid 325 thr \ ough 332 or (resid 333 and (name N or name CA or name C or name O or name CB )) \ or resid 334 through 528 or (resid 529 and (name N or name CA or name C or name \ O or name CB )) or resid 530 through 553 or (resid 554 and (name N or name CA or \ name C or name O or name CB )) or resid 555 through 793 or (resid 794 and (name \ N or name CA or name C or name O or name CB )) or resid 795 or (resid 796 and ( \ name N or name CA or name C or name O or name CB )) or resid 797 through 810 or \ (resid 811 and (name N or name CA or name C or name O or name CB )) or resid 813 \ through 827 or resid 856 through 866 or (resid 867 through 868 and (name N or n \ ame CA or name C or name O or name CB )) or resid 869 through 939 or (resid 940 \ and (name N or name CA or name C or name O or name CB )) or resid 941 through 98 \ 4 or (resid 985 and (name N or name CA or name C or name O or name CB )) or resi \ d 986 through 987 or (resid 988 through 989 and (name N or name CA or name C or \ name O or name CB )) or resid 990 through 1141 or (resid 1142 and (name N or nam \ e CA or name C or name O or name CB )) or resid 1143 through 1144 or (resid 1145 \ through 1146 and (name N or name CA or name C or name O or name CB )) or resid \ 1147 or resid 1301 through 1303)) selection = (chain 'B' and (resid 27 through 45 or (resid 46 and (name N or name CA or name \ C or name O or name CB )) or resid 47 through 66 or resid 82 through 87 or (resi \ d 88 and (name N or name CA or name C or name O or name CB )) or resid 89 throug \ h 96 or (resid 97 and (name N or name CA or name C or name O or name CB )) or re \ sid 98 or (resid 99 and (name N or name CA or name C or name O or name CB )) or \ resid 100 through 109 or (resid 110 through 113 and (name N or name CA or name C \ or name O or name CB )) or resid 116 through 128 or (resid 129 and (name N or n \ ame CA or name C or name O or name CB )) or resid 130 through 134 or (resid 135 \ through 138 and (name N or name CA or name C or name O or name CB )) or resid 13 \ 9 through 140 or resid 166 through 168 or (resid 169 and (name N or name CA or n \ ame C or name O or name CB )) or resid 170 through 187 or (resid 188 and (name N \ or name CA or name C or name O or name CB )) or resid 189 through 190 or (resid \ 191 and (name N or name CA or name C or name O or name CB )) or resid 192 throu \ gh 195 or (resid 196 and (name N or name CA or name C or name O or name CB )) or \ resid 200 through 210 or (resid 211 through 215 and (name N or name CA or name \ C or name O or name CB )) or resid 216 through 241 or (resid 242 through 263 and \ (name N or name CA or name C or name O or name CB )) or resid 265 through 280 o \ r (resid 281 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 82 through 323 or (resid 324 and (name N or name CA or name C or name O or name \ CB )) or resid 325 through 567 or (resid 568 and (name N or name CA or name C or \ name O or name CB )) or resid 569 through 570 or (resid 571 and (name N or name \ CA or name C or name O or name CB )) or resid 572 through 581 or (resid 582 thr \ ough 583 and (name N or name CA or name C or name O or name CB )) or resid 584 t \ hrough 585 or (resid 586 and (name N or name CA or name C or name O or name CB ) \ ) or resid 587 through 613 or (resid 614 and (name N or name CA or name C or nam \ e O or name CB )) or resid 615 through 618 or (resid 619 and (name N or name CA \ or name C or name O or name CB )) or resid 620 through 676 or resid 690 through \ 744 or (resid 745 and (name N or name CA or name C or name O or name CB )) or re \ sid 746 through 810 or (resid 811 and (name N or name CA or name C or name O or \ name CB )) or resid 813 through 827 or resid 856 through 866 or (resid 867 throu \ gh 868 and (name N or name CA or name C or name O or name CB )) or resid 869 thr \ ough 920 or (resid 921 and (name N or name CA or name C or name O or name CB )) \ or resid 922 through 939 or (resid 940 and (name N or name CA or name C or name \ O or name CB )) or resid 941 through 984 or (resid 985 and (name N or name CA or \ name C or name O or name CB )) or resid 986 through 987 or (resid 988 through 9 \ 89 and (name N or name CA or name C or name O or name CB )) or resid 990 through \ 1072 or (resid 1073 and (name N or name CA or name C or name O or name CB )) or \ resid 1074 through 1117 or (resid 1118 and (name N or name CA or name C or name \ O or name CB )) or resid 1119 through 1143 or (resid 1144 through 1146 and (nam \ e N or name CA or name C or name O or name CB )) or resid 1147 or resid 1301 thr \ ough 1303)) selection = (chain 'C' and (resid 27 through 52 or (resid 53 and (name N or name CA or name \ C or name O or name CB )) or resid 54 through 66 or resid 82 through 95 or (resi \ d 96 through 97 and (name N or name CA or name C or name O or name CB )) or resi \ d 98 or (resid 99 and (name N or name CA or name C or name O or name CB )) or re \ sid 100 through 110 or (resid 111 through 113 and (name N or name CA or name C o \ r name O or name CB )) or resid 116 through 134 or (resid 135 through 138 and (n \ ame N or name CA or name C or name O or name CB )) or resid 139 through 140 or r \ esid 166 through 187 or (resid 188 and (name N or name CA or name C or name O or \ name CB )) or resid 189 through 195 or (resid 196 and (name N or name CA or nam \ e C or name O or name CB )) or resid 200 through 211 or resid 215 through 217 or \ (resid 218 and (name N or name CA or name C or name O or name CB )) or resid 21 \ 9 through 223 or (resid 224 and (name N or name CA or name C or name O or name C \ B )) or resid 225 through 238 or (resid 239 and (name N or name CA or name C or \ name O or name CB )) or resid 240 through 308 or (resid 309 and (name N or name \ CA or name C or name O or name CB )) or resid 310 through 332 or (resid 333 and \ (name N or name CA or name C or name O or name CB )) or resid 334 through 528 or \ (resid 529 and (name N or name CA or name C or name O or name CB )) or resid 53 \ 0 through 553 or (resid 554 and (name N or name CA or name C or name O or name C \ B )) or resid 555 through 567 or (resid 568 and (name N or name CA or name C or \ name O or name CB )) or resid 569 through 570 or (resid 571 and (name N or name \ CA or name C or name O or name CB )) or resid 572 through 581 or (resid 582 thro \ ugh 583 and (name N or name CA or name C or name O or name CB )) or resid 584 th \ rough 585 or (resid 586 and (name N or name CA or name C or name O or name CB )) \ or resid 587 through 618 or (resid 619 and (name N or name CA or name C or name \ O or name CB )) or resid 620 through 645 or (resid 646 through 647 and (name N \ or name CA or name C or name O or name CB )) or resid 648 through 793 or (resid \ 794 and (name N or name CA or name C or name O or name CB )) or resid 795 or (re \ sid 796 and (name N or name CA or name C or name O or name CB )) or resid 797 th \ rough 920 or (resid 921 and (name N or name CA or name C or name O or name CB )) \ or resid 922 through 1072 or (resid 1073 and (name N or name CA or name C or na \ me O or name CB )) or resid 1074 through 1117 or (resid 1118 and (name N or name \ CA or name C or name O or name CB )) or resid 1119 through 1141 or (resid 1142 \ and (name N or name CA or name C or name O or name CB )) or resid 1143 or (resid \ 1144 through 1146 and (name N or name CA or name C or name O or name CB )) or r \ esid 1147 or resid 1301 through 1303)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'O' selection = chain 'P' selection = chain 'Q' } ncs_group { reference = chain 'H' selection = chain 'M' } ncs_group { reference = chain 'L' selection = chain 'N' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 10.470 Check model and map are aligned: 0.420 Set scattering table: 0.200 Process input model: 72.250 Find NCS groups from input model: 2.110 Set up NCS constraints: 0.250 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:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 92.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 26818 Z= 0.212 Angle : 0.624 10.329 36550 Z= 0.365 Chirality : 0.069 1.692 4351 Planarity : 0.003 0.066 4638 Dihedral : 13.789 112.013 9922 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.75 % Favored : 95.10 % Rotamer: Outliers : 0.15 % Allowed : 4.00 % Favored : 95.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.90 (0.13), residues: 3304 helix: -1.11 (0.18), residues: 650 sheet: -1.52 (0.19), residues: 616 loop : -2.45 (0.12), residues: 2038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP M 36 HIS 0.005 0.001 HIS A 66 PHE 0.017 0.001 PHE B 497 TYR 0.014 0.001 TYR L 91 ARG 0.003 0.000 ARG A 765 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6608 Ramachandran restraints generated. 3304 Oldfield, 0 Emsley, 3304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6608 Ramachandran restraints generated. 3304 Oldfield, 0 Emsley, 3304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 2960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 291 time to evaluate : 2.935 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 295 average time/residue: 0.4098 time to fit residues: 186.6461 Evaluate side-chains 160 residues out of total 2960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 158 time to evaluate : 3.022 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2214 time to fit residues: 4.8442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 282 optimal weight: 9.9990 chunk 253 optimal weight: 9.9990 chunk 140 optimal weight: 0.0870 chunk 86 optimal weight: 0.9990 chunk 171 optimal weight: 3.9990 chunk 135 optimal weight: 30.0000 chunk 262 optimal weight: 1.9990 chunk 101 optimal weight: 6.9990 chunk 159 optimal weight: 9.9990 chunk 195 optimal weight: 10.0000 chunk 304 optimal weight: 20.0000 overall best weight: 2.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 920 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 953 ASN A1011 GLN A1036 GLN ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 331 ASN ** B 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 437 ASN B 439 ASN B 448 ASN ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 580 GLN B 675 GLN ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 935 GLN B 949 GLN ** B 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 498 GLN C 804 GLN C 901 GLN C 965 GLN C1058 HIS ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 37 GLN N 92 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.1586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 26818 Z= 0.222 Angle : 0.604 10.170 36550 Z= 0.311 Chirality : 0.045 0.375 4351 Planarity : 0.004 0.065 4638 Dihedral : 8.334 96.966 4459 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 15.17 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.54 % Favored : 94.34 % Rotamer: Outliers : 1.28 % Allowed : 9.83 % Favored : 88.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.13 (0.13), residues: 3304 helix: -0.13 (0.19), residues: 668 sheet: -1.28 (0.18), residues: 670 loop : -2.00 (0.13), residues: 1966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP H 82 HIS 0.005 0.001 HIS C1048 PHE 0.028 0.001 PHE A 515 TYR 0.021 0.001 TYR H 91 ARG 0.024 0.001 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6608 Ramachandran restraints generated. 3304 Oldfield, 0 Emsley, 3304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6608 Ramachandran restraints generated. 3304 Oldfield, 0 Emsley, 3304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 2960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 167 time to evaluate : 2.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 19 residues processed: 192 average time/residue: 0.3907 time to fit residues: 120.3199 Evaluate side-chains 152 residues out of total 2960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 133 time to evaluate : 2.937 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.2670 time to fit residues: 12.9932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 169 optimal weight: 0.0570 chunk 94 optimal weight: 8.9990 chunk 253 optimal weight: 9.9990 chunk 207 optimal weight: 7.9990 chunk 83 optimal weight: 5.9990 chunk 304 optimal weight: 50.0000 chunk 329 optimal weight: 40.0000 chunk 271 optimal weight: 0.9990 chunk 302 optimal weight: 30.0000 chunk 103 optimal weight: 20.0000 chunk 244 optimal weight: 9.9990 overall best weight: 4.8106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 920 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1058 HIS ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 HIS ** B 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1011 GLN C 188 ASN ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 641 ASN ** C 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 953 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1101 HIS C1119 ASN H 3 GLN L 27 GLN ** L 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 92 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.2977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 26818 Z= 0.323 Angle : 0.663 10.461 36550 Z= 0.344 Chirality : 0.047 0.458 4351 Planarity : 0.005 0.065 4638 Dihedral : 6.833 87.497 4459 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 19.38 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.63 % Favored : 93.25 % Rotamer: Outliers : 1.69 % Allowed : 14.64 % Favored : 83.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: -1.89 (0.14), residues: 3304 helix: 0.14 (0.20), residues: 654 sheet: -1.30 (0.18), residues: 672 loop : -1.78 (0.13), residues: 1978 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP H 36 HIS 0.007 0.001 HIS A 49 PHE 0.023 0.002 PHE A 515 TYR 0.037 0.002 TYR H 91 ARG 0.007 0.001 ARG M 38 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6608 Ramachandran restraints generated. 3304 Oldfield, 0 Emsley, 3304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6608 Ramachandran restraints generated. 3304 Oldfield, 0 Emsley, 3304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 2960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 147 time to evaluate : 2.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 46 outliers final: 19 residues processed: 187 average time/residue: 0.3752 time to fit residues: 114.2501 Evaluate side-chains 137 residues out of total 2960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 118 time to evaluate : 2.946 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.2319 time to fit residues: 12.2350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 301 optimal weight: 0.0010 chunk 229 optimal weight: 20.0000 chunk 158 optimal weight: 1.9990 chunk 33 optimal weight: 9.9990 chunk 145 optimal weight: 5.9990 chunk 204 optimal weight: 30.0000 chunk 305 optimal weight: 40.0000 chunk 323 optimal weight: 40.0000 chunk 159 optimal weight: 3.9990 chunk 289 optimal weight: 8.9990 chunk 87 optimal weight: 3.9990 overall best weight: 3.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN ** A 920 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1011 GLN A1119 ASN B 66 HIS ** B 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 953 ASN H 3 GLN L 37 GLN ** L 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 100 GLN ** M 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.3320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 26818 Z= 0.226 Angle : 0.574 10.687 36550 Z= 0.296 Chirality : 0.044 0.385 4351 Planarity : 0.004 0.062 4638 Dihedral : 6.233 79.264 4459 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 15.83 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.84 % Favored : 94.04 % Rotamer: Outliers : 1.72 % Allowed : 17.13 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: -1.64 (0.14), residues: 3304 helix: 0.49 (0.20), residues: 650 sheet: -1.16 (0.19), residues: 670 loop : -1.65 (0.14), residues: 1984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP M 47 HIS 0.005 0.001 HIS C1048 PHE 0.015 0.001 PHE A1052 TYR 0.019 0.001 TYR H 91 ARG 0.013 0.000 ARG C1107 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6608 Ramachandran restraints generated. 3304 Oldfield, 0 Emsley, 3304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6608 Ramachandran restraints generated. 3304 Oldfield, 0 Emsley, 3304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 2960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 130 time to evaluate : 3.012 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 47 outliers final: 24 residues processed: 168 average time/residue: 0.3848 time to fit residues: 106.3219 Evaluate side-chains 140 residues out of total 2960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 116 time to evaluate : 3.123 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 24 outliers final: 1 residues processed: 24 average time/residue: 0.2538 time to fit residues: 15.4807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 269 optimal weight: 0.9980 chunk 183 optimal weight: 8.9990 chunk 4 optimal weight: 30.0000 chunk 241 optimal weight: 9.9990 chunk 133 optimal weight: 50.0000 chunk 276 optimal weight: 0.9980 chunk 223 optimal weight: 20.0000 chunk 0 optimal weight: 30.0000 chunk 165 optimal weight: 0.6980 chunk 290 optimal weight: 6.9990 chunk 81 optimal weight: 9.9990 overall best weight: 3.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 920 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1119 ASN ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.3761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 26818 Z= 0.254 Angle : 0.588 16.277 36550 Z= 0.301 Chirality : 0.044 0.386 4351 Planarity : 0.004 0.065 4638 Dihedral : 5.879 58.980 4459 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 16.85 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.78 % Favored : 93.10 % Rotamer: Outliers : 1.58 % Allowed : 18.42 % Favored : 80.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: -1.56 (0.14), residues: 3304 helix: 0.62 (0.20), residues: 649 sheet: -1.27 (0.18), residues: 711 loop : -1.56 (0.14), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP M 36 HIS 0.006 0.001 HIS C1048 PHE 0.019 0.001 PHE A1052 TYR 0.025 0.001 TYR M 79 ARG 0.011 0.000 ARG C1107 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6608 Ramachandran restraints generated. 3304 Oldfield, 0 Emsley, 3304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6608 Ramachandran restraints generated. 3304 Oldfield, 0 Emsley, 3304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 2960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 126 time to evaluate : 2.906 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 43 outliers final: 21 residues processed: 162 average time/residue: 0.3746 time to fit residues: 100.0361 Evaluate side-chains 135 residues out of total 2960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 114 time to evaluate : 3.006 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 21 outliers final: 1 residues processed: 21 average time/residue: 0.2523 time to fit residues: 14.1161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 108 optimal weight: 20.0000 chunk 291 optimal weight: 20.0000 chunk 64 optimal weight: 9.9990 chunk 190 optimal weight: 7.9990 chunk 79 optimal weight: 7.9990 chunk 324 optimal weight: 30.0000 chunk 269 optimal weight: 8.9990 chunk 150 optimal weight: 10.0000 chunk 26 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 170 optimal weight: 7.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 498 GLN A 536 ASN A 710 ASN ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 ASN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN ** B 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1011 GLN B1058 HIS ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1023 ASN ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.4979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.130 26818 Z= 0.399 Angle : 0.731 13.969 36550 Z= 0.380 Chirality : 0.047 0.448 4351 Planarity : 0.005 0.075 4638 Dihedral : 6.235 56.036 4459 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 24.67 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.11 % Favored : 91.77 % Rotamer: Outliers : 2.27 % Allowed : 18.86 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: -1.97 (0.14), residues: 3304 helix: 0.08 (0.20), residues: 652 sheet: -1.27 (0.18), residues: 683 loop : -1.86 (0.13), residues: 1969 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B1102 HIS 0.008 0.002 HIS C1048 PHE 0.035 0.003 PHE A1103 TYR 0.030 0.002 TYR C 756 ARG 0.011 0.001 ARG C1107 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6608 Ramachandran restraints generated. 3304 Oldfield, 0 Emsley, 3304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6608 Ramachandran restraints generated. 3304 Oldfield, 0 Emsley, 3304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 2960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 114 time to evaluate : 3.009 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 62 outliers final: 34 residues processed: 165 average time/residue: 0.3693 time to fit residues: 100.9499 Evaluate side-chains 138 residues out of total 2960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 104 time to evaluate : 2.879 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 34 outliers final: 1 residues processed: 34 average time/residue: 0.2349 time to fit residues: 18.9810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 312 optimal weight: 20.0000 chunk 36 optimal weight: 0.9990 chunk 184 optimal weight: 1.9990 chunk 236 optimal weight: 10.0000 chunk 183 optimal weight: 1.9990 chunk 272 optimal weight: 7.9990 chunk 180 optimal weight: 0.9990 chunk 322 optimal weight: 50.0000 chunk 202 optimal weight: 50.0000 chunk 196 optimal weight: 20.0000 chunk 149 optimal weight: 4.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 498 GLN A 658 ASN ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 ASN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 ASN ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN C 913 GLN ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.4963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 26818 Z= 0.201 Angle : 0.590 13.224 36550 Z= 0.300 Chirality : 0.045 0.377 4351 Planarity : 0.004 0.098 4638 Dihedral : 5.634 52.587 4459 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 17.28 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.93 % Favored : 93.95 % Rotamer: Outliers : 1.10 % Allowed : 19.85 % Favored : 79.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: -1.61 (0.14), residues: 3304 helix: 0.55 (0.20), residues: 653 sheet: -1.09 (0.19), residues: 684 loop : -1.68 (0.14), residues: 1967 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 103 HIS 0.005 0.001 HIS C1048 PHE 0.019 0.001 PHE C 759 TYR 0.022 0.001 TYR A 904 ARG 0.013 0.000 ARG B 357 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6608 Ramachandran restraints generated. 3304 Oldfield, 0 Emsley, 3304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6608 Ramachandran restraints generated. 3304 Oldfield, 0 Emsley, 3304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 2960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 122 time to evaluate : 2.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 13 residues processed: 147 average time/residue: 0.3871 time to fit residues: 93.2498 Evaluate side-chains 116 residues out of total 2960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 103 time to evaluate : 3.145 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.2373 time to fit residues: 9.8573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 199 optimal weight: 8.9990 chunk 128 optimal weight: 40.0000 chunk 192 optimal weight: 5.9990 chunk 97 optimal weight: 30.0000 chunk 63 optimal weight: 6.9990 chunk 62 optimal weight: 0.8980 chunk 205 optimal weight: 20.0000 chunk 219 optimal weight: 7.9990 chunk 159 optimal weight: 3.9990 chunk 30 optimal weight: 8.9990 chunk 253 optimal weight: 7.9990 overall best weight: 5.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 804 GLN ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 925 ASN H 3 GLN ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.5333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.091 26818 Z= 0.331 Angle : 0.652 12.702 36550 Z= 0.336 Chirality : 0.045 0.395 4351 Planarity : 0.004 0.058 4638 Dihedral : 5.738 56.097 4459 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 20.69 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.32 % Favored : 92.55 % Rotamer: Outliers : 1.17 % Allowed : 20.98 % Favored : 77.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: -1.74 (0.14), residues: 3304 helix: 0.31 (0.20), residues: 680 sheet: -1.22 (0.18), residues: 708 loop : -1.71 (0.14), residues: 1916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C1102 HIS 0.005 0.001 HIS A 49 PHE 0.028 0.002 PHE B1089 TYR 0.022 0.002 TYR A 873 ARG 0.010 0.001 ARG C1107 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6608 Ramachandran restraints generated. 3304 Oldfield, 0 Emsley, 3304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6608 Ramachandran restraints generated. 3304 Oldfield, 0 Emsley, 3304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 2960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 100 time to evaluate : 2.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 18 residues processed: 127 average time/residue: 0.4242 time to fit residues: 87.9042 Evaluate side-chains 117 residues out of total 2960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 99 time to evaluate : 2.967 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.2539 time to fit residues: 12.7781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 293 optimal weight: 50.0000 chunk 309 optimal weight: 40.0000 chunk 282 optimal weight: 4.9990 chunk 300 optimal weight: 7.9990 chunk 181 optimal weight: 1.9990 chunk 131 optimal weight: 50.0000 chunk 236 optimal weight: 20.0000 chunk 92 optimal weight: 0.9990 chunk 271 optimal weight: 6.9990 chunk 284 optimal weight: 6.9990 chunk 299 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 764 ASN ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1036 GLN ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.5547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 26818 Z= 0.264 Angle : 0.620 12.348 36550 Z= 0.317 Chirality : 0.045 0.377 4351 Planarity : 0.004 0.078 4638 Dihedral : 5.541 56.296 4459 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 19.56 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.60 % Favored : 93.28 % Rotamer: Outliers : 0.48 % Allowed : 21.28 % Favored : 78.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: -1.66 (0.14), residues: 3304 helix: 0.45 (0.20), residues: 672 sheet: -1.26 (0.18), residues: 724 loop : -1.65 (0.14), residues: 1908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 103 HIS 0.005 0.001 HIS A1048 PHE 0.024 0.002 PHE A 759 TYR 0.023 0.001 TYR A 904 ARG 0.016 0.001 ARG C1107 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6608 Ramachandran restraints generated. 3304 Oldfield, 0 Emsley, 3304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6608 Ramachandran restraints generated. 3304 Oldfield, 0 Emsley, 3304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 2960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 105 time to evaluate : 3.155 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 5 residues processed: 116 average time/residue: 0.4370 time to fit residues: 82.4251 Evaluate side-chains 103 residues out of total 2960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 98 time to evaluate : 3.295 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.3483 time to fit residues: 7.2020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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: 70.03 > 50: distance: 44 - 128: 29.929 distance: 61 - 118: 28.237 distance: 64 - 115: 32.668 distance: 85 - 90: 22.950 distance: 90 - 91: 7.030 distance: 91 - 92: 46.028 distance: 92 - 93: 28.167 distance: 92 - 94: 48.474 distance: 94 - 95: 11.616 distance: 95 - 96: 65.763 distance: 95 - 98: 35.200 distance: 96 - 97: 41.187 distance: 96 - 103: 67.265 distance: 98 - 99: 27.404 distance: 99 - 100: 22.328 distance: 100 - 101: 30.786 distance: 101 - 102: 46.601 distance: 103 - 104: 55.590 distance: 104 - 105: 24.248 distance: 104 - 107: 30.540 distance: 105 - 106: 32.867 distance: 105 - 108: 39.494 distance: 108 - 109: 16.660 distance: 108 - 114: 42.181 distance: 109 - 110: 46.456 distance: 109 - 112: 9.977 distance: 110 - 111: 51.739 distance: 110 - 115: 36.403 distance: 112 - 113: 45.562 distance: 113 - 114: 20.362 distance: 115 - 116: 3.624 distance: 116 - 117: 38.851 distance: 116 - 119: 70.030 distance: 117 - 118: 48.162 distance: 117 - 120: 46.463 distance: 120 - 121: 19.264 distance: 121 - 122: 38.906 distance: 121 - 124: 6.029 distance: 122 - 123: 35.971 distance: 122 - 128: 28.564 distance: 124 - 125: 38.076 distance: 125 - 126: 27.339 distance: 125 - 127: 22.685 distance: 128 - 129: 46.056 distance: 129 - 130: 29.026 distance: 129 - 132: 14.409 distance: 130 - 131: 24.209 distance: 130 - 136: 26.118 distance: 132 - 133: 18.069 distance: 133 - 134: 15.413 distance: 133 - 135: 10.495 distance: 136 - 137: 17.577 distance: 137 - 138: 46.960 distance: 137 - 140: 10.899 distance: 138 - 139: 23.291 distance: 138 - 144: 40.908 distance: 140 - 141: 38.213 distance: 140 - 142: 14.870 distance: 141 - 143: 44.469 distance: 144 - 145: 42.355 distance: 144 - 179: 26.690 distance: 145 - 146: 6.093 distance: 145 - 148: 47.427 distance: 146 - 147: 59.351 distance: 146 - 156: 15.639 distance: 147 - 176: 27.187 distance: 148 - 149: 40.229 distance: 149 - 150: 7.474 distance: 149 - 151: 8.117 distance: 150 - 152: 17.769 distance: 151 - 153: 11.172 distance: 152 - 154: 8.117 distance: 153 - 154: 11.020 distance: 154 - 155: 7.319 distance: 156 - 157: 5.716 distance: 157 - 158: 30.936 distance: 157 - 160: 61.710 distance: 158 - 159: 25.538 distance: 158 - 165: 30.322 distance: 161 - 162: 36.779 distance: 162 - 163: 11.141 distance: 162 - 164: 24.269