Starting phenix.real_space_refine (version: dev) on Sat Feb 25 21:21:24 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vrj_32100/02_2023/7vrj_32100_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vrj_32100/02_2023/7vrj_32100.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vrj_32100/02_2023/7vrj_32100.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vrj_32100/02_2023/7vrj_32100.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vrj_32100/02_2023/7vrj_32100_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vrj_32100/02_2023/7vrj_32100_updated.pdb" } resolution = 2.81 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 Process input model Symmetric amino acids flipped Residue "C TYR 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 26309 Number of models: 1 Model: "" Number of chains: 77 Chain: "C" Number of atoms: 2450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2450 Classifications: {'peptide': 313} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 285} Chain: "L" Number of atoms: 2212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2212 Classifications: {'peptide': 277} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 263} Chain: "M" Number of atoms: 2539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2539 Classifications: {'peptide': 318} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 298} Chain: "H" Number of atoms: 1989 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 259, 1987 Classifications: {'peptide': 259} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 20, 'TRANS': 235} Conformer: "B" Number of residues, atoms: 259, 1987 Classifications: {'peptide': 259} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 20, 'TRANS': 235} bond proxies already assigned to first conformer: 2037 Chain: "A" Number of atoms: 366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 366 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 41} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 359 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "D" Number of atoms: 411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 411 Classifications: {'peptide': 50} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 46} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 353 Classifications: {'peptide': 43} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 41} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "F" Number of atoms: 401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 401 Classifications: {'peptide': 49} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 45} Chain: "G" Number of atoms: 348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 348 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "I" Number of atoms: 366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 366 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 41} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "J" Number of atoms: 331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 331 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "K" Number of atoms: 366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 366 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 41} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "N" Number of atoms: 320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 320 Classifications: {'peptide': 38} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "O" Number of atoms: 366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 366 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 41} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "P" Number of atoms: 345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 345 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "Q" Number of atoms: 366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 366 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 41} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "R" Number of atoms: 339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 339 Classifications: {'peptide': 41} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 39} Chain: "S" Number of atoms: 419 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 419 Classifications: {'peptide': 52} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 48} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "T" Number of atoms: 348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 348 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "U" Number of atoms: 416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 416 Classifications: {'peptide': 51} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 47} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "V" Number of atoms: 348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 348 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "W" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 455 Classifications: {'peptide': 56} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 52} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "X" Number of atoms: 348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 348 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "Y" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 510 Classifications: {'peptide': 63} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 57} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "Z" Number of atoms: 342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 342 Classifications: {'peptide': 41} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 39} Chain: "1" Number of atoms: 366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 366 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 41} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "2" Number of atoms: 339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 339 Classifications: {'peptide': 41} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 39} Chain: "3" Number of atoms: 499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 499 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 5, 'TRANS': 59} Chain: "4" Number of atoms: 345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 345 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "5" Number of atoms: 355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 355 Classifications: {'peptide': 43} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 40} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "6" Number of atoms: 320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 320 Classifications: {'peptide': 38} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "7" Number of atoms: 362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 362 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 41} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "8" Number of atoms: 312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 312 Classifications: {'peptide': 37} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 35} Chain: "9" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 359 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 2, 'TRANS': 40} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "0" Number of atoms: 345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 345 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "C" Number of atoms: 233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 233 Unusual residues: {' MG': 1, 'DGA': 1, 'HEC': 4, 'PGV': 1, 'PLM': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 52 Planarities with less than four sites: {'PLM:plan-1': 1, 'PGV:plan-3': 1} Unresolved non-hydrogen planarities: 5 Chain: "L" Number of atoms: 584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 584 Unusual residues: {'BCL': 3, 'BPH': 1, 'CDL': 1, 'PGV': 4, 'UQ8': 3} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 142 Unresolved non-hydrogen angles: 151 Unresolved non-hydrogen dihedrals: 131 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PGV:plan-3': 4, 'UQ8:plan-6': 2, 'UQ8:plan-7': 2, 'UQ8:plan-8': 2, 'UQ8:plan-9': 2} Unresolved non-hydrogen planarities: 56 Chain: "M" Number of atoms: 520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 520 Unusual residues: {' FE': 1, 'BCL': 1, 'BPH': 1, 'CDL': 2, 'CRT': 1, 'MQ8': 2, 'PGV': 3} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 115 Unresolved non-hydrogen angles: 117 Unresolved non-hydrogen dihedrals: 110 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PGV:plan-3': 3, 'CDL:plan-4': 1} Unresolved non-hydrogen planarities: 14 Chain: "H" Number of atoms: 185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 185 Unusual residues: {'CDL': 2, 'LMT': 1, 'PGV': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 101 Unresolved non-hydrogen angles: 103 Unresolved non-hydrogen dihedrals: 98 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PGV:plan-3': 1, 'CDL:plan-1': 1} Unresolved non-hydrogen planarities: 8 Chain: "A" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 145 Unusual residues: {'BCL': 1, 'CRT': 1, 'LMT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 160 Unusual residues: {' CA': 1, 'BCL': 1, 'CDL': 1, 'PGV': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 58 Planarities with less than four sites: {'PGV:plan-3': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 145 Unusual residues: {'BCL': 1, 'CRT': 1, 'LMT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {' CA': 1, 'BCL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 145 Unusual residues: {'BCL': 1, 'CRT': 1, 'LMT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 117 Unusual residues: {'BCL': 1, 'CDL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 49 Chain: "J" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 180 Unusual residues: {'BCL': 1, 'CRT': 1, 'LMT': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "K" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 117 Unusual residues: {'BCL': 1, 'LDA': 1, 'LMT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "N" Number of atoms: 145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 145 Unusual residues: {'BCL': 1, 'CRT': 1, 'LMT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "O" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 82 Unusual residues: {'BCL': 1, 'LDA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "P" Number of atoms: 145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 145 Unusual residues: {'BCL': 1, 'CRT': 1, 'LMT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "Q" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 110 Unusual residues: {'BCL': 1, 'CRT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "R" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 110 Unusual residues: {'BCL': 1, 'CRT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "S" Number of atoms: 176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 176 Unusual residues: {' CA': 1, 'BCL': 1, 'CDL': 1, 'CRT': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 35 Chain: "T" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 101 Unusual residues: {'BCL': 1, 'LMT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "U" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {' CA': 1, 'BCL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "V" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 101 Unusual residues: {'BCL': 1, 'LMT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "W" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {' CA': 1, 'BCL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "X" Number of atoms: 145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 145 Unusual residues: {'BCL': 1, 'CRT': 1, 'LMT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "Y" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {' CA': 1, 'BCL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Z" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 101 Unusual residues: {'BCL': 1, 'LMT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "1" Number of atoms: 137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 137 Unusual residues: {'BCL': 1, 'CRT': 1, 'PGV': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PGV:plan-3': 1} Unresolved non-hydrogen planarities: 4 Chain: "2" Number of atoms: 145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 145 Unusual residues: {'BCL': 1, 'CRT': 1, 'LMT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "3" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "4" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 180 Unusual residues: {'BCL': 1, 'CRT': 1, 'LMT': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "5" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 110 Unusual residues: {'BCL': 1, 'PGV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Chain: "6" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 110 Unusual residues: {'BCL': 1, 'CRT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "7" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 105 Unusual residues: {'BCL': 1, 'CRT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "8" Number of atoms: 145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 145 Unusual residues: {'BCL': 1, 'CRT': 1, 'LMT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "9" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "0" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 101 Unusual residues: {'BCL': 1, 'LMT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Chain: "L" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "M" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "Y" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "3" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 16.56, per 1000 atoms: 0.63 Number of scatterers: 26309 At special positions: 0 Unit cell: (140.822, 136.752, 140.008, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Fe 5 26.01 Ca 6 19.99 S 102 16.00 P 28 15.00 Mg 37 11.99 O 4277 8.00 N 3570 7.00 C 18284 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=48, symmetry=0 Number of additional bonds: simple=48, symmetry=0 Coordination: Other bonds: Time building additional restraints: 12.00 Conformation dependent library (CDL) restraints added in 3.6 seconds 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4826 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 103 helices and 4 sheets defined 58.2% alpha, 1.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.40 Creating SS restraints... Processing helix chain 'C' and resid 46 through 55 removed outlier: 3.639A pdb=" N GLN C 55 " --> pdb=" O ALA C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 74 No H-bonds generated for 'chain 'C' and resid 72 through 74' Processing helix chain 'C' and resid 87 through 100 Processing helix chain 'C' and resid 122 through 140 removed outlier: 3.516A pdb=" N GLU C 132 " --> pdb=" O ARG C 128 " (cutoff:3.500A) Processing helix chain 'C' and resid 142 through 145 No H-bonds generated for 'chain 'C' and resid 142 through 145' Processing helix chain 'C' and resid 154 through 158 removed outlier: 3.598A pdb=" N CYS C 157 " --> pdb=" O CYS C 154 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N HIS C 158 " --> pdb=" O TYR C 155 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 154 through 158' Processing helix chain 'C' and resid 190 through 192 No H-bonds generated for 'chain 'C' and resid 190 through 192' Processing helix chain 'C' and resid 202 through 205 No H-bonds generated for 'chain 'C' and resid 202 through 205' Processing helix chain 'C' and resid 228 through 245 removed outlier: 3.849A pdb=" N GLU C 232 " --> pdb=" O LEU C 228 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N TRP C 233 " --> pdb=" O LYS C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 249 through 251 No H-bonds generated for 'chain 'C' and resid 249 through 251' Processing helix chain 'C' and resid 266 through 285 removed outlier: 3.688A pdb=" N THR C 270 " --> pdb=" O PRO C 266 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARG C 276 " --> pdb=" O TRP C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 291 removed outlier: 4.309A pdb=" N ASP C 291 " --> pdb=" O PRO C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 297 No H-bonds generated for 'chain 'C' and resid 295 through 297' Processing helix chain 'C' and resid 319 through 322 Processing helix chain 'C' and resid 330 through 332 No H-bonds generated for 'chain 'C' and resid 330 through 332' Processing helix chain 'L' and resid 7 through 9 No H-bonds generated for 'chain 'L' and resid 7 through 9' Processing helix chain 'L' and resid 32 through 55 Processing helix chain 'L' and resid 76 through 78 No H-bonds generated for 'chain 'L' and resid 76 through 78' Processing helix chain 'L' and resid 85 through 87 No H-bonds generated for 'chain 'L' and resid 85 through 87' Processing helix chain 'L' and resid 89 through 116 Processing helix chain 'L' and resid 121 through 137 removed outlier: 3.839A pdb=" N PHE L 128 " --> pdb=" O PHE L 124 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ALA L 129 " --> pdb=" O ALA L 125 " (cutoff:3.500A) Processing helix chain 'L' and resid 139 through 144 Processing helix chain 'L' and resid 147 through 149 No H-bonds generated for 'chain 'L' and resid 147 through 149' Processing helix chain 'L' and resid 157 through 169 removed outlier: 4.231A pdb=" N PHE L 169 " --> pdb=" O VAL L 165 " (cutoff:3.500A) Processing helix chain 'L' and resid 172 through 174 No H-bonds generated for 'chain 'L' and resid 172 through 174' Processing helix chain 'L' and resid 176 through 203 Processing helix chain 'L' and resid 214 through 224 removed outlier: 3.613A pdb=" N ASN L 218 " --> pdb=" O SER L 214 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N PHE L 221 " --> pdb=" O GLU L 217 " (cutoff:3.500A) Processing helix chain 'L' and resid 231 through 254 removed outlier: 4.059A pdb=" N HIS L 235 " --> pdb=" O ALA L 231 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL L 246 " --> pdb=" O ALA L 242 " (cutoff:3.500A) Processing helix chain 'L' and resid 265 through 272 removed outlier: 3.980A pdb=" N TRP L 270 " --> pdb=" O TRP L 267 " (cutoff:3.500A) Processing helix chain 'M' and resid 39 through 41 No H-bonds generated for 'chain 'M' and resid 39 through 41' Processing helix chain 'M' and resid 54 through 78 removed outlier: 3.944A pdb=" N VAL M 78 " --> pdb=" O MET M 74 " (cutoff:3.500A) Processing helix chain 'M' and resid 82 through 87 Processing helix chain 'M' and resid 99 through 101 No H-bonds generated for 'chain 'M' and resid 99 through 101' Processing helix chain 'M' and resid 108 through 110 No H-bonds generated for 'chain 'M' and resid 108 through 110' Processing helix chain 'M' and resid 112 through 138 Processing helix chain 'M' and resid 144 through 160 Processing helix chain 'M' and resid 162 through 167 Processing helix chain 'M' and resid 170 through 172 No H-bonds generated for 'chain 'M' and resid 170 through 172' Processing helix chain 'M' and resid 178 through 191 removed outlier: 3.615A pdb=" N LEU M 182 " --> pdb=" O ILE M 178 " (cutoff:3.500A) Processing helix chain 'M' and resid 195 through 197 No H-bonds generated for 'chain 'M' and resid 195 through 197' Processing helix chain 'M' and resid 199 through 224 Processing helix chain 'M' and resid 226 through 228 No H-bonds generated for 'chain 'M' and resid 226 through 228' Processing helix chain 'M' and resid 233 through 238 Processing helix chain 'M' and resid 242 through 255 removed outlier: 3.612A pdb=" N TRP M 251 " --> pdb=" O ALA M 247 " (cutoff:3.500A) Processing helix chain 'M' and resid 264 through 284 removed outlier: 3.527A pdb=" N ALA M 272 " --> pdb=" O ALA M 268 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR M 275 " --> pdb=" O CYS M 271 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL M 276 " --> pdb=" O ALA M 272 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA M 279 " --> pdb=" O THR M 275 " (cutoff:3.500A) Processing helix chain 'M' and resid 293 through 299 Processing helix chain 'H' and resid 11 through 36 removed outlier: 3.679A pdb=" N ILE H 16 " --> pdb=" O ALA H 12 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LYS H 35 " --> pdb=" O ARG H 31 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N ARG H 36 " --> pdb=" O ARG H 32 " (cutoff:3.500A) Processing helix chain 'H' and resid 44 through 48 Processing helix chain 'H' and resid 70 through 72 No H-bonds generated for 'chain 'H' and resid 70 through 72' Processing helix chain 'H' and resid 107 through 109 No H-bonds generated for 'chain 'H' and resid 107 through 109' Processing helix chain 'H' and resid 112 through 114 No H-bonds generated for 'chain 'H' and resid 112 through 114' Processing helix chain 'H' and resid 197 through 199 No H-bonds generated for 'chain 'H' and resid 197 through 199' Processing helix chain 'H' and resid 216 through 218 No H-bonds generated for 'chain 'H' and resid 216 through 218' Processing helix chain 'H' and resid 233 through 249 removed outlier: 3.803A pdb=" N GLY H 246 " --> pdb=" O TYR H 242 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LYS H 247 " --> pdb=" O TYR H 243 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N LEU H 248 " --> pdb=" O ALA H 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 7 through 10 Processing helix chain 'A' and resid 14 through 38 Processing helix chain 'B' and resid 12 through 43 removed outlier: 3.893A pdb=" N PHE B 18 " --> pdb=" O GLU B 14 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 10 removed outlier: 4.285A pdb=" N TRP D 6 " --> pdb=" O PRO D 3 " (cutoff:3.500A) Processing helix chain 'D' and resid 14 through 37 Processing helix chain 'E' and resid 12 through 41 removed outlier: 3.842A pdb=" N LYS E 16 " --> pdb=" O GLU E 12 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N GLU E 17 " --> pdb=" O ASP E 13 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLN E 24 " --> pdb=" O GLY E 20 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N PHE E 29 " --> pdb=" O SER E 25 " (cutoff:3.500A) Processing helix chain 'F' and resid 5 through 10 Processing helix chain 'F' and resid 14 through 38 removed outlier: 4.032A pdb=" N LEU F 18 " --> pdb=" O PRO F 14 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N ILE F 19 " --> pdb=" O ARG F 15 " (cutoff:3.500A) Processing helix chain 'G' and resid 12 through 43 removed outlier: 3.730A pdb=" N GLU G 17 " --> pdb=" O ASP G 13 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N MET G 28 " --> pdb=" O GLN G 24 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ILE G 34 " --> pdb=" O PHE G 30 " (cutoff:3.500A) Processing helix chain 'I' and resid 8 through 10 No H-bonds generated for 'chain 'I' and resid 8 through 10' Processing helix chain 'I' and resid 14 through 38 Processing helix chain 'J' and resid 14 through 43 removed outlier: 4.065A pdb=" N PHE J 18 " --> pdb=" O GLU J 14 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N HIS J 19 " --> pdb=" O ALA J 15 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLN J 24 " --> pdb=" O GLY J 20 " (cutoff:3.500A) Processing helix chain 'K' and resid 7 through 10 Processing helix chain 'K' and resid 14 through 38 Processing helix chain 'N' and resid 12 through 43 removed outlier: 3.691A pdb=" N HIS N 19 " --> pdb=" O ALA N 15 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE N 21 " --> pdb=" O GLU N 17 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL N 23 " --> pdb=" O HIS N 19 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N GLN N 24 " --> pdb=" O GLY N 20 " (cutoff:3.500A) Processing helix chain 'O' and resid 7 through 10 Processing helix chain 'O' and resid 14 through 38 Processing helix chain 'P' and resid 12 through 43 removed outlier: 3.673A pdb=" N GLU P 17 " --> pdb=" O GLN P 13 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE P 18 " --> pdb=" O GLU P 14 " (cutoff:3.500A) Processing helix chain 'Q' and resid 7 through 10 Processing helix chain 'Q' and resid 14 through 38 Processing helix chain 'R' and resid 12 through 43 removed outlier: 4.227A pdb=" N PHE R 18 " --> pdb=" O GLU R 14 " (cutoff:3.500A) Processing helix chain 'S' and resid 5 through 10 Processing helix chain 'S' and resid 14 through 38 removed outlier: 3.844A pdb=" N ILE S 19 " --> pdb=" O ARG S 15 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ALA S 20 " --> pdb=" O ARG S 16 " (cutoff:3.500A) Processing helix chain 'T' and resid 12 through 43 removed outlier: 3.624A pdb=" N GLY T 20 " --> pdb=" O LYS T 16 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ILE T 21 " --> pdb=" O GLU T 17 " (cutoff:3.500A) Processing helix chain 'U' and resid 3 through 10 removed outlier: 4.167A pdb=" N TRP U 6 " --> pdb=" O PRO U 3 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N TRP U 9 " --> pdb=" O TRP U 6 " (cutoff:3.500A) Processing helix chain 'U' and resid 14 through 37 Processing helix chain 'V' and resid 12 through 43 removed outlier: 3.677A pdb=" N PHE V 18 " --> pdb=" O GLU V 14 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N HIS V 19 " --> pdb=" O ALA V 15 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLY V 20 " --> pdb=" O LYS V 16 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE V 21 " --> pdb=" O GLU V 17 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N MET V 28 " --> pdb=" O GLN V 24 " (cutoff:3.500A) Processing helix chain 'W' and resid 5 through 10 removed outlier: 3.705A pdb=" N TRP W 9 " --> pdb=" O TRP W 6 " (cutoff:3.500A) Processing helix chain 'W' and resid 14 through 37 removed outlier: 3.715A pdb=" N ILE W 19 " --> pdb=" O ARG W 15 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N PHE W 24 " --> pdb=" O ALA W 20 " (cutoff:3.500A) Processing helix chain 'X' and resid 13 through 41 removed outlier: 4.010A pdb=" N GLU X 17 " --> pdb=" O ASP X 13 " (cutoff:3.500A) Processing helix chain 'Y' and resid 3 through 10 removed outlier: 4.362A pdb=" N TRP Y 6 " --> pdb=" O PRO Y 3 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS Y 7 " --> pdb=" O ASP Y 4 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TRP Y 9 " --> pdb=" O TRP Y 6 " (cutoff:3.500A) Processing helix chain 'Y' and resid 14 through 38 removed outlier: 3.793A pdb=" N ALA Y 20 " --> pdb=" O ARG Y 16 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N THR Y 26 " --> pdb=" O PHE Y 22 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ILE Y 27 " --> pdb=" O ALA Y 23 " (cutoff:3.500A) Processing helix chain 'Z' and resid 12 through 43 removed outlier: 3.870A pdb=" N LYS Z 16 " --> pdb=" O GLU Z 12 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N GLU Z 17 " --> pdb=" O ASP Z 13 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE Z 21 " --> pdb=" O GLU Z 17 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLN Z 24 " --> pdb=" O GLY Z 20 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE Z 35 " --> pdb=" O GLY Z 31 " (cutoff:3.500A) Processing helix chain '1' and resid 8 through 11 No H-bonds generated for 'chain '1' and resid 8 through 11' Processing helix chain '1' and resid 14 through 37 removed outlier: 3.699A pdb=" N VAL 1 19 " --> pdb=" O ARG 1 15 " (cutoff:3.500A) Processing helix chain '2' and resid 12 through 43 removed outlier: 4.016A pdb=" N PHE 2 18 " --> pdb=" O GLU 2 14 " (cutoff:3.500A) Processing helix chain '3' and resid 5 through 10 Processing helix chain '3' and resid 14 through 38 removed outlier: 3.747A pdb=" N ILE 3 19 " --> pdb=" O ARG 3 15 " (cutoff:3.500A) Processing helix chain '3' and resid 44 through 46 No H-bonds generated for 'chain '3' and resid 44 through 46' Processing helix chain '4' and resid 12 through 43 removed outlier: 3.875A pdb=" N GLN 4 16 " --> pdb=" O GLU 4 12 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLY 4 20 " --> pdb=" O GLN 4 16 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE 4 21 " --> pdb=" O GLU 4 17 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N THR 4 27 " --> pdb=" O VAL 4 23 " (cutoff:3.500A) Processing helix chain '5' and resid 7 through 10 Processing helix chain '5' and resid 14 through 38 removed outlier: 3.591A pdb=" N GLY 5 23 " --> pdb=" O VAL 5 19 " (cutoff:3.500A) Processing helix chain '6' and resid 17 through 43 removed outlier: 3.637A pdb=" N ILE 6 21 " --> pdb=" O GLU 6 17 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLN 6 24 " --> pdb=" O GLY 6 20 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE 6 32 " --> pdb=" O ALA 6 28 " (cutoff:3.500A) Processing helix chain '7' and resid 14 through 37 removed outlier: 4.042A pdb=" N VAL 7 19 " --> pdb=" O ARG 7 15 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ALA 7 20 " --> pdb=" O ARG 7 16 " (cutoff:3.500A) Processing helix chain '8' and resid 12 through 15 No H-bonds generated for 'chain '8' and resid 12 through 15' Processing helix chain '8' and resid 19 through 43 removed outlier: 3.983A pdb=" N GLN 8 24 " --> pdb=" O GLY 8 20 " (cutoff:3.500A) Processing helix chain '9' and resid 8 through 10 No H-bonds generated for 'chain '9' and resid 8 through 10' Processing helix chain '9' and resid 14 through 38 removed outlier: 3.850A pdb=" N VAL 9 19 " --> pdb=" O ARG 9 15 " (cutoff:3.500A) Processing helix chain '0' and resid 12 through 43 removed outlier: 3.627A pdb=" N ILE 0 21 " --> pdb=" O GLU 0 17 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ILE 0 32 " --> pdb=" O ALA 0 28 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL 0 33 " --> pdb=" O PHE 0 29 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'C' and resid 29 through 32 Processing sheet with id= B, first strand: chain 'H' and resid 66 through 69 removed outlier: 4.315A pdb=" N GLY H 74 " --> pdb=" O LEU H 69 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'H' and resid 133 through 135 removed outlier: 3.840A pdb=" N THR H 166 " --> pdb=" O ASP H 185 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N GLU H 183 " --> pdb=" O SER H 168 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N ILE H 170 " --> pdb=" O TYR H 181 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N TYR H 181 " --> pdb=" O ILE H 170 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LYS H 191 " --> pdb=" O VAL H 186 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'H' and resid 201 through 203 removed outlier: 6.778A pdb=" N THR H 155 " --> pdb=" O VAL H 209 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLY H 165 " --> pdb=" O VAL H 156 " (cutoff:3.500A) 1069 hydrogen bonds defined for protein. 3105 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: 7.20 Time building geometry restraints manager: 12.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.38: 9228 1.38 - 1.56: 17639 1.56 - 1.74: 56 1.74 - 1.93: 192 1.93 - 2.11: 156 Bond restraints: 27271 Sorted by residual: bond pdb=" CB7 CDL S 101 " pdb=" OB8 CDL S 101 " ideal model delta sigma weight residual 1.334 1.456 -0.122 1.10e-02 8.26e+03 1.24e+02 bond pdb=" CA7 CDL M 408 " pdb=" OA8 CDL M 408 " ideal model delta sigma weight residual 1.334 1.456 -0.122 1.10e-02 8.26e+03 1.24e+02 bond pdb=" CA7 CDL H 301 " pdb=" OA8 CDL H 301 " ideal model delta sigma weight residual 1.334 1.455 -0.121 1.10e-02 8.26e+03 1.22e+02 bond pdb=" CB7 CDL I 101 " pdb=" OB8 CDL I 101 " ideal model delta sigma weight residual 1.334 1.454 -0.120 1.10e-02 8.26e+03 1.20e+02 bond pdb=" CA7 CDL M 410 " pdb=" OA8 CDL M 410 " ideal model delta sigma weight residual 1.334 1.454 -0.120 1.10e-02 8.26e+03 1.19e+02 ... (remaining 27266 not shown) Histogram of bond angle deviations from ideal: 83.26 - 102.49: 527 102.49 - 121.72: 30861 121.72 - 140.94: 5954 140.94 - 160.17: 38 160.17 - 179.40: 80 Bond angle restraints: 37460 Sorted by residual: angle pdb=" C39 CRT S 104 " pdb=" C38 CRT S 104 " pdb=" O2 CRT S 104 " ideal model delta sigma weight residual 111.76 86.34 25.42 3.00e+00 1.11e-01 7.18e+01 angle pdb=" C39 CRT 2 103 " pdb=" C38 CRT 2 103 " pdb=" O2 CRT 2 103 " ideal model delta sigma weight residual 111.76 87.71 24.05 3.00e+00 1.11e-01 6.43e+01 angle pdb=" C1D BCL M 402 " pdb=" C2D BCL M 402 " pdb=" CMD BCL M 402 " ideal model delta sigma weight residual 125.57 139.92 -14.34 1.83e+00 2.99e-01 6.16e+01 angle pdb=" C40 CRT 2 103 " pdb=" C38 CRT 2 103 " pdb=" O2 CRT 2 103 " ideal model delta sigma weight residual 111.40 87.87 23.53 3.00e+00 1.11e-01 6.15e+01 angle pdb=" C3 CRT P 102 " pdb=" C1 CRT P 102 " pdb=" C4 CRT P 102 " ideal model delta sigma weight residual 108.82 85.50 23.32 3.00e+00 1.11e-01 6.04e+01 ... (remaining 37455 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.99: 13643 35.99 - 71.97: 533 71.97 - 107.96: 49 107.96 - 143.94: 7 143.94 - 179.93: 8 Dihedral angle restraints: 14240 sinusoidal: 6793 harmonic: 7447 Sorted by residual: dihedral pdb=" C1 BCL 0 102 " pdb=" CGA BCL 0 102 " pdb=" O2A BCL 0 102 " pdb=" CBA BCL 0 102 " ideal model delta sinusoidal sigma weight residual -180.00 -78.88 -101.12 1 6.00e+00 2.78e-02 3.18e+02 dihedral pdb=" C1 BCL Q 101 " pdb=" C2 BCL Q 101 " pdb=" C3 BCL Q 101 " pdb=" C5 BCL Q 101 " ideal model delta sinusoidal sigma weight residual -180.00 -0.07 -179.93 1 8.00e+00 1.56e-02 3.00e+02 dihedral pdb=" C1 BCL F 101 " pdb=" C2 BCL F 101 " pdb=" C3 BCL F 101 " pdb=" C5 BCL F 101 " ideal model delta sinusoidal sigma weight residual -180.00 -0.13 -179.87 1 8.00e+00 1.56e-02 3.00e+02 ... (remaining 14237 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 3213 0.074 - 0.147: 386 0.147 - 0.221: 136 0.221 - 0.295: 29 0.295 - 0.368: 5 Chirality restraints: 3769 Sorted by residual: chirality pdb=" C4' LMT 0 101 " pdb=" C3' LMT 0 101 " pdb=" C5' LMT 0 101 " pdb=" O1B LMT 0 101 " both_signs ideal model delta sigma weight residual False -2.76 -2.39 -0.37 2.00e-01 2.50e+01 3.39e+00 chirality pdb=" C4' LMT G 101 " pdb=" C3' LMT G 101 " pdb=" C5' LMT G 101 " pdb=" O1B LMT G 101 " both_signs ideal model delta sigma weight residual False -2.76 -2.44 -0.32 2.00e-01 2.50e+01 2.57e+00 chirality pdb=" C4' LMT E 101 " pdb=" C3' LMT E 101 " pdb=" C5' LMT E 101 " pdb=" O1B LMT E 101 " both_signs ideal model delta sigma weight residual False -2.76 -2.45 -0.32 2.00e-01 2.50e+01 2.49e+00 ... (remaining 3766 not shown) Planarity restraints: 4433 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 BCL K 103 " 0.386 3.00e-02 1.11e+03 3.15e-01 5.52e+02 pdb=" CBA BCL K 103 " 0.161 3.00e-02 1.11e+03 pdb=" CGA BCL K 103 " -0.087 3.00e-02 1.11e+03 pdb=" O1A BCL K 103 " 0.094 3.00e-02 1.11e+03 pdb=" O2A BCL K 103 " -0.553 3.00e-02 1.11e+03 delta sigma weight rms_deltas residual plane pdb=" C1 BCL T 102 " -0.369 3.00e-02 1.11e+03 3.08e-01 5.29e+02 pdb=" CBA BCL T 102 " -0.095 3.00e-02 1.11e+03 pdb=" CGA BCL T 102 " 0.075 3.00e-02 1.11e+03 pdb=" O1A BCL T 102 " -0.159 3.00e-02 1.11e+03 pdb=" O2A BCL T 102 " 0.548 3.00e-02 1.11e+03 delta sigma weight rms_deltas residual plane pdb=" C1 BCL L 509 " -0.371 3.00e-02 1.11e+03 3.07e-01 5.23e+02 pdb=" CBA BCL L 509 " -0.132 3.00e-02 1.11e+03 pdb=" CGA BCL L 509 " 0.079 3.00e-02 1.11e+03 pdb=" O1A BCL L 509 " -0.120 3.00e-02 1.11e+03 pdb=" O2A BCL L 509 " 0.544 3.00e-02 1.11e+03 ... (remaining 4430 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 260 2.63 - 3.20: 21089 3.20 - 3.77: 39483 3.77 - 4.33: 57920 4.33 - 4.90: 93107 Nonbonded interactions: 211859 Sorted by model distance: nonbonded pdb="MG MG C 505 " pdb=" O HOH C 606 " model vdw 2.064 2.170 nonbonded pdb="MG MG C 505 " pdb=" O HOH M 507 " model vdw 2.065 2.170 nonbonded pdb=" OE2 GLU M 233 " pdb="FE FE M 401 " model vdw 2.068 2.260 nonbonded pdb="MG MG C 505 " pdb=" O HOH C 602 " model vdw 2.071 2.170 nonbonded pdb=" O ILE W 49 " pdb="CA CA W 102 " model vdw 2.129 2.510 ... (remaining 211854 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 '0' and (resid 11 through 12 or resid 14 through 15 or resid 17 through 2 \ 2 or resid 24 through 27 or resid 29 through 33 or resid 35 through 47)) selection = (chain '2' and (resid 11 through 12 or resid 14 through 15 or resid 17 through 2 \ 2 or resid 24 through 27 or resid 29 through 33 or resid 35 through 47)) selection = (chain '4' and (resid 11 through 12 or resid 14 through 15 or resid 17 through 2 \ 2 or resid 24 through 27 or resid 29 through 33 or resid 35 through 47)) selection = (chain '6' and (resid 11 through 12 or resid 14 through 15 or resid 17 through 2 \ 2 or resid 24 through 27 or resid 29 through 33 or resid 35 through 47)) selection = (chain '8' and (resid 11 through 12 or resid 14 through 15 or resid 17 through 2 \ 2 or resid 24 through 27 or resid 29 through 33 or resid 35 through 47)) selection = (chain 'B' and (resid 11 through 12 or resid 14 through 15 or resid 17 through 2 \ 2 or resid 24 through 27 or resid 29 through 33 or resid 35 through 47)) selection = (chain 'E' and (resid 11 through 12 or resid 14 through 15 or resid 17 through 2 \ 2 or resid 24 through 27 or resid 29 through 33 or resid 35 through 47)) selection = (chain 'G' and (resid 11 through 12 or resid 14 through 15 or resid 17 through 2 \ 2 or resid 24 through 27 or resid 29 through 33 or resid 35 through 47)) selection = (chain 'J' and (resid 11 through 12 or resid 14 through 15 or resid 17 through 2 \ 2 or resid 24 through 27 or resid 29 through 33 or resid 35 through 47)) selection = (chain 'N' and (resid 11 through 12 or resid 14 through 15 or resid 17 through 2 \ 2 or resid 24 through 27 or resid 29 through 33 or resid 35 through 47)) selection = (chain 'P' and (resid 11 through 12 or resid 14 through 15 or resid 17 through 2 \ 2 or resid 24 through 27 or resid 29 through 33 or resid 35 through 47)) selection = (chain 'R' and (resid 11 through 12 or resid 14 through 15 or resid 17 through 2 \ 2 or resid 24 through 27 or resid 29 through 33 or resid 35 through 47)) selection = (chain 'T' and (resid 11 through 12 or resid 14 through 15 or resid 17 through 2 \ 2 or resid 24 through 27 or resid 29 through 33 or resid 35 through 47)) selection = (chain 'V' and (resid 11 through 12 or resid 14 through 15 or resid 17 through 2 \ 2 or resid 24 through 27 or resid 29 through 33 or resid 35 through 47)) selection = (chain 'X' and (resid 11 through 12 or resid 14 through 15 or resid 17 through 2 \ 2 or resid 24 through 27 or resid 29 through 33 or resid 35 through 47)) selection = (chain 'Z' and (resid 11 through 12 or resid 14 through 15 or resid 17 through 2 \ 2 or resid 24 through 27 or resid 29 through 33 or resid 35 through 47)) } ncs_group { reference = (chain '1' and (resid 5 through 6 or (resid 7 and (name N or name CA or name C o \ r name O or name CB )) or resid 8 through 47)) selection = (chain '5' and resid 5 through 47) selection = (chain '7' and resid 5 through 47) selection = (chain '9' and (resid 5 through 6 or (resid 7 and (name N or name CA or name C o \ r name O or name CB )) or resid 8 through 47)) selection = (chain 'A' and (resid 5 through 6 or (resid 7 and (name N or name CA or name C o \ r name O or name CB )) or resid 8 through 47)) selection = (chain 'I' and (resid 5 through 6 or (resid 7 and (name N or name CA or name C o \ r name O or name CB )) or resid 8 through 47)) selection = (chain 'K' and (resid 5 through 6 or (resid 7 and (name N or name CA or name C o \ r name O or name CB )) or resid 8 through 47)) selection = (chain 'O' and (resid 5 through 6 or (resid 7 and (name N or name CA or name C o \ r name O or name CB )) or resid 8 through 47)) selection = (chain 'Q' and (resid 5 through 6 or (resid 7 and (name N or name CA or name C o \ r name O or name CB )) or resid 8 through 47)) } ncs_group { reference = (chain 'D' and (resid 2 through 35 or (resid 36 and (name N or name CA or name C \ or name O or name CB or name CG )) or resid 37 through 50)) selection = (chain 'F' and (resid 2 through 35 or (resid 36 and (name N or name CA or name C \ or name O or name CB or name CG )) or resid 37 through 50)) selection = (chain 'S' and resid 2 through 50) selection = (chain 'U' and (resid 2 through 35 or (resid 36 and (name N or name CA or name C \ or name O or name CB or name CG )) or resid 37 through 50)) selection = (chain 'W' and (resid 2 through 35 or (resid 36 and (name N or name CA or name C \ or name O or name CB or name CG )) or resid 37 through 50)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians Ca 6 9.91 5 Fe 5 7.16 5 P 28 5.49 5 Mg 37 5.21 5 S 102 5.16 5 C 18284 2.51 5 N 3570 2.21 5 O 4277 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.530 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: 0.040 Extract box with map and model: 18.250 Check model and map are aligned: 0.400 Process input model: 67.240 Find NCS groups from input model: 1.430 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Set scattering table: 0.230 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:14.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 106.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 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 : 0.020 0.218 27271 Z= 0.985 Angle : 1.873 25.416 37460 Z= 0.830 Chirality : 0.062 0.368 3769 Planarity : 0.020 0.315 4433 Dihedral : 18.066 179.926 9414 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.86 % Favored : 97.10 % Rotamer Outliers : 1.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.75 % 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: 1.42 (0.17), residues: 2517 helix: 2.09 (0.14), residues: 1470 sheet: 0.29 (0.74), residues: 52 loop : -0.80 (0.20), residues: 995 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 2171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 376 time to evaluate : 2.955 Fit side-chains outliers start: 31 outliers final: 19 residues processed: 399 average time/residue: 1.2519 time to fit residues: 588.5267 Evaluate side-chains 324 residues out of total 2171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 305 time to evaluate : 2.799 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 17 residues processed: 2 average time/residue: 0.2494 time to fit residues: 4.4307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 208 optimal weight: 1.9990 chunk 187 optimal weight: 3.9990 chunk 103 optimal weight: 0.0470 chunk 63 optimal weight: 10.0000 chunk 126 optimal weight: 1.9990 chunk 100 optimal weight: 8.9990 chunk 193 optimal weight: 9.9990 chunk 74 optimal weight: 0.9990 chunk 117 optimal weight: 0.9990 chunk 144 optimal weight: 0.9990 chunk 224 optimal weight: 5.9990 overall best weight: 1.0086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 56 ASN C 78 ASN C 186 ASN L 206 GLN L 216 HIS M 258 ASN A 6 HIS B 16 GLN G 24 GLN J 16 GLN J 24 GLN K 10 GLN P 16 GLN 2 13 GLN 2 16 GLN 5 10 GLN 5 43 ASN 7 6 HIS ** 7 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 16 GLN 0 16 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.1069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 27271 Z= 0.156 Angle : 0.664 16.378 37460 Z= 0.254 Chirality : 0.038 0.146 3769 Planarity : 0.004 0.054 4433 Dihedral : 18.562 179.906 4805 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.15 % Favored : 97.81 % Rotamer Outliers : 2.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.75 % 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: 1.84 (0.17), residues: 2517 helix: 2.39 (0.14), residues: 1483 sheet: 0.31 (0.74), residues: 52 loop : -0.60 (0.20), residues: 982 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 2171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 317 time to evaluate : 2.921 Fit side-chains outliers start: 61 outliers final: 38 residues processed: 353 average time/residue: 1.1436 time to fit residues: 483.7327 Evaluate side-chains 326 residues out of total 2171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 288 time to evaluate : 2.774 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 26 residues processed: 14 average time/residue: 0.6617 time to fit residues: 15.9071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 124 optimal weight: 1.9990 chunk 69 optimal weight: 9.9990 chunk 186 optimal weight: 0.9990 chunk 152 optimal weight: 3.9990 chunk 61 optimal weight: 5.9990 chunk 224 optimal weight: 9.9990 chunk 242 optimal weight: 4.9990 chunk 200 optimal weight: 10.0000 chunk 222 optimal weight: 9.9990 chunk 76 optimal weight: 4.9990 chunk 180 optimal weight: 0.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 4 GLN H 122 HIS Z 24 GLN 5 10 GLN ** 7 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 16 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.1139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 27271 Z= 0.242 Angle : 0.749 20.879 37460 Z= 0.293 Chirality : 0.040 0.150 3769 Planarity : 0.004 0.058 4433 Dihedral : 18.305 179.874 4805 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.94 % Favored : 97.02 % Rotamer Outliers : 3.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.75 % 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: 1.62 (0.17), residues: 2517 helix: 2.24 (0.13), residues: 1476 sheet: 0.30 (0.73), residues: 52 loop : -0.72 (0.20), residues: 989 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 2171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 305 time to evaluate : 2.636 Fit side-chains outliers start: 83 outliers final: 52 residues processed: 352 average time/residue: 1.2393 time to fit residues: 521.2089 Evaluate side-chains 353 residues out of total 2171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 301 time to evaluate : 2.722 Switching outliers to nearest non-outliers outliers start: 52 outliers final: 31 residues processed: 21 average time/residue: 0.8115 time to fit residues: 25.3585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 222 optimal weight: 9.9990 chunk 168 optimal weight: 3.9990 chunk 116 optimal weight: 9.9990 chunk 24 optimal weight: 2.9990 chunk 107 optimal weight: 9.9990 chunk 150 optimal weight: 7.9990 chunk 225 optimal weight: 9.9990 chunk 238 optimal weight: 10.0000 chunk 117 optimal weight: 2.9990 chunk 213 optimal weight: 10.0000 chunk 64 optimal weight: 8.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 171 HIS H 122 HIS J 24 GLN K 10 GLN Z 24 GLN 5 10 GLN ** 7 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 16 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.1537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.068 27271 Z= 0.439 Angle : 0.955 27.490 37460 Z= 0.380 Chirality : 0.049 0.185 3769 Planarity : 0.006 0.073 4433 Dihedral : 19.432 179.966 4805 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.66 % Favored : 96.30 % Rotamer Outliers : 5.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.16), residues: 2517 helix: 1.70 (0.13), residues: 1469 sheet: -0.27 (0.82), residues: 42 loop : -0.97 (0.19), residues: 1006 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 2171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 309 time to evaluate : 2.844 Fit side-chains outliers start: 109 outliers final: 68 residues processed: 373 average time/residue: 1.2000 time to fit residues: 534.6225 Evaluate side-chains 365 residues out of total 2171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 297 time to evaluate : 2.689 Switching outliers to nearest non-outliers outliers start: 68 outliers final: 45 residues processed: 25 average time/residue: 0.6179 time to fit residues: 24.8275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 198 optimal weight: 0.0470 chunk 135 optimal weight: 9.9990 chunk 3 optimal weight: 0.5980 chunk 177 optimal weight: 2.9990 chunk 98 optimal weight: 8.9990 chunk 203 optimal weight: 10.0000 chunk 165 optimal weight: 0.9980 chunk 0 optimal weight: 7.9990 chunk 121 optimal weight: 6.9990 chunk 214 optimal weight: 7.9990 chunk 60 optimal weight: 8.9990 overall best weight: 2.3282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 122 HIS J 24 GLN K 10 GLN 4 13 GLN 5 10 GLN 7 10 GLN 0 16 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.1456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 27271 Z= 0.225 Angle : 0.736 17.747 37460 Z= 0.288 Chirality : 0.040 0.159 3769 Planarity : 0.005 0.057 4433 Dihedral : 18.441 179.872 4805 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.46 % Favored : 97.50 % Rotamer Outliers : 4.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.75 % 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: 1.40 (0.17), residues: 2517 helix: 2.11 (0.13), residues: 1469 sheet: -0.38 (0.81), residues: 42 loop : -0.83 (0.19), residues: 1006 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 2171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 305 time to evaluate : 2.751 Fit side-chains outliers start: 95 outliers final: 61 residues processed: 365 average time/residue: 1.1979 time to fit residues: 521.9622 Evaluate side-chains 354 residues out of total 2171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 293 time to evaluate : 2.683 Switching outliers to nearest non-outliers outliers start: 61 outliers final: 43 residues processed: 19 average time/residue: 0.5204 time to fit residues: 17.1395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 80 optimal weight: 1.9990 chunk 215 optimal weight: 10.0000 chunk 47 optimal weight: 1.9990 chunk 140 optimal weight: 7.9990 chunk 58 optimal weight: 10.0000 chunk 238 optimal weight: 10.0000 chunk 198 optimal weight: 4.9990 chunk 110 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 chunk 79 optimal weight: 1.9990 chunk 125 optimal weight: 6.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 171 HIS L 206 GLN H 122 HIS J 24 GLN K 10 GLN 5 10 GLN 0 16 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.1515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 27271 Z= 0.270 Angle : 0.784 17.291 37460 Z= 0.308 Chirality : 0.042 0.161 3769 Planarity : 0.005 0.058 4433 Dihedral : 18.510 179.899 4805 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.06 % Favored : 96.90 % Rotamer Outliers : 4.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.75 % 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: 1.31 (0.17), residues: 2517 helix: 2.03 (0.13), residues: 1475 sheet: -0.35 (0.81), residues: 42 loop : -0.89 (0.19), residues: 1000 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 2171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 297 time to evaluate : 2.701 Fit side-chains outliers start: 106 outliers final: 68 residues processed: 361 average time/residue: 1.2064 time to fit residues: 521.8577 Evaluate side-chains 362 residues out of total 2171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 294 time to evaluate : 2.980 Switching outliers to nearest non-outliers outliers start: 68 outliers final: 48 residues processed: 20 average time/residue: 0.6042 time to fit residues: 19.9285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 230 optimal weight: 2.9990 chunk 26 optimal weight: 0.0570 chunk 136 optimal weight: 10.0000 chunk 174 optimal weight: 5.9990 chunk 135 optimal weight: 0.8980 chunk 201 optimal weight: 3.9990 chunk 133 optimal weight: 8.9990 chunk 238 optimal weight: 9.9990 chunk 148 optimal weight: 4.9990 chunk 145 optimal weight: 7.9990 chunk 109 optimal weight: 9.9990 overall best weight: 2.5904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 171 HIS L 206 GLN H 122 HIS J 24 GLN K 10 GLN 5 10 GLN 6 24 GLN 0 16 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.1550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 27271 Z= 0.240 Angle : 0.743 16.865 37460 Z= 0.291 Chirality : 0.040 0.157 3769 Planarity : 0.005 0.058 4433 Dihedral : 18.235 179.866 4805 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.58 % Favored : 97.38 % Rotamer Outliers : 4.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.75 % 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: 1.45 (0.17), residues: 2517 helix: 2.14 (0.13), residues: 1467 sheet: 0.17 (0.74), residues: 52 loop : -0.83 (0.19), residues: 998 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 2171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 298 time to evaluate : 2.721 Fit side-chains outliers start: 91 outliers final: 70 residues processed: 358 average time/residue: 1.1392 time to fit residues: 489.2291 Evaluate side-chains 364 residues out of total 2171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 294 time to evaluate : 3.151 Switching outliers to nearest non-outliers outliers start: 70 outliers final: 50 residues processed: 20 average time/residue: 0.9027 time to fit residues: 27.3076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 147 optimal weight: 6.9990 chunk 95 optimal weight: 6.9990 chunk 142 optimal weight: 6.9990 chunk 71 optimal weight: 7.9990 chunk 46 optimal weight: 6.9990 chunk 151 optimal weight: 2.9990 chunk 162 optimal weight: 5.9990 chunk 117 optimal weight: 4.9990 chunk 22 optimal weight: 0.9990 chunk 187 optimal weight: 0.8980 chunk 216 optimal weight: 10.0000 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 171 HIS H 122 HIS J 24 GLN K 10 GLN 5 10 GLN 0 16 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.1609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.051 27271 Z= 0.281 Angle : 0.791 17.781 37460 Z= 0.311 Chirality : 0.042 0.162 3769 Planarity : 0.005 0.058 4433 Dihedral : 18.380 179.920 4805 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.14 % Favored : 96.82 % Rotamer Outliers : 4.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.75 % 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: 1.28 (0.17), residues: 2517 helix: 2.00 (0.13), residues: 1475 sheet: -0.25 (0.83), residues: 40 loop : -0.90 (0.19), residues: 1002 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 2171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 297 time to evaluate : 2.905 Fit side-chains outliers start: 97 outliers final: 72 residues processed: 356 average time/residue: 1.2008 time to fit residues: 510.1185 Evaluate side-chains 361 residues out of total 2171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 289 time to evaluate : 2.657 Switching outliers to nearest non-outliers outliers start: 72 outliers final: 53 residues processed: 20 average time/residue: 0.5346 time to fit residues: 18.1395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 228 optimal weight: 7.9990 chunk 208 optimal weight: 3.9990 chunk 221 optimal weight: 20.0000 chunk 133 optimal weight: 8.9990 chunk 96 optimal weight: 0.3980 chunk 174 optimal weight: 3.9990 chunk 68 optimal weight: 0.0870 chunk 200 optimal weight: 7.9990 chunk 209 optimal weight: 7.9990 chunk 145 optimal weight: 6.9990 chunk 234 optimal weight: 2.9990 overall best weight: 2.2964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 171 HIS H 122 HIS J 24 GLN K 10 GLN 5 10 GLN 0 16 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.1616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 27271 Z= 0.222 Angle : 0.729 16.692 37460 Z= 0.285 Chirality : 0.040 0.160 3769 Planarity : 0.005 0.058 4433 Dihedral : 17.993 179.873 4805 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer Outliers : 3.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.75 % 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: 1.47 (0.17), residues: 2517 helix: 2.15 (0.13), residues: 1472 sheet: -0.19 (0.83), residues: 40 loop : -0.78 (0.19), residues: 1005 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 2171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 294 time to evaluate : 2.703 Fit side-chains outliers start: 73 outliers final: 58 residues processed: 351 average time/residue: 1.1421 time to fit residues: 480.8056 Evaluate side-chains 347 residues out of total 2171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 289 time to evaluate : 4.697 Switching outliers to nearest non-outliers outliers start: 58 outliers final: 51 residues processed: 7 average time/residue: 0.5210 time to fit residues: 9.2049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 143 optimal weight: 2.9990 chunk 111 optimal weight: 9.9990 chunk 163 optimal weight: 7.9990 chunk 246 optimal weight: 9.9990 chunk 226 optimal weight: 2.9990 chunk 195 optimal weight: 9.9990 chunk 20 optimal weight: 8.9990 chunk 151 optimal weight: 1.9990 chunk 120 optimal weight: 9.9990 chunk 155 optimal weight: 10.0000 chunk 208 optimal weight: 10.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 56 ASN L 171 HIS H 122 HIS J 24 GLN K 10 GLN 5 10 GLN 0 16 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.065 27271 Z= 0.408 Angle : 0.912 20.027 37460 Z= 0.363 Chirality : 0.047 0.181 3769 Planarity : 0.006 0.067 4433 Dihedral : 18.813 179.994 4805 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer Outliers : 3.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.17), residues: 2517 helix: 1.69 (0.13), residues: 1474 sheet: -0.33 (0.82), residues: 40 loop : -1.04 (0.19), residues: 1003 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5034 Ramachandran restraints generated. 2517 Oldfield, 0 Emsley, 2517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 2171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 297 time to evaluate : 2.813 Fit side-chains outliers start: 75 outliers final: 67 residues processed: 355 average time/residue: 1.1455 time to fit residues: 486.1854 Evaluate side-chains 359 residues out of total 2171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 292 time to evaluate : 2.544 Switching outliers to nearest non-outliers outliers start: 67 outliers final: 53 residues processed: 15 average time/residue: 0.6309 time to fit residues: 15.7189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 60 optimal weight: 10.0000 chunk 180 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 54 optimal weight: 7.9990 chunk 196 optimal weight: 5.9990 chunk 82 optimal weight: 5.9990 chunk 201 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 172 optimal weight: 6.9990 chunk 11 optimal weight: 5.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 56 ASN L 171 HIS H 122 HIS J 24 GLN K 10 GLN 5 10 GLN 0 16 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.133411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.102713 restraints weight = 34036.532| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 1.30 r_work: 0.2972 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2847 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3608 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3608 r_free = 0.3608 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3608 r_free = 0.3608 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3608 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 moved from start: 0.1665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 27271 Z= 0.229 Angle : 0.745 16.632 37460 Z= 0.292 Chirality : 0.040 0.163 3769 Planarity : 0.005 0.058 4433 Dihedral : 18.139 179.887 4805 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer Outliers : 3.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.75 % 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: 1.32 (0.17), residues: 2517 helix: 2.04 (0.13), residues: 1470 sheet: -0.29 (0.82), residues: 40 loop : -0.87 (0.19), residues: 1007 =============================================================================== Job complete usr+sys time: 8635.90 seconds wall clock time: 155 minutes 1.66 seconds (9301.66 seconds total)