Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 27 21:22:10 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vrj_32100/04_2023/7vrj_32100_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vrj_32100/04_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_32100/04_2023/7vrj_32100.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vrj_32100/04_2023/7vrj_32100.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vrj_32100/04_2023/7vrj_32100_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vrj_32100/04_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 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. 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: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/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: 15.50, per 1000 atoms: 0.59 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: 11.84 Conformation dependent library (CDL) restraints added in 3.1 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: 1.31 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: 7.27 Time building geometry restraints manager: 12.39 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: 13647 35.99 - 71.97: 529 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 - 0.057: 2951 0.057 - 0.114: 608 0.114 - 0.172: 143 0.172 - 0.229: 55 0.229 - 0.286: 12 Chirality restraints: 3769 Sorted by residual: chirality pdb=" C05 PGV 5 101 " pdb=" C04 PGV 5 101 " pdb=" C06 PGV 5 101 " pdb=" O05 PGV 5 101 " both_signs ideal model delta sigma weight residual False 2.29 2.58 -0.29 2.00e-01 2.50e+01 2.05e+00 chirality pdb=" C05 PGV C 508 " pdb=" C04 PGV C 508 " pdb=" C06 PGV C 508 " pdb=" O05 PGV C 508 " both_signs ideal model delta sigma weight residual False 2.29 2.57 -0.28 2.00e-01 2.50e+01 1.94e+00 chirality pdb=" C05 PGV M 411 " pdb=" C04 PGV M 411 " pdb=" C06 PGV M 411 " pdb=" O05 PGV M 411 " both_signs ideal model delta sigma weight residual False 2.29 2.56 -0.27 2.00e-01 2.50e+01 1.79e+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 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: 4.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 16.110 Check model and map are aligned: 0.430 Set scattering table: 0.250 Process input model: 65.340 Find NCS groups from input model: 1.440 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:15.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 103.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 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 : 0.019 0.218 27271 Z= 0.975 Angle : 1.881 25.416 37460 Z= 0.826 Chirality : 0.056 0.286 3769 Planarity : 0.020 0.315 4433 Dihedral : 18.014 179.926 9414 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 9.41 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 : 2.538 Fit side-chains outliers start: 31 outliers final: 19 residues processed: 399 average time/residue: 1.1853 time to fit residues: 559.4346 Evaluate side-chains 324 residues out of total 2171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 305 time to evaluate : 2.770 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 17 residues processed: 2 average time/residue: 0.2564 time to fit residues: 4.3205 ------------------------------------------------------------------------------- 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: 0.0570 chunk 117 optimal weight: 0.9990 chunk 144 optimal weight: 0.9990 chunk 224 optimal weight: 5.9990 overall best weight: 0.8202 ------------------------------------------------------------------------------- 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: 0.8175 moved from start: 0.1124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 27271 Z= 0.147 Angle : 0.655 15.738 37460 Z= 0.248 Chirality : 0.037 0.148 3769 Planarity : 0.004 0.053 4433 Dihedral : 18.349 179.827 4805 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.07 % Favored : 97.89 % 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: 1.87 (0.17), residues: 2517 helix: 2.41 (0.14), residues: 1486 sheet: 0.31 (0.74), residues: 52 loop : -0.58 (0.20), residues: 979 *********************** 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 383 residues out of total 2171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 322 time to evaluate : 2.674 Fit side-chains outliers start: 61 outliers final: 38 residues processed: 358 average time/residue: 1.0981 time to fit residues: 472.2558 Evaluate side-chains 329 residues out of total 2171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 291 time to evaluate : 2.612 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 26 residues processed: 14 average time/residue: 0.6003 time to fit residues: 14.5678 ------------------------------------------------------------------------------- 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: 0.9980 chunk 69 optimal weight: 10.0000 chunk 186 optimal weight: 0.9980 chunk 152 optimal weight: 3.9990 chunk 61 optimal weight: 6.9990 chunk 224 optimal weight: 10.0000 chunk 242 optimal weight: 5.9990 chunk 200 optimal weight: 9.9990 chunk 222 optimal weight: 10.0000 chunk 76 optimal weight: 4.9990 chunk 180 optimal weight: 1.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- 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 2 13 GLN 5 10 GLN ** 7 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 43 ASN 0 16 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 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= 0.245 Angle : 0.754 20.535 37460 Z= 0.292 Chirality : 0.041 0.164 3769 Planarity : 0.004 0.060 4433 Dihedral : 18.121 179.907 4805 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.74 % Favored : 97.22 % Rotamer Outliers : 3.69 % 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: 1.65 (0.17), residues: 2517 helix: 2.27 (0.13), residues: 1476 sheet: 0.29 (0.73), residues: 52 loop : -0.71 (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 387 residues out of total 2171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 307 time to evaluate : 2.625 Fit side-chains outliers start: 80 outliers final: 50 residues processed: 353 average time/residue: 1.1638 time to fit residues: 490.5943 Evaluate side-chains 353 residues out of total 2171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 303 time to evaluate : 2.579 Switching outliers to nearest non-outliers outliers start: 50 outliers final: 32 residues processed: 19 average time/residue: 0.6207 time to fit residues: 18.8842 ------------------------------------------------------------------------------- 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: 10.0000 chunk 24 optimal weight: 5.9990 chunk 107 optimal weight: 10.0000 chunk 150 optimal weight: 6.9990 chunk 225 optimal weight: 9.9990 chunk 238 optimal weight: 10.0000 chunk 117 optimal weight: 3.9990 chunk 213 optimal weight: 9.9990 chunk 64 optimal weight: 8.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- 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: 0.8312 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.074 27271 Z= 0.480 Angle : 1.007 27.760 37460 Z= 0.396 Chirality : 0.051 0.230 3769 Planarity : 0.006 0.079 4433 Dihedral : 19.530 179.921 4805 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.78 % Favored : 96.18 % Rotamer Outliers : 5.08 % 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: 0.85 (0.16), residues: 2517 helix: 1.61 (0.13), residues: 1471 sheet: -0.33 (0.81), residues: 42 loop : -0.98 (0.19), residues: 1004 *********************** 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 423 residues out of total 2171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 313 time to evaluate : 2.735 Fit side-chains outliers start: 110 outliers final: 69 residues processed: 373 average time/residue: 1.2222 time to fit residues: 542.5239 Evaluate side-chains 373 residues out of total 2171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 304 time to evaluate : 2.719 Switching outliers to nearest non-outliers outliers start: 69 outliers final: 41 residues processed: 30 average time/residue: 0.6259 time to fit residues: 28.6383 ------------------------------------------------------------------------------- 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: 0.7980 chunk 135 optimal weight: 10.0000 chunk 3 optimal weight: 0.0870 chunk 177 optimal weight: 0.9990 chunk 98 optimal weight: 8.9990 chunk 203 optimal weight: 9.9990 chunk 165 optimal weight: 0.7980 chunk 0 optimal weight: 7.9990 chunk 121 optimal weight: 5.9990 chunk 214 optimal weight: 2.9990 chunk 60 optimal weight: 8.9990 overall best weight: 1.1362 ------------------------------------------------------------------------------- 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 5 10 GLN 7 10 GLN 0 16 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.1562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 27271 Z= 0.156 Angle : 0.661 14.834 37460 Z= 0.256 Chirality : 0.037 0.144 3769 Planarity : 0.004 0.057 4433 Dihedral : 17.880 179.959 4805 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.03 % Favored : 97.93 % Rotamer Outliers : 3.74 % 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: 1.69 (0.17), residues: 2517 helix: 2.33 (0.14), residues: 1464 sheet: 0.24 (0.74), residues: 52 loop : -0.70 (0.19), residues: 1001 *********************** 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 383 residues out of total 2171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 302 time to evaluate : 2.558 Fit side-chains outliers start: 81 outliers final: 48 residues processed: 354 average time/residue: 1.1400 time to fit residues: 482.8045 Evaluate side-chains 334 residues out of total 2171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 286 time to evaluate : 2.769 Switching outliers to nearest non-outliers outliers start: 48 outliers final: 36 residues processed: 12 average time/residue: 0.6270 time to fit residues: 13.4077 ------------------------------------------------------------------------------- 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: 4.9990 chunk 215 optimal weight: 10.0000 chunk 47 optimal weight: 3.9990 chunk 140 optimal weight: 2.9990 chunk 58 optimal weight: 10.0000 chunk 238 optimal weight: 10.0000 chunk 198 optimal weight: 4.9990 chunk 110 optimal weight: 8.9990 chunk 19 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 125 optimal weight: 6.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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 Z 24 GLN 5 10 GLN 0 16 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.1528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.055 27271 Z= 0.324 Angle : 0.836 17.703 37460 Z= 0.326 Chirality : 0.044 0.176 3769 Planarity : 0.005 0.056 4433 Dihedral : 18.506 179.938 4805 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.34 % Favored : 96.62 % Rotamer Outliers : 5.17 % 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: 2.01 (0.13), residues: 1474 sheet: 0.15 (0.74), residues: 52 loop : -0.86 (0.19), residues: 991 *********************** 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 408 residues out of total 2171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 296 time to evaluate : 2.791 Fit side-chains outliers start: 112 outliers final: 69 residues processed: 358 average time/residue: 1.1658 time to fit residues: 498.8920 Evaluate side-chains 362 residues out of total 2171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 293 time to evaluate : 2.669 Switching outliers to nearest non-outliers outliers start: 69 outliers final: 45 residues processed: 24 average time/residue: 0.7116 time to fit residues: 25.9510 ------------------------------------------------------------------------------- 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: 2.9990 chunk 136 optimal weight: 10.0000 chunk 174 optimal weight: 0.0870 chunk 135 optimal weight: 2.9990 chunk 201 optimal weight: 0.0000 chunk 133 optimal weight: 7.9990 chunk 238 optimal weight: 10.0000 chunk 148 optimal weight: 0.9990 chunk 145 optimal weight: 5.9990 chunk 109 optimal weight: 8.9990 overall best weight: 1.4168 ------------------------------------------------------------------------------- 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: 0.8219 moved from start: 0.1612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 27271 Z= 0.168 Angle : 0.672 15.369 37460 Z= 0.258 Chirality : 0.038 0.144 3769 Planarity : 0.004 0.058 4433 Dihedral : 17.644 179.942 4805 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.31 % Favored : 97.66 % 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: 1.73 (0.17), residues: 2517 helix: 2.33 (0.14), residues: 1472 sheet: 0.28 (0.74), residues: 52 loop : -0.66 (0.20), residues: 993 *********************** 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 370 residues out of total 2171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 295 time to evaluate : 2.684 Fit side-chains outliers start: 75 outliers final: 54 residues processed: 348 average time/residue: 1.1977 time to fit residues: 497.0378 Evaluate side-chains 341 residues out of total 2171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 287 time to evaluate : 2.531 Switching outliers to nearest non-outliers outliers start: 54 outliers final: 46 residues processed: 9 average time/residue: 0.8478 time to fit residues: 12.6712 ------------------------------------------------------------------------------- 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: 0.0670 chunk 142 optimal weight: 7.9990 chunk 71 optimal weight: 9.9990 chunk 46 optimal weight: 5.9990 chunk 151 optimal weight: 10.0000 chunk 162 optimal weight: 0.0770 chunk 117 optimal weight: 6.9990 chunk 22 optimal weight: 0.9980 chunk 187 optimal weight: 10.0000 chunk 216 optimal weight: 0.8980 overall best weight: 1.6078 ------------------------------------------------------------------------------- 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: 0.8226 moved from start: 0.1636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 27271 Z= 0.181 Angle : 0.689 15.791 37460 Z= 0.263 Chirality : 0.038 0.147 3769 Planarity : 0.004 0.057 4433 Dihedral : 17.412 179.887 4805 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer Outliers : 3.60 % 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: 1.74 (0.17), residues: 2517 helix: 2.33 (0.13), residues: 1475 sheet: 0.55 (0.76), residues: 50 loop : -0.65 (0.20), residues: 992 *********************** 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 371 residues out of total 2171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 293 time to evaluate : 2.658 Fit side-chains outliers start: 78 outliers final: 56 residues processed: 347 average time/residue: 1.1857 time to fit residues: 493.0501 Evaluate side-chains 345 residues out of total 2171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 289 time to evaluate : 2.626 Switching outliers to nearest non-outliers outliers start: 56 outliers final: 46 residues processed: 12 average time/residue: 0.6321 time to fit residues: 13.4805 ------------------------------------------------------------------------------- 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: 8.9990 chunk 208 optimal weight: 9.9990 chunk 221 optimal weight: 30.0000 chunk 133 optimal weight: 5.9990 chunk 96 optimal weight: 0.0070 chunk 174 optimal weight: 3.9990 chunk 68 optimal weight: 0.7980 chunk 200 optimal weight: 10.0000 chunk 209 optimal weight: 7.9990 chunk 145 optimal weight: 7.9990 chunk 234 optimal weight: 7.9990 overall best weight: 3.7604 ------------------------------------------------------------------------------- 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 M 4 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: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.1649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.054 27271 Z= 0.322 Angle : 0.839 18.328 37460 Z= 0.327 Chirality : 0.044 0.171 3769 Planarity : 0.005 0.057 4433 Dihedral : 18.189 179.957 4805 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer Outliers : 4.11 % 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: 1.30 (0.17), residues: 2517 helix: 1.97 (0.13), residues: 1482 sheet: 0.39 (0.75), residues: 50 loop : -0.86 (0.19), residues: 985 *********************** 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 379 residues out of total 2171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 290 time to evaluate : 2.742 Fit side-chains outliers start: 89 outliers final: 63 residues processed: 344 average time/residue: 1.1544 time to fit residues: 473.9622 Evaluate side-chains 348 residues out of total 2171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 285 time to evaluate : 2.636 Switching outliers to nearest non-outliers outliers start: 63 outliers final: 44 residues processed: 20 average time/residue: 0.5540 time to fit residues: 18.5235 ------------------------------------------------------------------------------- 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: 8.9990 chunk 111 optimal weight: 10.0000 chunk 163 optimal weight: 7.9990 chunk 246 optimal weight: 4.9990 chunk 226 optimal weight: 3.9990 chunk 195 optimal weight: 8.9990 chunk 20 optimal weight: 4.9990 chunk 151 optimal weight: 3.9990 chunk 120 optimal weight: 7.9990 chunk 155 optimal weight: 6.9990 chunk 208 optimal weight: 8.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- 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: 0.8302 moved from start: 0.1773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.063 27271 Z= 0.407 Angle : 0.935 19.928 37460 Z= 0.366 Chirality : 0.048 0.209 3769 Planarity : 0.005 0.059 4433 Dihedral : 18.871 179.995 4805 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer Outliers : 3.09 % 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: 0.89 (0.17), residues: 2517 helix: 1.64 (0.13), residues: 1477 sheet: 0.16 (0.75), residues: 50 loop : -1.03 (0.19), residues: 990 ********************** 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 362 residues out of total 2171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 295 time to evaluate : 2.590 Fit side-chains outliers start: 67 outliers final: 52 residues processed: 346 average time/residue: 1.1962 time to fit residues: 493.7615 Evaluate side-chains 343 residues out of total 2171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 291 time to evaluate : 2.485 Switching outliers to nearest non-outliers outliers start: 52 outliers final: 43 residues processed: 10 average time/residue: 0.5898 time to fit residues: 11.3957 ------------------------------------------------------------------------------- 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: 7.9990 chunk 180 optimal weight: 7.9990 chunk 28 optimal weight: 2.9990 chunk 54 optimal weight: 7.9990 chunk 196 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 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: 2.9990 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 H 122 HIS J 24 GLN K 10 GLN 5 10 GLN 0 16 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.131727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.102859 restraints weight = 34112.389| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 1.29 r_work: 0.2955 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2818 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2805 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2805 r_free = 0.2805 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2805 r_free = 0.2805 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2805 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.1714 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 : 0.801 17.395 37460 Z= 0.311 Chirality : 0.042 0.165 3769 Planarity : 0.005 0.057 4433 Dihedral : 18.326 179.893 4805 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer Outliers : 2.77 % 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: 1.18 (0.17), residues: 2517 helix: 1.90 (0.13), residues: 1469 sheet: -0.29 (0.82), residues: 40 loop : -0.88 (0.19), residues: 1008 =============================================================================== Job complete usr+sys time: 8514.37 seconds wall clock time: 151 minutes 59.34 seconds (9119.34 seconds total)