Starting phenix.real_space_refine on Tue Feb 20 00:49:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vrj_32100/02_2024/7vrj_32100_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vrj_32100/02_2024/7vrj_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_2024/7vrj_32100.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vrj_32100/02_2024/7vrj_32100.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vrj_32100/02_2024/7vrj_32100_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vrj_32100/02_2024/7vrj_32100_updated.pdb" } resolution = 2.81 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 54 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: 135 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: 114 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: 102 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: 25 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: 15.56, 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: 62.01 Conformation dependent library (CDL) restraints added in 4.1 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: 12.41 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: 5.54 Time building geometry restraints manager: 11.89 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: 14529 35.99 - 71.97: 763 71.97 - 107.96: 192 107.96 - 143.94: 63 143.94 - 179.93: 8 Dihedral angle restraints: 15555 sinusoidal: 8108 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 15552 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: 10.120 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: 0.000 Extract box with map and model: 12.890 Check model and map are aligned: 0.380 Set scattering table: 0.240 Process input model: 63.400 Find NCS groups from input model: 1.040 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 101.800 ------------------------------------------------------------------------------- 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 : 23.420 179.926 10729 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 % Allowed : 4.80 % Favored : 93.77 % 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: 1.42 (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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP U 9 HIS 0.008 0.001 HIS M 181 PHE 0.018 0.002 PHE 1 26 TYR 0.013 0.002 TYR H 234 ARG 0.003 0.000 ARG 2 44 *********************** 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 : 2.533 Fit side-chains REVERT: M 58 LEU cc_start: 0.8062 (mm) cc_final: 0.7840 (mp) REVERT: M 141 MET cc_start: 0.8111 (mtp) cc_final: 0.7773 (mtm) REVERT: M 215 PHE cc_start: 0.9257 (OUTLIER) cc_final: 0.7945 (t80) REVERT: H 124 ASP cc_start: 0.7354 (t0) cc_final: 0.6996 (t70) REVERT: H 190 LYS cc_start: 0.7162 (mppt) cc_final: 0.6902 (mmtm) REVERT: F 16 ARG cc_start: 0.6877 (mtt-85) cc_final: 0.6669 (mtt-85) REVERT: I 7 LYS cc_start: 0.7840 (OUTLIER) cc_final: 0.7508 (ttmt) REVERT: P 13 GLN cc_start: 0.6962 (tp-100) cc_final: 0.6665 (pp30) REVERT: P 14 GLU cc_start: 0.6644 (tt0) cc_final: 0.6248 (mt-10) REVERT: U 27 ILE cc_start: 0.8385 (mt) cc_final: 0.8153 (mp) REVERT: W 40 THR cc_start: 0.8618 (t) cc_final: 0.8392 (m) REVERT: X 26 MET cc_start: 0.7286 (ttp) cc_final: 0.7071 (ttm) REVERT: Z 26 MET cc_start: 0.6769 (mtp) cc_final: 0.6496 (mtp) REVERT: Z 28 MET cc_start: 0.6018 (tpp) cc_final: 0.5804 (tmt) REVERT: 2 8 THR cc_start: 0.5524 (p) cc_final: 0.5055 (m) REVERT: 3 6 TYR cc_start: 0.6744 (p90) cc_final: 0.6413 (p90) REVERT: 7 22 PHE cc_start: 0.7300 (m-10) cc_final: 0.6687 (m-80) outliers start: 31 outliers final: 19 residues processed: 399 average time/residue: 1.1676 time to fit residues: 552.7914 Evaluate side-chains 327 residues out of total 2171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 306 time to evaluate : 2.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 252 CYS Chi-restraints excluded: chain M residue 55 THR Chi-restraints excluded: chain M residue 174 VAL Chi-restraints excluded: chain M residue 215 PHE Chi-restraints excluded: chain M residue 242 THR Chi-restraints excluded: chain M residue 298 ILE Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 160 ASP Chi-restraints excluded: chain H residue 189 THR Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain I residue 7 LYS Chi-restraints excluded: chain N residue 34 VAL Chi-restraints excluded: chain P residue 11 THR Chi-restraints excluded: chain P residue 38 ILE Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain S residue 13 ASP Chi-restraints excluded: chain W residue 30 LEU Chi-restraints excluded: chain X residue 33 VAL Chi-restraints excluded: chain X residue 37 HIS Chi-restraints excluded: chain Z residue 21 ILE Chi-restraints excluded: chain 8 residue 21 ILE 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: 9.9990 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 4 GLN M 258 ASN A 6 HIS B 16 GLN G 24 GLN J 16 GLN J 24 GLN K 10 GLN P 13 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: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.1271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 27271 Z= 0.155 Angle : 0.709 16.912 37460 Z= 0.260 Chirality : 0.039 0.284 3769 Planarity : 0.004 0.052 4433 Dihedral : 19.258 179.899 6153 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.91 % Favored : 98.05 % Rotamer: Outliers : 2.49 % Allowed : 9.88 % Favored : 87.63 % 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: 1.90 (0.17), residues: 2517 helix: 2.44 (0.14), residues: 1484 sheet: 0.32 (0.74), residues: 52 loop : -0.56 (0.20), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP M 267 HIS 0.008 0.001 HIS L 158 PHE 0.020 0.001 PHE 1 26 TYR 0.014 0.001 TYR H 234 ARG 0.003 0.000 ARG F 15 *********************** 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 381 residues out of total 2171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 327 time to evaluate : 2.437 Fit side-chains REVERT: C 217 GLN cc_start: 0.8242 (OUTLIER) cc_final: 0.8024 (mt0) REVERT: L 206 GLN cc_start: 0.8198 (OUTLIER) cc_final: 0.7416 (mp-120) REVERT: M 262 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.7023 (tm-30) REVERT: H 124 ASP cc_start: 0.7290 (t0) cc_final: 0.7034 (t70) REVERT: H 190 LYS cc_start: 0.7192 (mppt) cc_final: 0.6953 (mmpt) REVERT: I 7 LYS cc_start: 0.7715 (ptpt) cc_final: 0.7222 (mtmt) REVERT: J 26 MET cc_start: 0.6934 (ttm) cc_final: 0.6732 (ttm) REVERT: P 13 GLN cc_start: 0.6914 (tp40) cc_final: 0.6632 (pp30) REVERT: U 27 ILE cc_start: 0.8388 (mt) cc_final: 0.8159 (mp) REVERT: Z 26 MET cc_start: 0.6781 (mtp) cc_final: 0.6463 (mtp) REVERT: Z 28 MET cc_start: 0.6020 (tpp) cc_final: 0.5803 (tmt) REVERT: 2 8 THR cc_start: 0.5523 (p) cc_final: 0.5097 (m) REVERT: 7 22 PHE cc_start: 0.7159 (m-10) cc_final: 0.6595 (m-80) outliers start: 54 outliers final: 28 residues processed: 357 average time/residue: 1.0969 time to fit residues: 468.3529 Evaluate side-chains 322 residues out of total 2171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 291 time to evaluate : 2.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 143 GLN Chi-restraints excluded: chain C residue 217 GLN Chi-restraints excluded: chain L residue 55 ILE Chi-restraints excluded: chain L residue 171 HIS Chi-restraints excluded: chain L residue 206 GLN Chi-restraints excluded: chain L residue 252 CYS Chi-restraints excluded: chain M residue 174 VAL Chi-restraints excluded: chain M residue 242 THR Chi-restraints excluded: chain M residue 262 GLU Chi-restraints excluded: chain H residue 10 ASP Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 189 THR Chi-restraints excluded: chain H residue 237 ASP Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain J residue 32 ILE Chi-restraints excluded: chain P residue 11 THR Chi-restraints excluded: chain P residue 38 ILE Chi-restraints excluded: chain S residue 12 ILE Chi-restraints excluded: chain S residue 13 ASP Chi-restraints excluded: chain V residue 7 MET Chi-restraints excluded: chain W residue 30 LEU Chi-restraints excluded: chain X residue 11 THR Chi-restraints excluded: chain Y residue 5 LEU Chi-restraints excluded: chain Y residue 40 THR Chi-restraints excluded: chain Z residue 21 ILE Chi-restraints excluded: chain 1 residue 7 LYS Chi-restraints excluded: chain 1 residue 17 THR Chi-restraints excluded: chain 3 residue 60 SER Chi-restraints excluded: chain 4 residue 42 LEU Chi-restraints excluded: chain 8 residue 21 ILE Chi-restraints excluded: chain 8 residue 25 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 124 optimal weight: 0.9990 chunk 69 optimal weight: 10.0000 chunk 186 optimal weight: 1.9990 chunk 152 optimal weight: 6.9990 chunk 61 optimal weight: 1.9990 chunk 224 optimal weight: 9.9990 chunk 242 optimal weight: 4.9990 chunk 200 optimal weight: 10.0000 chunk 222 optimal weight: 10.0000 chunk 76 optimal weight: 1.9990 chunk 180 optimal weight: 1.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 122 HIS 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.1261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 27271 Z= 0.194 Angle : 0.698 18.546 37460 Z= 0.268 Chirality : 0.039 0.230 3769 Planarity : 0.004 0.059 4433 Dihedral : 17.947 179.999 6136 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.54 % Favored : 97.42 % Rotamer: Outliers : 3.65 % Allowed : 10.80 % Favored : 85.56 % 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: 1.83 (0.17), residues: 2517 helix: 2.41 (0.14), residues: 1486 sheet: 0.30 (0.73), residues: 52 loop : -0.67 (0.20), residues: 979 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP U 9 HIS 0.011 0.001 HIS L 158 PHE 0.026 0.001 PHE 1 26 TYR 0.012 0.002 TYR L 167 ARG 0.004 0.000 ARG H 48 *********************** 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: 79 poor density : 308 time to evaluate : 2.412 Fit side-chains REVERT: M 58 LEU cc_start: 0.7987 (OUTLIER) cc_final: 0.7787 (mp) REVERT: M 215 PHE cc_start: 0.9198 (OUTLIER) cc_final: 0.7667 (t80) REVERT: M 262 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7035 (tm-30) REVERT: H 124 ASP cc_start: 0.7306 (t0) cc_final: 0.7001 (t70) REVERT: H 190 LYS cc_start: 0.7192 (mppt) cc_final: 0.6969 (mmpt) REVERT: I 7 LYS cc_start: 0.7832 (ptpt) cc_final: 0.7320 (mtmt) REVERT: P 13 GLN cc_start: 0.7050 (tp40) cc_final: 0.6672 (pp30) REVERT: P 14 GLU cc_start: 0.6595 (tt0) cc_final: 0.6121 (mt-10) REVERT: S 16 ARG cc_start: 0.7160 (OUTLIER) cc_final: 0.6296 (mtt180) REVERT: T 13 ASP cc_start: 0.6203 (OUTLIER) cc_final: 0.5911 (m-30) REVERT: U 27 ILE cc_start: 0.8440 (mt) cc_final: 0.8216 (mp) REVERT: W 7 LYS cc_start: 0.8334 (OUTLIER) cc_final: 0.7528 (tptt) REVERT: X 26 MET cc_start: 0.7298 (OUTLIER) cc_final: 0.6941 (ttp) REVERT: Z 26 MET cc_start: 0.6806 (mtp) cc_final: 0.6471 (mtp) REVERT: Z 28 MET cc_start: 0.6083 (tpp) cc_final: 0.5820 (tmt) REVERT: 2 8 THR cc_start: 0.5579 (p) cc_final: 0.5129 (m) REVERT: 2 13 GLN cc_start: 0.6242 (mm110) cc_final: 0.4735 (tp40) REVERT: 2 32 ILE cc_start: 0.8510 (mt) cc_final: 0.8214 (mp) REVERT: 5 21 LEU cc_start: 0.8379 (tp) cc_final: 0.8141 (tp) REVERT: 7 22 PHE cc_start: 0.7236 (m-10) cc_final: 0.6634 (m-80) REVERT: 8 19 HIS cc_start: 0.6312 (t70) cc_final: 0.6081 (t70) outliers start: 79 outliers final: 43 residues processed: 350 average time/residue: 1.1630 time to fit residues: 485.7242 Evaluate side-chains 340 residues out of total 2171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 290 time to evaluate : 2.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 143 GLN Chi-restraints excluded: chain L residue 55 ILE Chi-restraints excluded: chain L residue 85 LEU Chi-restraints excluded: chain L residue 252 CYS Chi-restraints excluded: chain M residue 55 THR Chi-restraints excluded: chain M residue 58 LEU Chi-restraints excluded: chain M residue 174 VAL Chi-restraints excluded: chain M residue 215 PHE Chi-restraints excluded: chain M residue 242 THR Chi-restraints excluded: chain M residue 262 GLU Chi-restraints excluded: chain M residue 276 VAL Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 160 ASP Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain H residue 189 THR Chi-restraints excluded: chain H residue 237 ASP Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain F residue 12 ILE Chi-restraints excluded: chain F residue 41 GLU Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain J residue 27 THR Chi-restraints excluded: chain J residue 32 ILE Chi-restraints excluded: chain P residue 11 THR Chi-restraints excluded: chain P residue 38 ILE Chi-restraints excluded: chain Q residue 38 SER Chi-restraints excluded: chain R residue 35 ILE Chi-restraints excluded: chain S residue 12 ILE Chi-restraints excluded: chain S residue 13 ASP Chi-restraints excluded: chain S residue 16 ARG Chi-restraints excluded: chain T residue 13 ASP Chi-restraints excluded: chain T residue 16 LYS Chi-restraints excluded: chain V residue 26 MET Chi-restraints excluded: chain W residue 7 LYS Chi-restraints excluded: chain W residue 12 ILE Chi-restraints excluded: chain W residue 30 LEU Chi-restraints excluded: chain W residue 40 THR Chi-restraints excluded: chain X residue 11 THR Chi-restraints excluded: chain X residue 26 MET Chi-restraints excluded: chain X residue 33 VAL Chi-restraints excluded: chain Y residue 5 LEU Chi-restraints excluded: chain Y residue 38 SER Chi-restraints excluded: chain Y residue 40 THR Chi-restraints excluded: chain Z residue 21 ILE Chi-restraints excluded: chain 1 residue 7 LYS Chi-restraints excluded: chain 3 residue 60 SER Chi-restraints excluded: chain 4 residue 42 LEU Chi-restraints excluded: chain 8 residue 13 GLN Chi-restraints excluded: chain 8 residue 25 SER 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: 0.9990 chunk 116 optimal weight: 10.0000 chunk 24 optimal weight: 3.9990 chunk 107 optimal weight: 9.9990 chunk 150 optimal weight: 5.9990 chunk 225 optimal weight: 9.9990 chunk 238 optimal weight: 10.0000 chunk 117 optimal weight: 5.9990 chunk 213 optimal weight: 8.9990 chunk 64 optimal weight: 8.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- 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 7 10 GLN 7 43 ASN 0 16 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.1530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 27271 Z= 0.424 Angle : 0.951 27.060 37460 Z= 0.372 Chirality : 0.048 0.219 3769 Planarity : 0.006 0.069 4433 Dihedral : 19.559 179.952 6134 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.54 % Favored : 96.42 % Rotamer: Outliers : 4.85 % Allowed : 11.35 % Favored : 83.80 % 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: 1.13 (0.17), residues: 2517 helix: 1.88 (0.13), residues: 1454 sheet: -0.27 (0.81), residues: 42 loop : -0.91 (0.19), residues: 1021 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 168 HIS 0.014 0.002 HIS M 181 PHE 0.044 0.003 PHE 1 26 TYR 0.020 0.003 TYR C 259 ARG 0.006 0.001 ARG L 12 *********************** 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 411 residues out of total 2171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 306 time to evaluate : 2.354 Fit side-chains REVERT: L 206 GLN cc_start: 0.8267 (OUTLIER) cc_final: 0.7496 (mp-120) REVERT: M 215 PHE cc_start: 0.9276 (OUTLIER) cc_final: 0.8007 (t80) REVERT: M 262 GLU cc_start: 0.8269 (OUTLIER) cc_final: 0.7194 (tm-30) REVERT: H 190 LYS cc_start: 0.7175 (mppt) cc_final: 0.6911 (mmpt) REVERT: K 31 LEU cc_start: 0.8461 (OUTLIER) cc_final: 0.8222 (tp) REVERT: P 7 MET cc_start: 0.6117 (OUTLIER) cc_final: 0.4398 (mpt) REVERT: P 13 GLN cc_start: 0.7030 (tp40) cc_final: 0.6646 (pp30) REVERT: P 14 GLU cc_start: 0.6894 (tt0) cc_final: 0.6367 (mt-10) REVERT: Q 7 LYS cc_start: 0.8186 (ptpt) cc_final: 0.7970 (ptpt) REVERT: S 16 ARG cc_start: 0.7156 (OUTLIER) cc_final: 0.6291 (mtt180) REVERT: V 17 GLU cc_start: 0.7406 (OUTLIER) cc_final: 0.7076 (tm-30) REVERT: W 7 LYS cc_start: 0.8413 (OUTLIER) cc_final: 0.7672 (tptt) REVERT: Z 26 MET cc_start: 0.6896 (mtp) cc_final: 0.6578 (mtp) REVERT: Z 28 MET cc_start: 0.6330 (tpp) cc_final: 0.5996 (tmt) REVERT: 2 8 THR cc_start: 0.5418 (p) cc_final: 0.4963 (m) REVERT: 5 21 LEU cc_start: 0.8554 (tp) cc_final: 0.8339 (tp) REVERT: 6 42 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.8156 (mp) REVERT: 7 10 GLN cc_start: 0.2064 (OUTLIER) cc_final: 0.1018 (mm110) REVERT: 7 22 PHE cc_start: 0.7397 (m-10) cc_final: 0.6770 (m-80) REVERT: 9 15 ARG cc_start: 0.7294 (mmm160) cc_final: 0.6994 (mmm160) outliers start: 105 outliers final: 62 residues processed: 368 average time/residue: 1.1930 time to fit residues: 519.5992 Evaluate side-chains 368 residues out of total 2171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 296 time to evaluate : 2.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain L residue 17 ILE Chi-restraints excluded: chain L residue 55 ILE Chi-restraints excluded: chain L residue 85 LEU Chi-restraints excluded: chain L residue 206 GLN Chi-restraints excluded: chain L residue 252 CYS Chi-restraints excluded: chain M residue 55 THR Chi-restraints excluded: chain M residue 141 MET Chi-restraints excluded: chain M residue 174 VAL Chi-restraints excluded: chain M residue 181 HIS Chi-restraints excluded: chain M residue 215 PHE Chi-restraints excluded: chain M residue 242 THR Chi-restraints excluded: chain M residue 262 GLU Chi-restraints excluded: chain H residue 10 ASP Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 160 ASP Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain H residue 189 THR Chi-restraints excluded: chain H residue 237 ASP Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain F residue 12 ILE Chi-restraints excluded: chain F residue 27 ILE Chi-restraints excluded: chain F residue 41 GLU Chi-restraints excluded: chain G residue 26 MET Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain J residue 27 THR Chi-restraints excluded: chain J residue 32 ILE Chi-restraints excluded: chain K residue 31 LEU Chi-restraints excluded: chain N residue 26 MET Chi-restraints excluded: chain P residue 7 MET Chi-restraints excluded: chain P residue 11 THR Chi-restraints excluded: chain P residue 32 ILE Chi-restraints excluded: chain P residue 33 VAL Chi-restraints excluded: chain P residue 42 LEU Chi-restraints excluded: chain Q residue 8 ILE Chi-restraints excluded: chain Q residue 38 SER Chi-restraints excluded: chain R residue 35 ILE Chi-restraints excluded: chain S residue 12 ILE Chi-restraints excluded: chain S residue 13 ASP Chi-restraints excluded: chain S residue 16 ARG Chi-restraints excluded: chain S residue 27 ILE Chi-restraints excluded: chain T residue 16 LYS Chi-restraints excluded: chain U residue 8 ILE Chi-restraints excluded: chain V residue 11 THR Chi-restraints excluded: chain V residue 17 GLU Chi-restraints excluded: chain V residue 26 MET Chi-restraints excluded: chain W residue 7 LYS Chi-restraints excluded: chain W residue 12 ILE Chi-restraints excluded: chain W residue 30 LEU Chi-restraints excluded: chain X residue 11 THR Chi-restraints excluded: chain X residue 33 VAL Chi-restraints excluded: chain Y residue 5 LEU Chi-restraints excluded: chain Y residue 17 VAL Chi-restraints excluded: chain Y residue 38 SER Chi-restraints excluded: chain Y residue 40 THR Chi-restraints excluded: chain Z residue 21 ILE Chi-restraints excluded: chain 1 residue 7 LYS Chi-restraints excluded: chain 1 residue 17 THR Chi-restraints excluded: chain 2 residue 33 VAL Chi-restraints excluded: chain 3 residue 53 VAL Chi-restraints excluded: chain 3 residue 60 SER Chi-restraints excluded: chain 6 residue 33 VAL Chi-restraints excluded: chain 6 residue 38 ILE Chi-restraints excluded: chain 6 residue 42 LEU Chi-restraints excluded: chain 7 residue 10 GLN Chi-restraints excluded: chain 8 residue 13 GLN Chi-restraints excluded: chain 8 residue 25 SER Chi-restraints excluded: chain 9 residue 8 ILE Chi-restraints excluded: chain 0 residue 38 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 198 optimal weight: 10.0000 chunk 135 optimal weight: 9.9990 chunk 3 optimal weight: 30.0000 chunk 177 optimal weight: 1.9990 chunk 98 optimal weight: 10.0000 chunk 203 optimal weight: 0.0470 chunk 165 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 121 optimal weight: 6.9990 chunk 214 optimal weight: 8.9990 chunk 60 optimal weight: 10.0000 overall best weight: 3.8086 ------------------------------------------------------------------------------- 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 7 10 GLN 0 16 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.1538 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= 0.321 Angle : 0.843 24.667 37460 Z= 0.328 Chirality : 0.044 0.213 3769 Planarity : 0.005 0.057 4433 Dihedral : 18.976 179.911 6132 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.02 % Favored : 96.94 % Rotamer: Outliers : 4.98 % Allowed : 12.14 % Favored : 82.88 % 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: 1.13 (0.17), residues: 2517 helix: 1.86 (0.13), residues: 1476 sheet: -0.32 (0.82), residues: 42 loop : -0.93 (0.19), residues: 999 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 168 HIS 0.013 0.002 HIS M 181 PHE 0.038 0.002 PHE 1 26 TYR 0.016 0.002 TYR L 167 ARG 0.004 0.001 ARG C 47 *********************** 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 410 residues out of total 2171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 302 time to evaluate : 2.958 Fit side-chains REVERT: M 215 PHE cc_start: 0.9246 (OUTLIER) cc_final: 0.7819 (t80) REVERT: M 262 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7110 (tm-30) REVERT: H 190 LYS cc_start: 0.7213 (mppt) cc_final: 0.6949 (mmpt) REVERT: E 28 MET cc_start: 0.6207 (OUTLIER) cc_final: 0.5771 (mmt) REVERT: F 41 GLU cc_start: 0.7486 (OUTLIER) cc_final: 0.7016 (tm-30) REVERT: K 31 LEU cc_start: 0.8447 (OUTLIER) cc_final: 0.8192 (tp) REVERT: P 7 MET cc_start: 0.6124 (OUTLIER) cc_final: 0.4347 (mpt) REVERT: P 13 GLN cc_start: 0.6977 (tp40) cc_final: 0.6678 (pp30) REVERT: P 14 GLU cc_start: 0.6899 (tt0) cc_final: 0.6402 (mt-10) REVERT: Q 13 ASP cc_start: 0.6853 (t70) cc_final: 0.6399 (p0) REVERT: S 16 ARG cc_start: 0.7172 (OUTLIER) cc_final: 0.6316 (mtt180) REVERT: T 13 ASP cc_start: 0.6449 (OUTLIER) cc_final: 0.6106 (m-30) REVERT: Z 26 MET cc_start: 0.6899 (mtp) cc_final: 0.6616 (mtp) REVERT: Z 28 MET cc_start: 0.6322 (tpp) cc_final: 0.5968 (tmt) REVERT: 2 8 THR cc_start: 0.5500 (p) cc_final: 0.5058 (m) REVERT: 5 21 LEU cc_start: 0.8528 (tp) cc_final: 0.8314 (tp) REVERT: 6 42 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.8126 (mp) REVERT: 7 10 GLN cc_start: 0.1757 (OUTLIER) cc_final: 0.1153 (mm110) REVERT: 7 22 PHE cc_start: 0.7366 (m-10) cc_final: 0.6772 (m-80) REVERT: 8 19 HIS cc_start: 0.6541 (OUTLIER) cc_final: 0.6232 (t-90) outliers start: 108 outliers final: 66 residues processed: 364 average time/residue: 1.1486 time to fit residues: 498.4036 Evaluate side-chains 368 residues out of total 2171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 291 time to evaluate : 2.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 178 SER Chi-restraints excluded: chain L residue 55 ILE Chi-restraints excluded: chain L residue 85 LEU Chi-restraints excluded: chain L residue 113 CYS Chi-restraints excluded: chain L residue 252 CYS Chi-restraints excluded: chain M residue 55 THR Chi-restraints excluded: chain M residue 174 VAL Chi-restraints excluded: chain M residue 181 HIS Chi-restraints excluded: chain M residue 215 PHE Chi-restraints excluded: chain M residue 242 THR Chi-restraints excluded: chain M residue 262 GLU Chi-restraints excluded: chain M residue 276 VAL Chi-restraints excluded: chain H residue 10 ASP Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 160 ASP Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain H residue 189 THR Chi-restraints excluded: chain H residue 237 ASP Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain E residue 28 MET Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain F residue 12 ILE Chi-restraints excluded: chain F residue 40 THR Chi-restraints excluded: chain F residue 41 GLU Chi-restraints excluded: chain G residue 26 MET Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain J residue 27 THR Chi-restraints excluded: chain K residue 31 LEU Chi-restraints excluded: chain P residue 7 MET Chi-restraints excluded: chain P residue 11 THR Chi-restraints excluded: chain P residue 33 VAL Chi-restraints excluded: chain P residue 38 ILE Chi-restraints excluded: chain P residue 42 LEU Chi-restraints excluded: chain Q residue 8 ILE Chi-restraints excluded: chain Q residue 38 SER Chi-restraints excluded: chain R residue 35 ILE Chi-restraints excluded: chain S residue 12 ILE Chi-restraints excluded: chain S residue 13 ASP Chi-restraints excluded: chain S residue 16 ARG Chi-restraints excluded: chain T residue 13 ASP Chi-restraints excluded: chain T residue 16 LYS Chi-restraints excluded: chain T residue 26 MET Chi-restraints excluded: chain U residue 8 ILE Chi-restraints excluded: chain U residue 19 ILE Chi-restraints excluded: chain V residue 7 MET Chi-restraints excluded: chain V residue 11 THR Chi-restraints excluded: chain V residue 17 GLU Chi-restraints excluded: chain V residue 26 MET Chi-restraints excluded: chain W residue 12 ILE Chi-restraints excluded: chain W residue 30 LEU Chi-restraints excluded: chain W residue 40 THR Chi-restraints excluded: chain X residue 11 THR Chi-restraints excluded: chain X residue 28 MET Chi-restraints excluded: chain X residue 33 VAL Chi-restraints excluded: chain Y residue 5 LEU Chi-restraints excluded: chain Y residue 17 VAL Chi-restraints excluded: chain Y residue 38 SER Chi-restraints excluded: chain Y residue 40 THR Chi-restraints excluded: chain Z residue 21 ILE Chi-restraints excluded: chain 1 residue 7 LYS Chi-restraints excluded: chain 2 residue 33 VAL Chi-restraints excluded: chain 3 residue 60 SER Chi-restraints excluded: chain 4 residue 42 LEU Chi-restraints excluded: chain 5 residue 17 THR Chi-restraints excluded: chain 6 residue 38 ILE Chi-restraints excluded: chain 6 residue 42 LEU Chi-restraints excluded: chain 7 residue 8 ILE Chi-restraints excluded: chain 7 residue 10 GLN Chi-restraints excluded: chain 8 residue 13 GLN Chi-restraints excluded: chain 8 residue 19 HIS Chi-restraints excluded: chain 8 residue 25 SER Chi-restraints excluded: chain 9 residue 8 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 80 optimal weight: 0.8980 chunk 215 optimal weight: 10.0000 chunk 47 optimal weight: 1.9990 chunk 140 optimal weight: 1.9990 chunk 58 optimal weight: 9.9990 chunk 238 optimal weight: 10.0000 chunk 198 optimal weight: 0.1980 chunk 110 optimal weight: 7.9990 chunk 19 optimal weight: 5.9990 chunk 79 optimal weight: 1.9990 chunk 125 optimal weight: 5.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- 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 Z 24 GLN 5 10 GLN 7 10 GLN 0 16 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.1611 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= 0.172 Angle : 0.664 15.405 37460 Z= 0.256 Chirality : 0.038 0.177 3769 Planarity : 0.004 0.059 4433 Dihedral : 17.793 179.949 6132 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.31 % Favored : 97.66 % Rotamer: Outliers : 3.51 % Allowed : 14.17 % Favored : 82.33 % 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: 2.31 (0.14), residues: 1471 sheet: -0.00 (0.82), residues: 40 loop : -0.68 (0.19), residues: 1006 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 43 HIS 0.011 0.001 HIS L 158 PHE 0.026 0.001 PHE 1 26 TYR 0.011 0.001 TYR H 234 ARG 0.003 0.000 ARG H 48 *********************** 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 376 residues out of total 2171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 300 time to evaluate : 2.680 Fit side-chains REVERT: M 58 LEU cc_start: 0.7933 (OUTLIER) cc_final: 0.7709 (mp) REVERT: M 215 PHE cc_start: 0.9183 (OUTLIER) cc_final: 0.7526 (t80) REVERT: H 190 LYS cc_start: 0.7209 (mppt) cc_final: 0.6978 (mmpt) REVERT: F 41 GLU cc_start: 0.7433 (OUTLIER) cc_final: 0.7215 (tm-30) REVERT: K 27 VAL cc_start: 0.8548 (t) cc_final: 0.8296 (t) REVERT: N 42 LEU cc_start: 0.8098 (OUTLIER) cc_final: 0.7880 (mp) REVERT: P 13 GLN cc_start: 0.7009 (tp40) cc_final: 0.6667 (pp30) REVERT: P 14 GLU cc_start: 0.6856 (tt0) cc_final: 0.6267 (mt-10) REVERT: S 16 ARG cc_start: 0.7145 (OUTLIER) cc_final: 0.6301 (mtt180) REVERT: T 13 ASP cc_start: 0.6250 (OUTLIER) cc_final: 0.5981 (m-30) REVERT: U 10 LEU cc_start: 0.7864 (pp) cc_final: 0.7611 (pp) REVERT: Z 26 MET cc_start: 0.6772 (mtp) cc_final: 0.6462 (mtp) REVERT: Z 28 MET cc_start: 0.6149 (tpp) cc_final: 0.5878 (tmt) REVERT: 2 8 THR cc_start: 0.5556 (p) cc_final: 0.5080 (m) REVERT: 2 32 ILE cc_start: 0.8541 (mt) cc_final: 0.8248 (mp) REVERT: 7 8 ILE cc_start: 0.6854 (OUTLIER) cc_final: 0.6339 (tt) REVERT: 7 10 GLN cc_start: 0.1395 (OUTLIER) cc_final: 0.1079 (mm110) REVERT: 7 22 PHE cc_start: 0.7265 (m-10) cc_final: 0.6644 (m-80) REVERT: 8 19 HIS cc_start: 0.6527 (t70) cc_final: 0.6255 (t-90) outliers start: 76 outliers final: 42 residues processed: 342 average time/residue: 1.1647 time to fit residues: 473.2155 Evaluate side-chains 338 residues out of total 2171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 288 time to evaluate : 2.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 143 GLN Chi-restraints excluded: chain L residue 55 ILE Chi-restraints excluded: chain L residue 252 CYS Chi-restraints excluded: chain M residue 55 THR Chi-restraints excluded: chain M residue 58 LEU Chi-restraints excluded: chain M residue 141 MET Chi-restraints excluded: chain M residue 174 VAL Chi-restraints excluded: chain M residue 215 PHE Chi-restraints excluded: chain M residue 242 THR Chi-restraints excluded: chain M residue 276 VAL Chi-restraints excluded: chain M residue 298 ILE Chi-restraints excluded: chain H residue 10 ASP Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 160 ASP Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain H residue 189 THR Chi-restraints excluded: chain H residue 237 ASP Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain F residue 41 GLU Chi-restraints excluded: chain J residue 27 THR Chi-restraints excluded: chain N residue 42 LEU Chi-restraints excluded: chain P residue 11 THR Chi-restraints excluded: chain P residue 38 ILE Chi-restraints excluded: chain R residue 35 ILE Chi-restraints excluded: chain S residue 12 ILE Chi-restraints excluded: chain S residue 13 ASP Chi-restraints excluded: chain S residue 16 ARG Chi-restraints excluded: chain T residue 13 ASP Chi-restraints excluded: chain V residue 7 MET Chi-restraints excluded: chain V residue 11 THR Chi-restraints excluded: chain W residue 30 LEU Chi-restraints excluded: chain W residue 40 THR Chi-restraints excluded: chain X residue 11 THR Chi-restraints excluded: chain X residue 33 VAL Chi-restraints excluded: chain Y residue 5 LEU Chi-restraints excluded: chain Y residue 38 SER Chi-restraints excluded: chain Y residue 40 THR Chi-restraints excluded: chain Y residue 58 THR Chi-restraints excluded: chain Z residue 21 ILE Chi-restraints excluded: chain 1 residue 7 LYS Chi-restraints excluded: chain 2 residue 33 VAL Chi-restraints excluded: chain 3 residue 60 SER Chi-restraints excluded: chain 5 residue 17 THR Chi-restraints excluded: chain 6 residue 33 VAL Chi-restraints excluded: chain 6 residue 38 ILE Chi-restraints excluded: chain 7 residue 8 ILE Chi-restraints excluded: chain 7 residue 10 GLN Chi-restraints excluded: chain 8 residue 13 GLN Chi-restraints excluded: chain 8 residue 21 ILE Chi-restraints excluded: chain 8 residue 25 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 230 optimal weight: 6.9990 chunk 26 optimal weight: 1.9990 chunk 136 optimal weight: 10.0000 chunk 174 optimal weight: 5.9990 chunk 135 optimal weight: 4.9990 chunk 201 optimal weight: 5.9990 chunk 133 optimal weight: 9.9990 chunk 238 optimal weight: 9.9990 chunk 148 optimal weight: 6.9990 chunk 145 optimal weight: 4.9990 chunk 109 optimal weight: 0.9980 overall best weight: 3.7988 ------------------------------------------------------------------------------- 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 7 10 GLN 0 16 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 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 : 0.005 0.054 27271 Z= 0.327 Angle : 0.841 18.304 37460 Z= 0.328 Chirality : 0.044 0.177 3769 Planarity : 0.005 0.058 4433 Dihedral : 18.644 179.934 6132 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.38 % Favored : 96.58 % Rotamer: Outliers : 4.98 % Allowed : 13.38 % Favored : 81.63 % 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: 1.96 (0.13), residues: 1477 sheet: -0.03 (0.84), residues: 40 loop : -0.84 (0.19), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 168 HIS 0.013 0.002 HIS L 158 PHE 0.040 0.002 PHE 1 26 TYR 0.017 0.002 TYR C 259 ARG 0.005 0.001 ARG L 12 *********************** 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 406 residues out of total 2171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 298 time to evaluate : 2.499 Fit side-chains REVERT: M 215 PHE cc_start: 0.9229 (OUTLIER) cc_final: 0.7925 (t80) REVERT: M 262 GLU cc_start: 0.8210 (OUTLIER) cc_final: 0.7079 (tm-30) REVERT: H 124 ASP cc_start: 0.7281 (t0) cc_final: 0.6922 (t70) REVERT: H 190 LYS cc_start: 0.7224 (mppt) cc_final: 0.6963 (mmpt) REVERT: F 41 GLU cc_start: 0.7479 (OUTLIER) cc_final: 0.6939 (tm-30) REVERT: P 7 MET cc_start: 0.6125 (OUTLIER) cc_final: 0.4352 (mpt) REVERT: P 13 GLN cc_start: 0.6960 (tp40) cc_final: 0.6639 (pp30) REVERT: P 14 GLU cc_start: 0.6919 (tt0) cc_final: 0.6389 (mt-10) REVERT: S 16 ARG cc_start: 0.7199 (OUTLIER) cc_final: 0.6339 (mtt180) REVERT: T 13 ASP cc_start: 0.6441 (OUTLIER) cc_final: 0.6098 (m-30) REVERT: Y 49 ILE cc_start: 0.8413 (OUTLIER) cc_final: 0.8181 (mm) REVERT: Z 26 MET cc_start: 0.6851 (mtp) cc_final: 0.6575 (mtp) REVERT: Z 28 MET cc_start: 0.6293 (tpp) cc_final: 0.5947 (tmt) REVERT: 2 8 THR cc_start: 0.5541 (p) cc_final: 0.5082 (m) REVERT: 7 10 GLN cc_start: 0.1679 (OUTLIER) cc_final: 0.0807 (mm110) REVERT: 7 22 PHE cc_start: 0.7372 (m-10) cc_final: 0.6748 (m-80) REVERT: 8 19 HIS cc_start: 0.6442 (OUTLIER) cc_final: 0.6157 (t-90) outliers start: 108 outliers final: 61 residues processed: 358 average time/residue: 1.1372 time to fit residues: 485.9983 Evaluate side-chains 360 residues out of total 2171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 290 time to evaluate : 2.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 143 GLN Chi-restraints excluded: chain L residue 17 ILE Chi-restraints excluded: chain L residue 55 ILE Chi-restraints excluded: chain L residue 252 CYS Chi-restraints excluded: chain M residue 55 THR Chi-restraints excluded: chain M residue 174 VAL Chi-restraints excluded: chain M residue 181 HIS Chi-restraints excluded: chain M residue 215 PHE Chi-restraints excluded: chain M residue 242 THR Chi-restraints excluded: chain M residue 262 GLU Chi-restraints excluded: chain M residue 276 VAL Chi-restraints excluded: chain M residue 309 VAL Chi-restraints excluded: chain H residue 10 ASP Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 160 ASP Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain H residue 189 THR Chi-restraints excluded: chain H residue 237 ASP Chi-restraints excluded: chain B residue 11 THR Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain F residue 12 ILE Chi-restraints excluded: chain F residue 41 GLU Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain J residue 27 THR Chi-restraints excluded: chain J residue 35 ILE Chi-restraints excluded: chain N residue 38 ILE Chi-restraints excluded: chain P residue 7 MET Chi-restraints excluded: chain P residue 11 THR Chi-restraints excluded: chain P residue 33 VAL Chi-restraints excluded: chain P residue 38 ILE Chi-restraints excluded: chain P residue 42 LEU Chi-restraints excluded: chain Q residue 8 ILE Chi-restraints excluded: chain Q residue 38 SER Chi-restraints excluded: chain R residue 35 ILE Chi-restraints excluded: chain S residue 12 ILE Chi-restraints excluded: chain S residue 13 ASP Chi-restraints excluded: chain S residue 16 ARG Chi-restraints excluded: chain T residue 13 ASP Chi-restraints excluded: chain T residue 16 LYS Chi-restraints excluded: chain U residue 8 ILE Chi-restraints excluded: chain V residue 7 MET Chi-restraints excluded: chain V residue 11 THR Chi-restraints excluded: chain W residue 12 ILE Chi-restraints excluded: chain W residue 30 LEU Chi-restraints excluded: chain X residue 11 THR Chi-restraints excluded: chain X residue 28 MET Chi-restraints excluded: chain X residue 33 VAL Chi-restraints excluded: chain Y residue 5 LEU Chi-restraints excluded: chain Y residue 38 SER Chi-restraints excluded: chain Y residue 40 THR Chi-restraints excluded: chain Y residue 49 ILE Chi-restraints excluded: chain Z residue 21 ILE Chi-restraints excluded: chain 1 residue 7 LYS Chi-restraints excluded: chain 2 residue 33 VAL Chi-restraints excluded: chain 3 residue 53 VAL Chi-restraints excluded: chain 3 residue 60 SER Chi-restraints excluded: chain 5 residue 17 THR Chi-restraints excluded: chain 6 residue 33 VAL Chi-restraints excluded: chain 6 residue 38 ILE Chi-restraints excluded: chain 7 residue 8 ILE Chi-restraints excluded: chain 7 residue 10 GLN Chi-restraints excluded: chain 8 residue 13 GLN Chi-restraints excluded: chain 8 residue 19 HIS Chi-restraints excluded: chain 8 residue 21 ILE Chi-restraints excluded: chain 8 residue 25 SER Chi-restraints excluded: chain 9 residue 8 ILE Chi-restraints excluded: chain 0 residue 38 ILE 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: 8.9990 chunk 142 optimal weight: 0.6980 chunk 71 optimal weight: 0.7980 chunk 46 optimal weight: 3.9990 chunk 151 optimal weight: 4.9990 chunk 162 optimal weight: 0.9980 chunk 117 optimal weight: 4.9990 chunk 22 optimal weight: 0.7980 chunk 187 optimal weight: 9.9990 chunk 216 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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: 0.8203 moved from start: 0.1754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 27271 Z= 0.150 Angle : 0.645 14.940 37460 Z= 0.248 Chirality : 0.037 0.154 3769 Planarity : 0.004 0.059 4433 Dihedral : 17.421 179.994 6132 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 3.05 % Allowed : 15.09 % Favored : 81.86 % 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: 1.80 (0.17), residues: 2517 helix: 2.39 (0.14), residues: 1469 sheet: 0.05 (0.83), residues: 40 loop : -0.60 (0.20), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP U 9 HIS 0.011 0.001 HIS L 158 PHE 0.026 0.001 PHE 1 26 TYR 0.010 0.001 TYR C 202 ARG 0.003 0.000 ARG H 48 *********************** 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 361 residues out of total 2171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 295 time to evaluate : 2.624 Fit side-chains REVERT: L 206 GLN cc_start: 0.8222 (OUTLIER) cc_final: 0.7383 (mp-120) REVERT: M 58 LEU cc_start: 0.8004 (OUTLIER) cc_final: 0.7761 (mp) REVERT: M 215 PHE cc_start: 0.9168 (OUTLIER) cc_final: 0.7711 (t80) REVERT: M 262 GLU cc_start: 0.8129 (OUTLIER) cc_final: 0.6993 (tm-30) REVERT: H 124 ASP cc_start: 0.7303 (t0) cc_final: 0.6973 (t70) REVERT: H 190 LYS cc_start: 0.7218 (mppt) cc_final: 0.6993 (mmpt) REVERT: F 41 GLU cc_start: 0.7405 (OUTLIER) cc_final: 0.7134 (tm-30) REVERT: K 27 VAL cc_start: 0.8521 (t) cc_final: 0.8268 (t) REVERT: P 13 GLN cc_start: 0.6982 (tp40) cc_final: 0.6674 (pp30) REVERT: P 14 GLU cc_start: 0.6842 (tt0) cc_final: 0.6286 (mt-10) REVERT: S 16 ARG cc_start: 0.7183 (OUTLIER) cc_final: 0.6331 (mtt180) REVERT: T 13 ASP cc_start: 0.6205 (OUTLIER) cc_final: 0.5931 (m-30) REVERT: U 10 LEU cc_start: 0.7874 (pp) cc_final: 0.7632 (pp) REVERT: Z 28 MET cc_start: 0.6114 (tpp) cc_final: 0.5861 (tmt) REVERT: 2 8 THR cc_start: 0.5573 (p) cc_final: 0.5096 (m) REVERT: 2 32 ILE cc_start: 0.8533 (mt) cc_final: 0.8249 (mp) REVERT: 7 22 PHE cc_start: 0.7219 (m-10) cc_final: 0.6592 (m-80) outliers start: 66 outliers final: 40 residues processed: 338 average time/residue: 1.1743 time to fit residues: 471.4615 Evaluate side-chains 328 residues out of total 2171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 281 time to evaluate : 2.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 143 GLN Chi-restraints excluded: chain L residue 55 ILE Chi-restraints excluded: chain L residue 85 LEU Chi-restraints excluded: chain L residue 206 GLN Chi-restraints excluded: chain L residue 252 CYS Chi-restraints excluded: chain M residue 55 THR Chi-restraints excluded: chain M residue 58 LEU Chi-restraints excluded: chain M residue 174 VAL Chi-restraints excluded: chain M residue 215 PHE Chi-restraints excluded: chain M residue 242 THR Chi-restraints excluded: chain M residue 262 GLU Chi-restraints excluded: chain M residue 276 VAL Chi-restraints excluded: chain M residue 298 ILE Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 160 ASP Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain H residue 189 THR Chi-restraints excluded: chain H residue 237 ASP Chi-restraints excluded: chain B residue 11 THR Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain F residue 41 GLU Chi-restraints excluded: chain J residue 27 THR Chi-restraints excluded: chain P residue 11 THR Chi-restraints excluded: chain Q residue 38 SER Chi-restraints excluded: chain R residue 35 ILE Chi-restraints excluded: chain S residue 13 ASP Chi-restraints excluded: chain S residue 16 ARG Chi-restraints excluded: chain T residue 13 ASP Chi-restraints excluded: chain V residue 7 MET Chi-restraints excluded: chain W residue 30 LEU Chi-restraints excluded: chain W residue 40 THR Chi-restraints excluded: chain X residue 11 THR Chi-restraints excluded: chain X residue 33 VAL Chi-restraints excluded: chain Y residue 5 LEU Chi-restraints excluded: chain Y residue 38 SER Chi-restraints excluded: chain Y residue 40 THR Chi-restraints excluded: chain Y residue 58 THR Chi-restraints excluded: chain Z residue 21 ILE Chi-restraints excluded: chain 1 residue 7 LYS Chi-restraints excluded: chain 2 residue 33 VAL Chi-restraints excluded: chain 3 residue 60 SER Chi-restraints excluded: chain 5 residue 17 THR Chi-restraints excluded: chain 6 residue 33 VAL Chi-restraints excluded: chain 6 residue 38 ILE Chi-restraints excluded: chain 8 residue 21 ILE Chi-restraints excluded: chain 8 residue 25 SER Chi-restraints excluded: chain 8 residue 32 ILE 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: 5.9990 chunk 221 optimal weight: 20.0000 chunk 133 optimal weight: 9.9990 chunk 96 optimal weight: 2.9990 chunk 174 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 200 optimal weight: 10.0000 chunk 209 optimal weight: 3.9990 chunk 145 optimal weight: 2.9990 chunk 234 optimal weight: 7.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- 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 2 13 GLN 5 10 GLN 0 16 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 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 : 0.004 0.045 27271 Z= 0.241 Angle : 0.751 17.341 37460 Z= 0.290 Chirality : 0.040 0.155 3769 Planarity : 0.005 0.058 4433 Dihedral : 17.805 179.892 6132 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 3.37 % Allowed : 15.18 % Favored : 81.45 % 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: 1.58 (0.17), residues: 2517 helix: 2.22 (0.13), residues: 1473 sheet: 0.01 (0.83), residues: 40 loop : -0.73 (0.20), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP U 9 HIS 0.016 0.002 HIS M 181 PHE 0.034 0.002 PHE 1 26 TYR 0.015 0.002 TYR L 167 ARG 0.005 0.000 ARG L 12 *********************** 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 363 residues out of total 2171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 290 time to evaluate : 2.767 Fit side-chains REVERT: M 215 PHE cc_start: 0.9212 (OUTLIER) cc_final: 0.7738 (t80) REVERT: H 124 ASP cc_start: 0.7258 (t0) cc_final: 0.6928 (t70) REVERT: H 190 LYS cc_start: 0.7226 (mppt) cc_final: 0.6996 (mmpt) REVERT: A 21 LEU cc_start: 0.8338 (tt) cc_final: 0.8131 (tm) REVERT: F 41 GLU cc_start: 0.7434 (OUTLIER) cc_final: 0.7183 (tm-30) REVERT: N 42 LEU cc_start: 0.8153 (OUTLIER) cc_final: 0.7917 (mp) REVERT: P 13 GLN cc_start: 0.6964 (tp40) cc_final: 0.6627 (pp30) REVERT: P 14 GLU cc_start: 0.6929 (tt0) cc_final: 0.6430 (mt-10) REVERT: S 16 ARG cc_start: 0.7227 (OUTLIER) cc_final: 0.6385 (mtt180) REVERT: T 13 ASP cc_start: 0.6300 (OUTLIER) cc_final: 0.6027 (m-30) REVERT: Z 28 MET cc_start: 0.6183 (tpp) cc_final: 0.5882 (tmt) REVERT: 2 8 THR cc_start: 0.5574 (p) cc_final: 0.5094 (m) REVERT: 7 22 PHE cc_start: 0.7288 (m-10) cc_final: 0.6672 (m-80) outliers start: 73 outliers final: 50 residues processed: 335 average time/residue: 1.1352 time to fit residues: 453.1010 Evaluate side-chains 342 residues out of total 2171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 287 time to evaluate : 2.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 143 GLN Chi-restraints excluded: chain L residue 55 ILE Chi-restraints excluded: chain L residue 85 LEU Chi-restraints excluded: chain L residue 252 CYS Chi-restraints excluded: chain M residue 55 THR Chi-restraints excluded: chain M residue 174 VAL Chi-restraints excluded: chain M residue 215 PHE Chi-restraints excluded: chain M residue 242 THR Chi-restraints excluded: chain M residue 276 VAL Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 160 ASP Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain H residue 189 THR Chi-restraints excluded: chain H residue 237 ASP Chi-restraints excluded: chain B residue 11 THR Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain F residue 12 ILE Chi-restraints excluded: chain F residue 41 GLU Chi-restraints excluded: chain J residue 27 THR Chi-restraints excluded: chain J residue 35 ILE Chi-restraints excluded: chain N residue 38 ILE Chi-restraints excluded: chain N residue 42 LEU Chi-restraints excluded: chain P residue 11 THR Chi-restraints excluded: chain P residue 33 VAL Chi-restraints excluded: chain P residue 38 ILE Chi-restraints excluded: chain Q residue 38 SER Chi-restraints excluded: chain R residue 35 ILE Chi-restraints excluded: chain S residue 12 ILE Chi-restraints excluded: chain S residue 13 ASP Chi-restraints excluded: chain S residue 16 ARG Chi-restraints excluded: chain T residue 13 ASP Chi-restraints excluded: chain V residue 7 MET Chi-restraints excluded: chain V residue 11 THR Chi-restraints excluded: chain W residue 30 LEU Chi-restraints excluded: chain W residue 40 THR Chi-restraints excluded: chain X residue 11 THR Chi-restraints excluded: chain X residue 28 MET Chi-restraints excluded: chain X residue 33 VAL Chi-restraints excluded: chain Y residue 5 LEU Chi-restraints excluded: chain Y residue 17 VAL Chi-restraints excluded: chain Y residue 38 SER Chi-restraints excluded: chain Y residue 40 THR Chi-restraints excluded: chain Y residue 58 THR Chi-restraints excluded: chain Z residue 21 ILE Chi-restraints excluded: chain 1 residue 7 LYS Chi-restraints excluded: chain 1 residue 11 ILE Chi-restraints excluded: chain 2 residue 33 VAL Chi-restraints excluded: chain 3 residue 53 VAL Chi-restraints excluded: chain 3 residue 60 SER Chi-restraints excluded: chain 4 residue 42 LEU Chi-restraints excluded: chain 5 residue 17 THR Chi-restraints excluded: chain 6 residue 33 VAL Chi-restraints excluded: chain 6 residue 38 ILE Chi-restraints excluded: chain 8 residue 21 ILE Chi-restraints excluded: chain 8 residue 25 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 143 optimal weight: 20.0000 chunk 111 optimal weight: 10.0000 chunk 163 optimal weight: 7.9990 chunk 246 optimal weight: 10.0000 chunk 226 optimal weight: 2.9990 chunk 195 optimal weight: 10.0000 chunk 20 optimal weight: 0.9980 chunk 151 optimal weight: 4.9990 chunk 120 optimal weight: 10.0000 chunk 155 optimal weight: 8.9990 chunk 208 optimal weight: 4.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- 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 2 13 GLN 5 10 GLN 0 16 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 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 : 0.006 0.060 27271 Z= 0.365 Angle : 0.882 19.321 37460 Z= 0.346 Chirality : 0.046 0.172 3769 Planarity : 0.005 0.059 4433 Dihedral : 18.725 179.976 6132 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 3.51 % Allowed : 14.95 % Favored : 81.54 % 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: 1.13 (0.17), residues: 2517 helix: 1.83 (0.13), residues: 1477 sheet: -0.16 (0.82), residues: 40 loop : -0.89 (0.19), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 168 HIS 0.019 0.002 HIS M 181 PHE 0.046 0.002 PHE 1 26 TYR 0.018 0.002 TYR C 259 ARG 0.006 0.001 ARG L 12 ********************** 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 373 residues out of total 2171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 297 time to evaluate : 2.480 Fit side-chains REVERT: L 206 GLN cc_start: 0.8231 (OUTLIER) cc_final: 0.7413 (mp-120) REVERT: M 215 PHE cc_start: 0.9254 (OUTLIER) cc_final: 0.7960 (t80) REVERT: M 262 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7039 (tm-30) REVERT: H 124 ASP cc_start: 0.7245 (t0) cc_final: 0.6872 (t70) REVERT: H 190 LYS cc_start: 0.7232 (mppt) cc_final: 0.6970 (mmpt) REVERT: F 41 GLU cc_start: 0.7470 (OUTLIER) cc_final: 0.6846 (tm-30) REVERT: P 7 MET cc_start: 0.6050 (OUTLIER) cc_final: 0.4278 (mpt) REVERT: P 13 GLN cc_start: 0.6957 (tp40) cc_final: 0.6611 (pp30) REVERT: P 14 GLU cc_start: 0.6974 (tt0) cc_final: 0.6442 (mt-10) REVERT: Q 7 LYS cc_start: 0.8176 (ptpt) cc_final: 0.7935 (ptpt) REVERT: S 16 ARG cc_start: 0.7181 (OUTLIER) cc_final: 0.6326 (mtt180) REVERT: T 13 ASP cc_start: 0.6477 (OUTLIER) cc_final: 0.6134 (m-30) REVERT: Z 28 MET cc_start: 0.6283 (tpp) cc_final: 0.5938 (tmt) REVERT: 2 8 THR cc_start: 0.5521 (p) cc_final: 0.5072 (m) REVERT: 7 22 PHE cc_start: 0.7393 (m-10) cc_final: 0.6751 (m-80) REVERT: 8 19 HIS cc_start: 0.6387 (t70) cc_final: 0.6138 (t-90) outliers start: 76 outliers final: 53 residues processed: 343 average time/residue: 1.1640 time to fit residues: 472.8843 Evaluate side-chains 350 residues out of total 2171 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 290 time to evaluate : 2.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 175 ASN Chi-restraints excluded: chain L residue 55 ILE Chi-restraints excluded: chain L residue 85 LEU Chi-restraints excluded: chain L residue 206 GLN Chi-restraints excluded: chain L residue 252 CYS Chi-restraints excluded: chain M residue 55 THR Chi-restraints excluded: chain M residue 174 VAL Chi-restraints excluded: chain M residue 215 PHE Chi-restraints excluded: chain M residue 242 THR Chi-restraints excluded: chain M residue 262 GLU Chi-restraints excluded: chain M residue 276 VAL Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 160 ASP Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain H residue 189 THR Chi-restraints excluded: chain H residue 237 ASP Chi-restraints excluded: chain B residue 11 THR Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain F residue 12 ILE Chi-restraints excluded: chain F residue 41 GLU Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain J residue 27 THR Chi-restraints excluded: chain J residue 35 ILE Chi-restraints excluded: chain P residue 7 MET Chi-restraints excluded: chain P residue 11 THR Chi-restraints excluded: chain P residue 33 VAL Chi-restraints excluded: chain P residue 38 ILE Chi-restraints excluded: chain Q residue 8 ILE Chi-restraints excluded: chain Q residue 38 SER Chi-restraints excluded: chain R residue 35 ILE Chi-restraints excluded: chain S residue 12 ILE Chi-restraints excluded: chain S residue 13 ASP Chi-restraints excluded: chain S residue 16 ARG Chi-restraints excluded: chain T residue 13 ASP Chi-restraints excluded: chain U residue 19 ILE Chi-restraints excluded: chain V residue 7 MET Chi-restraints excluded: chain V residue 11 THR Chi-restraints excluded: chain V residue 17 GLU Chi-restraints excluded: chain W residue 30 LEU Chi-restraints excluded: chain X residue 11 THR Chi-restraints excluded: chain X residue 28 MET Chi-restraints excluded: chain X residue 33 VAL Chi-restraints excluded: chain Y residue 5 LEU Chi-restraints excluded: chain Y residue 17 VAL Chi-restraints excluded: chain Y residue 38 SER Chi-restraints excluded: chain Y residue 40 THR Chi-restraints excluded: chain Z residue 21 ILE Chi-restraints excluded: chain 1 residue 7 LYS Chi-restraints excluded: chain 2 residue 33 VAL Chi-restraints excluded: chain 3 residue 53 VAL Chi-restraints excluded: chain 3 residue 60 SER Chi-restraints excluded: chain 5 residue 17 THR Chi-restraints excluded: chain 6 residue 33 VAL Chi-restraints excluded: chain 6 residue 38 ILE Chi-restraints excluded: chain 8 residue 21 ILE Chi-restraints excluded: chain 8 residue 25 SER Chi-restraints excluded: chain 0 residue 38 ILE 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: 9.9990 chunk 28 optimal weight: 3.9990 chunk 54 optimal weight: 7.9990 chunk 196 optimal weight: 4.9990 chunk 82 optimal weight: 8.9990 chunk 201 optimal weight: 3.9990 chunk 24 optimal weight: 6.9990 chunk 36 optimal weight: 5.9990 chunk 172 optimal weight: 7.9990 chunk 11 optimal weight: 1.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.130861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.103142 restraints weight = 33955.275| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 1.30 r_work: 0.2912 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2788 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2771 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2771 r_free = 0.2771 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2771 r_free = 0.2771 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2771 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.1735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.179 27271 Z= 0.372 Angle : 0.987 59.181 37460 Z= 0.435 Chirality : 0.046 0.546 3769 Planarity : 0.005 0.059 4433 Dihedral : 18.726 179.970 6132 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 3.51 % Allowed : 14.95 % Favored : 81.54 % Cbeta Deviations : 0.04 % 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: 1.07 (0.17), residues: 2517 helix: 1.80 (0.13), residues: 1481 sheet: -0.17 (0.82), residues: 40 loop : -0.94 (0.19), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 168 HIS 0.018 0.002 HIS M 181 PHE 0.045 0.002 PHE 1 26 TYR 0.018 0.002 TYR C 259 ARG 0.007 0.001 ARG L 12 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8659.52 seconds wall clock time: 160 minutes 52.80 seconds (9652.80 seconds total)