Starting phenix.real_space_refine (version: 1.21rc1) on Tue May 9 12:53:13 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7voy_32062/05_2023/7voy_32062_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7voy_32062/05_2023/7voy_32062.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7voy_32062/05_2023/7voy_32062.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7voy_32062/05_2023/7voy_32062.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7voy_32062/05_2023/7voy_32062_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7voy_32062/05_2023/7voy_32062_updated.pdb" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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: 6 Type Number sf(0) Gaussians Fe 1 7.16 5 Mg 38 5.21 5 S 96 5.16 5 C 15044 2.51 5 N 3398 2.21 5 O 3542 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 45": "OE1" <-> "OE2" Residue "A ARG 53": "NH1" <-> "NH2" Residue "B ARG 46": "NH1" <-> "NH2" Residue "D PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 53": "NH1" <-> "NH2" Residue "E ARG 46": "NH1" <-> "NH2" Residue "F ARG 14": "NH1" <-> "NH2" Residue "F PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 53": "NH1" <-> "NH2" Residue "G ARG 46": "NH1" <-> "NH2" Residue "I TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 15": "NH1" <-> "NH2" Residue "I TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 53": "NH1" <-> "NH2" Residue "J ARG 46": "NH1" <-> "NH2" Residue "K PHE 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 14": "NH1" <-> "NH2" Residue "K TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 53": "NH1" <-> "NH2" Residue "N ARG 46": "NH1" <-> "NH2" Residue "O TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 12": "OD1" <-> "OD2" Residue "O TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 53": "NH1" <-> "NH2" Residue "P TYR 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 46": "NH1" <-> "NH2" Residue "Q PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 45": "OE1" <-> "OE2" Residue "Q ARG 53": "NH1" <-> "NH2" Residue "R TYR 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 46": "NH1" <-> "NH2" Residue "S TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 15": "NH1" <-> "NH2" Residue "S GLU 45": "OE1" <-> "OE2" Residue "S ARG 53": "NH1" <-> "NH2" Residue "T ARG 46": "NH1" <-> "NH2" Residue "U TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 15": "NH1" <-> "NH2" Residue "U PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 53": "NH1" <-> "NH2" Residue "V ARG 46": "NH1" <-> "NH2" Residue "W TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 15": "NH1" <-> "NH2" Residue "W PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 46": "NH1" <-> "NH2" Residue "Y ARG 15": "NH1" <-> "NH2" Residue "Y PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 45": "OE1" <-> "OE2" Residue "Y TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 53": "NH1" <-> "NH2" Residue "Z ARG 46": "NH1" <-> "NH2" Residue "1 PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 GLU 45": "OE1" <-> "OE2" Residue "1 ARG 53": "NH1" <-> "NH2" Residue "2 ARG 46": "NH1" <-> "NH2" Residue "7 ASP 12": "OD1" <-> "OD2" Residue "7 PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 TYR 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 ARG 46": "NH1" <-> "NH2" Residue "9 PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 ARG 14": "NH1" <-> "NH2" Residue "9 TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 GLU 45": "OE1" <-> "OE2" Residue "9 ARG 53": "NH1" <-> "NH2" Residue "0 ARG 46": "NH1" <-> "NH2" Residue "4 TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ARG 53": "NH1" <-> "NH2" Residue "t TYR 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t ARG 46": "NH1" <-> "NH2" Residue "6 TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ARG 53": "NH1" <-> "NH2" Residue "5 TYR 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ARG 46": "NH1" <-> "NH2" Residue "C TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 53": "NH1" <-> "NH2" Residue "3 ARG 46": "NH1" <-> "NH2" Residue "L TYR 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 109": "NH1" <-> "NH2" Residue "L TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 217": "NH1" <-> "NH2" Residue "L ARG 231": "NH1" <-> "NH2" Residue "M PHE 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 17": "OD1" <-> "OD2" Residue "M ARG 87": "NH1" <-> "NH2" Residue "M PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 136": "NH1" <-> "NH2" Residue "M GLU 173": "OE1" <-> "OE2" Residue "M ASP 240": "OD1" <-> "OD2" Residue "M ARG 253": "NH1" <-> "NH2" Residue "M GLU 263": "OE1" <-> "OE2" Residue "H PHE 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 43": "OE1" <-> "OE2" Residue "H PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 89": "NH1" <-> "NH2" Residue "H PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 118": "NH1" <-> "NH2" Residue "H GLU 122": "OE1" <-> "OE2" Residue "H GLU 173": "OE1" <-> "OE2" Residue "H ARG 177": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/chem_data/mon_lib" Total number of atoms: 22119 Number of models: 1 Model: "" Number of chains: 71 Chain: "A" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "B" Number of atoms: 365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 365 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 1, 'TRANS': 43} Chain: "D" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "E" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "F" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "G" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "I" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "J" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "K" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "N" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "O" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "P" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "Q" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "R" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "S" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "T" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "U" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "V" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "W" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "X" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "Y" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "Z" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 343 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "1" Number of atoms: 447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 447 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "2" Number of atoms: 327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 327 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "7" Number of atoms: 392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 392 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 2, 'TRANS': 43} Chain: "8" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 359 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "9" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "0" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 359 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "4" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "t" Number of atoms: 365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 365 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 1, 'TRANS': 43} Chain: "6" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "5" Number of atoms: 365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 365 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 1, 'TRANS': 43} Chain: "C" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "3" Number of atoms: 365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 365 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 1, 'TRANS': 43} Chain: "L" Number of atoms: 2232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2232 Classifications: {'peptide': 281} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 266} Chain: "M" Number of atoms: 2431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2431 Classifications: {'peptide': 305} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 292} Chain: "H" Number of atoms: 1875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1875 Classifications: {'peptide': 247} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 223} Chain: "A" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'BCL:plan_0002': 1} Unresolved non-hydrogen planarities: 6 Chain: "B" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'BCL:plan_0002': 1} Unresolved non-hydrogen planarities: 6 Chain: "E" Number of atoms: 92 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 92 Unusual residues: {'BCL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'BCL:plan_0002': 2} Unresolved non-hydrogen planarities: 12 Chain: "F" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'BCL:plan_0002': 1} Unresolved non-hydrogen planarities: 6 Chain: "G" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'BCL:plan_0002': 1} Unresolved non-hydrogen planarities: 6 Chain: "I" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'BCL:plan_0002': 1} Unresolved non-hydrogen planarities: 6 Chain: "J" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'BCL:plan_0002': 1} Unresolved non-hydrogen planarities: 6 Chain: "K" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'BCL:plan_0002': 1} Unresolved non-hydrogen planarities: 6 Chain: "N" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'BCL:plan_0002': 1} Unresolved non-hydrogen planarities: 6 Chain: "O" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'BCL:plan_0002': 1} Unresolved non-hydrogen planarities: 6 Chain: "P" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'BCL:plan_0002': 1} Unresolved non-hydrogen planarities: 6 Chain: "Q" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'BCL:plan_0002': 1} Unresolved non-hydrogen planarities: 6 Chain: "R" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'BCL:plan_0002': 1} Unresolved non-hydrogen planarities: 6 Chain: "S" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'BCL:plan_0002': 1} Unresolved non-hydrogen planarities: 6 Chain: "T" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'BCL:plan_0002': 1} Unresolved non-hydrogen planarities: 6 Chain: "U" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'BCL:plan_0002': 1} Unresolved non-hydrogen planarities: 6 Chain: "V" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'BCL:plan_0002': 1} Unresolved non-hydrogen planarities: 6 Chain: "W" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'BCL:plan_0002': 1} Unresolved non-hydrogen planarities: 6 Chain: "X" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'BCL:plan_0002': 1} Unresolved non-hydrogen planarities: 6 Chain: "Y" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'BCL:plan_0002': 1} Unresolved non-hydrogen planarities: 6 Chain: "Z" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'BCL:plan_0002': 1} Unresolved non-hydrogen planarities: 6 Chain: "1" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'BCL:plan_0002': 1} Unresolved non-hydrogen planarities: 6 Chain: "2" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'BCL:plan_0002': 1} Unresolved non-hydrogen planarities: 6 Chain: "7" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'BCL:plan_0002': 1} Unresolved non-hydrogen planarities: 6 Chain: "8" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'BCL:plan_0002': 1} Unresolved non-hydrogen planarities: 6 Chain: "9" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'BCL:plan_0002': 1} Unresolved non-hydrogen planarities: 6 Chain: "0" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'BCL:plan_0002': 1} Unresolved non-hydrogen planarities: 6 Chain: "4" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'BCL:plan_0002': 1} Unresolved non-hydrogen planarities: 6 Chain: "t" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'BCL:plan_0002': 1} Unresolved non-hydrogen planarities: 6 Chain: "5" Number of atoms: 92 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 92 Unusual residues: {'BCL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'BCL:plan_0002': 2} Unresolved non-hydrogen planarities: 12 Chain: "C" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'BCL:plan_0002': 1} Unresolved non-hydrogen planarities: 6 Chain: "3" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'BCL:plan_0002': 1} Unresolved non-hydrogen planarities: 6 Chain: "L" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 105 Unusual residues: {'BCL': 1, 'BPH': 1, 'U10': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 107 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'BCL:plan_0002': 1, 'BPH:plan-1': 1, 'U10:plan-8': 1, 'U10:plan-9': 1, 'U10:plan-11': 1, 'U10:plan-4': 1, 'U10:plan-5': 1, 'U10:plan-6': 1, 'U10:plan-7': 1, 'U10:plan-10': 1, 'U10:plan-2': 1, 'U10:plan-3': 1} Unresolved non-hydrogen planarities: 51 Chain: "M" Number of atoms: 241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 241 Unusual residues: {'BCL': 3, 'BPH': 1, 'FE2': 1, 'SPN': 1, 'U10': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 129 Unresolved non-hydrogen angles: 155 Unresolved non-hydrogen dihedrals: 98 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'BCL:plan_0002': 3, 'BPH:plan-1': 1, 'U10:plan-8': 1, 'U10:plan-9': 1, 'U10:plan-11': 1, 'U10:plan-4': 1, 'U10:plan-5': 1, 'U10:plan-6': 1, 'U10:plan-7': 1, 'U10:plan-10': 1, 'U10:plan-2': 1, 'U10:plan-3': 1} Unresolved non-hydrogen planarities: 63 Time building chain proxies: 11.72, per 1000 atoms: 0.53 Number of scatterers: 22119 At special positions: 0 Unit cell: (139.92, 137.8, 119.78, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 1 26.01 S 96 16.00 Mg 38 11.99 O 3542 8.00 N 3398 7.00 C 15044 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=30, symmetry=0 Number of additional bonds: simple=30, symmetry=0 Coordination: Other bonds: Time building additional restraints: 10.11 Conformation dependent library (CDL) restraints added in 3.0 seconds 4810 Ramachandran restraints generated. 2405 Oldfield, 0 Emsley, 2405 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4638 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 101 helices and 4 sheets defined 65.2% alpha, 1.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.09 Creating SS restraints... Processing helix chain 'A' and resid 4 through 10 removed outlier: 3.528A pdb=" N TRP A 8 " --> pdb=" O TYR A 5 " (cutoff:3.500A) Processing helix chain 'A' and resid 13 through 37 Processing helix chain 'A' and resid 43 through 50 Processing helix chain 'B' and resid 14 through 45 Processing helix chain 'D' and resid 5 through 10 Processing helix chain 'D' and resid 13 through 37 Processing helix chain 'D' and resid 43 through 50 Processing helix chain 'E' and resid 14 through 45 Processing helix chain 'F' and resid 5 through 10 Processing helix chain 'F' and resid 13 through 37 removed outlier: 3.922A pdb=" N PHE F 17 " --> pdb=" O PRO F 13 " (cutoff:3.500A) Processing helix chain 'F' and resid 43 through 50 Processing helix chain 'G' and resid 14 through 45 Processing helix chain 'I' and resid 3 through 9 removed outlier: 4.018A pdb=" N ILE I 7 " --> pdb=" O PHE I 4 " (cutoff:3.500A) Processing helix chain 'I' and resid 13 through 37 Processing helix chain 'I' and resid 43 through 50 Processing helix chain 'J' and resid 14 through 45 Processing helix chain 'K' and resid 4 through 10 Processing helix chain 'K' and resid 13 through 36 Processing helix chain 'K' and resid 43 through 51 Processing helix chain 'N' and resid 14 through 45 Processing helix chain 'O' and resid 3 through 9 Processing helix chain 'O' and resid 13 through 37 Processing helix chain 'O' and resid 43 through 50 Processing helix chain 'P' and resid 14 through 45 Processing helix chain 'Q' and resid 4 through 9 removed outlier: 3.882A pdb=" N TRP Q 8 " --> pdb=" O TYR Q 5 " (cutoff:3.500A) Processing helix chain 'Q' and resid 13 through 37 Processing helix chain 'Q' and resid 43 through 50 Processing helix chain 'R' and resid 14 through 45 Processing helix chain 'S' and resid 5 through 10 removed outlier: 4.395A pdb=" N MET S 9 " --> pdb=" O TYR S 5 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ILE S 10 " --> pdb=" O LYS S 6 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 5 through 10' Processing helix chain 'S' and resid 13 through 37 Processing helix chain 'S' and resid 43 through 50 Processing helix chain 'T' and resid 14 through 45 Processing helix chain 'U' and resid 4 through 9 Processing helix chain 'U' and resid 13 through 37 Processing helix chain 'U' and resid 43 through 50 Processing helix chain 'V' and resid 14 through 45 Processing helix chain 'W' and resid 4 through 10 Processing helix chain 'W' and resid 13 through 37 Processing helix chain 'W' and resid 43 through 51 Processing helix chain 'X' and resid 14 through 45 Processing helix chain 'Y' and resid 2 through 10 removed outlier: 3.959A pdb=" N TYR Y 5 " --> pdb=" O SER Y 2 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS Y 6 " --> pdb=" O LYS Y 3 " (cutoff:3.500A) Processing helix chain 'Y' and resid 13 through 37 Processing helix chain 'Y' and resid 43 through 50 Processing helix chain 'Z' and resid 14 through 45 Processing helix chain '1' and resid 6 through 10 Processing helix chain '1' and resid 13 through 37 Processing helix chain '1' and resid 43 through 50 Processing helix chain '2' and resid 14 through 45 Processing helix chain '7' and resid 5 through 10 Processing helix chain '7' and resid 13 through 37 Processing helix chain '7' and resid 43 through 45 No H-bonds generated for 'chain '7' and resid 43 through 45' Processing helix chain '8' and resid 14 through 45 Processing helix chain '9' and resid 2 through 10 removed outlier: 3.741A pdb=" N TYR 9 5 " --> pdb=" O SER 9 2 " (cutoff:3.500A) Processing helix chain '9' and resid 13 through 37 Processing helix chain '9' and resid 43 through 51 Processing helix chain '0' and resid 14 through 45 Processing helix chain '4' and resid 5 through 10 Processing helix chain '4' and resid 13 through 37 Processing helix chain '4' and resid 43 through 51 removed outlier: 3.695A pdb=" N SER 4 47 " --> pdb=" O TRP 4 43 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA 4 48 " --> pdb=" O LEU 4 44 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA 4 49 " --> pdb=" O GLU 4 45 " (cutoff:3.500A) Processing helix chain 't' and resid 14 through 45 Processing helix chain '6' and resid 5 through 10 removed outlier: 3.550A pdb=" N TRP 6 8 " --> pdb=" O TYR 6 5 " (cutoff:3.500A) Processing helix chain '6' and resid 13 through 37 Processing helix chain '6' and resid 43 through 51 removed outlier: 3.517A pdb=" N ALA 6 48 " --> pdb=" O LEU 6 44 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYS 6 50 " --> pdb=" O ILE 6 46 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N TYR 6 51 " --> pdb=" O SER 6 47 " (cutoff:3.500A) Processing helix chain '5' and resid 14 through 45 Processing helix chain 'C' and resid 4 through 10 removed outlier: 3.695A pdb=" N TRP C 8 " --> pdb=" O TYR C 5 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 37 Processing helix chain 'C' and resid 39 through 41 No H-bonds generated for 'chain 'C' and resid 39 through 41' Processing helix chain 'C' and resid 43 through 50 removed outlier: 3.613A pdb=" N SER C 47 " --> pdb=" O TRP C 43 " (cutoff:3.500A) Processing helix chain '3' and resid 14 through 45 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 33 through 56 removed outlier: 3.749A pdb=" N ALA L 37 " --> pdb=" O PHE L 33 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N THR L 38 " --> pdb=" O PHE L 34 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N PHE L 39 " --> pdb=" O GLY L 35 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LEU L 44 " --> pdb=" O PHE L 40 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ILE L 47 " --> pdb=" O ALA L 43 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE L 49 " --> pdb=" O GLY L 45 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA L 53 " --> pdb=" O ILE L 49 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N VAL L 54 " --> pdb=" O ALA L 50 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU L 55 " --> pdb=" O TRP L 51 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLN L 56 " --> pdb=" O SER L 52 " (cutoff:3.500A) Processing helix chain 'L' and resid 61 through 63 No H-bonds generated for 'chain 'L' and resid 61 through 63' Processing helix chain 'L' and resid 86 through 111 removed outlier: 3.701A pdb=" N ILE L 91 " --> pdb=" O GLN L 87 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL L 105 " --> pdb=" O ALA L 101 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N GLU L 106 " --> pdb=" O LEU L 102 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ILE L 107 " --> pdb=" O ARG L 103 " (cutoff:3.500A) Processing helix chain 'L' and resid 116 through 129 removed outlier: 3.902A pdb=" N ALA L 127 " --> pdb=" O PHE L 123 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N TYR L 128 " --> pdb=" O ALA L 124 " (cutoff:3.500A) Processing helix chain 'L' and resid 135 through 139 removed outlier: 3.645A pdb=" N MET L 139 " --> pdb=" O ARG L 135 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 135 through 139' Processing helix chain 'L' and resid 142 through 144 No H-bonds generated for 'chain 'L' and resid 142 through 144' Processing helix chain 'L' and resid 157 through 160 No H-bonds generated for 'chain 'L' and resid 157 through 160' Processing helix chain 'L' and resid 162 through 164 No H-bonds generated for 'chain 'L' and resid 162 through 164' Processing helix chain 'L' and resid 167 through 169 No H-bonds generated for 'chain 'L' and resid 167 through 169' Processing helix chain 'L' and resid 171 through 198 removed outlier: 3.775A pdb=" N SER L 178 " --> pdb=" O MET L 174 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N PHE L 180 " --> pdb=" O ALA L 176 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N PHE L 181 " --> pdb=" O ILE L 177 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ALA L 188 " --> pdb=" O ALA L 184 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N LEU L 189 " --> pdb=" O LEU L 185 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N HIS L 190 " --> pdb=" O ALA L 186 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL L 194 " --> pdb=" O HIS L 190 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LEU L 195 " --> pdb=" O GLY L 191 " (cutoff:3.500A) Processing helix chain 'L' and resid 209 through 220 removed outlier: 4.249A pdb=" N ASP L 213 " --> pdb=" O PRO L 209 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N THR L 214 " --> pdb=" O ASP L 210 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N PHE L 215 " --> pdb=" O HIS L 211 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N PHE L 216 " --> pdb=" O GLU L 212 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU L 219 " --> pdb=" O PHE L 215 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL L 220 " --> pdb=" O PHE L 216 " (cutoff:3.500A) Processing helix chain 'L' and resid 226 through 251 removed outlier: 3.767A pdb=" N CYS L 247 " --> pdb=" O PHE L 243 " (cutoff:3.500A) Processing helix chain 'L' and resid 259 through 267 Processing helix chain 'M' and resid 38 through 42 Processing helix chain 'M' and resid 54 through 78 removed outlier: 3.890A pdb=" N ILE M 70 " --> pdb=" O TRP M 66 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N GLY M 71 " --> pdb=" O PHE M 67 " (cutoff:3.500A) Processing helix chain 'M' and resid 82 through 87 Processing helix chain 'M' and resid 113 through 140 removed outlier: 3.810A pdb=" N PHE M 121 " --> pdb=" O ILE M 117 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N TRP M 127 " --> pdb=" O PHE M 123 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N TRP M 130 " --> pdb=" O VAL M 126 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N GLY M 131 " --> pdb=" O TRP M 127 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ARG M 132 " --> pdb=" O SER M 128 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ARG M 136 " --> pdb=" O ARG M 132 " (cutoff:3.500A) Processing helix chain 'M' and resid 144 through 161 removed outlier: 4.490A pdb=" N ALA M 149 " --> pdb=" O THR M 146 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU M 151 " --> pdb=" O TRP M 148 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N TRP M 155 " --> pdb=" O SER M 152 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N MET M 158 " --> pdb=" O TRP M 155 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU M 160 " --> pdb=" O TRP M 157 " (cutoff:3.500A) Processing helix chain 'M' and resid 164 through 168 removed outlier: 3.881A pdb=" N MET M 168 " --> pdb=" O ARG M 164 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 164 through 168' Processing helix chain 'M' and resid 181 through 192 removed outlier: 3.714A pdb=" N SER M 190 " --> pdb=" O THR M 186 " (cutoff:3.500A) Processing helix chain 'M' and resid 196 through 198 No H-bonds generated for 'chain 'M' and resid 196 through 198' Processing helix chain 'M' and resid 200 through 225 removed outlier: 3.670A pdb=" N ALA M 207 " --> pdb=" O GLY M 203 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N PHE M 208 " --> pdb=" O LEU M 204 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N TYR M 210 " --> pdb=" O ILE M 206 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA M 213 " --> pdb=" O LEU M 209 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N MET M 218 " --> pdb=" O LEU M 214 " (cutoff:3.500A) Processing helix chain 'M' and resid 234 through 237 No H-bonds generated for 'chain 'M' and resid 234 through 237' Processing helix chain 'M' and resid 243 through 256 removed outlier: 4.313A pdb=" N ALA M 248 " --> pdb=" O ALA M 244 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALA M 249 " --> pdb=" O ALA M 245 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LEU M 250 " --> pdb=" O GLU M 246 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE M 251 " --> pdb=" O ARG M 247 " (cutoff:3.500A) Processing helix chain 'M' and resid 262 through 289 removed outlier: 4.065A pdb=" N HIS M 266 " --> pdb=" O MET M 262 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ARG M 267 " --> pdb=" O GLU M 263 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N TRP M 268 " --> pdb=" O GLY M 264 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ALA M 269 " --> pdb=" O ILE M 265 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ILE M 270 " --> pdb=" O HIS M 266 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LEU M 275 " --> pdb=" O TRP M 271 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N VAL M 276 " --> pdb=" O MET M 272 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N THR M 277 " --> pdb=" O ALA M 273 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR M 279 " --> pdb=" O LEU M 275 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N GLY M 280 " --> pdb=" O VAL M 276 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ILE M 282 " --> pdb=" O LEU M 278 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU M 285 " --> pdb=" O GLY M 281 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU M 286 " --> pdb=" O ILE M 282 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N SER M 287 " --> pdb=" O GLY M 283 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N GLY M 288 " --> pdb=" O ILE M 284 " (cutoff:3.500A) Processing helix chain 'M' and resid 294 through 301 removed outlier: 4.189A pdb=" N GLN M 299 " --> pdb=" O TYR M 295 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ASN M 300 " --> pdb=" O VAL M 296 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N HIS M 301 " --> pdb=" O TRP M 297 " (cutoff:3.500A) Processing helix chain 'H' and resid 12 through 34 removed outlier: 3.692A pdb=" N ILE H 17 " --> pdb=" O ALA H 13 " (cutoff:3.500A) Processing helix chain 'H' and resid 104 through 107 No H-bonds generated for 'chain 'H' and resid 104 through 107' Processing helix chain 'H' and resid 110 through 112 No H-bonds generated for 'chain 'H' and resid 110 through 112' Processing helix chain 'H' and resid 210 through 213 No H-bonds generated for 'chain 'H' and resid 210 through 213' Processing helix chain 'H' and resid 227 through 243 removed outlier: 3.786A pdb=" N ASP H 231 " --> pdb=" O LEU H 227 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLY H 240 " --> pdb=" O TYR H 236 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N LEU H 241 " --> pdb=" O VAL H 237 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N MET H 242 " --> pdb=" O ALA H 238 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N TYR H 243 " --> pdb=" O GLY H 239 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'H' and resid 63 through 65 removed outlier: 4.196A pdb=" N LEU H 73 " --> pdb=" O PHE H 64 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'H' and resid 87 through 89 Processing sheet with id= C, first strand: chain 'H' and resid 131 through 133 removed outlier: 5.644A pdb=" N ASP H 170 " --> pdb=" O ALA H 176 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N ALA H 176 " --> pdb=" O ASP H 170 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'H' and resid 152 through 154 1153 hydrogen bonds defined for protein. 3267 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: 5.75 Time building geometry restraints manager: 10.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.35: 6296 1.35 - 1.56: 16463 1.56 - 1.76: 21 1.76 - 1.97: 187 1.97 - 2.17: 152 Bond restraints: 23119 Sorted by residual: bond pdb=" C29 SPN M 407 " pdb=" C30 SPN M 407 " ideal model delta sigma weight residual 1.336 1.545 -0.209 2.00e-02 2.50e+03 1.09e+02 bond pdb=" C8 SPN M 407 " pdb=" C9 SPN M 407 " ideal model delta sigma weight residual 1.336 1.533 -0.197 2.00e-02 2.50e+03 9.74e+01 bond pdb=" C14 SPN M 407 " pdb=" C15 SPN M 407 " ideal model delta sigma weight residual 1.530 1.336 0.194 2.00e-02 2.50e+03 9.38e+01 bond pdb=" C16 SPN M 407 " pdb=" C17 SPN M 407 " ideal model delta sigma weight residual 1.530 1.344 0.186 2.00e-02 2.50e+03 8.66e+01 bond pdb=" C26 SPN M 407 " pdb=" CM8 SPN M 407 " ideal model delta sigma weight residual 1.502 1.318 0.184 2.00e-02 2.50e+03 8.45e+01 ... (remaining 23114 not shown) Histogram of bond angle deviations from ideal: 73.66 - 91.50: 154 91.50 - 109.35: 2684 109.35 - 127.19: 28234 127.19 - 145.03: 996 145.03 - 162.87: 114 Bond angle restraints: 32182 Sorted by residual: angle pdb=" C3B BCL E 101 " pdb=" CAB BCL E 101 " pdb=" OBB BCL E 101 " ideal model delta sigma weight residual 122.70 73.66 49.04 2.78e+00 1.29e-01 3.10e+02 angle pdb=" CBB BCL E 101 " pdb=" CAB BCL E 101 " pdb=" OBB BCL E 101 " ideal model delta sigma weight residual 116.79 80.19 36.60 2.39e+00 1.75e-01 2.34e+02 angle pdb=" C3B BCL E 101 " pdb=" CAB BCL E 101 " pdb=" CBB BCL E 101 " ideal model delta sigma weight residual 120.43 153.85 -33.42 2.41e+00 1.73e-01 1.93e+02 angle pdb=" C TYR 0 9 " pdb=" N THR 0 10 " pdb=" CA THR 0 10 " ideal model delta sigma weight residual 121.92 106.03 15.89 1.73e+00 3.34e-01 8.44e+01 angle pdb=" C TYR 3 9 " pdb=" N THR 3 10 " pdb=" CA THR 3 10 " ideal model delta sigma weight residual 122.24 110.42 11.82 1.57e+00 4.06e-01 5.67e+01 ... (remaining 32177 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.41: 10849 17.41 - 34.82: 873 34.82 - 52.23: 212 52.23 - 69.65: 42 69.65 - 87.06: 32 Dihedral angle restraints: 12008 sinusoidal: 4801 harmonic: 7207 Sorted by residual: dihedral pdb=" CA TYR V 9 " pdb=" C TYR V 9 " pdb=" N THR V 10 " pdb=" CA THR V 10 " ideal model delta harmonic sigma weight residual 180.00 140.79 39.21 0 5.00e+00 4.00e-02 6.15e+01 dihedral pdb=" CA TYR 0 9 " pdb=" C TYR 0 9 " pdb=" N THR 0 10 " pdb=" CA THR 0 10 " ideal model delta harmonic sigma weight residual -180.00 -144.55 -35.45 0 5.00e+00 4.00e-02 5.03e+01 dihedral pdb=" CA TYR P 9 " pdb=" C TYR P 9 " pdb=" N THR P 10 " pdb=" CA THR P 10 " ideal model delta harmonic sigma weight residual 180.00 144.80 35.20 0 5.00e+00 4.00e-02 4.96e+01 ... (remaining 12005 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.048: 3296 1.048 - 2.096: 0 2.096 - 3.144: 0 3.144 - 4.192: 0 4.192 - 5.240: 1 Chirality restraints: 3297 Sorted by residual: chirality pdb=" C22 SPN M 407 " pdb=" C21 SPN M 407 " pdb=" C23 SPN M 407 " pdb=" CM7 SPN M 407 " both_signs ideal model delta sigma weight residual False -2.58 2.66 -5.24 2.00e-01 2.50e+01 6.86e+02 chirality pdb=" C3C BPH M 405 " pdb=" C2C BPH M 405 " pdb=" C4C BPH M 405 " pdb=" CAC BPH M 405 " both_signs ideal model delta sigma weight residual False 2.83 2.60 0.23 2.00e-01 2.50e+01 1.37e+00 chirality pdb=" CA TYR P 9 " pdb=" N TYR P 9 " pdb=" C TYR P 9 " pdb=" CB TYR P 9 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.37e+00 ... (remaining 3294 not shown) Planarity restraints: 3861 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C28 SPN M 407 " -0.176 2.00e-02 2.50e+03 2.26e-01 6.41e+02 pdb=" C29 SPN M 407 " 0.345 2.00e-02 2.50e+03 pdb=" C30 SPN M 407 " -0.289 2.00e-02 2.50e+03 pdb=" CM9 SPN M 407 " 0.150 2.00e-02 2.50e+03 pdb=" CMB SPN M 407 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 SPN M 407 " -0.094 2.00e-02 2.50e+03 1.68e-01 3.51e+02 pdb=" C7 SPN M 407 " 0.021 2.00e-02 2.50e+03 pdb=" C8 SPN M 407 " -0.132 2.00e-02 2.50e+03 pdb=" C9 SPN M 407 " 0.318 2.00e-02 2.50e+03 pdb=" CM4 SPN M 407 " -0.113 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" ND BPH M 405 " -0.020 2.00e-02 2.50e+03 1.12e-01 2.80e+02 pdb=" C1D BPH M 405 " -0.029 2.00e-02 2.50e+03 pdb=" C2D BPH M 405 " 0.055 2.00e-02 2.50e+03 pdb=" C3D BPH M 405 " 0.088 2.00e-02 2.50e+03 pdb=" C4D BPH M 405 " 0.071 2.00e-02 2.50e+03 pdb=" CAD BPH M 405 " -0.250 2.00e-02 2.50e+03 pdb=" CHA BPH M 405 " 0.095 2.00e-02 2.50e+03 pdb=" CHD BPH M 405 " -0.113 2.00e-02 2.50e+03 pdb=" CMD BPH M 405 " 0.104 2.00e-02 2.50e+03 ... (remaining 3858 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.62: 336 2.62 - 3.19: 20770 3.19 - 3.76: 36554 3.76 - 4.33: 47633 4.33 - 4.90: 76528 Nonbonded interactions: 181821 Sorted by model distance: nonbonded pdb=" OG1 THR K 38 " pdb=" O SER K 40 " model vdw 2.056 2.440 nonbonded pdb=" OG1 THR L 15 " pdb=" O GLY L 18 " model vdw 2.063 2.440 nonbonded pdb=" O TRP R 48 " pdb=" OG SER S 47 " model vdw 2.066 2.440 nonbonded pdb=" O PRO V 47 " pdb=" NH2 ARG W 53 " model vdw 2.094 2.520 nonbonded pdb=" O TYR L 30 " pdb=" NH2 ARG L 103 " model vdw 2.118 2.520 ... (remaining 181816 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 10 through 49 or resid 101)) selection = chain '2' selection = (chain '3' and (resid 10 through 49 or resid 101)) selection = (chain '5' and (resid 10 through 49 or resid 101)) selection = (chain '8' and (resid 10 through 49 or resid 101)) selection = (chain 'B' and (resid 10 through 49 or resid 101)) selection = (chain 'E' and (resid 10 through 49 or resid 101)) selection = (chain 'G' and (resid 10 through 49 or resid 101)) selection = (chain 'J' and (resid 10 through 49 or resid 101)) selection = (chain 'N' and (resid 10 through 49 or resid 101)) selection = (chain 'P' and (resid 10 through 49 or resid 101)) selection = (chain 'R' and (resid 10 through 49 or resid 101)) selection = (chain 'T' and (resid 10 through 49 or resid 101)) selection = (chain 'V' and (resid 10 through 49 or resid 101)) selection = (chain 'X' and (resid 10 through 49 or resid 101)) selection = (chain 'Z' and (resid 10 through 49 or resid 101)) selection = (chain 't' and (resid 10 through 49 or resid 101)) } ncs_group { reference = (chain '1' and resid 2 through 46) selection = (chain '4' and resid 2 through 46) selection = (chain '6' and resid 2 through 46) selection = (chain '7' and resid 2 through 46) selection = (chain '9' and resid 2 through 46) selection = (chain 'A' and resid 2 through 46) selection = (chain 'C' and resid 2 through 46) selection = (chain 'D' and resid 2 through 46) selection = (chain 'F' and resid 2 through 46) selection = (chain 'I' and resid 2 through 46) selection = (chain 'K' and resid 2 through 46) selection = (chain 'O' and resid 2 through 46) selection = (chain 'Q' and resid 2 through 46) selection = (chain 'S' and resid 2 through 46) selection = (chain 'U' and resid 2 through 46) selection = (chain 'W' and resid 2 through 46) selection = (chain 'Y' and resid 2 through 46) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 5.710 Check model and map are aligned: 0.340 Set scattering table: 0.200 Process input model: 55.300 Find NCS groups from input model: 1.420 Set up NCS constraints: 0.210 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6715 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 : 0.009 0.209 23119 Z= 0.512 Angle : 0.975 49.038 32182 Z= 0.454 Chirality : 0.101 5.240 3297 Planarity : 0.008 0.226 3861 Dihedral : 14.409 87.057 7370 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 16.17 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.57 % Favored : 95.38 % Rotamer Outliers : 1.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.17), residues: 2405 helix: 1.72 (0.13), residues: 1501 sheet: -2.51 (0.84), residues: 22 loop : -1.15 (0.21), residues: 882 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4810 Ramachandran restraints generated. 2405 Oldfield, 0 Emsley, 2405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4810 Ramachandran restraints generated. 2405 Oldfield, 0 Emsley, 2405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 891 residues out of total 2086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 865 time to evaluate : 2.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 2 residues processed: 877 average time/residue: 0.3166 time to fit residues: 436.0231 Evaluate side-chains 695 residues out of total 2086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 693 time to evaluate : 2.208 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2794 time to fit residues: 3.7303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 197 optimal weight: 5.9990 chunk 177 optimal weight: 0.0060 chunk 98 optimal weight: 5.9990 chunk 60 optimal weight: 0.7980 chunk 119 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 183 optimal weight: 5.9990 chunk 70 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 chunk 136 optimal weight: 2.9990 chunk 212 optimal weight: 7.9990 overall best weight: 1.5602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 20 GLN U 20 GLN W 20 GLN ** Z 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 16 GLN 6 52 ASN C 20 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6688 moved from start: 0.2316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 23119 Z= 0.198 Angle : 0.728 48.029 32182 Z= 0.338 Chirality : 0.040 0.300 3297 Planarity : 0.004 0.060 3861 Dihedral : 8.796 88.255 2981 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer Outliers : 0.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.17), residues: 2405 helix: 2.14 (0.13), residues: 1522 sheet: -0.37 (1.41), residues: 12 loop : -0.82 (0.22), residues: 871 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4810 Ramachandran restraints generated. 2405 Oldfield, 0 Emsley, 2405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4810 Ramachandran restraints generated. 2405 Oldfield, 0 Emsley, 2405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 806 residues out of total 2086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 801 time to evaluate : 2.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 0 residues processed: 801 average time/residue: 0.3101 time to fit residues: 391.9760 Evaluate side-chains 693 residues out of total 2086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 693 time to evaluate : 2.342 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.0204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 118 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 176 optimal weight: 5.9990 chunk 144 optimal weight: 1.9990 chunk 58 optimal weight: 8.9990 chunk 212 optimal weight: 6.9990 chunk 229 optimal weight: 20.0000 chunk 189 optimal weight: 8.9990 chunk 211 optimal weight: 0.4980 chunk 72 optimal weight: 10.0000 chunk 170 optimal weight: 9.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 GLN ** E 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 16 GLN N 18 GLN O 20 GLN 6 52 ASN ** 5 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6705 moved from start: 0.2832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 23119 Z= 0.213 Angle : 0.719 47.362 32182 Z= 0.331 Chirality : 0.039 0.238 3297 Planarity : 0.004 0.052 3861 Dihedral : 8.625 83.008 2981 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer Outliers : 0.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.17), residues: 2405 helix: 1.95 (0.12), residues: 1535 sheet: -0.16 (1.73), residues: 12 loop : -0.82 (0.22), residues: 858 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4810 Ramachandran restraints generated. 2405 Oldfield, 0 Emsley, 2405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4810 Ramachandran restraints generated. 2405 Oldfield, 0 Emsley, 2405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 777 residues out of total 2086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 773 time to evaluate : 2.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 773 average time/residue: 0.3181 time to fit residues: 393.0170 Evaluate side-chains 685 residues out of total 2086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 684 time to evaluate : 2.341 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2799 time to fit residues: 3.4300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 210 optimal weight: 20.0000 chunk 160 optimal weight: 0.9980 chunk 110 optimal weight: 0.9980 chunk 23 optimal weight: 9.9990 chunk 101 optimal weight: 7.9990 chunk 142 optimal weight: 9.9990 chunk 213 optimal weight: 5.9990 chunk 226 optimal weight: 6.9990 chunk 111 optimal weight: 2.9990 chunk 202 optimal weight: 5.9990 chunk 60 optimal weight: 5.9990 overall best weight: 3.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 20 GLN ** Z 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 21 HIS 6 52 ASN ** 5 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 168 HIS M 202 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6739 moved from start: 0.3179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.065 23119 Z= 0.270 Angle : 0.752 47.417 32182 Z= 0.344 Chirality : 0.039 0.193 3297 Planarity : 0.004 0.049 3861 Dihedral : 8.707 83.366 2981 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer Outliers : 0.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.17), residues: 2405 helix: 1.92 (0.13), residues: 1530 sheet: -0.14 (1.75), residues: 12 loop : -0.89 (0.22), residues: 863 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4810 Ramachandran restraints generated. 2405 Oldfield, 0 Emsley, 2405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4810 Ramachandran restraints generated. 2405 Oldfield, 0 Emsley, 2405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 766 residues out of total 2086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 762 time to evaluate : 2.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 0 residues processed: 762 average time/residue: 0.3000 time to fit residues: 366.3905 Evaluate side-chains 688 residues out of total 2086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 688 time to evaluate : 2.353 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.0299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 188 optimal weight: 8.9990 chunk 128 optimal weight: 0.8980 chunk 3 optimal weight: 5.9990 chunk 168 optimal weight: 9.9990 chunk 93 optimal weight: 3.9990 chunk 193 optimal weight: 20.0000 chunk 156 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 115 optimal weight: 5.9990 chunk 203 optimal weight: 10.0000 chunk 57 optimal weight: 0.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 20 GLN Y 20 GLN ** Z 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 21 HIS 4 52 ASN 5 16 GLN ** 3 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 202 HIS ** M 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6755 moved from start: 0.3425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.062 23119 Z= 0.272 Angle : 0.760 47.342 32182 Z= 0.347 Chirality : 0.040 0.191 3297 Planarity : 0.004 0.057 3861 Dihedral : 8.721 84.261 2981 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer Outliers : 0.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % 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: 1.26 (0.17), residues: 2405 helix: 1.81 (0.13), residues: 1530 sheet: -2.07 (1.05), residues: 22 loop : -0.91 (0.22), residues: 853 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4810 Ramachandran restraints generated. 2405 Oldfield, 0 Emsley, 2405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4810 Ramachandran restraints generated. 2405 Oldfield, 0 Emsley, 2405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 771 residues out of total 2086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 766 time to evaluate : 2.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 0 residues processed: 767 average time/residue: 0.3048 time to fit residues: 372.8298 Evaluate side-chains 678 residues out of total 2086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 678 time to evaluate : 2.416 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.1382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 76 optimal weight: 6.9990 chunk 203 optimal weight: 0.0970 chunk 44 optimal weight: 3.9990 chunk 132 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 226 optimal weight: 7.9990 chunk 187 optimal weight: 0.9990 chunk 104 optimal weight: 10.0000 chunk 18 optimal weight: 10.0000 chunk 74 optimal weight: 4.9990 chunk 118 optimal weight: 0.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 21 HIS ** 3 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 35 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6715 moved from start: 0.3672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 23119 Z= 0.179 Angle : 0.703 47.746 32182 Z= 0.321 Chirality : 0.038 0.249 3297 Planarity : 0.004 0.052 3861 Dihedral : 8.512 88.559 2981 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % 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: 1.43 (0.17), residues: 2405 helix: 1.96 (0.13), residues: 1533 sheet: -1.95 (1.08), residues: 22 loop : -0.88 (0.22), residues: 850 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4810 Ramachandran restraints generated. 2405 Oldfield, 0 Emsley, 2405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4810 Ramachandran restraints generated. 2405 Oldfield, 0 Emsley, 2405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 760 residues out of total 2086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 760 time to evaluate : 2.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 760 average time/residue: 0.3046 time to fit residues: 369.7403 Evaluate side-chains 679 residues out of total 2086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 679 time to evaluate : 2.430 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.8252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 218 optimal weight: 0.0870 chunk 25 optimal weight: 5.9990 chunk 128 optimal weight: 10.0000 chunk 165 optimal weight: 20.0000 chunk 190 optimal weight: 20.0000 chunk 126 optimal weight: 0.9990 chunk 225 optimal weight: 0.0020 chunk 141 optimal weight: 10.0000 chunk 137 optimal weight: 2.9990 chunk 104 optimal weight: 7.9990 chunk 139 optimal weight: 20.0000 overall best weight: 2.0172 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 18 GLN ** E 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 20 GLN ** T 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 21 HIS ** 7 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 21 HIS 3 16 GLN ** L 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6716 moved from start: 0.3832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.057 23119 Z= 0.195 Angle : 0.714 47.674 32182 Z= 0.325 Chirality : 0.039 0.164 3297 Planarity : 0.004 0.058 3861 Dihedral : 8.481 87.157 2981 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % 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: 1.44 (0.17), residues: 2405 helix: 1.95 (0.13), residues: 1536 sheet: -1.69 (1.12), residues: 22 loop : -0.84 (0.22), residues: 847 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4810 Ramachandran restraints generated. 2405 Oldfield, 0 Emsley, 2405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4810 Ramachandran restraints generated. 2405 Oldfield, 0 Emsley, 2405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 749 residues out of total 2086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 749 time to evaluate : 2.269 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 749 average time/residue: 0.3038 time to fit residues: 366.6187 Evaluate side-chains 681 residues out of total 2086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 681 time to evaluate : 2.334 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.1289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 90 optimal weight: 10.0000 chunk 134 optimal weight: 9.9990 chunk 67 optimal weight: 10.0000 chunk 44 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 143 optimal weight: 5.9990 chunk 153 optimal weight: 20.0000 chunk 111 optimal weight: 5.9990 chunk 21 optimal weight: 0.5980 chunk 177 optimal weight: 0.6980 chunk 205 optimal weight: 10.0000 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 20 GLN ** Z 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 21 HIS ** 7 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 21 HIS 3 16 GLN ** L 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6716 moved from start: 0.3992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 23119 Z= 0.195 Angle : 0.724 47.689 32182 Z= 0.330 Chirality : 0.039 0.162 3297 Planarity : 0.004 0.050 3861 Dihedral : 8.462 87.796 2981 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % 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: 1.41 (0.17), residues: 2405 helix: 1.92 (0.13), residues: 1537 sheet: -1.52 (1.13), residues: 22 loop : -0.85 (0.22), residues: 846 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4810 Ramachandran restraints generated. 2405 Oldfield, 0 Emsley, 2405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4810 Ramachandran restraints generated. 2405 Oldfield, 0 Emsley, 2405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 752 residues out of total 2086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 752 time to evaluate : 2.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 752 average time/residue: 0.2927 time to fit residues: 353.5418 Evaluate side-chains 683 residues out of total 2086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 683 time to evaluate : 2.310 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.0115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 216 optimal weight: 9.9990 chunk 197 optimal weight: 30.0000 chunk 210 optimal weight: 0.0070 chunk 126 optimal weight: 1.9990 chunk 91 optimal weight: 0.0770 chunk 165 optimal weight: 9.9990 chunk 64 optimal weight: 8.9990 chunk 189 optimal weight: 4.9990 chunk 198 optimal weight: 5.9990 chunk 209 optimal weight: 9.9990 chunk 138 optimal weight: 2.9990 overall best weight: 2.0162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 20 GLN ** T 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 21 HIS 3 16 GLN ** M 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6715 moved from start: 0.4071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.057 23119 Z= 0.196 Angle : 0.725 47.718 32182 Z= 0.330 Chirality : 0.039 0.235 3297 Planarity : 0.004 0.056 3861 Dihedral : 8.434 87.994 2981 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.17), residues: 2405 helix: 1.93 (0.13), residues: 1535 sheet: -1.36 (1.15), residues: 22 loop : -0.90 (0.22), residues: 848 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4810 Ramachandran restraints generated. 2405 Oldfield, 0 Emsley, 2405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4810 Ramachandran restraints generated. 2405 Oldfield, 0 Emsley, 2405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 738 residues out of total 2086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 738 time to evaluate : 2.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 738 average time/residue: 0.2945 time to fit residues: 350.3266 Evaluate side-chains 678 residues out of total 2086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 678 time to evaluate : 2.516 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.2340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 222 optimal weight: 0.0060 chunk 135 optimal weight: 6.9990 chunk 105 optimal weight: 4.9990 chunk 154 optimal weight: 8.9990 chunk 233 optimal weight: 6.9990 chunk 214 optimal weight: 5.9990 chunk 185 optimal weight: 4.9990 chunk 19 optimal weight: 6.9990 chunk 143 optimal weight: 5.9990 chunk 113 optimal weight: 0.9980 chunk 147 optimal weight: 3.9990 overall best weight: 3.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 20 GLN ** T 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 21 HIS t 18 GLN 3 16 GLN ** M 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6736 moved from start: 0.4149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.061 23119 Z= 0.240 Angle : 0.757 47.508 32182 Z= 0.346 Chirality : 0.040 0.182 3297 Planarity : 0.004 0.055 3861 Dihedral : 8.514 85.478 2981 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.17), residues: 2405 helix: 1.84 (0.13), residues: 1537 sheet: -1.33 (1.15), residues: 22 loop : -0.90 (0.22), residues: 846 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4810 Ramachandran restraints generated. 2405 Oldfield, 0 Emsley, 2405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4810 Ramachandran restraints generated. 2405 Oldfield, 0 Emsley, 2405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 727 residues out of total 2086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 727 time to evaluate : 2.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 727 average time/residue: 0.2982 time to fit residues: 348.9352 Evaluate side-chains 671 residues out of total 2086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 671 time to evaluate : 2.352 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.0794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/iotbx/cli_parser.py", line 872, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 70.7494 > 50: distance: 136 - 140: 30.972 distance: 140 - 141: 16.381 distance: 141 - 142: 47.906 distance: 141 - 144: 50.858 distance: 142 - 154: 69.377 distance: 144 - 145: 13.197 distance: 145 - 146: 33.925 distance: 145 - 147: 17.680 distance: 146 - 148: 24.451 distance: 147 - 149: 49.023 distance: 147 - 150: 20.915 distance: 148 - 149: 34.180 distance: 149 - 151: 38.384 distance: 150 - 152: 3.019 distance: 151 - 153: 47.148 distance: 152 - 153: 32.065 distance: 154 - 155: 12.691 distance: 155 - 156: 29.043 distance: 155 - 158: 33.973 distance: 156 - 157: 54.722 distance: 158 - 159: 40.511 distance: 160 - 161: 56.107 distance: 161 - 162: 40.129 distance: 162 - 163: 56.234 distance: 164 - 165: 18.973 distance: 165 - 166: 26.678 distance: 166 - 167: 24.944 distance: 166 - 168: 25.729 distance: 169 - 170: 15.085 distance: 170 - 171: 41.698 distance: 170 - 173: 61.448 distance: 171 - 174: 56.942 distance: 174 - 175: 4.065 distance: 175 - 176: 56.889 distance: 175 - 178: 41.119 distance: 176 - 181: 57.087 distance: 178 - 179: 39.724 distance: 178 - 180: 48.427 distance: 181 - 182: 5.291 distance: 181 - 187: 40.655 distance: 182 - 183: 52.741 distance: 182 - 185: 40.358 distance: 183 - 188: 14.889 distance: 188 - 189: 41.078 distance: 189 - 190: 25.966 distance: 189 - 192: 58.867 distance: 190 - 200: 39.244 distance: 193 - 194: 69.977 distance: 194 - 196: 39.733 distance: 195 - 197: 18.522 distance: 197 - 198: 45.662 distance: 198 - 199: 40.270 distance: 201 - 202: 69.508 distance: 202 - 203: 14.317 distance: 202 - 204: 34.328 distance: 204 - 205: 39.149 distance: 205 - 206: 56.972 distance: 205 - 208: 13.937 distance: 206 - 207: 41.494 distance: 206 - 212: 41.216 distance: 208 - 209: 24.415 distance: 208 - 210: 49.528 distance: 209 - 211: 47.471 distance: 214 - 215: 39.403 distance: 214 - 223: 35.202 distance: 217 - 219: 39.876 distance: 218 - 220: 41.256 distance: 220 - 222: 41.252 distance: 221 - 222: 38.256