Starting phenix.real_space_refine (version: dev) on Mon May 16 12:18:55 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k43_9913/05_2022/6k43_9913_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k43_9913/05_2022/6k43_9913.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k43_9913/05_2022/6k43_9913.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k43_9913/05_2022/6k43_9913.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k43_9913/05_2022/6k43_9913_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k43_9913/05_2022/6k43_9913_trim_updated.pdb" } resolution = 3.7 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= 0.030 sd= 1.242 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "C TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 127": "OE1" <-> "OE2" Residue "E TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 127": "OE1" <-> "OE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib" Total number of atoms: 31808 Number of models: 1 Model: "" Number of chains: 48 Chain: "A" Number of atoms: 1315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1315 Classifications: {'peptide': 162} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 157} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 1318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1318 Classifications: {'peptide': 162} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 157} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 1310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1310 Classifications: {'peptide': 161} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 156} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 1304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1304 Classifications: {'peptide': 161} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 156} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "G" Number of atoms: 1304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1304 Classifications: {'peptide': 161} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 156} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "H" Number of atoms: 1304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1304 Classifications: {'peptide': 161} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 156} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "I" Number of atoms: 1304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1304 Classifications: {'peptide': 161} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 156} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "J" Number of atoms: 1315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1315 Classifications: {'peptide': 162} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 157} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "K" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "L" Number of atoms: 1318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1318 Classifications: {'peptide': 162} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 157} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "M" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "N" Number of atoms: 1310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1310 Classifications: {'peptide': 161} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 156} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "O" Number of atoms: 1315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1315 Classifications: {'peptide': 162} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 157} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "P" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "Q" Number of atoms: 1318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1318 Classifications: {'peptide': 162} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 157} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "R" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "S" Number of atoms: 1310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1310 Classifications: {'peptide': 161} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 156} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "T" Number of atoms: 1315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1315 Classifications: {'peptide': 162} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 157} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "U" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "V" Number of atoms: 1318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1318 Classifications: {'peptide': 162} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 157} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "W" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "X" Number of atoms: 1310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1310 Classifications: {'peptide': 161} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 156} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {'HEM': 1, 'FE2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {'HEM': 1, 'FE2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {'HEM': 1, 'FE2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {'HEM': 1, 'FE2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {'HEM': 1, 'FE2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {'HEM': 1, 'FE2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "O" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {'HEM': 1, 'FE2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {'HEM': 1, 'FE2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 1} Chain: "S" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {'HEM': 1, 'FE2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "T" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {'HEM': 1, 'FE2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "V" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {'HEM': 1, 'FE2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "W" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 1} Chain: "X" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {'HEM': 1, 'FE2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 16.36, per 1000 atoms: 0.51 Number of scatterers: 31808 At special positions: 0 Unit cell: (132.09, 132.09, 132.09, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Fe 36 26.01 S 96 16.00 O 6116 8.00 N 5428 7.00 C 20132 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=29, symmetry=0 Number of additional bonds: simple=29, symmetry=0 Coordination: Other bonds: Time building additional restraints: 13.18 Conformation dependent library (CDL) restraints added in 4.4 seconds 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7384 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 120 helices and 0 sheets defined 77.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.43 Creating SS restraints... Processing helix chain 'A' and resid 5 through 35 removed outlier: 3.695A pdb=" N LYS A 35 " --> pdb=" O LEU A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 64 Processing helix chain 'A' and resid 83 through 109 Processing helix chain 'A' and resid 114 through 144 Processing helix chain 'A' and resid 146 through 152 removed outlier: 4.695A pdb=" N THR A 152 " --> pdb=" O LEU A 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 35 removed outlier: 3.711A pdb=" N LYS B 35 " --> pdb=" O LEU B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 64 removed outlier: 3.810A pdb=" N TYR B 43 " --> pdb=" O LYS B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 111 removed outlier: 3.821A pdb=" N LYS B 111 " --> pdb=" O VAL B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 144 Processing helix chain 'B' and resid 146 through 152 removed outlier: 3.832A pdb=" N THR B 152 " --> pdb=" O LEU B 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 35 removed outlier: 3.698A pdb=" N LYS C 35 " --> pdb=" O LEU C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 39 through 64 Processing helix chain 'C' and resid 83 through 111 removed outlier: 3.833A pdb=" N LYS C 111 " --> pdb=" O VAL C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 144 Processing helix chain 'C' and resid 146 through 152 removed outlier: 4.683A pdb=" N THR C 152 " --> pdb=" O LEU C 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 5 through 35 removed outlier: 3.695A pdb=" N LYS D 35 " --> pdb=" O LEU D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 64 removed outlier: 3.851A pdb=" N TYR D 43 " --> pdb=" O LYS D 39 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 109 Processing helix chain 'D' and resid 115 through 144 Processing helix chain 'D' and resid 146 through 152 removed outlier: 4.618A pdb=" N THR D 152 " --> pdb=" O LEU D 148 " (cutoff:3.500A) Processing helix chain 'F' and resid 5 through 35 removed outlier: 3.680A pdb=" N LYS F 35 " --> pdb=" O LEU F 31 " (cutoff:3.500A) Processing helix chain 'F' and resid 38 through 64 removed outlier: 3.518A pdb=" N TYR F 43 " --> pdb=" O LYS F 39 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 111 removed outlier: 3.817A pdb=" N LYS F 111 " --> pdb=" O VAL F 107 " (cutoff:3.500A) Processing helix chain 'F' and resid 114 through 144 Processing helix chain 'F' and resid 146 through 152 removed outlier: 4.642A pdb=" N THR F 152 " --> pdb=" O LEU F 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 35 removed outlier: 3.711A pdb=" N LYS E 35 " --> pdb=" O LEU E 31 " (cutoff:3.500A) Processing helix chain 'E' and resid 39 through 64 Processing helix chain 'E' and resid 83 through 111 removed outlier: 3.845A pdb=" N LYS E 111 " --> pdb=" O VAL E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 114 through 144 Processing helix chain 'E' and resid 146 through 152 removed outlier: 4.690A pdb=" N THR E 152 " --> pdb=" O LEU E 148 " (cutoff:3.500A) Processing helix chain 'G' and resid 5 through 35 removed outlier: 3.723A pdb=" N LYS G 35 " --> pdb=" O LEU G 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 39 through 64 Processing helix chain 'G' and resid 83 through 111 removed outlier: 3.825A pdb=" N LYS G 111 " --> pdb=" O VAL G 107 " (cutoff:3.500A) Processing helix chain 'G' and resid 114 through 144 Processing helix chain 'G' and resid 146 through 152 removed outlier: 4.681A pdb=" N THR G 152 " --> pdb=" O LEU G 148 " (cutoff:3.500A) Processing helix chain 'H' and resid 5 through 35 removed outlier: 3.715A pdb=" N LYS H 35 " --> pdb=" O LEU H 31 " (cutoff:3.500A) Processing helix chain 'H' and resid 39 through 64 Processing helix chain 'H' and resid 83 through 111 removed outlier: 3.814A pdb=" N LYS H 111 " --> pdb=" O VAL H 107 " (cutoff:3.500A) Processing helix chain 'H' and resid 114 through 144 Processing helix chain 'H' and resid 146 through 152 removed outlier: 3.905A pdb=" N THR H 152 " --> pdb=" O LEU H 148 " (cutoff:3.500A) Processing helix chain 'I' and resid 5 through 35 removed outlier: 3.720A pdb=" N LYS I 35 " --> pdb=" O LEU I 31 " (cutoff:3.500A) Processing helix chain 'I' and resid 39 through 64 Processing helix chain 'I' and resid 83 through 109 Processing helix chain 'I' and resid 114 through 144 Processing helix chain 'I' and resid 146 through 152 removed outlier: 3.896A pdb=" N THR I 152 " --> pdb=" O LEU I 148 " (cutoff:3.500A) Processing helix chain 'J' and resid 5 through 35 removed outlier: 3.707A pdb=" N LYS J 35 " --> pdb=" O LEU J 31 " (cutoff:3.500A) Processing helix chain 'J' and resid 39 through 64 Processing helix chain 'J' and resid 83 through 109 Processing helix chain 'J' and resid 114 through 144 Processing helix chain 'J' and resid 146 through 152 removed outlier: 4.698A pdb=" N THR J 152 " --> pdb=" O LEU J 148 " (cutoff:3.500A) Processing helix chain 'K' and resid 5 through 35 removed outlier: 3.743A pdb=" N LYS K 35 " --> pdb=" O LEU K 31 " (cutoff:3.500A) Processing helix chain 'K' and resid 38 through 64 removed outlier: 3.768A pdb=" N TYR K 43 " --> pdb=" O LYS K 39 " (cutoff:3.500A) Processing helix chain 'K' and resid 83 through 111 removed outlier: 3.842A pdb=" N LYS K 111 " --> pdb=" O VAL K 107 " (cutoff:3.500A) Processing helix chain 'K' and resid 114 through 144 Processing helix chain 'K' and resid 146 through 152 removed outlier: 3.826A pdb=" N THR K 152 " --> pdb=" O LEU K 148 " (cutoff:3.500A) Processing helix chain 'L' and resid 5 through 35 removed outlier: 3.699A pdb=" N LYS L 35 " --> pdb=" O LEU L 31 " (cutoff:3.500A) Processing helix chain 'L' and resid 39 through 64 Processing helix chain 'L' and resid 83 through 111 removed outlier: 3.834A pdb=" N LYS L 111 " --> pdb=" O VAL L 107 " (cutoff:3.500A) Processing helix chain 'L' and resid 114 through 144 Processing helix chain 'L' and resid 146 through 152 removed outlier: 4.685A pdb=" N THR L 152 " --> pdb=" O LEU L 148 " (cutoff:3.500A) Processing helix chain 'M' and resid 5 through 35 removed outlier: 3.745A pdb=" N LYS M 35 " --> pdb=" O LEU M 31 " (cutoff:3.500A) Processing helix chain 'M' and resid 38 through 64 removed outlier: 3.827A pdb=" N TYR M 43 " --> pdb=" O LYS M 39 " (cutoff:3.500A) Processing helix chain 'M' and resid 83 through 109 Processing helix chain 'M' and resid 115 through 144 Processing helix chain 'M' and resid 146 through 152 removed outlier: 4.599A pdb=" N THR M 152 " --> pdb=" O LEU M 148 " (cutoff:3.500A) Processing helix chain 'N' and resid 5 through 35 removed outlier: 3.708A pdb=" N LYS N 35 " --> pdb=" O LEU N 31 " (cutoff:3.500A) Processing helix chain 'N' and resid 38 through 64 Processing helix chain 'N' and resid 83 through 111 removed outlier: 3.815A pdb=" N LYS N 111 " --> pdb=" O VAL N 107 " (cutoff:3.500A) Processing helix chain 'N' and resid 114 through 144 Processing helix chain 'N' and resid 146 through 152 removed outlier: 4.680A pdb=" N THR N 152 " --> pdb=" O LEU N 148 " (cutoff:3.500A) Processing helix chain 'O' and resid 5 through 35 removed outlier: 3.709A pdb=" N LYS O 35 " --> pdb=" O LEU O 31 " (cutoff:3.500A) Processing helix chain 'O' and resid 39 through 64 Processing helix chain 'O' and resid 83 through 109 Processing helix chain 'O' and resid 114 through 144 Processing helix chain 'O' and resid 146 through 152 removed outlier: 3.878A pdb=" N THR O 152 " --> pdb=" O LEU O 148 " (cutoff:3.500A) Processing helix chain 'P' and resid 5 through 35 removed outlier: 3.737A pdb=" N LYS P 35 " --> pdb=" O LEU P 31 " (cutoff:3.500A) Processing helix chain 'P' and resid 38 through 64 removed outlier: 3.815A pdb=" N TYR P 43 " --> pdb=" O LYS P 39 " (cutoff:3.500A) Processing helix chain 'P' and resid 83 through 111 removed outlier: 3.833A pdb=" N LYS P 111 " --> pdb=" O VAL P 107 " (cutoff:3.500A) Processing helix chain 'P' and resid 114 through 144 Processing helix chain 'P' and resid 146 through 152 removed outlier: 3.805A pdb=" N THR P 152 " --> pdb=" O LEU P 148 " (cutoff:3.500A) Processing helix chain 'Q' and resid 5 through 35 removed outlier: 3.680A pdb=" N LYS Q 35 " --> pdb=" O LEU Q 31 " (cutoff:3.500A) Processing helix chain 'Q' and resid 39 through 64 Processing helix chain 'Q' and resid 83 through 109 Processing helix chain 'Q' and resid 114 through 144 Processing helix chain 'Q' and resid 146 through 152 removed outlier: 4.684A pdb=" N THR Q 152 " --> pdb=" O LEU Q 148 " (cutoff:3.500A) Processing helix chain 'R' and resid 5 through 35 removed outlier: 3.745A pdb=" N LYS R 35 " --> pdb=" O LEU R 31 " (cutoff:3.500A) Processing helix chain 'R' and resid 38 through 64 removed outlier: 3.845A pdb=" N TYR R 43 " --> pdb=" O LYS R 39 " (cutoff:3.500A) Processing helix chain 'R' and resid 83 through 111 removed outlier: 3.820A pdb=" N LYS R 111 " --> pdb=" O VAL R 107 " (cutoff:3.500A) Processing helix chain 'R' and resid 114 through 144 Processing helix chain 'R' and resid 146 through 152 removed outlier: 4.599A pdb=" N THR R 152 " --> pdb=" O LEU R 148 " (cutoff:3.500A) Processing helix chain 'S' and resid 5 through 35 removed outlier: 3.683A pdb=" N LYS S 35 " --> pdb=" O LEU S 31 " (cutoff:3.500A) Processing helix chain 'S' and resid 38 through 64 removed outlier: 3.598A pdb=" N TYR S 43 " --> pdb=" O LYS S 39 " (cutoff:3.500A) Processing helix chain 'S' and resid 83 through 111 removed outlier: 3.821A pdb=" N LYS S 111 " --> pdb=" O VAL S 107 " (cutoff:3.500A) Processing helix chain 'S' and resid 114 through 144 Processing helix chain 'S' and resid 146 through 152 removed outlier: 4.677A pdb=" N THR S 152 " --> pdb=" O LEU S 148 " (cutoff:3.500A) Processing helix chain 'T' and resid 5 through 35 removed outlier: 3.685A pdb=" N LYS T 35 " --> pdb=" O LEU T 31 " (cutoff:3.500A) Processing helix chain 'T' and resid 39 through 64 Processing helix chain 'T' and resid 83 through 109 Processing helix chain 'T' and resid 114 through 144 Processing helix chain 'T' and resid 146 through 152 removed outlier: 3.876A pdb=" N THR T 152 " --> pdb=" O LEU T 148 " (cutoff:3.500A) Processing helix chain 'U' and resid 5 through 35 removed outlier: 3.746A pdb=" N LYS U 35 " --> pdb=" O LEU U 31 " (cutoff:3.500A) Processing helix chain 'U' and resid 38 through 64 removed outlier: 3.749A pdb=" N TYR U 43 " --> pdb=" O LYS U 39 " (cutoff:3.500A) Processing helix chain 'U' and resid 83 through 111 removed outlier: 3.831A pdb=" N LYS U 111 " --> pdb=" O VAL U 107 " (cutoff:3.500A) Processing helix chain 'U' and resid 114 through 144 Processing helix chain 'U' and resid 146 through 152 removed outlier: 3.850A pdb=" N THR U 152 " --> pdb=" O LEU U 148 " (cutoff:3.500A) Processing helix chain 'V' and resid 5 through 35 removed outlier: 3.682A pdb=" N LYS V 35 " --> pdb=" O LEU V 31 " (cutoff:3.500A) Processing helix chain 'V' and resid 39 through 64 Processing helix chain 'V' and resid 83 through 111 removed outlier: 3.829A pdb=" N LYS V 111 " --> pdb=" O VAL V 107 " (cutoff:3.500A) Processing helix chain 'V' and resid 114 through 144 Processing helix chain 'V' and resid 146 through 152 removed outlier: 4.684A pdb=" N THR V 152 " --> pdb=" O LEU V 148 " (cutoff:3.500A) Processing helix chain 'W' and resid 5 through 35 removed outlier: 3.742A pdb=" N LYS W 35 " --> pdb=" O LEU W 31 " (cutoff:3.500A) Processing helix chain 'W' and resid 38 through 64 removed outlier: 3.814A pdb=" N TYR W 43 " --> pdb=" O LYS W 39 " (cutoff:3.500A) Processing helix chain 'W' and resid 83 through 111 removed outlier: 3.831A pdb=" N LYS W 111 " --> pdb=" O VAL W 107 " (cutoff:3.500A) Processing helix chain 'W' and resid 114 through 144 Processing helix chain 'W' and resid 146 through 152 removed outlier: 4.626A pdb=" N THR W 152 " --> pdb=" O LEU W 148 " (cutoff:3.500A) Processing helix chain 'X' and resid 5 through 35 removed outlier: 3.743A pdb=" N LYS X 35 " --> pdb=" O LEU X 31 " (cutoff:3.500A) Processing helix chain 'X' and resid 38 through 64 removed outlier: 3.586A pdb=" N TYR X 43 " --> pdb=" O LYS X 39 " (cutoff:3.500A) Processing helix chain 'X' and resid 83 through 111 removed outlier: 3.822A pdb=" N LYS X 111 " --> pdb=" O VAL X 107 " (cutoff:3.500A) Processing helix chain 'X' and resid 114 through 144 Processing helix chain 'X' and resid 146 through 152 removed outlier: 4.671A pdb=" N THR X 152 " --> pdb=" O LEU X 148 " (cutoff:3.500A) 2415 hydrogen bonds defined for protein. 7245 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: 8.85 Time building geometry restraints manager: 14.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.39: 13491 1.39 - 1.56: 18653 1.56 - 1.73: 0 1.73 - 1.90: 192 1.90 - 2.07: 48 Bond restraints: 32384 Sorted by residual: bond pdb=" C ASP R 99 " pdb=" O ASP R 99 " ideal model delta sigma weight residual 1.236 1.251 -0.015 1.15e-02 7.56e+03 1.60e+00 bond pdb=" C ASP W 99 " pdb=" O ASP W 99 " ideal model delta sigma weight residual 1.236 1.251 -0.014 1.15e-02 7.56e+03 1.51e+00 bond pdb=" C ASP A 99 " pdb=" O ASP A 99 " ideal model delta sigma weight residual 1.236 1.250 -0.014 1.15e-02 7.56e+03 1.46e+00 bond pdb=" C ASP T 99 " pdb=" O ASP T 99 " ideal model delta sigma weight residual 1.236 1.250 -0.014 1.15e-02 7.56e+03 1.46e+00 bond pdb=" C ASP O 99 " pdb=" O ASP O 99 " ideal model delta sigma weight residual 1.236 1.250 -0.014 1.15e-02 7.56e+03 1.46e+00 ... (remaining 32379 not shown) Histogram of bond angle deviations from ideal: 85.34 - 104.16: 285 104.16 - 122.98: 41844 122.98 - 141.80: 1783 141.80 - 160.62: 0 160.62 - 179.44: 24 Bond angle restraints: 43936 Sorted by residual: angle pdb=" C TYR R 25 " pdb=" N PHE R 26 " pdb=" CA PHE R 26 " ideal model delta sigma weight residual 120.29 116.11 4.18 1.42e+00 4.96e-01 8.65e+00 angle pdb=" C TYR W 25 " pdb=" N PHE W 26 " pdb=" CA PHE W 26 " ideal model delta sigma weight residual 120.29 116.25 4.04 1.42e+00 4.96e-01 8.09e+00 angle pdb=" C TYR I 25 " pdb=" N PHE I 26 " pdb=" CA PHE I 26 " ideal model delta sigma weight residual 120.29 116.26 4.03 1.42e+00 4.96e-01 8.05e+00 angle pdb=" C TYR G 25 " pdb=" N PHE G 26 " pdb=" CA PHE G 26 " ideal model delta sigma weight residual 120.29 116.33 3.96 1.42e+00 4.96e-01 7.76e+00 angle pdb=" C TYR N 25 " pdb=" N PHE N 26 " pdb=" CA PHE N 26 " ideal model delta sigma weight residual 120.29 116.34 3.95 1.42e+00 4.96e-01 7.74e+00 ... (remaining 43931 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.05: 16832 18.05 - 36.11: 2149 36.11 - 54.16: 286 54.16 - 72.22: 66 72.22 - 90.27: 51 Dihedral angle restraints: 19384 sinusoidal: 8064 harmonic: 11320 Sorted by residual: dihedral pdb=" C2B HEM K 301 " pdb=" C3B HEM K 301 " pdb=" CAB HEM K 301 " pdb=" CBB HEM K 301 " ideal model delta sinusoidal sigma weight residual -0.00 -39.28 39.28 2 1.00e+01 1.00e-02 1.92e+01 dihedral pdb=" CA PRO T 159 " pdb=" C PRO T 159 " pdb=" N ASP T 160 " pdb=" CA ASP T 160 " ideal model delta harmonic sigma weight residual -180.00 -158.46 -21.54 0 5.00e+00 4.00e-02 1.86e+01 dihedral pdb=" C2C HEM X 201 " pdb=" C3C HEM X 201 " pdb=" CAC HEM X 201 " pdb=" CBC HEM X 201 " ideal model delta sinusoidal sigma weight residual 0.00 37.74 -37.74 2 1.00e+01 1.00e-02 1.80e+01 ... (remaining 19381 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 2435 0.024 - 0.049: 1594 0.049 - 0.073: 595 0.073 - 0.097: 161 0.097 - 0.121: 91 Chirality restraints: 4876 Sorted by residual: chirality pdb=" CA PRO J 159 " pdb=" N PRO J 159 " pdb=" C PRO J 159 " pdb=" CB PRO J 159 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.68e-01 chirality pdb=" CA PRO L 161 " pdb=" N PRO L 161 " pdb=" C PRO L 161 " pdb=" CB PRO L 161 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.53e-01 chirality pdb=" CA PRO Q 161 " pdb=" N PRO Q 161 " pdb=" C PRO Q 161 " pdb=" CB PRO Q 161 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.44e-01 ... (remaining 4873 not shown) Planarity restraints: 5680 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" NB HEM K 301 " 0.002 2.00e-02 2.50e+03 1.07e-02 2.58e+00 pdb=" C1B HEM K 301 " -0.008 2.00e-02 2.50e+03 pdb=" C2B HEM K 301 " 0.009 2.00e-02 2.50e+03 pdb=" C3B HEM K 301 " -0.019 2.00e-02 2.50e+03 pdb=" C4B HEM K 301 " -0.008 2.00e-02 2.50e+03 pdb=" CAB HEM K 301 " 0.016 2.00e-02 2.50e+03 pdb=" CHB HEM K 301 " 0.011 2.00e-02 2.50e+03 pdb=" CHC HEM K 301 " 0.004 2.00e-02 2.50e+03 pdb=" CMB HEM K 301 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP G 37 " -0.016 2.00e-02 2.50e+03 9.74e-03 2.37e+00 pdb=" CG TRP G 37 " 0.025 2.00e-02 2.50e+03 pdb=" CD1 TRP G 37 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 TRP G 37 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP G 37 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP G 37 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP G 37 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP G 37 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP G 37 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP G 37 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" NB HEM O 202 " -0.024 2.00e-02 2.50e+03 1.03e-02 2.37e+00 pdb=" C1B HEM O 202 " 0.005 2.00e-02 2.50e+03 pdb=" C2B HEM O 202 " 0.006 2.00e-02 2.50e+03 pdb=" C3B HEM O 202 " -0.005 2.00e-02 2.50e+03 pdb=" C4B HEM O 202 " 0.000 2.00e-02 2.50e+03 pdb=" CAB HEM O 202 " -0.001 2.00e-02 2.50e+03 pdb=" CHB HEM O 202 " 0.010 2.00e-02 2.50e+03 pdb=" CHC HEM O 202 " 0.013 2.00e-02 2.50e+03 pdb=" CMB HEM O 202 " -0.004 2.00e-02 2.50e+03 ... (remaining 5677 not shown) Histogram of nonbonded interaction distances: 1.27 - 1.99: 26 1.99 - 2.72: 2837 2.72 - 3.45: 46904 3.45 - 4.17: 62780 4.17 - 4.90: 122129 Nonbonded interactions: 234676 Sorted by model distance: nonbonded pdb=" OE1 GLU J 18 " pdb=" OE1 GLU J 51 " model vdw 1.266 3.040 nonbonded pdb=" OE1 GLU B 18 " pdb=" OE1 GLU B 51 " model vdw 1.287 3.040 nonbonded pdb=" OE1 GLU T 18 " pdb=" OE1 GLU T 51 " model vdw 1.303 3.040 nonbonded pdb=" OE1 GLU P 18 " pdb=" OE1 GLU P 51 " model vdw 1.308 3.040 nonbonded pdb=" OE1 GLU L 18 " pdb=" OE1 GLU L 51 " model vdw 1.319 3.040 ... (remaining 234671 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 156 or (resid 157 and (name N or name CA or name \ C or name O or name CB )))) selection = (chain 'B' and resid 1 through 157) selection = (chain 'C' and (resid 1 through 156 or (resid 157 and (name N or name CA or name \ C or name O or name CB )))) selection = (chain 'D' and resid 1 through 157) selection = (chain 'E' and resid 1 through 157) selection = (chain 'F' and resid 1 through 157) selection = (chain 'G' and resid 1 through 157) selection = (chain 'H' and resid 1 through 157) selection = (chain 'I' and resid 1 through 157) selection = (chain 'J' and (resid 1 through 156 or (resid 157 and (name N or name CA or name \ C or name O or name CB )))) selection = (chain 'K' and resid 1 through 157) selection = (chain 'L' and (resid 1 through 156 or (resid 157 and (name N or name CA or name \ C or name O or name CB )))) selection = (chain 'M' and resid 1 through 157) selection = (chain 'N' and resid 1 through 157) selection = (chain 'O' and (resid 1 through 156 or (resid 157 and (name N or name CA or name \ C or name O or name CB )))) selection = (chain 'P' and resid 1 through 157) selection = (chain 'Q' and (resid 1 through 156 or (resid 157 and (name N or name CA or name \ C or name O or name CB )))) selection = (chain 'R' and resid 1 through 157) selection = (chain 'S' and resid 1 through 157) selection = (chain 'T' and (resid 1 through 156 or (resid 157 and (name N or name CA or name \ C or name O or name CB )))) selection = (chain 'U' and resid 1 through 157) selection = (chain 'V' and (resid 1 through 156 or (resid 157 and (name N or name CA or name \ C or name O or name CB )))) selection = (chain 'W' and resid 1 through 157) selection = (chain 'X' and resid 1 through 157) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Fe 36 7.16 5 S 96 5.16 5 C 20132 2.51 5 N 5428 2.21 5 O 6116 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 0.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 6.010 Check model and map are aligned: 0.460 Convert atoms to be neutral: 0.260 Process input model: 72.950 Find NCS groups from input model: 2.700 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Set scattering table: 0.020 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 86.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 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 : 0.007 0.082 32384 Z= 0.485 Angle : 0.716 15.729 43936 Z= 0.393 Chirality : 0.037 0.121 4876 Planarity : 0.003 0.027 5680 Dihedral : 15.846 90.272 12000 Min Nonbonded Distance : 1.266 Molprobity Statistics. All-atom Clashscore : 17.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer Outliers : 0.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.02 (0.11), residues: 3792 helix: -0.37 (0.08), residues: 2888 sheet: None (None), residues: 0 loop : -4.43 (0.15), residues: 904 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1015 residues out of total 3408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 1011 time to evaluate : 3.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP C 160 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP L 160 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP Q 160 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP V 160 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 4 residues processed: 1015 average time/residue: 0.4316 time to fit residues: 683.3911 Evaluate side-chains 669 residues out of total 3408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 665 time to evaluate : 3.955 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "ASP C 160 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP L 160 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP Q 160 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP V 160 " (corrupted residue). Skipping it. outliers start: 4 outliers final: 4 residues processed: 4 average time/residue: 0.2587 time to fit residues: 7.5525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 317 optimal weight: 1.9990 chunk 284 optimal weight: 2.9990 chunk 158 optimal weight: 10.0000 chunk 97 optimal weight: 4.9990 chunk 192 optimal weight: 2.9990 chunk 152 optimal weight: 4.9990 chunk 294 optimal weight: 7.9990 chunk 114 optimal weight: 5.9990 chunk 179 optimal weight: 0.3980 chunk 219 optimal weight: 0.1980 chunk 341 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 24 GLN B 130 HIS C 24 GLN D 24 GLN D 156 GLN F 24 GLN F 118 ASN F 156 GLN E 24 GLN E 130 HIS G 24 GLN H 24 GLN I 24 GLN J 24 GLN K 24 GLN L 24 GLN M 24 GLN M 156 GLN N 24 GLN N 118 ASN O 24 GLN P 129 HIS Q 24 GLN R 24 GLN S 24 GLN S 118 ASN S 130 HIS S 156 GLN T 24 GLN U 24 GLN U 130 HIS V 24 GLN W 24 GLN W 156 GLN X 118 ASN X 156 GLN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.3621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.054 32384 Z= 0.217 Angle : 0.629 11.623 43936 Z= 0.301 Chirality : 0.034 0.135 4876 Planarity : 0.003 0.020 5680 Dihedral : 6.778 87.084 4272 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer Outliers : 2.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.52 (0.13), residues: 3792 helix: 3.11 (0.08), residues: 2908 sheet: None (None), residues: 0 loop : -3.80 (0.16), residues: 884 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 892 residues out of total 3408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 818 time to evaluate : 3.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP C 160 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP L 160 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP Q 160 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP V 160 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash outliers start: 74 outliers final: 63 residues processed: 823 average time/residue: 0.3839 time to fit residues: 515.8609 Evaluate side-chains 708 residues out of total 3408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 645 time to evaluate : 3.772 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "ASP C 160 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP L 160 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP Q 160 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP V 160 " (corrupted residue). Skipping it. outliers start: 63 outliers final: 4 residues processed: 63 average time/residue: 0.2591 time to fit residues: 36.5771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 189 optimal weight: 10.0000 chunk 105 optimal weight: 10.0000 chunk 284 optimal weight: 8.9990 chunk 232 optimal weight: 4.9990 chunk 94 optimal weight: 10.0000 chunk 342 optimal weight: 3.9990 chunk 369 optimal weight: 6.9990 chunk 304 optimal weight: 0.0010 chunk 339 optimal weight: 20.0000 chunk 116 optimal weight: 7.9990 chunk 274 optimal weight: 2.9990 overall best weight: 3.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 GLN A 158 GLN B 28 HIS B 137 GLN C 28 HIS C 72 GLN D 72 GLN F 72 GLN E 28 HIS G 28 HIS H 28 HIS H 137 GLN I 28 HIS I 137 GLN J 158 GLN K 28 HIS K 137 GLN L 28 HIS M 72 GLN N 72 GLN O 137 GLN P 28 HIS Q 28 HIS Q 72 GLN R 72 GLN S 137 GLN T 137 GLN T 158 GLN U 28 HIS V 28 HIS V 72 GLN W 72 GLN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.3906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.065 32384 Z= 0.320 Angle : 0.675 22.917 43936 Z= 0.330 Chirality : 0.035 0.130 4876 Planarity : 0.003 0.023 5680 Dihedral : 6.919 89.605 4272 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer Outliers : 2.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.90 (0.13), residues: 3792 helix: 3.32 (0.08), residues: 2904 sheet: None (None), residues: 0 loop : -3.36 (0.21), residues: 888 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 776 residues out of total 3408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 681 time to evaluate : 4.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP C 160 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP L 160 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP Q 160 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP V 160 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash outliers start: 95 outliers final: 77 residues processed: 760 average time/residue: 0.4062 time to fit residues: 497.6632 Evaluate side-chains 702 residues out of total 3408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 625 time to evaluate : 3.780 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "ASP C 160 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP L 160 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP Q 160 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP V 160 " (corrupted residue). Skipping it. outliers start: 77 outliers final: 4 residues processed: 77 average time/residue: 0.2712 time to fit residues: 44.6904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 337 optimal weight: 1.9990 chunk 257 optimal weight: 6.9990 chunk 177 optimal weight: 3.9990 chunk 37 optimal weight: 5.9990 chunk 163 optimal weight: 0.8980 chunk 229 optimal weight: 5.9990 chunk 343 optimal weight: 0.8980 chunk 363 optimal weight: 0.7980 chunk 179 optimal weight: 7.9990 chunk 325 optimal weight: 4.9990 chunk 97 optimal weight: 0.0010 overall best weight: 0.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 28 HIS C 28 HIS F 137 GLN E 28 HIS G 28 HIS H 28 HIS I 28 HIS K 28 HIS L 28 HIS M 156 GLN P 28 HIS Q 28 HIS S 137 GLN U 28 HIS V 28 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.4990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 32384 Z= 0.179 Angle : 0.567 20.625 43936 Z= 0.264 Chirality : 0.032 0.127 4876 Planarity : 0.002 0.021 5680 Dihedral : 6.911 89.394 4272 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer Outliers : 1.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.81 (0.14), residues: 3792 helix: 3.95 (0.08), residues: 2952 sheet: None (None), residues: 0 loop : -3.41 (0.20), residues: 840 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 678 residues out of total 3408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 618 time to evaluate : 3.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP C 160 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP L 160 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP Q 160 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP V 160 " (corrupted residue). Skipping it. revert: symmetry clash outliers start: 60 outliers final: 32 residues processed: 642 average time/residue: 0.4022 time to fit residues: 419.9090 Evaluate side-chains 580 residues out of total 3408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 548 time to evaluate : 3.767 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "ASP C 160 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP L 160 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP Q 160 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP V 160 " (corrupted residue). Skipping it. outliers start: 32 outliers final: 4 residues processed: 32 average time/residue: 0.2765 time to fit residues: 22.1272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 302 optimal weight: 3.9990 chunk 206 optimal weight: 8.9990 chunk 5 optimal weight: 2.9990 chunk 270 optimal weight: 0.6980 chunk 149 optimal weight: 8.9990 chunk 310 optimal weight: 0.9980 chunk 251 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 185 optimal weight: 0.9980 chunk 326 optimal weight: 6.9990 chunk 91 optimal weight: 0.7980 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 137 GLN J 54 HIS J 137 GLN L 156 GLN N 156 GLN ** V 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 156 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.5166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.074 32384 Z= 0.186 Angle : 0.540 18.210 43936 Z= 0.254 Chirality : 0.032 0.135 4876 Planarity : 0.002 0.014 5680 Dihedral : 6.751 85.601 4272 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer Outliers : 1.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.99 (0.14), residues: 3792 helix: 4.05 (0.08), residues: 2960 sheet: None (None), residues: 0 loop : -3.26 (0.21), residues: 832 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 596 residues out of total 3408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 548 time to evaluate : 3.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP C 160 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP L 160 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP Q 160 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP V 160 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash outliers start: 48 outliers final: 40 residues processed: 563 average time/residue: 0.4377 time to fit residues: 401.3323 Evaluate side-chains 575 residues out of total 3408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 535 time to evaluate : 4.081 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "ASP C 160 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP L 160 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP Q 160 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP V 160 " (corrupted residue). Skipping it. outliers start: 40 outliers final: 4 residues processed: 40 average time/residue: 0.2770 time to fit residues: 26.7993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 122 optimal weight: 10.0000 chunk 327 optimal weight: 10.0000 chunk 71 optimal weight: 0.9990 chunk 213 optimal weight: 6.9990 chunk 89 optimal weight: 0.0570 chunk 363 optimal weight: 7.9990 chunk 301 optimal weight: 10.0000 chunk 168 optimal weight: 0.9990 chunk 30 optimal weight: 4.9990 chunk 120 optimal weight: 6.9990 chunk 190 optimal weight: 1.9990 overall best weight: 1.8106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 137 GLN L 54 HIS M 156 GLN N 156 GLN R 54 HIS R 137 GLN ** V 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.5120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.086 32384 Z= 0.212 Angle : 0.582 20.534 43936 Z= 0.272 Chirality : 0.032 0.156 4876 Planarity : 0.003 0.116 5680 Dihedral : 6.830 89.971 4272 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer Outliers : 1.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.99 (0.14), residues: 3792 helix: 4.03 (0.08), residues: 2960 sheet: None (None), residues: 0 loop : -3.19 (0.21), residues: 832 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 616 residues out of total 3408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 557 time to evaluate : 3.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP C 160 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP L 160 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP Q 160 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP V 160 " (corrupted residue). Skipping it. revert: symmetry clash outliers start: 59 outliers final: 45 residues processed: 579 average time/residue: 0.4082 time to fit residues: 380.7630 Evaluate side-chains 585 residues out of total 3408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 540 time to evaluate : 3.884 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "ASP C 160 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP L 160 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP Q 160 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP V 160 " (corrupted residue). Skipping it. outliers start: 45 outliers final: 4 residues processed: 45 average time/residue: 0.2617 time to fit residues: 27.8061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 350 optimal weight: 6.9990 chunk 41 optimal weight: 4.9990 chunk 207 optimal weight: 6.9990 chunk 265 optimal weight: 7.9990 chunk 205 optimal weight: 2.9990 chunk 306 optimal weight: 0.5980 chunk 203 optimal weight: 8.9990 chunk 362 optimal weight: 8.9990 chunk 226 optimal weight: 2.9990 chunk 220 optimal weight: 10.0000 chunk 167 optimal weight: 0.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 137 GLN L 156 GLN M 156 GLN N 137 GLN N 156 GLN R 137 GLN U 156 GLN V 137 GLN V 156 GLN X 137 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.5040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.089 32384 Z= 0.252 Angle : 0.611 20.437 43936 Z= 0.291 Chirality : 0.033 0.132 4876 Planarity : 0.003 0.074 5680 Dihedral : 6.908 88.684 4272 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer Outliers : 1.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.97 (0.14), residues: 3792 helix: 4.01 (0.08), residues: 2920 sheet: None (None), residues: 0 loop : -2.81 (0.23), residues: 872 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 594 residues out of total 3408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 548 time to evaluate : 3.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP C 160 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP L 160 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP Q 160 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP V 160 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash outliers start: 46 outliers final: 33 residues processed: 573 average time/residue: 0.4176 time to fit residues: 384.3450 Evaluate side-chains 567 residues out of total 3408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 534 time to evaluate : 4.755 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "ASP C 160 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP L 160 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP Q 160 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP V 160 " (corrupted residue). Skipping it. outliers start: 33 outliers final: 4 residues processed: 33 average time/residue: 0.2868 time to fit residues: 23.3129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 224 optimal weight: 6.9990 chunk 144 optimal weight: 0.9990 chunk 216 optimal weight: 0.9980 chunk 109 optimal weight: 0.0030 chunk 71 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 230 optimal weight: 1.9990 chunk 246 optimal weight: 5.9990 chunk 179 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 284 optimal weight: 0.8980 overall best weight: 0.7592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 54 HIS D 137 GLN H 54 HIS M 54 HIS N 156 GLN O 54 HIS P 54 HIS U 156 GLN ** V 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 54 HIS X 54 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.5830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.065 32384 Z= 0.186 Angle : 0.582 17.132 43936 Z= 0.272 Chirality : 0.032 0.134 4876 Planarity : 0.003 0.080 5680 Dihedral : 6.957 89.676 4272 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer Outliers : 0.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 4.40 (0.14), residues: 3792 helix: 4.35 (0.08), residues: 2904 sheet: None (None), residues: 0 loop : -2.65 (0.22), residues: 888 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 558 residues out of total 3408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 533 time to evaluate : 4.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP C 160 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP L 160 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP Q 160 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP V 160 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 17 residues processed: 544 average time/residue: 0.4293 time to fit residues: 371.0510 Evaluate side-chains 511 residues out of total 3408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 494 time to evaluate : 3.677 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "ASP C 160 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP L 160 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP Q 160 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP V 160 " (corrupted residue). Skipping it. outliers start: 17 outliers final: 4 residues processed: 17 average time/residue: 0.2628 time to fit residues: 13.4666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 329 optimal weight: 6.9990 chunk 347 optimal weight: 8.9990 chunk 316 optimal weight: 7.9990 chunk 337 optimal weight: 0.0040 chunk 203 optimal weight: 0.9990 chunk 147 optimal weight: 10.0000 chunk 265 optimal weight: 0.9990 chunk 103 optimal weight: 8.9990 chunk 305 optimal weight: 7.9990 chunk 319 optimal weight: 6.9990 chunk 336 optimal weight: 3.9990 overall best weight: 2.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 137 GLN F 54 HIS G 54 HIS N 156 GLN P 72 GLN R 156 GLN U 72 GLN U 156 GLN ** V 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 137 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.5255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.077 32384 Z= 0.260 Angle : 0.627 14.914 43936 Z= 0.307 Chirality : 0.034 0.152 4876 Planarity : 0.003 0.064 5680 Dihedral : 6.958 88.809 4272 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer Outliers : 1.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.98 (0.14), residues: 3792 helix: 3.98 (0.08), residues: 2928 sheet: None (None), residues: 0 loop : -2.72 (0.22), residues: 864 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 585 residues out of total 3408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 545 time to evaluate : 3.921 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP C 160 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP L 160 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP Q 160 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP V 160 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash outliers start: 40 outliers final: 29 residues processed: 560 average time/residue: 0.4256 time to fit residues: 378.2370 Evaluate side-chains 547 residues out of total 3408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 518 time to evaluate : 4.038 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "ASP C 160 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP L 160 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP Q 160 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP V 160 " (corrupted residue). Skipping it. outliers start: 29 outliers final: 4 residues processed: 29 average time/residue: 0.2563 time to fit residues: 19.2631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 221 optimal weight: 1.9990 chunk 357 optimal weight: 0.9990 chunk 217 optimal weight: 4.9990 chunk 169 optimal weight: 7.9990 chunk 248 optimal weight: 9.9990 chunk 374 optimal weight: 7.9990 chunk 344 optimal weight: 0.1980 chunk 298 optimal weight: 0.0020 chunk 30 optimal weight: 0.0470 chunk 230 optimal weight: 2.9990 chunk 182 optimal weight: 0.9990 overall best weight: 0.4490 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 HIS ** A 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 54 HIS ** C 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 137 GLN I 54 HIS N 156 GLN R 156 GLN U 156 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.6194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.057 32384 Z= 0.192 Angle : 0.600 13.044 43936 Z= 0.286 Chirality : 0.032 0.150 4876 Planarity : 0.003 0.083 5680 Dihedral : 7.008 87.397 4272 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer Outliers : 0.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 4.38 (0.14), residues: 3792 helix: 4.33 (0.08), residues: 2904 sheet: None (None), residues: 0 loop : -2.64 (0.21), residues: 888 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 534 residues out of total 3408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 520 time to evaluate : 3.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP C 160 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP L 160 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP Q 160 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP V 160 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 12 residues processed: 525 average time/residue: 0.4267 time to fit residues: 360.6945 Evaluate side-chains 494 residues out of total 3408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 482 time to evaluate : 3.416 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "ASP C 160 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP L 160 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP Q 160 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP V 160 " (corrupted residue). Skipping it. outliers start: 12 outliers final: 4 residues processed: 12 average time/residue: 0.2557 time to fit residues: 10.8634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 236 optimal weight: 10.0000 chunk 317 optimal weight: 5.9990 chunk 91 optimal weight: 0.7980 chunk 275 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 298 optimal weight: 4.9990 chunk 125 optimal weight: 0.1980 chunk 306 optimal weight: 0.0770 chunk 37 optimal weight: 6.9990 chunk 55 optimal weight: 5.9990 overall best weight: 1.0140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 137 GLN E 54 HIS L 72 GLN N 156 GLN R 156 GLN T 54 HIS U 156 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.156016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.139607 restraints weight = 48914.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.143188 restraints weight = 28522.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.145580 restraints weight = 19071.446| |-----------------------------------------------------------------------------| r_work (final): 0.3773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.6111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.062 32384 Z= 0.200 Angle : 0.606 14.886 43936 Z= 0.285 Chirality : 0.032 0.125 4876 Planarity : 0.003 0.062 5680 Dihedral : 6.809 88.125 4272 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer Outliers : 0.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 4.46 (0.14), residues: 3792 helix: 4.28 (0.08), residues: 2920 sheet: None (None), residues: 0 loop : -2.28 (0.22), residues: 872 =============================================================================== Job complete usr+sys time: 6926.91 seconds wall clock time: 125 minutes 41.63 seconds (7541.63 seconds total)