Starting phenix.real_space_refine (version: dev) on Fri May 13 11:19:44 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mrw_9214/05_2022/6mrw_9214_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mrw_9214/05_2022/6mrw_9214.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mrw_9214/05_2022/6mrw_9214.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mrw_9214/05_2022/6mrw_9214.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mrw_9214/05_2022/6mrw_9214_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mrw_9214/05_2022/6mrw_9214_neut.pdb" } resolution = 4.3 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= 0.001 sd= 0.005 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 "A ARG 49": "NH1" <-> "NH2" Residue "B ARG 49": "NH1" <-> "NH2" Residue "C ARG 49": "NH1" <-> "NH2" Residue "D ARG 49": "NH1" <-> "NH2" Residue "E ARG 49": "NH1" <-> "NH2" Residue "F ARG 49": "NH1" <-> "NH2" Residue "G ARG 49": "NH1" <-> "NH2" Residue "H ARG 49": "NH1" <-> "NH2" Residue "I ARG 49": "NH1" <-> "NH2" Residue "J ARG 49": "NH1" <-> "NH2" Residue "K ARG 49": "NH1" <-> "NH2" Residue "L ARG 49": "NH1" <-> "NH2" Residue "M ARG 49": "NH1" <-> "NH2" Residue "N ARG 49": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib" Total number of atoms: 31346 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2239 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 3, 'TRANS': 281} Chain: "B" Number of atoms: 2239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2239 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 3, 'TRANS': 281} Chain: "C" Number of atoms: 2239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2239 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 3, 'TRANS': 281} Chain: "D" Number of atoms: 2239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2239 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 3, 'TRANS': 281} Chain: "E" Number of atoms: 2239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2239 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 3, 'TRANS': 281} Chain: "F" Number of atoms: 2239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2239 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 3, 'TRANS': 281} Chain: "G" Number of atoms: 2239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2239 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 3, 'TRANS': 281} Chain: "H" Number of atoms: 2239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2239 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 3, 'TRANS': 281} Chain: "I" Number of atoms: 2239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2239 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 3, 'TRANS': 281} Chain: "J" Number of atoms: 2239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2239 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 3, 'TRANS': 281} Chain: "K" Number of atoms: 2239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2239 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 3, 'TRANS': 281} Chain: "L" Number of atoms: 2239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2239 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 3, 'TRANS': 281} Chain: "M" Number of atoms: 2239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2239 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 3, 'TRANS': 281} Chain: "N" Number of atoms: 2239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2239 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 3, 'TRANS': 281} Time building chain proxies: 12.85, per 1000 atoms: 0.41 Number of scatterers: 31346 At special positions: 0 Unit cell: (146.59, 144.45, 156.22, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 70 16.00 O 6230 8.00 N 5040 7.00 C 20006 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=0, symmetry=0 Time building additional restraints: 9.76 Conformation dependent library (CDL) restraints added in 4.2 seconds 7924 Ramachandran restraints generated. 3962 Oldfield, 0 Emsley, 3962 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7644 Finding SS restraints... Secondary structure from input PDB file: 98 helices and 0 sheets defined 92.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'A' and resid 8 through 35 removed outlier: 3.560A pdb=" N GLU A 18 " --> pdb=" O LYS A 14 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLN A 33 " --> pdb=" O LYS A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 101 removed outlier: 3.631A pdb=" N LYS A 51 " --> pdb=" O LEU A 47 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N VAL A 60 " --> pdb=" O GLN A 56 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LEU A 61 " --> pdb=" O ALA A 57 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N VAL A 89 " --> pdb=" O GLU A 85 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLN A 92 " --> pdb=" O GLY A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 140 removed outlier: 3.562A pdb=" N ASP A 114 " --> pdb=" O SER A 110 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N THR A 125 " --> pdb=" O ASP A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 181 removed outlier: 3.924A pdb=" N LEU A 149 " --> pdb=" O SER A 145 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER A 160 " --> pdb=" O THR A 156 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASP A 171 " --> pdb=" O GLN A 167 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS A 172 " --> pdb=" O SER A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 202 removed outlier: 3.603A pdb=" N LEU A 192 " --> pdb=" O GLY A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 265 removed outlier: 3.560A pdb=" N ILE A 253 " --> pdb=" O ALA A 249 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU A 256 " --> pdb=" O GLU A 252 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ASP A 265 " --> pdb=" O ARG A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 291 Processing helix chain 'B' and resid 9 through 35 removed outlier: 3.561A pdb=" N GLU B 18 " --> pdb=" O LYS B 14 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLN B 33 " --> pdb=" O LYS B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 101 removed outlier: 3.631A pdb=" N LYS B 51 " --> pdb=" O LEU B 47 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N VAL B 60 " --> pdb=" O GLN B 56 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LEU B 61 " --> pdb=" O ALA B 57 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N VAL B 89 " --> pdb=" O GLU B 85 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLN B 92 " --> pdb=" O GLY B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 140 removed outlier: 3.562A pdb=" N ASP B 114 " --> pdb=" O SER B 110 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N THR B 125 " --> pdb=" O ASP B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 181 removed outlier: 3.925A pdb=" N LEU B 149 " --> pdb=" O SER B 145 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER B 160 " --> pdb=" O THR B 156 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASP B 171 " --> pdb=" O GLN B 167 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYS B 172 " --> pdb=" O SER B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 202 removed outlier: 3.605A pdb=" N LEU B 192 " --> pdb=" O GLY B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 265 removed outlier: 3.561A pdb=" N ILE B 253 " --> pdb=" O ALA B 249 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU B 256 " --> pdb=" O GLU B 252 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ASP B 265 " --> pdb=" O ARG B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 291 Processing helix chain 'C' and resid 9 through 35 removed outlier: 3.561A pdb=" N GLU C 18 " --> pdb=" O LYS C 14 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLN C 33 " --> pdb=" O LYS C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 36 through 101 removed outlier: 3.631A pdb=" N LYS C 51 " --> pdb=" O LEU C 47 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N VAL C 60 " --> pdb=" O GLN C 56 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LEU C 61 " --> pdb=" O ALA C 57 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N VAL C 89 " --> pdb=" O GLU C 85 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLN C 92 " --> pdb=" O GLY C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 140 removed outlier: 3.563A pdb=" N ASP C 114 " --> pdb=" O SER C 110 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N THR C 125 " --> pdb=" O ASP C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 181 removed outlier: 3.925A pdb=" N LEU C 149 " --> pdb=" O SER C 145 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER C 160 " --> pdb=" O THR C 156 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASP C 171 " --> pdb=" O GLN C 167 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYS C 172 " --> pdb=" O SER C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 188 through 202 removed outlier: 3.604A pdb=" N LEU C 192 " --> pdb=" O GLY C 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 265 removed outlier: 3.560A pdb=" N ILE C 253 " --> pdb=" O ALA C 249 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU C 256 " --> pdb=" O GLU C 252 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ASP C 265 " --> pdb=" O ARG C 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 291 Processing helix chain 'D' and resid 9 through 35 removed outlier: 3.561A pdb=" N GLU D 18 " --> pdb=" O LYS D 14 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLN D 33 " --> pdb=" O LYS D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 36 through 101 removed outlier: 3.631A pdb=" N LYS D 51 " --> pdb=" O LEU D 47 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N VAL D 60 " --> pdb=" O GLN D 56 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LEU D 61 " --> pdb=" O ALA D 57 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N VAL D 89 " --> pdb=" O GLU D 85 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLN D 92 " --> pdb=" O GLY D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 140 removed outlier: 3.563A pdb=" N ASP D 114 " --> pdb=" O SER D 110 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N THR D 125 " --> pdb=" O ASP D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 141 through 181 removed outlier: 3.925A pdb=" N LEU D 149 " --> pdb=" O SER D 145 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N SER D 160 " --> pdb=" O THR D 156 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASP D 171 " --> pdb=" O GLN D 167 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS D 172 " --> pdb=" O SER D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 188 through 202 removed outlier: 3.605A pdb=" N LEU D 192 " --> pdb=" O GLY D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 265 removed outlier: 3.560A pdb=" N ILE D 253 " --> pdb=" O ALA D 249 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU D 256 " --> pdb=" O GLU D 252 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ASP D 265 " --> pdb=" O ARG D 261 " (cutoff:3.500A) Processing helix chain 'D' and resid 271 through 291 Processing helix chain 'E' and resid 9 through 35 removed outlier: 3.561A pdb=" N GLU E 18 " --> pdb=" O LYS E 14 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLN E 33 " --> pdb=" O LYS E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 101 removed outlier: 3.631A pdb=" N LYS E 51 " --> pdb=" O LEU E 47 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N VAL E 60 " --> pdb=" O GLN E 56 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LEU E 61 " --> pdb=" O ALA E 57 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N VAL E 89 " --> pdb=" O GLU E 85 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLN E 92 " --> pdb=" O GLY E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 140 removed outlier: 3.563A pdb=" N ASP E 114 " --> pdb=" O SER E 110 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N THR E 125 " --> pdb=" O ASP E 121 " (cutoff:3.500A) Processing helix chain 'E' and resid 141 through 181 removed outlier: 3.925A pdb=" N LEU E 149 " --> pdb=" O SER E 145 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER E 160 " --> pdb=" O THR E 156 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASP E 171 " --> pdb=" O GLN E 167 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS E 172 " --> pdb=" O SER E 168 " (cutoff:3.500A) Processing helix chain 'E' and resid 188 through 202 removed outlier: 3.604A pdb=" N LEU E 192 " --> pdb=" O GLY E 188 " (cutoff:3.500A) Processing helix chain 'E' and resid 206 through 265 removed outlier: 3.560A pdb=" N ILE E 253 " --> pdb=" O ALA E 249 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLU E 256 " --> pdb=" O GLU E 252 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ASP E 265 " --> pdb=" O ARG E 261 " (cutoff:3.500A) Processing helix chain 'E' and resid 271 through 291 Processing helix chain 'F' and resid 9 through 35 removed outlier: 3.561A pdb=" N GLU F 18 " --> pdb=" O LYS F 14 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLN F 33 " --> pdb=" O LYS F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 36 through 101 removed outlier: 3.630A pdb=" N LYS F 51 " --> pdb=" O LEU F 47 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N VAL F 60 " --> pdb=" O GLN F 56 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LEU F 61 " --> pdb=" O ALA F 57 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N VAL F 89 " --> pdb=" O GLU F 85 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLN F 92 " --> pdb=" O GLY F 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 108 through 140 removed outlier: 3.563A pdb=" N ASP F 114 " --> pdb=" O SER F 110 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N THR F 125 " --> pdb=" O ASP F 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 141 through 181 removed outlier: 3.925A pdb=" N LEU F 149 " --> pdb=" O SER F 145 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N SER F 160 " --> pdb=" O THR F 156 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASP F 171 " --> pdb=" O GLN F 167 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYS F 172 " --> pdb=" O SER F 168 " (cutoff:3.500A) Processing helix chain 'F' and resid 188 through 202 removed outlier: 3.604A pdb=" N LEU F 192 " --> pdb=" O GLY F 188 " (cutoff:3.500A) Processing helix chain 'F' and resid 206 through 265 removed outlier: 3.560A pdb=" N ILE F 253 " --> pdb=" O ALA F 249 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU F 256 " --> pdb=" O GLU F 252 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ASP F 265 " --> pdb=" O ARG F 261 " (cutoff:3.500A) Processing helix chain 'F' and resid 271 through 291 Processing helix chain 'G' and resid 9 through 35 removed outlier: 3.560A pdb=" N GLU G 18 " --> pdb=" O LYS G 14 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLN G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 36 through 101 removed outlier: 3.630A pdb=" N LYS G 51 " --> pdb=" O LEU G 47 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N VAL G 60 " --> pdb=" O GLN G 56 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LEU G 61 " --> pdb=" O ALA G 57 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N VAL G 89 " --> pdb=" O GLU G 85 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLN G 92 " --> pdb=" O GLY G 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 108 through 140 removed outlier: 3.562A pdb=" N ASP G 114 " --> pdb=" O SER G 110 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N THR G 125 " --> pdb=" O ASP G 121 " (cutoff:3.500A) Processing helix chain 'G' and resid 141 through 181 removed outlier: 3.924A pdb=" N LEU G 149 " --> pdb=" O SER G 145 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER G 160 " --> pdb=" O THR G 156 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASP G 171 " --> pdb=" O GLN G 167 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYS G 172 " --> pdb=" O SER G 168 " (cutoff:3.500A) Processing helix chain 'G' and resid 188 through 202 removed outlier: 3.603A pdb=" N LEU G 192 " --> pdb=" O GLY G 188 " (cutoff:3.500A) Processing helix chain 'G' and resid 206 through 265 removed outlier: 3.560A pdb=" N ILE G 253 " --> pdb=" O ALA G 249 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU G 256 " --> pdb=" O GLU G 252 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ASP G 265 " --> pdb=" O ARG G 261 " (cutoff:3.500A) Processing helix chain 'G' and resid 271 through 291 Processing helix chain 'H' and resid 9 through 35 removed outlier: 3.561A pdb=" N GLU H 18 " --> pdb=" O LYS H 14 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLN H 33 " --> pdb=" O LYS H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 36 through 101 removed outlier: 3.631A pdb=" N LYS H 51 " --> pdb=" O LEU H 47 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N VAL H 60 " --> pdb=" O GLN H 56 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LEU H 61 " --> pdb=" O ALA H 57 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N VAL H 89 " --> pdb=" O GLU H 85 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLN H 92 " --> pdb=" O GLY H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 108 through 140 removed outlier: 3.562A pdb=" N ASP H 114 " --> pdb=" O SER H 110 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N THR H 125 " --> pdb=" O ASP H 121 " (cutoff:3.500A) Processing helix chain 'H' and resid 141 through 181 removed outlier: 3.925A pdb=" N LEU H 149 " --> pdb=" O SER H 145 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER H 160 " --> pdb=" O THR H 156 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASP H 171 " --> pdb=" O GLN H 167 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS H 172 " --> pdb=" O SER H 168 " (cutoff:3.500A) Processing helix chain 'H' and resid 188 through 202 removed outlier: 3.604A pdb=" N LEU H 192 " --> pdb=" O GLY H 188 " (cutoff:3.500A) Processing helix chain 'H' and resid 206 through 265 removed outlier: 3.560A pdb=" N ILE H 253 " --> pdb=" O ALA H 249 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLU H 256 " --> pdb=" O GLU H 252 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ASP H 265 " --> pdb=" O ARG H 261 " (cutoff:3.500A) Processing helix chain 'H' and resid 271 through 291 Processing helix chain 'I' and resid 9 through 35 removed outlier: 3.560A pdb=" N GLU I 18 " --> pdb=" O LYS I 14 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLN I 33 " --> pdb=" O LYS I 29 " (cutoff:3.500A) Processing helix chain 'I' and resid 36 through 101 removed outlier: 3.631A pdb=" N LYS I 51 " --> pdb=" O LEU I 47 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N VAL I 60 " --> pdb=" O GLN I 56 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LEU I 61 " --> pdb=" O ALA I 57 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N VAL I 89 " --> pdb=" O GLU I 85 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLN I 92 " --> pdb=" O GLY I 88 " (cutoff:3.500A) Processing helix chain 'I' and resid 108 through 140 removed outlier: 3.563A pdb=" N ASP I 114 " --> pdb=" O SER I 110 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N THR I 125 " --> pdb=" O ASP I 121 " (cutoff:3.500A) Processing helix chain 'I' and resid 141 through 181 removed outlier: 3.924A pdb=" N LEU I 149 " --> pdb=" O SER I 145 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER I 160 " --> pdb=" O THR I 156 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASP I 171 " --> pdb=" O GLN I 167 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYS I 172 " --> pdb=" O SER I 168 " (cutoff:3.500A) Processing helix chain 'I' and resid 188 through 202 removed outlier: 3.604A pdb=" N LEU I 192 " --> pdb=" O GLY I 188 " (cutoff:3.500A) Processing helix chain 'I' and resid 206 through 265 removed outlier: 3.560A pdb=" N ILE I 253 " --> pdb=" O ALA I 249 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU I 256 " --> pdb=" O GLU I 252 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ASP I 265 " --> pdb=" O ARG I 261 " (cutoff:3.500A) Processing helix chain 'I' and resid 271 through 291 Processing helix chain 'J' and resid 9 through 35 removed outlier: 3.559A pdb=" N GLU J 18 " --> pdb=" O LYS J 14 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLN J 33 " --> pdb=" O LYS J 29 " (cutoff:3.500A) Processing helix chain 'J' and resid 36 through 101 removed outlier: 3.630A pdb=" N LYS J 51 " --> pdb=" O LEU J 47 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N VAL J 60 " --> pdb=" O GLN J 56 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LEU J 61 " --> pdb=" O ALA J 57 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N VAL J 89 " --> pdb=" O GLU J 85 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLN J 92 " --> pdb=" O GLY J 88 " (cutoff:3.500A) Processing helix chain 'J' and resid 108 through 140 removed outlier: 3.562A pdb=" N ASP J 114 " --> pdb=" O SER J 110 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N THR J 125 " --> pdb=" O ASP J 121 " (cutoff:3.500A) Processing helix chain 'J' and resid 141 through 181 removed outlier: 3.925A pdb=" N LEU J 149 " --> pdb=" O SER J 145 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER J 160 " --> pdb=" O THR J 156 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASP J 171 " --> pdb=" O GLN J 167 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS J 172 " --> pdb=" O SER J 168 " (cutoff:3.500A) Processing helix chain 'J' and resid 188 through 202 removed outlier: 3.604A pdb=" N LEU J 192 " --> pdb=" O GLY J 188 " (cutoff:3.500A) Processing helix chain 'J' and resid 206 through 265 removed outlier: 3.560A pdb=" N ILE J 253 " --> pdb=" O ALA J 249 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU J 256 " --> pdb=" O GLU J 252 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ASP J 265 " --> pdb=" O ARG J 261 " (cutoff:3.500A) Processing helix chain 'J' and resid 271 through 291 Processing helix chain 'K' and resid 9 through 35 removed outlier: 3.560A pdb=" N GLU K 18 " --> pdb=" O LYS K 14 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLN K 33 " --> pdb=" O LYS K 29 " (cutoff:3.500A) Processing helix chain 'K' and resid 36 through 101 removed outlier: 3.630A pdb=" N LYS K 51 " --> pdb=" O LEU K 47 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N VAL K 60 " --> pdb=" O GLN K 56 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LEU K 61 " --> pdb=" O ALA K 57 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N VAL K 89 " --> pdb=" O GLU K 85 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLN K 92 " --> pdb=" O GLY K 88 " (cutoff:3.500A) Processing helix chain 'K' and resid 108 through 140 removed outlier: 3.562A pdb=" N ASP K 114 " --> pdb=" O SER K 110 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N THR K 125 " --> pdb=" O ASP K 121 " (cutoff:3.500A) Processing helix chain 'K' and resid 141 through 181 removed outlier: 3.925A pdb=" N LEU K 149 " --> pdb=" O SER K 145 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER K 160 " --> pdb=" O THR K 156 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASP K 171 " --> pdb=" O GLN K 167 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYS K 172 " --> pdb=" O SER K 168 " (cutoff:3.500A) Processing helix chain 'K' and resid 188 through 202 removed outlier: 3.604A pdb=" N LEU K 192 " --> pdb=" O GLY K 188 " (cutoff:3.500A) Processing helix chain 'K' and resid 206 through 265 removed outlier: 3.559A pdb=" N ILE K 253 " --> pdb=" O ALA K 249 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU K 256 " --> pdb=" O GLU K 252 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ASP K 265 " --> pdb=" O ARG K 261 " (cutoff:3.500A) Processing helix chain 'K' and resid 271 through 291 Processing helix chain 'L' and resid 9 through 35 removed outlier: 3.561A pdb=" N GLU L 18 " --> pdb=" O LYS L 14 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLN L 33 " --> pdb=" O LYS L 29 " (cutoff:3.500A) Processing helix chain 'L' and resid 36 through 101 removed outlier: 3.630A pdb=" N LYS L 51 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N VAL L 60 " --> pdb=" O GLN L 56 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LEU L 61 " --> pdb=" O ALA L 57 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N VAL L 89 " --> pdb=" O GLU L 85 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLN L 92 " --> pdb=" O GLY L 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 108 through 140 removed outlier: 3.563A pdb=" N ASP L 114 " --> pdb=" O SER L 110 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N THR L 125 " --> pdb=" O ASP L 121 " (cutoff:3.500A) Processing helix chain 'L' and resid 141 through 181 removed outlier: 3.924A pdb=" N LEU L 149 " --> pdb=" O SER L 145 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N SER L 160 " --> pdb=" O THR L 156 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASP L 171 " --> pdb=" O GLN L 167 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS L 172 " --> pdb=" O SER L 168 " (cutoff:3.500A) Processing helix chain 'L' and resid 188 through 202 removed outlier: 3.604A pdb=" N LEU L 192 " --> pdb=" O GLY L 188 " (cutoff:3.500A) Processing helix chain 'L' and resid 206 through 265 removed outlier: 3.560A pdb=" N ILE L 253 " --> pdb=" O ALA L 249 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU L 256 " --> pdb=" O GLU L 252 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ASP L 265 " --> pdb=" O ARG L 261 " (cutoff:3.500A) Processing helix chain 'L' and resid 271 through 291 Processing helix chain 'M' and resid 9 through 35 removed outlier: 3.561A pdb=" N GLU M 18 " --> pdb=" O LYS M 14 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLN M 33 " --> pdb=" O LYS M 29 " (cutoff:3.500A) Processing helix chain 'M' and resid 36 through 101 removed outlier: 3.632A pdb=" N LYS M 51 " --> pdb=" O LEU M 47 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N VAL M 60 " --> pdb=" O GLN M 56 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LEU M 61 " --> pdb=" O ALA M 57 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N VAL M 89 " --> pdb=" O GLU M 85 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLN M 92 " --> pdb=" O GLY M 88 " (cutoff:3.500A) Processing helix chain 'M' and resid 108 through 140 removed outlier: 3.563A pdb=" N ASP M 114 " --> pdb=" O SER M 110 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N THR M 125 " --> pdb=" O ASP M 121 " (cutoff:3.500A) Processing helix chain 'M' and resid 141 through 181 removed outlier: 3.925A pdb=" N LEU M 149 " --> pdb=" O SER M 145 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER M 160 " --> pdb=" O THR M 156 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASP M 171 " --> pdb=" O GLN M 167 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYS M 172 " --> pdb=" O SER M 168 " (cutoff:3.500A) Processing helix chain 'M' and resid 188 through 202 removed outlier: 3.603A pdb=" N LEU M 192 " --> pdb=" O GLY M 188 " (cutoff:3.500A) Processing helix chain 'M' and resid 206 through 265 removed outlier: 3.560A pdb=" N ILE M 253 " --> pdb=" O ALA M 249 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLU M 256 " --> pdb=" O GLU M 252 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ASP M 265 " --> pdb=" O ARG M 261 " (cutoff:3.500A) Processing helix chain 'M' and resid 271 through 291 Processing helix chain 'N' and resid 9 through 35 removed outlier: 3.561A pdb=" N GLU N 18 " --> pdb=" O LYS N 14 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLN N 33 " --> pdb=" O LYS N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 36 through 101 removed outlier: 3.631A pdb=" N LYS N 51 " --> pdb=" O LEU N 47 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N VAL N 60 " --> pdb=" O GLN N 56 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LEU N 61 " --> pdb=" O ALA N 57 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N VAL N 89 " --> pdb=" O GLU N 85 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLN N 92 " --> pdb=" O GLY N 88 " (cutoff:3.500A) Processing helix chain 'N' and resid 108 through 140 removed outlier: 3.562A pdb=" N ASP N 114 " --> pdb=" O SER N 110 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N THR N 125 " --> pdb=" O ASP N 121 " (cutoff:3.500A) Processing helix chain 'N' and resid 141 through 181 removed outlier: 3.925A pdb=" N LEU N 149 " --> pdb=" O SER N 145 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N SER N 160 " --> pdb=" O THR N 156 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASP N 171 " --> pdb=" O GLN N 167 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYS N 172 " --> pdb=" O SER N 168 " (cutoff:3.500A) Processing helix chain 'N' and resid 188 through 202 removed outlier: 3.604A pdb=" N LEU N 192 " --> pdb=" O GLY N 188 " (cutoff:3.500A) Processing helix chain 'N' and resid 206 through 265 removed outlier: 3.560A pdb=" N ILE N 253 " --> pdb=" O ALA N 249 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU N 256 " --> pdb=" O GLU N 252 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ASP N 265 " --> pdb=" O ARG N 261 " (cutoff:3.500A) Processing helix chain 'N' and resid 271 through 291 3053 hydrogen bonds defined for protein. 9159 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.37 Time building geometry restraints manager: 10.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9848 1.34 - 1.45: 4378 1.45 - 1.57: 17442 1.57 - 1.69: 0 1.69 - 1.80: 112 Bond restraints: 31780 Sorted by residual: bond pdb=" CA ILE H 208 " pdb=" C ILE H 208 " ideal model delta sigma weight residual 1.520 1.535 -0.015 8.80e-03 1.29e+04 3.02e+00 bond pdb=" CA ILE D 208 " pdb=" C ILE D 208 " ideal model delta sigma weight residual 1.520 1.535 -0.015 8.80e-03 1.29e+04 3.00e+00 bond pdb=" CA ILE N 208 " pdb=" C ILE N 208 " ideal model delta sigma weight residual 1.520 1.535 -0.015 8.80e-03 1.29e+04 2.98e+00 bond pdb=" CA ILE G 208 " pdb=" C ILE G 208 " ideal model delta sigma weight residual 1.520 1.535 -0.015 8.80e-03 1.29e+04 2.91e+00 bond pdb=" CA ILE I 208 " pdb=" C ILE I 208 " ideal model delta sigma weight residual 1.520 1.535 -0.015 8.80e-03 1.29e+04 2.90e+00 ... (remaining 31775 not shown) Histogram of bond angle deviations from ideal: 98.89 - 105.90: 210 105.90 - 112.90: 17698 112.90 - 119.91: 11445 119.91 - 126.91: 13445 126.91 - 133.92: 112 Bond angle restraints: 42910 Sorted by residual: angle pdb=" C LEU K 207 " pdb=" N ILE K 208 " pdb=" CA ILE K 208 " ideal model delta sigma weight residual 120.24 124.34 -4.10 6.30e-01 2.52e+00 4.23e+01 angle pdb=" C LEU N 207 " pdb=" N ILE N 208 " pdb=" CA ILE N 208 " ideal model delta sigma weight residual 120.24 124.32 -4.08 6.30e-01 2.52e+00 4.20e+01 angle pdb=" C LEU B 207 " pdb=" N ILE B 208 " pdb=" CA ILE B 208 " ideal model delta sigma weight residual 120.24 124.31 -4.07 6.30e-01 2.52e+00 4.16e+01 angle pdb=" C LEU A 207 " pdb=" N ILE A 208 " pdb=" CA ILE A 208 " ideal model delta sigma weight residual 120.24 124.30 -4.06 6.30e-01 2.52e+00 4.16e+01 angle pdb=" C LEU D 207 " pdb=" N ILE D 208 " pdb=" CA ILE D 208 " ideal model delta sigma weight residual 120.24 124.30 -4.06 6.30e-01 2.52e+00 4.15e+01 ... (remaining 42905 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.31: 18480 15.31 - 30.61: 602 30.61 - 45.92: 294 45.92 - 61.22: 0 61.22 - 76.53: 28 Dihedral angle restraints: 19404 sinusoidal: 7602 harmonic: 11802 Sorted by residual: dihedral pdb=" CA PHE D 141 " pdb=" C PHE D 141 " pdb=" N ASN D 142 " pdb=" CA ASN D 142 " ideal model delta harmonic sigma weight residual 180.00 -146.88 -33.12 0 5.00e+00 4.00e-02 4.39e+01 dihedral pdb=" CA PHE G 141 " pdb=" C PHE G 141 " pdb=" N ASN G 142 " pdb=" CA ASN G 142 " ideal model delta harmonic sigma weight residual 180.00 -146.88 -33.12 0 5.00e+00 4.00e-02 4.39e+01 dihedral pdb=" CA PHE M 141 " pdb=" C PHE M 141 " pdb=" N ASN M 142 " pdb=" CA ASN M 142 " ideal model delta harmonic sigma weight residual 180.00 -146.89 -33.11 0 5.00e+00 4.00e-02 4.38e+01 ... (remaining 19401 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 3244 0.035 - 0.070: 1415 0.070 - 0.105: 290 0.105 - 0.140: 71 0.140 - 0.175: 34 Chirality restraints: 5054 Sorted by residual: chirality pdb=" CA TYR B 54 " pdb=" N TYR B 54 " pdb=" C TYR B 54 " pdb=" CB TYR B 54 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.70e-01 chirality pdb=" CA TYR A 54 " pdb=" N TYR A 54 " pdb=" C TYR A 54 " pdb=" CB TYR A 54 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.18 2.00e-01 2.50e+01 7.69e-01 chirality pdb=" CA TYR F 54 " pdb=" N TYR F 54 " pdb=" C TYR F 54 " pdb=" CB TYR F 54 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.60e-01 ... (remaining 5051 not shown) Planarity restraints: 5404 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B 35 " -0.029 5.00e-02 4.00e+02 4.44e-02 3.16e+00 pdb=" N PRO B 36 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO B 36 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 36 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE M 35 " -0.029 5.00e-02 4.00e+02 4.43e-02 3.14e+00 pdb=" N PRO M 36 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO M 36 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO M 36 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE D 35 " -0.029 5.00e-02 4.00e+02 4.43e-02 3.14e+00 pdb=" N PRO D 36 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO D 36 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO D 36 " -0.025 5.00e-02 4.00e+02 ... (remaining 5401 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 308 2.64 - 3.21: 30315 3.21 - 3.77: 51717 3.77 - 4.34: 65191 4.34 - 4.90: 107320 Nonbonded interactions: 254851 Sorted by model distance: nonbonded pdb=" OD1 ASP L 21 " pdb=" NZ LYS M 29 " model vdw 2.080 2.520 nonbonded pdb=" OH TYR K 54 " pdb=" OD2 ASP K 158 " model vdw 2.131 2.440 nonbonded pdb=" OH TYR N 54 " pdb=" OD2 ASP N 158 " model vdw 2.132 2.440 nonbonded pdb=" OH TYR F 54 " pdb=" OD2 ASP F 158 " model vdw 2.132 2.440 nonbonded pdb=" OH TYR I 54 " pdb=" OD2 ASP I 158 " model vdw 2.132 2.440 ... (remaining 254846 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' } 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: 4 Type Number sf(0) Gaussians S 70 5.16 5 C 20006 2.51 5 N 5040 2.21 5 O 6230 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: 0.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.270 Construct map_model_manager: 0.020 Extract box with map and model: 6.380 Check model and map are aligned: 0.350 Convert atoms to be neutral: 0.200 Process input model: 58.170 Find NCS groups from input model: 1.520 Set up NCS constraints: 0.160 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:2.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 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 : 0.006 0.044 31780 Z= 0.373 Angle : 0.982 8.194 42910 Z= 0.651 Chirality : 0.042 0.175 5054 Planarity : 0.005 0.044 5404 Dihedral : 10.348 76.525 11760 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer Outliers : 0.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.36 % 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: -0.19 (0.12), residues: 3962 helix: 0.25 (0.08), residues: 3626 sheet: None (None), residues: 0 loop : -3.14 (0.28), residues: 336 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7924 Ramachandran restraints generated. 3962 Oldfield, 0 Emsley, 3962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7924 Ramachandran restraints generated. 3962 Oldfield, 0 Emsley, 3962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 3430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 269 time to evaluate : 2.838 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 0 residues processed: 283 average time/residue: 0.3116 time to fit residues: 144.1200 Evaluate side-chains 129 residues out of total 3430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 129 time to evaluate : 2.812 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.7453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 331 optimal weight: 4.9990 chunk 297 optimal weight: 40.0000 chunk 164 optimal weight: 3.9990 chunk 101 optimal weight: 40.0000 chunk 200 optimal weight: 6.9990 chunk 158 optimal weight: 40.0000 chunk 307 optimal weight: 9.9990 chunk 118 optimal weight: 0.8980 chunk 186 optimal weight: 30.0000 chunk 228 optimal weight: 5.9990 chunk 355 optimal weight: 8.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 227 ASN A 233 ASN A 289 GLN B 227 ASN B 233 ASN B 289 GLN C 227 ASN C 289 GLN D 227 ASN D 289 GLN E 220 ASN E 227 ASN E 289 GLN F 220 ASN F 227 ASN F 289 GLN G 227 ASN G 289 GLN H 227 ASN H 289 GLN I 227 ASN I 289 GLN J 220 ASN J 227 ASN J 289 GLN K 227 ASN K 289 GLN L 227 ASN L 289 GLN ** M 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 227 ASN M 289 GLN N 220 ASN N 227 ASN N 289 GLN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 31780 Z= 0.211 Angle : 0.544 8.432 42910 Z= 0.298 Chirality : 0.034 0.138 5054 Planarity : 0.003 0.083 5404 Dihedral : 4.232 26.282 4214 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer Outliers : 0.06 % 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: 3.14 (0.13), residues: 3962 helix: 2.45 (0.08), residues: 3626 sheet: None (None), residues: 0 loop : -2.54 (0.27), residues: 336 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7924 Ramachandran restraints generated. 3962 Oldfield, 0 Emsley, 3962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7924 Ramachandran restraints generated. 3962 Oldfield, 0 Emsley, 3962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 3430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 225 time to evaluate : 2.895 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 225 average time/residue: 0.3344 time to fit residues: 121.3035 Evaluate side-chains 117 residues out of total 3430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 2.823 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.7902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 197 optimal weight: 5.9990 chunk 110 optimal weight: 20.0000 chunk 296 optimal weight: 8.9990 chunk 242 optimal weight: 10.0000 chunk 98 optimal weight: 5.9990 chunk 356 optimal weight: 8.9990 chunk 385 optimal weight: 5.9990 chunk 317 optimal weight: 0.6980 chunk 353 optimal weight: 50.0000 chunk 121 optimal weight: 6.9990 chunk 286 optimal weight: 0.7980 overall best weight: 3.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 ASN A 233 ASN ** B 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 233 ASN C 169 GLN C 220 ASN D 220 ASN ** E 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 220 ASN ** H 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 220 ASN ** I 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 220 ASN ** K 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 220 ASN ** L 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 220 ASN ** M 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 220 ASN ** N 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 169 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.2250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 31780 Z= 0.184 Angle : 0.485 7.346 42910 Z= 0.267 Chirality : 0.033 0.138 5054 Planarity : 0.003 0.034 5404 Dihedral : 3.898 24.404 4214 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer Outliers : 0.00 % 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: 4.36 (0.13), residues: 3962 helix: 3.29 (0.08), residues: 3626 sheet: None (None), residues: 0 loop : -2.66 (0.24), residues: 336 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7924 Ramachandran restraints generated. 3962 Oldfield, 0 Emsley, 3962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7924 Ramachandran restraints generated. 3962 Oldfield, 0 Emsley, 3962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 3430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 200 time to evaluate : 2.845 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 200 average time/residue: 0.3469 time to fit residues: 110.7758 Evaluate side-chains 112 residues out of total 3430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 2.797 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.7241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 352 optimal weight: 3.9990 chunk 268 optimal weight: 3.9990 chunk 185 optimal weight: 5.9990 chunk 39 optimal weight: 0.9980 chunk 170 optimal weight: 10.0000 chunk 239 optimal weight: 8.9990 chunk 357 optimal weight: 5.9990 chunk 378 optimal weight: 10.0000 chunk 186 optimal weight: 9.9990 chunk 339 optimal weight: 20.0000 chunk 102 optimal weight: 20.0000 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 283 ASN ** B 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 169 GLN B 220 ASN B 283 ASN ** C 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 283 ASN ** D 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 283 ASN ** E 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 169 GLN E 283 ASN F 283 ASN ** G 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 169 GLN G 283 ASN H 283 ASN I 283 ASN ** J 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 283 ASN ** K 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 283 ASN ** L 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 283 ASN ** M 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 283 ASN ** N 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 283 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.2636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 31780 Z= 0.197 Angle : 0.493 6.607 42910 Z= 0.272 Chirality : 0.033 0.140 5054 Planarity : 0.003 0.032 5404 Dihedral : 3.765 23.515 4214 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer Outliers : 0.00 % 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: 4.66 (0.13), residues: 3962 helix: 3.50 (0.08), residues: 3626 sheet: None (None), residues: 0 loop : -2.84 (0.24), residues: 336 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7924 Ramachandran restraints generated. 3962 Oldfield, 0 Emsley, 3962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7924 Ramachandran restraints generated. 3962 Oldfield, 0 Emsley, 3962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 3430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 189 time to evaluate : 2.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 189 average time/residue: 0.3629 time to fit residues: 110.0787 Evaluate side-chains 103 residues out of total 3430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 103 time to evaluate : 2.824 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.7588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 315 optimal weight: 1.9990 chunk 215 optimal weight: 8.9990 chunk 5 optimal weight: 9.9990 chunk 282 optimal weight: 3.9990 chunk 156 optimal weight: 9.9990 chunk 323 optimal weight: 3.9990 chunk 261 optimal weight: 8.9990 chunk 0 optimal weight: 50.0000 chunk 193 optimal weight: 9.9990 chunk 340 optimal weight: 10.0000 chunk 95 optimal weight: 3.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 33 GLN ** E 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 33 GLN ** M 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.2883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.074 31780 Z= 0.206 Angle : 0.519 18.000 42910 Z= 0.286 Chirality : 0.034 0.140 5054 Planarity : 0.003 0.056 5404 Dihedral : 3.726 23.472 4214 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer Outliers : 0.03 % 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: 4.77 (0.12), residues: 3962 helix: 3.57 (0.08), residues: 3626 sheet: None (None), residues: 0 loop : -2.72 (0.25), residues: 336 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7924 Ramachandran restraints generated. 3962 Oldfield, 0 Emsley, 3962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7924 Ramachandran restraints generated. 3962 Oldfield, 0 Emsley, 3962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 3430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 172 time to evaluate : 2.840 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 172 average time/residue: 0.3253 time to fit residues: 92.0622 Evaluate side-chains 92 residues out of total 3430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 2.820 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.7342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 127 optimal weight: 6.9990 chunk 341 optimal weight: 9.9990 chunk 74 optimal weight: 2.9990 chunk 222 optimal weight: 0.9990 chunk 93 optimal weight: 8.9990 chunk 379 optimal weight: 3.9990 chunk 314 optimal weight: 0.9990 chunk 175 optimal weight: 0.9980 chunk 31 optimal weight: 5.9990 chunk 125 optimal weight: 9.9990 chunk 199 optimal weight: 20.0000 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 33 GLN ** B 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 169 GLN ** G 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 169 GLN ** M 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.3128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.161 31780 Z= 0.156 Angle : 0.487 18.245 42910 Z= 0.265 Chirality : 0.032 0.141 5054 Planarity : 0.003 0.064 5404 Dihedral : 3.569 20.751 4214 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer Outliers : 0.06 % 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: 5.52 (0.12), residues: 3962 helix: 4.02 (0.08), residues: 3640 sheet: None (None), residues: 0 loop : -2.30 (0.25), residues: 322 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7924 Ramachandran restraints generated. 3962 Oldfield, 0 Emsley, 3962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7924 Ramachandran restraints generated. 3962 Oldfield, 0 Emsley, 3962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 3430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 179 time to evaluate : 2.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 181 average time/residue: 0.3349 time to fit residues: 99.9848 Evaluate side-chains 101 residues out of total 3430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 99 time to evaluate : 2.837 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1977 time to fit residues: 4.5935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 365 optimal weight: 7.9990 chunk 42 optimal weight: 0.8980 chunk 216 optimal weight: 8.9990 chunk 276 optimal weight: 6.9990 chunk 214 optimal weight: 9.9990 chunk 319 optimal weight: 7.9990 chunk 211 optimal weight: 4.9990 chunk 377 optimal weight: 8.9990 chunk 236 optimal weight: 3.9990 chunk 230 optimal weight: 0.9990 chunk 174 optimal weight: 1.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 169 GLN ** I 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 169 GLN ** J 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 33 GLN ** K 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 169 GLN ** N 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.3318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.261 31780 Z= 0.159 Angle : 0.503 22.799 42910 Z= 0.271 Chirality : 0.032 0.141 5054 Planarity : 0.003 0.081 5404 Dihedral : 3.503 20.841 4214 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer Outliers : 0.09 % 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: 5.63 (0.12), residues: 3962 helix: 4.08 (0.08), residues: 3654 sheet: None (None), residues: 0 loop : -2.39 (0.26), residues: 308 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7924 Ramachandran restraints generated. 3962 Oldfield, 0 Emsley, 3962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7924 Ramachandran restraints generated. 3962 Oldfield, 0 Emsley, 3962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 3430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 164 time to evaluate : 2.834 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 165 average time/residue: 0.3086 time to fit residues: 86.3907 Evaluate side-chains 93 residues out of total 3430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 92 time to evaluate : 2.813 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1957 time to fit residues: 4.1219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 233 optimal weight: 0.0010 chunk 150 optimal weight: 2.9990 chunk 225 optimal weight: 8.9990 chunk 113 optimal weight: 6.9990 chunk 74 optimal weight: 7.9990 chunk 73 optimal weight: 6.9990 chunk 240 optimal weight: 6.9990 chunk 257 optimal weight: 8.9990 chunk 186 optimal weight: 9.9990 chunk 35 optimal weight: 2.9990 chunk 296 optimal weight: 2.9990 overall best weight: 3.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 169 GLN ** K 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 33 GLN ** L 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.3434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.068 31780 Z= 0.156 Angle : 0.477 16.126 42910 Z= 0.257 Chirality : 0.032 0.137 5054 Planarity : 0.003 0.042 5404 Dihedral : 3.483 21.142 4214 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer Outliers : 0.03 % 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: 5.67 (0.12), residues: 3962 helix: 4.10 (0.08), residues: 3654 sheet: None (None), residues: 0 loop : -2.36 (0.26), residues: 308 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7924 Ramachandran restraints generated. 3962 Oldfield, 0 Emsley, 3962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7924 Ramachandran restraints generated. 3962 Oldfield, 0 Emsley, 3962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 3430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 165 time to evaluate : 2.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 165 average time/residue: 0.3042 time to fit residues: 86.3336 Evaluate side-chains 95 residues out of total 3430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 95 time to evaluate : 2.793 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.7385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 343 optimal weight: 1.9990 chunk 361 optimal weight: 0.0870 chunk 330 optimal weight: 1.9990 chunk 352 optimal weight: 2.9990 chunk 211 optimal weight: 6.9990 chunk 153 optimal weight: 10.0000 chunk 276 optimal weight: 7.9990 chunk 108 optimal weight: 5.9990 chunk 318 optimal weight: 6.9990 chunk 332 optimal weight: 7.9990 chunk 350 optimal weight: 6.9990 overall best weight: 2.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 169 GLN ** E 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 169 GLN ** L 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.3552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.048 31780 Z= 0.140 Angle : 0.449 9.230 42910 Z= 0.241 Chirality : 0.032 0.135 5054 Planarity : 0.003 0.062 5404 Dihedral : 3.431 20.543 4214 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer Outliers : 0.00 % 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: 5.83 (0.12), residues: 3962 helix: 4.21 (0.08), residues: 3654 sheet: None (None), residues: 0 loop : -2.35 (0.26), residues: 308 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7924 Ramachandran restraints generated. 3962 Oldfield, 0 Emsley, 3962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7924 Ramachandran restraints generated. 3962 Oldfield, 0 Emsley, 3962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 3430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 164 time to evaluate : 3.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 164 average time/residue: 0.3012 time to fit residues: 86.0283 Evaluate side-chains 95 residues out of total 3430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 95 time to evaluate : 2.833 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.7543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 231 optimal weight: 2.9990 chunk 372 optimal weight: 5.9990 chunk 227 optimal weight: 10.0000 chunk 176 optimal weight: 1.9990 chunk 258 optimal weight: 0.5980 chunk 390 optimal weight: 10.0000 chunk 359 optimal weight: 1.9990 chunk 310 optimal weight: 7.9990 chunk 32 optimal weight: 3.9990 chunk 240 optimal weight: 10.0000 chunk 190 optimal weight: 2.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.3654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.994 31780 Z= 0.330 Angle : 0.645 84.417 42910 Z= 0.308 Chirality : 0.032 0.199 5054 Planarity : 0.003 0.107 5404 Dihedral : 3.409 20.079 4214 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.07 % Favored : 97.91 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.03 % 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: 5.95 (0.12), residues: 3962 helix: 4.29 (0.08), residues: 3654 sheet: None (None), residues: 0 loop : -2.38 (0.26), residues: 308 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7924 Ramachandran restraints generated. 3962 Oldfield, 0 Emsley, 3962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7924 Ramachandran restraints generated. 3962 Oldfield, 0 Emsley, 3962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 3430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 165 time to evaluate : 2.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 165 average time/residue: 0.3016 time to fit residues: 86.0388 Evaluate side-chains 92 residues out of total 3430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 2.823 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.7931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 247 optimal weight: 1.9990 chunk 331 optimal weight: 7.9990 chunk 95 optimal weight: 1.9990 chunk 286 optimal weight: 0.8980 chunk 45 optimal weight: 6.9990 chunk 86 optimal weight: 10.0000 chunk 311 optimal weight: 6.9990 chunk 130 optimal weight: 10.0000 chunk 319 optimal weight: 6.9990 chunk 39 optimal weight: 4.9990 chunk 57 optimal weight: 0.7980 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 289 GLN ** D 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.049155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.032629 restraints weight = 225795.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.033312 restraints weight = 164359.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.033779 restraints weight = 126929.533| |-----------------------------------------------------------------------------| r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.3764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.995 31780 Z= 0.332 Angle : 0.614 79.386 42910 Z= 0.293 Chirality : 0.032 0.263 5054 Planarity : 0.003 0.110 5404 Dihedral : 3.372 19.888 4214 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.97 % Favored : 98.01 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.03 % 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: 6.06 (0.12), residues: 3962 helix: 4.36 (0.08), residues: 3654 sheet: None (None), residues: 0 loop : -2.28 (0.26), residues: 308 =============================================================================== Job complete usr+sys time: 3120.29 seconds wall clock time: 58 minutes 43.49 seconds (3523.49 seconds total)