Starting phenix.real_space_refine (version: dev) on Fri Apr 8 01:22:16 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5l93_4015/04_2022/5l93_4015.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5l93_4015/04_2022/5l93_4015.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5l93_4015/04_2022/5l93_4015.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5l93_4015/04_2022/5l93_4015.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5l93_4015/04_2022/5l93_4015.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5l93_4015/04_2022/5l93_4015.pdb" } resolution = 3.9 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= 0.042 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 150": "NH1" <-> "NH2" Residue "A ARG 232": "NH1" <-> "NH2" Residue "A ARG 294": "NH1" <-> "NH2" Residue "A ARG 305": "NH1" <-> "NH2" Residue "B ARG 150": "NH1" <-> "NH2" Residue "B ARG 232": "NH1" <-> "NH2" Residue "B ARG 294": "NH1" <-> "NH2" Residue "B ARG 305": "NH1" <-> "NH2" Residue "C ARG 150": "NH1" <-> "NH2" Residue "C ARG 232": "NH1" <-> "NH2" Residue "C ARG 294": "NH1" <-> "NH2" Residue "C ARG 305": "NH1" <-> "NH2" Residue "D ARG 150": "NH1" <-> "NH2" Residue "D ARG 232": "NH1" <-> "NH2" Residue "D ARG 294": "NH1" <-> "NH2" Residue "D ARG 305": "NH1" <-> "NH2" Residue "E ARG 150": "NH1" <-> "NH2" Residue "E ARG 232": "NH1" <-> "NH2" Residue "E ARG 294": "NH1" <-> "NH2" Residue "E ARG 305": "NH1" <-> "NH2" Residue "F ARG 150": "NH1" <-> "NH2" Residue "F ARG 232": "NH1" <-> "NH2" Residue "F ARG 294": "NH1" <-> "NH2" Residue "F ARG 305": "NH1" <-> "NH2" Residue "G ARG 150": "NH1" <-> "NH2" Residue "G ARG 232": "NH1" <-> "NH2" Residue "G ARG 294": "NH1" <-> "NH2" Residue "G ARG 305": "NH1" <-> "NH2" Residue "H ARG 150": "NH1" <-> "NH2" Residue "H ARG 232": "NH1" <-> "NH2" Residue "H ARG 294": "NH1" <-> "NH2" Residue "H ARG 305": "NH1" <-> "NH2" Residue "I ARG 150": "NH1" <-> "NH2" Residue "I ARG 232": "NH1" <-> "NH2" Residue "I ARG 294": "NH1" <-> "NH2" Residue "I ARG 305": "NH1" <-> "NH2" Residue "J ARG 150": "NH1" <-> "NH2" Residue "J ARG 232": "NH1" <-> "NH2" Residue "J ARG 294": "NH1" <-> "NH2" Residue "J ARG 305": "NH1" <-> "NH2" Residue "K ARG 150": "NH1" <-> "NH2" Residue "K ARG 232": "NH1" <-> "NH2" Residue "K ARG 294": "NH1" <-> "NH2" Residue "K ARG 305": "NH1" <-> "NH2" Residue "L ARG 150": "NH1" <-> "NH2" Residue "L ARG 232": "NH1" <-> "NH2" Residue "L ARG 294": "NH1" <-> "NH2" Residue "L ARG 305": "NH1" <-> "NH2" Residue "M ARG 150": "NH1" <-> "NH2" Residue "M ARG 232": "NH1" <-> "NH2" Residue "M ARG 294": "NH1" <-> "NH2" Residue "M ARG 305": "NH1" <-> "NH2" Residue "N ARG 150": "NH1" <-> "NH2" Residue "N ARG 232": "NH1" <-> "NH2" Residue "N ARG 294": "NH1" <-> "NH2" Residue "N ARG 305": "NH1" <-> "NH2" Residue "O ARG 150": "NH1" <-> "NH2" Residue "O ARG 232": "NH1" <-> "NH2" Residue "O ARG 294": "NH1" <-> "NH2" Residue "O ARG 305": "NH1" <-> "NH2" Residue "P ARG 150": "NH1" <-> "NH2" Residue "P ARG 232": "NH1" <-> "NH2" Residue "P ARG 294": "NH1" <-> "NH2" Residue "P ARG 305": "NH1" <-> "NH2" Residue "Q ARG 150": "NH1" <-> "NH2" Residue "Q ARG 232": "NH1" <-> "NH2" Residue "Q ARG 294": "NH1" <-> "NH2" Residue "Q ARG 305": "NH1" <-> "NH2" Residue "R ARG 150": "NH1" <-> "NH2" Residue "R ARG 232": "NH1" <-> "NH2" Residue "R ARG 294": "NH1" <-> "NH2" Residue "R ARG 305": "NH1" <-> "NH2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 31212 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 1734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1734 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 15, 'TRANS': 206, 'PCIS': 2} Chain: "B" Number of atoms: 1734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1734 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 15, 'TRANS': 206, 'PCIS': 2} Chain: "C" Number of atoms: 1734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1734 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 15, 'TRANS': 206, 'PCIS': 2} Chain: "D" Number of atoms: 1734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1734 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 15, 'TRANS': 206, 'PCIS': 2} Chain: "E" Number of atoms: 1734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1734 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 15, 'TRANS': 206, 'PCIS': 2} Chain: "F" Number of atoms: 1734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1734 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 15, 'TRANS': 206, 'PCIS': 2} Chain: "G" Number of atoms: 1734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1734 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 15, 'TRANS': 206, 'PCIS': 2} Chain: "H" Number of atoms: 1734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1734 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 15, 'TRANS': 206, 'PCIS': 2} Chain: "I" Number of atoms: 1734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1734 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 15, 'TRANS': 206, 'PCIS': 2} Chain: "J" Number of atoms: 1734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1734 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 15, 'TRANS': 206, 'PCIS': 2} Chain: "K" Number of atoms: 1734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1734 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 15, 'TRANS': 206, 'PCIS': 2} Chain: "L" Number of atoms: 1734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1734 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 15, 'TRANS': 206, 'PCIS': 2} Chain: "M" Number of atoms: 1734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1734 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 15, 'TRANS': 206, 'PCIS': 2} Chain: "N" Number of atoms: 1734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1734 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 15, 'TRANS': 206, 'PCIS': 2} Chain: "O" Number of atoms: 1734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1734 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 15, 'TRANS': 206, 'PCIS': 2} Chain: "P" Number of atoms: 1734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1734 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 15, 'TRANS': 206, 'PCIS': 2} Chain: "Q" Number of atoms: 1734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1734 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 15, 'TRANS': 206, 'PCIS': 2} Chain: "R" Number of atoms: 1734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1734 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 15, 'TRANS': 206, 'PCIS': 2} Time building chain proxies: 16.62, per 1000 atoms: 0.53 Number of scatterers: 31212 At special positions: 0 Unit cell: (179.55, 163.35, 116.1, 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 234 16.00 O 5868 8.00 N 5472 7.00 C 19638 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: 12.28 Conformation dependent library (CDL) restraints added in 4.6 seconds 7992 Ramachandran restraints generated. 3996 Oldfield, 0 Emsley, 3996 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7452 Finding SS restraints... Secondary structure from input PDB file: 216 helices and 0 sheets defined 73.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.11 Creating SS restraints... Processing helix chain 'A' and resid 148 through 161 removed outlier: 3.715A pdb=" N GLU A 161 " --> pdb=" O LYS A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 177 Processing helix chain 'A' and resid 180 through 190 Processing helix chain 'A' and resid 195 through 216 Processing helix chain 'A' and resid 232 through 237 removed outlier: 3.966A pdb=" N ALA A 237 " --> pdb=" O GLY A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 252 Processing helix chain 'A' and resid 257 through 277 Processing helix chain 'A' and resid 292 through 307 removed outlier: 3.505A pdb=" N TYR A 296 " --> pdb=" O PRO A 292 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA A 306 " --> pdb=" O LYS A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 325 Processing helix chain 'A' and resid 327 through 336 Processing helix chain 'A' and resid 342 through 352 removed outlier: 3.604A pdb=" N MET A 346 " --> pdb=" O THR A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 371 Processing helix chain 'B' and resid 149 through 161 removed outlier: 3.714A pdb=" N GLU B 161 " --> pdb=" O LYS B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 177 removed outlier: 3.508A pdb=" N GLU B 177 " --> pdb=" O SER B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 190 Processing helix chain 'B' and resid 195 through 216 Processing helix chain 'B' and resid 232 through 237 removed outlier: 3.964A pdb=" N ALA B 237 " --> pdb=" O GLY B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 252 Processing helix chain 'B' and resid 257 through 277 Processing helix chain 'B' and resid 292 through 307 removed outlier: 3.574A pdb=" N ALA B 306 " --> pdb=" O LYS B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 325 Processing helix chain 'B' and resid 327 through 336 Processing helix chain 'B' and resid 342 through 352 removed outlier: 3.625A pdb=" N MET B 346 " --> pdb=" O THR B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 371 Processing helix chain 'C' and resid 149 through 161 removed outlier: 3.714A pdb=" N GLU C 161 " --> pdb=" O LYS C 157 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 177 Processing helix chain 'C' and resid 180 through 190 Processing helix chain 'C' and resid 195 through 216 Processing helix chain 'C' and resid 232 through 237 removed outlier: 3.960A pdb=" N ALA C 237 " --> pdb=" O GLY C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 252 Processing helix chain 'C' and resid 257 through 277 Processing helix chain 'C' and resid 292 through 307 removed outlier: 3.502A pdb=" N TYR C 296 " --> pdb=" O PRO C 292 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA C 306 " --> pdb=" O LYS C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 310 through 325 Processing helix chain 'C' and resid 327 through 336 Processing helix chain 'C' and resid 342 through 352 removed outlier: 3.604A pdb=" N MET C 346 " --> pdb=" O THR C 342 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 371 Processing helix chain 'D' and resid 148 through 161 removed outlier: 3.715A pdb=" N GLU D 161 " --> pdb=" O LYS D 157 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 177 Processing helix chain 'D' and resid 180 through 190 Processing helix chain 'D' and resid 195 through 216 Processing helix chain 'D' and resid 232 through 237 removed outlier: 3.965A pdb=" N ALA D 237 " --> pdb=" O GLY D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 252 Processing helix chain 'D' and resid 257 through 277 Processing helix chain 'D' and resid 292 through 307 removed outlier: 3.506A pdb=" N TYR D 296 " --> pdb=" O PRO D 292 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA D 306 " --> pdb=" O LYS D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 310 through 325 Processing helix chain 'D' and resid 327 through 336 Processing helix chain 'D' and resid 342 through 352 removed outlier: 3.604A pdb=" N MET D 346 " --> pdb=" O THR D 342 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 371 Processing helix chain 'E' and resid 149 through 161 removed outlier: 3.714A pdb=" N GLU E 161 " --> pdb=" O LYS E 157 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 177 removed outlier: 3.508A pdb=" N GLU E 177 " --> pdb=" O SER E 173 " (cutoff:3.500A) Processing helix chain 'E' and resid 180 through 190 Processing helix chain 'E' and resid 195 through 216 Processing helix chain 'E' and resid 232 through 237 removed outlier: 3.964A pdb=" N ALA E 237 " --> pdb=" O GLY E 233 " (cutoff:3.500A) Processing helix chain 'E' and resid 242 through 252 Processing helix chain 'E' and resid 257 through 277 Processing helix chain 'E' and resid 292 through 307 removed outlier: 3.574A pdb=" N ALA E 306 " --> pdb=" O LYS E 302 " (cutoff:3.500A) Processing helix chain 'E' and resid 310 through 325 Processing helix chain 'E' and resid 327 through 336 Processing helix chain 'E' and resid 342 through 352 removed outlier: 3.625A pdb=" N MET E 346 " --> pdb=" O THR E 342 " (cutoff:3.500A) Processing helix chain 'E' and resid 355 through 371 Processing helix chain 'F' and resid 149 through 161 removed outlier: 3.713A pdb=" N GLU F 161 " --> pdb=" O LYS F 157 " (cutoff:3.500A) Processing helix chain 'F' and resid 167 through 177 Processing helix chain 'F' and resid 180 through 190 Processing helix chain 'F' and resid 195 through 216 Processing helix chain 'F' and resid 232 through 237 removed outlier: 3.960A pdb=" N ALA F 237 " --> pdb=" O GLY F 233 " (cutoff:3.500A) Processing helix chain 'F' and resid 242 through 252 Processing helix chain 'F' and resid 257 through 277 Processing helix chain 'F' and resid 292 through 307 removed outlier: 3.502A pdb=" N TYR F 296 " --> pdb=" O PRO F 292 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA F 306 " --> pdb=" O LYS F 302 " (cutoff:3.500A) Processing helix chain 'F' and resid 310 through 325 Processing helix chain 'F' and resid 327 through 336 Processing helix chain 'F' and resid 342 through 352 removed outlier: 3.603A pdb=" N MET F 346 " --> pdb=" O THR F 342 " (cutoff:3.500A) Processing helix chain 'F' and resid 355 through 371 Processing helix chain 'G' and resid 148 through 161 removed outlier: 3.716A pdb=" N GLU G 161 " --> pdb=" O LYS G 157 " (cutoff:3.500A) Processing helix chain 'G' and resid 167 through 177 Processing helix chain 'G' and resid 180 through 190 Processing helix chain 'G' and resid 195 through 216 Processing helix chain 'G' and resid 232 through 237 removed outlier: 3.965A pdb=" N ALA G 237 " --> pdb=" O GLY G 233 " (cutoff:3.500A) Processing helix chain 'G' and resid 242 through 252 Processing helix chain 'G' and resid 257 through 277 Processing helix chain 'G' and resid 292 through 307 removed outlier: 3.506A pdb=" N TYR G 296 " --> pdb=" O PRO G 292 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA G 306 " --> pdb=" O LYS G 302 " (cutoff:3.500A) Processing helix chain 'G' and resid 310 through 325 Processing helix chain 'G' and resid 327 through 336 Processing helix chain 'G' and resid 342 through 352 removed outlier: 3.604A pdb=" N MET G 346 " --> pdb=" O THR G 342 " (cutoff:3.500A) Processing helix chain 'G' and resid 355 through 371 Processing helix chain 'H' and resid 149 through 161 removed outlier: 3.714A pdb=" N GLU H 161 " --> pdb=" O LYS H 157 " (cutoff:3.500A) Processing helix chain 'H' and resid 167 through 177 removed outlier: 3.508A pdb=" N GLU H 177 " --> pdb=" O SER H 173 " (cutoff:3.500A) Processing helix chain 'H' and resid 180 through 190 Processing helix chain 'H' and resid 195 through 216 Processing helix chain 'H' and resid 232 through 237 removed outlier: 3.964A pdb=" N ALA H 237 " --> pdb=" O GLY H 233 " (cutoff:3.500A) Processing helix chain 'H' and resid 242 through 252 Processing helix chain 'H' and resid 257 through 277 Processing helix chain 'H' and resid 292 through 307 removed outlier: 3.574A pdb=" N ALA H 306 " --> pdb=" O LYS H 302 " (cutoff:3.500A) Processing helix chain 'H' and resid 310 through 325 Processing helix chain 'H' and resid 327 through 336 Processing helix chain 'H' and resid 342 through 352 removed outlier: 3.625A pdb=" N MET H 346 " --> pdb=" O THR H 342 " (cutoff:3.500A) Processing helix chain 'H' and resid 355 through 371 Processing helix chain 'I' and resid 149 through 161 removed outlier: 3.714A pdb=" N GLU I 161 " --> pdb=" O LYS I 157 " (cutoff:3.500A) Processing helix chain 'I' and resid 167 through 177 Processing helix chain 'I' and resid 180 through 190 Processing helix chain 'I' and resid 195 through 216 Processing helix chain 'I' and resid 232 through 237 removed outlier: 3.960A pdb=" N ALA I 237 " --> pdb=" O GLY I 233 " (cutoff:3.500A) Processing helix chain 'I' and resid 242 through 252 Processing helix chain 'I' and resid 257 through 277 Processing helix chain 'I' and resid 292 through 307 removed outlier: 3.502A pdb=" N TYR I 296 " --> pdb=" O PRO I 292 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA I 306 " --> pdb=" O LYS I 302 " (cutoff:3.500A) Processing helix chain 'I' and resid 310 through 325 Processing helix chain 'I' and resid 327 through 336 Processing helix chain 'I' and resid 342 through 352 removed outlier: 3.604A pdb=" N MET I 346 " --> pdb=" O THR I 342 " (cutoff:3.500A) Processing helix chain 'I' and resid 355 through 371 Processing helix chain 'J' and resid 148 through 161 removed outlier: 3.715A pdb=" N GLU J 161 " --> pdb=" O LYS J 157 " (cutoff:3.500A) Processing helix chain 'J' and resid 167 through 177 Processing helix chain 'J' and resid 180 through 190 Processing helix chain 'J' and resid 195 through 216 Processing helix chain 'J' and resid 232 through 237 removed outlier: 3.966A pdb=" N ALA J 237 " --> pdb=" O GLY J 233 " (cutoff:3.500A) Processing helix chain 'J' and resid 242 through 252 Processing helix chain 'J' and resid 257 through 277 Processing helix chain 'J' and resid 292 through 307 removed outlier: 3.505A pdb=" N TYR J 296 " --> pdb=" O PRO J 292 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA J 306 " --> pdb=" O LYS J 302 " (cutoff:3.500A) Processing helix chain 'J' and resid 310 through 325 Processing helix chain 'J' and resid 327 through 336 Processing helix chain 'J' and resid 342 through 352 removed outlier: 3.604A pdb=" N MET J 346 " --> pdb=" O THR J 342 " (cutoff:3.500A) Processing helix chain 'J' and resid 355 through 371 Processing helix chain 'K' and resid 149 through 161 removed outlier: 3.714A pdb=" N GLU K 161 " --> pdb=" O LYS K 157 " (cutoff:3.500A) Processing helix chain 'K' and resid 167 through 177 removed outlier: 3.508A pdb=" N GLU K 177 " --> pdb=" O SER K 173 " (cutoff:3.500A) Processing helix chain 'K' and resid 180 through 190 Processing helix chain 'K' and resid 195 through 216 Processing helix chain 'K' and resid 232 through 237 removed outlier: 3.964A pdb=" N ALA K 237 " --> pdb=" O GLY K 233 " (cutoff:3.500A) Processing helix chain 'K' and resid 242 through 252 Processing helix chain 'K' and resid 257 through 277 Processing helix chain 'K' and resid 292 through 307 removed outlier: 3.574A pdb=" N ALA K 306 " --> pdb=" O LYS K 302 " (cutoff:3.500A) Processing helix chain 'K' and resid 310 through 325 Processing helix chain 'K' and resid 327 through 336 Processing helix chain 'K' and resid 342 through 352 removed outlier: 3.625A pdb=" N MET K 346 " --> pdb=" O THR K 342 " (cutoff:3.500A) Processing helix chain 'K' and resid 355 through 371 Processing helix chain 'L' and resid 149 through 161 removed outlier: 3.714A pdb=" N GLU L 161 " --> pdb=" O LYS L 157 " (cutoff:3.500A) Processing helix chain 'L' and resid 167 through 177 Processing helix chain 'L' and resid 180 through 190 Processing helix chain 'L' and resid 195 through 216 Processing helix chain 'L' and resid 232 through 237 removed outlier: 3.960A pdb=" N ALA L 237 " --> pdb=" O GLY L 233 " (cutoff:3.500A) Processing helix chain 'L' and resid 242 through 252 Processing helix chain 'L' and resid 257 through 277 Processing helix chain 'L' and resid 292 through 307 removed outlier: 3.502A pdb=" N TYR L 296 " --> pdb=" O PRO L 292 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA L 306 " --> pdb=" O LYS L 302 " (cutoff:3.500A) Processing helix chain 'L' and resid 310 through 325 Processing helix chain 'L' and resid 327 through 336 Processing helix chain 'L' and resid 342 through 352 removed outlier: 3.604A pdb=" N MET L 346 " --> pdb=" O THR L 342 " (cutoff:3.500A) Processing helix chain 'L' and resid 355 through 371 Processing helix chain 'M' and resid 148 through 161 removed outlier: 3.715A pdb=" N GLU M 161 " --> pdb=" O LYS M 157 " (cutoff:3.500A) Processing helix chain 'M' and resid 167 through 177 Processing helix chain 'M' and resid 180 through 190 Processing helix chain 'M' and resid 195 through 216 Processing helix chain 'M' and resid 232 through 237 removed outlier: 3.965A pdb=" N ALA M 237 " --> pdb=" O GLY M 233 " (cutoff:3.500A) Processing helix chain 'M' and resid 242 through 252 Processing helix chain 'M' and resid 257 through 277 Processing helix chain 'M' and resid 292 through 307 removed outlier: 3.506A pdb=" N TYR M 296 " --> pdb=" O PRO M 292 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA M 306 " --> pdb=" O LYS M 302 " (cutoff:3.500A) Processing helix chain 'M' and resid 310 through 325 Processing helix chain 'M' and resid 327 through 336 Processing helix chain 'M' and resid 342 through 352 removed outlier: 3.604A pdb=" N MET M 346 " --> pdb=" O THR M 342 " (cutoff:3.500A) Processing helix chain 'M' and resid 355 through 371 Processing helix chain 'N' and resid 149 through 161 removed outlier: 3.714A pdb=" N GLU N 161 " --> pdb=" O LYS N 157 " (cutoff:3.500A) Processing helix chain 'N' and resid 167 through 177 removed outlier: 3.508A pdb=" N GLU N 177 " --> pdb=" O SER N 173 " (cutoff:3.500A) Processing helix chain 'N' and resid 180 through 190 Processing helix chain 'N' and resid 195 through 216 Processing helix chain 'N' and resid 232 through 237 removed outlier: 3.964A pdb=" N ALA N 237 " --> pdb=" O GLY N 233 " (cutoff:3.500A) Processing helix chain 'N' and resid 242 through 252 Processing helix chain 'N' and resid 257 through 277 Processing helix chain 'N' and resid 292 through 307 removed outlier: 3.574A pdb=" N ALA N 306 " --> pdb=" O LYS N 302 " (cutoff:3.500A) Processing helix chain 'N' and resid 310 through 325 Processing helix chain 'N' and resid 327 through 336 Processing helix chain 'N' and resid 342 through 352 removed outlier: 3.625A pdb=" N MET N 346 " --> pdb=" O THR N 342 " (cutoff:3.500A) Processing helix chain 'N' and resid 355 through 371 Processing helix chain 'O' and resid 149 through 161 removed outlier: 3.713A pdb=" N GLU O 161 " --> pdb=" O LYS O 157 " (cutoff:3.500A) Processing helix chain 'O' and resid 167 through 177 Processing helix chain 'O' and resid 180 through 190 Processing helix chain 'O' and resid 195 through 216 Processing helix chain 'O' and resid 232 through 237 removed outlier: 3.960A pdb=" N ALA O 237 " --> pdb=" O GLY O 233 " (cutoff:3.500A) Processing helix chain 'O' and resid 242 through 252 Processing helix chain 'O' and resid 257 through 277 Processing helix chain 'O' and resid 292 through 307 removed outlier: 3.502A pdb=" N TYR O 296 " --> pdb=" O PRO O 292 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA O 306 " --> pdb=" O LYS O 302 " (cutoff:3.500A) Processing helix chain 'O' and resid 310 through 325 Processing helix chain 'O' and resid 327 through 336 Processing helix chain 'O' and resid 342 through 352 removed outlier: 3.603A pdb=" N MET O 346 " --> pdb=" O THR O 342 " (cutoff:3.500A) Processing helix chain 'O' and resid 355 through 371 Processing helix chain 'P' and resid 148 through 161 removed outlier: 3.716A pdb=" N GLU P 161 " --> pdb=" O LYS P 157 " (cutoff:3.500A) Processing helix chain 'P' and resid 167 through 177 Processing helix chain 'P' and resid 180 through 190 Processing helix chain 'P' and resid 195 through 216 Processing helix chain 'P' and resid 232 through 237 removed outlier: 3.965A pdb=" N ALA P 237 " --> pdb=" O GLY P 233 " (cutoff:3.500A) Processing helix chain 'P' and resid 242 through 252 Processing helix chain 'P' and resid 257 through 277 Processing helix chain 'P' and resid 292 through 307 removed outlier: 3.506A pdb=" N TYR P 296 " --> pdb=" O PRO P 292 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA P 306 " --> pdb=" O LYS P 302 " (cutoff:3.500A) Processing helix chain 'P' and resid 310 through 325 Processing helix chain 'P' and resid 327 through 336 Processing helix chain 'P' and resid 342 through 352 removed outlier: 3.604A pdb=" N MET P 346 " --> pdb=" O THR P 342 " (cutoff:3.500A) Processing helix chain 'P' and resid 355 through 371 Processing helix chain 'Q' and resid 149 through 161 removed outlier: 3.714A pdb=" N GLU Q 161 " --> pdb=" O LYS Q 157 " (cutoff:3.500A) Processing helix chain 'Q' and resid 167 through 177 removed outlier: 3.508A pdb=" N GLU Q 177 " --> pdb=" O SER Q 173 " (cutoff:3.500A) Processing helix chain 'Q' and resid 180 through 190 Processing helix chain 'Q' and resid 195 through 216 Processing helix chain 'Q' and resid 232 through 237 removed outlier: 3.964A pdb=" N ALA Q 237 " --> pdb=" O GLY Q 233 " (cutoff:3.500A) Processing helix chain 'Q' and resid 242 through 252 Processing helix chain 'Q' and resid 257 through 277 Processing helix chain 'Q' and resid 292 through 307 removed outlier: 3.574A pdb=" N ALA Q 306 " --> pdb=" O LYS Q 302 " (cutoff:3.500A) Processing helix chain 'Q' and resid 310 through 325 Processing helix chain 'Q' and resid 327 through 336 Processing helix chain 'Q' and resid 342 through 352 removed outlier: 3.625A pdb=" N MET Q 346 " --> pdb=" O THR Q 342 " (cutoff:3.500A) Processing helix chain 'Q' and resid 355 through 371 Processing helix chain 'R' and resid 149 through 161 removed outlier: 3.714A pdb=" N GLU R 161 " --> pdb=" O LYS R 157 " (cutoff:3.500A) Processing helix chain 'R' and resid 167 through 177 Processing helix chain 'R' and resid 180 through 190 Processing helix chain 'R' and resid 195 through 216 Processing helix chain 'R' and resid 232 through 237 removed outlier: 3.960A pdb=" N ALA R 237 " --> pdb=" O GLY R 233 " (cutoff:3.500A) Processing helix chain 'R' and resid 242 through 252 Processing helix chain 'R' and resid 257 through 277 Processing helix chain 'R' and resid 292 through 307 removed outlier: 3.502A pdb=" N TYR R 296 " --> pdb=" O PRO R 292 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA R 306 " --> pdb=" O LYS R 302 " (cutoff:3.500A) Processing helix chain 'R' and resid 310 through 325 Processing helix chain 'R' and resid 327 through 336 Processing helix chain 'R' and resid 342 through 352 removed outlier: 3.604A pdb=" N MET R 346 " --> pdb=" O THR R 342 " (cutoff:3.500A) Processing helix chain 'R' and resid 355 through 371 2022 hydrogen bonds defined for protein. 6066 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: 9.39 Time building geometry restraints manager: 13.27 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: 10174 1.34 - 1.46: 3746 1.46 - 1.57: 17562 1.57 - 1.69: 0 1.69 - 1.81: 432 Bond restraints: 31914 Sorted by residual: bond pdb=" C SER E 278 " pdb=" O SER E 278 " ideal model delta sigma weight residual 1.246 1.230 0.016 9.20e-03 1.18e+04 3.03e+00 bond pdb=" C SER N 278 " pdb=" O SER N 278 " ideal model delta sigma weight residual 1.246 1.230 0.016 9.20e-03 1.18e+04 3.03e+00 bond pdb=" C SER Q 278 " pdb=" O SER Q 278 " ideal model delta sigma weight residual 1.246 1.230 0.016 9.20e-03 1.18e+04 2.94e+00 bond pdb=" C SER H 278 " pdb=" O SER H 278 " ideal model delta sigma weight residual 1.246 1.230 0.016 9.20e-03 1.18e+04 2.94e+00 bond pdb=" C SER K 278 " pdb=" O SER K 278 " ideal model delta sigma weight residual 1.246 1.231 0.015 9.20e-03 1.18e+04 2.82e+00 ... (remaining 31909 not shown) Histogram of bond angle deviations from ideal: 100.73 - 107.38: 1782 107.38 - 114.03: 18108 114.03 - 120.68: 10924 120.68 - 127.33: 12024 127.33 - 133.98: 524 Bond angle restraints: 43362 Sorted by residual: angle pdb=" N VAL A 168 " pdb=" CA VAL A 168 " pdb=" C VAL A 168 " ideal model delta sigma weight residual 111.17 115.49 -4.32 1.38e+00 5.25e-01 9.79e+00 angle pdb=" N VAL J 168 " pdb=" CA VAL J 168 " pdb=" C VAL J 168 " ideal model delta sigma weight residual 111.17 115.49 -4.32 1.38e+00 5.25e-01 9.79e+00 angle pdb=" N VAL G 168 " pdb=" CA VAL G 168 " pdb=" C VAL G 168 " ideal model delta sigma weight residual 111.17 115.47 -4.30 1.38e+00 5.25e-01 9.73e+00 angle pdb=" N VAL P 168 " pdb=" CA VAL P 168 " pdb=" C VAL P 168 " ideal model delta sigma weight residual 111.17 115.47 -4.30 1.38e+00 5.25e-01 9.73e+00 angle pdb=" N VAL B 168 " pdb=" CA VAL B 168 " pdb=" C VAL B 168 " ideal model delta sigma weight residual 111.17 115.47 -4.30 1.38e+00 5.25e-01 9.73e+00 ... (remaining 43357 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.21: 17922 11.21 - 22.42: 1200 22.42 - 33.63: 342 33.63 - 44.84: 60 44.84 - 56.05: 6 Dihedral angle restraints: 19530 sinusoidal: 7992 harmonic: 11538 Sorted by residual: dihedral pdb=" N LEU K 334 " pdb=" CA LEU K 334 " pdb=" CB LEU K 334 " pdb=" CG LEU K 334 " ideal model delta sinusoidal sigma weight residual -60.00 -103.29 43.29 3 1.50e+01 4.44e-03 7.78e+00 dihedral pdb=" N LEU B 334 " pdb=" CA LEU B 334 " pdb=" CB LEU B 334 " pdb=" CG LEU B 334 " ideal model delta sinusoidal sigma weight residual -60.00 -103.29 43.29 3 1.50e+01 4.44e-03 7.78e+00 dihedral pdb=" N LEU H 334 " pdb=" CA LEU H 334 " pdb=" CB LEU H 334 " pdb=" CG LEU H 334 " ideal model delta sinusoidal sigma weight residual -60.00 -103.26 43.26 3 1.50e+01 4.44e-03 7.77e+00 ... (remaining 19527 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 3500 0.026 - 0.053: 694 0.053 - 0.079: 180 0.079 - 0.105: 292 0.105 - 0.132: 158 Chirality restraints: 4824 Sorted by residual: chirality pdb=" CA ILE D 256 " pdb=" N ILE D 256 " pdb=" C ILE D 256 " pdb=" CB ILE D 256 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.34e-01 chirality pdb=" CA ILE M 256 " pdb=" N ILE M 256 " pdb=" C ILE M 256 " pdb=" CB ILE M 256 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.34e-01 chirality pdb=" CA ILE H 256 " pdb=" N ILE H 256 " pdb=" C ILE H 256 " pdb=" CB ILE H 256 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.29e-01 ... (remaining 4821 not shown) Planarity restraints: 5670 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN J 327 " 0.030 5.00e-02 4.00e+02 4.59e-02 3.37e+00 pdb=" N PRO J 328 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO J 328 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO J 328 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 327 " -0.030 5.00e-02 4.00e+02 4.59e-02 3.37e+00 pdb=" N PRO A 328 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO A 328 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 328 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN Q 327 " -0.030 5.00e-02 4.00e+02 4.59e-02 3.37e+00 pdb=" N PRO Q 328 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO Q 328 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO Q 328 " -0.025 5.00e-02 4.00e+02 ... (remaining 5667 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.23: 72 2.23 - 2.90: 11370 2.90 - 3.57: 48944 3.57 - 4.23: 66604 4.23 - 4.90: 118106 Nonbonded interactions: 245096 Sorted by model distance: nonbonded pdb=" CG GLU N 177 " pdb=" OE2 GLU P 260 " model vdw 1.566 3.440 nonbonded pdb=" CG GLU E 177 " pdb=" OE2 GLU G 260 " model vdw 1.566 3.440 nonbonded pdb=" CG GLU K 177 " pdb=" OE2 GLU M 260 " model vdw 1.566 3.440 nonbonded pdb=" CG GLU B 177 " pdb=" OE2 GLU D 260 " model vdw 1.566 3.440 nonbonded pdb=" CG GLU H 177 " pdb=" OE2 GLU J 260 " model vdw 1.566 3.440 ... (remaining 245091 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' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' } 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 234 5.16 5 C 19638 2.51 5 N 5472 2.21 5 O 5868 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: 0.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 4.840 Check model and map are aligned: 0.440 Convert atoms to be neutral: 0.250 Process input model: 73.870 Find NCS groups from input model: 1.910 Set up NCS constraints: 0.230 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 84.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 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 : 0.004 0.032 31914 Z= 0.291 Angle : 0.917 5.981 43362 Z= 0.639 Chirality : 0.038 0.132 4824 Planarity : 0.005 0.046 5670 Dihedral : 8.715 56.049 12078 Min Nonbonded Distance : 1.566 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.76 % Favored : 90.24 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.97 (0.11), residues: 3996 helix: -1.43 (0.08), residues: 2682 sheet: None (None), residues: 0 loop : -2.92 (0.13), residues: 1314 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7992 Ramachandran restraints generated. 3996 Oldfield, 0 Emsley, 3996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7992 Ramachandran restraints generated. 3996 Oldfield, 0 Emsley, 3996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1451 residues out of total 3366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1451 time to evaluate : 3.358 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 outliers start: 0 outliers final: 0 residues processed: 1451 average time/residue: 0.4115 time to fit residues: 945.6167 Evaluate side-chains 816 residues out of total 3366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 816 time to evaluate : 3.656 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.9492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 334 optimal weight: 8.9990 chunk 300 optimal weight: 3.9990 chunk 166 optimal weight: 5.9990 chunk 102 optimal weight: 3.9990 chunk 202 optimal weight: 0.9990 chunk 160 optimal weight: 5.9990 chunk 310 optimal weight: 5.9990 chunk 120 optimal weight: 8.9990 chunk 188 optimal weight: 5.9990 chunk 231 optimal weight: 3.9990 chunk 359 optimal weight: 9.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 ASN ** B 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 189 ASN ** C 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 185 ASN D 189 ASN ** E 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 185 ASN F 189 ASN ** F 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 185 ASN G 189 ASN ** G 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 369 GLN I 185 ASN ** I 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 185 ASN ** K 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 189 ASN ** L 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 185 ASN M 189 ASN ** N 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 185 ASN O 189 ASN ** O 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 185 ASN P 189 ASN ** P 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 185 ASN ** R 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.4562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.062 31914 Z= 0.276 Angle : 0.674 7.504 43362 Z= 0.345 Chirality : 0.042 0.161 4824 Planarity : 0.006 0.067 5670 Dihedral : 4.050 16.901 4284 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer Outliers : 5.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.13), residues: 3996 helix: 0.59 (0.10), residues: 2754 sheet: None (None), residues: 0 loop : -2.73 (0.15), residues: 1242 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7992 Ramachandran restraints generated. 3996 Oldfield, 0 Emsley, 3996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7992 Ramachandran restraints generated. 3996 Oldfield, 0 Emsley, 3996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1161 residues out of total 3366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 196 poor density : 965 time to evaluate : 3.691 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 outliers start: 196 outliers final: 129 residues processed: 1108 average time/residue: 0.4333 time to fit residues: 743.5315 Evaluate side-chains 876 residues out of total 3366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 747 time to evaluate : 3.970 Switching outliers to nearest non-outliers outliers start: 129 outliers final: 0 residues processed: 129 average time/residue: 0.2689 time to fit residues: 72.0482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 199 optimal weight: 0.0070 chunk 111 optimal weight: 7.9990 chunk 299 optimal weight: 8.9990 chunk 244 optimal weight: 7.9990 chunk 99 optimal weight: 2.9990 chunk 360 optimal weight: 1.9990 chunk 389 optimal weight: 2.9990 chunk 320 optimal weight: 9.9990 chunk 357 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 289 optimal weight: 8.9990 overall best weight: 2.2006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 ASN ** A 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 358 HIS B 189 ASN ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 358 HIS C 246 GLN E 153 ASN E 325 ASN F 246 GLN ** F 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 185 ASN G 358 HIS H 189 ASN ** H 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 369 GLN I 185 ASN I 189 ASN ** I 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 185 ASN ** J 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 358 HIS K 189 ASN ** K 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 358 HIS L 246 GLN ** L 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 153 ASN N 325 ASN O 246 GLN ** O 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 185 ASN P 358 HIS Q 189 ASN ** Q 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 369 GLN R 185 ASN R 189 ASN ** R 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.5205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.072 31914 Z= 0.213 Angle : 0.611 6.090 43362 Z= 0.313 Chirality : 0.040 0.147 4824 Planarity : 0.005 0.066 5670 Dihedral : 3.959 16.993 4284 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer Outliers : 2.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.13), residues: 3996 helix: 1.18 (0.10), residues: 2754 sheet: None (None), residues: 0 loop : -2.55 (0.15), residues: 1242 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7992 Ramachandran restraints generated. 3996 Oldfield, 0 Emsley, 3996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7992 Ramachandran restraints generated. 3996 Oldfield, 0 Emsley, 3996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 945 residues out of total 3366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 866 time to evaluate : 3.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 79 outliers final: 30 residues processed: 921 average time/residue: 0.3961 time to fit residues: 586.7530 Evaluate side-chains 780 residues out of total 3366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 750 time to evaluate : 3.695 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 0 residues processed: 30 average time/residue: 0.2843 time to fit residues: 20.6694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 355 optimal weight: 9.9990 chunk 270 optimal weight: 20.0000 chunk 186 optimal weight: 30.0000 chunk 39 optimal weight: 9.9990 chunk 171 optimal weight: 9.9990 chunk 241 optimal weight: 4.9990 chunk 361 optimal weight: 7.9990 chunk 382 optimal weight: 2.9990 chunk 188 optimal weight: 9.9990 chunk 342 optimal weight: 9.9990 chunk 103 optimal weight: 9.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 189 ASN ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 246 GLN ** C 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 252 HIS F 308 GLN G 185 ASN ** H 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 185 ASN ** I 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 189 ASN ** K 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 185 ASN ** Q 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 185 ASN ** R 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.6469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.097 31914 Z= 0.395 Angle : 0.741 6.447 43362 Z= 0.387 Chirality : 0.045 0.186 4824 Planarity : 0.006 0.064 5670 Dihedral : 4.722 19.553 4284 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 14.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer Outliers : 5.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.13), residues: 3996 helix: 0.86 (0.10), residues: 2772 sheet: None (None), residues: 0 loop : -2.69 (0.15), residues: 1224 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7992 Ramachandran restraints generated. 3996 Oldfield, 0 Emsley, 3996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7992 Ramachandran restraints generated. 3996 Oldfield, 0 Emsley, 3996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 957 residues out of total 3366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 181 poor density : 776 time to evaluate : 3.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 181 outliers final: 105 residues processed: 896 average time/residue: 0.4298 time to fit residues: 607.9687 Evaluate side-chains 807 residues out of total 3366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 702 time to evaluate : 3.739 Switching outliers to nearest non-outliers outliers start: 105 outliers final: 0 residues processed: 105 average time/residue: 0.2822 time to fit residues: 59.7962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 318 optimal weight: 7.9990 chunk 217 optimal weight: 2.9990 chunk 5 optimal weight: 7.9990 chunk 285 optimal weight: 9.9990 chunk 157 optimal weight: 8.9990 chunk 326 optimal weight: 8.9990 chunk 264 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 195 optimal weight: 8.9990 chunk 343 optimal weight: 7.9990 chunk 96 optimal weight: 20.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 185 ASN G 216 HIS H 189 ASN ** H 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 185 ASN ** I 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 185 ASN P 216 HIS Q 189 ASN ** Q 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 185 ASN ** R 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.6874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.079 31914 Z= 0.382 Angle : 0.721 6.239 43362 Z= 0.376 Chirality : 0.044 0.142 4824 Planarity : 0.006 0.064 5670 Dihedral : 4.673 18.509 4284 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 13.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer Outliers : 2.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.13), residues: 3996 helix: 0.90 (0.10), residues: 2754 sheet: None (None), residues: 0 loop : -2.86 (0.15), residues: 1242 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7992 Ramachandran restraints generated. 3996 Oldfield, 0 Emsley, 3996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7992 Ramachandran restraints generated. 3996 Oldfield, 0 Emsley, 3996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 852 residues out of total 3366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 755 time to evaluate : 3.871 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 97 outliers final: 58 residues processed: 826 average time/residue: 0.4133 time to fit residues: 543.9729 Evaluate side-chains 761 residues out of total 3366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 703 time to evaluate : 3.731 Switching outliers to nearest non-outliers outliers start: 58 outliers final: 0 residues processed: 58 average time/residue: 0.2625 time to fit residues: 34.0850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 128 optimal weight: 0.9990 chunk 344 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 224 optimal weight: 5.9990 chunk 94 optimal weight: 8.9990 chunk 383 optimal weight: 1.9990 chunk 318 optimal weight: 0.5980 chunk 177 optimal weight: 0.7980 chunk 31 optimal weight: 6.9990 chunk 126 optimal weight: 4.9990 chunk 201 optimal weight: 7.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 324 GLN ** F 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 308 GLN G 185 ASN H 189 ASN I 185 ASN I 246 GLN ** I 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 253 ASN ** K 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 308 GLN P 185 ASN Q 189 ASN ** Q 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 185 ASN R 246 GLN ** R 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 253 ASN R 311 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.6733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.114 31914 Z= 0.207 Angle : 0.628 7.065 43362 Z= 0.326 Chirality : 0.040 0.148 4824 Planarity : 0.005 0.081 5670 Dihedral : 4.209 16.601 4284 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer Outliers : 1.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.13), residues: 3996 helix: 1.25 (0.10), residues: 2736 sheet: None (None), residues: 0 loop : -2.69 (0.15), residues: 1260 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7992 Ramachandran restraints generated. 3996 Oldfield, 0 Emsley, 3996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7992 Ramachandran restraints generated. 3996 Oldfield, 0 Emsley, 3996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 872 residues out of total 3366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 820 time to evaluate : 3.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 52 outliers final: 22 residues processed: 857 average time/residue: 0.4089 time to fit residues: 557.8497 Evaluate side-chains 752 residues out of total 3366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 730 time to evaluate : 3.874 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.2698 time to fit residues: 16.2578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 369 optimal weight: 5.9990 chunk 43 optimal weight: 0.3980 chunk 218 optimal weight: 10.0000 chunk 279 optimal weight: 9.9990 chunk 216 optimal weight: 6.9990 chunk 322 optimal weight: 0.6980 chunk 213 optimal weight: 2.9990 chunk 381 optimal weight: 7.9990 chunk 238 optimal weight: 0.5980 chunk 232 optimal weight: 5.9990 chunk 176 optimal weight: 0.9980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 ASN ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 185 ASN F 252 HIS F 308 GLN I 185 ASN ** I 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 327 ASN J 185 ASN ** K 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 324 GLN M 185 ASN ** O 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 185 ASN ** R 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 253 ASN R 327 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.6751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.144 31914 Z= 0.201 Angle : 0.636 9.099 43362 Z= 0.326 Chirality : 0.040 0.146 4824 Planarity : 0.005 0.093 5670 Dihedral : 4.048 16.706 4284 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer Outliers : 1.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.13), residues: 3996 helix: 1.38 (0.10), residues: 2736 sheet: None (None), residues: 0 loop : -2.63 (0.15), residues: 1260 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7992 Ramachandran restraints generated. 3996 Oldfield, 0 Emsley, 3996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7992 Ramachandran restraints generated. 3996 Oldfield, 0 Emsley, 3996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 867 residues out of total 3366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 810 time to evaluate : 3.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 57 outliers final: 24 residues processed: 846 average time/residue: 0.4127 time to fit residues: 555.2927 Evaluate side-chains 756 residues out of total 3366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 732 time to evaluate : 3.972 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.2786 time to fit residues: 17.7725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 236 optimal weight: 9.9990 chunk 152 optimal weight: 2.9990 chunk 227 optimal weight: 6.9990 chunk 114 optimal weight: 9.9990 chunk 74 optimal weight: 4.9990 chunk 73 optimal weight: 0.0000 chunk 242 optimal weight: 20.0000 chunk 260 optimal weight: 7.9990 chunk 188 optimal weight: 7.9990 chunk 35 optimal weight: 0.3980 chunk 300 optimal weight: 10.0000 overall best weight: 3.0790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 ASN ** A 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 185 ASN ** F 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 185 ASN H 246 GLN ** H 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 185 ASN ** I 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 185 ASN ** J 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 185 ASN ** O 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 308 GLN P 185 ASN Q 246 GLN R 185 ASN ** R 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 253 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.6907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.161 31914 Z= 0.243 Angle : 0.677 10.411 43362 Z= 0.346 Chirality : 0.041 0.186 4824 Planarity : 0.005 0.099 5670 Dihedral : 4.131 17.041 4284 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.11 % Favored : 92.74 % Rotamer Outliers : 1.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.13), residues: 3996 helix: 1.34 (0.10), residues: 2736 sheet: None (None), residues: 0 loop : -2.64 (0.15), residues: 1260 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7992 Ramachandran restraints generated. 3996 Oldfield, 0 Emsley, 3996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7992 Ramachandran restraints generated. 3996 Oldfield, 0 Emsley, 3996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 784 residues out of total 3366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 733 time to evaluate : 3.912 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 51 outliers final: 28 residues processed: 765 average time/residue: 0.4079 time to fit residues: 500.4177 Evaluate side-chains 729 residues out of total 3366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 701 time to evaluate : 3.290 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.2537 time to fit residues: 18.1346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 347 optimal weight: 10.0000 chunk 365 optimal weight: 7.9990 chunk 333 optimal weight: 5.9990 chunk 355 optimal weight: 0.9990 chunk 214 optimal weight: 6.9990 chunk 154 optimal weight: 20.0000 chunk 279 optimal weight: 5.9990 chunk 109 optimal weight: 10.0000 chunk 321 optimal weight: 6.9990 chunk 336 optimal weight: 10.0000 chunk 354 optimal weight: 0.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 ASN ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 185 ASN ** I 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 185 ASN ** K 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 185 ASN ** R 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.7133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.259 31914 Z= 0.301 Angle : 0.709 14.663 43362 Z= 0.365 Chirality : 0.042 0.168 4824 Planarity : 0.006 0.106 5670 Dihedral : 4.294 17.809 4284 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.63 % Favored : 92.22 % Rotamer Outliers : 1.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.13), residues: 3996 helix: 1.25 (0.10), residues: 2736 sheet: None (None), residues: 0 loop : -2.73 (0.14), residues: 1260 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7992 Ramachandran restraints generated. 3996 Oldfield, 0 Emsley, 3996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7992 Ramachandran restraints generated. 3996 Oldfield, 0 Emsley, 3996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 761 residues out of total 3366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 711 time to evaluate : 3.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 50 outliers final: 26 residues processed: 737 average time/residue: 0.4163 time to fit residues: 490.5233 Evaluate side-chains 719 residues out of total 3366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 693 time to evaluate : 3.564 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.2746 time to fit residues: 17.7719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 233 optimal weight: 3.9990 chunk 376 optimal weight: 3.9990 chunk 229 optimal weight: 5.9990 chunk 178 optimal weight: 8.9990 chunk 261 optimal weight: 8.9990 chunk 394 optimal weight: 5.9990 chunk 363 optimal weight: 3.9990 chunk 314 optimal weight: 0.9980 chunk 32 optimal weight: 0.0060 chunk 242 optimal weight: 20.0000 chunk 192 optimal weight: 8.9990 overall best weight: 2.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 ASN ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 308 GLN ** H 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 185 ASN ** I 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 185 ASN ** K 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 185 ASN ** R 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.7099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.126 31914 Z= 0.237 Angle : 0.692 11.188 43362 Z= 0.353 Chirality : 0.041 0.178 4824 Planarity : 0.005 0.079 5670 Dihedral : 4.198 17.424 4284 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.41 % Favored : 92.44 % Rotamer Outliers : 0.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.13), residues: 3996 helix: 1.37 (0.10), residues: 2718 sheet: None (None), residues: 0 loop : -2.60 (0.15), residues: 1278 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7992 Ramachandran restraints generated. 3996 Oldfield, 0 Emsley, 3996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7992 Ramachandran restraints generated. 3996 Oldfield, 0 Emsley, 3996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 752 residues out of total 3366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 736 time to evaluate : 3.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 6 residues processed: 747 average time/residue: 0.4068 time to fit residues: 487.5900 Evaluate side-chains 704 residues out of total 3366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 698 time to evaluate : 3.727 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2766 time to fit residues: 8.0304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 249 optimal weight: 0.7980 chunk 334 optimal weight: 0.0060 chunk 96 optimal weight: 3.9990 chunk 289 optimal weight: 6.9990 chunk 46 optimal weight: 7.9990 chunk 87 optimal weight: 7.9990 chunk 314 optimal weight: 8.9990 chunk 131 optimal weight: 2.9990 chunk 323 optimal weight: 5.9990 chunk 39 optimal weight: 0.9990 chunk 57 optimal weight: 20.0000 overall best weight: 1.7602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 ASN ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 252 HIS E 324 GLN ** F 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 246 GLN ** H 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 185 ASN ** I 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 185 ASN ** K 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 324 GLN ** O 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 246 GLN R 185 ASN ** R 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.127928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.113763 restraints weight = 57310.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.115305 restraints weight = 38968.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.116476 restraints weight = 29538.950| |-----------------------------------------------------------------------------| r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.7111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.534 31914 Z= 0.274 Angle : 0.706 22.723 43362 Z= 0.364 Chirality : 0.040 0.261 4824 Planarity : 0.005 0.126 5670 Dihedral : 4.109 16.684 4284 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.36 % Favored : 92.49 % Rotamer Outliers : 0.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.13), residues: 3996 helix: 1.42 (0.10), residues: 2718 sheet: None (None), residues: 0 loop : -2.61 (0.15), residues: 1278 =============================================================================== Job complete usr+sys time: 8610.72 seconds wall clock time: 155 minutes 22.77 seconds (9322.77 seconds total)