Starting phenix.real_space_refine (version: dev) on Sun Feb 26 20:47:55 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pig_20350/02_2023/6pig_20350.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pig_20350/02_2023/6pig_20350.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pig_20350/02_2023/6pig_20350.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pig_20350/02_2023/6pig_20350.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pig_20350/02_2023/6pig_20350.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pig_20350/02_2023/6pig_20350.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.005 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 Process input model Symmetric amino acids flipped Residue "A ARG 37": "NH1" <-> "NH2" Residue "A GLU 44": "OE1" <-> "OE2" Residue "A GLU 96": "OE1" <-> "OE2" Residue "A ARG 178": "NH1" <-> "NH2" Residue "A GLU 192": "OE1" <-> "OE2" Residue "A ARG 210": "NH1" <-> "NH2" Residue "A GLU 229": "OE1" <-> "OE2" Residue "A GLU 231": "OE1" <-> "OE2" Residue "A GLU 277": "OE1" <-> "OE2" Residue "A GLU 314": "OE1" <-> "OE2" Residue "B ARG 37": "NH1" <-> "NH2" Residue "B GLU 164": "OE1" <-> "OE2" Residue "B ARG 178": "NH1" <-> "NH2" Residue "B ARG 210": "NH1" <-> "NH2" Residue "C ARG 37": "NH1" <-> "NH2" Residue "C GLU 169": "OE1" <-> "OE2" Residue "C ARG 178": "NH1" <-> "NH2" Residue "C ARG 210": "NH1" <-> "NH2" Residue "C GLU 292": "OE1" <-> "OE2" Residue "D ARG 37": "NH1" <-> "NH2" Residue "D GLU 44": "OE1" <-> "OE2" Residue "D GLU 164": "OE1" <-> "OE2" Residue "D ARG 178": "NH1" <-> "NH2" Residue "D ARG 210": "NH1" <-> "NH2" Residue "D GLU 229": "OE1" <-> "OE2" Residue "D GLU 254": "OE1" <-> "OE2" Residue "D GLU 292": "OE1" <-> "OE2" Residue "D GLU 318": "OE1" <-> "OE2" Residue "E TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 37": "NH1" <-> "NH2" Residue "E ARG 178": "NH1" <-> "NH2" Residue "E ARG 210": "NH1" <-> "NH2" Residue "E GLU 229": "OE1" <-> "OE2" Residue "E GLU 329": "OE1" <-> "OE2" Residue "F ARG 37": "NH1" <-> "NH2" Residue "F ARG 178": "NH1" <-> "NH2" Residue "F ARG 210": "NH1" <-> "NH2" Residue "F GLU 229": "OE1" <-> "OE2" Residue "F GLU 318": "OE1" <-> "OE2" Residue "F GLU 329": "OE1" <-> "OE2" Residue "G ARG 21": "NH1" <-> "NH2" Residue "G ARG 24": "NH1" <-> "NH2" Residue "G ARG 67": "NH1" <-> "NH2" Residue "G GLU 69": "OE1" <-> "OE2" Residue "G ARG 82": "NH1" <-> "NH2" Residue "G ARG 93": "NH1" <-> "NH2" Residue "G GLU 151": "OE1" <-> "OE2" Residue "G ARG 228": "NH1" <-> "NH2" Residue "G ARG 234": "NH1" <-> "NH2" Residue "G ARG 259": "NH1" <-> "NH2" Residue "G GLU 436": "OE1" <-> "OE2" Residue "G ARG 503": "NH1" <-> "NH2" Residue "G GLU 526": "OE1" <-> "OE2" Residue "G GLU 530": "OE1" <-> "OE2" Residue "G GLU 535": "OE1" <-> "OE2" Residue "G ARG 584": "NH1" <-> "NH2" Residue "G ARG 628": "NH1" <-> "NH2" Residue "H GLU 13": "OE1" <-> "OE2" Residue "H GLU 36": "OE1" <-> "OE2" Residue "H GLU 65": "OE1" <-> "OE2" Residue "H GLU 94": "OE1" <-> "OE2" Residue "H ARG 103": "NH1" <-> "NH2" Residue "H ARG 117": "NH1" <-> "NH2" Residue "H ARG 120": "NH1" <-> "NH2" Residue "H ARG 121": "NH1" <-> "NH2" Residue "H ARG 125": "NH1" <-> "NH2" Residue "H GLU 131": "OE1" <-> "OE2" Residue "H GLU 154": "OE1" <-> "OE2" Residue "H ARG 168": "NH1" <-> "NH2" Residue "H GLU 190": "OE1" <-> "OE2" Residue "I ARG 5": "NH1" <-> "NH2" Residue "I GLU 12": "OE1" <-> "OE2" Residue "I GLU 35": "OE1" <-> "OE2" Residue "I GLU 85": "OE1" <-> "OE2" Residue "I GLU 148": "OE1" <-> "OE2" Residue "I ARG 249": "NH1" <-> "NH2" Residue "I GLU 264": "OE1" <-> "OE2" Residue "I ARG 281": "NH1" <-> "NH2" Residue "I GLU 291": "OE1" <-> "OE2" Residue "I GLU 302": "OE1" <-> "OE2" Residue "I ARG 310": "NH1" <-> "NH2" Residue "I GLU 327": "OE1" <-> "OE2" Residue "I ARG 346": "NH1" <-> "NH2" Residue "I GLU 384": "OE1" <-> "OE2" Residue "I ARG 387": "NH1" <-> "NH2" Residue "J ARG 20": "NH1" <-> "NH2" Residue "J ARG 32": "NH1" <-> "NH2" Residue "J GLU 88": "OE1" <-> "OE2" Residue "J ARG 121": "NH1" <-> "NH2" Residue "J GLU 134": "OE1" <-> "OE2" Residue "J GLU 148": "OE1" <-> "OE2" Residue "J GLU 166": "OE1" <-> "OE2" Residue "J GLU 208": "OE1" <-> "OE2" Residue "J ARG 220": "NH1" <-> "NH2" Residue "J GLU 256": "OE1" <-> "OE2" Residue "J GLU 258": "OE1" <-> "OE2" Residue "J GLU 260": "OE1" <-> "OE2" Residue "J ARG 274": "NH1" <-> "NH2" Residue "J ARG 281": "NH1" <-> "NH2" Residue "J GLU 291": "OE1" <-> "OE2" Residue "J GLU 302": "OE1" <-> "OE2" Residue "J GLU 308": "OE1" <-> "OE2" Residue "J ARG 310": "NH1" <-> "NH2" Residue "J GLU 327": "OE1" <-> "OE2" Residue "J ARG 346": "NH1" <-> "NH2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 28867 Number of models: 1 Model: "" Number of chains: 11 Chain: "1" Number of atoms: 1271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 1271 Classifications: {'RNA': 60} Modifications used: {'5*END': 1, 'rna2p_pur': 9, 'rna2p_pyr': 14, 'rna3p_pur': 20, 'rna3p_pyr': 17} Link IDs: {'rna2p': 23, 'rna3p': 36} Chain: "A" Number of atoms: 2742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2742 Classifications: {'peptide': 343} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 323} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 2714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2714 Classifications: {'peptide': 339} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 4, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 317} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 2705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2705 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 317} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "D" Number of atoms: 2705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2705 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 317} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 2705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2705 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 317} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "F" Number of atoms: 2509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2509 Classifications: {'peptide': 310} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 15, 'TRANS': 291} Chain breaks: 2 Chain: "G" Number of atoms: 4009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 511, 4009 Classifications: {'peptide': 511} Link IDs: {'PCIS': 3, 'PTRANS': 21, 'TRANS': 486} Chain breaks: 2 Chain: "H" Number of atoms: 1606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1606 Classifications: {'peptide': 197} Link IDs: {'CIS': 2, 'PTRANS': 7, 'TRANS': 187} Chain: "I" Number of atoms: 2923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 2923 Classifications: {'peptide': 357} Link IDs: {'CIS': 4, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 335} Chain breaks: 3 Chain: "J" Number of atoms: 2978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2978 Classifications: {'peptide': 368} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 347} Chain breaks: 2 Time building chain proxies: 17.93, per 1000 atoms: 0.62 Number of scatterers: 28867 At special positions: 0 Unit cell: (133, 161.5, 185.25, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 142 16.00 P 59 15.00 O 5533 8.00 N 4990 7.00 C 18143 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: 11.93 Conformation dependent library (CDL) restraints added in 4.4 seconds 6782 Ramachandran restraints generated. 3391 Oldfield, 0 Emsley, 3391 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6552 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 36 sheets defined 26.7% alpha, 12.4% beta 6 base pairs and 27 stacking pairs defined. Time for finding SS restraints: 7.53 Creating SS restraints... Processing helix chain 'A' and resid 105 through 123 Processing helix chain 'A' and resid 125 through 134 Processing helix chain 'A' and resid 177 through 182 removed outlier: 3.558A pdb=" N PHE A 181 " --> pdb=" O SER A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 200 removed outlier: 3.783A pdb=" N ILE A 190 " --> pdb=" O ASN A 186 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ILE A 194 " --> pdb=" O ILE A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 268 Processing helix chain 'A' and resid 309 through 313 Processing helix chain 'A' and resid 316 through 321 removed outlier: 4.112A pdb=" N LEU A 320 " --> pdb=" O TYR A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 342 removed outlier: 4.028A pdb=" N ASN A 332 " --> pdb=" O GLN A 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 123 Processing helix chain 'B' and resid 125 through 134 Processing helix chain 'B' and resid 139 through 143 removed outlier: 3.574A pdb=" N LEU B 142 " --> pdb=" O GLY B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 182 removed outlier: 3.799A pdb=" N PHE B 181 " --> pdb=" O SER B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 191 removed outlier: 3.551A pdb=" N ILE B 190 " --> pdb=" O ASN B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 200 Processing helix chain 'B' and resid 305 through 311 removed outlier: 3.789A pdb=" N GLN B 311 " --> pdb=" O PHE B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 322 removed outlier: 3.560A pdb=" N GLU B 318 " --> pdb=" O GLU B 314 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL B 319 " --> pdb=" O HIS B 315 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ALA B 322 " --> pdb=" O GLU B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 344 removed outlier: 3.689A pdb=" N LYS B 343 " --> pdb=" O ALA B 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 49 removed outlier: 3.808A pdb=" N ALA C 49 " --> pdb=" O LYS C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 123 removed outlier: 3.633A pdb=" N THR C 111 " --> pdb=" O LYS C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 135 removed outlier: 3.895A pdb=" N ASN C 135 " --> pdb=" O ARG C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 143 Processing helix chain 'C' and resid 178 through 182 Processing helix chain 'C' and resid 187 through 192 removed outlier: 4.061A pdb=" N GLU C 192 " --> pdb=" O SER C 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 269 removed outlier: 3.854A pdb=" N ILE C 268 " --> pdb=" O THR C 264 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA C 269 " --> pdb=" O GLY C 265 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 264 through 269' Processing helix chain 'C' and resid 305 through 311 removed outlier: 3.646A pdb=" N GLN C 311 " --> pdb=" O PHE C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 312 through 320 removed outlier: 3.802A pdb=" N GLU C 318 " --> pdb=" O GLU C 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 343 removed outlier: 3.894A pdb=" N LYS C 343 " --> pdb=" O ALA C 339 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 123 removed outlier: 3.680A pdb=" N THR D 111 " --> pdb=" O LYS D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 138 removed outlier: 3.832A pdb=" N ASN D 135 " --> pdb=" O ARG D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 182 Processing helix chain 'D' and resid 194 through 199 Processing helix chain 'D' and resid 262 through 269 removed outlier: 3.939A pdb=" N ILE D 268 " --> pdb=" O THR D 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 311 Processing helix chain 'D' and resid 312 through 320 removed outlier: 3.637A pdb=" N TYR D 316 " --> pdb=" O GLN D 312 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N GLU D 318 " --> pdb=" O GLU D 314 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL D 319 " --> pdb=" O HIS D 315 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LEU D 320 " --> pdb=" O TYR D 316 " (cutoff:3.500A) Processing helix chain 'D' and resid 330 through 343 removed outlier: 3.797A pdb=" N PHE D 336 " --> pdb=" O ASN D 332 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LYS D 343 " --> pdb=" O ALA D 339 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 49 removed outlier: 3.809A pdb=" N ALA E 49 " --> pdb=" O LYS E 46 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 67 removed outlier: 3.683A pdb=" N GLN E 67 " --> pdb=" O ALA E 64 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 123 Processing helix chain 'E' and resid 125 through 137 removed outlier: 3.772A pdb=" N ASN E 135 " --> pdb=" O ARG E 131 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ILE E 136 " --> pdb=" O TYR E 132 " (cutoff:3.500A) Processing helix chain 'E' and resid 194 through 200 removed outlier: 3.549A pdb=" N SER E 200 " --> pdb=" O THR E 196 " (cutoff:3.500A) Processing helix chain 'E' and resid 305 through 311 Processing helix chain 'E' and resid 312 through 320 removed outlier: 3.820A pdb=" N GLU E 318 " --> pdb=" O GLU E 314 " (cutoff:3.500A) Processing helix chain 'E' and resid 330 through 344 removed outlier: 3.513A pdb=" N PHE E 336 " --> pdb=" O ASN E 332 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS E 343 " --> pdb=" O ALA E 339 " (cutoff:3.500A) Processing helix chain 'F' and resid 107 through 123 removed outlier: 4.022A pdb=" N THR F 111 " --> pdb=" O LYS F 107 " (cutoff:3.500A) Processing helix chain 'F' and resid 125 through 135 removed outlier: 3.870A pdb=" N ASN F 135 " --> pdb=" O ARG F 131 " (cutoff:3.500A) Processing helix chain 'F' and resid 139 through 143 Processing helix chain 'F' and resid 177 through 182 removed outlier: 3.629A pdb=" N PHE F 181 " --> pdb=" O SER F 177 " (cutoff:3.500A) Processing helix chain 'F' and resid 183 through 188 removed outlier: 3.995A pdb=" N TRP F 187 " --> pdb=" O ASN F 183 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N SER F 188 " --> pdb=" O ASN F 184 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 183 through 188' Processing helix chain 'F' and resid 194 through 200 Processing helix chain 'F' and resid 307 through 312 removed outlier: 3.512A pdb=" N GLN F 311 " --> pdb=" O PHE F 307 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLN F 312 " --> pdb=" O SER F 308 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 307 through 312' Processing helix chain 'F' and resid 312 through 320 removed outlier: 3.742A pdb=" N GLU F 318 " --> pdb=" O GLU F 314 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU F 320 " --> pdb=" O TYR F 316 " (cutoff:3.500A) Processing helix chain 'F' and resid 330 through 342 removed outlier: 3.749A pdb=" N PHE F 336 " --> pdb=" O ASN F 332 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 10 Processing helix chain 'G' and resid 17 through 24 Processing helix chain 'G' and resid 36 through 44 removed outlier: 4.003A pdb=" N THR G 41 " --> pdb=" O ILE G 37 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE G 42 " --> pdb=" O ASP G 38 " (cutoff:3.500A) Processing helix chain 'G' and resid 63 through 68 removed outlier: 4.266A pdb=" N ASP G 68 " --> pdb=" O GLN G 64 " (cutoff:3.500A) Processing helix chain 'G' and resid 71 through 77 Processing helix chain 'G' and resid 112 through 116 removed outlier: 3.736A pdb=" N ILE G 116 " --> pdb=" O SER G 113 " (cutoff:3.500A) Processing helix chain 'G' and resid 148 through 153 removed outlier: 3.556A pdb=" N LEU G 153 " --> pdb=" O LEU G 149 " (cutoff:3.500A) Processing helix chain 'G' and resid 161 through 167 removed outlier: 3.918A pdb=" N LEU G 167 " --> pdb=" O THR G 163 " (cutoff:3.500A) Processing helix chain 'G' and resid 173 through 181 removed outlier: 3.735A pdb=" N MET G 177 " --> pdb=" O THR G 173 " (cutoff:3.500A) Processing helix chain 'G' and resid 219 through 229 removed outlier: 4.023A pdb=" N SER G 223 " --> pdb=" O LEU G 219 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU G 229 " --> pdb=" O PHE G 225 " (cutoff:3.500A) Processing helix chain 'G' and resid 248 through 253 Processing helix chain 'G' and resid 411 through 427 removed outlier: 3.892A pdb=" N PHE G 415 " --> pdb=" O SER G 411 " (cutoff:3.500A) Processing helix chain 'G' and resid 494 through 499 removed outlier: 3.919A pdb=" N SER G 499 " --> pdb=" O THR G 495 " (cutoff:3.500A) Processing helix chain 'G' and resid 524 through 529 Processing helix chain 'G' and resid 550 through 557 Processing helix chain 'H' and resid 16 through 31 removed outlier: 3.798A pdb=" N LYS H 23 " --> pdb=" O SER H 19 " (cutoff:3.500A) Processing helix chain 'H' and resid 63 through 70 removed outlier: 3.529A pdb=" N ASP H 67 " --> pdb=" O LYS H 63 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LEU H 68 " --> pdb=" O ILE H 64 " (cutoff:3.500A) Processing helix chain 'H' and resid 73 through 80 removed outlier: 3.593A pdb=" N GLN H 77 " --> pdb=" O HIS H 73 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLN H 80 " --> pdb=" O VAL H 76 " (cutoff:3.500A) Processing helix chain 'H' and resid 106 through 110 Processing helix chain 'H' and resid 111 through 125 removed outlier: 3.582A pdb=" N ARG H 117 " --> pdb=" O ALA H 113 " (cutoff:3.500A) Processing helix chain 'H' and resid 126 through 128 No H-bonds generated for 'chain 'H' and resid 126 through 128' Processing helix chain 'I' and resid 16 through 21 Processing helix chain 'I' and resid 30 through 45 removed outlier: 4.299A pdb=" N LEU I 34 " --> pdb=" O VAL I 30 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ILE I 44 " --> pdb=" O PHE I 40 " (cutoff:3.500A) Processing helix chain 'I' and resid 68 through 81 removed outlier: 4.386A pdb=" N LEU I 81 " --> pdb=" O LYS I 77 " (cutoff:3.500A) Processing helix chain 'I' and resid 196 through 201 removed outlier: 3.857A pdb=" N VAL I 200 " --> pdb=" O ALA I 196 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N SER I 201 " --> pdb=" O ALA I 197 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 196 through 201' Processing helix chain 'I' and resid 216 through 228 removed outlier: 3.965A pdb=" N ARG I 220 " --> pdb=" O PRO I 216 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N TRP I 221 " --> pdb=" O LYS I 217 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLY I 222 " --> pdb=" O SER I 218 " (cutoff:3.500A) Processing helix chain 'I' and resid 246 through 265 removed outlier: 3.863A pdb=" N PHE I 251 " --> pdb=" O TRP I 247 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N HIS I 252 " --> pdb=" O PRO I 248 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N SER I 253 " --> pdb=" O ARG I 249 " (cutoff:3.500A) Processing helix chain 'I' and resid 280 through 285 removed outlier: 3.950A pdb=" N PHE I 284 " --> pdb=" O GLY I 280 " (cutoff:3.500A) Processing helix chain 'I' and resid 297 through 310 removed outlier: 3.901A pdb=" N GLY I 301 " --> pdb=" O ASN I 297 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N GLU I 302 " --> pdb=" O ILE I 298 " (cutoff:3.500A) Processing helix chain 'I' and resid 327 through 333 Processing helix chain 'I' and resid 336 through 345 removed outlier: 3.999A pdb=" N ALA I 340 " --> pdb=" O LEU I 336 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N SER I 341 " --> pdb=" O ASP I 337 " (cutoff:3.500A) Processing helix chain 'I' and resid 368 through 379 removed outlier: 3.502A pdb=" N ILE I 372 " --> pdb=" O HIS I 368 " (cutoff:3.500A) Processing helix chain 'J' and resid 15 through 24 removed outlier: 3.916A pdb=" N LYS J 24 " --> pdb=" O ARG J 20 " (cutoff:3.500A) Processing helix chain 'J' and resid 32 through 43 Processing helix chain 'J' and resid 68 through 81 removed outlier: 3.806A pdb=" N LEU J 81 " --> pdb=" O LYS J 77 " (cutoff:3.500A) Processing helix chain 'J' and resid 196 through 206 removed outlier: 3.626A pdb=" N ALA J 205 " --> pdb=" O SER J 201 " (cutoff:3.500A) Processing helix chain 'J' and resid 217 through 231 removed outlier: 4.151A pdb=" N TRP J 221 " --> pdb=" O LYS J 217 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N GLY J 222 " --> pdb=" O SER J 218 " (cutoff:3.500A) Processing helix chain 'J' and resid 237 through 244 removed outlier: 3.861A pdb=" N VAL J 241 " --> pdb=" O HIS J 237 " (cutoff:3.500A) Processing helix chain 'J' and resid 246 through 260 removed outlier: 3.644A pdb=" N PHE J 251 " --> pdb=" O TRP J 247 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N HIS J 252 " --> pdb=" O PRO J 248 " (cutoff:3.500A) Processing helix chain 'J' and resid 280 through 285 Processing helix chain 'J' and resid 297 through 310 Processing helix chain 'J' and resid 328 through 333 removed outlier: 3.982A pdb=" N LEU J 332 " --> pdb=" O ALA J 328 " (cutoff:3.500A) Processing helix chain 'J' and resid 338 through 345 Processing helix chain 'J' and resid 369 through 380 Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 31 removed outlier: 3.556A pdb=" N HIS A 84 " --> pdb=" O VAL A 23 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE A 206 " --> pdb=" O TRP A 159 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N CYS A 151 " --> pdb=" O HIS A 214 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 35 through 41 Processing sheet with id=AA3, first strand: chain 'A' and resid 248 through 251 Processing sheet with id=AA4, first strand: chain 'A' and resid 270 through 272 Processing sheet with id=AA5, first strand: chain 'A' and resid 289 through 290 removed outlier: 3.909A pdb=" N HIS A 290 " --> pdb=" O THR A 295 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N THR A 295 " --> pdb=" O HIS A 290 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 29 through 31 removed outlier: 3.848A pdb=" N CYS B 151 " --> pdb=" O HIS B 214 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 34 through 41 Processing sheet with id=AA8, first strand: chain 'B' and resid 248 through 251 Processing sheet with id=AA9, first strand: chain 'C' and resid 13 through 15 Processing sheet with id=AB1, first strand: chain 'C' and resid 13 through 15 removed outlier: 3.718A pdb=" N CYS C 151 " --> pdb=" O HIS C 214 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 35 through 41 Processing sheet with id=AB3, first strand: chain 'C' and resid 248 through 251 Processing sheet with id=AB4, first strand: chain 'D' and resid 13 through 14 Processing sheet with id=AB5, first strand: chain 'D' and resid 13 through 14 removed outlier: 3.719A pdb=" N CYS D 151 " --> pdb=" O HIS D 214 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU D 156 " --> pdb=" O VAL D 166 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 35 through 41 Processing sheet with id=AB7, first strand: chain 'D' and resid 248 through 251 Processing sheet with id=AB8, first strand: chain 'D' and resid 270 through 272 Processing sheet with id=AB9, first strand: chain 'E' and resid 13 through 14 Processing sheet with id=AC1, first strand: chain 'E' and resid 13 through 14 removed outlier: 3.893A pdb=" N CYS E 151 " --> pdb=" O HIS E 214 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 35 through 41 Processing sheet with id=AC3, first strand: chain 'E' and resid 248 through 251 Processing sheet with id=AC4, first strand: chain 'F' and resid 13 through 14 Processing sheet with id=AC5, first strand: chain 'F' and resid 13 through 14 removed outlier: 3.606A pdb=" N VAL F 166 " --> pdb=" O LEU F 156 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 35 through 38 Processing sheet with id=AC7, first strand: chain 'F' and resid 248 through 251 Processing sheet with id=AC8, first strand: chain 'G' and resid 85 through 86 Processing sheet with id=AC9, first strand: chain 'G' and resid 201 through 204 Processing sheet with id=AD1, first strand: chain 'G' and resid 438 through 444 removed outlier: 6.590A pdb=" N VAL G 478 " --> pdb=" O HIS G 443 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N LEU G 481 " --> pdb=" O PRO G 391 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N LEU G 483 " --> pdb=" O VAL G 389 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N VAL G 389 " --> pdb=" O LEU G 483 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 398 through 399 Processing sheet with id=AD3, first strand: chain 'G' and resid 539 through 541 Processing sheet with id=AD4, first strand: chain 'G' and resid 569 through 572 removed outlier: 3.878A pdb=" N GLY G 569 " --> pdb=" O ILE G 594 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 615 through 616 Processing sheet with id=AD6, first strand: chain 'H' and resid 4 through 5 Processing sheet with id=AD7, first strand: chain 'H' and resid 55 through 56 removed outlier: 3.535A pdb=" N THR H 9 " --> pdb=" O HIS H 85 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N HIS H 85 " --> pdb=" O THR H 9 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'H' and resid 99 through 100 Processing sheet with id=AD9, first strand: chain 'J' and resid 322 through 324 753 hydrogen bonds defined for protein. 2076 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 15 hydrogen bonds 22 hydrogen bond angles 0 basepair planarities 6 basepair parallelities 27 stacking parallelities Total time for adding SS restraints: 8.74 Time building geometry restraints manager: 12.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5482 1.33 - 1.46: 7938 1.46 - 1.58: 15985 1.58 - 1.70: 118 1.70 - 1.82: 205 Bond restraints: 29728 Sorted by residual: bond pdb=" N ILE J 125 " pdb=" CA ILE J 125 " ideal model delta sigma weight residual 1.460 1.495 -0.035 7.50e-03 1.78e+04 2.22e+01 bond pdb=" N ILE E 190 " pdb=" CA ILE E 190 " ideal model delta sigma weight residual 1.459 1.500 -0.042 9.10e-03 1.21e+04 2.10e+01 bond pdb=" N VAL G 497 " pdb=" CA VAL G 497 " ideal model delta sigma weight residual 1.458 1.498 -0.040 9.00e-03 1.23e+04 2.01e+01 bond pdb=" N ILE A 271 " pdb=" CA ILE A 271 " ideal model delta sigma weight residual 1.456 1.499 -0.042 9.50e-03 1.11e+04 1.99e+01 bond pdb=" N LEU H 11 " pdb=" CA LEU H 11 " ideal model delta sigma weight residual 1.463 1.494 -0.031 6.90e-03 2.10e+04 1.96e+01 ... (remaining 29723 not shown) Histogram of bond angle deviations from ideal: 96.50 - 104.11: 599 104.11 - 111.72: 11866 111.72 - 119.33: 15406 119.33 - 126.95: 12174 126.95 - 134.56: 582 Bond angle restraints: 40627 Sorted by residual: angle pdb=" N PRO G 533 " pdb=" CA PRO G 533 " pdb=" CB PRO G 533 " ideal model delta sigma weight residual 103.25 96.50 6.75 1.05e+00 9.07e-01 4.13e+01 angle pdb=" N PRO C 276 " pdb=" CA PRO C 276 " pdb=" CB PRO C 276 " ideal model delta sigma weight residual 103.25 96.88 6.37 1.05e+00 9.07e-01 3.68e+01 angle pdb=" C GLN B 67 " pdb=" N GLY B 68 " pdb=" CA GLY B 68 " ideal model delta sigma weight residual 119.92 125.43 -5.51 9.60e-01 1.09e+00 3.29e+01 angle pdb=" CA ILE G 201 " pdb=" C ILE G 201 " pdb=" O ILE G 201 " ideal model delta sigma weight residual 121.68 117.44 4.24 7.90e-01 1.60e+00 2.88e+01 angle pdb=" C LYS D 343 " pdb=" N GLY D 344 " pdb=" CA GLY D 344 " ideal model delta sigma weight residual 120.44 126.25 -5.81 1.09e+00 8.42e-01 2.84e+01 ... (remaining 40622 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.97: 17110 35.97 - 71.94: 404 71.94 - 107.91: 27 107.91 - 143.88: 2 143.88 - 179.85: 2 Dihedral angle restraints: 17545 sinusoidal: 7460 harmonic: 10085 Sorted by residual: dihedral pdb=" CA TRP A 24 " pdb=" C TRP A 24 " pdb=" N PRO A 25 " pdb=" CA PRO A 25 " ideal model delta harmonic sigma weight residual 180.00 -100.77 -79.23 0 5.00e+00 4.00e-02 2.51e+02 dihedral pdb=" CA ILE I 125 " pdb=" C ILE I 125 " pdb=" N PRO I 126 " pdb=" CA PRO I 126 " ideal model delta harmonic sigma weight residual 180.00 110.99 69.01 0 5.00e+00 4.00e-02 1.91e+02 dihedral pdb=" CA LYS J 7 " pdb=" C LYS J 7 " pdb=" N PRO J 8 " pdb=" CA PRO J 8 " ideal model delta harmonic sigma weight residual -180.00 -125.64 -54.36 0 5.00e+00 4.00e-02 1.18e+02 ... (remaining 17542 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 2212 0.061 - 0.122: 1583 0.122 - 0.184: 588 0.184 - 0.245: 105 0.245 - 0.306: 1 Chirality restraints: 4489 Sorted by residual: chirality pdb=" CA HIS A 349 " pdb=" N HIS A 349 " pdb=" C HIS A 349 " pdb=" CB HIS A 349 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.34e+00 chirality pdb=" C2' G 1 41 " pdb=" C3' G 1 41 " pdb=" O2' G 1 41 " pdb=" C1' G 1 41 " both_signs ideal model delta sigma weight residual False -2.75 -2.51 -0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" CA ILE B 85 " pdb=" N ILE B 85 " pdb=" C ILE B 85 " pdb=" CB ILE B 85 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.24 2.00e-01 2.50e+01 1.40e+00 ... (remaining 4486 not shown) Planarity restraints: 4986 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G 1 48 " -0.017 2.00e-02 2.50e+03 1.47e-02 6.52e+00 pdb=" N9 G 1 48 " 0.018 2.00e-02 2.50e+03 pdb=" C8 G 1 48 " 0.004 2.00e-02 2.50e+03 pdb=" N7 G 1 48 " 0.000 2.00e-02 2.50e+03 pdb=" C5 G 1 48 " -0.001 2.00e-02 2.50e+03 pdb=" C6 G 1 48 " 0.016 2.00e-02 2.50e+03 pdb=" O6 G 1 48 " -0.029 2.00e-02 2.50e+03 pdb=" N1 G 1 48 " 0.026 2.00e-02 2.50e+03 pdb=" C2 G 1 48 " -0.013 2.00e-02 2.50e+03 pdb=" N2 G 1 48 " -0.001 2.00e-02 2.50e+03 pdb=" N3 G 1 48 " -0.004 2.00e-02 2.50e+03 pdb=" C4 G 1 48 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE I 125 " -0.042 5.00e-02 4.00e+02 6.33e-02 6.41e+00 pdb=" N PRO I 126 " 0.110 5.00e-02 4.00e+02 pdb=" CA PRO I 126 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO I 126 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP H 67 " 0.012 2.00e-02 2.50e+03 2.44e-02 5.95e+00 pdb=" C ASP H 67 " -0.042 2.00e-02 2.50e+03 pdb=" O ASP H 67 " 0.016 2.00e-02 2.50e+03 pdb=" N LEU H 68 " 0.015 2.00e-02 2.50e+03 ... (remaining 4983 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 1033 2.72 - 3.26: 26356 3.26 - 3.81: 42513 3.81 - 4.35: 57282 4.35 - 4.90: 94986 Nonbonded interactions: 222170 Sorted by model distance: nonbonded pdb=" O GLU H 154 " pdb=" O PHE H 163 " model vdw 2.173 3.040 nonbonded pdb=" O LEU H 152 " pdb=" NH1 ARG H 164 " model vdw 2.327 2.520 nonbonded pdb=" O ASP A 14 " pdb=" NZ LYS G 510 " model vdw 2.348 2.520 nonbonded pdb=" O LYS G 517 " pdb=" N ILE G 519 " model vdw 2.356 2.520 nonbonded pdb=" O ASP G 608 " pdb=" OG1 THR G 611 " model vdw 2.377 2.440 ... (remaining 222165 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 43 or resid 70 through 230 or resid 243 through \ 349)) selection = (chain 'B' and (resid 2 through 43 or resid 70 through 230 or resid 243 through \ 349)) selection = (chain 'C' and (resid 2 through 43 or resid 70 through 230 or resid 243 through \ 349)) selection = (chain 'D' and (resid 2 through 43 or resid 70 through 230 or resid 243 through \ 349)) selection = (chain 'E' and (resid 2 through 43 or resid 70 through 230 or resid 243 through \ 349)) selection = chain 'F' } ncs_group { reference = (chain 'I' and (resid 1 through 193 or resid 195 through 232 or resid 236 throug \ h 351 or resid 361 through 378 or resid 380 through 393)) selection = (chain 'J' and (resid 1 through 162 or resid 164 or resid 166 or resid 196 throu \ gh 351 or resid 361 through 378 or resid 380 through 393)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 59 5.49 5 S 142 5.16 5 C 18143 2.51 5 N 4990 2.21 5 O 5533 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: 4.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 8.170 Check model and map are aligned: 0.440 Process input model: 79.530 Find NCS groups from input model: 1.910 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Set scattering table: 0.270 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:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 98.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 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 : 0.014 0.047 29728 Z= 0.894 Angle : 1.754 8.247 40627 Z= 1.237 Chirality : 0.085 0.306 4489 Planarity : 0.004 0.063 4986 Dihedral : 16.070 179.853 10993 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 1.98 Ramachandran Plot: Outliers : 3.45 % Allowed : 15.16 % Favored : 81.39 % Rotamer Outliers : 1.58 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.77 % Twisted Proline : 6.06 % Twisted General : 1.35 % 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: -4.85 (0.12), residues: 3391 helix: -2.89 (0.13), residues: 868 sheet: -2.09 (0.21), residues: 484 loop : -3.87 (0.11), residues: 2039 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6782 Ramachandran restraints generated. 3391 Oldfield, 0 Emsley, 3391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6782 Ramachandran restraints generated. 3391 Oldfield, 0 Emsley, 3391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 3040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 414 time to evaluate : 3.135 Fit side-chains revert: symmetry clash outliers start: 48 outliers final: 17 residues processed: 460 average time/residue: 0.4267 time to fit residues: 305.0229 Evaluate side-chains 282 residues out of total 3040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 265 time to evaluate : 3.429 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 3 residues processed: 17 average time/residue: 0.2436 time to fit residues: 12.6661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 290 optimal weight: 0.7980 chunk 260 optimal weight: 5.9990 chunk 144 optimal weight: 6.9990 chunk 89 optimal weight: 0.9990 chunk 175 optimal weight: 5.9990 chunk 139 optimal weight: 0.9980 chunk 269 optimal weight: 3.9990 chunk 104 optimal weight: 9.9990 chunk 163 optimal weight: 0.9990 chunk 200 optimal weight: 2.9990 chunk 312 optimal weight: 6.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 GLN ** A 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 174 ASN A 312 GLN B 35 ASN B 145 ASN B 174 ASN B 183 ASN B 348 GLN C 104 ASN C 174 ASN C 179 GLN C 214 HIS C 311 GLN D 135 ASN D 183 ASN D 328 GLN E 99 GLN E 241 GLN E 311 GLN E 349 HIS F 174 ASN F 183 ASN G 227 GLN G 230 GLN G 246 ASN G 518 HIS G 618 ASN H 17 ASN H 162 ASN H 166 ASN I 60 ASN I 95 ASN I 154 ASN I 207 HIS J 23 ASN J 66 ASN ** J 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 95 ASN J 313 GLN J 345 GLN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.2053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 29728 Z= 0.195 Angle : 0.765 12.931 40627 Z= 0.398 Chirality : 0.045 0.214 4489 Planarity : 0.005 0.078 4986 Dihedral : 12.906 179.906 4425 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.80 % Allowed : 14.45 % Favored : 84.75 % Rotamer Outliers : 2.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.77 % Twisted Proline : 4.85 % Twisted General : 1.11 % 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: -3.94 (0.13), residues: 3391 helix: -1.63 (0.16), residues: 946 sheet: -1.60 (0.22), residues: 500 loop : -3.59 (0.12), residues: 1945 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6782 Ramachandran restraints generated. 3391 Oldfield, 0 Emsley, 3391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6782 Ramachandran restraints generated. 3391 Oldfield, 0 Emsley, 3391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 3040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 305 time to evaluate : 3.489 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 82 outliers final: 37 residues processed: 362 average time/residue: 0.3869 time to fit residues: 230.7661 Evaluate side-chains 282 residues out of total 3040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 245 time to evaluate : 3.365 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 0 residues processed: 37 average time/residue: 0.2570 time to fit residues: 22.2574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 173 optimal weight: 0.9990 chunk 96 optimal weight: 0.8980 chunk 259 optimal weight: 20.0000 chunk 212 optimal weight: 0.0980 chunk 86 optimal weight: 1.9990 chunk 312 optimal weight: 0.0010 chunk 338 optimal weight: 5.9990 chunk 278 optimal weight: 5.9990 chunk 310 optimal weight: 9.9990 chunk 106 optimal weight: 4.9990 chunk 251 optimal weight: 20.0000 overall best weight: 0.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 348 GLN ** B 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 299 HIS F 311 GLN J 46 HIS ** J 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.2603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.046 29728 Z= 0.157 Angle : 0.707 15.024 40627 Z= 0.360 Chirality : 0.044 0.207 4489 Planarity : 0.005 0.081 4986 Dihedral : 12.378 178.697 4425 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.62 % Allowed : 15.33 % Favored : 84.05 % Rotamer Outliers : 2.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.80 % Twisted Proline : 4.24 % Twisted General : 0.89 % 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: -3.46 (0.13), residues: 3391 helix: -1.07 (0.17), residues: 958 sheet: -1.27 (0.23), residues: 496 loop : -3.41 (0.12), residues: 1937 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6782 Ramachandran restraints generated. 3391 Oldfield, 0 Emsley, 3391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6782 Ramachandran restraints generated. 3391 Oldfield, 0 Emsley, 3391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 3040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 311 time to evaluate : 3.605 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 72 outliers final: 35 residues processed: 360 average time/residue: 0.3950 time to fit residues: 233.7640 Evaluate side-chains 276 residues out of total 3040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 241 time to evaluate : 3.471 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 0 residues processed: 35 average time/residue: 0.2651 time to fit residues: 21.9724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 309 optimal weight: 8.9990 chunk 235 optimal weight: 7.9990 chunk 162 optimal weight: 0.9980 chunk 34 optimal weight: 8.9990 chunk 149 optimal weight: 9.9990 chunk 210 optimal weight: 7.9990 chunk 314 optimal weight: 3.9990 chunk 332 optimal weight: 0.3980 chunk 164 optimal weight: 2.9990 chunk 297 optimal weight: 20.0000 chunk 89 optimal weight: 9.9990 overall best weight: 3.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 174 ASN E 42 GLN F 311 GLN ** J 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.2670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 29728 Z= 0.285 Angle : 0.759 11.863 40627 Z= 0.387 Chirality : 0.046 0.226 4489 Planarity : 0.005 0.080 4986 Dihedral : 12.379 175.648 4425 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.74 % Allowed : 15.54 % Favored : 83.72 % Rotamer Outliers : 2.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.80 % Twisted Proline : 4.85 % Twisted General : 0.77 % 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: -3.40 (0.13), residues: 3391 helix: -1.05 (0.17), residues: 953 sheet: -1.16 (0.23), residues: 496 loop : -3.38 (0.13), residues: 1942 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6782 Ramachandran restraints generated. 3391 Oldfield, 0 Emsley, 3391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6782 Ramachandran restraints generated. 3391 Oldfield, 0 Emsley, 3391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 3040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 263 time to evaluate : 3.692 Fit side-chains outliers start: 86 outliers final: 44 residues processed: 328 average time/residue: 0.4090 time to fit residues: 225.3662 Evaluate side-chains 285 residues out of total 3040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 241 time to evaluate : 3.512 Switching outliers to nearest non-outliers outliers start: 44 outliers final: 0 residues processed: 44 average time/residue: 0.2826 time to fit residues: 27.7511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 276 optimal weight: 10.0000 chunk 188 optimal weight: 0.7980 chunk 4 optimal weight: 10.0000 chunk 247 optimal weight: 8.9990 chunk 137 optimal weight: 8.9990 chunk 283 optimal weight: 1.9990 chunk 229 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 169 optimal weight: 9.9990 chunk 298 optimal weight: 0.9990 chunk 83 optimal weight: 7.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 214 HIS ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 214 HIS F 311 GLN G 85 HIS ** G 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 123 HIS I 135 ASN I 338 GLN ** J 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 237 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.2784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.046 29728 Z= 0.341 Angle : 0.793 12.880 40627 Z= 0.403 Chirality : 0.048 0.238 4489 Planarity : 0.006 0.080 4986 Dihedral : 12.509 174.225 4425 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.74 % Allowed : 16.46 % Favored : 82.81 % Rotamer Outliers : 2.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.80 % Twisted Proline : 4.24 % Twisted General : 0.80 % 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: -3.44 (0.14), residues: 3391 helix: -1.15 (0.16), residues: 953 sheet: -1.22 (0.23), residues: 513 loop : -3.36 (0.13), residues: 1925 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6782 Ramachandran restraints generated. 3391 Oldfield, 0 Emsley, 3391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6782 Ramachandran restraints generated. 3391 Oldfield, 0 Emsley, 3391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 3040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 249 time to evaluate : 3.678 Fit side-chains revert: symmetry clash outliers start: 73 outliers final: 43 residues processed: 301 average time/residue: 0.3756 time to fit residues: 190.1760 Evaluate side-chains 276 residues out of total 3040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 233 time to evaluate : 3.659 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 0 residues processed: 43 average time/residue: 0.2660 time to fit residues: 26.0562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 111 optimal weight: 6.9990 chunk 299 optimal weight: 10.0000 chunk 65 optimal weight: 4.9990 chunk 195 optimal weight: 5.9990 chunk 82 optimal weight: 2.9990 chunk 332 optimal weight: 8.9990 chunk 276 optimal weight: 6.9990 chunk 154 optimal weight: 1.9990 chunk 27 optimal weight: 7.9990 chunk 110 optimal weight: 7.9990 chunk 174 optimal weight: 0.0870 overall best weight: 3.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 323 ASN G 158 HIS ** G 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 338 GLN ** J 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.2902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 29728 Z= 0.280 Angle : 0.765 12.870 40627 Z= 0.388 Chirality : 0.046 0.229 4489 Planarity : 0.005 0.080 4986 Dihedral : 12.411 175.497 4425 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.71 % Allowed : 16.40 % Favored : 82.90 % Rotamer Outliers : 1.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.80 % Twisted Proline : 3.64 % Twisted General : 0.83 % 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: -3.35 (0.14), residues: 3391 helix: -1.06 (0.17), residues: 954 sheet: -1.22 (0.23), residues: 517 loop : -3.31 (0.13), residues: 1920 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6782 Ramachandran restraints generated. 3391 Oldfield, 0 Emsley, 3391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6782 Ramachandran restraints generated. 3391 Oldfield, 0 Emsley, 3391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 3040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 252 time to evaluate : 3.548 Fit side-chains revert: symmetry clash outliers start: 55 outliers final: 30 residues processed: 292 average time/residue: 0.3842 time to fit residues: 186.2333 Evaluate side-chains 260 residues out of total 3040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 230 time to evaluate : 3.351 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 0 residues processed: 30 average time/residue: 0.2657 time to fit residues: 19.4509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 320 optimal weight: 20.0000 chunk 37 optimal weight: 9.9990 chunk 189 optimal weight: 8.9990 chunk 243 optimal weight: 10.0000 chunk 188 optimal weight: 0.9980 chunk 280 optimal weight: 8.9990 chunk 185 optimal weight: 0.1980 chunk 331 optimal weight: 3.9990 chunk 207 optimal weight: 20.0000 chunk 202 optimal weight: 0.9990 chunk 153 optimal weight: 0.7980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 158 HIS I 225 HIS I 295 GLN ** J 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.3144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 29728 Z= 0.173 Angle : 0.711 13.450 40627 Z= 0.358 Chirality : 0.044 0.247 4489 Planarity : 0.005 0.080 4986 Dihedral : 12.169 179.562 4425 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.56 % Allowed : 15.66 % Favored : 83.78 % Rotamer Outliers : 1.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.80 % Twisted Proline : 3.64 % Twisted General : 0.58 % 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: -3.12 (0.14), residues: 3391 helix: -0.83 (0.17), residues: 951 sheet: -1.08 (0.23), residues: 517 loop : -3.18 (0.13), residues: 1923 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6782 Ramachandran restraints generated. 3391 Oldfield, 0 Emsley, 3391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6782 Ramachandran restraints generated. 3391 Oldfield, 0 Emsley, 3391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 3040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 278 time to evaluate : 3.384 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 19 residues processed: 301 average time/residue: 0.4004 time to fit residues: 197.8821 Evaluate side-chains 266 residues out of total 3040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 247 time to evaluate : 3.441 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.2771 time to fit residues: 14.7110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 205 optimal weight: 0.7980 chunk 132 optimal weight: 0.4980 chunk 198 optimal weight: 5.9990 chunk 99 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 chunk 210 optimal weight: 0.0010 chunk 225 optimal weight: 10.0000 chunk 163 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 chunk 260 optimal weight: 20.0000 overall best weight: 0.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 ASN ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 214 HIS F 218 ASN G 131 ASN ** J 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.3487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.043 29728 Z= 0.152 Angle : 0.697 13.075 40627 Z= 0.351 Chirality : 0.043 0.245 4489 Planarity : 0.005 0.079 4986 Dihedral : 11.998 179.622 4425 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.53 % Allowed : 15.25 % Favored : 84.22 % Rotamer Outliers : 0.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.80 % Twisted Proline : 3.64 % Twisted General : 0.46 % 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: -2.94 (0.14), residues: 3391 helix: -0.60 (0.17), residues: 955 sheet: -0.92 (0.23), residues: 517 loop : -3.13 (0.13), residues: 1919 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6782 Ramachandran restraints generated. 3391 Oldfield, 0 Emsley, 3391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6782 Ramachandran restraints generated. 3391 Oldfield, 0 Emsley, 3391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 3040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 302 time to evaluate : 3.785 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 7 residues processed: 316 average time/residue: 0.4091 time to fit residues: 213.1213 Evaluate side-chains 266 residues out of total 3040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 259 time to evaluate : 3.633 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2683 time to fit residues: 8.5821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 301 optimal weight: 1.9990 chunk 317 optimal weight: 9.9990 chunk 289 optimal weight: 40.0000 chunk 308 optimal weight: 0.8980 chunk 185 optimal weight: 0.9990 chunk 134 optimal weight: 10.0000 chunk 242 optimal weight: 0.0980 chunk 94 optimal weight: 9.9990 chunk 279 optimal weight: 8.9990 chunk 292 optimal weight: 5.9990 chunk 307 optimal weight: 0.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 222 GLN ** H 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.3614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.043 29728 Z= 0.161 Angle : 0.699 14.268 40627 Z= 0.352 Chirality : 0.043 0.233 4489 Planarity : 0.005 0.080 4986 Dihedral : 11.845 179.314 4425 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.50 % Allowed : 15.45 % Favored : 84.05 % Rotamer Outliers : 0.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.80 % Twisted Proline : 3.64 % Twisted General : 0.43 % 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: -2.85 (0.14), residues: 3391 helix: -0.50 (0.17), residues: 961 sheet: -0.90 (0.23), residues: 523 loop : -3.10 (0.13), residues: 1907 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6782 Ramachandran restraints generated. 3391 Oldfield, 0 Emsley, 3391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6782 Ramachandran restraints generated. 3391 Oldfield, 0 Emsley, 3391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 3040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 271 time to evaluate : 3.520 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 12 residues processed: 279 average time/residue: 0.3900 time to fit residues: 181.1858 Evaluate side-chains 261 residues out of total 3040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 249 time to evaluate : 3.394 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.2815 time to fit residues: 10.8374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 202 optimal weight: 0.7980 chunk 326 optimal weight: 8.9990 chunk 199 optimal weight: 6.9990 chunk 154 optimal weight: 1.9990 chunk 227 optimal weight: 3.9990 chunk 342 optimal weight: 10.0000 chunk 315 optimal weight: 3.9990 chunk 272 optimal weight: 20.0000 chunk 28 optimal weight: 3.9990 chunk 210 optimal weight: 0.0770 chunk 167 optimal weight: 6.9990 overall best weight: 2.1744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 42 GLN ** E 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 315 HIS ** G 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.3563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 29728 Z= 0.217 Angle : 0.728 13.686 40627 Z= 0.367 Chirality : 0.045 0.220 4489 Planarity : 0.005 0.077 4986 Dihedral : 11.849 177.965 4425 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.50 % Allowed : 15.90 % Favored : 83.60 % Rotamer Outliers : 0.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.80 % Twisted Proline : 3.64 % Twisted General : 0.49 % 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: -2.86 (0.14), residues: 3391 helix: -0.50 (0.18), residues: 951 sheet: -0.92 (0.23), residues: 525 loop : -3.09 (0.13), residues: 1915 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6782 Ramachandran restraints generated. 3391 Oldfield, 0 Emsley, 3391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6782 Ramachandran restraints generated. 3391 Oldfield, 0 Emsley, 3391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 3040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 264 time to evaluate : 3.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 8 residues processed: 269 average time/residue: 0.4081 time to fit residues: 179.1865 Evaluate side-chains 260 residues out of total 3040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 252 time to evaluate : 3.328 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.2796 time to fit residues: 8.6966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 216 optimal weight: 8.9990 chunk 290 optimal weight: 5.9990 chunk 83 optimal weight: 8.9990 chunk 251 optimal weight: 6.9990 chunk 40 optimal weight: 3.9990 chunk 75 optimal weight: 0.0010 chunk 273 optimal weight: 20.0000 chunk 114 optimal weight: 4.9990 chunk 280 optimal weight: 30.0000 chunk 34 optimal weight: 7.9990 chunk 50 optimal weight: 4.9990 overall best weight: 3.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 84 ASN ** J 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 333 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.163507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.128080 restraints weight = 43854.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.126112 restraints weight = 58711.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.127343 restraints weight = 58249.179| |-----------------------------------------------------------------------------| r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.3432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.044 29728 Z= 0.333 Angle : 0.791 13.265 40627 Z= 0.401 Chirality : 0.047 0.257 4489 Planarity : 0.006 0.077 4986 Dihedral : 12.051 174.527 4425 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.56 % Allowed : 17.16 % Favored : 82.28 % Rotamer Outliers : 0.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.80 % Twisted Proline : 3.64 % Twisted General : 0.52 % 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: -3.03 (0.14), residues: 3391 helix: -0.75 (0.17), residues: 951 sheet: -0.96 (0.23), residues: 526 loop : -3.16 (0.13), residues: 1914 =============================================================================== Job complete usr+sys time: 4962.82 seconds wall clock time: 93 minutes 1.60 seconds (5581.60 seconds total)