Starting phenix.real_space_refine (version: dev) on Wed Feb 22 01:57:46 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nuw_0523/02_2023/6nuw_0523.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nuw_0523/02_2023/6nuw_0523.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nuw_0523/02_2023/6nuw_0523.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nuw_0523/02_2023/6nuw_0523.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nuw_0523/02_2023/6nuw_0523.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nuw_0523/02_2023/6nuw_0523.pdb" } resolution = 4.25 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= 0.004 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 "B ARG 55": "NH1" <-> "NH2" Residue "B TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 171": "NH1" <-> "NH2" Residue "C ARG 205": "NH1" <-> "NH2" Residue "C ARG 227": "NH1" <-> "NH2" Residue "C ARG 270": "NH1" <-> "NH2" Residue "C ARG 282": "NH1" <-> "NH2" Residue "D ARG 127": "NH1" <-> "NH2" Residue "D ARG 153": "NH1" <-> "NH2" Residue "D ARG 172": "NH1" <-> "NH2" Residue "E PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 158": "NH1" <-> "NH2" Residue "E TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 280": "NH1" <-> "NH2" Residue "E ARG 323": "NH1" <-> "NH2" Residue "G TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 71": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 16292 Number of models: 1 Model: "" Number of chains: 13 Chain: "B" Number of atoms: 1962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1962 Classifications: {'peptide': 244} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 9, 'TRANS': 232} Chain: "C" Number of atoms: 1601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1601 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 4, 'TRANS': 189} Chain breaks: 2 Chain: "D" Number of atoms: 1578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1578 Classifications: {'peptide': 196} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 7, 'TRANS': 188} Chain breaks: 5 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 23 Chain: "E" Number of atoms: 2851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 2851 Classifications: {'peptide': 369} Incomplete info: {'backbone_only': 2, 'truncation_to_alanine': 45} Link IDs: {'PTRANS': 19, 'TRANS': 349} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 171 Unresolved non-hydrogen angles: 214 Unresolved non-hydrogen dihedrals: 142 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 6, 'TYR:plan': 1, 'ASN:plan1': 5, 'HIS:plan': 1, 'PHE:plan': 4, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 94 Chain: "F" Number of atoms: 1360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1360 Classifications: {'peptide': 190} Incomplete info: {'truncation_to_alanine': 64} Link IDs: {'PTRANS': 3, 'TRANS': 186} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 233 Unresolved non-hydrogen angles: 288 Unresolved non-hydrogen dihedrals: 191 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 4, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 7, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 112 Chain: "G" Number of atoms: 1114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1114 Classifications: {'peptide': 176} Incomplete info: {'truncation_to_alanine': 89} Link IDs: {'PTRANS': 4, 'TRANS': 171} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 285 Unresolved non-hydrogen angles: 367 Unresolved non-hydrogen dihedrals: 223 Unresolved non-hydrogen chiralities: 31 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 5, 'ASN:plan1': 9, 'ASP:plan': 11, 'PHE:plan': 2, 'GLU:plan': 7, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 152 Chain: "I" Number of atoms: 1295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1295 Classifications: {'peptide': 168} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 1, 'TRANS': 166} Chain breaks: 2 Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 97 Unresolved non-hydrogen dihedrals: 55 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 1, 'PHE:plan': 2, 'ASN:plan1': 2, 'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 32 Chain: "H" Number of atoms: 1668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 1668 Classifications: {'peptide': 302} Incomplete info: {'truncation_to_alanine': 237} Link IDs: {'PTRANS': 15, 'TRANS': 286} Chain breaks: 5 Unresolved chain link angles: 15 Unresolved non-hydrogen bonds: 839 Unresolved non-hydrogen angles: 1077 Unresolved non-hydrogen dihedrals: 723 Unresolved non-hydrogen chiralities: 79 Planarities with less than four sites: {'GLN:plan1': 11, 'ARG:plan': 12, 'TYR:plan': 5, 'ASN:plan1': 12, 'TRP:plan': 8, 'HIS:plan': 9, 'PHE:plan': 9, 'GLU:plan': 8, 'ASP:plan': 10} Unresolved non-hydrogen planarities: 408 Chain: "J" Number of atoms: 997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 997 Classifications: {'peptide': 147} Incomplete info: {'truncation_to_alanine': 64} Link IDs: {'PTRANS': 2, 'TRANS': 144} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 217 Unresolved non-hydrogen angles: 279 Unresolved non-hydrogen dihedrals: 168 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 6, 'TYR:plan': 3, 'ASN:plan1': 5, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 119 Chain: "Y" Number of atoms: 746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 746 Classifications: {'peptide': 150} Incomplete info: {'truncation_to_alanine': 143} Link IDs: {'PTRANS': 2, 'TRANS': 147} Chain breaks: 6 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 469 Unresolved non-hydrogen angles: 615 Unresolved non-hydrogen dihedrals: 377 Unresolved non-hydrogen chiralities: 33 Planarities with less than four sites: {'GLN:plan1': 3, 'UNK:plan-1': 37, 'ASP:plan': 5, 'TYR:plan': 3, 'ASN:plan1': 9, 'TRP:plan': 3, 'HIS:plan': 6, 'PHE:plan': 5, 'GLU:plan': 5, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 249 Chain: "X" Number of atoms: 630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 630 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 126} Link IDs: {'TRANS': 125} Chain breaks: 2 Unresolved non-hydrogen bonds: 252 Unresolved non-hydrogen angles: 378 Unresolved non-hydrogen dihedrals: 126 Planarities with less than four sites: {'UNK:plan-1': 126} Unresolved non-hydrogen planarities: 126 Chain: "M" Number of atoms: 375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 375 Classifications: {'peptide': 75} Incomplete info: {'truncation_to_alanine': 75} Link IDs: {'TRANS': 74} Chain breaks: 1 Unresolved non-hydrogen bonds: 150 Unresolved non-hydrogen angles: 225 Unresolved non-hydrogen dihedrals: 75 Planarities with less than four sites: {'UNK:plan-1': 75} Unresolved non-hydrogen planarities: 75 Chain: "U" Number of atoms: 115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 115 Classifications: {'peptide': 23} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'TRANS': 22} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'UNK:plan-1': 23} Unresolved non-hydrogen planarities: 23 Time building chain proxies: 9.66, per 1000 atoms: 0.59 Number of scatterers: 16292 At special positions: 0 Unit cell: (147.6, 143.91, 188.19, 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 49 16.00 O 3086 8.00 N 2921 7.00 C 10236 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: 7.55 Conformation dependent library (CDL) restraints added in 2.8 seconds 4046 Ramachandran restraints generated. 2023 Oldfield, 0 Emsley, 2023 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4570 Finding SS restraints... Secondary structure from input PDB file: 95 helices and 9 sheets defined 74.3% alpha, 3.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.68 Creating SS restraints... Processing helix chain 'B' and resid 19 through 28 Processing helix chain 'B' and resid 94 through 108 removed outlier: 4.185A pdb=" N VAL B 98 " --> pdb=" O ASN B 94 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N TYR B 107 " --> pdb=" O LEU B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 128 Processing helix chain 'B' and resid 153 through 157 removed outlier: 3.936A pdb=" N LYS B 156 " --> pdb=" O THR B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 176 Processing helix chain 'B' and resid 182 through 187 Processing helix chain 'B' and resid 187 through 197 Processing helix chain 'B' and resid 229 through 240 removed outlier: 3.935A pdb=" N ILE B 240 " --> pdb=" O VAL B 236 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 173 Processing helix chain 'C' and resid 246 through 252 Processing helix chain 'C' and resid 253 through 257 Processing helix chain 'C' and resid 261 through 286 removed outlier: 4.155A pdb=" N VAL C 278 " --> pdb=" O GLN C 274 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 292 Processing helix chain 'C' and resid 338 through 345 Processing helix chain 'C' and resid 347 through 359 removed outlier: 3.921A pdb=" N LEU C 352 " --> pdb=" O LEU C 348 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ASP C 353 " --> pdb=" O LEU C 349 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LEU C 359 " --> pdb=" O LEU C 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 133 through 140 removed outlier: 3.846A pdb=" N GLU D 137 " --> pdb=" O ASN D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 151 through 160 Processing helix chain 'D' and resid 226 through 232 Processing helix chain 'D' and resid 236 through 263 removed outlier: 4.260A pdb=" N ASN D 260 " --> pdb=" O GLY D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 334 through 345 Processing helix chain 'D' and resid 349 through 363 removed outlier: 3.814A pdb=" N LEU D 354 " --> pdb=" O VAL D 350 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N LYS D 355 " --> pdb=" O LYS D 351 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE D 363 " --> pdb=" O ASN D 359 " (cutoff:3.500A) Processing helix chain 'E' and resid 17 through 27 removed outlier: 3.863A pdb=" N LYS E 26 " --> pdb=" O LYS E 22 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU E 27 " --> pdb=" O GLN E 23 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 41 Processing helix chain 'E' and resid 51 through 64 removed outlier: 3.921A pdb=" N GLU E 56 " --> pdb=" O TYR E 52 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU E 60 " --> pdb=" O GLU E 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 70 through 79 Processing helix chain 'E' and resid 87 through 99 removed outlier: 3.717A pdb=" N ASP E 93 " --> pdb=" O LEU E 89 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N CYS E 94 " --> pdb=" O ALA E 90 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N HIS E 95 " --> pdb=" O GLU E 91 " (cutoff:3.500A) Processing helix chain 'E' and resid 127 through 136 Processing helix chain 'E' and resid 220 through 232 removed outlier: 3.610A pdb=" N ARG E 230 " --> pdb=" O GLN E 226 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ILE E 232 " --> pdb=" O ILE E 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 251 through 256 Processing helix chain 'E' and resid 270 through 275 Processing helix chain 'E' and resid 285 through 290 removed outlier: 3.893A pdb=" N HIS E 289 " --> pdb=" O ASP E 285 " (cutoff:3.500A) Processing helix chain 'E' and resid 301 through 309 Processing helix chain 'E' and resid 318 through 334 Processing helix chain 'E' and resid 408 through 418 removed outlier: 3.506A pdb=" N GLY E 412 " --> pdb=" O ASP E 408 " (cutoff:3.500A) Processing helix chain 'E' and resid 423 through 427 Processing helix chain 'E' and resid 428 through 433 Processing helix chain 'F' and resid 163 through 190 Processing helix chain 'F' and resid 197 through 221 Processing helix chain 'F' and resid 234 through 293 removed outlier: 4.174A pdb=" N GLN F 293 " --> pdb=" O GLU F 289 " (cutoff:3.500A) Processing helix chain 'F' and resid 324 through 330 Processing helix chain 'F' and resid 346 through 355 removed outlier: 4.422A pdb=" N LYS F 350 " --> pdb=" O ARG F 347 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU F 351 " --> pdb=" O LEU F 348 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N VAL F 353 " --> pdb=" O LYS F 350 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU F 354 " --> pdb=" O GLU F 351 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N SER F 355 " --> pdb=" O GLU F 352 " (cutoff:3.500A) Processing helix chain 'F' and resid 356 through 375 Processing helix chain 'F' and resid 376 through 381 removed outlier: 3.667A pdb=" N ASP F 380 " --> pdb=" O MET F 377 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 27 removed outlier: 3.746A pdb=" N LEU G 19 " --> pdb=" O GLU G 15 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N LEU G 20 " --> pdb=" O LEU G 16 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 34 removed outlier: 3.803A pdb=" N LEU G 34 " --> pdb=" O LEU G 30 " (cutoff:3.500A) Processing helix chain 'G' and resid 42 through 84 removed outlier: 4.494A pdb=" N GLY G 57 " --> pdb=" O ALA G 53 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N LYS G 58 " --> pdb=" O MET G 54 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLN G 59 " --> pdb=" O SER G 55 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N TYR G 67 " --> pdb=" O SER G 63 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 97 Processing helix chain 'G' and resid 104 through 113 Processing helix chain 'G' and resid 140 through 177 removed outlier: 3.715A pdb=" N GLU G 161 " --> pdb=" O LEU G 157 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N THR G 171 " --> pdb=" O ILE G 167 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N ASN G 172 " --> pdb=" O LEU G 168 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N SER G 173 " --> pdb=" O SER G 169 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ILE G 174 " --> pdb=" O GLN G 170 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N ASN G 175 " --> pdb=" O THR G 171 " (cutoff:3.500A) Processing helix chain 'G' and resid 188 through 204 Processing helix chain 'I' and resid 125 through 150 removed outlier: 3.537A pdb=" N ASP I 149 " --> pdb=" O LEU I 145 " (cutoff:3.500A) Processing helix chain 'I' and resid 171 through 230 removed outlier: 4.580A pdb=" N TYR I 204 " --> pdb=" O ASN I 200 " (cutoff:3.500A) Processing helix chain 'I' and resid 236 through 250 removed outlier: 3.612A pdb=" N GLN I 240 " --> pdb=" O TRP I 236 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N ASN I 247 " --> pdb=" O GLN I 243 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N ASP I 248 " --> pdb=" O ALA I 244 " (cutoff:3.500A) Processing helix chain 'I' and resid 250 through 266 Processing helix chain 'I' and resid 268 through 273 Processing helix chain 'I' and resid 290 through 300 Processing helix chain 'I' and resid 302 through 321 Processing helix chain 'H' and resid 44 through 54 Processing helix chain 'H' and resid 57 through 65 Processing helix chain 'H' and resid 83 through 88 Processing helix chain 'H' and resid 105 through 120 Processing helix chain 'H' and resid 130 through 146 removed outlier: 5.106A pdb=" N TRP H 136 " --> pdb=" O SER H 132 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N LEU H 137 " --> pdb=" O SER H 133 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N PHE H 142 " --> pdb=" O HIS H 138 " (cutoff:3.500A) Processing helix chain 'H' and resid 153 through 164 Proline residue: H 160 - end of helix Processing helix chain 'H' and resid 167 through 183 removed outlier: 3.789A pdb=" N HIS H 177 " --> pdb=" O ARG H 173 " (cutoff:3.500A) Proline residue: H 178 - end of helix Processing helix chain 'H' and resid 189 through 201 removed outlier: 3.697A pdb=" N ARG H 193 " --> pdb=" O LEU H 189 " (cutoff:3.500A) Processing helix chain 'H' and resid 201 through 209 removed outlier: 3.547A pdb=" N THR H 205 " --> pdb=" O SER H 201 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ILE H 209 " --> pdb=" O THR H 205 " (cutoff:3.500A) Processing helix chain 'H' and resid 211 through 232 removed outlier: 3.526A pdb=" N ARG H 215 " --> pdb=" O ILE H 211 " (cutoff:3.500A) Processing helix chain 'H' and resid 298 through 324 Proline residue: H 304 - end of helix Proline residue: H 309 - end of helix Proline residue: H 318 - end of helix Processing helix chain 'H' and resid 326 through 348 Processing helix chain 'H' and resid 355 through 374 removed outlier: 4.259A pdb=" N HIS H 370 " --> pdb=" O ARG H 366 " (cutoff:3.500A) Processing helix chain 'H' and resid 380 through 386 Processing helix chain 'H' and resid 387 through 396 Processing helix chain 'H' and resid 412 through 430 Proline residue: H 422 - end of helix Proline residue: H 426 - end of helix Processing helix chain 'H' and resid 437 through 457 removed outlier: 3.587A pdb=" N ALA H 441 " --> pdb=" O VAL H 437 " (cutoff:3.500A) Processing helix chain 'J' and resid 3 through 29 removed outlier: 3.884A pdb=" N LEU J 15 " --> pdb=" O VAL J 11 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N THR J 18 " --> pdb=" O SER J 14 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N LYS J 26 " --> pdb=" O PHE J 22 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N GLN J 27 " --> pdb=" O GLN J 23 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLN J 28 " --> pdb=" O GLU J 24 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU J 29 " --> pdb=" O PHE J 25 " (cutoff:3.500A) Processing helix chain 'J' and resid 36 through 46 Processing helix chain 'J' and resid 50 through 73 removed outlier: 5.574A pdb=" N PHE J 64 " --> pdb=" O ARG J 60 " (cutoff:3.500A) Processing helix chain 'J' and resid 86 through 127 removed outlier: 4.024A pdb=" N PHE J 122 " --> pdb=" O GLU J 118 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLU J 123 " --> pdb=" O LEU J 119 " (cutoff:3.500A) Processing helix chain 'J' and resid 134 through 153 removed outlier: 3.571A pdb=" N GLY J 138 " --> pdb=" O ASN J 134 " (cutoff:3.500A) Processing helix chain 'Y' and resid 315 through 326 Processing helix chain 'Y' and resid 329 through 335 Processing helix chain 'Y' and resid 340 through 369 removed outlier: 3.906A pdb=" N ILE Y 344 " --> pdb=" O TYR Y 340 " (cutoff:3.500A) Proline residue: Y 356 - end of helix Processing helix chain 'Y' and resid 480 through 490 removed outlier: 3.801A pdb=" N GLN Y 490 " --> pdb=" O LEU Y 486 " (cutoff:3.500A) Processing helix chain 'Y' and resid 655 through 666 Processing helix chain 'Y' and resid 673 through 678 removed outlier: 3.778A pdb=" N HIS Y 677 " --> pdb=" O PHE Y 673 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N HIS Y 678 " --> pdb=" O PHE Y 674 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 673 through 678' Processing helix chain 'Y' and resid 684 through 696 Processing helix chain 'Y' and resid 1197 through 1204 Processing helix chain 'Y' and resid 1206 through 1212 Processing helix chain 'Y' and resid 1668 through 1681 removed outlier: 4.334A pdb=" N UNK Y1675 " --> pdb=" O UNK Y1671 " (cutoff:3.500A) Processing helix chain 'X' and resid 72 through 128 removed outlier: 4.464A pdb=" N UNK X 111 " --> pdb=" O UNK X 107 " (cutoff:3.500A) Processing helix chain 'X' and resid 137 through 167 Processing helix chain 'X' and resid 177 through 206 Processing helix chain 'M' and resid 72 through 127 removed outlier: 3.799A pdb=" N UNK M 76 " --> pdb=" O UNK M 72 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N UNK M 78 " --> pdb=" O UNK M 74 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N UNK M 82 " --> pdb=" O UNK M 78 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N UNK M 103 " --> pdb=" O UNK M 99 " (cutoff:3.500A) Processing helix chain 'M' and resid 150 through 164 removed outlier: 5.227A pdb=" N UNK M 156 " --> pdb=" O UNK M 152 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N UNK M 159 " --> pdb=" O UNK M 155 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N UNK M 160 " --> pdb=" O UNK M 156 " (cutoff:3.500A) Processing helix chain 'U' and resid 2 through 23 Processing sheet with id=AA1, first strand: chain 'B' and resid 3 through 4 Processing sheet with id=AA2, first strand: chain 'B' and resid 75 through 77 removed outlier: 4.675A pdb=" N MET B 85 " --> pdb=" O ILE B 10 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N TRP B 112 " --> pdb=" O GLY B 9 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 32 through 38 removed outlier: 3.804A pdb=" N GLN B 36 " --> pdb=" O ARG B 55 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 148 through 149 removed outlier: 3.546A pdb=" N TYR B 148 " --> pdb=" O SER B 207 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 209 through 210 removed outlier: 3.532A pdb=" N THR B 214 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 175 through 177 removed outlier: 3.691A pdb=" N TYR C 221 " --> pdb=" O THR C 239 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 298 through 299 removed outlier: 3.667A pdb=" N PHE C 308 " --> pdb=" O VAL C 315 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 108 through 109 removed outlier: 4.537A pdb=" N ARG E 198 " --> pdb=" O GLN E 160 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N GLN E 160 " --> pdb=" O ARG E 198 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 397 through 403 removed outlier: 3.671A pdb=" N ILE E 442 " --> pdb=" O THR E 388 " (cutoff:3.500A) 1125 hydrogen bonds defined for protein. 3327 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: 4.50 Time building geometry restraints manager: 8.08 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: 4018 1.33 - 1.45: 3185 1.45 - 1.57: 9177 1.57 - 1.69: 0 1.69 - 1.81: 80 Bond restraints: 16460 Sorted by residual: bond pdb=" CB TRP E 106 " pdb=" CG TRP E 106 " ideal model delta sigma weight residual 1.498 1.371 0.127 3.10e-02 1.04e+03 1.68e+01 bond pdb=" C TYR D 187 " pdb=" N LYS D 188 " ideal model delta sigma weight residual 1.333 1.279 0.054 1.34e-02 5.57e+03 1.65e+01 bond pdb=" CA ASN E 277 " pdb=" C ASN E 277 " ideal model delta sigma weight residual 1.523 1.472 0.051 1.34e-02 5.57e+03 1.46e+01 bond pdb=" N PRO E 260 " pdb=" CD PRO E 260 " ideal model delta sigma weight residual 1.473 1.526 -0.053 1.40e-02 5.10e+03 1.46e+01 bond pdb=" CA HIS E 284 " pdb=" CB HIS E 284 " ideal model delta sigma weight residual 1.535 1.478 0.057 1.69e-02 3.50e+03 1.13e+01 ... (remaining 16455 not shown) Histogram of bond angle deviations from ideal: 97.80 - 106.05: 291 106.05 - 114.30: 9571 114.30 - 122.55: 10445 122.55 - 130.80: 2001 130.80 - 139.05: 54 Bond angle restraints: 22362 Sorted by residual: angle pdb=" CA PRO E 260 " pdb=" N PRO E 260 " pdb=" CD PRO E 260 " ideal model delta sigma weight residual 112.00 99.54 12.46 1.40e+00 5.10e-01 7.92e+01 angle pdb=" C LEU E 283 " pdb=" N HIS E 284 " pdb=" CA HIS E 284 " ideal model delta sigma weight residual 122.56 110.10 12.46 1.50e+00 4.44e-01 6.90e+01 angle pdb=" N PRO J 129 " pdb=" CA PRO J 129 " pdb=" CB PRO J 129 " ideal model delta sigma weight residual 103.25 111.85 -8.60 1.05e+00 9.07e-01 6.71e+01 angle pdb=" N PRO H 184 " pdb=" CA PRO H 184 " pdb=" CB PRO H 184 " ideal model delta sigma weight residual 103.25 111.11 -7.86 1.05e+00 9.07e-01 5.60e+01 angle pdb=" N PRO H 104 " pdb=" CA PRO H 104 " pdb=" CB PRO H 104 " ideal model delta sigma weight residual 103.00 110.54 -7.54 1.10e+00 8.26e-01 4.70e+01 ... (remaining 22357 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.47: 9020 16.47 - 32.93: 756 32.93 - 49.40: 183 49.40 - 65.86: 32 65.86 - 82.33: 14 Dihedral angle restraints: 10005 sinusoidal: 3073 harmonic: 6932 Sorted by residual: dihedral pdb=" CA ASN D 149 " pdb=" C ASN D 149 " pdb=" N MET D 150 " pdb=" CA MET D 150 " ideal model delta harmonic sigma weight residual -180.00 -120.99 -59.01 0 5.00e+00 4.00e-02 1.39e+02 dihedral pdb=" CA VAL E 29 " pdb=" C VAL E 29 " pdb=" N THR E 30 " pdb=" CA THR E 30 " ideal model delta harmonic sigma weight residual -180.00 -128.68 -51.32 0 5.00e+00 4.00e-02 1.05e+02 dihedral pdb=" CA LYS G 90 " pdb=" C LYS G 90 " pdb=" N TYR G 91 " pdb=" CA TYR G 91 " ideal model delta harmonic sigma weight residual 180.00 -134.61 -45.39 0 5.00e+00 4.00e-02 8.24e+01 ... (remaining 10002 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 2330 0.097 - 0.194: 335 0.194 - 0.292: 61 0.292 - 0.389: 5 0.389 - 0.486: 2 Chirality restraints: 2733 Sorted by residual: chirality pdb=" CB ILE H 57 " pdb=" CA ILE H 57 " pdb=" CG1 ILE H 57 " pdb=" CG2 ILE H 57 " both_signs ideal model delta sigma weight residual False 2.64 2.16 0.49 2.00e-01 2.50e+01 5.90e+00 chirality pdb=" CB VAL E 120 " pdb=" CA VAL E 120 " pdb=" CG1 VAL E 120 " pdb=" CG2 VAL E 120 " both_signs ideal model delta sigma weight residual False -2.63 -2.23 -0.40 2.00e-01 2.50e+01 4.01e+00 chirality pdb=" CB ILE E 251 " pdb=" CA ILE E 251 " pdb=" CG1 ILE E 251 " pdb=" CG2 ILE E 251 " both_signs ideal model delta sigma weight residual False 2.64 2.26 0.38 2.00e-01 2.50e+01 3.61e+00 ... (remaining 2730 not shown) Planarity restraints: 2919 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS E 149 " 0.096 5.00e-02 4.00e+02 1.46e-01 3.43e+01 pdb=" N PRO E 150 " -0.253 5.00e-02 4.00e+02 pdb=" CA PRO E 150 " 0.081 5.00e-02 4.00e+02 pdb=" CD PRO E 150 " 0.076 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY E 268 " 0.080 5.00e-02 4.00e+02 1.19e-01 2.28e+01 pdb=" N PRO E 269 " -0.206 5.00e-02 4.00e+02 pdb=" CA PRO E 269 " 0.064 5.00e-02 4.00e+02 pdb=" CD PRO E 269 " 0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 106 " 0.036 2.00e-02 2.50e+03 2.99e-02 2.24e+01 pdb=" CG TRP E 106 " -0.082 2.00e-02 2.50e+03 pdb=" CD1 TRP E 106 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 TRP E 106 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP E 106 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP E 106 " 0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP E 106 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 106 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 106 " 0.009 2.00e-02 2.50e+03 pdb=" CH2 TRP E 106 " -0.006 2.00e-02 2.50e+03 ... (remaining 2916 not shown) Histogram of nonbonded interaction distances: 1.22 - 1.96: 8 1.96 - 2.69: 835 2.69 - 3.43: 25435 3.43 - 4.16: 37680 4.16 - 4.90: 63092 Nonbonded interactions: 127050 Sorted by model distance: nonbonded pdb=" CB PHE C 209 " pdb=" OE1 GLN D 238 " model vdw 1.219 3.440 nonbonded pdb=" OE2 GLU C 302 " pdb=" CG ASN E 207 " model vdw 1.757 3.270 nonbonded pdb=" OD1 ASP C 300 " pdb=" O MET C 305 " model vdw 1.839 3.040 nonbonded pdb=" OD2 ASP C 300 " pdb=" N MET C 305 " model vdw 1.853 2.520 nonbonded pdb=" C THR D 234 " pdb=" NH1 ARG D 235 " model vdw 1.903 3.350 ... (remaining 127045 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 49 5.16 5 C 10236 2.51 5 N 2921 2.21 5 O 3086 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=0.97 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: 1.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 7.150 Check model and map are aligned: 0.210 Process input model: 43.200 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Set scattering table: 0.140 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 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 : 0.012 0.127 16460 Z= 0.781 Angle : 1.448 14.505 22362 Z= 0.807 Chirality : 0.074 0.486 2733 Planarity : 0.009 0.146 2919 Dihedral : 14.250 82.328 5435 Min Nonbonded Distance : 1.219 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.79 % Allowed : 15.22 % Favored : 83.98 % Rotamer Outliers : 6.01 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.05 % Twisted Proline : 4.55 % Twisted General : 0.75 % 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: -4.70 (0.15), residues: 2023 helix: -2.32 (0.11), residues: 1191 sheet: -4.41 (0.34), residues: 139 loop : -4.05 (0.20), residues: 693 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4046 Ramachandran restraints generated. 2023 Oldfield, 0 Emsley, 2023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4046 Ramachandran restraints generated. 2023 Oldfield, 0 Emsley, 2023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 1958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 359 time to evaluate : 2.006 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 79 outliers final: 24 residues processed: 413 average time/residue: 0.3026 time to fit residues: 178.8031 Evaluate side-chains 271 residues out of total 1958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 247 time to evaluate : 1.995 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 24 outliers final: 1 residues processed: 24 average time/residue: 0.1567 time to fit residues: 9.1404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 181 optimal weight: 1.9990 chunk 162 optimal weight: 5.9990 chunk 90 optimal weight: 0.9980 chunk 55 optimal weight: 0.8980 chunk 109 optimal weight: 10.0000 chunk 87 optimal weight: 0.9980 chunk 168 optimal weight: 2.9990 chunk 65 optimal weight: 8.9990 chunk 102 optimal weight: 6.9990 chunk 125 optimal weight: 5.9990 chunk 195 optimal weight: 4.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 215 GLN C 220 HIS D 151 ASN D 186 ASN ** D 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 95 HIS E 143 HIS E 149 HIS E 207 ASN E 226 GLN ** E 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 423 ASN ** F 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 330 HIS F 376 GLN F 382 HIS ** G 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 200 ASN ** I 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 228 GLN I 294 HIS ** J 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.2657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 16460 Z= 0.272 Angle : 0.819 11.027 22362 Z= 0.432 Chirality : 0.046 0.269 2733 Planarity : 0.006 0.119 2919 Dihedral : 7.047 47.018 2440 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 15.59 Ramachandran Plot: Outliers : 0.20 % Allowed : 11.91 % Favored : 87.89 % Rotamer Outliers : 1.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -3.01 (0.17), residues: 2023 helix: -0.67 (0.14), residues: 1206 sheet: -3.66 (0.41), residues: 119 loop : -4.09 (0.20), residues: 698 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4046 Ramachandran restraints generated. 2023 Oldfield, 0 Emsley, 2023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4046 Ramachandran restraints generated. 2023 Oldfield, 0 Emsley, 2023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 1958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 369 time to evaluate : 1.855 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 9 residues processed: 376 average time/residue: 0.2973 time to fit residues: 161.0714 Evaluate side-chains 295 residues out of total 1958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 286 time to evaluate : 1.754 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1465 time to fit residues: 4.7111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 108 optimal weight: 6.9990 chunk 60 optimal weight: 0.6980 chunk 162 optimal weight: 8.9990 chunk 132 optimal weight: 20.0000 chunk 53 optimal weight: 0.9980 chunk 195 optimal weight: 5.9990 chunk 211 optimal weight: 8.9990 chunk 174 optimal weight: 10.0000 chunk 193 optimal weight: 20.0000 chunk 66 optimal weight: 9.9990 chunk 156 optimal weight: 0.9990 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 215 GLN ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 151 ASN ** D 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 407 ASN ** F 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 278 ASN F 330 HIS ** I 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.3068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.075 16460 Z= 0.426 Angle : 0.871 11.694 22362 Z= 0.462 Chirality : 0.047 0.252 2733 Planarity : 0.006 0.113 2919 Dihedral : 6.854 47.190 2440 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 19.72 Ramachandran Plot: Outliers : 0.15 % Allowed : 15.27 % Favored : 84.58 % Rotamer Outliers : 0.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.52 (0.18), residues: 2023 helix: -0.15 (0.15), residues: 1199 sheet: -3.36 (0.42), residues: 120 loop : -4.15 (0.20), residues: 704 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4046 Ramachandran restraints generated. 2023 Oldfield, 0 Emsley, 2023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4046 Ramachandran restraints generated. 2023 Oldfield, 0 Emsley, 2023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 1958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 335 time to evaluate : 1.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 7 residues processed: 343 average time/residue: 0.2852 time to fit residues: 143.6228 Evaluate side-chains 282 residues out of total 1958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 275 time to evaluate : 2.092 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1530 time to fit residues: 4.6233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 193 optimal weight: 5.9990 chunk 147 optimal weight: 10.0000 chunk 101 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 93 optimal weight: 0.7980 chunk 131 optimal weight: 5.9990 chunk 196 optimal weight: 3.9990 chunk 207 optimal weight: 6.9990 chunk 102 optimal weight: 9.9990 chunk 186 optimal weight: 10.0000 chunk 56 optimal weight: 8.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 215 GLN ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 423 ASN ** F 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 278 ASN F 330 HIS ** I 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 41 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.3405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.078 16460 Z= 0.438 Angle : 0.884 12.628 22362 Z= 0.465 Chirality : 0.049 0.577 2733 Planarity : 0.006 0.116 2919 Dihedral : 6.754 47.254 2440 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 21.33 Ramachandran Plot: Outliers : 0.15 % Allowed : 15.13 % Favored : 84.73 % Rotamer Outliers : 0.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -2.43 (0.18), residues: 2023 helix: -0.03 (0.15), residues: 1211 sheet: -3.34 (0.42), residues: 128 loop : -4.25 (0.20), residues: 684 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4046 Ramachandran restraints generated. 2023 Oldfield, 0 Emsley, 2023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4046 Ramachandran restraints generated. 2023 Oldfield, 0 Emsley, 2023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 1958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 334 time to evaluate : 1.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 6 residues processed: 341 average time/residue: 0.2994 time to fit residues: 148.8002 Evaluate side-chains 274 residues out of total 1958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 268 time to evaluate : 1.769 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1449 time to fit residues: 4.3058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 173 optimal weight: 2.9990 chunk 117 optimal weight: 6.9990 chunk 3 optimal weight: 4.9990 chunk 154 optimal weight: 0.8980 chunk 85 optimal weight: 0.9980 chunk 177 optimal weight: 10.0000 chunk 143 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 106 optimal weight: 0.9990 chunk 186 optimal weight: 3.9990 chunk 52 optimal weight: 0.6980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 143 HIS ** E 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 423 ASN ** F 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 330 HIS ** F 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 106 GLN I 196 ASN I 200 ASN ** I 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.3905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 16460 Z= 0.218 Angle : 0.770 11.858 22362 Z= 0.391 Chirality : 0.045 0.371 2733 Planarity : 0.006 0.114 2919 Dihedral : 6.114 42.298 2440 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 16.20 Ramachandran Plot: Outliers : 0.15 % Allowed : 12.36 % Favored : 87.49 % Rotamer Outliers : 0.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.19), residues: 2023 helix: 0.62 (0.15), residues: 1218 sheet: -3.07 (0.43), residues: 126 loop : -3.95 (0.21), residues: 679 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4046 Ramachandran restraints generated. 2023 Oldfield, 0 Emsley, 2023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4046 Ramachandran restraints generated. 2023 Oldfield, 0 Emsley, 2023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 1958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 366 time to evaluate : 1.893 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 367 average time/residue: 0.2866 time to fit residues: 152.9917 Evaluate side-chains 287 residues out of total 1958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 284 time to evaluate : 1.724 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1494 time to fit residues: 3.1358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 69 optimal weight: 5.9990 chunk 187 optimal weight: 20.0000 chunk 41 optimal weight: 5.9990 chunk 122 optimal weight: 9.9990 chunk 51 optimal weight: 3.9990 chunk 208 optimal weight: 4.9990 chunk 172 optimal weight: 1.9990 chunk 96 optimal weight: 0.2980 chunk 17 optimal weight: 0.9980 chunk 68 optimal weight: 0.2980 chunk 109 optimal weight: 7.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 143 HIS ** E 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 423 ASN ** F 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 330 HIS ** I 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.4148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.055 16460 Z= 0.260 Angle : 0.772 10.966 22362 Z= 0.396 Chirality : 0.045 0.329 2733 Planarity : 0.006 0.130 2919 Dihedral : 5.964 40.210 2440 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 16.70 Ramachandran Plot: Outliers : 0.15 % Allowed : 12.90 % Favored : 86.95 % Rotamer Outliers : 0.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.20), residues: 2023 helix: 0.83 (0.15), residues: 1220 sheet: -3.16 (0.44), residues: 123 loop : -3.86 (0.21), residues: 680 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4046 Ramachandran restraints generated. 2023 Oldfield, 0 Emsley, 2023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4046 Ramachandran restraints generated. 2023 Oldfield, 0 Emsley, 2023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 1958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 343 time to evaluate : 1.920 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 343 average time/residue: 0.2954 time to fit residues: 147.5759 Evaluate side-chains 272 residues out of total 1958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 272 time to evaluate : 1.960 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.6111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 200 optimal weight: 6.9990 chunk 23 optimal weight: 0.8980 chunk 118 optimal weight: 40.0000 chunk 151 optimal weight: 0.0570 chunk 117 optimal weight: 4.9990 chunk 175 optimal weight: 9.9990 chunk 116 optimal weight: 10.0000 chunk 207 optimal weight: 7.9990 chunk 129 optimal weight: 20.0000 chunk 126 optimal weight: 5.9990 chunk 95 optimal weight: 0.9980 overall best weight: 2.5902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 143 HIS ** E 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 330 HIS G 106 GLN ** I 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.4195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.076 16460 Z= 0.368 Angle : 0.844 11.040 22362 Z= 0.439 Chirality : 0.047 0.327 2733 Planarity : 0.006 0.137 2919 Dihedral : 6.165 40.978 2440 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 20.62 Ramachandran Plot: Outliers : 0.15 % Allowed : 13.89 % Favored : 85.96 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.19), residues: 2023 helix: 0.80 (0.15), residues: 1209 sheet: -3.20 (0.45), residues: 123 loop : -3.84 (0.21), residues: 691 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4046 Ramachandran restraints generated. 2023 Oldfield, 0 Emsley, 2023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4046 Ramachandran restraints generated. 2023 Oldfield, 0 Emsley, 2023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 1958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 338 time to evaluate : 2.097 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 338 average time/residue: 0.2981 time to fit residues: 146.9973 Evaluate side-chains 265 residues out of total 1958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 265 time to evaluate : 1.900 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.5061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 128 optimal weight: 10.0000 chunk 82 optimal weight: 0.8980 chunk 123 optimal weight: 7.9990 chunk 62 optimal weight: 1.9990 chunk 40 optimal weight: 7.9990 chunk 131 optimal weight: 5.9990 chunk 141 optimal weight: 0.8980 chunk 102 optimal weight: 20.0000 chunk 19 optimal weight: 0.6980 chunk 162 optimal weight: 1.9990 chunk 188 optimal weight: 10.0000 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 284 HIS ** F 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 254 ASN F 330 HIS G 106 GLN ** I 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.4511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.064 16460 Z= 0.246 Angle : 0.804 12.161 22362 Z= 0.407 Chirality : 0.046 0.281 2733 Planarity : 0.006 0.125 2919 Dihedral : 5.894 38.135 2440 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 17.67 Ramachandran Plot: Outliers : 0.15 % Allowed : 12.16 % Favored : 87.69 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.20), residues: 2023 helix: 1.07 (0.16), residues: 1219 sheet: -2.94 (0.45), residues: 122 loop : -3.76 (0.22), residues: 682 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4046 Ramachandran restraints generated. 2023 Oldfield, 0 Emsley, 2023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4046 Ramachandran restraints generated. 2023 Oldfield, 0 Emsley, 2023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 1958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 341 time to evaluate : 2.033 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 341 average time/residue: 0.2851 time to fit residues: 144.7349 Evaluate side-chains 276 residues out of total 1958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 276 time to evaluate : 1.890 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.4830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 198 optimal weight: 9.9990 chunk 181 optimal weight: 5.9990 chunk 193 optimal weight: 20.0000 chunk 116 optimal weight: 9.9990 chunk 84 optimal weight: 2.9990 chunk 151 optimal weight: 8.9990 chunk 59 optimal weight: 9.9990 chunk 174 optimal weight: 5.9990 chunk 182 optimal weight: 6.9990 chunk 192 optimal weight: 20.0000 chunk 126 optimal weight: 6.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B -1 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 64 ASN ** C 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 143 HIS ** E 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 330 HIS G 106 GLN I 200 ASN ** I 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 44 GLN ** H 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.4284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.011 0.128 16460 Z= 0.719 Angle : 1.102 13.508 22362 Z= 0.582 Chirality : 0.055 0.486 2733 Planarity : 0.008 0.119 2919 Dihedral : 6.936 46.334 2440 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 29.18 Ramachandran Plot: Outliers : 0.15 % Allowed : 17.35 % Favored : 82.50 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -2.14 (0.19), residues: 2023 helix: 0.18 (0.15), residues: 1198 sheet: -3.47 (0.41), residues: 140 loop : -3.96 (0.21), residues: 685 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4046 Ramachandran restraints generated. 2023 Oldfield, 0 Emsley, 2023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4046 Ramachandran restraints generated. 2023 Oldfield, 0 Emsley, 2023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 302 time to evaluate : 1.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 302 average time/residue: 0.3006 time to fit residues: 132.7230 Evaluate side-chains 249 residues out of total 1958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 249 time to evaluate : 1.895 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.4944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 204 optimal weight: 4.9990 chunk 124 optimal weight: 7.9990 chunk 96 optimal weight: 0.8980 chunk 141 optimal weight: 0.8980 chunk 214 optimal weight: 30.0000 chunk 197 optimal weight: 2.9990 chunk 170 optimal weight: 6.9990 chunk 17 optimal weight: 0.5980 chunk 131 optimal weight: 1.9990 chunk 104 optimal weight: 10.0000 chunk 135 optimal weight: 20.0000 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 64 ASN C 168 ASN ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 143 HIS ** F 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 330 HIS G 106 GLN I 200 ASN ** I 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.4521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.062 16460 Z= 0.272 Angle : 0.861 13.806 22362 Z= 0.435 Chirality : 0.048 0.407 2733 Planarity : 0.006 0.117 2919 Dihedral : 6.242 41.535 2440 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 19.45 Ramachandran Plot: Outliers : 0.15 % Allowed : 13.00 % Favored : 86.85 % Rotamer Outliers : 0.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.20), residues: 2023 helix: 0.80 (0.15), residues: 1210 sheet: -3.34 (0.41), residues: 137 loop : -3.89 (0.22), residues: 676 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4046 Ramachandran restraints generated. 2023 Oldfield, 0 Emsley, 2023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4046 Ramachandran restraints generated. 2023 Oldfield, 0 Emsley, 2023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 1958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 332 time to evaluate : 2.080 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: 1 outliers final: 0 residues processed: 333 average time/residue: 0.3068 time to fit residues: 147.9171 Evaluate side-chains 265 residues out of total 1958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 265 time to evaluate : 1.858 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.4311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 181 optimal weight: 4.9990 chunk 52 optimal weight: 5.9990 chunk 157 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 47 optimal weight: 5.9990 chunk 170 optimal weight: 0.0970 chunk 71 optimal weight: 2.9990 chunk 175 optimal weight: 8.9990 chunk 21 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 149 optimal weight: 8.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 207 ASN ** F 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 330 HIS G 106 GLN ** I 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 2 ASN ** J 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.099185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.078002 restraints weight = 70266.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.077440 restraints weight = 43574.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.077871 restraints weight = 41291.998| |-----------------------------------------------------------------------------| r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3791 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3791 r_free = 0.3791 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.97 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3791 r_free = 0.3791 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3791 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.4825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.059 16460 Z= 0.235 Angle : 0.829 14.269 22362 Z= 0.414 Chirality : 0.046 0.338 2733 Planarity : 0.006 0.109 2919 Dihedral : 5.852 36.762 2440 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 17.27 Ramachandran Plot: Outliers : 0.15 % Allowed : 12.65 % Favored : 87.20 % Rotamer Outliers : 0.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.05 % Twisted Proline : 1.52 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.20), residues: 2023 helix: 1.11 (0.16), residues: 1234 sheet: -2.98 (0.42), residues: 136 loop : -3.74 (0.22), residues: 653 =============================================================================== Job complete usr+sys time: 3250.77 seconds wall clock time: 59 minutes 32.91 seconds (3572.91 seconds total)