Starting phenix.real_space_refine on Sat Aug 23 23:15:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wui_37855/08_2025/8wui_37855_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wui_37855/08_2025/8wui_37855.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8wui_37855/08_2025/8wui_37855_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wui_37855/08_2025/8wui_37855_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8wui_37855/08_2025/8wui_37855.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wui_37855/08_2025/8wui_37855.map" } resolution = 3.4 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- 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= 0.002 sd= 0.032 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 Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 92 5.16 5 C 10130 2.51 5 N 2498 2.21 5 O 2618 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15340 Number of models: 1 Model: "" Number of chains: 8 Chain: "B" Number of atoms: 3706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 3706 Classifications: {'peptide': 449} Link IDs: {'PTRANS': 13, 'TRANS': 435} Chain breaks: 1 Chain: "A" Number of atoms: 3832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3832 Classifications: {'peptide': 464} Link IDs: {'PTRANS': 13, 'TRANS': 450} Chain breaks: 1 Chain: "D" Number of atoms: 3706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 3706 Classifications: {'peptide': 449} Link IDs: {'PTRANS': 13, 'TRANS': 435} Chain breaks: 1 Chain: "C" Number of atoms: 3832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3832 Classifications: {'peptide': 464} Link IDs: {'PTRANS': 13, 'TRANS': 450} Chain breaks: 1 Chain: "B" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 51 Unusual residues: {'PC1': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 138 Unresolved non-hydrogen dihedrals: 102 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PC1:plan-1': 3, 'PC1:plan-2': 3} Unresolved non-hydrogen planarities: 18 Chain: "A" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 81 Unusual residues: {'PC1': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 135 Unresolved non-hydrogen angles: 165 Unresolved non-hydrogen dihedrals: 124 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PC1:plan-1': 3, 'PC1:plan-2': 3} Unresolved non-hydrogen planarities: 18 Chain: "D" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 51 Unusual residues: {'PC1': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 138 Unresolved non-hydrogen dihedrals: 102 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PC1:plan-1': 3, 'PC1:plan-2': 3} Unresolved non-hydrogen planarities: 18 Chain: "C" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 81 Unusual residues: {'PC1': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 135 Unresolved non-hydrogen angles: 165 Unresolved non-hydrogen dihedrals: 124 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PC1:plan-1': 3, 'PC1:plan-2': 3} Unresolved non-hydrogen planarities: 18 Time building chain proxies: 3.59, per 1000 atoms: 0.23 Number of scatterers: 15340 At special positions: 0 Unit cell: (117.52, 115.44, 125.84, 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 92 16.00 P 2 15.00 O 2618 8.00 N 2498 7.00 C 10130 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 - 3.00 Amino acid : True - 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=8, symmetry=0 Number of additional bonds: simple=8, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.42 Conformation dependent library (CDL) restraints added in 583.3 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3468 Finding SS restraints... Secondary structure from input PDB file: 91 helices and 10 sheets defined 67.4% alpha, 5.8% 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 79 through 97 Processing helix chain 'B' and resid 99 through 105 Processing helix chain 'B' and resid 114 through 132 removed outlier: 3.582A pdb=" N PHE B 125 " --> pdb=" O GLY B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 158 removed outlier: 3.895A pdb=" N TYR B 156 " --> pdb=" O ILE B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 167 Processing helix chain 'B' and resid 170 through 178 Processing helix chain 'B' and resid 181 through 193 removed outlier: 3.514A pdb=" N VAL B 184 " --> pdb=" O LYS B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 208 removed outlier: 4.240A pdb=" N VAL B 198 " --> pdb=" O ARG B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 243 removed outlier: 3.670A pdb=" N ILE B 218 " --> pdb=" O LEU B 214 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEU B 226 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ALA B 233 " --> pdb=" O THR B 229 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE B 236 " --> pdb=" O ALA B 232 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA B 240 " --> pdb=" O PHE B 236 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N LEU B 243 " --> pdb=" O LEU B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 248 Processing helix chain 'B' and resid 265 through 269 Processing helix chain 'B' and resid 270 through 287 Processing helix chain 'B' and resid 299 through 330 removed outlier: 3.508A pdb=" N ALA B 317 " --> pdb=" O MET B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 351 removed outlier: 4.130A pdb=" N PHE B 336 " --> pdb=" O LYS B 332 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ARG B 337 " --> pdb=" O THR B 333 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ASP B 338 " --> pdb=" O GLU B 334 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS B 339 " --> pdb=" O ARG B 335 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE B 343 " --> pdb=" O LYS B 339 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ARG B 345 " --> pdb=" O ALA B 341 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ASN B 348 " --> pdb=" O MET B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 369 Processing helix chain 'B' and resid 382 through 394 removed outlier: 5.277A pdb=" N LYS B 388 " --> pdb=" O SER B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 400 removed outlier: 4.038A pdb=" N LYS B 400 " --> pdb=" O PRO B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 405 Processing helix chain 'B' and resid 408 through 418 removed outlier: 3.575A pdb=" N ARG B 418 " --> pdb=" O GLN B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 479 removed outlier: 3.837A pdb=" N ILE B 476 " --> pdb=" O GLY B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 509 Processing helix chain 'B' and resid 509 through 524 Processing helix chain 'A' and resid 79 through 98 removed outlier: 3.720A pdb=" N SER A 96 " --> pdb=" O TRP A 92 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE A 98 " --> pdb=" O LEU A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 105 Processing helix chain 'A' and resid 113 through 131 removed outlier: 4.018A pdb=" N LEU A 117 " --> pdb=" O ASN A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 160 removed outlier: 4.131A pdb=" N ALA A 153 " --> pdb=" O ARG A 149 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N LEU A 154 " --> pdb=" O SER A 150 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N ARG A 155 " --> pdb=" O SER A 151 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N TYR A 156 " --> pdb=" O ILE A 152 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N LYS A 158 " --> pdb=" O LEU A 154 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR A 160 " --> pdb=" O TYR A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 167 removed outlier: 3.603A pdb=" N LEU A 166 " --> pdb=" O ILE A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 178 Processing helix chain 'A' and resid 181 through 187 removed outlier: 4.441A pdb=" N ARG A 185 " --> pdb=" O LYS A 181 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N TYR A 186 " --> pdb=" O GLU A 182 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LEU A 187 " --> pdb=" O GLU A 183 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 181 through 187' Processing helix chain 'A' and resid 188 through 193 Processing helix chain 'A' and resid 194 through 208 removed outlier: 4.187A pdb=" N VAL A 198 " --> pdb=" O ARG A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 242 removed outlier: 3.847A pdb=" N CYS A 228 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE A 235 " --> pdb=" O THR A 231 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N TYR A 238 " --> pdb=" O CYS A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 251 removed outlier: 3.557A pdb=" N THR A 251 " --> pdb=" O GLU A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 269 Processing helix chain 'A' and resid 270 through 287 removed outlier: 3.591A pdb=" N SER A 278 " --> pdb=" O ARG A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 330 Processing helix chain 'A' and resid 331 through 351 Processing helix chain 'A' and resid 353 through 380 removed outlier: 3.988A pdb=" N ARG A 357 " --> pdb=" O GLY A 353 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASP A 380 " --> pdb=" O ALA A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 394 Processing helix chain 'A' and resid 394 through 400 removed outlier: 4.102A pdb=" N LYS A 400 " --> pdb=" O PRO A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 418 removed outlier: 3.768A pdb=" N ILE A 417 " --> pdb=" O ASN A 413 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ARG A 418 " --> pdb=" O GLN A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 478 Processing helix chain 'A' and resid 499 through 509 removed outlier: 3.561A pdb=" N ILE A 508 " --> pdb=" O ASN A 504 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE A 509 " --> pdb=" O ILE A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 521 removed outlier: 3.516A pdb=" N ARG A 515 " --> pdb=" O HIS A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 545 removed outlier: 4.208A pdb=" N PHE A 539 " --> pdb=" O SER A 535 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N HIS A 540 " --> pdb=" O ASP A 536 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE A 541 " --> pdb=" O ILE A 537 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 97 Processing helix chain 'D' and resid 99 through 105 Processing helix chain 'D' and resid 114 through 132 removed outlier: 3.582A pdb=" N PHE D 125 " --> pdb=" O GLY D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 158 removed outlier: 3.894A pdb=" N TYR D 156 " --> pdb=" O ILE D 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 167 Processing helix chain 'D' and resid 170 through 178 Processing helix chain 'D' and resid 181 through 193 removed outlier: 3.515A pdb=" N VAL D 184 " --> pdb=" O LYS D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 208 removed outlier: 4.241A pdb=" N VAL D 198 " --> pdb=" O ARG D 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 221 removed outlier: 3.670A pdb=" N ILE D 218 " --> pdb=" O LEU D 214 " (cutoff:3.500A) Processing helix chain 'D' and resid 223 through 243 removed outlier: 4.217A pdb=" N THR D 229 " --> pdb=" O GLU D 225 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N HIS D 230 " --> pdb=" O LEU D 226 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE D 236 " --> pdb=" O ALA D 232 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA D 240 " --> pdb=" O PHE D 236 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N LEU D 243 " --> pdb=" O LEU D 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 248 Processing helix chain 'D' and resid 265 through 269 Processing helix chain 'D' and resid 270 through 287 Processing helix chain 'D' and resid 299 through 330 removed outlier: 3.508A pdb=" N ALA D 317 " --> pdb=" O MET D 313 " (cutoff:3.500A) Processing helix chain 'D' and resid 332 through 351 removed outlier: 4.130A pdb=" N PHE D 336 " --> pdb=" O LYS D 332 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ARG D 337 " --> pdb=" O THR D 333 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ASP D 338 " --> pdb=" O GLU D 334 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS D 339 " --> pdb=" O ARG D 335 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE D 343 " --> pdb=" O LYS D 339 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ARG D 345 " --> pdb=" O ALA D 341 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ASN D 348 " --> pdb=" O MET D 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 353 through 369 Processing helix chain 'D' and resid 382 through 394 removed outlier: 5.277A pdb=" N LYS D 388 " --> pdb=" O SER D 384 " (cutoff:3.500A) Processing helix chain 'D' and resid 394 through 400 removed outlier: 4.038A pdb=" N LYS D 400 " --> pdb=" O PRO D 396 " (cutoff:3.500A) Processing helix chain 'D' and resid 401 through 405 Processing helix chain 'D' and resid 408 through 418 removed outlier: 3.576A pdb=" N ARG D 418 " --> pdb=" O GLN D 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 479 removed outlier: 3.838A pdb=" N ILE D 476 " --> pdb=" O GLY D 472 " (cutoff:3.500A) Processing helix chain 'D' and resid 499 through 509 Processing helix chain 'D' and resid 509 through 524 Processing helix chain 'C' and resid 79 through 98 removed outlier: 3.719A pdb=" N SER C 96 " --> pdb=" O TRP C 92 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE C 98 " --> pdb=" O LEU C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 105 Processing helix chain 'C' and resid 113 through 131 removed outlier: 4.018A pdb=" N LEU C 117 " --> pdb=" O ASN C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 160 removed outlier: 4.131A pdb=" N ALA C 153 " --> pdb=" O ARG C 149 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N LEU C 154 " --> pdb=" O SER C 150 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N ARG C 155 " --> pdb=" O SER C 151 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N TYR C 156 " --> pdb=" O ILE C 152 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N LYS C 158 " --> pdb=" O LEU C 154 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR C 160 " --> pdb=" O TYR C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 167 removed outlier: 3.603A pdb=" N LEU C 166 " --> pdb=" O ILE C 162 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 178 Processing helix chain 'C' and resid 181 through 187 removed outlier: 4.441A pdb=" N ARG C 185 " --> pdb=" O LYS C 181 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N TYR C 186 " --> pdb=" O GLU C 182 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LEU C 187 " --> pdb=" O GLU C 183 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 181 through 187' Processing helix chain 'C' and resid 188 through 193 Processing helix chain 'C' and resid 194 through 208 removed outlier: 4.188A pdb=" N VAL C 198 " --> pdb=" O ARG C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 242 removed outlier: 3.961A pdb=" N CYS C 228 " --> pdb=" O VAL C 224 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE C 235 " --> pdb=" O THR C 231 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N TYR C 238 " --> pdb=" O CYS C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 251 removed outlier: 3.557A pdb=" N THR C 251 " --> pdb=" O GLU C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 265 through 269 Processing helix chain 'C' and resid 270 through 287 removed outlier: 3.591A pdb=" N SER C 278 " --> pdb=" O ARG C 274 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 330 Processing helix chain 'C' and resid 331 through 351 Processing helix chain 'C' and resid 353 through 380 removed outlier: 3.988A pdb=" N ARG C 357 " --> pdb=" O GLY C 353 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASP C 380 " --> pdb=" O ALA C 376 " (cutoff:3.500A) Processing helix chain 'C' and resid 382 through 394 Processing helix chain 'C' and resid 394 through 400 removed outlier: 4.102A pdb=" N LYS C 400 " --> pdb=" O PRO C 396 " (cutoff:3.500A) Processing helix chain 'C' and resid 408 through 418 removed outlier: 3.768A pdb=" N ILE C 417 " --> pdb=" O ASN C 413 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ARG C 418 " --> pdb=" O GLN C 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 473 through 478 Processing helix chain 'C' and resid 499 through 509 removed outlier: 3.561A pdb=" N ILE C 508 " --> pdb=" O ASN C 504 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N PHE C 509 " --> pdb=" O ILE C 505 " (cutoff:3.500A) Processing helix chain 'C' and resid 509 through 521 removed outlier: 3.516A pdb=" N ARG C 515 " --> pdb=" O HIS C 511 " (cutoff:3.500A) Processing helix chain 'C' and resid 532 through 545 removed outlier: 4.208A pdb=" N PHE C 539 " --> pdb=" O SER C 535 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N HIS C 540 " --> pdb=" O ASP C 536 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE C 541 " --> pdb=" O ILE C 537 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 137 through 139 removed outlier: 3.758A pdb=" N TYR B 137 " --> pdb=" O ILE B 146 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASP B 139 " --> pdb=" O ARG B 144 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ARG B 144 " --> pdb=" O ASP B 139 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 420 through 424 removed outlier: 3.563A pdb=" N GLU B 422 " --> pdb=" O ILE B 494 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE B 494 " --> pdb=" O GLU B 422 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N PHE B 424 " --> pdb=" O CYS B 492 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N CYS B 492 " --> pdb=" O PHE B 424 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ARG B 493 " --> pdb=" O CYS B 444 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N TYR B 441 " --> pdb=" O PHE B 471 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N PHE B 471 " --> pdb=" O TYR B 441 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 460 through 465 removed outlier: 6.620A pdb=" N GLU B 450 " --> pdb=" O VAL B 462 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N VAL B 464 " --> pdb=" O LEU B 448 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N LEU B 448 " --> pdb=" O VAL B 464 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLU B 449 " --> pdb=" O ARG B 487 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 420 through 421 Processing sheet with id=AA5, first strand: chain 'A' and resid 463 through 465 removed outlier: 3.502A pdb=" N ALA A 463 " --> pdb=" O GLU A 450 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N VAL A 447 " --> pdb=" O ALA A 489 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 137 through 139 removed outlier: 3.759A pdb=" N TYR D 137 " --> pdb=" O ILE D 146 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASP D 139 " --> pdb=" O ARG D 144 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG D 144 " --> pdb=" O ASP D 139 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 420 through 424 removed outlier: 3.563A pdb=" N GLU D 422 " --> pdb=" O ILE D 494 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE D 494 " --> pdb=" O GLU D 422 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N PHE D 424 " --> pdb=" O CYS D 492 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N CYS D 492 " --> pdb=" O PHE D 424 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ARG D 493 " --> pdb=" O CYS D 444 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N TYR D 441 " --> pdb=" O PHE D 471 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N PHE D 471 " --> pdb=" O TYR D 441 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 460 through 465 removed outlier: 6.621A pdb=" N GLU D 450 " --> pdb=" O VAL D 462 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N VAL D 464 " --> pdb=" O LEU D 448 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N LEU D 448 " --> pdb=" O VAL D 464 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU D 449 " --> pdb=" O ARG D 487 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 420 through 421 Processing sheet with id=AB1, first strand: chain 'C' and resid 463 through 465 removed outlier: 3.502A pdb=" N ALA C 463 " --> pdb=" O GLU C 450 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N VAL C 447 " --> pdb=" O ALA C 489 " (cutoff:3.500A) 837 hydrogen bonds defined for protein. 2355 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: 2.63 Time building geometry restraints manager: 1.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 2302 1.30 - 1.43: 4363 1.43 - 1.56: 8865 1.56 - 1.69: 8 1.69 - 1.82: 156 Bond restraints: 15694 Sorted by residual: bond pdb=" C ASN A 355 " pdb=" O ASN A 355 " ideal model delta sigma weight residual 1.235 1.310 -0.075 1.26e-02 6.30e+03 3.52e+01 bond pdb=" C ASN C 355 " pdb=" O ASN C 355 " ideal model delta sigma weight residual 1.235 1.309 -0.074 1.26e-02 6.30e+03 3.45e+01 bond pdb=" C SER A 331 " pdb=" O SER A 331 " ideal model delta sigma weight residual 1.235 1.170 0.065 1.32e-02 5.74e+03 2.40e+01 bond pdb=" C SER C 331 " pdb=" O SER C 331 " ideal model delta sigma weight residual 1.235 1.171 0.064 1.32e-02 5.74e+03 2.35e+01 bond pdb=" C GLN A 359 " pdb=" O GLN A 359 " ideal model delta sigma weight residual 1.236 1.290 -0.053 1.15e-02 7.56e+03 2.15e+01 ... (remaining 15689 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.58: 20930 3.58 - 7.16: 177 7.16 - 10.75: 25 10.75 - 14.33: 0 14.33 - 17.91: 2 Bond angle restraints: 21134 Sorted by residual: angle pdb=" N ASN A 348 " pdb=" CA ASN A 348 " pdb=" C ASN A 348 " ideal model delta sigma weight residual 112.23 101.94 10.29 1.26e+00 6.30e-01 6.67e+01 angle pdb=" N ASN C 348 " pdb=" CA ASN C 348 " pdb=" C ASN C 348 " ideal model delta sigma weight residual 112.23 101.96 10.27 1.26e+00 6.30e-01 6.65e+01 angle pdb=" N LEU D 226 " pdb=" CA LEU D 226 " pdb=" C LEU D 226 " ideal model delta sigma weight residual 113.72 104.00 9.72 1.30e+00 5.92e-01 5.60e+01 angle pdb=" N LYS C 332 " pdb=" CA LYS C 332 " pdb=" C LYS C 332 " ideal model delta sigma weight residual 111.14 103.08 8.06 1.08e+00 8.57e-01 5.58e+01 angle pdb=" N LYS A 332 " pdb=" CA LYS A 332 " pdb=" C LYS A 332 " ideal model delta sigma weight residual 111.14 103.10 8.04 1.08e+00 8.57e-01 5.54e+01 ... (remaining 21129 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.75: 7694 17.75 - 35.50: 1141 35.50 - 53.25: 408 53.25 - 71.00: 91 71.00 - 88.75: 22 Dihedral angle restraints: 9356 sinusoidal: 3958 harmonic: 5398 Sorted by residual: dihedral pdb=" CA GLU D 112 " pdb=" C GLU D 112 " pdb=" N ASN D 113 " pdb=" CA ASN D 113 " ideal model delta harmonic sigma weight residual -180.00 -159.59 -20.41 0 5.00e+00 4.00e-02 1.67e+01 dihedral pdb=" CA GLU B 112 " pdb=" C GLU B 112 " pdb=" N ASN B 113 " pdb=" CA ASN B 113 " ideal model delta harmonic sigma weight residual -180.00 -159.61 -20.39 0 5.00e+00 4.00e-02 1.66e+01 dihedral pdb=" C CYS D 228 " pdb=" N CYS D 228 " pdb=" CA CYS D 228 " pdb=" CB CYS D 228 " ideal model delta harmonic sigma weight residual -122.60 -131.35 8.75 0 2.50e+00 1.60e-01 1.23e+01 ... (remaining 9353 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 1916 0.061 - 0.121: 331 0.121 - 0.182: 52 0.182 - 0.243: 22 0.243 - 0.304: 7 Chirality restraints: 2328 Sorted by residual: chirality pdb=" CA CYS D 228 " pdb=" N CYS D 228 " pdb=" C CYS D 228 " pdb=" CB CYS D 228 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.30e+00 chirality pdb=" CA ASN C 350 " pdb=" N ASN C 350 " pdb=" C ASN C 350 " pdb=" CB ASN C 350 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.08e+00 chirality pdb=" CA ASN A 350 " pdb=" N ASN A 350 " pdb=" C ASN A 350 " pdb=" CB ASN A 350 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.06e+00 ... (remaining 2325 not shown) Planarity restraints: 2592 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP C 380 " -0.027 2.00e-02 2.50e+03 5.40e-02 2.92e+01 pdb=" C ASP C 380 " 0.094 2.00e-02 2.50e+03 pdb=" O ASP C 380 " -0.034 2.00e-02 2.50e+03 pdb=" N ILE C 381 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 380 " 0.027 2.00e-02 2.50e+03 5.39e-02 2.91e+01 pdb=" C ASP A 380 " -0.093 2.00e-02 2.50e+03 pdb=" O ASP A 380 " 0.034 2.00e-02 2.50e+03 pdb=" N ILE A 381 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 270 " 0.070 5.00e-02 4.00e+02 1.00e-01 1.61e+01 pdb=" N PRO A 271 " -0.173 5.00e-02 4.00e+02 pdb=" CA PRO A 271 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO A 271 " 0.054 5.00e-02 4.00e+02 ... (remaining 2589 not shown) Histogram of nonbonded interaction distances: 1.05 - 1.82: 11 1.82 - 2.59: 198 2.59 - 3.36: 20841 3.36 - 4.13: 37714 4.13 - 4.90: 68846 Nonbonded interactions: 127610 Sorted by model distance: nonbonded pdb=" CG1 ILE A 360 " pdb=" CD1 ILE D 385 " model vdw 1.049 3.860 nonbonded pdb=" CG1 ILE A 360 " pdb=" CG1 ILE D 385 " model vdw 1.127 3.840 nonbonded pdb=" NH2 ARG A 345 " pdb=" OE1 GLU D 374 " model vdw 1.261 3.120 nonbonded pdb=" CD1 ILE B 385 " pdb=" CG1 ILE C 360 " model vdw 1.395 3.860 nonbonded pdb=" CD1 ILE A 360 " pdb=" CG1 ILE D 385 " model vdw 1.405 3.860 ... (remaining 127605 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 73 through 525 or resid 902 or (resid 903 and (name C21 or \ name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C2 \ 8 or name C29 or name C2A)) or resid 904)) selection = (chain 'B' and (resid 73 through 452 or resid 462 through 901 or (resid 902 and \ (name C21 or name C22 or name C23 or name C24 or name C25 or name C26 or name C2 \ 7 or name C28 or name C29 or name C2A)) or resid 903)) selection = (chain 'C' and (resid 73 through 525 or resid 902 or (resid 903 and (name C21 or \ name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C2 \ 8 or name C29 or name C2A)) or resid 904)) selection = (chain 'D' and (resid 73 through 452 or resid 462 through 901 or (resid 902 and \ (name C21 or name C22 or name C23 or name C24 or name C25 or name C26 or name C2 \ 7 or name C28 or name C29 or name C2A)) or resid 903)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators 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 individual isotropic 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: 1.990 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: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 15.260 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 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:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6584 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 0.884 15702 Z= 1.124 Angle : 0.838 17.910 21134 Z= 0.532 Chirality : 0.053 0.304 2328 Planarity : 0.006 0.100 2592 Dihedral : 19.522 88.748 5888 Min Nonbonded Distance : 1.049 Molprobity Statistics. All-atom Clashscore : 21.56 Ramachandran Plot: Outliers : 0.72 % Allowed : 6.24 % Favored : 93.04 % Rotamer: Outliers : 5.09 % Allowed : 27.30 % Favored : 67.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.15 (0.20), residues: 1810 helix: -0.98 (0.16), residues: 1040 sheet: -0.97 (0.97), residues: 34 loop : -0.12 (0.25), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 194 TYR 0.013 0.001 TYR B 237 PHE 0.030 0.002 PHE D 223 TRP 0.018 0.001 TRP C 171 HIS 0.004 0.001 HIS C 295 Details of bonding type rmsd covalent geometry : bond 0.00576 (15694) covalent geometry : angle 0.83753 (21134) hydrogen bonds : bond 0.26261 ( 837) hydrogen bonds : angle 9.26269 ( 2355) Misc. bond : bond 0.47052 ( 8) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 235 time to evaluate : 0.507 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: B 377 VAL cc_start: 0.6841 (OUTLIER) cc_final: 0.6435 (t) REVERT: B 468 ASP cc_start: 0.5185 (t0) cc_final: 0.4524 (t0) REVERT: A 145 MET cc_start: 0.6947 (tpp) cc_final: 0.6699 (tpp) REVERT: A 351 LYS cc_start: 0.3960 (OUTLIER) cc_final: 0.3582 (mttp) REVERT: A 365 ARG cc_start: 0.0571 (OUTLIER) cc_final: 0.0068 (ttp-170) REVERT: D 128 ASP cc_start: 0.7860 (t0) cc_final: 0.7657 (t70) REVERT: D 468 ASP cc_start: 0.5363 (t0) cc_final: 0.5022 (t0) REVERT: C 183 GLU cc_start: 0.5865 (tm-30) cc_final: 0.5435 (tt0) REVERT: C 365 ARG cc_start: 0.1331 (OUTLIER) cc_final: 0.0352 (ttp-170) REVERT: C 369 GLU cc_start: 0.2964 (OUTLIER) cc_final: 0.2456 (pt0) outliers start: 83 outliers final: 31 residues processed: 306 average time/residue: 0.1511 time to fit residues: 66.1539 Evaluate side-chains 227 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 191 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 385 ILE Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 336 PHE Chi-restraints excluded: chain A residue 340 MET Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain A residue 351 LYS Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 354 ARG Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 365 ARG Chi-restraints excluded: chain A residue 369 GLU Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 380 ASP Chi-restraints excluded: chain D residue 224 VAL Chi-restraints excluded: chain D residue 377 VAL Chi-restraints excluded: chain D residue 385 ILE Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 336 PHE Chi-restraints excluded: chain C residue 340 MET Chi-restraints excluded: chain C residue 344 MET Chi-restraints excluded: chain C residue 351 LYS Chi-restraints excluded: chain C residue 352 LEU Chi-restraints excluded: chain C residue 360 ILE Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain C residue 365 ARG Chi-restraints excluded: chain C residue 367 GLN Chi-restraints excluded: chain C residue 369 GLU Chi-restraints excluded: chain C residue 377 VAL Chi-restraints excluded: chain C residue 379 GLN Chi-restraints excluded: chain C residue 380 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 20.0000 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 9.9990 chunk 77 optimal weight: 20.0000 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 0.5980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 439 GLN D 295 HIS D 312 ASN D 439 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4844 r_free = 0.4844 target = 0.261150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.193200 restraints weight = 18871.919| |-----------------------------------------------------------------------------| r_work (start): 0.4197 rms_B_bonded: 2.24 r_work: 0.3738 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3615 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 15702 Z= 0.166 Angle : 0.658 11.205 21134 Z= 0.345 Chirality : 0.044 0.165 2328 Planarity : 0.006 0.073 2592 Dihedral : 11.756 93.630 2358 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 13.53 Ramachandran Plot: Outliers : 0.44 % Allowed : 5.52 % Favored : 94.03 % Rotamer: Outliers : 4.91 % Allowed : 25.58 % Favored : 69.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.39 (0.20), residues: 1810 helix: -0.27 (0.16), residues: 1074 sheet: -0.63 (1.18), residues: 20 loop : 0.07 (0.25), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 357 TYR 0.016 0.001 TYR A 368 PHE 0.024 0.002 PHE D 281 TRP 0.014 0.001 TRP D 92 HIS 0.004 0.001 HIS C 295 Details of bonding type rmsd covalent geometry : bond 0.00356 (15694) covalent geometry : angle 0.65784 (21134) hydrogen bonds : bond 0.05523 ( 837) hydrogen bonds : angle 5.83922 ( 2355) Misc. bond : bond 0.00267 ( 8) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3620 Ramachandran restraints generated. 1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 221 time to evaluate : 0.591 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: B 87 MET cc_start: 0.7507 (mmp) cc_final: 0.6453 (mmm) REVERT: B 218 ILE cc_start: 0.6316 (OUTLIER) cc_final: 0.5361 (tt) REVERT: B 367 GLN cc_start: 0.7924 (mt0) cc_final: 0.7530 (mp10) REVERT: A 89 ILE cc_start: 0.8275 (OUTLIER) cc_final: 0.8004 (tp) REVERT: A 145 MET cc_start: 0.8240 (tpp) cc_final: 0.7749 (tpp) REVERT: A 260 ASP cc_start: 0.8116 (m-30) cc_final: 0.7780 (t70) REVERT: A 339 LYS cc_start: 0.6560 (mmtt) cc_final: 0.6168 (pttm) REVERT: A 355 ASN cc_start: 0.6294 (OUTLIER) cc_final: 0.5533 (p0) REVERT: A 360 ILE cc_start: 0.4276 (OUTLIER) cc_final: 0.3868 (mm) REVERT: A 368 TYR cc_start: 0.3829 (OUTLIER) cc_final: 0.3177 (p90) REVERT: A 369 GLU cc_start: 0.0290 (OUTLIER) cc_final: 0.0060 (pt0) REVERT: A 404 PHE cc_start: 0.7490 (OUTLIER) cc_final: 0.7275 (t80) REVERT: D 421 GLU cc_start: 0.6934 (mt-10) cc_final: 0.6503 (tm-30) REVERT: C 89 ILE cc_start: 0.7847 (OUTLIER) cc_final: 0.7483 (tp) REVERT: C 92 TRP cc_start: 0.7724 (m100) cc_final: 0.7497 (m100) REVERT: C 171 TRP cc_start: 0.7761 (m100) cc_final: 0.7311 (m100) REVERT: C 211 ILE cc_start: 0.7806 (OUTLIER) cc_final: 0.7282 (mp) REVERT: C 221 LEU cc_start: 0.7953 (mm) cc_final: 0.7560 (mt) REVERT: C 359 GLN cc_start: 0.4510 (tm-30) cc_final: 0.4132 (mm110) REVERT: C 369 GLU cc_start: 0.1305 (OUTLIER) cc_final: 0.0986 (pt0) REVERT: C 393 LEU cc_start: 0.7230 (tt) cc_final: 0.6836 (pp) REVERT: C 404 PHE cc_start: 0.7518 (OUTLIER) cc_final: 0.7165 (t80) outliers start: 80 outliers final: 37 residues processed: 286 average time/residue: 0.1151 time to fit residues: 51.9098 Evaluate side-chains 230 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 182 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 301 GLU Chi-restraints excluded: chain B residue 302 MET Chi-restraints excluded: chain B residue 310 SER Chi-restraints excluded: chain B residue 445 HIS Chi-restraints excluded: chain B residue 516 ILE Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 301 GLU Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain A residue 336 PHE Chi-restraints excluded: chain A residue 354 ARG Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 368 TYR Chi-restraints excluded: chain A residue 369 GLU Chi-restraints excluded: chain A residue 380 ASP Chi-restraints excluded: chain A residue 404 PHE Chi-restraints excluded: chain A residue 407 CYS Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 211 ILE Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 301 GLU Chi-restraints excluded: chain D residue 302 MET Chi-restraints excluded: chain D residue 319 LEU Chi-restraints excluded: chain D residue 364 LEU Chi-restraints excluded: chain D residue 377 VAL Chi-restraints excluded: chain D residue 445 HIS Chi-restraints excluded: chain D residue 516 ILE Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 301 GLU Chi-restraints excluded: chain C residue 310 SER Chi-restraints excluded: chain C residue 336 PHE Chi-restraints excluded: chain C residue 344 MET Chi-restraints excluded: chain C residue 360 ILE Chi-restraints excluded: chain C residue 369 GLU Chi-restraints excluded: chain C residue 380 ASP Chi-restraints excluded: chain C residue 404 PHE Chi-restraints excluded: chain C residue 407 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 58.1714 > 50: distance: 62 - 85: 15.542 distance: 67 - 93: 9.096 distance: 73 - 101: 17.827 distance: 76 - 85: 14.671 distance: 77 - 110: 14.274 distance: 85 - 86: 5.934 distance: 86 - 87: 10.145 distance: 86 - 89: 14.723 distance: 87 - 88: 8.501 distance: 87 - 93: 9.666 distance: 88 - 118: 19.807 distance: 89 - 90: 6.543 distance: 89 - 91: 24.932 distance: 90 - 92: 12.657 distance: 93 - 94: 6.747 distance: 94 - 95: 3.856 distance: 94 - 97: 11.127 distance: 95 - 96: 6.102 distance: 95 - 101: 15.260 distance: 96 - 125: 14.188 distance: 97 - 98: 21.119 distance: 98 - 99: 4.566 distance: 98 - 100: 6.271 distance: 101 - 102: 9.101 distance: 102 - 103: 7.679 distance: 102 - 105: 5.163 distance: 103 - 104: 15.654 distance: 103 - 110: 8.376 distance: 105 - 106: 11.918 distance: 106 - 107: 11.566 distance: 107 - 108: 18.277 distance: 107 - 109: 20.772 distance: 110 - 111: 4.245 distance: 111 - 112: 16.528 distance: 112 - 113: 15.195 distance: 112 - 118: 7.014 distance: 114 - 115: 10.631 distance: 114 - 116: 18.490 distance: 115 - 117: 11.704 distance: 118 - 119: 18.083 distance: 119 - 120: 17.776 distance: 119 - 122: 32.521 distance: 120 - 121: 14.510 distance: 120 - 125: 5.259 distance: 122 - 123: 4.728 distance: 122 - 124: 22.421 distance: 125 - 126: 4.410 distance: 126 - 127: 5.986 distance: 126 - 129: 10.935 distance: 127 - 128: 9.990 distance: 127 - 133: 13.308 distance: 129 - 130: 17.110 distance: 129 - 131: 25.539 distance: 130 - 132: 11.738 distance: 133 - 134: 23.484 distance: 134 - 135: 7.071 distance: 134 - 137: 9.453 distance: 135 - 136: 9.012 distance: 135 - 144: 7.061 distance: 137 - 138: 17.471 distance: 138 - 139: 26.394 distance: 139 - 140: 4.906 distance: 140 - 141: 5.591 distance: 141 - 142: 5.419 distance: 141 - 143: 17.052 distance: 145 - 146: 20.744 distance: 145 - 148: 5.337 distance: 146 - 147: 21.122 distance: 146 - 152: 30.121 distance: 148 - 149: 16.306 distance: 149 - 150: 21.801 distance: 149 - 151: 13.372 distance: 152 - 153: 24.043 distance: 152 - 202: 14.045 distance: 153 - 154: 4.822 distance: 153 - 156: 4.372 distance: 154 - 155: 11.487 distance: 154 - 162: 13.066 distance: 155 - 199: 22.078 distance: 156 - 157: 10.086 distance: 157 - 158: 21.899 distance: 157 - 159: 10.661 distance: 158 - 160: 11.700 distance: 160 - 161: 18.407 distance: 162 - 163: 15.241 distance: 163 - 164: 18.266 distance: 163 - 166: 6.791 distance: 164 - 165: 16.140 distance: 164 - 171: 9.159 distance: 166 - 167: 6.956 distance: 167 - 168: 25.804 distance: 168 - 169: 18.654 distance: 168 - 170: 16.457