Starting phenix.real_space_refine on Fri Aug 9 05:03:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qzp_18779/08_2024/8qzp_18779.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qzp_18779/08_2024/8qzp_18779.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qzp_18779/08_2024/8qzp_18779.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qzp_18779/08_2024/8qzp_18779.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qzp_18779/08_2024/8qzp_18779.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qzp_18779/08_2024/8qzp_18779.cif" } resolution = 4.15 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.008 sd= 0.107 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: 4 Type Number sf(0) Gaussians S 112 5.16 5 C 16273 2.51 5 N 4419 2.21 5 O 4589 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 485": "OE1" <-> "OE2" Residue "B ASP 460": "OD1" <-> "OD2" Residue "C TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 396": "OE1" <-> "OE2" Residue "C GLU 436": "OE1" <-> "OE2" Residue "D GLU 331": "OE1" <-> "OE2" Residue "E GLU 409": "OE1" <-> "OE2" Residue "F GLU 257": "OE1" <-> "OE2" Residue "F TYR 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 485": "OE1" <-> "OE2" Residue "G GLU 351": "OE1" <-> "OE2" Residue "H GLU 139": "OE1" <-> "OE2" Residue "H GLU 159": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 25393 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 413, 3201 Classifications: {'peptide': 413} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 14} Link IDs: {'PTRANS': 26, 'TRANS': 386} Chain breaks: 1 Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 28 Chain: "B" Number of atoms: 3208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3208 Classifications: {'peptide': 414} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 26, 'TRANS': 387} Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 2, 'ARG:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 35 Chain: "C" Number of atoms: 3217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 3217 Classifications: {'peptide': 416} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 26, 'TRANS': 389} Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 2, 'ARG:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 35 Chain: "D" Number of atoms: 3407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3407 Classifications: {'peptide': 441} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 26, 'TRANS': 414} Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 2, 'ARG:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 35 Chain: "E" Number of atoms: 3112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 3112 Classifications: {'peptide': 401} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 13} Link IDs: {'PTRANS': 25, 'TRANS': 375} Chain breaks: 1 Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "F" Number of atoms: 3090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 397, 3090 Classifications: {'peptide': 397} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 24, 'TRANS': 372} Chain breaks: 1 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 23 Chain: "G" Number of atoms: 3068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 3068 Classifications: {'peptide': 394} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 23, 'TRANS': 370} Chain breaks: 2 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 23 Chain: "H" Number of atoms: 3090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 397, 3090 Classifications: {'peptide': 397} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 24, 'TRANS': 372} Chain breaks: 1 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 23 Time building chain proxies: 14.23, per 1000 atoms: 0.56 Number of scatterers: 25393 At special positions: 0 Unit cell: (104.64, 150.42, 149.33, 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 112 16.00 O 4589 8.00 N 4419 7.00 C 16273 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: 10.99 Conformation dependent library (CDL) restraints added in 5.1 seconds 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6090 Finding SS restraints... Secondary structure from input PDB file: 181 helices and 13 sheets defined 63.5% alpha, 1.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.46 Creating SS restraints... Processing helix chain 'A' and resid 128 through 133 Processing helix chain 'A' and resid 136 through 147 Processing helix chain 'A' and resid 151 through 166 Processing helix chain 'A' and resid 169 through 179 Processing helix chain 'A' and resid 184 through 199 removed outlier: 3.628A pdb=" N VAL A 188 " --> pdb=" O HIS A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 208 removed outlier: 3.751A pdb=" N LEU A 207 " --> pdb=" O ASN A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 214 Processing helix chain 'A' and resid 215 through 243 removed outlier: 3.956A pdb=" N ARG A 219 " --> pdb=" O SER A 215 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASP A 220 " --> pdb=" O LYS A 216 " (cutoff:3.500A) Proline residue: A 231 - end of helix removed outlier: 3.599A pdb=" N ALA A 242 " --> pdb=" O TYR A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 265 Processing helix chain 'A' and resid 274 through 288 removed outlier: 3.631A pdb=" N ILE A 286 " --> pdb=" O ASP A 282 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LEU A 287 " --> pdb=" O ILE A 283 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N HIS A 288 " --> pdb=" O LEU A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 306 Processing helix chain 'A' and resid 309 through 322 removed outlier: 3.562A pdb=" N ALA A 313 " --> pdb=" O ASP A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 327 removed outlier: 3.581A pdb=" N HIS A 326 " --> pdb=" O GLY A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 341 removed outlier: 3.943A pdb=" N GLY A 341 " --> pdb=" O LEU A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 355 Processing helix chain 'A' and resid 372 through 390 Processing helix chain 'A' and resid 392 through 408 removed outlier: 3.905A pdb=" N SER A 407 " --> pdb=" O LYS A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 413 Processing helix chain 'A' and resid 419 through 432 removed outlier: 3.619A pdb=" N TYR A 423 " --> pdb=" O ASN A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 436 No H-bonds generated for 'chain 'A' and resid 434 through 436' Processing helix chain 'A' and resid 437 through 442 removed outlier: 3.974A pdb=" N LEU A 441 " --> pdb=" O PHE A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 446 No H-bonds generated for 'chain 'A' and resid 444 through 446' Processing helix chain 'A' and resid 447 through 460 Processing helix chain 'A' and resid 482 through 486 Processing helix chain 'B' and resid 128 through 135 Processing helix chain 'B' and resid 136 through 146 Processing helix chain 'B' and resid 151 through 165 Processing helix chain 'B' and resid 169 through 179 removed outlier: 3.677A pdb=" N LEU B 173 " --> pdb=" O PRO B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 199 Processing helix chain 'B' and resid 200 through 208 Proline residue: B 205 - end of helix Processing helix chain 'B' and resid 215 through 243 removed outlier: 3.633A pdb=" N ARG B 219 " --> pdb=" O SER B 215 " (cutoff:3.500A) Proline residue: B 231 - end of helix removed outlier: 3.902A pdb=" N ALA B 242 " --> pdb=" O TYR B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 264 Processing helix chain 'B' and resid 274 through 288 Processing helix chain 'B' and resid 294 through 306 Processing helix chain 'B' and resid 309 through 320 Processing helix chain 'B' and resid 321 through 327 Proline residue: B 324 - end of helix removed outlier: 3.808A pdb=" N GLY B 327 " --> pdb=" O PRO B 324 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 321 through 327' Processing helix chain 'B' and resid 329 through 340 removed outlier: 3.869A pdb=" N VAL B 333 " --> pdb=" O ALA B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 344 No H-bonds generated for 'chain 'B' and resid 342 through 344' Processing helix chain 'B' and resid 345 through 355 Processing helix chain 'B' and resid 372 through 390 removed outlier: 4.084A pdb=" N LYS B 376 " --> pdb=" O ASP B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 408 removed outlier: 3.577A pdb=" N SER B 407 " --> pdb=" O LYS B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 413 Processing helix chain 'B' and resid 419 through 432 removed outlier: 4.354A pdb=" N TYR B 423 " --> pdb=" O ASN B 419 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 459 removed outlier: 3.957A pdb=" N LEU B 441 " --> pdb=" O PHE B 437 " (cutoff:3.500A) Proline residue: B 445 - end of helix removed outlier: 4.425A pdb=" N ALA B 448 " --> pdb=" O ILE B 444 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLY B 449 " --> pdb=" O PRO B 445 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU B 458 " --> pdb=" O TRP B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 503 through 507 removed outlier: 3.829A pdb=" N ARG B 506 " --> pdb=" O ALA B 503 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ARG B 507 " --> pdb=" O THR B 504 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 503 through 507' Processing helix chain 'C' and resid 128 through 135 Processing helix chain 'C' and resid 136 through 145 Processing helix chain 'C' and resid 151 through 165 Processing helix chain 'C' and resid 169 through 178 removed outlier: 3.836A pdb=" N LEU C 173 " --> pdb=" O PRO C 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 200 removed outlier: 3.576A pdb=" N VAL C 188 " --> pdb=" O HIS C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 214 removed outlier: 3.974A pdb=" N TYR C 213 " --> pdb=" O GLN C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 215 through 242 Proline residue: C 231 - end of helix removed outlier: 3.681A pdb=" N ALA C 242 " --> pdb=" O TYR C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 264 Processing helix chain 'C' and resid 274 through 287 Processing helix chain 'C' and resid 294 through 306 Processing helix chain 'C' and resid 309 through 322 Processing helix chain 'C' and resid 329 through 341 removed outlier: 4.024A pdb=" N VAL C 333 " --> pdb=" O ALA C 329 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLY C 341 " --> pdb=" O LEU C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 342 through 344 No H-bonds generated for 'chain 'C' and resid 342 through 344' Processing helix chain 'C' and resid 345 through 355 removed outlier: 3.623A pdb=" N PHE C 349 " --> pdb=" O ASN C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 372 through 389 removed outlier: 3.872A pdb=" N LYS C 376 " --> pdb=" O ASP C 372 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLU C 383 " --> pdb=" O ARG C 379 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N GLU C 384 " --> pdb=" O LYS C 380 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL C 385 " --> pdb=" O LEU C 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 392 through 408 removed outlier: 3.932A pdb=" N GLU C 396 " --> pdb=" O ASP C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 408 through 414 removed outlier: 3.649A pdb=" N ILE C 412 " --> pdb=" O ASP C 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 419 through 431 removed outlier: 3.799A pdb=" N TYR C 423 " --> pdb=" O ASN C 419 " (cutoff:3.500A) Processing helix chain 'C' and resid 434 through 443 Proline residue: C 439 - end of helix Processing helix chain 'C' and resid 444 through 445 No H-bonds generated for 'chain 'C' and resid 444 through 445' Processing helix chain 'C' and resid 446 through 458 removed outlier: 4.694A pdb=" N ALA C 452 " --> pdb=" O ALA C 448 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU C 458 " --> pdb=" O TRP C 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 507 removed outlier: 4.050A pdb=" N ARG C 506 " --> pdb=" O ASN C 502 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 82 Processing helix chain 'D' and resid 127 through 135 Processing helix chain 'D' and resid 136 through 147 Processing helix chain 'D' and resid 151 through 165 Processing helix chain 'D' and resid 169 through 179 removed outlier: 3.934A pdb=" N LEU D 173 " --> pdb=" O PRO D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 184 through 200 removed outlier: 3.722A pdb=" N HIS D 200 " --> pdb=" O LEU D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 201 through 204 Processing helix chain 'D' and resid 211 through 214 Processing helix chain 'D' and resid 215 through 242 Proline residue: D 231 - end of helix Processing helix chain 'D' and resid 254 through 264 removed outlier: 3.763A pdb=" N ASP D 264 " --> pdb=" O LEU D 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 288 Processing helix chain 'D' and resid 294 through 305 Processing helix chain 'D' and resid 309 through 321 removed outlier: 3.909A pdb=" N ALA D 313 " --> pdb=" O ASP D 309 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU D 321 " --> pdb=" O ALA D 317 " (cutoff:3.500A) Processing helix chain 'D' and resid 329 through 341 removed outlier: 4.046A pdb=" N GLY D 341 " --> pdb=" O LEU D 337 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 355 removed outlier: 3.731A pdb=" N PHE D 349 " --> pdb=" O ASN D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 390 removed outlier: 3.707A pdb=" N LYS D 376 " --> pdb=" O ASP D 372 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLY D 390 " --> pdb=" O PHE D 386 " (cutoff:3.500A) Processing helix chain 'D' and resid 392 through 407 removed outlier: 3.993A pdb=" N GLU D 396 " --> pdb=" O ASP D 392 " (cutoff:3.500A) Processing helix chain 'D' and resid 408 through 413 Processing helix chain 'D' and resid 419 through 431 removed outlier: 3.816A pdb=" N TYR D 423 " --> pdb=" O ASN D 419 " (cutoff:3.500A) Processing helix chain 'D' and resid 434 through 436 No H-bonds generated for 'chain 'D' and resid 434 through 436' Processing helix chain 'D' and resid 437 through 442 removed outlier: 3.836A pdb=" N LEU D 441 " --> pdb=" O PHE D 437 " (cutoff:3.500A) Processing helix chain 'D' and resid 443 through 460 removed outlier: 4.462A pdb=" N ALA D 448 " --> pdb=" O ILE D 444 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N GLY D 449 " --> pdb=" O PRO D 445 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N SER D 457 " --> pdb=" O HIS D 453 " (cutoff:3.500A) Processing helix chain 'D' and resid 482 through 486 removed outlier: 3.876A pdb=" N GLU D 485 " --> pdb=" O PRO D 482 " (cutoff:3.500A) Processing helix chain 'D' and resid 501 through 509 Processing helix chain 'E' and resid 128 through 135 Processing helix chain 'E' and resid 136 through 147 Processing helix chain 'E' and resid 151 through 164 removed outlier: 3.584A pdb=" N TRP E 158 " --> pdb=" O GLN E 154 " (cutoff:3.500A) Processing helix chain 'E' and resid 169 through 178 removed outlier: 3.800A pdb=" N LEU E 173 " --> pdb=" O PRO E 169 " (cutoff:3.500A) Processing helix chain 'E' and resid 184 through 200 Processing helix chain 'E' and resid 201 through 204 Processing helix chain 'E' and resid 211 through 214 removed outlier: 3.555A pdb=" N LYS E 214 " --> pdb=" O ASP E 211 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 211 through 214' Processing helix chain 'E' and resid 215 through 242 removed outlier: 3.688A pdb=" N ARG E 219 " --> pdb=" O SER E 215 " (cutoff:3.500A) Proline residue: E 231 - end of helix Processing helix chain 'E' and resid 254 through 264 Processing helix chain 'E' and resid 274 through 288 Processing helix chain 'E' and resid 294 through 306 removed outlier: 3.792A pdb=" N HIS E 302 " --> pdb=" O ALA E 298 " (cutoff:3.500A) Processing helix chain 'E' and resid 309 through 323 removed outlier: 4.256A pdb=" N GLY E 323 " --> pdb=" O GLY E 319 " (cutoff:3.500A) Processing helix chain 'E' and resid 323 through 328 Processing helix chain 'E' and resid 329 through 341 Processing helix chain 'E' and resid 342 through 345 Processing helix chain 'E' and resid 346 through 355 Processing helix chain 'E' and resid 365 through 369 removed outlier: 4.255A pdb=" N LYS E 369 " --> pdb=" O ARG E 366 " (cutoff:3.500A) Processing helix chain 'E' and resid 372 through 390 removed outlier: 4.166A pdb=" N LYS E 376 " --> pdb=" O ASP E 372 " (cutoff:3.500A) Processing helix chain 'E' and resid 392 through 408 Processing helix chain 'E' and resid 408 through 414 removed outlier: 3.937A pdb=" N ILE E 412 " --> pdb=" O ASP E 408 " (cutoff:3.500A) Processing helix chain 'E' and resid 419 through 431 removed outlier: 3.594A pdb=" N TYR E 423 " --> pdb=" O ASN E 419 " (cutoff:3.500A) Processing helix chain 'E' and resid 434 through 436 No H-bonds generated for 'chain 'E' and resid 434 through 436' Processing helix chain 'E' and resid 437 through 442 removed outlier: 4.035A pdb=" N LEU E 441 " --> pdb=" O PHE E 437 " (cutoff:3.500A) Processing helix chain 'E' and resid 445 through 459 removed outlier: 4.029A pdb=" N GLY E 449 " --> pdb=" O PRO E 445 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ARG E 455 " --> pdb=" O LEU E 451 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLU E 456 " --> pdb=" O ALA E 452 " (cutoff:3.500A) Processing helix chain 'E' and resid 502 through 507 removed outlier: 3.993A pdb=" N ARG E 506 " --> pdb=" O ASN E 502 " (cutoff:3.500A) Processing helix chain 'F' and resid 128 through 135 removed outlier: 4.148A pdb=" N SER F 134 " --> pdb=" O GLU F 130 " (cutoff:3.500A) Processing helix chain 'F' and resid 136 through 147 Processing helix chain 'F' and resid 151 through 165 removed outlier: 3.563A pdb=" N HIS F 165 " --> pdb=" O ALA F 161 " (cutoff:3.500A) Processing helix chain 'F' and resid 170 through 179 Processing helix chain 'F' and resid 184 through 199 Processing helix chain 'F' and resid 200 through 203 Processing helix chain 'F' and resid 204 through 209 removed outlier: 3.589A pdb=" N ARG F 208 " --> pdb=" O ASN F 204 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLY F 209 " --> pdb=" O PRO F 205 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 204 through 209' Processing helix chain 'F' and resid 210 through 214 Processing helix chain 'F' and resid 215 through 242 Proline residue: F 231 - end of helix removed outlier: 3.907A pdb=" N ALA F 242 " --> pdb=" O TYR F 238 " (cutoff:3.500A) Processing helix chain 'F' and resid 254 through 264 Processing helix chain 'F' and resid 274 through 288 removed outlier: 4.026A pdb=" N HIS F 288 " --> pdb=" O LEU F 284 " (cutoff:3.500A) Processing helix chain 'F' and resid 294 through 305 Processing helix chain 'F' and resid 309 through 320 removed outlier: 3.843A pdb=" N ALA F 317 " --> pdb=" O ALA F 313 " (cutoff:3.500A) Processing helix chain 'F' and resid 321 through 323 No H-bonds generated for 'chain 'F' and resid 321 through 323' Processing helix chain 'F' and resid 328 through 341 removed outlier: 3.602A pdb=" N GLY F 341 " --> pdb=" O LEU F 337 " (cutoff:3.500A) Processing helix chain 'F' and resid 342 through 344 No H-bonds generated for 'chain 'F' and resid 342 through 344' Processing helix chain 'F' and resid 345 through 355 removed outlier: 3.656A pdb=" N LYS F 354 " --> pdb=" O ILE F 350 " (cutoff:3.500A) Processing helix chain 'F' and resid 372 through 390 removed outlier: 3.810A pdb=" N LYS F 376 " --> pdb=" O ASP F 372 " (cutoff:3.500A) Processing helix chain 'F' and resid 392 through 408 removed outlier: 3.940A pdb=" N LEU F 406 " --> pdb=" O GLU F 402 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N SER F 407 " --> pdb=" O LYS F 403 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASP F 408 " --> pdb=" O ALA F 404 " (cutoff:3.500A) Processing helix chain 'F' and resid 408 through 415 removed outlier: 3.880A pdb=" N ILE F 412 " --> pdb=" O ASP F 408 " (cutoff:3.500A) Processing helix chain 'F' and resid 419 through 431 removed outlier: 3.944A pdb=" N TYR F 423 " --> pdb=" O ASN F 419 " (cutoff:3.500A) Processing helix chain 'F' and resid 434 through 436 No H-bonds generated for 'chain 'F' and resid 434 through 436' Processing helix chain 'F' and resid 437 through 460 Proline residue: F 445 - end of helix removed outlier: 4.761A pdb=" N ALA F 448 " --> pdb=" O ILE F 444 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N GLY F 449 " --> pdb=" O PRO F 445 " (cutoff:3.500A) Processing helix chain 'F' and resid 503 through 508 Processing helix chain 'G' and resid 129 through 131 No H-bonds generated for 'chain 'G' and resid 129 through 131' Processing helix chain 'G' and resid 136 through 147 Processing helix chain 'G' and resid 151 through 165 removed outlier: 3.734A pdb=" N HIS G 165 " --> pdb=" O ALA G 161 " (cutoff:3.500A) Processing helix chain 'G' and resid 171 through 177 removed outlier: 3.530A pdb=" N GLN G 177 " --> pdb=" O LEU G 173 " (cutoff:3.500A) Processing helix chain 'G' and resid 184 through 197 Processing helix chain 'G' and resid 215 through 229 removed outlier: 4.450A pdb=" N LYS G 229 " --> pdb=" O ARG G 225 " (cutoff:3.500A) Processing helix chain 'G' and resid 229 through 234 Processing helix chain 'G' and resid 237 through 243 removed outlier: 3.582A pdb=" N LEU G 241 " --> pdb=" O ALA G 237 " (cutoff:3.500A) Processing helix chain 'G' and resid 254 through 264 Processing helix chain 'G' and resid 276 through 288 removed outlier: 3.843A pdb=" N VAL G 280 " --> pdb=" O ARG G 276 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N PHE G 285 " --> pdb=" O LEU G 281 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ILE G 286 " --> pdb=" O ASP G 282 " (cutoff:3.500A) Processing helix chain 'G' and resid 295 through 307 removed outlier: 3.851A pdb=" N ALA G 299 " --> pdb=" O CYS G 295 " (cutoff:3.500A) Processing helix chain 'G' and resid 310 through 322 removed outlier: 3.909A pdb=" N TYR G 322 " --> pdb=" O VAL G 318 " (cutoff:3.500A) Processing helix chain 'G' and resid 330 through 340 removed outlier: 3.780A pdb=" N LEU G 334 " --> pdb=" O ASN G 330 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LYS G 335 " --> pdb=" O GLU G 331 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N MET G 336 " --> pdb=" O ALA G 332 " (cutoff:3.500A) Processing helix chain 'G' and resid 342 through 344 No H-bonds generated for 'chain 'G' and resid 342 through 344' Processing helix chain 'G' and resid 345 through 355 removed outlier: 3.598A pdb=" N PHE G 349 " --> pdb=" O ASN G 345 " (cutoff:3.500A) Processing helix chain 'G' and resid 372 through 390 removed outlier: 3.771A pdb=" N LYS G 376 " --> pdb=" O ASP G 372 " (cutoff:3.500A) Processing helix chain 'G' and resid 392 through 406 Processing helix chain 'G' and resid 408 through 414 Processing helix chain 'G' and resid 419 through 431 removed outlier: 4.023A pdb=" N TYR G 423 " --> pdb=" O ASN G 419 " (cutoff:3.500A) Processing helix chain 'G' and resid 439 through 458 removed outlier: 3.780A pdb=" N ILE G 444 " --> pdb=" O VAL G 440 " (cutoff:3.500A) Proline residue: G 445 - end of helix removed outlier: 4.389A pdb=" N ALA G 448 " --> pdb=" O ILE G 444 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLY G 449 " --> pdb=" O PRO G 445 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA G 452 " --> pdb=" O ALA G 448 " (cutoff:3.500A) Processing helix chain 'G' and resid 482 through 486 Processing helix chain 'G' and resid 502 through 508 Processing helix chain 'H' and resid 127 through 134 removed outlier: 3.516A pdb=" N LEU H 131 " --> pdb=" O PRO H 127 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N SER H 134 " --> pdb=" O GLU H 130 " (cutoff:3.500A) Processing helix chain 'H' and resid 136 through 146 Processing helix chain 'H' and resid 151 through 165 Processing helix chain 'H' and resid 171 through 176 Processing helix chain 'H' and resid 184 through 200 removed outlier: 4.337A pdb=" N VAL H 188 " --> pdb=" O HIS H 184 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N VAL H 198 " --> pdb=" O SER H 194 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N HIS H 200 " --> pdb=" O LEU H 196 " (cutoff:3.500A) Processing helix chain 'H' and resid 215 through 230 removed outlier: 4.118A pdb=" N VAL H 230 " --> pdb=" O ILE H 226 " (cutoff:3.500A) Processing helix chain 'H' and resid 230 through 240 removed outlier: 3.909A pdb=" N ALA H 236 " --> pdb=" O THR H 232 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N TYR H 238 " --> pdb=" O ALA H 234 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ARG H 240 " --> pdb=" O ALA H 236 " (cutoff:3.500A) Processing helix chain 'H' and resid 254 through 262 Processing helix chain 'H' and resid 275 through 288 Processing helix chain 'H' and resid 296 through 302 Processing helix chain 'H' and resid 302 through 307 removed outlier: 4.245A pdb=" N SER H 306 " --> pdb=" O HIS H 302 " (cutoff:3.500A) Processing helix chain 'H' and resid 310 through 321 Processing helix chain 'H' and resid 332 through 338 removed outlier: 4.146A pdb=" N MET H 336 " --> pdb=" O ALA H 332 " (cutoff:3.500A) Processing helix chain 'H' and resid 345 through 355 removed outlier: 3.754A pdb=" N LYS H 354 " --> pdb=" O ILE H 350 " (cutoff:3.500A) Processing helix chain 'H' and resid 372 through 387 removed outlier: 4.450A pdb=" N LYS H 376 " --> pdb=" O ASP H 372 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N VAL H 377 " --> pdb=" O PRO H 373 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER H 387 " --> pdb=" O GLU H 383 " (cutoff:3.500A) Processing helix chain 'H' and resid 392 through 405 removed outlier: 3.747A pdb=" N GLU H 396 " --> pdb=" O ASP H 392 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL H 397 " --> pdb=" O PRO H 393 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ALA H 398 " --> pdb=" O LEU H 394 " (cutoff:3.500A) Processing helix chain 'H' and resid 408 through 414 Processing helix chain 'H' and resid 419 through 432 removed outlier: 3.711A pdb=" N GLY H 432 " --> pdb=" O TYR H 428 " (cutoff:3.500A) Processing helix chain 'H' and resid 442 through 460 removed outlier: 3.754A pdb=" N ALA H 448 " --> pdb=" O ILE H 444 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 107 through 109 removed outlier: 3.631A pdb=" N VAL B 471 " --> pdb=" O VAL A 107 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 122 through 123 Processing sheet with id=AA3, first strand: chain 'B' and resid 122 through 123 Processing sheet with id=AA4, first strand: chain 'C' and resid 104 through 105 Processing sheet with id=AA5, first strand: chain 'C' and resid 108 through 109 Processing sheet with id=AA6, first strand: chain 'C' and resid 114 through 115 Processing sheet with id=AA7, first strand: chain 'C' and resid 471 through 472 removed outlier: 5.664A pdb=" N VAL C 471 " --> pdb=" O SER D 109 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'D' and resid 112 through 115 Processing sheet with id=AA9, first strand: chain 'E' and resid 122 through 123 Processing sheet with id=AB1, first strand: chain 'F' and resid 113 through 115 removed outlier: 3.601A pdb=" N TYR F 126 " --> pdb=" O TYR F 123 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 122 through 123 Processing sheet with id=AB3, first strand: chain 'G' and resid 471 through 472 removed outlier: 6.866A pdb=" N VAL G 471 " --> pdb=" O SER H 109 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'H' and resid 113 through 114 1247 hydrogen bonds defined for protein. 3621 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.23 Time building geometry restraints manager: 11.96 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: 5696 1.33 - 1.45: 5667 1.45 - 1.57: 14452 1.57 - 1.69: 0 1.69 - 1.82: 200 Bond restraints: 26015 Sorted by residual: bond pdb=" CA ALA B 234 " pdb=" C ALA B 234 " ideal model delta sigma weight residual 1.524 1.437 0.088 1.28e-02 6.10e+03 4.71e+01 bond pdb=" CA ALA B 236 " pdb=" C ALA B 236 " ideal model delta sigma weight residual 1.524 1.448 0.075 1.44e-02 4.82e+03 2.74e+01 bond pdb=" CA THR B 232 " pdb=" C THR B 232 " ideal model delta sigma weight residual 1.524 1.459 0.065 1.26e-02 6.30e+03 2.65e+01 bond pdb=" CA VAL B 230 " pdb=" C VAL B 230 " ideal model delta sigma weight residual 1.524 1.475 0.049 1.05e-02 9.07e+03 2.20e+01 bond pdb=" CA SER F 197 " pdb=" C SER F 197 " ideal model delta sigma weight residual 1.524 1.469 0.055 1.24e-02 6.50e+03 1.95e+01 ... (remaining 26010 not shown) Histogram of bond angle deviations from ideal: 93.38 - 101.73: 84 101.73 - 110.08: 4041 110.08 - 118.43: 15896 118.43 - 126.78: 14932 126.78 - 135.12: 358 Bond angle restraints: 35311 Sorted by residual: angle pdb=" N ALA E 156 " pdb=" CA ALA E 156 " pdb=" C ALA E 156 " ideal model delta sigma weight residual 111.07 100.40 10.67 1.07e+00 8.73e-01 9.95e+01 angle pdb=" N GLU B 485 " pdb=" CA GLU B 485 " pdb=" C GLU B 485 " ideal model delta sigma weight residual 112.54 102.94 9.60 1.22e+00 6.72e-01 6.19e+01 angle pdb=" N GLU A 485 " pdb=" CA GLU A 485 " pdb=" C GLU A 485 " ideal model delta sigma weight residual 112.72 103.92 8.80 1.14e+00 7.69e-01 5.96e+01 angle pdb=" N SER F 197 " pdb=" CA SER F 197 " pdb=" C SER F 197 " ideal model delta sigma weight residual 110.97 103.56 7.41 1.09e+00 8.42e-01 4.62e+01 angle pdb=" N GLN B 484 " pdb=" CA GLN B 484 " pdb=" C GLN B 484 " ideal model delta sigma weight residual 113.12 104.96 8.16 1.25e+00 6.40e-01 4.26e+01 ... (remaining 35306 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 14150 17.89 - 35.79: 1235 35.79 - 53.68: 196 53.68 - 71.58: 42 71.58 - 89.47: 28 Dihedral angle restraints: 15651 sinusoidal: 6126 harmonic: 9525 Sorted by residual: dihedral pdb=" CA LEU H 325 " pdb=" C LEU H 325 " pdb=" N HIS H 326 " pdb=" CA HIS H 326 " ideal model delta harmonic sigma weight residual 180.00 153.67 26.33 0 5.00e+00 4.00e-02 2.77e+01 dihedral pdb=" CA GLU C 292 " pdb=" C GLU C 292 " pdb=" N MET C 293 " pdb=" CA MET C 293 " ideal model delta harmonic sigma weight residual -180.00 -154.74 -25.26 0 5.00e+00 4.00e-02 2.55e+01 dihedral pdb=" CA ASP B 493 " pdb=" C ASP B 493 " pdb=" N LYS B 494 " pdb=" CA LYS B 494 " ideal model delta harmonic sigma weight residual 180.00 155.75 24.25 0 5.00e+00 4.00e-02 2.35e+01 ... (remaining 15648 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 3467 0.072 - 0.144: 367 0.144 - 0.215: 20 0.215 - 0.287: 1 0.287 - 0.359: 1 Chirality restraints: 3856 Sorted by residual: chirality pdb=" CG LEU B 483 " pdb=" CB LEU B 483 " pdb=" CD1 LEU B 483 " pdb=" CD2 LEU B 483 " both_signs ideal model delta sigma weight residual False -2.59 -2.23 -0.36 2.00e-01 2.50e+01 3.22e+00 chirality pdb=" CA ASN C 148 " pdb=" N ASN C 148 " pdb=" C ASN C 148 " pdb=" CB ASN C 148 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.89e+00 chirality pdb=" CB ILE C 395 " pdb=" CA ILE C 395 " pdb=" CG1 ILE C 395 " pdb=" CG2 ILE C 395 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.21 2.00e-01 2.50e+01 1.06e+00 ... (remaining 3853 not shown) Planarity restraints: 4594 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU B 227 " -0.026 2.00e-02 2.50e+03 5.39e-02 2.91e+01 pdb=" C LEU B 227 " 0.093 2.00e-02 2.50e+03 pdb=" O LEU B 227 " -0.035 2.00e-02 2.50e+03 pdb=" N GLY B 228 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG F 414 " -0.024 2.00e-02 2.50e+03 4.80e-02 2.31e+01 pdb=" C ARG F 414 " 0.083 2.00e-02 2.50e+03 pdb=" O ARG F 414 " -0.031 2.00e-02 2.50e+03 pdb=" N LYS F 415 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA D 430 " -0.018 2.00e-02 2.50e+03 3.69e-02 1.36e+01 pdb=" C ALA D 430 " 0.064 2.00e-02 2.50e+03 pdb=" O ALA D 430 " -0.024 2.00e-02 2.50e+03 pdb=" N MET D 431 " -0.021 2.00e-02 2.50e+03 ... (remaining 4591 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 3061 2.74 - 3.28: 29111 3.28 - 3.82: 44265 3.82 - 4.36: 51423 4.36 - 4.90: 81496 Nonbonded interactions: 209356 Sorted by model distance: nonbonded pdb=" OG1 THR B 342 " pdb=" OD1 ASN B 345 " model vdw 2.205 3.040 nonbonded pdb=" OH TYR G 261 " pdb=" O ARG G 269 " model vdw 2.208 3.040 nonbonded pdb=" O TRP D 454 " pdb=" OG SER D 457 " model vdw 2.214 3.040 nonbonded pdb=" O HIS G 302 " pdb=" OG SER G 305 " model vdw 2.220 3.040 nonbonded pdb=" O MET C 179 " pdb=" NH2 ARG C 240 " model vdw 2.222 3.120 ... (remaining 209351 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 106 through 460 or resid 464 through 486 or resid 498 thro \ ugh 500 or (resid 501 through 502 and (name N or name CA or name C or name O )) \ or resid 503 through 508)) selection = (chain 'B' and (resid 106 through 460 or resid 464 through 486 or resid 498 thro \ ugh 500 or (resid 501 through 502 and (name N or name CA or name C or name O )) \ or resid 503 through 508)) selection = (chain 'C' and (resid 106 through 460 or resid 464 through 486 or resid 498 thro \ ugh 500 or (resid 501 through 502 and (name N or name CA or name C or name O )) \ or resid 503 through 508)) selection = (chain 'D' and (resid 106 through 460 or resid 464 through 486 or resid 498 thro \ ugh 500 or (resid 501 through 502 and (name N or name CA or name C or name O )) \ or resid 503 through 508)) selection = (chain 'E' and (resid 106 through 460 or resid 464 through 486 or resid 498 thro \ ugh 501 or (resid 502 and (name N or name CA or name C or name O )) or resid 503 \ through 508)) selection = (chain 'F' and (resid 106 through 460 or resid 464 through 486 or resid 488 thro \ ugh 496 or (resid 497 through 498 and (name N or name CA or name C or name O )) \ or resid 499 through 504)) selection = (chain 'G' and (resid 106 through 486 or resid 488 through 496 or (resid 497 thr \ ough 498 and (name N or name CA or name C or name O )) or resid 499 through 504) \ ) selection = (chain 'H' and (resid 106 through 460 or resid 464 through 486 or resid 488 thro \ ugh 496 or (resid 497 through 498 and (name N or name CA or name C or name O )) \ or resid 499 through 504)) } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.050 Check model and map are aligned: 0.200 Set scattering table: 0.260 Process input model: 68.460 Find NCS groups from input model: 1.370 Set up NCS constraints: 0.090 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: 0.010 Load rotamer database and sin/cos tables:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 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 : 0.005 0.088 26015 Z= 0.305 Angle : 0.799 10.835 35311 Z= 0.440 Chirality : 0.044 0.359 3856 Planarity : 0.006 0.091 4594 Dihedral : 14.084 89.469 9561 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 22.06 Ramachandran Plot: Outliers : 0.55 % Allowed : 8.04 % Favored : 91.40 % Rotamer: Outliers : 1.23 % Allowed : 0.61 % Favored : 98.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.14), residues: 3245 helix: -0.36 (0.12), residues: 1778 sheet: -0.73 (1.70), residues: 10 loop : -1.78 (0.16), residues: 1457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP F 454 HIS 0.011 0.001 HIS E 302 PHE 0.031 0.002 PHE H 311 TYR 0.028 0.001 TYR E 428 ARG 0.010 0.001 ARG G 391 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 2723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 462 time to evaluate : 2.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 LYS cc_start: 0.8851 (OUTLIER) cc_final: 0.8522 (mmtt) REVERT: A 179 MET cc_start: 0.8498 (mmm) cc_final: 0.8182 (mmm) REVERT: A 293 MET cc_start: 0.6366 (mmp) cc_final: 0.6089 (mmp) REVERT: A 422 PHE cc_start: 0.9236 (t80) cc_final: 0.8950 (t80) REVERT: C 124 ARG cc_start: 0.7599 (OUTLIER) cc_final: 0.6252 (tpp80) REVERT: C 229 LYS cc_start: 0.8577 (mmmt) cc_final: 0.8357 (mptt) REVERT: C 297 THR cc_start: 0.9071 (p) cc_final: 0.8440 (p) REVERT: C 450 TYR cc_start: 0.8103 (m-10) cc_final: 0.7660 (m-10) REVERT: D 124 ARG cc_start: 0.7591 (OUTLIER) cc_final: 0.6651 (mmm160) REVERT: D 193 MET cc_start: 0.8605 (mmt) cc_final: 0.8118 (mmt) REVERT: D 334 LEU cc_start: 0.9150 (tt) cc_final: 0.8580 (tt) REVERT: D 336 MET cc_start: 0.8822 (tmm) cc_final: 0.8584 (ppp) REVERT: D 337 LEU cc_start: 0.7448 (tp) cc_final: 0.7080 (tp) REVERT: E 409 GLU cc_start: 0.8458 (mm-30) cc_final: 0.8128 (pm20) REVERT: F 175 ILE cc_start: 0.9274 (mm) cc_final: 0.8966 (mm) REVERT: F 217 GLN cc_start: 0.9407 (pt0) cc_final: 0.9140 (tp40) REVERT: F 220 ASP cc_start: 0.9086 (OUTLIER) cc_final: 0.8785 (m-30) REVERT: G 227 LEU cc_start: 0.8839 (tp) cc_final: 0.8563 (tp) REVERT: G 261 TYR cc_start: 0.7833 (t80) cc_final: 0.7374 (t80) REVERT: G 262 MET cc_start: 0.8016 (ppp) cc_final: 0.7518 (ppp) REVERT: H 276 ARG cc_start: 0.8296 (mmp80) cc_final: 0.8068 (mmp80) REVERT: H 379 ARG cc_start: 0.8625 (tmt-80) cc_final: 0.8400 (tpt90) REVERT: H 383 GLU cc_start: 0.8725 (pp20) cc_final: 0.7960 (tp30) REVERT: H 431 MET cc_start: 0.6026 (mmp) cc_final: 0.5683 (mmm) outliers start: 32 outliers final: 13 residues processed: 490 average time/residue: 0.3779 time to fit residues: 289.5263 Evaluate side-chains 390 residues out of total 2723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 373 time to evaluate : 3.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 273 optimal weight: 30.0000 chunk 245 optimal weight: 40.0000 chunk 136 optimal weight: 0.7980 chunk 83 optimal weight: 2.9990 chunk 165 optimal weight: 50.0000 chunk 131 optimal weight: 2.9990 chunk 253 optimal weight: 10.0000 chunk 98 optimal weight: 9.9990 chunk 154 optimal weight: 9.9990 chunk 189 optimal weight: 30.0000 chunk 294 optimal weight: 10.0000 overall best weight: 5.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 294 ASN B 338 ASN ** C 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 338 ASN E 164 GLN E 177 GLN ** E 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 177 GLN ** F 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 288 HIS H 181 HIS H 204 ASN ** H 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.1179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 26015 Z= 0.318 Angle : 0.704 10.236 35311 Z= 0.363 Chirality : 0.043 0.197 3856 Planarity : 0.006 0.056 4594 Dihedral : 5.112 25.247 3636 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 16.90 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.83 % Favored : 92.05 % Rotamer: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.14), residues: 3245 helix: -0.25 (0.12), residues: 1827 sheet: -0.49 (1.86), residues: 10 loop : -1.82 (0.16), residues: 1408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 158 HIS 0.008 0.001 HIS F 302 PHE 0.022 0.002 PHE B 422 TYR 0.024 0.002 TYR B 450 ARG 0.006 0.001 ARG F 486 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 2723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 465 time to evaluate : 3.019 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 MET cc_start: 0.6448 (mmp) cc_final: 0.5960 (mmp) REVERT: A 422 PHE cc_start: 0.9261 (t80) cc_final: 0.8941 (t80) REVERT: B 179 MET cc_start: 0.8774 (mpp) cc_final: 0.8050 (mpp) REVERT: B 450 TYR cc_start: 0.8031 (m-80) cc_final: 0.7692 (m-80) REVERT: C 297 THR cc_start: 0.9073 (p) cc_final: 0.8445 (t) REVERT: C 450 TYR cc_start: 0.8168 (m-10) cc_final: 0.7776 (m-10) REVERT: C 466 MET cc_start: 0.8760 (pmm) cc_final: 0.8530 (pmm) REVERT: D 148 ASN cc_start: 0.8883 (t0) cc_final: 0.8499 (t0) REVERT: D 337 LEU cc_start: 0.7571 (tp) cc_final: 0.7269 (tp) REVERT: D 406 LEU cc_start: 0.8995 (pp) cc_final: 0.8564 (mt) REVERT: E 409 GLU cc_start: 0.8554 (mm-30) cc_final: 0.8185 (pm20) REVERT: F 175 ILE cc_start: 0.9303 (mm) cc_final: 0.8964 (mm) REVERT: F 257 GLU cc_start: 0.8056 (pm20) cc_final: 0.7671 (pm20) REVERT: G 227 LEU cc_start: 0.8870 (tp) cc_final: 0.8577 (tp) REVERT: G 261 TYR cc_start: 0.8112 (t80) cc_final: 0.7705 (t80) REVERT: G 360 MET cc_start: 0.2220 (mmm) cc_final: 0.1847 (mmm) REVERT: H 379 ARG cc_start: 0.8681 (tmt-80) cc_final: 0.8085 (tpt90) REVERT: H 383 GLU cc_start: 0.8749 (pp20) cc_final: 0.8528 (pp20) outliers start: 0 outliers final: 0 residues processed: 465 average time/residue: 0.3557 time to fit residues: 263.1026 Evaluate side-chains 358 residues out of total 2723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 358 time to evaluate : 3.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 163 optimal weight: 10.0000 chunk 91 optimal weight: 1.9990 chunk 244 optimal weight: 1.9990 chunk 200 optimal weight: 0.1980 chunk 81 optimal weight: 30.0000 chunk 294 optimal weight: 20.0000 chunk 318 optimal weight: 2.9990 chunk 262 optimal weight: 30.0000 chunk 292 optimal weight: 10.0000 chunk 100 optimal weight: 4.9990 chunk 236 optimal weight: 2.9990 overall best weight: 2.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 ASN ** A 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 365 HIS D 210 GLN ** D 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 365 HIS D 469 GLN E 177 GLN E 204 ASN ** F 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 181 HIS H 200 HIS ** H 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 26015 Z= 0.207 Angle : 0.641 9.437 35311 Z= 0.325 Chirality : 0.042 0.154 3856 Planarity : 0.005 0.073 4594 Dihedral : 4.882 26.708 3636 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.56 % Favored : 93.31 % Rotamer: Outliers : 0.08 % Allowed : 3.49 % Favored : 96.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.14), residues: 3245 helix: -0.04 (0.12), residues: 1832 sheet: -0.40 (1.93), residues: 10 loop : -1.67 (0.17), residues: 1403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP G 454 HIS 0.008 0.001 HIS E 165 PHE 0.025 0.002 PHE H 438 TYR 0.023 0.001 TYR D 450 ARG 0.005 0.000 ARG B 240 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 503 residues out of total 2723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 501 time to evaluate : 2.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 422 PHE cc_start: 0.9241 (t80) cc_final: 0.8916 (t80) REVERT: B 179 MET cc_start: 0.8385 (mpp) cc_final: 0.7997 (mpp) REVERT: B 450 TYR cc_start: 0.7922 (m-80) cc_final: 0.7722 (m-80) REVERT: C 297 THR cc_start: 0.8900 (p) cc_final: 0.8196 (t) REVERT: C 365 HIS cc_start: 0.6524 (m-70) cc_final: 0.6207 (m90) REVERT: C 450 TYR cc_start: 0.8020 (m-10) cc_final: 0.7572 (m-10) REVERT: D 112 CYS cc_start: 0.7450 (m) cc_final: 0.7151 (m) REVERT: D 186 MET cc_start: 0.8499 (mmm) cc_final: 0.8255 (tpp) REVERT: D 193 MET cc_start: 0.9034 (mmp) cc_final: 0.8745 (mmt) REVERT: D 257 GLU cc_start: 0.8721 (mp0) cc_final: 0.8400 (mp0) REVERT: D 337 LEU cc_start: 0.7417 (tp) cc_final: 0.6902 (pp) REVERT: D 406 LEU cc_start: 0.8973 (pp) cc_final: 0.8541 (mt) REVERT: D 466 MET cc_start: 0.8345 (pmm) cc_final: 0.8127 (pmm) REVERT: E 155 LEU cc_start: 0.8120 (tt) cc_final: 0.7668 (pp) REVERT: E 409 GLU cc_start: 0.8653 (mm-30) cc_final: 0.8222 (pm20) REVERT: F 174 ASP cc_start: 0.9659 (m-30) cc_final: 0.9407 (m-30) REVERT: F 175 ILE cc_start: 0.9306 (mm) cc_final: 0.9011 (mm) REVERT: F 450 TYR cc_start: 0.8730 (m-80) cc_final: 0.8516 (m-80) REVERT: G 145 MET cc_start: 0.7729 (mmm) cc_final: 0.7264 (mmm) REVERT: G 227 LEU cc_start: 0.8771 (tp) cc_final: 0.8448 (tp) REVERT: G 261 TYR cc_start: 0.8189 (t80) cc_final: 0.7760 (t80) REVERT: G 360 MET cc_start: 0.2456 (mmm) cc_final: 0.2093 (mmm) REVERT: G 447 MET cc_start: 0.8204 (ptt) cc_final: 0.7466 (ptt) REVERT: G 450 TYR cc_start: 0.8000 (m-10) cc_final: 0.7609 (m-10) REVERT: H 276 ARG cc_start: 0.8364 (mmp80) cc_final: 0.8159 (mmp80) REVERT: H 379 ARG cc_start: 0.8670 (tmt-80) cc_final: 0.7999 (tpt90) REVERT: H 383 GLU cc_start: 0.8769 (pp20) cc_final: 0.8499 (pp20) REVERT: H 429 ARG cc_start: 0.7338 (tmt170) cc_final: 0.7022 (tpt90) REVERT: H 450 TYR cc_start: 0.8886 (m-10) cc_final: 0.8556 (m-80) outliers start: 2 outliers final: 0 residues processed: 501 average time/residue: 0.3605 time to fit residues: 289.3832 Evaluate side-chains 381 residues out of total 2723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 381 time to evaluate : 3.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 291 optimal weight: 7.9990 chunk 221 optimal weight: 40.0000 chunk 152 optimal weight: 8.9990 chunk 32 optimal weight: 10.0000 chunk 140 optimal weight: 6.9990 chunk 197 optimal weight: 40.0000 chunk 295 optimal weight: 4.9990 chunk 313 optimal weight: 2.9990 chunk 154 optimal weight: 6.9990 chunk 280 optimal weight: 20.0000 chunk 84 optimal weight: 2.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 469 GLN ** E 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 177 GLN E 204 ASN H 181 HIS ** H 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 26015 Z= 0.293 Angle : 0.673 9.587 35311 Z= 0.343 Chirality : 0.043 0.169 3856 Planarity : 0.005 0.059 4594 Dihedral : 4.919 24.483 3636 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 16.72 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.01 % Favored : 91.90 % Rotamer: Outliers : 0.04 % Allowed : 3.49 % Favored : 96.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.14), residues: 3245 helix: -0.09 (0.12), residues: 1842 sheet: -0.26 (1.99), residues: 10 loop : -1.66 (0.17), residues: 1393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP G 158 HIS 0.006 0.001 HIS F 302 PHE 0.026 0.002 PHE B 422 TYR 0.024 0.002 TYR A 322 ARG 0.005 0.000 ARG E 429 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 2723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 464 time to evaluate : 2.988 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: A 422 PHE cc_start: 0.9249 (t80) cc_final: 0.8943 (t80) REVERT: B 164 GLN cc_start: 0.8163 (tp40) cc_final: 0.7852 (tp40) REVERT: B 179 MET cc_start: 0.8702 (mpp) cc_final: 0.8147 (mpp) REVERT: B 276 ARG cc_start: 0.8857 (mmp-170) cc_final: 0.8463 (mmp80) REVERT: B 450 TYR cc_start: 0.7985 (m-80) cc_final: 0.7722 (m-80) REVERT: C 297 THR cc_start: 0.8972 (p) cc_final: 0.8452 (t) REVERT: C 365 HIS cc_start: 0.6780 (m-70) cc_final: 0.6526 (m90) REVERT: C 411 PHE cc_start: 0.8788 (m-80) cc_final: 0.8548 (m-10) REVERT: C 450 TYR cc_start: 0.8037 (m-10) cc_final: 0.7606 (m-10) REVERT: D 112 CYS cc_start: 0.7364 (m) cc_final: 0.7143 (m) REVERT: D 337 LEU cc_start: 0.7370 (tp) cc_final: 0.6909 (pp) REVERT: D 397 VAL cc_start: 0.8752 (t) cc_final: 0.8504 (t) REVERT: D 406 LEU cc_start: 0.9023 (pp) cc_final: 0.8571 (mt) REVERT: E 155 LEU cc_start: 0.8327 (tt) cc_final: 0.7939 (pp) REVERT: E 179 MET cc_start: 0.7420 (mmt) cc_final: 0.6813 (mmt) REVERT: E 297 THR cc_start: 0.8568 (m) cc_final: 0.7992 (p) REVERT: E 409 GLU cc_start: 0.8654 (mm-30) cc_final: 0.8252 (pm20) REVERT: F 174 ASP cc_start: 0.9681 (m-30) cc_final: 0.9435 (m-30) REVERT: F 175 ILE cc_start: 0.9220 (mm) cc_final: 0.8871 (mm) REVERT: F 257 GLU cc_start: 0.8107 (pm20) cc_final: 0.7704 (pm20) REVERT: G 261 TYR cc_start: 0.8204 (t80) cc_final: 0.7960 (t80) REVERT: G 360 MET cc_start: 0.2223 (mmm) cc_final: 0.1789 (mmm) REVERT: G 447 MET cc_start: 0.8448 (ptt) cc_final: 0.7909 (ptt) REVERT: G 450 TYR cc_start: 0.8041 (m-10) cc_final: 0.7702 (m-80) REVERT: H 379 ARG cc_start: 0.8679 (tmt-80) cc_final: 0.8001 (tpt90) REVERT: H 383 GLU cc_start: 0.8832 (pp20) cc_final: 0.8585 (pp20) REVERT: H 429 ARG cc_start: 0.7569 (tmt170) cc_final: 0.7199 (tpt90) outliers start: 1 outliers final: 0 residues processed: 465 average time/residue: 0.3625 time to fit residues: 264.4393 Evaluate side-chains 358 residues out of total 2723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 358 time to evaluate : 2.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 260 optimal weight: 20.0000 chunk 177 optimal weight: 40.0000 chunk 4 optimal weight: 6.9990 chunk 233 optimal weight: 30.0000 chunk 129 optimal weight: 1.9990 chunk 267 optimal weight: 7.9990 chunk 216 optimal weight: 9.9990 chunk 0 optimal weight: 30.0000 chunk 159 optimal weight: 8.9990 chunk 281 optimal weight: 5.9990 chunk 79 optimal weight: 0.0970 overall best weight: 4.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 HIS ** A 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 326 HIS D 210 GLN D 291 HIS ** D 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 154 GLN ** E 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 177 GLN E 204 ASN E 302 HIS F 177 GLN H 181 HIS ** H 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.1998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 26015 Z= 0.274 Angle : 0.678 11.265 35311 Z= 0.342 Chirality : 0.043 0.170 3856 Planarity : 0.005 0.056 4594 Dihedral : 4.926 24.352 3636 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 16.05 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.73 % Favored : 92.14 % Rotamer: Outliers : 0.04 % Allowed : 3.61 % Favored : 96.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.14), residues: 3245 helix: -0.09 (0.12), residues: 1857 sheet: -0.35 (1.99), residues: 10 loop : -1.69 (0.17), residues: 1378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP G 454 HIS 0.008 0.001 HIS E 302 PHE 0.029 0.002 PHE H 438 TYR 0.021 0.002 TYR F 450 ARG 0.006 0.000 ARG B 301 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 2723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 472 time to evaluate : 3.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 MET cc_start: 0.7217 (mmp) cc_final: 0.6732 (mmp) REVERT: A 422 PHE cc_start: 0.9247 (t80) cc_final: 0.8937 (t80) REVERT: B 164 GLN cc_start: 0.8129 (tp40) cc_final: 0.7843 (tp40) REVERT: B 179 MET cc_start: 0.8811 (mpp) cc_final: 0.8162 (mpp) REVERT: B 276 ARG cc_start: 0.8853 (mmp-170) cc_final: 0.8533 (mmp80) REVERT: B 409 GLU cc_start: 0.8933 (pp20) cc_final: 0.8648 (pp20) REVERT: B 447 MET cc_start: 0.8389 (ttm) cc_final: 0.8186 (ttm) REVERT: B 450 TYR cc_start: 0.7971 (m-10) cc_final: 0.7702 (m-80) REVERT: C 297 THR cc_start: 0.8972 (p) cc_final: 0.8411 (t) REVERT: C 365 HIS cc_start: 0.6704 (m-70) cc_final: 0.6502 (m90) REVERT: C 411 PHE cc_start: 0.8787 (m-80) cc_final: 0.8549 (m-10) REVERT: C 450 TYR cc_start: 0.8063 (m-10) cc_final: 0.7613 (m-10) REVERT: D 112 CYS cc_start: 0.7519 (m) cc_final: 0.7166 (m) REVERT: D 337 LEU cc_start: 0.7401 (tp) cc_final: 0.6905 (pp) REVERT: D 397 VAL cc_start: 0.8768 (t) cc_final: 0.8528 (t) REVERT: D 406 LEU cc_start: 0.9042 (pp) cc_final: 0.8584 (mt) REVERT: E 155 LEU cc_start: 0.8663 (tt) cc_final: 0.8398 (pp) REVERT: E 179 MET cc_start: 0.7730 (mmt) cc_final: 0.7031 (mmt) REVERT: E 193 MET cc_start: 0.8579 (tmm) cc_final: 0.8229 (tmm) REVERT: E 297 THR cc_start: 0.8567 (m) cc_final: 0.8119 (p) REVERT: F 174 ASP cc_start: 0.9654 (m-30) cc_final: 0.9398 (m-30) REVERT: F 175 ILE cc_start: 0.9199 (mm) cc_final: 0.8894 (mm) REVERT: F 257 GLU cc_start: 0.8175 (pm20) cc_final: 0.7723 (pm20) REVERT: G 261 TYR cc_start: 0.8352 (t80) cc_final: 0.7967 (t80) REVERT: G 360 MET cc_start: 0.2272 (mmm) cc_final: 0.1739 (mmm) REVERT: G 447 MET cc_start: 0.8438 (ptt) cc_final: 0.7967 (ptt) REVERT: G 450 TYR cc_start: 0.8085 (m-10) cc_final: 0.7690 (m-80) REVERT: H 121 LEU cc_start: 0.8100 (tp) cc_final: 0.7783 (tp) REVERT: H 379 ARG cc_start: 0.8676 (tmt-80) cc_final: 0.8036 (tpt90) REVERT: H 396 GLU cc_start: 0.7355 (mp0) cc_final: 0.7148 (pm20) REVERT: H 429 ARG cc_start: 0.7461 (tmt170) cc_final: 0.7058 (tpt90) REVERT: H 450 TYR cc_start: 0.8861 (m-10) cc_final: 0.8541 (m-80) outliers start: 1 outliers final: 0 residues processed: 473 average time/residue: 0.3520 time to fit residues: 263.1557 Evaluate side-chains 369 residues out of total 2723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 369 time to evaluate : 2.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 105 optimal weight: 8.9990 chunk 282 optimal weight: 20.0000 chunk 61 optimal weight: 20.0000 chunk 183 optimal weight: 20.0000 chunk 77 optimal weight: 0.1980 chunk 313 optimal weight: 10.0000 chunk 260 optimal weight: 20.0000 chunk 145 optimal weight: 9.9990 chunk 26 optimal weight: 30.0000 chunk 103 optimal weight: 0.9990 chunk 164 optimal weight: 0.4980 overall best weight: 4.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 177 GLN F 177 GLN G 222 GLN H 181 HIS ** H 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 26015 Z= 0.261 Angle : 0.679 12.604 35311 Z= 0.341 Chirality : 0.043 0.170 3856 Planarity : 0.005 0.056 4594 Dihedral : 4.881 23.557 3636 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 16.31 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.73 % Favored : 92.17 % Rotamer: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.14), residues: 3245 helix: -0.03 (0.12), residues: 1848 sheet: -0.27 (2.01), residues: 10 loop : -1.67 (0.17), residues: 1387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP G 158 HIS 0.006 0.001 HIS E 165 PHE 0.030 0.002 PHE H 438 TYR 0.047 0.002 TYR F 450 ARG 0.004 0.000 ARG B 240 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 2723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 465 time to evaluate : 3.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 MET cc_start: 0.6364 (mmp) cc_final: 0.5975 (mmp) REVERT: A 422 PHE cc_start: 0.9245 (t80) cc_final: 0.8952 (t80) REVERT: B 179 MET cc_start: 0.8853 (mpp) cc_final: 0.8143 (mpp) REVERT: B 409 GLU cc_start: 0.8916 (pp20) cc_final: 0.8559 (pp20) REVERT: B 413 LYS cc_start: 0.8758 (mppt) cc_final: 0.8551 (mmtm) REVERT: B 447 MET cc_start: 0.8395 (ttm) cc_final: 0.8191 (ttm) REVERT: B 450 TYR cc_start: 0.7943 (m-10) cc_final: 0.7710 (m-80) REVERT: C 297 THR cc_start: 0.8935 (p) cc_final: 0.8273 (p) REVERT: C 365 HIS cc_start: 0.6820 (m-70) cc_final: 0.6615 (m90) REVERT: C 411 PHE cc_start: 0.8773 (m-80) cc_final: 0.8534 (m-10) REVERT: C 450 TYR cc_start: 0.8011 (m-10) cc_final: 0.7548 (m-10) REVERT: D 112 CYS cc_start: 0.7491 (m) cc_final: 0.7156 (m) REVERT: D 337 LEU cc_start: 0.7450 (tp) cc_final: 0.6971 (pp) REVERT: D 397 VAL cc_start: 0.8765 (t) cc_final: 0.8530 (t) REVERT: D 406 LEU cc_start: 0.9012 (pp) cc_final: 0.8565 (mt) REVERT: E 155 LEU cc_start: 0.8788 (tt) cc_final: 0.8586 (pp) REVERT: E 179 MET cc_start: 0.7857 (mmt) cc_final: 0.7138 (mmt) REVERT: E 297 THR cc_start: 0.8671 (m) cc_final: 0.8295 (p) REVERT: E 466 MET cc_start: 0.6811 (pmm) cc_final: 0.6603 (pmm) REVERT: F 174 ASP cc_start: 0.9652 (m-30) cc_final: 0.9368 (m-30) REVERT: F 175 ILE cc_start: 0.9198 (mm) cc_final: 0.8884 (mm) REVERT: F 257 GLU cc_start: 0.8213 (pm20) cc_final: 0.7725 (pm20) REVERT: G 145 MET cc_start: 0.7496 (mmm) cc_final: 0.7258 (mmm) REVERT: G 261 TYR cc_start: 0.8359 (t80) cc_final: 0.8016 (t80) REVERT: G 360 MET cc_start: 0.2362 (mmm) cc_final: 0.1834 (mmm) REVERT: G 447 MET cc_start: 0.8433 (ptt) cc_final: 0.7995 (ptt) REVERT: G 450 TYR cc_start: 0.8077 (m-10) cc_final: 0.7736 (m-80) REVERT: H 379 ARG cc_start: 0.8634 (tmt-80) cc_final: 0.8060 (tpt90) REVERT: H 383 GLU cc_start: 0.8622 (pp20) cc_final: 0.8358 (pp20) REVERT: H 429 ARG cc_start: 0.7445 (tmt170) cc_final: 0.7023 (tpt90) REVERT: H 450 TYR cc_start: 0.8809 (m-10) cc_final: 0.8505 (m-80) outliers start: 0 outliers final: 0 residues processed: 465 average time/residue: 0.3527 time to fit residues: 260.5861 Evaluate side-chains 368 residues out of total 2723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 368 time to evaluate : 3.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 302 optimal weight: 8.9990 chunk 35 optimal weight: 6.9990 chunk 178 optimal weight: 10.0000 chunk 228 optimal weight: 30.0000 chunk 177 optimal weight: 40.0000 chunk 263 optimal weight: 7.9990 chunk 175 optimal weight: 10.0000 chunk 312 optimal weight: 7.9990 chunk 195 optimal weight: 7.9990 chunk 190 optimal weight: 10.0000 chunk 144 optimal weight: 0.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 210 GLN ** D 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 177 GLN E 294 ASN H 181 HIS ** H 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 26015 Z= 0.347 Angle : 0.737 12.839 35311 Z= 0.373 Chirality : 0.045 0.209 3856 Planarity : 0.006 0.092 4594 Dihedral : 5.089 23.868 3636 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 18.49 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.32 % Favored : 91.59 % Rotamer: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.14), residues: 3245 helix: -0.23 (0.12), residues: 1850 sheet: -0.65 (1.86), residues: 10 loop : -1.72 (0.17), residues: 1385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP F 454 HIS 0.007 0.001 HIS G 326 PHE 0.038 0.002 PHE A 285 TYR 0.036 0.002 TYR F 450 ARG 0.011 0.001 ARG D 276 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 2723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 458 time to evaluate : 2.801 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 422 PHE cc_start: 0.9255 (t80) cc_final: 0.8956 (t80) REVERT: B 179 MET cc_start: 0.8743 (mpp) cc_final: 0.8324 (mpp) REVERT: B 409 GLU cc_start: 0.8953 (pp20) cc_final: 0.8573 (pp20) REVERT: B 413 LYS cc_start: 0.8709 (mppt) cc_final: 0.8483 (mmtm) REVERT: B 447 MET cc_start: 0.8493 (ttm) cc_final: 0.8225 (ttm) REVERT: B 450 TYR cc_start: 0.7971 (m-10) cc_final: 0.7716 (m-80) REVERT: C 297 THR cc_start: 0.8993 (p) cc_final: 0.8443 (p) REVERT: C 365 HIS cc_start: 0.6789 (m-70) cc_final: 0.6567 (m90) REVERT: C 411 PHE cc_start: 0.8813 (m-80) cc_final: 0.8571 (m-10) REVERT: C 450 TYR cc_start: 0.8171 (m-10) cc_final: 0.7693 (m-10) REVERT: D 406 LEU cc_start: 0.9061 (pp) cc_final: 0.8566 (mt) REVERT: E 179 MET cc_start: 0.8213 (mmt) cc_final: 0.7657 (mmt) REVERT: E 193 MET cc_start: 0.8625 (tmm) cc_final: 0.8333 (tmm) REVERT: E 297 THR cc_start: 0.8665 (m) cc_final: 0.8360 (p) REVERT: F 174 ASP cc_start: 0.9666 (m-30) cc_final: 0.9395 (m-30) REVERT: F 175 ILE cc_start: 0.9153 (mm) cc_final: 0.8854 (mm) REVERT: F 257 GLU cc_start: 0.8256 (pm20) cc_final: 0.7815 (pm20) REVERT: G 145 MET cc_start: 0.7735 (mmm) cc_final: 0.7410 (mmm) REVERT: G 261 TYR cc_start: 0.8396 (t80) cc_final: 0.8054 (t80) REVERT: G 360 MET cc_start: 0.2413 (mmm) cc_final: 0.1808 (mmm) REVERT: G 447 MET cc_start: 0.8584 (ptt) cc_final: 0.7809 (ptt) REVERT: G 450 TYR cc_start: 0.8064 (m-10) cc_final: 0.7746 (m-80) REVERT: H 348 ASP cc_start: 0.8782 (t70) cc_final: 0.8430 (m-30) REVERT: H 379 ARG cc_start: 0.8660 (tmt-80) cc_final: 0.8091 (tpt90) REVERT: H 383 GLU cc_start: 0.8646 (pp20) cc_final: 0.8409 (pp20) REVERT: H 429 ARG cc_start: 0.7533 (tmt170) cc_final: 0.7035 (tpt90) outliers start: 0 outliers final: 0 residues processed: 458 average time/residue: 0.3567 time to fit residues: 258.4523 Evaluate side-chains 355 residues out of total 2723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 355 time to evaluate : 2.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 193 optimal weight: 10.0000 chunk 124 optimal weight: 0.0470 chunk 186 optimal weight: 10.0000 chunk 94 optimal weight: 2.9990 chunk 61 optimal weight: 20.0000 chunk 60 optimal weight: 5.9990 chunk 198 optimal weight: 9.9990 chunk 212 optimal weight: 20.0000 chunk 154 optimal weight: 0.9980 chunk 29 optimal weight: 6.9990 chunk 245 optimal weight: 4.9990 overall best weight: 3.0084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 355 ASN C 469 GLN ** D 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 177 GLN H 181 HIS H 330 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 26015 Z= 0.231 Angle : 0.686 13.540 35311 Z= 0.341 Chirality : 0.043 0.182 3856 Planarity : 0.005 0.058 4594 Dihedral : 4.900 24.210 3636 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 15.47 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.30 % Favored : 92.60 % Rotamer: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.15), residues: 3245 helix: 0.06 (0.12), residues: 1847 sheet: -0.34 (1.95), residues: 10 loop : -1.64 (0.17), residues: 1388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP F 454 HIS 0.006 0.001 HIS G 291 PHE 0.042 0.002 PHE F 437 TYR 0.037 0.001 TYR F 450 ARG 0.009 0.000 ARG F 240 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 2723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 475 time to evaluate : 3.056 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 MET cc_start: 0.6898 (mmp) cc_final: 0.6543 (mmp) REVERT: A 422 PHE cc_start: 0.9211 (t80) cc_final: 0.8945 (t80) REVERT: B 164 GLN cc_start: 0.8284 (tp40) cc_final: 0.7998 (tp40) REVERT: B 179 MET cc_start: 0.8647 (mpp) cc_final: 0.8224 (mpp) REVERT: B 409 GLU cc_start: 0.8958 (pp20) cc_final: 0.8646 (pp20) REVERT: B 447 MET cc_start: 0.8334 (ttm) cc_final: 0.8121 (ttm) REVERT: B 450 TYR cc_start: 0.7984 (m-10) cc_final: 0.7755 (m-80) REVERT: C 262 MET cc_start: 0.7809 (mtm) cc_final: 0.7292 (mtt) REVERT: C 297 THR cc_start: 0.8916 (p) cc_final: 0.8188 (p) REVERT: C 365 HIS cc_start: 0.6664 (m-70) cc_final: 0.6426 (m90) REVERT: C 411 PHE cc_start: 0.8741 (m-80) cc_final: 0.8492 (m-80) REVERT: C 450 TYR cc_start: 0.8045 (m-10) cc_final: 0.7534 (m-10) REVERT: D 112 CYS cc_start: 0.7481 (m) cc_final: 0.7060 (m) REVERT: D 325 LEU cc_start: 0.9241 (mp) cc_final: 0.8903 (pt) REVERT: D 337 LEU cc_start: 0.7812 (tp) cc_final: 0.7209 (pp) REVERT: D 397 VAL cc_start: 0.8782 (t) cc_final: 0.8581 (t) REVERT: D 406 LEU cc_start: 0.9037 (pp) cc_final: 0.8577 (mt) REVERT: E 179 MET cc_start: 0.8035 (mmt) cc_final: 0.7658 (mmt) REVERT: E 297 THR cc_start: 0.8678 (m) cc_final: 0.8399 (p) REVERT: E 409 GLU cc_start: 0.8549 (mm-30) cc_final: 0.8256 (pm20) REVERT: F 174 ASP cc_start: 0.9655 (m-30) cc_final: 0.9369 (m-30) REVERT: F 175 ILE cc_start: 0.9158 (mm) cc_final: 0.8879 (mm) REVERT: G 145 MET cc_start: 0.7684 (mmm) cc_final: 0.7465 (mmm) REVERT: G 261 TYR cc_start: 0.8321 (t80) cc_final: 0.7995 (t80) REVERT: G 447 MET cc_start: 0.8496 (ptt) cc_final: 0.8179 (ptt) REVERT: G 450 TYR cc_start: 0.8142 (m-10) cc_final: 0.7754 (m-80) REVERT: H 379 ARG cc_start: 0.8595 (tmt-80) cc_final: 0.8045 (tpt90) REVERT: H 383 GLU cc_start: 0.8614 (pp20) cc_final: 0.8367 (pp20) REVERT: H 450 TYR cc_start: 0.8744 (m-10) cc_final: 0.8383 (m-80) outliers start: 0 outliers final: 0 residues processed: 475 average time/residue: 0.3601 time to fit residues: 269.6822 Evaluate side-chains 369 residues out of total 2723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 369 time to evaluate : 3.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 284 optimal weight: 50.0000 chunk 299 optimal weight: 0.9980 chunk 272 optimal weight: 20.0000 chunk 291 optimal weight: 10.0000 chunk 175 optimal weight: 0.9990 chunk 126 optimal weight: 2.9990 chunk 228 optimal weight: 9.9990 chunk 89 optimal weight: 7.9990 chunk 262 optimal weight: 20.0000 chunk 275 optimal weight: 5.9990 chunk 289 optimal weight: 0.0370 overall best weight: 2.2064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 HIS ** B 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 210 GLN ** D 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 177 GLN ** F 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 181 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.2488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 26015 Z= 0.214 Angle : 0.686 14.951 35311 Z= 0.340 Chirality : 0.043 0.276 3856 Planarity : 0.005 0.058 4594 Dihedral : 4.798 23.494 3636 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 15.39 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.12 % Favored : 92.76 % Rotamer: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.15), residues: 3245 helix: 0.12 (0.12), residues: 1848 sheet: None (None), residues: 0 loop : -1.57 (0.17), residues: 1397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP F 454 HIS 0.005 0.001 HIS F 302 PHE 0.042 0.002 PHE B 442 TYR 0.036 0.001 TYR F 450 ARG 0.008 0.000 ARG B 429 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 2723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 472 time to evaluate : 3.155 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 MET cc_start: 0.7144 (mmp) cc_final: 0.6729 (mmp) REVERT: A 422 PHE cc_start: 0.9173 (t80) cc_final: 0.8926 (t80) REVERT: A 431 MET cc_start: 0.5044 (tpt) cc_final: 0.4803 (tpt) REVERT: A 483 LEU cc_start: 0.8889 (mm) cc_final: 0.8533 (tt) REVERT: B 164 GLN cc_start: 0.8249 (tp40) cc_final: 0.7968 (tp40) REVERT: B 179 MET cc_start: 0.8594 (mpp) cc_final: 0.8169 (mpp) REVERT: B 409 GLU cc_start: 0.8868 (pp20) cc_final: 0.8590 (pp20) REVERT: B 413 LYS cc_start: 0.8868 (mppt) cc_final: 0.8509 (mmtm) REVERT: C 262 MET cc_start: 0.7751 (mtm) cc_final: 0.7280 (mtm) REVERT: C 297 THR cc_start: 0.8884 (p) cc_final: 0.8038 (p) REVERT: C 411 PHE cc_start: 0.8739 (m-80) cc_final: 0.8450 (m-10) REVERT: C 450 TYR cc_start: 0.7920 (m-10) cc_final: 0.7509 (m-10) REVERT: D 112 CYS cc_start: 0.7407 (m) cc_final: 0.7024 (m) REVERT: D 337 LEU cc_start: 0.7733 (tp) cc_final: 0.7151 (pp) REVERT: D 397 VAL cc_start: 0.8743 (t) cc_final: 0.8534 (t) REVERT: D 406 LEU cc_start: 0.9033 (pp) cc_final: 0.8586 (mt) REVERT: E 179 MET cc_start: 0.8124 (mmt) cc_final: 0.7493 (mmt) REVERT: E 297 THR cc_start: 0.8771 (m) cc_final: 0.8539 (p) REVERT: E 409 GLU cc_start: 0.8572 (mm-30) cc_final: 0.8283 (pm20) REVERT: E 450 TYR cc_start: 0.8459 (m-10) cc_final: 0.7885 (m-80) REVERT: E 466 MET cc_start: 0.6687 (pmm) cc_final: 0.6297 (pmm) REVERT: F 174 ASP cc_start: 0.9648 (m-30) cc_final: 0.9371 (m-30) REVERT: F 175 ILE cc_start: 0.9174 (mm) cc_final: 0.8725 (mm) REVERT: G 261 TYR cc_start: 0.8343 (t80) cc_final: 0.7982 (t80) REVERT: G 447 MET cc_start: 0.8580 (ptt) cc_final: 0.8279 (ptt) REVERT: G 450 TYR cc_start: 0.8116 (m-10) cc_final: 0.7748 (m-80) REVERT: H 181 HIS cc_start: 0.6143 (p90) cc_final: 0.5895 (p-80) REVERT: H 276 ARG cc_start: 0.8229 (mmp80) cc_final: 0.7849 (mmm160) REVERT: H 348 ASP cc_start: 0.8721 (t70) cc_final: 0.8356 (m-30) REVERT: H 379 ARG cc_start: 0.8608 (tmt-80) cc_final: 0.8064 (tpt90) REVERT: H 383 GLU cc_start: 0.8612 (pp20) cc_final: 0.8363 (pp20) REVERT: H 450 TYR cc_start: 0.8831 (m-10) cc_final: 0.8425 (m-80) outliers start: 0 outliers final: 0 residues processed: 472 average time/residue: 0.3509 time to fit residues: 263.1417 Evaluate side-chains 371 residues out of total 2723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 371 time to evaluate : 3.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 191 optimal weight: 7.9990 chunk 307 optimal weight: 4.9990 chunk 187 optimal weight: 30.0000 chunk 145 optimal weight: 7.9990 chunk 213 optimal weight: 0.5980 chunk 322 optimal weight: 7.9990 chunk 297 optimal weight: 6.9990 chunk 257 optimal weight: 5.9990 chunk 26 optimal weight: 30.0000 chunk 198 optimal weight: 3.9990 chunk 157 optimal weight: 4.9990 overall best weight: 4.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 177 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.2555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 26015 Z= 0.268 Angle : 0.711 12.923 35311 Z= 0.354 Chirality : 0.044 0.214 3856 Planarity : 0.005 0.072 4594 Dihedral : 4.859 23.635 3636 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 16.42 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.77 % Favored : 92.14 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.15), residues: 3245 helix: 0.05 (0.12), residues: 1853 sheet: -0.26 (1.91), residues: 10 loop : -1.60 (0.17), residues: 1382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP F 454 HIS 0.006 0.001 HIS H 479 PHE 0.028 0.002 PHE F 437 TYR 0.037 0.002 TYR A 142 ARG 0.013 0.001 ARG H 414 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 2723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 460 time to evaluate : 3.263 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: A 117 ASP cc_start: 0.8386 (m-30) cc_final: 0.7250 (p0) REVERT: A 422 PHE cc_start: 0.9207 (t80) cc_final: 0.8949 (t80) REVERT: A 483 LEU cc_start: 0.8877 (mm) cc_final: 0.8514 (tt) REVERT: B 164 GLN cc_start: 0.8327 (tp40) cc_final: 0.8029 (tp40) REVERT: B 179 MET cc_start: 0.8704 (mpp) cc_final: 0.8208 (mpp) REVERT: B 409 GLU cc_start: 0.8931 (pp20) cc_final: 0.8633 (pp20) REVERT: B 413 LYS cc_start: 0.8828 (mppt) cc_final: 0.8538 (mmtm) REVERT: B 450 TYR cc_start: 0.8104 (m-80) cc_final: 0.7803 (m-80) REVERT: C 297 THR cc_start: 0.8935 (p) cc_final: 0.8103 (p) REVERT: C 411 PHE cc_start: 0.8789 (m-80) cc_final: 0.8490 (m-80) REVERT: C 450 TYR cc_start: 0.8031 (m-10) cc_final: 0.7571 (m-10) REVERT: C 466 MET cc_start: 0.8940 (pmm) cc_final: 0.8424 (pmm) REVERT: D 337 LEU cc_start: 0.7813 (tp) cc_final: 0.7201 (pp) REVERT: D 397 VAL cc_start: 0.8788 (t) cc_final: 0.8571 (t) REVERT: D 406 LEU cc_start: 0.9071 (pp) cc_final: 0.8598 (mt) REVERT: E 179 MET cc_start: 0.8261 (mmt) cc_final: 0.7880 (mmt) REVERT: E 297 THR cc_start: 0.8629 (m) cc_final: 0.8382 (p) REVERT: E 409 GLU cc_start: 0.8559 (mm-30) cc_final: 0.8266 (pm20) REVERT: E 466 MET cc_start: 0.7008 (pmm) cc_final: 0.6660 (pmm) REVERT: F 174 ASP cc_start: 0.9655 (m-30) cc_final: 0.9382 (m-30) REVERT: F 175 ILE cc_start: 0.9176 (mm) cc_final: 0.8733 (mm) REVERT: G 261 TYR cc_start: 0.8413 (t80) cc_final: 0.7997 (t80) REVERT: G 447 MET cc_start: 0.8623 (ptt) cc_final: 0.8016 (ptt) REVERT: G 450 TYR cc_start: 0.8069 (m-10) cc_final: 0.7688 (m-80) REVERT: H 276 ARG cc_start: 0.8244 (mmp80) cc_final: 0.7872 (mmm160) REVERT: H 348 ASP cc_start: 0.8709 (t70) cc_final: 0.8347 (m-30) REVERT: H 379 ARG cc_start: 0.8651 (tmt-80) cc_final: 0.8104 (tpt90) REVERT: H 383 GLU cc_start: 0.8644 (pp20) cc_final: 0.8401 (pp20) outliers start: 0 outliers final: 0 residues processed: 460 average time/residue: 0.3751 time to fit residues: 276.4444 Evaluate side-chains 366 residues out of total 2723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 366 time to evaluate : 3.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 204 optimal weight: 50.0000 chunk 273 optimal weight: 5.9990 chunk 78 optimal weight: 3.9990 chunk 237 optimal weight: 30.0000 chunk 37 optimal weight: 10.0000 chunk 71 optimal weight: 9.9990 chunk 257 optimal weight: 9.9990 chunk 107 optimal weight: 5.9990 chunk 264 optimal weight: 7.9990 chunk 32 optimal weight: 3.9990 chunk 47 optimal weight: 0.9980 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 210 GLN ** D 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 177 GLN ** F 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.140506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.105745 restraints weight = 81965.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.104171 restraints weight = 67178.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.104790 restraints weight = 46717.292| |-----------------------------------------------------------------------------| r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.2627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 26015 Z= 0.267 Angle : 0.714 15.071 35311 Z= 0.356 Chirality : 0.044 0.197 3856 Planarity : 0.005 0.059 4594 Dihedral : 4.879 23.378 3636 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 16.68 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.73 % Favored : 92.17 % Rotamer: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.15), residues: 3245 helix: 0.04 (0.12), residues: 1855 sheet: -0.23 (1.90), residues: 10 loop : -1.63 (0.17), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP F 454 HIS 0.005 0.001 HIS H 479 PHE 0.034 0.002 PHE E 160 TYR 0.034 0.002 TYR F 450 ARG 0.006 0.000 ARG F 240 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5492.16 seconds wall clock time: 99 minutes 17.59 seconds (5957.59 seconds total)