Starting phenix.real_space_refine on Sun Aug 4 00:59:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yiy_33866/08_2024/7yiy_33866.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yiy_33866/08_2024/7yiy_33866.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yiy_33866/08_2024/7yiy_33866.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yiy_33866/08_2024/7yiy_33866.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yiy_33866/08_2024/7yiy_33866.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yiy_33866/08_2024/7yiy_33866.cif" } resolution = 2.7 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= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 52 5.16 5 C 5971 2.51 5 N 1559 2.21 5 O 1674 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 61": "OE1" <-> "OE2" Residue "B PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 64": "OE1" <-> "OE2" Residue "B ARG 88": "NH1" <-> "NH2" Residue "B GLU 107": "OE1" <-> "OE2" Residue "B ASP 110": "OD1" <-> "OD2" Residue "B ARG 129": "NH1" <-> "NH2" Residue "B ARG 151": "NH1" <-> "NH2" Residue "B ASP 155": "OD1" <-> "OD2" Residue "B GLU 190": "OE1" <-> "OE2" Residue "B GLU 198": "OE1" <-> "OE2" Residue "B TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 207": "NH1" <-> "NH2" Residue "B PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 271": "NH1" <-> "NH2" Residue "B ARG 278": "NH1" <-> "NH2" Residue "B ASP 294": "OD1" <-> "OD2" Residue "B ARG 304": "NH1" <-> "NH2" Residue "B ARG 305": "NH1" <-> "NH2" Residue "B TYR 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 326": "NH1" <-> "NH2" Residue "B GLU 329": "OE1" <-> "OE2" Residue "B TYR 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 345": "OE1" <-> "OE2" Residue "B ASP 369": "OD1" <-> "OD2" Residue "B ASP 371": "OD1" <-> "OD2" Residue "B TYR 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 393": "OE1" <-> "OE2" Residue "B GLU 437": "OE1" <-> "OE2" Residue "B ARG 447": "NH1" <-> "NH2" Residue "B ARG 450": "NH1" <-> "NH2" Residue "B GLU 464": "OE1" <-> "OE2" Residue "B ASP 465": "OD1" <-> "OD2" Residue "B ARG 489": "NH1" <-> "NH2" Residue "B GLU 505": "OE1" <-> "OE2" Residue "B ARG 507": "NH1" <-> "NH2" Residue "B ARG 509": "NH1" <-> "NH2" Residue "B GLU 530": "OE1" <-> "OE2" Residue "B ARG 541": "NH1" <-> "NH2" Residue "E ARG 37": "NH1" <-> "NH2" Residue "E TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 76": "OD1" <-> "OD2" Residue "D PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 34": "NH1" <-> "NH2" Residue "C TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 51": "OD1" <-> "OD2" Residue "A GLU 58": "OE1" <-> "OE2" Residue "A GLU 59": "OE1" <-> "OE2" Residue "A PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 116": "NH1" <-> "NH2" Residue "A ASP 150": "OD1" <-> "OD2" Residue "A ARG 151": "NH1" <-> "NH2" Residue "A GLU 159": "OE1" <-> "OE2" Residue "A TYR 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 189": "NH1" <-> "NH2" Residue "A ARG 203": "NH1" <-> "NH2" Residue "A PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 225": "OE1" <-> "OE2" Residue "A ARG 233": "NH1" <-> "NH2" Residue "A ARG 239": "NH1" <-> "NH2" Residue "A TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 259": "OE1" <-> "OE2" Residue "A ARG 270": "NH1" <-> "NH2" Residue "A ARG 287": "NH1" <-> "NH2" Residue "A GLU 308": "OE1" <-> "OE2" Residue "A ARG 329": "NH1" <-> "NH2" Residue "A GLU 357": "OE1" <-> "OE2" Residue "A PHE 394": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 405": "NH1" <-> "NH2" Residue "A GLU 414": "OE1" <-> "OE2" Residue "A ASP 417": "OD1" <-> "OD2" Residue "A GLU 435": "OE1" <-> "OE2" Residue "A ARG 459": "NH1" <-> "NH2" Residue "A GLU 466": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 9257 Number of models: 1 Model: "" Number of chains: 7 Chain: "B" Number of atoms: 3940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 499, 3940 Classifications: {'peptide': 499} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 17, 'TRANS': 481} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "E" Number of atoms: 324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 324 Classifications: {'peptide': 41} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 39} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'TYR:plan': 1, 'GLN:plan1': 1, 'TRP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "D" Number of atoms: 1236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1236 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 8, 'TRANS': 144} Chain: "C" Number of atoms: 411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 411 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 1, 'TRANS': 46} Chain: "A" Number of atoms: 3285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 3285 Classifications: {'peptide': 423} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 21, 'TRANS': 401} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'PLP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "D" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'Z1T': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.74, per 1000 atoms: 0.62 Number of scatterers: 9257 At special positions: 0 Unit cell: (91.8, 85.32, 122.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 52 16.00 P 1 15.00 O 1674 8.00 N 1559 7.00 C 5971 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.61 Conformation dependent library (CDL) restraints added in 1.7 seconds 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2156 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 11 sheets defined 53.9% alpha, 9.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.92 Creating SS restraints... Processing helix chain 'B' and resid 67 through 92 removed outlier: 3.855A pdb=" N TYR B 75 " --> pdb=" O ALA B 71 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL B 76 " --> pdb=" O VAL B 72 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLY B 77 " --> pdb=" O LEU B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 109 removed outlier: 3.530A pdb=" N GLN B 108 " --> pdb=" O ARG B 105 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS B 109 " --> pdb=" O GLU B 106 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 105 through 109' Processing helix chain 'B' and resid 120 through 126 Processing helix chain 'B' and resid 127 through 134 removed outlier: 3.942A pdb=" N ARG B 131 " --> pdb=" O MET B 128 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N ASP B 132 " --> pdb=" O ARG B 129 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TRP B 134 " --> pdb=" O ARG B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 181 removed outlier: 4.281A pdb=" N PHE B 181 " --> pdb=" O TYR B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 199 removed outlier: 3.513A pdb=" N GLU B 190 " --> pdb=" O GLY B 186 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLU B 198 " --> pdb=" O LYS B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 228 removed outlier: 3.614A pdb=" N GLU B 217 " --> pdb=" O LEU B 213 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA B 224 " --> pdb=" O GLU B 220 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG B 225 " --> pdb=" O GLU B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 244 removed outlier: 3.781A pdb=" N ASN B 242 " --> pdb=" O GLY B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 249 Processing helix chain 'B' and resid 263 through 274 removed outlier: 4.033A pdb=" N GLY B 274 " --> pdb=" O ALA B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 299 removed outlier: 3.692A pdb=" N ILE B 296 " --> pdb=" O LEU B 292 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL B 297 " --> pdb=" O LYS B 293 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N TYR B 298 " --> pdb=" O ASP B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 337 removed outlier: 3.803A pdb=" N LYS B 336 " --> pdb=" O ALA B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 363 removed outlier: 4.133A pdb=" N GLU B 361 " --> pdb=" O ARG B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 370 Processing helix chain 'B' and resid 391 through 402 removed outlier: 3.749A pdb=" N THR B 400 " --> pdb=" O ASP B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 408 removed outlier: 3.507A pdb=" N VAL B 406 " --> pdb=" O SER B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 428 removed outlier: 3.522A pdb=" N GLN B 418 " --> pdb=" O PRO B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 455 removed outlier: 3.713A pdb=" N GLU B 437 " --> pdb=" O SER B 433 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N CYS B 438 " --> pdb=" O LEU B 434 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL B 439 " --> pdb=" O GLY B 435 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA B 443 " --> pdb=" O VAL B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 489 removed outlier: 3.942A pdb=" N GLY B 480 " --> pdb=" O PRO B 476 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLY B 483 " --> pdb=" O ILE B 479 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ARG B 484 " --> pdb=" O GLY B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 517 through 536 Processing helix chain 'E' and resid 10 through 19 Processing helix chain 'E' and resid 21 through 40 removed outlier: 3.527A pdb=" N LEU E 25 " --> pdb=" O PRO E 21 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LEU E 27 " --> pdb=" O TYR E 23 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLU E 28 " --> pdb=" O HIS E 24 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG E 37 " --> pdb=" O LEU E 33 " (cutoff:3.500A) Processing helix chain 'D' and resid 11 through 19 removed outlier: 3.766A pdb=" N ARG D 15 " --> pdb=" O PRO D 12 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N VAL D 16 " --> pdb=" O ASN D 13 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N MET D 17 " --> pdb=" O THR D 14 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 39 removed outlier: 3.599A pdb=" N ILE D 30 " --> pdb=" O TYR D 26 " (cutoff:3.500A) Processing helix chain 'D' and resid 44 through 66 Processing helix chain 'D' and resid 84 through 89 Processing helix chain 'D' and resid 90 through 93 Processing helix chain 'D' and resid 96 through 116 Proline residue: D 106 - end of helix Processing helix chain 'D' and resid 120 through 133 removed outlier: 3.789A pdb=" N VAL D 125 " --> pdb=" O GLN D 121 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU D 126 " --> pdb=" O ILE D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 134 through 143 Proline residue: D 137 - end of helix Proline residue: D 140 - end of helix removed outlier: 3.531A pdb=" N HIS D 143 " --> pdb=" O PRO D 140 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 134 through 143' Processing helix chain 'D' and resid 146 through 150 Processing helix chain 'C' and resid 10 through 24 Processing helix chain 'C' and resid 25 through 29 removed outlier: 3.614A pdb=" N MET C 28 " --> pdb=" O ALA C 25 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 55 removed outlier: 3.614A pdb=" N VAL C 36 " --> pdb=" O TRP C 32 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE C 37 " --> pdb=" O GLU C 33 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ILE C 44 " --> pdb=" O MET C 40 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR C 51 " --> pdb=" O MET C 47 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TYR C 53 " --> pdb=" O LEU C 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 64 removed outlier: 3.527A pdb=" N LYS A 57 " --> pdb=" O THR A 53 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLU A 58 " --> pdb=" O VAL A 54 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLU A 59 " --> pdb=" O LYS A 55 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TRP A 64 " --> pdb=" O LEU A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 129 removed outlier: 3.676A pdb=" N LYS A 127 " --> pdb=" O ALA A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 157 Processing helix chain 'A' and resid 168 through 179 removed outlier: 3.756A pdb=" N ALA A 172 " --> pdb=" O PHE A 168 " (cutoff:3.500A) Proline residue: A 176 - end of helix Processing helix chain 'A' and resid 192 through 202 Processing helix chain 'A' and resid 213 through 230 removed outlier: 3.789A pdb=" N LEU A 217 " --> pdb=" O ASP A 213 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE A 226 " --> pdb=" O LYS A 222 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLU A 227 " --> pdb=" O GLU A 223 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYS A 230 " --> pdb=" O ILE A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 236 Processing helix chain 'A' and resid 257 through 268 removed outlier: 3.641A pdb=" N LYS A 262 " --> pdb=" O PRO A 258 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU A 263 " --> pdb=" O GLU A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 294 Processing helix chain 'A' and resid 296 through 300 removed outlier: 3.545A pdb=" N ILE A 300 " --> pdb=" O ILE A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 326 Processing helix chain 'A' and resid 332 through 337 Processing helix chain 'A' and resid 342 through 359 removed outlier: 3.537A pdb=" N GLU A 351 " --> pdb=" O ALA A 347 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASN A 359 " --> pdb=" O ILE A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 377 removed outlier: 3.942A pdb=" N GLN A 372 " --> pdb=" O GLU A 368 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ILE A 373 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N HIS A 374 " --> pdb=" O CYS A 370 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LYS A 375 " --> pdb=" O GLY A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 420 removed outlier: 3.695A pdb=" N ASP A 408 " --> pdb=" O SER A 404 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE A 415 " --> pdb=" O LEU A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 436 removed outlier: 4.138A pdb=" N GLU A 436 " --> pdb=" O GLU A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 469 Processing sheet with id=AA1, first strand: chain 'B' and resid 47 through 48 Processing sheet with id=AA2, first strand: chain 'B' and resid 61 through 62 Processing sheet with id=AA3, first strand: chain 'B' and resid 137 through 138 Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 152 removed outlier: 5.156A pdb=" N ILE B 148 " --> pdb=" O LYS B 168 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N LYS B 168 " --> pdb=" O ILE B 148 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N GLU B 150 " --> pdb=" O ILE B 166 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ILE B 166 " --> pdb=" O GLU B 150 " (cutoff:3.500A) removed outlier: 11.136A pdb=" N GLN B 152 " --> pdb=" O GLY B 164 " (cutoff:3.500A) removed outlier: 9.614A pdb=" N GLY B 164 " --> pdb=" O GLN B 152 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N GLY B 492 " --> pdb=" O GLY B 169 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ILE B 171 " --> pdb=" O GLY B 492 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 231 through 234 removed outlier: 8.201A pdb=" N GLU B 315 " --> pdb=" O ASP B 259 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 317 through 318 removed outlier: 3.575A pdb=" N SER B 323 " --> pdb=" O TYR B 318 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 468 through 472 removed outlier: 3.833A pdb=" N VAL B 494 " --> pdb=" O ARG B 509 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 92 through 94 removed outlier: 7.433A pdb=" N ALA A 425 " --> pdb=" O GLU A 99 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ILE A 101 " --> pdb=" O ALA A 425 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 160 through 164 removed outlier: 8.558A pdb=" N SER A 304 " --> pdb=" O ILE A 271 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N LEU A 273 " --> pdb=" O SER A 304 " (cutoff:3.500A) removed outlier: 9.095A pdb=" N ASN A 306 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ARG A 240 " --> pdb=" O ARG A 270 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N PHE A 272 " --> pdb=" O ARG A 240 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ILE A 242 " --> pdb=" O PHE A 272 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N GLU A 274 " --> pdb=" O ILE A 242 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N VAL A 244 " --> pdb=" O GLU A 274 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N GLU A 245 " --> pdb=" O ASP A 188 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 383 through 386 Processing sheet with id=AB2, first strand: chain 'A' and resid 427 through 428 removed outlier: 4.507A pdb=" N THR A 427 " --> pdb=" O ARG A 445 " (cutoff:3.500A) 419 hydrogen bonds defined for protein. 1173 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.49 Time building geometry restraints manager: 3.91 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: 2604 1.33 - 1.45: 1510 1.45 - 1.57: 5255 1.57 - 1.69: 1 1.69 - 1.81: 87 Bond restraints: 9457 Sorted by residual: bond pdb=" C14 Z1T D 201 " pdb=" C15 Z1T D 201 " ideal model delta sigma weight residual 1.329 1.523 -0.194 2.00e-02 2.50e+03 9.45e+01 bond pdb=" C2 PLP B 601 " pdb=" C3 PLP B 601 " ideal model delta sigma weight residual 1.390 1.485 -0.095 2.00e-02 2.50e+03 2.24e+01 bond pdb=" C4 PLP B 601 " pdb=" C5 PLP B 601 " ideal model delta sigma weight residual 1.390 1.483 -0.093 2.00e-02 2.50e+03 2.14e+01 bond pdb=" C3 PLP B 601 " pdb=" C4 PLP B 601 " ideal model delta sigma weight residual 1.390 1.480 -0.090 2.00e-02 2.50e+03 2.04e+01 bond pdb=" C PHE B 498 " pdb=" O PHE B 498 " ideal model delta sigma weight residual 1.241 1.212 0.029 9.80e-03 1.04e+04 8.78e+00 ... (remaining 9452 not shown) Histogram of bond angle deviations from ideal: 98.19 - 105.37: 174 105.37 - 112.55: 4682 112.55 - 119.72: 3441 119.72 - 126.90: 4388 126.90 - 134.07: 102 Bond angle restraints: 12787 Sorted by residual: angle pdb=" N ILE B 503 " pdb=" CA ILE B 503 " pdb=" C ILE B 503 " ideal model delta sigma weight residual 110.62 118.43 -7.81 1.02e+00 9.61e-01 5.86e+01 angle pdb=" N GLN B 116 " pdb=" CA GLN B 116 " pdb=" C GLN B 116 " ideal model delta sigma weight residual 109.76 99.56 10.20 1.59e+00 3.96e-01 4.12e+01 angle pdb=" N PRO A 78 " pdb=" CA PRO A 78 " pdb=" CB PRO A 78 " ideal model delta sigma weight residual 103.44 109.98 -6.54 1.12e+00 7.97e-01 3.41e+01 angle pdb=" N GLY B 497 " pdb=" CA GLY B 497 " pdb=" C GLY B 497 " ideal model delta sigma weight residual 112.81 120.13 -7.32 1.38e+00 5.25e-01 2.82e+01 angle pdb=" N ASN B 60 " pdb=" CA ASN B 60 " pdb=" C ASN B 60 " ideal model delta sigma weight residual 108.34 116.90 -8.56 1.64e+00 3.72e-01 2.72e+01 ... (remaining 12782 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.31: 4933 16.31 - 32.63: 482 32.63 - 48.94: 174 48.94 - 65.26: 66 65.26 - 81.57: 12 Dihedral angle restraints: 5667 sinusoidal: 2298 harmonic: 3369 Sorted by residual: dihedral pdb=" CA ASN B 120 " pdb=" C ASN B 120 " pdb=" N PHE B 121 " pdb=" CA PHE B 121 " ideal model delta harmonic sigma weight residual 180.00 155.33 24.67 0 5.00e+00 4.00e-02 2.43e+01 dihedral pdb=" CA ILE B 96 " pdb=" C ILE B 96 " pdb=" N GLU B 97 " pdb=" CA GLU B 97 " ideal model delta harmonic sigma weight residual -180.00 -158.19 -21.81 0 5.00e+00 4.00e-02 1.90e+01 dihedral pdb=" C TYR E 44 " pdb=" N TYR E 44 " pdb=" CA TYR E 44 " pdb=" CB TYR E 44 " ideal model delta harmonic sigma weight residual -122.60 -132.97 10.37 0 2.50e+00 1.60e-01 1.72e+01 ... (remaining 5664 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 1247 0.087 - 0.174: 157 0.174 - 0.261: 19 0.261 - 0.347: 2 0.347 - 0.434: 3 Chirality restraints: 1428 Sorted by residual: chirality pdb=" CA LYS B 168 " pdb=" N LYS B 168 " pdb=" C LYS B 168 " pdb=" CB LYS B 168 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.71e+00 chirality pdb=" CA TYR E 44 " pdb=" N TYR E 44 " pdb=" C TYR E 44 " pdb=" CB TYR E 44 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.59e+00 chirality pdb=" CA PHE B 498 " pdb=" N PHE B 498 " pdb=" C PHE B 498 " pdb=" CB PHE B 498 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.41 2.00e-01 2.50e+01 4.10e+00 ... (remaining 1425 not shown) Planarity restraints: 1619 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 501 " -0.057 5.00e-02 4.00e+02 8.65e-02 1.20e+01 pdb=" N PRO B 502 " 0.150 5.00e-02 4.00e+02 pdb=" CA PRO B 502 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO B 502 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 166 " 0.022 2.00e-02 2.50e+03 1.68e-02 5.62e+00 pdb=" CG TYR A 166 " -0.039 2.00e-02 2.50e+03 pdb=" CD1 TYR A 166 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 TYR A 166 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR A 166 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR A 166 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR A 166 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR A 166 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 501 " -0.011 2.00e-02 2.50e+03 2.23e-02 4.98e+00 pdb=" C THR B 501 " 0.039 2.00e-02 2.50e+03 pdb=" O THR B 501 " -0.015 2.00e-02 2.50e+03 pdb=" N PRO B 502 " -0.013 2.00e-02 2.50e+03 ... (remaining 1616 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 1023 2.74 - 3.28: 8357 3.28 - 3.82: 14320 3.82 - 4.36: 18141 4.36 - 4.90: 31287 Nonbonded interactions: 73128 Sorted by model distance: nonbonded pdb=" O ALA B 201 " pdb=" OG SER B 412 " model vdw 2.205 3.040 nonbonded pdb=" OH TYR B 407 " pdb=" OE2 GLU A 436 " model vdw 2.218 3.040 nonbonded pdb=" O THR B 66 " pdb=" NH1 ARG D 20 " model vdw 2.240 3.120 nonbonded pdb=" OG1 THR B 432 " pdb=" CD2 LEU B 434 " model vdw 2.261 3.460 nonbonded pdb=" NZ LYS B 338 " pdb=" O TRP A 64 " model vdw 2.296 3.120 ... (remaining 73123 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.80 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.850 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: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 27.800 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 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:11.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 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 : 0.008 0.194 9457 Z= 0.503 Angle : 0.981 12.129 12787 Z= 0.587 Chirality : 0.063 0.434 1428 Planarity : 0.006 0.086 1619 Dihedral : 16.225 81.572 3511 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.61 % Allowed : 5.20 % Favored : 94.19 % Rotamer: Outliers : 4.77 % Allowed : 2.44 % Favored : 92.79 % 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: -1.48 (0.24), residues: 1154 helix: -0.40 (0.22), residues: 505 sheet: -0.01 (0.50), residues: 118 loop : -1.77 (0.25), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 134 HIS 0.005 0.001 HIS A 91 PHE 0.032 0.003 PHE A 138 TYR 0.039 0.003 TYR A 166 ARG 0.007 0.001 ARG D 81 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 125 time to evaluate : 0.967 Fit side-chains REVERT: B 93 TYR cc_start: 0.7030 (OUTLIER) cc_final: 0.6711 (m-10) REVERT: B 152 GLN cc_start: 0.8448 (OUTLIER) cc_final: 0.8163 (pm20) REVERT: B 183 ARG cc_start: 0.8313 (OUTLIER) cc_final: 0.8112 (ptm160) REVERT: B 281 LYS cc_start: 0.8394 (mttp) cc_final: 0.8153 (mttt) REVERT: B 344 ASP cc_start: 0.8647 (t0) cc_final: 0.8445 (t70) REVERT: B 427 MET cc_start: 0.9006 (mtm) cc_final: 0.8589 (mtm) REVERT: B 434 LEU cc_start: 0.7579 (OUTLIER) cc_final: 0.6958 (tp) REVERT: B 436 LYS cc_start: 0.8540 (OUTLIER) cc_final: 0.7592 (mtpp) REVERT: B 518 LYS cc_start: 0.8464 (OUTLIER) cc_final: 0.8162 (tppt) REVERT: E 42 LYS cc_start: 0.7051 (OUTLIER) cc_final: 0.6616 (mmtm) REVERT: C 11 LYS cc_start: 0.7709 (OUTLIER) cc_final: 0.7289 (tmtt) REVERT: C 13 MET cc_start: 0.8194 (OUTLIER) cc_final: 0.7928 (mmp) REVERT: A 56 GLU cc_start: 0.7933 (OUTLIER) cc_final: 0.7444 (mp0) REVERT: A 375 LYS cc_start: 0.8657 (tttm) cc_final: 0.8448 (tttp) REVERT: A 434 LYS cc_start: 0.8703 (OUTLIER) cc_final: 0.8239 (mmpt) REVERT: A 435 GLU cc_start: 0.6858 (OUTLIER) cc_final: 0.6522 (mp0) REVERT: A 459 ARG cc_start: 0.8059 (OUTLIER) cc_final: 0.7018 (tmm-80) outliers start: 47 outliers final: 22 residues processed: 149 average time/residue: 1.6705 time to fit residues: 261.4156 Evaluate side-chains 145 residues out of total 997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 110 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 93 TYR Chi-restraints excluded: chain B residue 109 LYS Chi-restraints excluded: chain B residue 150 GLU Chi-restraints excluded: chain B residue 152 GLN Chi-restraints excluded: chain B residue 168 LYS Chi-restraints excluded: chain B residue 183 ARG Chi-restraints excluded: chain B residue 189 GLN Chi-restraints excluded: chain B residue 190 GLU Chi-restraints excluded: chain B residue 194 LYS Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 436 LYS Chi-restraints excluded: chain B residue 496 VAL Chi-restraints excluded: chain B residue 518 LYS Chi-restraints excluded: chain B residue 526 LYS Chi-restraints excluded: chain B residue 530 GLU Chi-restraints excluded: chain B residue 541 ARG Chi-restraints excluded: chain E residue 42 LYS Chi-restraints excluded: chain E residue 44 TYR Chi-restraints excluded: chain E residue 45 LYS Chi-restraints excluded: chain C residue 11 LYS Chi-restraints excluded: chain C residue 13 MET Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 58 GLU Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 133 CYS Chi-restraints excluded: chain A residue 326 ASP Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 420 MET Chi-restraints excluded: chain A residue 422 ARG Chi-restraints excluded: chain A residue 434 LYS Chi-restraints excluded: chain A residue 435 GLU Chi-restraints excluded: chain A residue 459 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 0.8980 chunk 86 optimal weight: 0.7980 chunk 47 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 46 optimal weight: 0.6980 chunk 89 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 189 GLN ** B 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 229 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.1211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9457 Z= 0.245 Angle : 0.641 8.088 12787 Z= 0.344 Chirality : 0.048 0.183 1428 Planarity : 0.005 0.054 1619 Dihedral : 11.363 73.126 1423 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 2.84 % Allowed : 9.64 % Favored : 87.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.68 (0.24), residues: 1154 helix: 0.59 (0.23), residues: 527 sheet: 0.24 (0.49), residues: 117 loop : -1.75 (0.26), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 134 HIS 0.004 0.001 HIS B 516 PHE 0.018 0.002 PHE A 138 TYR 0.020 0.002 TYR A 166 ARG 0.003 0.000 ARG D 20 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 123 time to evaluate : 0.888 Fit side-chains REVERT: B 93 TYR cc_start: 0.7112 (OUTLIER) cc_final: 0.6670 (m-10) REVERT: B 150 GLU cc_start: 0.7978 (OUTLIER) cc_final: 0.7417 (tm-30) REVERT: B 152 GLN cc_start: 0.8412 (OUTLIER) cc_final: 0.8179 (pm20) REVERT: B 197 GLU cc_start: 0.7993 (tm-30) cc_final: 0.7762 (tp30) REVERT: B 281 LYS cc_start: 0.8251 (mttp) cc_final: 0.8025 (mttt) REVERT: B 427 MET cc_start: 0.8723 (mtm) cc_final: 0.8348 (mtm) REVERT: B 434 LEU cc_start: 0.7831 (OUTLIER) cc_final: 0.7006 (tp) REVERT: B 518 LYS cc_start: 0.8144 (OUTLIER) cc_final: 0.7933 (tppt) REVERT: B 526 LYS cc_start: 0.8209 (OUTLIER) cc_final: 0.7994 (ttpp) REVERT: D 19 SER cc_start: 0.8934 (m) cc_final: 0.8639 (m) REVERT: C 11 LYS cc_start: 0.7717 (OUTLIER) cc_final: 0.7421 (mptt) REVERT: A 56 GLU cc_start: 0.7751 (OUTLIER) cc_final: 0.7316 (mp0) REVERT: A 107 ASN cc_start: 0.8487 (p0) cc_final: 0.8277 (p0) REVERT: A 205 ASP cc_start: 0.8031 (m-30) cc_final: 0.7826 (m-30) REVERT: A 434 LYS cc_start: 0.8501 (mmtm) cc_final: 0.8137 (mmpt) REVERT: A 435 GLU cc_start: 0.6878 (OUTLIER) cc_final: 0.6628 (mm-30) outliers start: 28 outliers final: 9 residues processed: 137 average time/residue: 1.6801 time to fit residues: 241.6498 Evaluate side-chains 130 residues out of total 997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 112 time to evaluate : 1.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 93 TYR Chi-restraints excluded: chain B residue 109 LYS Chi-restraints excluded: chain B residue 150 GLU Chi-restraints excluded: chain B residue 152 GLN Chi-restraints excluded: chain B residue 189 GLN Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 518 LYS Chi-restraints excluded: chain B residue 519 GLU Chi-restraints excluded: chain B residue 526 LYS Chi-restraints excluded: chain E residue 44 TYR Chi-restraints excluded: chain C residue 11 LYS Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 326 ASP Chi-restraints excluded: chain A residue 422 ARG Chi-restraints excluded: chain A residue 435 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 57 optimal weight: 0.0000 chunk 32 optimal weight: 0.7980 chunk 86 optimal weight: 6.9990 chunk 70 optimal weight: 0.7980 chunk 28 optimal weight: 0.5980 chunk 103 optimal weight: 2.9990 chunk 112 optimal weight: 3.9990 chunk 92 optimal weight: 0.5980 chunk 102 optimal weight: 0.7980 chunk 35 optimal weight: 0.8980 chunk 83 optimal weight: 0.7980 overall best weight: 0.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 440 GLN B 463 ASN A 229 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9457 Z= 0.142 Angle : 0.524 7.910 12787 Z= 0.280 Chirality : 0.043 0.181 1428 Planarity : 0.004 0.047 1619 Dihedral : 9.375 69.566 1366 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 1.93 % Allowed : 12.08 % Favored : 85.99 % 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: 0.02 (0.25), residues: 1154 helix: 1.37 (0.24), residues: 531 sheet: 0.26 (0.48), residues: 119 loop : -1.58 (0.26), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 134 HIS 0.002 0.000 HIS B 47 PHE 0.012 0.001 PHE A 209 TYR 0.012 0.001 TYR B 235 ARG 0.003 0.000 ARG B 271 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 121 time to evaluate : 1.144 Fit side-chains REVERT: B 93 TYR cc_start: 0.7100 (OUTLIER) cc_final: 0.6678 (m-10) REVERT: B 109 LYS cc_start: 0.8652 (OUTLIER) cc_final: 0.8247 (mmtt) REVERT: B 152 GLN cc_start: 0.8392 (OUTLIER) cc_final: 0.8180 (pm20) REVERT: B 189 GLN cc_start: 0.7731 (OUTLIER) cc_final: 0.7057 (mm-40) REVERT: B 427 MET cc_start: 0.8672 (mtm) cc_final: 0.8329 (mtm) REVERT: B 518 LYS cc_start: 0.8049 (OUTLIER) cc_final: 0.7844 (mmmm) REVERT: B 526 LYS cc_start: 0.8202 (OUTLIER) cc_final: 0.7999 (ttpp) REVERT: D 19 SER cc_start: 0.8825 (m) cc_final: 0.8477 (m) REVERT: A 434 LYS cc_start: 0.8493 (mmtm) cc_final: 0.8153 (mmpt) REVERT: A 435 GLU cc_start: 0.7100 (OUTLIER) cc_final: 0.6857 (mm-30) outliers start: 19 outliers final: 5 residues processed: 133 average time/residue: 1.6707 time to fit residues: 233.5835 Evaluate side-chains 124 residues out of total 997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 112 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 93 TYR Chi-restraints excluded: chain B residue 109 LYS Chi-restraints excluded: chain B residue 152 GLN Chi-restraints excluded: chain B residue 189 GLN Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 496 VAL Chi-restraints excluded: chain B residue 518 LYS Chi-restraints excluded: chain B residue 526 LYS Chi-restraints excluded: chain E residue 44 TYR Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 326 ASP Chi-restraints excluded: chain A residue 435 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 102 optimal weight: 0.8980 chunk 77 optimal weight: 4.9990 chunk 53 optimal weight: 8.9990 chunk 11 optimal weight: 5.9990 chunk 49 optimal weight: 0.9990 chunk 69 optimal weight: 4.9990 chunk 104 optimal weight: 2.9990 chunk 110 optimal weight: 3.9990 chunk 54 optimal weight: 0.6980 chunk 98 optimal weight: 5.9990 chunk 29 optimal weight: 4.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.1601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9457 Z= 0.288 Angle : 0.637 8.259 12787 Z= 0.338 Chirality : 0.048 0.201 1428 Planarity : 0.005 0.060 1619 Dihedral : 8.660 68.864 1348 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 2.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 2.34 % Allowed : 13.50 % Favored : 84.16 % 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: 0.03 (0.25), residues: 1154 helix: 1.42 (0.23), residues: 526 sheet: 0.11 (0.47), residues: 124 loop : -1.58 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 134 HIS 0.003 0.001 HIS B 47 PHE 0.019 0.002 PHE A 138 TYR 0.015 0.002 TYR B 235 ARG 0.003 0.000 ARG B 271 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 114 time to evaluate : 1.117 Fit side-chains REVERT: B 93 TYR cc_start: 0.7343 (OUTLIER) cc_final: 0.6536 (m-10) REVERT: B 109 LYS cc_start: 0.8678 (OUTLIER) cc_final: 0.8250 (mmtt) REVERT: B 189 GLN cc_start: 0.7745 (OUTLIER) cc_final: 0.7010 (mm-40) REVERT: B 427 MET cc_start: 0.8672 (mtm) cc_final: 0.8293 (mtm) REVERT: D 19 SER cc_start: 0.8937 (m) cc_final: 0.8599 (m) REVERT: A 107 ASN cc_start: 0.8605 (p0) cc_final: 0.8387 (p0) REVERT: A 434 LYS cc_start: 0.8616 (mmtm) cc_final: 0.8247 (mmpt) REVERT: A 435 GLU cc_start: 0.7431 (OUTLIER) cc_final: 0.7187 (mm-30) outliers start: 23 outliers final: 8 residues processed: 125 average time/residue: 1.6608 time to fit residues: 218.9459 Evaluate side-chains 125 residues out of total 997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 113 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 93 TYR Chi-restraints excluded: chain B residue 109 LYS Chi-restraints excluded: chain B residue 189 GLN Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain E residue 44 TYR Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 435 GLU Chi-restraints excluded: chain A residue 456 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 91 optimal weight: 4.9990 chunk 62 optimal weight: 4.9990 chunk 1 optimal weight: 0.9990 chunk 82 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 94 optimal weight: 4.9990 chunk 76 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 56 optimal weight: 5.9990 chunk 98 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.1604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 9457 Z= 0.318 Angle : 0.661 8.369 12787 Z= 0.350 Chirality : 0.049 0.204 1428 Planarity : 0.005 0.055 1619 Dihedral : 7.983 58.599 1335 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 2.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 3.15 % Allowed : 13.10 % Favored : 83.76 % 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: -0.06 (0.25), residues: 1154 helix: 1.34 (0.23), residues: 526 sheet: -0.01 (0.47), residues: 126 loop : -1.60 (0.27), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 134 HIS 0.004 0.001 HIS B 516 PHE 0.020 0.002 PHE A 138 TYR 0.018 0.002 TYR B 235 ARG 0.003 0.001 ARG B 136 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 116 time to evaluate : 1.048 Fit side-chains REVERT: B 93 TYR cc_start: 0.7370 (OUTLIER) cc_final: 0.6491 (m-10) REVERT: B 152 GLN cc_start: 0.8533 (OUTLIER) cc_final: 0.7205 (pm20) REVERT: B 427 MET cc_start: 0.8633 (mtm) cc_final: 0.8332 (mtm) REVERT: B 436 LYS cc_start: 0.8511 (mtmm) cc_final: 0.7775 (mtpt) REVERT: A 107 ASN cc_start: 0.8510 (p0) cc_final: 0.8290 (p0) REVERT: A 144 VAL cc_start: 0.8623 (OUTLIER) cc_final: 0.8404 (p) REVERT: A 423 SER cc_start: 0.8659 (m) cc_final: 0.8097 (p) REVERT: A 434 LYS cc_start: 0.8662 (mmtm) cc_final: 0.8294 (mmpt) outliers start: 31 outliers final: 19 residues processed: 133 average time/residue: 1.5869 time to fit residues: 222.3591 Evaluate side-chains 135 residues out of total 997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 113 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 93 TYR Chi-restraints excluded: chain B residue 109 LYS Chi-restraints excluded: chain B residue 152 GLN Chi-restraints excluded: chain B residue 183 ARG Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 189 GLN Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 496 VAL Chi-restraints excluded: chain B residue 542 HIS Chi-restraints excluded: chain E residue 44 TYR Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 326 ASP Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 435 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 37 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 64 optimal weight: 4.9990 chunk 27 optimal weight: 0.4980 chunk 110 optimal weight: 0.5980 chunk 91 optimal weight: 4.9990 chunk 51 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 57 optimal weight: 10.0000 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.1923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9457 Z= 0.162 Angle : 0.537 7.570 12787 Z= 0.287 Chirality : 0.044 0.188 1428 Planarity : 0.004 0.049 1619 Dihedral : 7.477 59.377 1335 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.64 % Allowed : 14.01 % Favored : 83.35 % 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: 0.31 (0.25), residues: 1154 helix: 1.73 (0.24), residues: 528 sheet: 0.07 (0.46), residues: 124 loop : -1.49 (0.27), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 134 HIS 0.002 0.001 HIS A 292 PHE 0.014 0.001 PHE A 209 TYR 0.012 0.001 TYR B 235 ARG 0.006 0.000 ARG B 271 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 120 time to evaluate : 1.178 Fit side-chains REVERT: B 93 TYR cc_start: 0.7283 (OUTLIER) cc_final: 0.6498 (m-10) REVERT: B 109 LYS cc_start: 0.8648 (OUTLIER) cc_final: 0.8244 (mmtt) REVERT: B 152 GLN cc_start: 0.8476 (OUTLIER) cc_final: 0.7202 (pm20) REVERT: B 189 GLN cc_start: 0.7687 (OUTLIER) cc_final: 0.6989 (mm-40) REVERT: B 427 MET cc_start: 0.8595 (mtm) cc_final: 0.8273 (mtm) REVERT: B 475 MET cc_start: 0.8568 (OUTLIER) cc_final: 0.7078 (mtp) REVERT: E 13 MET cc_start: 0.6857 (OUTLIER) cc_final: 0.6445 (mtt) REVERT: D 19 SER cc_start: 0.8888 (m) cc_final: 0.8552 (m) REVERT: A 56 GLU cc_start: 0.7326 (OUTLIER) cc_final: 0.6917 (mp0) REVERT: A 144 VAL cc_start: 0.8597 (OUTLIER) cc_final: 0.8343 (p) REVERT: A 423 SER cc_start: 0.8668 (m) cc_final: 0.8135 (p) REVERT: A 434 LYS cc_start: 0.8615 (mmtm) cc_final: 0.8283 (mmpt) REVERT: A 435 GLU cc_start: 0.7735 (OUTLIER) cc_final: 0.7494 (mm-30) outliers start: 26 outliers final: 10 residues processed: 134 average time/residue: 1.5786 time to fit residues: 222.9038 Evaluate side-chains 133 residues out of total 997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 114 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 93 TYR Chi-restraints excluded: chain B residue 109 LYS Chi-restraints excluded: chain B residue 152 GLN Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 189 GLN Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 475 MET Chi-restraints excluded: chain B residue 496 VAL Chi-restraints excluded: chain B residue 519 GLU Chi-restraints excluded: chain B residue 542 HIS Chi-restraints excluded: chain E residue 13 MET Chi-restraints excluded: chain E residue 44 TYR Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 326 ASP Chi-restraints excluded: chain A residue 435 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 106 optimal weight: 5.9990 chunk 12 optimal weight: 0.8980 chunk 62 optimal weight: 5.9990 chunk 80 optimal weight: 3.9990 chunk 92 optimal weight: 0.0170 chunk 61 optimal weight: 0.7980 chunk 109 optimal weight: 6.9990 chunk 68 optimal weight: 4.9990 chunk 66 optimal weight: 0.0670 chunk 50 optimal weight: 5.9990 chunk 67 optimal weight: 0.8980 overall best weight: 0.5356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 GLN A 407 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9457 Z= 0.142 Angle : 0.516 8.613 12787 Z= 0.274 Chirality : 0.043 0.182 1428 Planarity : 0.004 0.047 1619 Dihedral : 7.135 59.519 1335 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.03 % Allowed : 14.42 % Favored : 83.55 % 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: 0.57 (0.26), residues: 1154 helix: 1.88 (0.24), residues: 540 sheet: 0.19 (0.47), residues: 123 loop : -1.36 (0.27), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 134 HIS 0.002 0.000 HIS B 47 PHE 0.015 0.001 PHE B 121 TYR 0.010 0.001 TYR B 235 ARG 0.007 0.000 ARG B 271 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 118 time to evaluate : 1.099 Fit side-chains REVERT: B 93 TYR cc_start: 0.7163 (OUTLIER) cc_final: 0.6464 (m-10) REVERT: B 109 LYS cc_start: 0.8491 (OUTLIER) cc_final: 0.8199 (mmtt) REVERT: B 427 MET cc_start: 0.8562 (mtm) cc_final: 0.8245 (mtm) REVERT: B 475 MET cc_start: 0.8443 (OUTLIER) cc_final: 0.6892 (mtp) REVERT: D 19 SER cc_start: 0.8837 (m) cc_final: 0.8481 (m) REVERT: A 144 VAL cc_start: 0.8571 (OUTLIER) cc_final: 0.8314 (p) REVERT: A 407 GLN cc_start: 0.7634 (mt0) cc_final: 0.7220 (mt0) REVERT: A 423 SER cc_start: 0.8668 (m) cc_final: 0.8135 (p) REVERT: A 434 LYS cc_start: 0.8595 (mmtm) cc_final: 0.8275 (mmpt) REVERT: A 435 GLU cc_start: 0.7784 (OUTLIER) cc_final: 0.7520 (mm-30) outliers start: 20 outliers final: 8 residues processed: 127 average time/residue: 1.6944 time to fit residues: 226.3562 Evaluate side-chains 125 residues out of total 997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 112 time to evaluate : 1.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 93 TYR Chi-restraints excluded: chain B residue 109 LYS Chi-restraints excluded: chain B residue 189 GLN Chi-restraints excluded: chain B residue 423 MET Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 475 MET Chi-restraints excluded: chain B residue 488 LYS Chi-restraints excluded: chain B residue 496 VAL Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 326 ASP Chi-restraints excluded: chain A residue 435 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 72.714 > 50: distance: 18 - 24: 3.016 distance: 55 - 61: 35.624 distance: 63 - 64: 56.162 distance: 65 - 66: 40.946 distance: 66 - 67: 56.179 distance: 68 - 70: 38.941 distance: 69 - 71: 39.568 distance: 73 - 74: 30.382 distance: 74 - 75: 12.184 distance: 74 - 77: 50.768 distance: 75 - 76: 41.272 distance: 75 - 81: 39.851 distance: 76 - 102: 42.931 distance: 77 - 78: 38.579 distance: 78 - 79: 68.257 distance: 79 - 80: 41.691 distance: 81 - 82: 55.737 distance: 81 - 87: 57.067 distance: 82 - 83: 38.910 distance: 82 - 85: 39.835 distance: 83 - 84: 57.509 distance: 83 - 88: 55.446 distance: 86 - 87: 38.958 distance: 89 - 90: 17.836 distance: 89 - 92: 56.255 distance: 90 - 91: 53.237 distance: 90 - 93: 61.558 distance: 91 - 114: 44.398 distance: 94 - 95: 40.979 distance: 95 - 96: 39.447 distance: 95 - 102: 51.950 distance: 96 - 119: 49.317 distance: 97 - 98: 46.573 distance: 98 - 99: 47.802 distance: 99 - 100: 40.128 distance: 100 - 101: 56.356 distance: 102 - 103: 8.394 distance: 103 - 104: 63.754 distance: 103 - 106: 52.164 distance: 104 - 105: 59.489 distance: 104 - 110: 40.182 distance: 106 - 107: 69.550 distance: 106 - 108: 37.527 distance: 107 - 109: 70.381 distance: 110 - 111: 56.226 distance: 111 - 112: 57.820 distance: 112 - 114: 38.975 distance: 114 - 115: 56.895 distance: 115 - 116: 11.751 distance: 115 - 118: 40.213 distance: 116 - 117: 12.191 distance: 116 - 119: 42.559 distance: 117 - 144: 29.243 distance: 119 - 120: 14.367 distance: 120 - 121: 56.152 distance: 120 - 123: 55.938 distance: 121 - 122: 39.846 distance: 121 - 130: 63.636 distance: 122 - 152: 32.612 distance: 123 - 124: 44.502 distance: 124 - 125: 18.688 distance: 124 - 126: 46.859 distance: 125 - 127: 41.451 distance: 126 - 128: 50.553 distance: 127 - 129: 27.247 distance: 130 - 131: 12.503 distance: 131 - 132: 43.414 distance: 132 - 133: 26.894 distance: 132 - 134: 28.321 distance: 133 - 160: 32.839