Starting phenix.real_space_refine (version: dev) on Sun Dec 18 12:37:32 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cqk_30442/12_2022/7cqk_30442_updated_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cqk_30442/12_2022/7cqk_30442.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cqk_30442/12_2022/7cqk_30442_updated_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cqk_30442/12_2022/7cqk_30442_updated_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cqk_30442/12_2022/7cqk_30442_updated_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cqk_30442/12_2022/7cqk_30442.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cqk_30442/12_2022/7cqk_30442.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cqk_30442/12_2022/7cqk_30442_updated_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cqk_30442/12_2022/7cqk_30442_updated_updated.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 22 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "S PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 113": "OD1" <-> "OD2" Residue "S ARG 116": "NH1" <-> "NH2" Residue "S PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 151": "NH1" <-> "NH2" Residue "S TYR 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 181": "NH1" <-> "NH2" Residue "S ARG 189": "NH1" <-> "NH2" Residue "S ARG 236": "NH1" <-> "NH2" Residue "S ARG 239": "NH1" <-> "NH2" Residue "S TYR 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 270": "NH1" <-> "NH2" Residue "S ARG 287": "NH1" <-> "NH2" Residue "S ARG 321": "NH1" <-> "NH2" Residue "S ARG 329": "NH1" <-> "NH2" Residue "S PHE 394": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 405": "NH1" <-> "NH2" Residue "S GLU 414": "OE1" <-> "OE2" Residue "S ARG 459": "NH1" <-> "NH2" Residue "T GLU 61": "OE1" <-> "OE2" Residue "T ARG 88": "NH1" <-> "NH2" Residue "T GLU 106": "OE1" <-> "OE2" Residue "T PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 129": "NH1" <-> "NH2" Residue "T ARG 151": "NH1" <-> "NH2" Residue "T ARG 207": "NH1" <-> "NH2" Residue "T ARG 278": "NH1" <-> "NH2" Residue "T ARG 326": "NH1" <-> "NH2" Residue "T TYR 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 344": "OD1" <-> "OD2" Residue "T TYR 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 447": "NH1" <-> "NH2" Residue "T ARG 450": "NH1" <-> "NH2" Residue "T ARG 489": "NH1" <-> "NH2" Residue "T PHE 498": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 505": "OE1" <-> "OE2" Residue "T ARG 507": "NH1" <-> "NH2" Residue "T ARG 509": "NH1" <-> "NH2" Residue "T TYR 539": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 541": "NH1" <-> "NH2" Residue "A ARG 20": "NH1" <-> "NH2" Residue "A TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 34": "NH1" <-> "NH2" Residue "C ARG 37": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 8859 Number of models: 1 Model: "" Number of chains: 7 Chain: "S" Number of atoms: 3268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 421, 3268 Classifications: {'peptide': 421} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 21, 'TRANS': 399} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "T" Number of atoms: 3907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 497, 3907 Classifications: {'peptide': 497} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 18, 'TRANS': 478} Chain breaks: 1 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 3, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 29 Chain: "A" Number of atoms: 1030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1030 Classifications: {'peptide': 130} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 7, 'TRANS': 122} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "E" Number of atoms: 389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 389 Classifications: {'peptide': 46} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "C" Number of atoms: 177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 177 Classifications: {'peptide': 22} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 20} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "T" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Classifications: {'peptide': 1} Chain: "A" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'GE0': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.34, per 1000 atoms: 0.60 Number of scatterers: 8859 At special positions: 0 Unit cell: (92.88, 82.08, 120.96, 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 51 16.00 P 4 15.00 O 1616 8.00 N 1482 7.00 C 5706 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: 3.31 Conformation dependent library (CDL) restraints added in 1.4 seconds 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2068 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 39 helices and 8 sheets defined 39.2% alpha, 5.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain 'S' and resid 55 through 61 Processing helix chain 'S' and resid 115 through 128 removed outlier: 3.524A pdb=" N SER S 124 " --> pdb=" O ALA S 120 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N LYS S 127 " --> pdb=" O ALA S 123 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TYR S 128 " --> pdb=" O SER S 124 " (cutoff:3.500A) Processing helix chain 'S' and resid 143 through 155 removed outlier: 3.606A pdb=" N ALA S 153 " --> pdb=" O GLU S 149 " (cutoff:3.500A) Processing helix chain 'S' and resid 193 through 202 removed outlier: 3.573A pdb=" N GLY S 198 " --> pdb=" O ALA S 194 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ALA S 201 " --> pdb=" O LYS S 197 " (cutoff:3.500A) Processing helix chain 'S' and resid 214 through 231 removed outlier: 3.811A pdb=" N GLU S 223 " --> pdb=" O ARG S 219 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLN S 224 " --> pdb=" O LEU S 220 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLU S 227 " --> pdb=" O GLU S 223 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLN S 229 " --> pdb=" O GLU S 225 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASN S 231 " --> pdb=" O GLU S 227 " (cutoff:3.500A) Processing helix chain 'S' and resid 258 through 261 No H-bonds generated for 'chain 'S' and resid 258 through 261' Processing helix chain 'S' and resid 290 through 293 No H-bonds generated for 'chain 'S' and resid 290 through 293' Processing helix chain 'S' and resid 322 through 331 removed outlier: 3.629A pdb=" N ASP S 326 " --> pdb=" O SER S 322 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N HIS S 327 " --> pdb=" O PHE S 323 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N GLN S 328 " --> pdb=" O VAL S 324 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ARG S 329 " --> pdb=" O ILE S 325 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N LEU S 330 " --> pdb=" O ASP S 326 " (cutoff:3.500A) Processing helix chain 'S' and resid 333 through 336 No H-bonds generated for 'chain 'S' and resid 333 through 336' Processing helix chain 'S' and resid 343 through 358 removed outlier: 3.663A pdb=" N ALA S 347 " --> pdb=" O PRO S 343 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA S 348 " --> pdb=" O LEU S 344 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU S 351 " --> pdb=" O ALA S 347 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N MET S 356 " --> pdb=" O ALA S 352 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLU S 357 " --> pdb=" O LEU S 353 " (cutoff:3.500A) Processing helix chain 'S' and resid 362 through 367 Processing helix chain 'S' and resid 369 through 376 removed outlier: 3.835A pdb=" N ILE S 373 " --> pdb=" O LYS S 369 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N HIS S 374 " --> pdb=" O CYS S 370 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA S 376 " --> pdb=" O GLN S 372 " (cutoff:3.500A) Processing helix chain 'S' and resid 405 through 421 removed outlier: 3.928A pdb=" N ILE S 415 " --> pdb=" O LEU S 411 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N MET S 420 " --> pdb=" O VAL S 416 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ASN S 421 " --> pdb=" O ASP S 417 " (cutoff:3.500A) Processing helix chain 'S' and resid 455 through 466 removed outlier: 3.659A pdb=" N ARG S 459 " --> pdb=" O GLU S 455 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA S 460 " --> pdb=" O GLU S 456 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ILE S 464 " --> pdb=" O ALA S 460 " (cutoff:3.500A) Processing helix chain 'T' and resid 70 through 90 removed outlier: 4.394A pdb=" N TYR T 75 " --> pdb=" O ALA T 71 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL T 76 " --> pdb=" O VAL T 72 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TYR T 86 " --> pdb=" O THR T 82 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N LEU T 87 " --> pdb=" O LEU T 83 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ARG T 88 " --> pdb=" O PHE T 84 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ASP T 89 " --> pdb=" O GLY T 85 " (cutoff:3.500A) Processing helix chain 'T' and resid 131 through 133 No H-bonds generated for 'chain 'T' and resid 131 through 133' Processing helix chain 'T' and resid 178 through 180 No H-bonds generated for 'chain 'T' and resid 178 through 180' Processing helix chain 'T' and resid 187 through 199 removed outlier: 3.611A pdb=" N TYR T 199 " --> pdb=" O VAL T 195 " (cutoff:3.500A) Processing helix chain 'T' and resid 215 through 227 removed outlier: 3.708A pdb=" N LEU T 222 " --> pdb=" O GLU T 218 " (cutoff:3.500A) Processing helix chain 'T' and resid 238 through 249 removed outlier: 3.603A pdb=" N ASN T 242 " --> pdb=" O GLY T 238 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SER T 243 " --> pdb=" O PHE T 239 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N MET T 244 " --> pdb=" O ALA T 240 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE T 246 " --> pdb=" O ASN T 242 " (cutoff:3.500A) Proline residue: T 247 - end of helix Processing helix chain 'T' and resid 264 through 269 Processing helix chain 'T' and resid 286 through 293 removed outlier: 3.854A pdb=" N LEU T 291 " --> pdb=" O SER T 287 " (cutoff:3.500A) Processing helix chain 'T' and resid 327 through 337 removed outlier: 3.957A pdb=" N LEU T 333 " --> pdb=" O GLU T 329 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LYS T 335 " --> pdb=" O ILE T 331 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N LYS T 336 " --> pdb=" O ALA T 332 " (cutoff:3.500A) Processing helix chain 'T' and resid 358 through 362 removed outlier: 3.788A pdb=" N TYR T 362 " --> pdb=" O GLY T 358 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 358 through 362' Processing helix chain 'T' and resid 392 through 401 removed outlier: 3.790A pdb=" N TYR T 397 " --> pdb=" O GLU T 393 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N THR T 400 " --> pdb=" O ASP T 396 " (cutoff:3.500A) Processing helix chain 'T' and resid 403 through 407 Processing helix chain 'T' and resid 413 through 427 removed outlier: 3.704A pdb=" N GLU T 417 " --> pdb=" O PRO T 413 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLN T 418 " --> pdb=" O PRO T 414 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ILE T 419 " --> pdb=" O VAL T 415 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER T 422 " --> pdb=" O GLN T 418 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N CYS T 425 " --> pdb=" O THR T 421 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ILE T 426 " --> pdb=" O SER T 422 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N MET T 427 " --> pdb=" O MET T 423 " (cutoff:3.500A) Processing helix chain 'T' and resid 436 through 454 removed outlier: 3.626A pdb=" N GLN T 440 " --> pdb=" O LYS T 436 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU T 444 " --> pdb=" O GLN T 440 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR T 446 " --> pdb=" O LEU T 442 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ARG T 447 " --> pdb=" O ALA T 443 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU T 453 " --> pdb=" O PHE T 449 " (cutoff:3.500A) Processing helix chain 'T' and resid 476 through 488 removed outlier: 3.846A pdb=" N GLY T 480 " --> pdb=" O PRO T 476 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLY T 483 " --> pdb=" O ILE T 479 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ARG T 484 " --> pdb=" O GLY T 480 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LEU T 487 " --> pdb=" O GLY T 483 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LYS T 488 " --> pdb=" O ARG T 484 " (cutoff:3.500A) Processing helix chain 'T' and resid 498 through 500 No H-bonds generated for 'chain 'T' and resid 498 through 500' Processing helix chain 'T' and resid 518 through 532 removed outlier: 3.539A pdb=" N THR T 523 " --> pdb=" O GLU T 519 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU T 527 " --> pdb=" O THR T 523 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU T 530 " --> pdb=" O LYS T 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 37 Processing helix chain 'A' and resid 48 through 65 removed outlier: 3.637A pdb=" N MET A 58 " --> pdb=" O LEU A 54 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE A 62 " --> pdb=" O MET A 58 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE A 63 " --> pdb=" O GLY A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 92 removed outlier: 6.833A pdb=" N ASP A 90 " --> pdb=" O TRP A 86 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N TYR A 91 " --> pdb=" O GLU A 87 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLY A 92 " --> pdb=" O GLN A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 115 removed outlier: 3.698A pdb=" N PHE A 101 " --> pdb=" O ALA A 97 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N THR A 103 " --> pdb=" O ARG A 99 " (cutoff:3.500A) Proline residue: A 106 - end of helix removed outlier: 3.932A pdb=" N TYR A 110 " --> pdb=" O PRO A 106 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER A 114 " --> pdb=" O TYR A 110 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N PHE A 115 " --> pdb=" O PHE A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 135 removed outlier: 4.215A pdb=" N VAL A 134 " --> pdb=" O SER A 130 " (cutoff:3.500A) Processing helix chain 'E' and resid 11 through 22 removed outlier: 3.673A pdb=" N SER E 14 " --> pdb=" O LYS E 11 " (cutoff:3.500A) Processing helix chain 'E' and resid 34 through 54 removed outlier: 3.817A pdb=" N VAL E 42 " --> pdb=" O ASN E 38 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ALA E 48 " --> pdb=" O ILE E 44 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N TYR E 50 " --> pdb=" O GLY E 46 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N THR E 51 " --> pdb=" O MET E 47 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLY E 52 " --> pdb=" O ALA E 48 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N TYR E 53 " --> pdb=" O LEU E 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 24 through 39 removed outlier: 3.703A pdb=" N ILE C 30 " --> pdb=" O ILE C 26 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE C 36 " --> pdb=" O ILE C 32 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'S' and resid 92 through 94 Processing sheet with id= B, first strand: chain 'S' and resid 160 through 164 Processing sheet with id= C, first strand: chain 'S' and resid 205 through 208 Processing sheet with id= D, first strand: chain 'S' and resid 393 through 397 removed outlier: 3.865A pdb=" N PHE S 394 " --> pdb=" O VAL S 446 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE S 444 " --> pdb=" O LEU S 396 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'T' and resid 151 through 153 Processing sheet with id= F, first strand: chain 'T' and resid 231 through 234 removed outlier: 3.909A pdb=" N ALA T 231 " --> pdb=" O GLY T 390 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLY T 375 " --> pdb=" O TYR T 387 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'T' and resid 276 through 279 Processing sheet with id= H, first strand: chain 'T' and resid 494 through 496 removed outlier: 3.978A pdb=" N VAL T 494 " --> pdb=" O ARG T 509 " (cutoff:3.500A) 229 hydrogen bonds defined for protein. 651 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: 2.25 Time building geometry restraints manager: 3.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2770 1.34 - 1.46: 2027 1.46 - 1.58: 4160 1.58 - 1.71: 10 1.71 - 1.83: 84 Bond restraints: 9051 Sorted by residual: bond pdb=" C1' GE0 A 201 " pdb=" C2' GE0 A 201 " ideal model delta sigma weight residual 1.297 1.499 -0.202 2.00e-02 2.50e+03 1.02e+02 bond pdb=" C1' GE0 A 201 " pdb=" O4' GE0 A 201 " ideal model delta sigma weight residual 1.623 1.433 0.190 2.00e-02 2.50e+03 8.99e+01 bond pdb=" C4' GE0 A 201 " pdb=" O4' GE0 A 201 " ideal model delta sigma weight residual 1.273 1.440 -0.167 2.00e-02 2.50e+03 6.98e+01 bond pdb=" C4 PLS T 601 " pdb=" C5 PLS T 601 " ideal model delta sigma weight residual 1.352 1.483 -0.131 2.00e-02 2.50e+03 4.30e+01 bond pdb=" C6 GE0 A 201 " pdb=" N6 GE0 A 201 " ideal model delta sigma weight residual 1.450 1.330 0.120 2.00e-02 2.50e+03 3.60e+01 ... (remaining 9046 not shown) Histogram of bond angle deviations from ideal: 98.39 - 105.56: 216 105.56 - 112.73: 4574 112.73 - 119.90: 3257 119.90 - 127.06: 4120 127.06 - 134.23: 91 Bond angle restraints: 12258 Sorted by residual: angle pdb=" C PHE T 498 " pdb=" N PRO T 499 " pdb=" CA PRO T 499 " ideal model delta sigma weight residual 119.84 130.70 -10.86 1.25e+00 6.40e-01 7.55e+01 angle pdb=" N GLU S 399 " pdb=" CA GLU S 399 " pdb=" C GLU S 399 " ideal model delta sigma weight residual 111.28 120.49 -9.21 1.09e+00 8.42e-01 7.15e+01 angle pdb=" N MET T 423 " pdb=" CA MET T 423 " pdb=" C MET T 423 " ideal model delta sigma weight residual 111.69 101.72 9.97 1.23e+00 6.61e-01 6.57e+01 angle pdb=" C GLU E 30 " pdb=" N PRO E 31 " pdb=" CA PRO E 31 " ideal model delta sigma weight residual 119.84 129.77 -9.93 1.25e+00 6.40e-01 6.32e+01 angle pdb=" N ASN S 212 " pdb=" CA ASN S 212 " pdb=" C ASN S 212 " ideal model delta sigma weight residual 112.86 121.12 -8.26 1.22e+00 6.72e-01 4.59e+01 ... (remaining 12253 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.52: 4634 17.52 - 35.04: 405 35.04 - 52.55: 250 52.55 - 70.07: 92 70.07 - 87.59: 12 Dihedral angle restraints: 5393 sinusoidal: 2163 harmonic: 3230 Sorted by residual: dihedral pdb=" C VAL T 372 " pdb=" N VAL T 372 " pdb=" CA VAL T 372 " pdb=" CB VAL T 372 " ideal model delta harmonic sigma weight residual -122.00 -134.83 12.83 0 2.50e+00 1.60e-01 2.63e+01 dihedral pdb=" N ARG S 189 " pdb=" C ARG S 189 " pdb=" CA ARG S 189 " pdb=" CB ARG S 189 " ideal model delta harmonic sigma weight residual 122.80 134.15 -11.35 0 2.50e+00 1.60e-01 2.06e+01 dihedral pdb=" N VAL T 372 " pdb=" C VAL T 372 " pdb=" CA VAL T 372 " pdb=" CB VAL T 372 " ideal model delta harmonic sigma weight residual 123.40 134.31 -10.91 0 2.50e+00 1.60e-01 1.90e+01 ... (remaining 5390 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 1004 0.080 - 0.160: 294 0.160 - 0.241: 55 0.241 - 0.321: 12 0.321 - 0.401: 8 Chirality restraints: 1373 Sorted by residual: chirality pdb=" CA VAL T 372 " pdb=" N VAL T 372 " pdb=" C VAL T 372 " pdb=" CB VAL T 372 " both_signs ideal model delta sigma weight residual False 2.44 2.04 0.40 2.00e-01 2.50e+01 4.02e+00 chirality pdb=" CA ALA T 144 " pdb=" N ALA T 144 " pdb=" C ALA T 144 " pdb=" CB ALA T 144 " both_signs ideal model delta sigma weight residual False 2.48 2.09 0.40 2.00e-01 2.50e+01 3.91e+00 chirality pdb=" CA ARG S 189 " pdb=" N ARG S 189 " pdb=" C ARG S 189 " pdb=" CB ARG S 189 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.57e+00 ... (remaining 1370 not shown) Planarity restraints: 1547 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE T 498 " 0.055 5.00e-02 4.00e+02 8.19e-02 1.07e+01 pdb=" N PRO T 499 " -0.142 5.00e-02 4.00e+02 pdb=" CA PRO T 499 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO T 499 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU T 444 " -0.015 2.00e-02 2.50e+03 3.07e-02 9.42e+00 pdb=" C GLU T 444 " 0.053 2.00e-02 2.50e+03 pdb=" O GLU T 444 " -0.020 2.00e-02 2.50e+03 pdb=" N ASN T 445 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU S 63 " -0.015 2.00e-02 2.50e+03 3.07e-02 9.42e+00 pdb=" C GLU S 63 " 0.053 2.00e-02 2.50e+03 pdb=" O GLU S 63 " -0.020 2.00e-02 2.50e+03 pdb=" N TRP S 64 " -0.018 2.00e-02 2.50e+03 ... (remaining 1544 not shown) Histogram of nonbonded interaction distances: 0.96 - 1.75: 5 1.75 - 2.54: 81 2.54 - 3.33: 10150 3.33 - 4.11: 20048 4.11 - 4.90: 38195 Warning: very small nonbonded interaction distances. Nonbonded interactions: 68479 Sorted by model distance: nonbonded pdb=" OG SER S 423 " pdb=" NH2 ARG S 459 " model vdw 0.963 2.520 nonbonded pdb=" O LEU T 91 " pdb=" NE1 TRP T 94 " model vdw 1.487 2.520 nonbonded pdb=" OD2 ASP T 344 " pdb=" CE MET T 374 " model vdw 1.568 3.460 nonbonded pdb=" CD1 LEU T 196 " pdb=" CB GLU T 417 " model vdw 1.668 3.860 nonbonded pdb=" CG LEU T 196 " pdb=" OE1 GLU T 417 " model vdw 1.735 3.470 ... (remaining 68474 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 51 5.16 5 C 5706 2.51 5 N 1482 2.21 5 O 1616 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.80 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: 0.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 4.260 Check model and map are aligned: 0.130 Convert atoms to be neutral: 0.070 Process input model: 24.740 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 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 : 0.010 0.202 9051 Z= 0.685 Angle : 1.346 15.047 12258 Z= 0.812 Chirality : 0.082 0.401 1373 Planarity : 0.007 0.082 1547 Dihedral : 19.235 87.590 3325 Min Nonbonded Distance : 0.963 Molprobity Statistics. All-atom Clashscore : 30.09 Ramachandran Plot: Outliers : 1.00 % Allowed : 11.32 % Favored : 87.68 % Rotamer Outliers : 21.66 % Cbeta Deviations : 0.29 % 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: -5.35 (0.19), residues: 1104 helix: -4.21 (0.14), residues: 449 sheet: -2.77 (0.49), residues: 100 loop : -3.09 (0.22), residues: 555 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 203 poor density : 208 time to evaluate : 1.191 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 203 outliers final: 101 residues processed: 372 average time/residue: 0.2395 time to fit residues: 116.4702 Evaluate side-chains 242 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 141 time to evaluate : 0.959 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 101 outliers final: 2 residues processed: 101 average time/residue: 0.1279 time to fit residues: 21.6791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 chunk 46 optimal weight: 0.0970 chunk 28 optimal weight: 0.6980 chunk 56 optimal weight: 0.6980 chunk 44 optimal weight: 2.9990 chunk 86 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 99 optimal weight: 4.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 77 HIS S 211 HIS S 309 ASN S 413 GLN T 263 HIS T 445 ASN A 18 ASN A 53 ASN A 57 ASN A 85 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.2950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 9051 Z= 0.190 Angle : 0.686 8.370 12258 Z= 0.344 Chirality : 0.045 0.168 1373 Planarity : 0.005 0.061 1547 Dihedral : 7.414 68.670 1245 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.34 % Favored : 94.38 % Rotamer Outliers : 3.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.08 % 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: -3.84 (0.22), residues: 1104 helix: -2.71 (0.20), residues: 433 sheet: -2.26 (0.51), residues: 99 loop : -2.45 (0.23), residues: 572 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 157 time to evaluate : 0.818 Fit side-chains outliers start: 32 outliers final: 13 residues processed: 179 average time/residue: 0.1935 time to fit residues: 48.9402 Evaluate side-chains 139 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 126 time to evaluate : 1.036 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1104 time to fit residues: 3.7840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 83 optimal weight: 4.9990 chunk 68 optimal weight: 0.9980 chunk 27 optimal weight: 0.7980 chunk 100 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 89 optimal weight: 0.7980 chunk 99 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 80 optimal weight: 3.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 65 GLN T 47 HIS T 51 ASN ** T 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 245 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.3288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.052 9051 Z= 0.234 Angle : 0.656 8.466 12258 Z= 0.321 Chirality : 0.045 0.156 1373 Planarity : 0.005 0.061 1547 Dihedral : 6.650 62.422 1245 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.16 % Favored : 93.75 % Rotamer Outliers : 1.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.08 % 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: -3.11 (0.24), residues: 1104 helix: -1.83 (0.23), residues: 447 sheet: -2.14 (0.51), residues: 102 loop : -2.21 (0.25), residues: 555 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 132 time to evaluate : 1.082 Fit side-chains outliers start: 18 outliers final: 8 residues processed: 147 average time/residue: 0.1837 time to fit residues: 39.3709 Evaluate side-chains 132 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 124 time to evaluate : 1.097 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1308 time to fit residues: 3.2777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 51 optimal weight: 9.9990 chunk 11 optimal weight: 3.9990 chunk 47 optimal weight: 5.9990 chunk 67 optimal weight: 0.0010 chunk 100 optimal weight: 2.9990 chunk 106 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 overall best weight: 1.7392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 107 ASN ** T 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.3540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.055 9051 Z= 0.280 Angle : 0.640 8.268 12258 Z= 0.319 Chirality : 0.045 0.165 1373 Planarity : 0.005 0.071 1547 Dihedral : 6.385 63.748 1245 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.71 % Favored : 94.20 % Rotamer Outliers : 2.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.08 % 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: -2.61 (0.25), residues: 1104 helix: -1.30 (0.24), residues: 458 sheet: -1.65 (0.49), residues: 114 loop : -2.11 (0.26), residues: 532 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 126 time to evaluate : 1.126 Fit side-chains outliers start: 27 outliers final: 12 residues processed: 147 average time/residue: 0.1923 time to fit residues: 40.6530 Evaluate side-chains 132 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 120 time to evaluate : 1.057 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.0917 time to fit residues: 3.4043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 0.0070 chunk 60 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 43 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 54 optimal weight: 3.9990 chunk 95 optimal weight: 6.9990 chunk 26 optimal weight: 2.9990 overall best weight: 1.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 354 ASN ** T 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 85 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.3738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.050 9051 Z= 0.230 Angle : 0.604 8.653 12258 Z= 0.297 Chirality : 0.044 0.159 1373 Planarity : 0.005 0.078 1547 Dihedral : 6.155 65.574 1245 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.80 % Favored : 94.11 % Rotamer Outliers : 2.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.08 % 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: -2.29 (0.25), residues: 1104 helix: -0.95 (0.25), residues: 452 sheet: -1.38 (0.51), residues: 110 loop : -2.04 (0.26), residues: 542 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 128 time to evaluate : 1.084 Fit side-chains outliers start: 19 outliers final: 6 residues processed: 144 average time/residue: 0.1915 time to fit residues: 39.5062 Evaluate side-chains 123 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 117 time to evaluate : 1.018 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0804 time to fit residues: 2.2917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 6.9990 chunk 95 optimal weight: 0.0980 chunk 21 optimal weight: 0.0010 chunk 62 optimal weight: 0.0370 chunk 26 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 chunk 49 optimal weight: 4.9990 chunk 8 optimal weight: 0.1980 chunk 55 optimal weight: 2.9990 chunk 102 optimal weight: 5.9990 overall best weight: 0.6666 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 372 GLN ** T 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 85 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.3965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.046 9051 Z= 0.154 Angle : 0.568 10.413 12258 Z= 0.276 Chirality : 0.043 0.259 1373 Planarity : 0.004 0.081 1547 Dihedral : 5.899 64.065 1245 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.16 % Favored : 94.75 % Rotamer Outliers : 1.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.08 % 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: -1.93 (0.26), residues: 1104 helix: -0.53 (0.26), residues: 447 sheet: -1.11 (0.51), residues: 122 loop : -1.96 (0.26), residues: 535 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 122 time to evaluate : 0.922 Fit side-chains outliers start: 15 outliers final: 5 residues processed: 134 average time/residue: 0.1858 time to fit residues: 36.2027 Evaluate side-chains 120 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 115 time to evaluate : 1.020 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0828 time to fit residues: 2.1640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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-4807/modules/cctbx_project/iotbx/cli_parser.py", line 864, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 736, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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-4807/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-4807/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-4807/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-4807/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-4807/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-4807/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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-4807/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-4807/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-4807/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-4807/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: 54.3768 > 50: distance: 0 - 1: 15.164 distance: 1 - 2: 22.067 distance: 1 - 4: 11.172 distance: 2 - 3: 18.964 distance: 2 - 8: 7.263 distance: 4 - 5: 11.973 distance: 4 - 6: 7.450 distance: 5 - 7: 8.970 distance: 8 - 9: 16.596 distance: 9 - 10: 3.449 distance: 9 - 12: 8.206 distance: 10 - 11: 22.907 distance: 10 - 18: 31.939 distance: 12 - 13: 6.993 distance: 13 - 14: 14.468 distance: 13 - 15: 7.887 distance: 14 - 16: 10.408 distance: 15 - 17: 13.639 distance: 16 - 17: 13.410 distance: 18 - 19: 17.461 distance: 19 - 20: 21.243 distance: 19 - 22: 12.409 distance: 20 - 21: 13.849 distance: 20 - 28: 17.282 distance: 22 - 23: 6.457 distance: 23 - 24: 3.266 distance: 23 - 25: 22.111 distance: 24 - 26: 11.725 distance: 25 - 27: 5.979 distance: 26 - 27: 16.184 distance: 28 - 29: 3.286 distance: 29 - 30: 6.371 distance: 29 - 32: 6.870 distance: 30 - 31: 6.136 distance: 30 - 35: 4.192 distance: 32 - 33: 8.346 distance: 32 - 34: 13.235 distance: 35 - 36: 5.692 distance: 36 - 37: 5.912 distance: 36 - 39: 9.087 distance: 37 - 38: 14.094 distance: 37 - 42: 9.829 distance: 39 - 40: 5.702 distance: 39 - 41: 21.295 distance: 43 - 44: 4.714 distance: 44 - 45: 8.645 distance: 46 - 47: 5.447 distance: 47 - 48: 5.325 distance: 48 - 50: 7.376 distance: 51 - 52: 7.426 distance: 52 - 53: 10.852 distance: 52 - 55: 8.006 distance: 53 - 54: 11.060 distance: 53 - 59: 11.158 distance: 55 - 56: 5.506 distance: 56 - 57: 6.658 distance: 56 - 58: 6.077 distance: 59 - 60: 7.692 distance: 60 - 61: 6.414 distance: 61 - 62: 3.967 distance: 61 - 63: 4.604 distance: 63 - 64: 7.769 distance: 64 - 65: 8.061 distance: 65 - 66: 5.178 distance: 65 - 67: 3.694