Starting phenix.real_space_refine (version: 1.21rc1) on Fri Apr 21 02:46:06 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cqk_30442/04_2023/7cqk_30442_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cqk_30442/04_2023/7cqk_30442.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cqk_30442/04_2023/7cqk_30442_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_30442/04_2023/7cqk_30442_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cqk_30442/04_2023/7cqk_30442_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cqk_30442/04_2023/7cqk_30442.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cqk_30442/04_2023/7cqk_30442.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cqk_30442/04_2023/7cqk_30442_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cqk_30442/04_2023/7cqk_30442_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 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. 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-1.21rc1-4938/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: 4.89, per 1000 atoms: 0.55 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: 3.21 Conformation dependent library (CDL) restraints added in 1.5 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: 0.86 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: 2.11 Time building geometry restraints manager: 3.50 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 1.300 1.499 -0.199 2.00e-02 2.50e+03 9.87e+01 bond pdb=" C1' GE0 A 201 " pdb=" O4' GE0 A 201 " ideal model delta sigma weight residual 1.619 1.433 0.186 2.00e-02 2.50e+03 8.61e+01 bond pdb=" C4' GE0 A 201 " pdb=" O4' GE0 A 201 " ideal model delta sigma weight residual 1.268 1.440 -0.172 2.00e-02 2.50e+03 7.40e+01 bond pdb=" CAE GE0 A 201 " pdb=" NAD GE0 A 201 " ideal model delta sigma weight residual 1.496 1.342 0.154 2.00e-02 2.50e+03 5.89e+01 bond pdb=" C6 GE0 A 201 " pdb=" N6 GE0 A 201 " ideal model delta sigma weight residual 1.459 1.330 0.129 2.00e-02 2.50e+03 4.16e+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 - 17.47: 4635 17.47 - 34.94: 402 34.94 - 52.41: 248 52.41 - 69.89: 96 69.89 - 87.36: 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: 295 0.160 - 0.241: 54 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 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: 0.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.010 Extract box with map and model: 4.400 Check model and map are aligned: 0.150 Set scattering table: 0.080 Process input model: 24.910 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 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 : 0.011 0.199 9051 Z= 0.700 Angle : 1.337 14.192 12258 Z= 0.810 Chirality : 0.082 0.401 1373 Planarity : 0.007 0.082 1547 Dihedral : 19.231 87.358 3325 Min Nonbonded Distance : 0.963 Molprobity Statistics. All-atom Clashscore : 29.97 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 : 1.091 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: 0.2667 time to fit residues: 128.3124 Evaluate side-chains 242 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 141 time to evaluate : 1.151 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 101 outliers final: 2 residues processed: 101 average time/residue: 0.1353 time to fit residues: 22.4805 ------------------------------------------------------------------------------- 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 65 GLN 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: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.2856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 9051 Z= 0.200 Angle : 0.697 8.598 12258 Z= 0.351 Chirality : 0.045 0.178 1373 Planarity : 0.005 0.061 1547 Dihedral : 7.169 64.827 1245 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.62 % Favored : 94.11 % Rotamer Outliers : 3.09 % 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: -3.86 (0.22), residues: 1104 helix: -2.74 (0.20), residues: 436 sheet: -2.26 (0.51), residues: 99 loop : -2.44 (0.24), residues: 569 *********************** 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 188 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 159 time to evaluate : 1.057 Fit side-chains revert: symmetry clash outliers start: 29 outliers final: 13 residues processed: 178 average time/residue: 0.2108 time to fit residues: 52.3459 Evaluate side-chains 140 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 127 time to evaluate : 1.070 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1124 time to fit residues: 3.8917 ------------------------------------------------------------------------------- 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: 3.9990 chunk 68 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 100 optimal weight: 0.6980 chunk 108 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 80 optimal weight: 5.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.3291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.056 9051 Z= 0.336 Angle : 0.714 9.359 12258 Z= 0.353 Chirality : 0.047 0.163 1373 Planarity : 0.005 0.061 1547 Dihedral : 6.955 58.524 1245 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.79 % Favored : 93.12 % Rotamer Outliers : 3.20 % 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: -3.17 (0.23), residues: 1104 helix: -1.85 (0.23), residues: 443 sheet: -2.03 (0.52), residues: 98 loop : -2.31 (0.24), residues: 563 *********************** 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 162 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 132 time to evaluate : 1.124 Fit side-chains revert: symmetry clash outliers start: 30 outliers final: 14 residues processed: 156 average time/residue: 0.1861 time to fit residues: 42.3786 Evaluate side-chains 136 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 122 time to evaluate : 0.973 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1099 time to fit residues: 4.0419 ------------------------------------------------------------------------------- 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: 3.9990 chunk 75 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 47 optimal weight: 5.9990 chunk 67 optimal weight: 2.9990 chunk 100 optimal weight: 0.7980 chunk 106 optimal weight: 0.0770 chunk 52 optimal weight: 1.9990 chunk 95 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 overall best weight: 1.3742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** T 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 85 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.3552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.054 9051 Z= 0.225 Angle : 0.611 8.654 12258 Z= 0.304 Chirality : 0.044 0.159 1373 Planarity : 0.005 0.071 1547 Dihedral : 6.720 59.375 1245 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.34 % Favored : 94.57 % Rotamer Outliers : 2.45 % 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: -2.59 (0.25), residues: 1104 helix: -1.27 (0.24), residues: 448 sheet: -1.54 (0.51), residues: 110 loop : -2.12 (0.26), residues: 546 *********************** 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 150 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 127 time to evaluate : 1.090 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 9 residues processed: 147 average time/residue: 0.1884 time to fit residues: 40.2676 Evaluate side-chains 129 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 120 time to evaluate : 1.098 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0891 time to fit residues: 2.9688 ------------------------------------------------------------------------------- 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: 4.9990 chunk 60 optimal weight: 2.9990 chunk 1 optimal weight: 0.0020 chunk 79 optimal weight: 4.9990 chunk 43 optimal weight: 0.7980 chunk 90 optimal weight: 5.9990 chunk 73 optimal weight: 0.4980 chunk 0 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 chunk 95 optimal weight: 6.9990 chunk 26 optimal weight: 3.9990 overall best weight: 1.4592 ------------------------------------------------------------------------------- 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: 0.8253 moved from start: 0.3709 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= 0.239 Angle : 0.608 9.109 12258 Z= 0.299 Chirality : 0.044 0.160 1373 Planarity : 0.005 0.078 1547 Dihedral : 6.556 58.815 1245 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.25 % Favored : 93.66 % Rotamer Outliers : 2.24 % 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: -2.34 (0.25), residues: 1104 helix: -0.95 (0.25), residues: 451 sheet: -1.46 (0.51), residues: 110 loop : -2.08 (0.26), residues: 543 *********************** 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 152 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 131 time to evaluate : 1.074 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 7 residues processed: 148 average time/residue: 0.2043 time to fit residues: 43.1989 Evaluate side-chains 127 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 120 time to evaluate : 1.065 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0859 time to fit residues: 2.5568 ------------------------------------------------------------------------------- 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: 9.9990 chunk 95 optimal weight: 6.9990 chunk 21 optimal weight: 0.0970 chunk 62 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 106 optimal weight: 2.9990 chunk 88 optimal weight: 0.0970 chunk 49 optimal weight: 0.9990 chunk 8 optimal weight: 0.5980 chunk 55 optimal weight: 0.7980 chunk 102 optimal weight: 7.9990 overall best weight: 0.5178 ------------------------------------------------------------------------------- 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: 0.8202 moved from start: 0.3959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.045 9051 Z= 0.141 Angle : 0.545 10.384 12258 Z= 0.269 Chirality : 0.042 0.147 1373 Planarity : 0.004 0.081 1547 Dihedral : 6.184 57.481 1245 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.80 % Favored : 95.11 % Rotamer Outliers : 2.24 % 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: -1.84 (0.26), residues: 1104 helix: -0.42 (0.26), residues: 444 sheet: -0.98 (0.53), residues: 118 loop : -1.98 (0.26), residues: 542 *********************** 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 149 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 128 time to evaluate : 1.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 10 residues processed: 144 average time/residue: 0.1839 time to fit residues: 38.8634 Evaluate side-chains 127 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 117 time to evaluate : 0.989 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0935 time to fit residues: 3.1339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 89 optimal weight: 5.9990 chunk 59 optimal weight: 0.7980 chunk 106 optimal weight: 1.9990 chunk 66 optimal weight: 0.0070 chunk 64 optimal weight: 4.9990 chunk 48 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 42 optimal weight: 0.0870 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 102 ASN T 125 ASN T 242 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.4131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.044 9051 Z= 0.145 Angle : 0.554 9.163 12258 Z= 0.269 Chirality : 0.042 0.143 1373 Planarity : 0.004 0.083 1547 Dihedral : 5.901 55.877 1245 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.43 % Favored : 94.47 % 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: -1.63 (0.26), residues: 1104 helix: -0.14 (0.27), residues: 441 sheet: -0.94 (0.52), residues: 118 loop : -1.93 (0.26), residues: 545 *********************** REFINEMENT MACRO_CYCLE 7 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 : 1.160 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 3 residues processed: 134 average time/residue: 0.1675 time to fit residues: 34.2648 Evaluate side-chains 118 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 115 time to evaluate : 1.103 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0874 time to fit residues: 1.9269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 20 optimal weight: 0.0970 chunk 67 optimal weight: 0.7980 chunk 72 optimal weight: 2.9990 chunk 52 optimal weight: 5.9990 chunk 9 optimal weight: 4.9990 chunk 83 optimal weight: 3.9990 chunk 96 optimal weight: 0.0770 chunk 101 optimal weight: 0.9980 chunk 92 optimal weight: 2.9990 overall best weight: 0.9938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 102 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.4164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 9051 Z= 0.183 Angle : 0.569 8.873 12258 Z= 0.280 Chirality : 0.044 0.160 1373 Planarity : 0.004 0.080 1547 Dihedral : 5.867 55.780 1245 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.07 % Favored : 94.84 % Rotamer Outliers : 0.75 % 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: -1.50 (0.26), residues: 1104 helix: -0.02 (0.27), residues: 448 sheet: -0.97 (0.52), residues: 118 loop : -1.87 (0.26), residues: 538 *********************** REFINEMENT MACRO_CYCLE 8 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 128 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 121 time to evaluate : 1.099 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 128 average time/residue: 0.1816 time to fit residues: 34.4987 Evaluate side-chains 119 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 115 time to evaluate : 1.081 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0849 time to fit residues: 2.0799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 7.9990 chunk 101 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 30 optimal weight: 0.4980 chunk 89 optimal weight: 0.8980 chunk 93 optimal weight: 10.0000 chunk 64 optimal weight: 3.9990 chunk 104 optimal weight: 0.0770 chunk 63 optimal weight: 0.6980 overall best weight: 0.8340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 102 ASN T 165 ASN A 85 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.4249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 9051 Z= 0.169 Angle : 0.556 8.353 12258 Z= 0.273 Chirality : 0.043 0.189 1373 Planarity : 0.004 0.081 1547 Dihedral : 5.822 55.291 1245 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.25 % Favored : 94.66 % Rotamer Outliers : 0.32 % 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: -1.38 (0.26), residues: 1104 helix: 0.16 (0.27), residues: 442 sheet: -1.00 (0.51), residues: 118 loop : -1.83 (0.26), residues: 544 *********************** REFINEMENT MACRO_CYCLE 9 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 123 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 120 time to evaluate : 1.164 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 122 average time/residue: 0.1767 time to fit residues: 32.3859 Evaluate side-chains 117 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 116 time to evaluate : 1.115 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0918 time to fit residues: 1.7337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 0.0370 chunk 72 optimal weight: 0.5980 chunk 109 optimal weight: 7.9990 chunk 100 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 67 optimal weight: 0.0970 chunk 53 optimal weight: 4.9990 chunk 69 optimal weight: 0.8980 chunk 92 optimal weight: 2.9990 chunk 26 optimal weight: 0.2980 overall best weight: 0.3856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 102 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.4417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.041 9051 Z= 0.133 Angle : 0.540 9.079 12258 Z= 0.264 Chirality : 0.042 0.185 1373 Planarity : 0.004 0.080 1547 Dihedral : 5.590 51.775 1245 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.71 % Favored : 95.20 % Rotamer Outliers : 0.43 % 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: -1.19 (0.26), residues: 1104 helix: 0.37 (0.27), residues: 442 sheet: -0.98 (0.52), residues: 117 loop : -1.75 (0.26), residues: 545 ********************** REFINEMENT MACRO_CYCLE 10 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 133 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 129 time to evaluate : 1.106 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 133 average time/residue: 0.1744 time to fit residues: 34.4832 Evaluate side-chains 122 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 121 time to evaluate : 1.002 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0874 time to fit residues: 1.5071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 0.0000 chunk 12 optimal weight: 0.2980 chunk 24 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 chunk 36 optimal weight: 0.0570 chunk 89 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 4 optimal weight: 0.0470 chunk 63 optimal weight: 4.9990 overall best weight: 0.2802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.128760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.103857 restraints weight = 13062.211| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 2.01 r_work: 0.3041 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2910 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2916 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2916 r_free = 0.2916 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2916 r_free = 0.2916 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2916 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.4512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.041 9051 Z= 0.127 Angle : 0.538 9.043 12258 Z= 0.263 Chirality : 0.042 0.155 1373 Planarity : 0.004 0.079 1547 Dihedral : 5.459 49.385 1245 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.80 % Favored : 95.11 % Rotamer Outliers : 0.11 % 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: -1.06 (0.26), residues: 1104 helix: 0.48 (0.27), residues: 442 sheet: -0.92 (0.52), residues: 115 loop : -1.68 (0.26), residues: 547 =============================================================================== Job complete usr+sys time: 2146.86 seconds wall clock time: 39 minutes 34.23 seconds (2374.23 seconds total)