Starting phenix.real_space_refine on Mon Mar 11 19:20:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cqk_30442/03_2024/7cqk_30442_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cqk_30442/03_2024/7cqk_30442.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cqk_30442/03_2024/7cqk_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_30442/03_2024/7cqk_30442_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cqk_30442/03_2024/7cqk_30442_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cqk_30442/03_2024/7cqk_30442.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cqk_30442/03_2024/7cqk_30442.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cqk_30442/03_2024/7cqk_30442_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cqk_30442/03_2024/7cqk_30442_updated.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs 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-dev-5265/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: 4.91, 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: 3.55 Conformation dependent library (CDL) restraints added in 1.8 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: 1.83 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: 2.12 Time building geometry restraints manager: 3.85 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 - 17.53: 4638 17.53 - 35.07: 410 35.07 - 52.60: 253 52.60 - 70.13: 90 70.13 - 87.66: 13 Dihedral angle restraints: 5404 sinusoidal: 2174 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 5401 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: 0.670 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: 4.000 Check model and map are aligned: 0.120 Set scattering table: 0.090 Process input model: 27.130 Find NCS groups from input model: 0.240 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:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.030 ------------------------------------------------------------------------------- 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 : 19.321 87.664 3336 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 % Allowed : 10.25 % Favored : 68.09 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP T 134 HIS 0.011 0.001 HIS S 91 PHE 0.036 0.003 PHE T 280 TYR 0.047 0.002 TYR T 474 ARG 0.010 0.001 ARG S 445 *********************** 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 : 0.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: S 57 LYS cc_start: 0.8370 (mtmt) cc_final: 0.7885 (tmtt) REVERT: S 160 GLU cc_start: 0.7702 (tt0) cc_final: 0.7499 (tt0) REVERT: S 203 ARG cc_start: 0.7888 (OUTLIER) cc_final: 0.7677 (mmt-90) REVERT: S 217 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8649 (tp) REVERT: S 264 LYS cc_start: 0.8827 (OUTLIER) cc_final: 0.8536 (tttt) REVERT: S 388 GLU cc_start: 0.8858 (OUTLIER) cc_final: 0.7850 (mp0) REVERT: S 401 SER cc_start: 0.8552 (OUTLIER) cc_final: 0.8322 (t) REVERT: S 418 GLN cc_start: 0.8483 (OUTLIER) cc_final: 0.8144 (tt0) REVERT: T 50 GLN cc_start: 0.6206 (OUTLIER) cc_final: 0.5875 (tp40) REVERT: T 57 ARG cc_start: 0.8168 (ttm170) cc_final: 0.7859 (ptm160) REVERT: T 88 ARG cc_start: 0.8687 (OUTLIER) cc_final: 0.7803 (mmm160) REVERT: T 113 SER cc_start: 0.7664 (OUTLIER) cc_final: 0.7380 (m) REVERT: T 189 GLN cc_start: 0.8727 (OUTLIER) cc_final: 0.7338 (tp40) REVERT: T 261 LEU cc_start: 0.8890 (OUTLIER) cc_final: 0.8653 (pp) REVERT: T 440 GLN cc_start: 0.8432 (mm110) cc_final: 0.8153 (mt0) REVERT: T 506 SER cc_start: 0.8386 (OUTLIER) cc_final: 0.8116 (p) REVERT: T 543 ARG cc_start: 0.7060 (OUTLIER) cc_final: 0.6459 (ttt180) REVERT: A 17 MET cc_start: 0.5155 (pp-130) cc_final: 0.3616 (mtt) REVERT: A 77 GLN cc_start: 0.8866 (OUTLIER) cc_final: 0.7950 (mp10) REVERT: A 138 LYS cc_start: 0.8136 (OUTLIER) cc_final: 0.7031 (mmtt) REVERT: A 146 ARG cc_start: 0.6922 (OUTLIER) cc_final: 0.5666 (mmm-85) REVERT: E 33 GLU cc_start: 0.8109 (OUTLIER) cc_final: 0.7296 (mp0) REVERT: C 37 ARG cc_start: 0.7030 (mpt-90) cc_final: 0.6145 (tpt90) outliers start: 203 outliers final: 101 residues processed: 372 average time/residue: 0.2588 time to fit residues: 124.8076 Evaluate side-chains 260 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 142 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 52 LEU Chi-restraints excluded: chain S residue 73 VAL Chi-restraints excluded: chain S residue 80 LEU Chi-restraints excluded: chain S residue 95 VAL Chi-restraints excluded: chain S residue 127 LYS Chi-restraints excluded: chain S residue 146 LEU Chi-restraints excluded: chain S residue 151 ARG Chi-restraints excluded: chain S residue 184 ILE Chi-restraints excluded: chain S residue 189 ARG Chi-restraints excluded: chain S residue 203 ARG Chi-restraints excluded: chain S residue 208 LEU Chi-restraints excluded: chain S residue 217 LEU Chi-restraints excluded: chain S residue 234 LYS Chi-restraints excluded: chain S residue 239 ARG Chi-restraints excluded: chain S residue 244 VAL Chi-restraints excluded: chain S residue 249 MET Chi-restraints excluded: chain S residue 251 THR Chi-restraints excluded: chain S residue 257 LEU Chi-restraints excluded: chain S residue 264 LYS Chi-restraints excluded: chain S residue 267 TYR Chi-restraints excluded: chain S residue 277 LEU Chi-restraints excluded: chain S residue 291 GLU Chi-restraints excluded: chain S residue 300 ILE Chi-restraints excluded: chain S residue 313 SER Chi-restraints excluded: chain S residue 331 SER Chi-restraints excluded: chain S residue 362 ILE Chi-restraints excluded: chain S residue 377 LEU Chi-restraints excluded: chain S residue 381 SER Chi-restraints excluded: chain S residue 388 GLU Chi-restraints excluded: chain S residue 396 LEU Chi-restraints excluded: chain S residue 401 SER Chi-restraints excluded: chain S residue 408 ASP Chi-restraints excluded: chain S residue 411 LEU Chi-restraints excluded: chain S residue 414 GLU Chi-restraints excluded: chain S residue 418 GLN Chi-restraints excluded: chain S residue 423 SER Chi-restraints excluded: chain S residue 435 GLU Chi-restraints excluded: chain S residue 448 VAL Chi-restraints excluded: chain S residue 449 THR Chi-restraints excluded: chain S residue 451 GLU Chi-restraints excluded: chain S residue 453 THR Chi-restraints excluded: chain S residue 459 ARG Chi-restraints excluded: chain S residue 467 VAL Chi-restraints excluded: chain T residue 50 GLN Chi-restraints excluded: chain T residue 54 LEU Chi-restraints excluded: chain T residue 61 GLU Chi-restraints excluded: chain T residue 64 GLU Chi-restraints excluded: chain T residue 66 THR Chi-restraints excluded: chain T residue 69 LEU Chi-restraints excluded: chain T residue 87 LEU Chi-restraints excluded: chain T residue 88 ARG Chi-restraints excluded: chain T residue 99 CYS Chi-restraints excluded: chain T residue 111 PHE Chi-restraints excluded: chain T residue 113 SER Chi-restraints excluded: chain T residue 114 LEU Chi-restraints excluded: chain T residue 116 GLN Chi-restraints excluded: chain T residue 124 ARG Chi-restraints excluded: chain T residue 163 THR Chi-restraints excluded: chain T residue 189 GLN Chi-restraints excluded: chain T residue 261 LEU Chi-restraints excluded: chain T residue 273 SER Chi-restraints excluded: chain T residue 297 VAL Chi-restraints excluded: chain T residue 300 GLN Chi-restraints excluded: chain T residue 314 VAL Chi-restraints excluded: chain T residue 315 GLU Chi-restraints excluded: chain T residue 320 MET Chi-restraints excluded: chain T residue 324 ILE Chi-restraints excluded: chain T residue 325 VAL Chi-restraints excluded: chain T residue 344 ASP Chi-restraints excluded: chain T residue 349 ILE Chi-restraints excluded: chain T residue 352 LEU Chi-restraints excluded: chain T residue 357 ARG Chi-restraints excluded: chain T residue 371 ASP Chi-restraints excluded: chain T residue 373 MET Chi-restraints excluded: chain T residue 374 MET Chi-restraints excluded: chain T residue 380 SER Chi-restraints excluded: chain T residue 406 VAL Chi-restraints excluded: chain T residue 465 ASP Chi-restraints excluded: chain T residue 496 VAL Chi-restraints excluded: chain T residue 503 ILE Chi-restraints excluded: chain T residue 504 ILE Chi-restraints excluded: chain T residue 506 SER Chi-restraints excluded: chain T residue 539 TYR Chi-restraints excluded: chain T residue 543 ARG Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 68 LYS Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 77 GLN Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 89 MET Chi-restraints excluded: chain A residue 94 GLN Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 138 LYS Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 146 ARG Chi-restraints excluded: chain E residue 11 LYS Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 32 TRP Chi-restraints excluded: chain E residue 33 GLU Chi-restraints excluded: chain E residue 40 MET Chi-restraints excluded: chain E residue 41 LEU Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 43 SER Chi-restraints excluded: chain E residue 44 ILE Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 28 GLU Chi-restraints excluded: chain C residue 32 ILE Chi-restraints excluded: chain C residue 34 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 4.9990 chunk 83 optimal weight: 2.9990 chunk 46 optimal weight: 0.2980 chunk 28 optimal weight: 0.4980 chunk 56 optimal weight: 0.9990 chunk 44 optimal weight: 4.9990 chunk 86 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- 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 47 HIS T 263 HIS T 286 GLN T 445 ASN A 18 ASN A 53 ASN A 57 ASN A 85 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.2587 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= 0.202 Angle : 0.691 8.426 12258 Z= 0.348 Chirality : 0.046 0.175 1373 Planarity : 0.006 0.061 1547 Dihedral : 15.840 109.616 1516 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.80 % Favored : 93.93 % Rotamer: Outliers : 9.50 % Allowed : 18.46 % Favored : 72.04 % 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: -3.91 (0.22), residues: 1104 helix: -2.73 (0.20), residues: 440 sheet: -2.14 (0.48), residues: 113 loop : -2.54 (0.24), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP T 134 HIS 0.005 0.001 HIS S 77 PHE 0.015 0.001 PHE T 111 TYR 0.017 0.001 TYR T 474 ARG 0.003 0.000 ARG S 459 *********************** 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 245 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 156 time to evaluate : 0.974 Fit side-chains revert: symmetry clash REVERT: S 57 LYS cc_start: 0.8164 (mtmt) cc_final: 0.7667 (tttt) REVERT: S 160 GLU cc_start: 0.7654 (tt0) cc_final: 0.7417 (tt0) REVERT: S 388 GLU cc_start: 0.8971 (OUTLIER) cc_final: 0.8085 (mp0) REVERT: S 390 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8516 (pp) REVERT: S 418 GLN cc_start: 0.8382 (OUTLIER) cc_final: 0.7995 (tt0) REVERT: S 423 SER cc_start: 0.6571 (OUTLIER) cc_final: 0.6049 (p) REVERT: S 464 ILE cc_start: 0.9091 (tt) cc_final: 0.8850 (tt) REVERT: T 57 ARG cc_start: 0.8015 (ttm170) cc_final: 0.7809 (ptm160) REVERT: T 88 ARG cc_start: 0.8706 (OUTLIER) cc_final: 0.7968 (mmm160) REVERT: T 261 LEU cc_start: 0.9059 (OUTLIER) cc_final: 0.8725 (pp) REVERT: T 327 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8549 (tp) REVERT: T 357 ARG cc_start: 0.9286 (OUTLIER) cc_final: 0.8828 (mmt-90) REVERT: A 17 MET cc_start: 0.5095 (pp-130) cc_final: 0.3398 (mtt) REVERT: A 138 LYS cc_start: 0.8012 (OUTLIER) cc_final: 0.7009 (mmtt) REVERT: A 146 ARG cc_start: 0.6698 (OUTLIER) cc_final: 0.5800 (mmm-85) REVERT: E 50 TYR cc_start: 0.7038 (t80) cc_final: 0.6729 (t80) outliers start: 89 outliers final: 49 residues processed: 221 average time/residue: 0.2118 time to fit residues: 63.8097 Evaluate side-chains 185 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 126 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 73 VAL Chi-restraints excluded: chain S residue 77 HIS Chi-restraints excluded: chain S residue 80 LEU Chi-restraints excluded: chain S residue 113 ASP Chi-restraints excluded: chain S residue 114 ASN Chi-restraints excluded: chain S residue 146 LEU Chi-restraints excluded: chain S residue 184 ILE Chi-restraints excluded: chain S residue 189 ARG Chi-restraints excluded: chain S residue 208 LEU Chi-restraints excluded: chain S residue 239 ARG Chi-restraints excluded: chain S residue 244 VAL Chi-restraints excluded: chain S residue 249 MET Chi-restraints excluded: chain S residue 251 THR Chi-restraints excluded: chain S residue 257 LEU Chi-restraints excluded: chain S residue 277 LEU Chi-restraints excluded: chain S residue 369 LYS Chi-restraints excluded: chain S residue 388 GLU Chi-restraints excluded: chain S residue 390 LEU Chi-restraints excluded: chain S residue 396 LEU Chi-restraints excluded: chain S residue 411 LEU Chi-restraints excluded: chain S residue 418 GLN Chi-restraints excluded: chain S residue 423 SER Chi-restraints excluded: chain S residue 426 LEU Chi-restraints excluded: chain S residue 448 VAL Chi-restraints excluded: chain S residue 454 GLU Chi-restraints excluded: chain T residue 54 LEU Chi-restraints excluded: chain T residue 64 GLU Chi-restraints excluded: chain T residue 66 THR Chi-restraints excluded: chain T residue 87 LEU Chi-restraints excluded: chain T residue 88 ARG Chi-restraints excluded: chain T residue 111 PHE Chi-restraints excluded: chain T residue 163 THR Chi-restraints excluded: chain T residue 261 LEU Chi-restraints excluded: chain T residue 300 GLN Chi-restraints excluded: chain T residue 317 ILE Chi-restraints excluded: chain T residue 327 LEU Chi-restraints excluded: chain T residue 344 ASP Chi-restraints excluded: chain T residue 357 ARG Chi-restraints excluded: chain T residue 371 ASP Chi-restraints excluded: chain T residue 372 VAL Chi-restraints excluded: chain T residue 465 ASP Chi-restraints excluded: chain T residue 496 VAL Chi-restraints excluded: chain T residue 504 ILE Chi-restraints excluded: chain T residue 539 TYR Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 89 MET Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 138 LYS Chi-restraints excluded: chain A residue 146 ARG Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 41 LEU Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 32 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 3.9990 chunk 31 optimal weight: 6.9990 chunk 83 optimal weight: 5.9990 chunk 68 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 100 optimal weight: 0.9990 chunk 108 optimal weight: 0.3980 chunk 89 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 chunk 34 optimal weight: 0.0670 chunk 80 optimal weight: 0.0470 overall best weight: 0.5018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: T 51 ASN T 245 ASN T 300 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.3086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 9051 Z= 0.155 Angle : 0.602 8.746 12258 Z= 0.298 Chirality : 0.043 0.149 1373 Planarity : 0.005 0.061 1547 Dihedral : 12.221 108.766 1356 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.98 % Favored : 93.93 % Rotamer: Outliers : 7.15 % Allowed : 21.34 % Favored : 71.50 % 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: -3.04 (0.24), residues: 1104 helix: -1.79 (0.23), residues: 436 sheet: -2.17 (0.50), residues: 102 loop : -2.14 (0.25), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 34 HIS 0.017 0.001 HIS S 77 PHE 0.013 0.001 PHE T 111 TYR 0.014 0.001 TYR A 61 ARG 0.003 0.000 ARG S 459 *********************** 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 207 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 140 time to evaluate : 0.994 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: S 57 LYS cc_start: 0.8146 (mtmt) cc_final: 0.7678 (tttt) REVERT: S 77 HIS cc_start: 0.6357 (OUTLIER) cc_final: 0.5102 (m90) REVERT: S 388 GLU cc_start: 0.8976 (OUTLIER) cc_final: 0.8117 (mp0) REVERT: S 418 GLN cc_start: 0.8379 (OUTLIER) cc_final: 0.8051 (tt0) REVERT: S 464 ILE cc_start: 0.9139 (tt) cc_final: 0.8899 (tt) REVERT: T 57 ARG cc_start: 0.7991 (ttm170) cc_final: 0.7764 (ptm160) REVERT: T 88 ARG cc_start: 0.8676 (OUTLIER) cc_final: 0.7952 (mmm160) REVERT: T 90 PHE cc_start: 0.7050 (m-10) cc_final: 0.6658 (t80) REVERT: T 126 LEU cc_start: 0.9022 (tt) cc_final: 0.8707 (mp) REVERT: T 257 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8578 (mt) REVERT: T 300 GLN cc_start: 0.8827 (OUTLIER) cc_final: 0.7762 (mp10) REVERT: T 305 ARG cc_start: 0.7393 (mtp180) cc_final: 0.7024 (mtp180) REVERT: T 327 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8480 (tp) REVERT: T 357 ARG cc_start: 0.9304 (OUTLIER) cc_final: 0.8850 (mmt-90) REVERT: A 17 MET cc_start: 0.4944 (pp-130) cc_final: 0.3513 (mtm) REVERT: A 135 LEU cc_start: 0.8387 (OUTLIER) cc_final: 0.8086 (mm) REVERT: A 138 LYS cc_start: 0.8061 (OUTLIER) cc_final: 0.7169 (mmtt) REVERT: A 146 ARG cc_start: 0.7069 (OUTLIER) cc_final: 0.5892 (mmm-85) REVERT: E 50 TYR cc_start: 0.7219 (t80) cc_final: 0.6951 (t80) outliers start: 67 outliers final: 39 residues processed: 195 average time/residue: 0.2072 time to fit residues: 55.7855 Evaluate side-chains 180 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 130 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 77 HIS Chi-restraints excluded: chain S residue 81 ASN Chi-restraints excluded: chain S residue 113 ASP Chi-restraints excluded: chain S residue 166 TYR Chi-restraints excluded: chain S residue 184 ILE Chi-restraints excluded: chain S residue 189 ARG Chi-restraints excluded: chain S residue 208 LEU Chi-restraints excluded: chain S residue 239 ARG Chi-restraints excluded: chain S residue 247 LEU Chi-restraints excluded: chain S residue 251 THR Chi-restraints excluded: chain S residue 369 LYS Chi-restraints excluded: chain S residue 388 GLU Chi-restraints excluded: chain S residue 396 LEU Chi-restraints excluded: chain S residue 418 GLN Chi-restraints excluded: chain S residue 426 LEU Chi-restraints excluded: chain S residue 448 VAL Chi-restraints excluded: chain S residue 453 THR Chi-restraints excluded: chain T residue 66 THR Chi-restraints excluded: chain T residue 87 LEU Chi-restraints excluded: chain T residue 88 ARG Chi-restraints excluded: chain T residue 89 ASP Chi-restraints excluded: chain T residue 111 PHE Chi-restraints excluded: chain T residue 196 LEU Chi-restraints excluded: chain T residue 257 LEU Chi-restraints excluded: chain T residue 261 LEU Chi-restraints excluded: chain T residue 300 GLN Chi-restraints excluded: chain T residue 317 ILE Chi-restraints excluded: chain T residue 327 LEU Chi-restraints excluded: chain T residue 344 ASP Chi-restraints excluded: chain T residue 355 THR Chi-restraints excluded: chain T residue 357 ARG Chi-restraints excluded: chain T residue 371 ASP Chi-restraints excluded: chain T residue 372 VAL Chi-restraints excluded: chain T residue 465 ASP Chi-restraints excluded: chain T residue 496 VAL Chi-restraints excluded: chain T residue 503 ILE Chi-restraints excluded: chain T residue 504 ILE Chi-restraints excluded: chain T residue 539 TYR Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 138 LYS Chi-restraints excluded: chain A residue 146 ARG Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 41 LEU Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 32 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 0.0770 chunk 75 optimal weight: 5.9990 chunk 51 optimal weight: 8.9990 chunk 11 optimal weight: 4.9990 chunk 47 optimal weight: 10.0000 chunk 67 optimal weight: 0.4980 chunk 100 optimal weight: 0.6980 chunk 106 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 95 optimal weight: 5.9990 chunk 28 optimal weight: 3.9990 overall best weight: 0.8540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 102 ASN S 107 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.3346 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= 0.178 Angle : 0.577 8.186 12258 Z= 0.286 Chirality : 0.043 0.166 1373 Planarity : 0.004 0.064 1547 Dihedral : 10.993 106.112 1328 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.53 % Favored : 94.38 % Rotamer: Outliers : 5.44 % Allowed : 22.73 % Favored : 71.82 % 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: -2.50 (0.25), residues: 1104 helix: -1.21 (0.25), residues: 444 sheet: -1.84 (0.52), residues: 102 loop : -1.98 (0.25), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 34 HIS 0.002 0.000 HIS S 77 PHE 0.014 0.001 PHE T 111 TYR 0.012 0.001 TYR T 539 ARG 0.002 0.000 ARG T 489 *********************** 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 189 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 138 time to evaluate : 1.063 Fit side-chains revert: symmetry clash REVERT: S 57 LYS cc_start: 0.8156 (mtmt) cc_final: 0.7661 (tttt) REVERT: S 388 GLU cc_start: 0.9063 (OUTLIER) cc_final: 0.8188 (mp0) REVERT: S 464 ILE cc_start: 0.9074 (tt) cc_final: 0.8865 (tt) REVERT: T 57 ARG cc_start: 0.8021 (OUTLIER) cc_final: 0.7788 (ptm160) REVERT: T 88 ARG cc_start: 0.8659 (OUTLIER) cc_final: 0.7876 (mmm160) REVERT: T 90 PHE cc_start: 0.7046 (m-10) cc_final: 0.6682 (t80) REVERT: T 261 LEU cc_start: 0.9112 (OUTLIER) cc_final: 0.8665 (pp) REVERT: T 300 GLN cc_start: 0.8833 (OUTLIER) cc_final: 0.7709 (mp10) REVERT: T 327 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8529 (tp) REVERT: T 357 ARG cc_start: 0.9344 (OUTLIER) cc_final: 0.8937 (mmt-90) REVERT: T 369 ASP cc_start: 0.7817 (m-30) cc_final: 0.7520 (m-30) REVERT: A 17 MET cc_start: 0.5310 (pp-130) cc_final: 0.3551 (mtm) REVERT: A 135 LEU cc_start: 0.8272 (OUTLIER) cc_final: 0.7970 (mm) REVERT: A 138 LYS cc_start: 0.7970 (OUTLIER) cc_final: 0.7107 (mmtt) REVERT: A 146 ARG cc_start: 0.6986 (OUTLIER) cc_final: 0.5832 (mmm-85) outliers start: 51 outliers final: 27 residues processed: 180 average time/residue: 0.2084 time to fit residues: 51.7229 Evaluate side-chains 171 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 134 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 77 HIS Chi-restraints excluded: chain S residue 90 SER Chi-restraints excluded: chain S residue 113 ASP Chi-restraints excluded: chain S residue 166 TYR Chi-restraints excluded: chain S residue 189 ARG Chi-restraints excluded: chain S residue 239 ARG Chi-restraints excluded: chain S residue 251 THR Chi-restraints excluded: chain S residue 369 LYS Chi-restraints excluded: chain S residue 388 GLU Chi-restraints excluded: chain S residue 396 LEU Chi-restraints excluded: chain S residue 419 CYS Chi-restraints excluded: chain S residue 426 LEU Chi-restraints excluded: chain S residue 453 THR Chi-restraints excluded: chain T residue 57 ARG Chi-restraints excluded: chain T residue 66 THR Chi-restraints excluded: chain T residue 88 ARG Chi-restraints excluded: chain T residue 111 PHE Chi-restraints excluded: chain T residue 196 LEU Chi-restraints excluded: chain T residue 261 LEU Chi-restraints excluded: chain T residue 300 GLN Chi-restraints excluded: chain T residue 317 ILE Chi-restraints excluded: chain T residue 327 LEU Chi-restraints excluded: chain T residue 344 ASP Chi-restraints excluded: chain T residue 357 ARG Chi-restraints excluded: chain T residue 371 ASP Chi-restraints excluded: chain T residue 372 VAL Chi-restraints excluded: chain T residue 465 ASP Chi-restraints excluded: chain T residue 496 VAL Chi-restraints excluded: chain T residue 504 ILE Chi-restraints excluded: chain T residue 539 TYR Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 138 LYS Chi-restraints excluded: chain A residue 146 ARG Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 41 LEU Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain C residue 32 ILE 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: 3.9990 chunk 1 optimal weight: 0.1980 chunk 79 optimal weight: 3.9990 chunk 43 optimal weight: 0.0670 chunk 90 optimal weight: 0.9980 chunk 73 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 54 optimal weight: 0.8980 chunk 95 optimal weight: 6.9990 chunk 26 optimal weight: 5.9990 overall best weight: 1.2320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 102 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: 0.8230 moved from start: 0.3500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9051 Z= 0.214 Angle : 0.574 7.787 12258 Z= 0.284 Chirality : 0.043 0.147 1373 Planarity : 0.005 0.072 1547 Dihedral : 10.181 102.765 1312 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.89 % Favored : 94.02 % Rotamer: Outliers : 5.23 % Allowed : 23.05 % Favored : 71.72 % 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: -2.21 (0.25), residues: 1104 helix: -0.90 (0.25), residues: 450 sheet: -1.41 (0.52), residues: 114 loop : -1.94 (0.26), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 34 HIS 0.002 0.000 HIS S 77 PHE 0.015 0.001 PHE T 111 TYR 0.015 0.001 TYR A 119 ARG 0.002 0.000 ARG S 151 *********************** 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 180 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 131 time to evaluate : 1.012 Fit side-chains revert: symmetry clash REVERT: S 57 LYS cc_start: 0.8130 (mtmt) cc_final: 0.7625 (tttt) REVERT: S 388 GLU cc_start: 0.9037 (OUTLIER) cc_final: 0.8097 (mp0) REVERT: S 464 ILE cc_start: 0.9079 (tt) cc_final: 0.8876 (tt) REVERT: T 57 ARG cc_start: 0.8026 (OUTLIER) cc_final: 0.7780 (ptm160) REVERT: T 88 ARG cc_start: 0.8660 (OUTLIER) cc_final: 0.7846 (mmm160) REVERT: T 90 PHE cc_start: 0.7093 (m-10) cc_final: 0.6706 (t80) REVERT: T 261 LEU cc_start: 0.9114 (OUTLIER) cc_final: 0.8680 (pp) REVERT: T 300 GLN cc_start: 0.8835 (OUTLIER) cc_final: 0.7724 (mp10) REVERT: T 327 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8566 (tp) REVERT: T 357 ARG cc_start: 0.9356 (OUTLIER) cc_final: 0.8899 (mmt-90) REVERT: T 369 ASP cc_start: 0.7796 (m-30) cc_final: 0.7522 (m-30) REVERT: A 17 MET cc_start: 0.5563 (pp-130) cc_final: 0.3550 (mtm) REVERT: A 120 ASP cc_start: 0.7257 (m-30) cc_final: 0.7028 (m-30) REVERT: A 135 LEU cc_start: 0.8276 (OUTLIER) cc_final: 0.7966 (mm) REVERT: A 138 LYS cc_start: 0.7967 (OUTLIER) cc_final: 0.7126 (mmtt) REVERT: A 146 ARG cc_start: 0.7055 (OUTLIER) cc_final: 0.5891 (mmm-85) outliers start: 49 outliers final: 30 residues processed: 171 average time/residue: 0.2204 time to fit residues: 51.5524 Evaluate side-chains 169 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 129 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 77 HIS Chi-restraints excluded: chain S residue 81 ASN Chi-restraints excluded: chain S residue 90 SER Chi-restraints excluded: chain S residue 113 ASP Chi-restraints excluded: chain S residue 166 TYR Chi-restraints excluded: chain S residue 189 ARG Chi-restraints excluded: chain S residue 239 ARG Chi-restraints excluded: chain S residue 251 THR Chi-restraints excluded: chain S residue 344 LEU Chi-restraints excluded: chain S residue 369 LYS Chi-restraints excluded: chain S residue 388 GLU Chi-restraints excluded: chain S residue 419 CYS Chi-restraints excluded: chain S residue 426 LEU Chi-restraints excluded: chain S residue 453 THR Chi-restraints excluded: chain T residue 57 ARG Chi-restraints excluded: chain T residue 66 THR Chi-restraints excluded: chain T residue 87 LEU Chi-restraints excluded: chain T residue 88 ARG Chi-restraints excluded: chain T residue 103 THR Chi-restraints excluded: chain T residue 111 PHE Chi-restraints excluded: chain T residue 261 LEU Chi-restraints excluded: chain T residue 300 GLN Chi-restraints excluded: chain T residue 317 ILE Chi-restraints excluded: chain T residue 327 LEU Chi-restraints excluded: chain T residue 344 ASP Chi-restraints excluded: chain T residue 355 THR Chi-restraints excluded: chain T residue 357 ARG Chi-restraints excluded: chain T residue 371 ASP Chi-restraints excluded: chain T residue 372 VAL Chi-restraints excluded: chain T residue 465 ASP Chi-restraints excluded: chain T residue 504 ILE Chi-restraints excluded: chain T residue 539 TYR Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 138 LYS Chi-restraints excluded: chain A residue 146 ARG Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 43 SER 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: 5.9990 chunk 62 optimal weight: 0.4980 chunk 26 optimal weight: 0.9990 chunk 106 optimal weight: 0.9990 chunk 88 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 55 optimal weight: 0.9980 chunk 102 optimal weight: 1.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 102 ASN S 327 HIS S 372 GLN T 242 ASN A 85 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.3676 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= 0.167 Angle : 0.545 7.248 12258 Z= 0.269 Chirality : 0.043 0.143 1373 Planarity : 0.004 0.076 1547 Dihedral : 9.642 101.269 1305 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.07 % Favored : 94.84 % Rotamer: Outliers : 5.66 % Allowed : 22.73 % Favored : 71.61 % 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: -1.96 (0.25), residues: 1104 helix: -0.61 (0.25), residues: 454 sheet: -1.07 (0.51), residues: 120 loop : -1.97 (0.26), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 34 HIS 0.002 0.000 HIS S 77 PHE 0.013 0.001 PHE T 111 TYR 0.014 0.001 TYR A 26 ARG 0.001 0.000 ARG T 489 *********************** 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 186 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 133 time to evaluate : 1.056 Fit side-chains revert: symmetry clash REVERT: S 57 LYS cc_start: 0.8084 (mtmt) cc_final: 0.7613 (tttt) REVERT: S 388 GLU cc_start: 0.9001 (OUTLIER) cc_final: 0.8056 (mp0) REVERT: S 418 GLN cc_start: 0.8443 (OUTLIER) cc_final: 0.8124 (tt0) REVERT: S 464 ILE cc_start: 0.9088 (tt) cc_final: 0.8884 (tt) REVERT: T 57 ARG cc_start: 0.8009 (OUTLIER) cc_final: 0.7752 (ptm160) REVERT: T 88 ARG cc_start: 0.8713 (OUTLIER) cc_final: 0.7919 (mmm160) REVERT: T 90 PHE cc_start: 0.7101 (m-10) cc_final: 0.6758 (t80) REVERT: T 261 LEU cc_start: 0.9106 (OUTLIER) cc_final: 0.8741 (pp) REVERT: T 300 GLN cc_start: 0.8723 (OUTLIER) cc_final: 0.7676 (mp10) REVERT: T 327 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8548 (tp) REVERT: T 357 ARG cc_start: 0.9344 (OUTLIER) cc_final: 0.9038 (mmt-90) REVERT: T 369 ASP cc_start: 0.7764 (m-30) cc_final: 0.7495 (m-30) REVERT: T 471 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.7926 (tt) REVERT: A 17 MET cc_start: 0.5581 (pp-130) cc_final: 0.3422 (mtm) REVERT: A 119 TYR cc_start: 0.6959 (m-80) cc_final: 0.6641 (m-80) REVERT: A 135 LEU cc_start: 0.8298 (OUTLIER) cc_final: 0.8020 (mm) REVERT: A 138 LYS cc_start: 0.7952 (OUTLIER) cc_final: 0.7267 (mptt) REVERT: A 146 ARG cc_start: 0.7039 (OUTLIER) cc_final: 0.6049 (mmm-85) REVERT: E 12 GLN cc_start: 0.8237 (pp30) cc_final: 0.7955 (pp30) outliers start: 53 outliers final: 31 residues processed: 176 average time/residue: 0.2155 time to fit residues: 51.9852 Evaluate side-chains 171 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 128 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 77 HIS Chi-restraints excluded: chain S residue 81 ASN Chi-restraints excluded: chain S residue 102 ASN Chi-restraints excluded: chain S residue 166 TYR Chi-restraints excluded: chain S residue 189 ARG Chi-restraints excluded: chain S residue 239 ARG Chi-restraints excluded: chain S residue 247 LEU Chi-restraints excluded: chain S residue 251 THR Chi-restraints excluded: chain S residue 344 LEU Chi-restraints excluded: chain S residue 369 LYS Chi-restraints excluded: chain S residue 388 GLU Chi-restraints excluded: chain S residue 418 GLN Chi-restraints excluded: chain S residue 419 CYS Chi-restraints excluded: chain S residue 426 LEU Chi-restraints excluded: chain S residue 453 THR Chi-restraints excluded: chain T residue 57 ARG Chi-restraints excluded: chain T residue 66 THR Chi-restraints excluded: chain T residue 88 ARG Chi-restraints excluded: chain T residue 111 PHE Chi-restraints excluded: chain T residue 261 LEU Chi-restraints excluded: chain T residue 300 GLN Chi-restraints excluded: chain T residue 317 ILE Chi-restraints excluded: chain T residue 327 LEU Chi-restraints excluded: chain T residue 344 ASP Chi-restraints excluded: chain T residue 355 THR Chi-restraints excluded: chain T residue 357 ARG Chi-restraints excluded: chain T residue 370 VAL Chi-restraints excluded: chain T residue 371 ASP Chi-restraints excluded: chain T residue 372 VAL Chi-restraints excluded: chain T residue 465 ASP Chi-restraints excluded: chain T residue 471 LEU Chi-restraints excluded: chain T residue 504 ILE Chi-restraints excluded: chain T residue 539 TYR Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 89 MET Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 138 LYS Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 146 ARG Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 43 SER Chi-restraints excluded: chain C residue 27 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 89 optimal weight: 0.0370 chunk 59 optimal weight: 0.9990 chunk 106 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 48 optimal weight: 5.9990 chunk 65 optimal weight: 3.9990 chunk 42 optimal weight: 10.0000 overall best weight: 1.0064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 0.8223 moved from start: 0.3735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9051 Z= 0.184 Angle : 0.547 7.908 12258 Z= 0.271 Chirality : 0.043 0.161 1373 Planarity : 0.004 0.079 1547 Dihedral : 9.461 99.704 1305 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.43 % Favored : 94.47 % Rotamer: Outliers : 5.34 % Allowed : 23.59 % Favored : 71.08 % 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: -1.80 (0.26), residues: 1104 helix: -0.41 (0.26), residues: 454 sheet: -1.06 (0.51), residues: 120 loop : -1.93 (0.26), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 34 HIS 0.001 0.000 HIS S 77 PHE 0.013 0.001 PHE T 111 TYR 0.014 0.001 TYR A 26 ARG 0.002 0.000 ARG T 489 *********************** 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 183 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 133 time to evaluate : 1.018 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: S 57 LYS cc_start: 0.8088 (mtmt) cc_final: 0.7608 (tttt) REVERT: S 239 ARG cc_start: 0.8521 (OUTLIER) cc_final: 0.7804 (ptt90) REVERT: S 388 GLU cc_start: 0.9012 (OUTLIER) cc_final: 0.8100 (mp0) REVERT: S 418 GLN cc_start: 0.8453 (OUTLIER) cc_final: 0.8141 (tt0) REVERT: T 57 ARG cc_start: 0.8027 (OUTLIER) cc_final: 0.7709 (ptm160) REVERT: T 88 ARG cc_start: 0.8728 (OUTLIER) cc_final: 0.7933 (mmm160) REVERT: T 90 PHE cc_start: 0.7110 (m-10) cc_final: 0.6765 (t80) REVERT: T 261 LEU cc_start: 0.9112 (OUTLIER) cc_final: 0.8739 (pp) REVERT: T 300 GLN cc_start: 0.8721 (OUTLIER) cc_final: 0.7670 (mp10) REVERT: T 311 LEU cc_start: 0.8988 (OUTLIER) cc_final: 0.8410 (tt) REVERT: T 327 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8553 (tp) REVERT: T 357 ARG cc_start: 0.9288 (OUTLIER) cc_final: 0.8937 (mmt-90) REVERT: T 369 ASP cc_start: 0.7770 (m-30) cc_final: 0.7497 (m-30) REVERT: T 471 LEU cc_start: 0.8457 (OUTLIER) cc_final: 0.8074 (tt) REVERT: T 491 ILE cc_start: 0.8637 (OUTLIER) cc_final: 0.8063 (mt) REVERT: A 17 MET cc_start: 0.5591 (pp-130) cc_final: 0.5052 (ptp) REVERT: A 119 TYR cc_start: 0.6945 (m-80) cc_final: 0.6590 (m-80) REVERT: A 135 LEU cc_start: 0.8289 (OUTLIER) cc_final: 0.8059 (mm) REVERT: A 138 LYS cc_start: 0.8013 (OUTLIER) cc_final: 0.7373 (mptt) REVERT: A 146 ARG cc_start: 0.7183 (OUTLIER) cc_final: 0.6035 (mmm-85) REVERT: E 12 GLN cc_start: 0.8267 (pp30) cc_final: 0.8003 (pp30) outliers start: 50 outliers final: 30 residues processed: 173 average time/residue: 0.2312 time to fit residues: 55.2215 Evaluate side-chains 173 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 128 time to evaluate : 1.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 81 ASN Chi-restraints excluded: chain S residue 90 SER Chi-restraints excluded: chain S residue 113 ASP Chi-restraints excluded: chain S residue 166 TYR Chi-restraints excluded: chain S residue 189 ARG Chi-restraints excluded: chain S residue 208 LEU Chi-restraints excluded: chain S residue 239 ARG Chi-restraints excluded: chain S residue 247 LEU Chi-restraints excluded: chain S residue 251 THR Chi-restraints excluded: chain S residue 344 LEU Chi-restraints excluded: chain S residue 369 LYS Chi-restraints excluded: chain S residue 388 GLU Chi-restraints excluded: chain S residue 418 GLN Chi-restraints excluded: chain S residue 419 CYS Chi-restraints excluded: chain S residue 426 LEU Chi-restraints excluded: chain S residue 453 THR Chi-restraints excluded: chain T residue 57 ARG Chi-restraints excluded: chain T residue 66 THR Chi-restraints excluded: chain T residue 88 ARG Chi-restraints excluded: chain T residue 111 PHE Chi-restraints excluded: chain T residue 196 LEU Chi-restraints excluded: chain T residue 261 LEU Chi-restraints excluded: chain T residue 300 GLN Chi-restraints excluded: chain T residue 311 LEU Chi-restraints excluded: chain T residue 317 ILE Chi-restraints excluded: chain T residue 327 LEU Chi-restraints excluded: chain T residue 344 ASP Chi-restraints excluded: chain T residue 355 THR Chi-restraints excluded: chain T residue 357 ARG Chi-restraints excluded: chain T residue 370 VAL Chi-restraints excluded: chain T residue 371 ASP Chi-restraints excluded: chain T residue 372 VAL Chi-restraints excluded: chain T residue 465 ASP Chi-restraints excluded: chain T residue 471 LEU Chi-restraints excluded: chain T residue 491 ILE Chi-restraints excluded: chain T residue 504 ILE Chi-restraints excluded: chain T residue 539 TYR Chi-restraints excluded: chain A residue 89 MET Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 138 LYS Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 146 ARG Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 43 SER 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: 3.9990 chunk 20 optimal weight: 0.4980 chunk 67 optimal weight: 0.6980 chunk 72 optimal weight: 4.9990 chunk 52 optimal weight: 5.9990 chunk 9 optimal weight: 0.9980 chunk 83 optimal weight: 4.9990 chunk 96 optimal weight: 0.0010 chunk 101 optimal weight: 0.4980 chunk 92 optimal weight: 7.9990 overall best weight: 0.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 77 HIS S 102 ASN S 107 ASN ** T 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 85 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.3930 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= 0.142 Angle : 0.527 7.583 12258 Z= 0.263 Chirality : 0.042 0.207 1373 Planarity : 0.004 0.080 1547 Dihedral : 8.997 98.605 1305 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.89 % Favored : 95.02 % Rotamer: Outliers : 4.70 % Allowed : 24.23 % Favored : 71.08 % 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: -1.48 (0.26), residues: 1104 helix: 0.00 (0.26), residues: 445 sheet: -0.99 (0.51), residues: 121 loop : -1.84 (0.26), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 34 HIS 0.001 0.000 HIS S 145 PHE 0.010 0.001 PHE T 111 TYR 0.022 0.001 TYR T 298 ARG 0.002 0.000 ARG S 151 *********************** 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 182 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 138 time to evaluate : 1.101 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: S 57 LYS cc_start: 0.8062 (mtmt) cc_final: 0.7561 (tttt) REVERT: S 239 ARG cc_start: 0.8434 (OUTLIER) cc_final: 0.7855 (ptt90) REVERT: S 388 GLU cc_start: 0.8981 (OUTLIER) cc_final: 0.8104 (mp0) REVERT: S 418 GLN cc_start: 0.8493 (OUTLIER) cc_final: 0.8189 (tt0) REVERT: T 57 ARG cc_start: 0.7978 (OUTLIER) cc_final: 0.7669 (ptm160) REVERT: T 88 ARG cc_start: 0.8670 (OUTLIER) cc_final: 0.7884 (mmm160) REVERT: T 90 PHE cc_start: 0.6941 (m-10) cc_final: 0.6635 (t80) REVERT: T 261 LEU cc_start: 0.9102 (OUTLIER) cc_final: 0.8760 (pp) REVERT: T 300 GLN cc_start: 0.8661 (OUTLIER) cc_final: 0.7465 (mp10) REVERT: T 311 LEU cc_start: 0.8977 (pp) cc_final: 0.8478 (tt) REVERT: T 327 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8529 (tp) REVERT: T 357 ARG cc_start: 0.9270 (OUTLIER) cc_final: 0.8918 (mmt-90) REVERT: T 471 LEU cc_start: 0.8361 (OUTLIER) cc_final: 0.7851 (tt) REVERT: T 491 ILE cc_start: 0.8610 (OUTLIER) cc_final: 0.8038 (mt) REVERT: A 17 MET cc_start: 0.5590 (pp-130) cc_final: 0.4965 (ptp) REVERT: A 119 TYR cc_start: 0.6957 (m-80) cc_final: 0.6600 (m-80) REVERT: A 135 LEU cc_start: 0.8252 (OUTLIER) cc_final: 0.8022 (mm) REVERT: A 138 LYS cc_start: 0.8012 (OUTLIER) cc_final: 0.7454 (mptt) REVERT: A 146 ARG cc_start: 0.7103 (OUTLIER) cc_final: 0.5967 (mmm-85) REVERT: E 12 GLN cc_start: 0.8252 (pp30) cc_final: 0.7998 (pp30) REVERT: E 13 MET cc_start: 0.6975 (OUTLIER) cc_final: 0.6552 (ptt) outliers start: 44 outliers final: 22 residues processed: 175 average time/residue: 0.2097 time to fit residues: 50.6405 Evaluate side-chains 167 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 130 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 81 ASN Chi-restraints excluded: chain S residue 102 ASN Chi-restraints excluded: chain S residue 113 ASP Chi-restraints excluded: chain S residue 166 TYR Chi-restraints excluded: chain S residue 189 ARG Chi-restraints excluded: chain S residue 239 ARG Chi-restraints excluded: chain S residue 247 LEU Chi-restraints excluded: chain S residue 251 THR Chi-restraints excluded: chain S residue 369 LYS Chi-restraints excluded: chain S residue 388 GLU Chi-restraints excluded: chain S residue 418 GLN Chi-restraints excluded: chain S residue 419 CYS Chi-restraints excluded: chain S residue 426 LEU Chi-restraints excluded: chain S residue 453 THR Chi-restraints excluded: chain T residue 57 ARG Chi-restraints excluded: chain T residue 88 ARG Chi-restraints excluded: chain T residue 111 PHE Chi-restraints excluded: chain T residue 196 LEU Chi-restraints excluded: chain T residue 261 LEU Chi-restraints excluded: chain T residue 300 GLN Chi-restraints excluded: chain T residue 317 ILE Chi-restraints excluded: chain T residue 327 LEU Chi-restraints excluded: chain T residue 344 ASP Chi-restraints excluded: chain T residue 355 THR Chi-restraints excluded: chain T residue 357 ARG Chi-restraints excluded: chain T residue 371 ASP Chi-restraints excluded: chain T residue 372 VAL Chi-restraints excluded: chain T residue 465 ASP Chi-restraints excluded: chain T residue 471 LEU Chi-restraints excluded: chain T residue 491 ILE Chi-restraints excluded: chain T residue 539 TYR Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 138 LYS Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 146 ARG Chi-restraints excluded: chain E residue 13 MET Chi-restraints excluded: chain E residue 24 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 10.0000 chunk 101 optimal weight: 0.6980 chunk 59 optimal weight: 0.0570 chunk 43 optimal weight: 0.7980 chunk 77 optimal weight: 5.9990 chunk 30 optimal weight: 0.8980 chunk 89 optimal weight: 0.6980 chunk 93 optimal weight: 6.9990 chunk 64 optimal weight: 0.8980 chunk 104 optimal weight: 0.8980 chunk 63 optimal weight: 0.9990 overall best weight: 0.6298 ------------------------------------------------------------------------------- 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 A 85 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.3970 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= 0.150 Angle : 0.534 7.835 12258 Z= 0.267 Chirality : 0.043 0.217 1373 Planarity : 0.005 0.081 1547 Dihedral : 8.806 97.743 1301 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.16 % Favored : 94.66 % Rotamer: Outliers : 4.16 % Allowed : 24.65 % Favored : 71.18 % 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: -1.30 (0.26), residues: 1104 helix: 0.20 (0.26), residues: 446 sheet: -0.99 (0.50), residues: 121 loop : -1.77 (0.26), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 34 HIS 0.001 0.000 HIS S 145 PHE 0.012 0.001 PHE S 103 TYR 0.017 0.001 TYR A 26 ARG 0.001 0.000 ARG T 489 *********************** 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 171 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 132 time to evaluate : 0.962 Fit side-chains revert: symmetry clash REVERT: S 57 LYS cc_start: 0.8059 (mtmt) cc_final: 0.7555 (tttt) REVERT: S 239 ARG cc_start: 0.8396 (OUTLIER) cc_final: 0.7858 (ptt90) REVERT: S 388 GLU cc_start: 0.9027 (OUTLIER) cc_final: 0.8122 (mp0) REVERT: S 418 GLN cc_start: 0.8494 (OUTLIER) cc_final: 0.8169 (tt0) REVERT: T 57 ARG cc_start: 0.7930 (OUTLIER) cc_final: 0.7669 (ptm160) REVERT: T 88 ARG cc_start: 0.8670 (OUTLIER) cc_final: 0.7886 (mmm160) REVERT: T 90 PHE cc_start: 0.6876 (m-10) cc_final: 0.6613 (t80) REVERT: T 261 LEU cc_start: 0.9105 (OUTLIER) cc_final: 0.8765 (pp) REVERT: T 300 GLN cc_start: 0.8675 (OUTLIER) cc_final: 0.7502 (mp10) REVERT: T 311 LEU cc_start: 0.8973 (pp) cc_final: 0.8481 (tt) REVERT: T 471 LEU cc_start: 0.8402 (OUTLIER) cc_final: 0.7889 (tt) REVERT: A 17 MET cc_start: 0.5582 (pp-130) cc_final: 0.4948 (ptp) REVERT: A 119 TYR cc_start: 0.6796 (m-80) cc_final: 0.6447 (m-80) REVERT: A 135 LEU cc_start: 0.8245 (OUTLIER) cc_final: 0.8027 (mm) REVERT: A 138 LYS cc_start: 0.7978 (OUTLIER) cc_final: 0.7418 (mptt) REVERT: A 146 ARG cc_start: 0.7148 (OUTLIER) cc_final: 0.5822 (mmm-85) REVERT: E 12 GLN cc_start: 0.8282 (pp30) cc_final: 0.8025 (pp30) REVERT: E 13 MET cc_start: 0.6978 (OUTLIER) cc_final: 0.6553 (ptt) outliers start: 39 outliers final: 22 residues processed: 165 average time/residue: 0.1967 time to fit residues: 45.5042 Evaluate side-chains 162 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 128 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 81 ASN Chi-restraints excluded: chain S residue 113 ASP Chi-restraints excluded: chain S residue 166 TYR Chi-restraints excluded: chain S residue 189 ARG Chi-restraints excluded: chain S residue 239 ARG Chi-restraints excluded: chain S residue 247 LEU Chi-restraints excluded: chain S residue 251 THR Chi-restraints excluded: chain S residue 301 ASP Chi-restraints excluded: chain S residue 369 LYS Chi-restraints excluded: chain S residue 388 GLU Chi-restraints excluded: chain S residue 418 GLN Chi-restraints excluded: chain S residue 419 CYS Chi-restraints excluded: chain S residue 426 LEU Chi-restraints excluded: chain S residue 453 THR Chi-restraints excluded: chain T residue 57 ARG Chi-restraints excluded: chain T residue 88 ARG Chi-restraints excluded: chain T residue 111 PHE Chi-restraints excluded: chain T residue 196 LEU Chi-restraints excluded: chain T residue 261 LEU Chi-restraints excluded: chain T residue 300 GLN Chi-restraints excluded: chain T residue 317 ILE Chi-restraints excluded: chain T residue 344 ASP Chi-restraints excluded: chain T residue 355 THR Chi-restraints excluded: chain T residue 371 ASP Chi-restraints excluded: chain T residue 471 LEU Chi-restraints excluded: chain T residue 491 ILE Chi-restraints excluded: chain T residue 539 TYR Chi-restraints excluded: chain A residue 30 ILE Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 138 LYS Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 146 ARG Chi-restraints excluded: chain E residue 13 MET Chi-restraints excluded: chain E residue 24 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 3.9990 chunk 72 optimal weight: 6.9990 chunk 109 optimal weight: 8.9990 chunk 100 optimal weight: 0.8980 chunk 87 optimal weight: 7.9990 chunk 9 optimal weight: 0.9990 chunk 67 optimal weight: 0.0270 chunk 53 optimal weight: 3.9990 chunk 69 optimal weight: 0.8980 chunk 92 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 overall best weight: 0.7642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 102 ASN A 85 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.4048 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= 0.161 Angle : 0.536 7.703 12258 Z= 0.267 Chirality : 0.043 0.167 1373 Planarity : 0.004 0.077 1547 Dihedral : 8.521 95.870 1295 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.25 % Favored : 94.66 % Rotamer: Outliers : 4.16 % Allowed : 24.87 % Favored : 70.97 % 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: -1.16 (0.26), residues: 1104 helix: 0.32 (0.26), residues: 449 sheet: -0.94 (0.50), residues: 122 loop : -1.69 (0.27), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 34 HIS 0.002 0.000 HIS S 77 PHE 0.012 0.001 PHE T 111 TYR 0.017 0.001 TYR A 26 ARG 0.001 0.000 ARG T 489 ********************** 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 174 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 135 time to evaluate : 1.167 Fit side-chains revert: symmetry clash REVERT: S 57 LYS cc_start: 0.8057 (mtmt) cc_final: 0.7551 (tttt) REVERT: S 239 ARG cc_start: 0.8368 (OUTLIER) cc_final: 0.7937 (ptt90) REVERT: S 388 GLU cc_start: 0.9011 (OUTLIER) cc_final: 0.8168 (mp0) REVERT: S 418 GLN cc_start: 0.8488 (OUTLIER) cc_final: 0.8163 (tt0) REVERT: T 57 ARG cc_start: 0.7933 (OUTLIER) cc_final: 0.7649 (ptm160) REVERT: T 90 PHE cc_start: 0.6881 (m-10) cc_final: 0.6659 (t80) REVERT: T 261 LEU cc_start: 0.9102 (OUTLIER) cc_final: 0.8751 (pp) REVERT: T 300 GLN cc_start: 0.8677 (OUTLIER) cc_final: 0.7538 (mp10) REVERT: T 311 LEU cc_start: 0.8971 (pp) cc_final: 0.8529 (tt) REVERT: T 471 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.7881 (tt) REVERT: A 17 MET cc_start: 0.5598 (pp-130) cc_final: 0.4988 (ptm) REVERT: A 119 TYR cc_start: 0.6774 (m-80) cc_final: 0.6442 (m-80) REVERT: A 135 LEU cc_start: 0.8165 (OUTLIER) cc_final: 0.7948 (mm) REVERT: A 138 LYS cc_start: 0.7951 (OUTLIER) cc_final: 0.7401 (mptt) REVERT: A 146 ARG cc_start: 0.7034 (OUTLIER) cc_final: 0.5763 (mmm-85) REVERT: E 12 GLN cc_start: 0.8286 (pp30) cc_final: 0.8029 (pp30) REVERT: E 13 MET cc_start: 0.6983 (OUTLIER) cc_final: 0.6498 (ptt) outliers start: 39 outliers final: 26 residues processed: 168 average time/residue: 0.2012 time to fit residues: 47.4089 Evaluate side-chains 167 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 130 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 81 ASN Chi-restraints excluded: chain S residue 90 SER Chi-restraints excluded: chain S residue 102 ASN Chi-restraints excluded: chain S residue 113 ASP Chi-restraints excluded: chain S residue 166 TYR Chi-restraints excluded: chain S residue 189 ARG Chi-restraints excluded: chain S residue 208 LEU Chi-restraints excluded: chain S residue 239 ARG Chi-restraints excluded: chain S residue 247 LEU Chi-restraints excluded: chain S residue 251 THR Chi-restraints excluded: chain S residue 301 ASP Chi-restraints excluded: chain S residue 369 LYS Chi-restraints excluded: chain S residue 388 GLU Chi-restraints excluded: chain S residue 418 GLN Chi-restraints excluded: chain S residue 419 CYS Chi-restraints excluded: chain S residue 426 LEU Chi-restraints excluded: chain S residue 453 THR Chi-restraints excluded: chain T residue 57 ARG Chi-restraints excluded: chain T residue 111 PHE Chi-restraints excluded: chain T residue 196 LEU Chi-restraints excluded: chain T residue 261 LEU Chi-restraints excluded: chain T residue 300 GLN Chi-restraints excluded: chain T residue 317 ILE Chi-restraints excluded: chain T residue 344 ASP Chi-restraints excluded: chain T residue 355 THR Chi-restraints excluded: chain T residue 370 VAL Chi-restraints excluded: chain T residue 371 ASP Chi-restraints excluded: chain T residue 471 LEU Chi-restraints excluded: chain T residue 491 ILE Chi-restraints excluded: chain T residue 539 TYR Chi-restraints excluded: chain A residue 30 ILE Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 138 LYS Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 146 ARG Chi-restraints excluded: chain E residue 13 MET Chi-restraints excluded: chain E residue 24 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 3.9990 chunk 12 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 chunk 87 optimal weight: 5.9990 chunk 36 optimal weight: 0.8980 chunk 89 optimal weight: 0.7980 chunk 11 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 63 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 102 ASN A 85 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.129105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.104903 restraints weight = 12794.879| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 1.92 r_work: 0.3040 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2934 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2934 r_free = 0.2934 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2934 r_free = 0.2934 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2934 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.4072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9051 Z= 0.169 Angle : 0.543 7.607 12258 Z= 0.271 Chirality : 0.043 0.199 1373 Planarity : 0.004 0.078 1547 Dihedral : 8.366 95.267 1291 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.43 % Favored : 94.47 % Rotamer: Outliers : 4.38 % Allowed : 24.65 % Favored : 70.97 % 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: -1.10 (0.26), residues: 1104 helix: 0.41 (0.26), residues: 447 sheet: -0.85 (0.52), residues: 116 loop : -1.70 (0.26), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 34 HIS 0.002 0.000 HIS S 77 PHE 0.015 0.001 PHE S 103 TYR 0.018 0.001 TYR A 26 ARG 0.001 0.000 ARG T 489 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2250.04 seconds wall clock time: 41 minutes 23.99 seconds (2483.99 seconds total)