Starting phenix.real_space_refine on Fri Feb 16 22:47:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7btr_30183/02_2024/7btr_30183.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7btr_30183/02_2024/7btr_30183.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7btr_30183/02_2024/7btr_30183.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7btr_30183/02_2024/7btr_30183.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7btr_30183/02_2024/7btr_30183.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7btr_30183/02_2024/7btr_30183.pdb" } resolution = 4.54 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 ------------------------------------------------------------------------------- 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= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 37 5.16 5 C 10711 2.51 5 N 2741 2.21 5 O 3248 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C ARG 65": "NH1" <-> "NH2" Residue "C ARG 131": "NH1" <-> "NH2" Residue "C ARG 149": "NH1" <-> "NH2" Residue "C TYR 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 352": "NH1" <-> "NH2" Residue "C TYR 429": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 456": "NH1" <-> "NH2" Residue "D ARG 104": "NH1" <-> "NH2" Residue "E TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 104": "NH1" <-> "NH2" Residue "A PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 142": "NH1" <-> "NH2" Residue "A ARG 364": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 16737 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 1334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1334 Classifications: {'peptide': 163} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 3, 'TRANS': 157} Chain: "C" Number of atoms: 3571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3571 Classifications: {'peptide': 436} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'CIS': 5, 'PTRANS': 9, 'TRANS': 421} Chain breaks: 2 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 1, 'HIS:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "D" Number of atoms: 3704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 472, 3704 Classifications: {'peptide': 472} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'CIS': 18, 'PTRANS': 13, 'TRANS': 440} Chain breaks: 3 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "E" Number of atoms: 3099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 3099 Classifications: {'peptide': 384} Link IDs: {'CIS': 5, 'PCIS': 2, 'PTRANS': 17, 'TRANS': 359} Chain: "F" Number of atoms: 1334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1334 Classifications: {'peptide': 163} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 3, 'TRANS': 157} Chain: "A" Number of atoms: 3695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3695 Classifications: {'peptide': 469} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'CIS': 18, 'PTRANS': 13, 'TRANS': 437} Chain breaks: 3 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Time building chain proxies: 8.94, per 1000 atoms: 0.53 Number of scatterers: 16737 At special positions: 0 Unit cell: (149.85, 112.05, 144.45, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 37 16.00 O 3248 8.00 N 2741 7.00 C 10711 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.41 Conformation dependent library (CDL) restraints added in 3.1 seconds 4118 Ramachandran restraints generated. 2059 Oldfield, 0 Emsley, 2059 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3964 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 18 sheets defined 39.7% alpha, 8.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.70 Creating SS restraints... Processing helix chain 'B' and resid 29 through 38 Processing helix chain 'B' and resid 62 through 76 Processing helix chain 'B' and resid 77 through 82 Processing helix chain 'B' and resid 83 through 91 removed outlier: 3.794A pdb=" N THR B 89 " --> pdb=" O SER B 85 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N HIS B 90 " --> pdb=" O ALA B 86 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE B 91 " --> pdb=" O LEU B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 100 removed outlier: 3.694A pdb=" N HIS B 100 " --> pdb=" O GLU B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 122 Processing helix chain 'B' and resid 139 through 151 Processing helix chain 'C' and resid 35 through 47 removed outlier: 3.726A pdb=" N GLU C 39 " --> pdb=" O ASP C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 72 removed outlier: 4.402A pdb=" N GLN C 69 " --> pdb=" O ARG C 65 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ASN C 70 " --> pdb=" O GLU C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 88 removed outlier: 3.671A pdb=" N TRP C 81 " --> pdb=" O ASN C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 105 Processing helix chain 'C' and resid 128 through 132 Processing helix chain 'C' and resid 174 through 179 removed outlier: 3.591A pdb=" N ASN C 178 " --> pdb=" O ARG C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 198 removed outlier: 3.731A pdb=" N TYR C 197 " --> pdb=" O LEU C 194 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU C 198 " --> pdb=" O PHE C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 248 Processing helix chain 'C' and resid 249 through 258 Processing helix chain 'C' and resid 273 through 293 Processing helix chain 'C' and resid 312 through 328 removed outlier: 3.708A pdb=" N ASP C 328 " --> pdb=" O ALA C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 342 through 353 removed outlier: 3.604A pdb=" N PHE C 353 " --> pdb=" O GLU C 349 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 373 Processing helix chain 'C' and resid 383 through 391 Processing helix chain 'C' and resid 416 through 425 Processing helix chain 'D' and resid 12 through 24 removed outlier: 3.936A pdb=" N ARG D 24 " --> pdb=" O ALA D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 31 through 53 removed outlier: 4.253A pdb=" N SER D 50 " --> pdb=" O SER D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 92 Processing helix chain 'D' and resid 121 through 126 Processing helix chain 'D' and resid 149 through 163 Processing helix chain 'D' and resid 180 through 185 Processing helix chain 'D' and resid 202 through 214 removed outlier: 3.783A pdb=" N MET D 214 " --> pdb=" O ALA D 210 " (cutoff:3.500A) Processing helix chain 'D' and resid 232 through 239 Processing helix chain 'D' and resid 256 through 270 removed outlier: 3.886A pdb=" N MET D 267 " --> pdb=" O ALA D 263 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N PHE D 268 " --> pdb=" O ARG D 264 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N HIS D 270 " --> pdb=" O ASN D 266 " (cutoff:3.500A) Processing helix chain 'D' and resid 315 through 320 removed outlier: 3.793A pdb=" N ASP D 320 " --> pdb=" O LEU D 317 " (cutoff:3.500A) Processing helix chain 'D' and resid 336 through 346 removed outlier: 4.037A pdb=" N VAL D 340 " --> pdb=" O ASP D 336 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU D 341 " --> pdb=" O PHE D 337 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 376 removed outlier: 4.506A pdb=" N LYS D 370 " --> pdb=" O GLY D 366 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N ILE D 371 " --> pdb=" O ALA D 367 " (cutoff:3.500A) Processing helix chain 'D' and resid 435 through 445 Processing helix chain 'D' and resid 459 through 464 Processing helix chain 'D' and resid 482 through 509 removed outlier: 3.503A pdb=" N ASN D 489 " --> pdb=" O ILE D 485 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ALA D 490 " --> pdb=" O ALA D 486 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ILE D 499 " --> pdb=" O THR D 495 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 120 removed outlier: 3.991A pdb=" N ASN E 119 " --> pdb=" O TYR E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 134 through 140 Processing helix chain 'E' and resid 151 through 193 removed outlier: 3.745A pdb=" N ILE E 161 " --> pdb=" O ILE E 157 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ASP E 191 " --> pdb=" O ASN E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 223 through 228 removed outlier: 4.096A pdb=" N ASN E 228 " --> pdb=" O GLU E 224 " (cutoff:3.500A) Processing helix chain 'E' and resid 254 through 258 Processing helix chain 'E' and resid 307 through 318 Processing helix chain 'E' and resid 318 through 326 removed outlier: 4.488A pdb=" N ARG E 324 " --> pdb=" O SER E 320 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ALA E 326 " --> pdb=" O ILE E 322 " (cutoff:3.500A) Processing helix chain 'E' and resid 353 through 369 removed outlier: 4.394A pdb=" N ILE E 357 " --> pdb=" O GLU E 353 " (cutoff:3.500A) Processing helix chain 'E' and resid 374 through 395 Processing helix chain 'F' and resid 29 through 38 Processing helix chain 'F' and resid 62 through 76 Processing helix chain 'F' and resid 77 through 82 Processing helix chain 'F' and resid 83 through 91 removed outlier: 3.794A pdb=" N THR F 89 " --> pdb=" O SER F 85 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N HIS F 90 " --> pdb=" O ALA F 86 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE F 91 " --> pdb=" O LEU F 87 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 100 removed outlier: 3.694A pdb=" N HIS F 100 " --> pdb=" O GLU F 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 112 through 122 Processing helix chain 'F' and resid 139 through 151 Processing helix chain 'A' and resid 12 through 22 Processing helix chain 'A' and resid 28 through 54 removed outlier: 3.686A pdb=" N PHE A 32 " --> pdb=" O ASP A 28 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N GLN A 34 " --> pdb=" O TRP A 30 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N TYR A 35 " --> pdb=" O ASP A 31 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU A 54 " --> pdb=" O SER A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 92 removed outlier: 4.854A pdb=" N TYR A 87 " --> pdb=" O GLY A 83 " (cutoff:3.500A) Proline residue: A 88 - end of helix Processing helix chain 'A' and resid 101 through 106 Processing helix chain 'A' and resid 115 through 123 removed outlier: 3.524A pdb=" N GLY A 122 " --> pdb=" O SER A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 163 Processing helix chain 'A' and resid 177 through 186 removed outlier: 3.678A pdb=" N TYR A 181 " --> pdb=" O PHE A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 214 Processing helix chain 'A' and resid 234 through 242 removed outlier: 3.819A pdb=" N LYS A 238 " --> pdb=" O LEU A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 270 removed outlier: 3.990A pdb=" N HIS A 270 " --> pdb=" O ASN A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 320 removed outlier: 3.737A pdb=" N ASP A 320 " --> pdb=" O LEU A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 346 Processing helix chain 'A' and resid 365 through 378 removed outlier: 4.196A pdb=" N ASN A 378 " --> pdb=" O TYR A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 445 removed outlier: 4.281A pdb=" N SER A 445 " --> pdb=" O GLN A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 464 Processing helix chain 'A' and resid 482 through 508 removed outlier: 4.030A pdb=" N ALA A 486 " --> pdb=" O ILE A 482 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 24 through 25 removed outlier: 3.771A pdb=" N ASP B 50 " --> pdb=" O TYR B 7 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 104 through 107 removed outlier: 3.862A pdb=" N THR B 152 " --> pdb=" O ILE B 163 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 108 through 112 Processing sheet with id=AA4, first strand: chain 'C' and resid 134 through 137 removed outlier: 6.760A pdb=" N VAL C 152 " --> pdb=" O GLN C 163 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N GLN C 163 " --> pdb=" O VAL C 152 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ILE C 154 " --> pdb=" O LEU C 161 " (cutoff:3.500A) removed outlier: 10.074A pdb=" N LEU C 200 " --> pdb=" O LEU C 159 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N LEU C 161 " --> pdb=" O LEU C 200 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N VAL C 202 " --> pdb=" O LEU C 161 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N GLN C 163 " --> pdb=" O VAL C 202 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N SER C 204 " --> pdb=" O GLN C 163 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N GLU C 165 " --> pdb=" O SER C 204 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 261 through 264 Processing sheet with id=AA6, first strand: chain 'C' and resid 358 through 359 removed outlier: 6.347A pdb=" N VAL C 333 " --> pdb=" O ILE C 379 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N THR C 381 " --> pdb=" O VAL C 333 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N PHE C 335 " --> pdb=" O THR C 381 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N LYS C 332 " --> pdb=" O VAL C 404 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N ILE C 406 " --> pdb=" O LYS C 332 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N PHE C 334 " --> pdb=" O ILE C 406 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N ASP C 408 " --> pdb=" O PHE C 334 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N VAL C 336 " --> pdb=" O ASP C 408 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N PHE C 434 " --> pdb=" O PHE C 407 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N ILE C 305 " --> pdb=" O THR C 435 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N TYR C 304 " --> pdb=" O LEU C 458 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N SER C 460 " --> pdb=" O TYR C 304 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N TRP C 306 " --> pdb=" O SER C 460 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 253 through 254 removed outlier: 4.254A pdb=" N GLU D 254 " --> pdb=" O LYS D 280 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'D' and resid 299 through 300 removed outlier: 6.741A pdb=" N ILE D 299 " --> pdb=" O ALA D 354 " (cutoff:3.500A) removed outlier: 8.958A pdb=" N VAL D 356 " --> pdb=" O ILE D 299 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 17 through 19 Processing sheet with id=AB1, first strand: chain 'E' and resid 25 through 28 removed outlier: 3.952A pdb=" N LYS E 99 " --> pdb=" O ILE E 76 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 202 through 205 removed outlier: 3.690A pdb=" N GLU E 202 " --> pdb=" O VAL E 348 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 249 through 251 removed outlier: 4.050A pdb=" N ASP E 249 " --> pdb=" O TRP E 233 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 286 through 287 Processing sheet with id=AB5, first strand: chain 'F' and resid 24 through 25 removed outlier: 3.772A pdb=" N ASP F 50 " --> pdb=" O TYR F 7 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 104 through 107 removed outlier: 3.863A pdb=" N THR F 152 " --> pdb=" O ILE F 163 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 252 through 254 removed outlier: 6.469A pdb=" N GLY A 252 " --> pdb=" O LYS A 280 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 296 through 300 removed outlier: 6.085A pdb=" N ASP A 297 " --> pdb=" O ARG A 352 " (cutoff:3.500A) removed outlier: 8.414A pdb=" N ALA A 354 " --> pdb=" O ASP A 297 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ILE A 299 " --> pdb=" O ALA A 354 " (cutoff:3.500A) removed outlier: 8.062A pdb=" N VAL A 356 " --> pdb=" O ILE A 299 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N THR A 383 " --> pdb=" O VAL A 403 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N SER A 405 " --> pdb=" O VAL A 381 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N VAL A 381 " --> pdb=" O SER A 405 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 412 through 413 removed outlier: 4.141A pdb=" N ASN A 412 " --> pdb=" O VAL A 456 " (cutoff:3.500A) 598 hydrogen bonds defined for protein. 1713 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: 4.71 Time building geometry restraints manager: 6.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3346 1.32 - 1.45: 4313 1.45 - 1.57: 9372 1.57 - 1.70: 0 1.70 - 1.82: 63 Bond restraints: 17094 Sorted by residual: bond pdb=" N ASP A 225 " pdb=" CA ASP A 225 " ideal model delta sigma weight residual 1.460 1.414 0.046 1.29e-02 6.01e+03 1.28e+01 bond pdb=" C ASP A 225 " pdb=" N PRO A 226 " ideal model delta sigma weight residual 1.333 1.295 0.038 1.20e-02 6.94e+03 9.93e+00 bond pdb=" C TYR D 87 " pdb=" N PRO D 88 " ideal model delta sigma weight residual 1.337 1.367 -0.030 1.06e-02 8.90e+03 8.23e+00 bond pdb=" CA ILE D 116 " pdb=" C ILE D 116 " ideal model delta sigma weight residual 1.523 1.556 -0.033 1.27e-02 6.20e+03 6.90e+00 bond pdb=" CD LYS D 150 " pdb=" CE LYS D 150 " ideal model delta sigma weight residual 1.520 1.445 0.075 3.00e-02 1.11e+03 6.27e+00 ... (remaining 17089 not shown) Histogram of bond angle deviations from ideal: 93.45 - 101.59: 30 101.59 - 109.73: 2567 109.73 - 117.88: 10064 117.88 - 126.02: 10222 126.02 - 134.16: 276 Bond angle restraints: 23159 Sorted by residual: angle pdb=" C GLY C 27 " pdb=" N ASP C 28 " pdb=" CA ASP C 28 " ideal model delta sigma weight residual 121.70 133.22 -11.52 1.80e+00 3.09e-01 4.10e+01 angle pdb=" N VAL C 398 " pdb=" CA VAL C 398 " pdb=" C VAL C 398 " ideal model delta sigma weight residual 111.77 105.22 6.55 1.04e+00 9.25e-01 3.96e+01 angle pdb=" C GLU D 420 " pdb=" N LEU D 421 " pdb=" CA LEU D 421 " ideal model delta sigma weight residual 121.70 132.49 -10.79 1.80e+00 3.09e-01 3.59e+01 angle pdb=" C SER C 266 " pdb=" N GLN C 267 " pdb=" CA GLN C 267 " ideal model delta sigma weight residual 121.70 132.42 -10.72 1.80e+00 3.09e-01 3.54e+01 angle pdb=" C GLU A 420 " pdb=" N LEU A 421 " pdb=" CA LEU A 421 " ideal model delta sigma weight residual 121.70 132.36 -10.66 1.80e+00 3.09e-01 3.51e+01 ... (remaining 23154 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.51: 9253 15.51 - 31.03: 737 31.03 - 46.54: 168 46.54 - 62.05: 9 62.05 - 77.57: 16 Dihedral angle restraints: 10183 sinusoidal: 4044 harmonic: 6139 Sorted by residual: dihedral pdb=" CA THR D 395 " pdb=" C THR D 395 " pdb=" N THR D 396 " pdb=" CA THR D 396 " ideal model delta harmonic sigma weight residual 0.00 -44.60 44.60 0 5.00e+00 4.00e-02 7.96e+01 dihedral pdb=" CA VAL A 474 " pdb=" C VAL A 474 " pdb=" N GLU A 475 " pdb=" CA GLU A 475 " ideal model delta harmonic sigma weight residual 180.00 136.12 43.88 0 5.00e+00 4.00e-02 7.70e+01 dihedral pdb=" CA PHE C 353 " pdb=" C PHE C 353 " pdb=" N SER C 354 " pdb=" CA SER C 354 " ideal model delta harmonic sigma weight residual -180.00 -137.69 -42.31 0 5.00e+00 4.00e-02 7.16e+01 ... (remaining 10180 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 2077 0.076 - 0.152: 413 0.152 - 0.228: 63 0.228 - 0.304: 8 0.304 - 0.380: 5 Chirality restraints: 2566 Sorted by residual: chirality pdb=" CB ILE D 361 " pdb=" CA ILE D 361 " pdb=" CG1 ILE D 361 " pdb=" CG2 ILE D 361 " both_signs ideal model delta sigma weight residual False 2.64 2.26 0.38 2.00e-01 2.50e+01 3.61e+00 chirality pdb=" CB ILE A 310 " pdb=" CA ILE A 310 " pdb=" CG1 ILE A 310 " pdb=" CG2 ILE A 310 " both_signs ideal model delta sigma weight residual False 2.64 2.29 0.36 2.00e-01 2.50e+01 3.16e+00 chirality pdb=" CB ILE D 116 " pdb=" CA ILE D 116 " pdb=" CG1 ILE D 116 " pdb=" CG2 ILE D 116 " both_signs ideal model delta sigma weight residual False 2.64 3.00 -0.35 2.00e-01 2.50e+01 3.12e+00 ... (remaining 2563 not shown) Planarity restraints: 2994 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA E 72 " 0.059 5.00e-02 4.00e+02 8.94e-02 1.28e+01 pdb=" N PRO E 73 " -0.155 5.00e-02 4.00e+02 pdb=" CA PRO E 73 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO E 73 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 358 " 0.047 5.00e-02 4.00e+02 7.17e-02 8.22e+00 pdb=" N PRO A 359 " -0.124 5.00e-02 4.00e+02 pdb=" CA PRO A 359 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 359 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE C 440 " 0.047 5.00e-02 4.00e+02 7.10e-02 8.08e+00 pdb=" N PRO C 441 " -0.123 5.00e-02 4.00e+02 pdb=" CA PRO C 441 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO C 441 " 0.039 5.00e-02 4.00e+02 ... (remaining 2991 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 241 2.61 - 3.18: 14877 3.18 - 3.75: 27383 3.75 - 4.33: 36585 4.33 - 4.90: 55675 Nonbonded interactions: 134761 Sorted by model distance: nonbonded pdb=" ND2 ASN A 390 " pdb=" O THR A 395 " model vdw 2.037 2.520 nonbonded pdb=" O GLY A 131 " pdb=" OH TYR A 274 " model vdw 2.214 2.440 nonbonded pdb=" OH TYR C 399 " pdb=" O LYS C 425 " model vdw 2.242 2.440 nonbonded pdb=" OD1 ASN B 136 " pdb=" OG1 THR D 396 " model vdw 2.251 2.440 nonbonded pdb=" OH TYR E 116 " pdb=" OD1 ASP E 166 " model vdw 2.266 2.440 ... (remaining 134756 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 11 through 79 or (resid 80 and (name N or name CA or name \ C or name O or name CB )) or resid 81 through 141 or (resid 142 and (name N or n \ ame CA or name C or name O or name CB )) or resid 143 through 414 or (resid 415 \ and (name N or name CA or name C or name O or name CB )) or resid 416 through 51 \ 0)) selection = (chain 'D' and (resid 11 through 189 or resid 200 through 510)) } ncs_group { reference = chain 'B' selection = chain 'F' } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 4.620 Check model and map are aligned: 0.250 Set scattering table: 0.160 Process input model: 44.650 Find NCS groups from input model: 0.940 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 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 : 0.007 0.139 17094 Z= 0.435 Angle : 1.229 17.247 23159 Z= 0.681 Chirality : 0.064 0.380 2566 Planarity : 0.008 0.089 2994 Dihedral : 12.091 77.566 6219 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.38 % Favored : 85.62 % Rotamer: Outliers : 0.99 % Allowed : 6.10 % Favored : 92.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 2.34 % Twisted Proline : 0.00 % Twisted General : 1.34 % 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: -4.59 (0.15), residues: 2059 helix: -2.33 (0.15), residues: 728 sheet: -3.04 (0.35), residues: 171 loop : -3.70 (0.15), residues: 1160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP F 23 HIS 0.011 0.002 HIS A 289 PHE 0.027 0.004 PHE A 49 TYR 0.034 0.003 TYR F 46 ARG 0.012 0.001 ARG C 65 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4118 Ramachandran restraints generated. 2059 Oldfield, 0 Emsley, 2059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4118 Ramachandran restraints generated. 2059 Oldfield, 0 Emsley, 2059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 1831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 327 time to evaluate : 2.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 5 GLN cc_start: 0.9134 (pt0) cc_final: 0.8933 (pm20) REVERT: B 72 MET cc_start: 0.9283 (mtm) cc_final: 0.9015 (mtt) REVERT: B 152 THR cc_start: 0.8726 (m) cc_final: 0.8456 (m) REVERT: C 103 ILE cc_start: 0.9403 (mm) cc_final: 0.9203 (mm) REVERT: C 347 MET cc_start: 0.9071 (tpt) cc_final: 0.8703 (tpt) REVERT: C 359 ASN cc_start: 0.8662 (p0) cc_final: 0.8224 (t0) REVERT: D 40 LEU cc_start: 0.8938 (tp) cc_final: 0.8665 (mm) REVERT: D 42 TYR cc_start: 0.8310 (t80) cc_final: 0.8085 (t80) REVERT: D 44 PHE cc_start: 0.9036 (t80) cc_final: 0.8400 (t80) REVERT: D 305 TYR cc_start: 0.7394 (t80) cc_final: 0.6968 (t80) REVERT: E 228 ASN cc_start: 0.8814 (m-40) cc_final: 0.8596 (m-40) REVERT: E 297 MET cc_start: 0.8387 (ptm) cc_final: 0.7010 (ptp) REVERT: E 315 ILE cc_start: 0.9586 (mm) cc_final: 0.9333 (mm) REVERT: F 6 VAL cc_start: 0.9062 (m) cc_final: 0.8816 (p) REVERT: F 113 MET cc_start: 0.8997 (tpp) cc_final: 0.8646 (tmm) REVERT: F 124 THR cc_start: 0.9101 (m) cc_final: 0.8827 (m) REVERT: A 265 MET cc_start: 0.8982 (ptm) cc_final: 0.8747 (ptm) outliers start: 18 outliers final: 3 residues processed: 345 average time/residue: 0.3651 time to fit residues: 174.9521 Evaluate side-chains 148 residues out of total 1831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 145 time to evaluate : 2.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 173 optimal weight: 2.9990 chunk 156 optimal weight: 0.6980 chunk 86 optimal weight: 10.0000 chunk 53 optimal weight: 5.9990 chunk 105 optimal weight: 0.8980 chunk 83 optimal weight: 2.9990 chunk 161 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 120 optimal weight: 0.6980 chunk 187 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 47 GLN ** C 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 72 ASN C 120 ASN ** C 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 214 ASN C 221 ASN C 295 ASN C 307 HIS ** C 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 414 GLN ** C 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 459 HIS D 18 GLN D 219 HIS E 64 HIS ** E 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 258 HIS E 303 HIS F 90 HIS A 13 HIS ** A 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 219 HIS A 379 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.2757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 17094 Z= 0.207 Angle : 0.775 9.980 23159 Z= 0.416 Chirality : 0.047 0.206 2566 Planarity : 0.006 0.094 2994 Dihedral : 8.256 60.634 2243 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 19.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.77 % Favored : 87.23 % Rotamer: Outliers : 0.16 % Allowed : 4.12 % Favored : 95.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 2.39 % Twisted Proline : 1.61 % Twisted General : 0.75 % 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: -3.63 (0.16), residues: 2059 helix: -1.09 (0.17), residues: 780 sheet: -2.79 (0.37), residues: 164 loop : -3.49 (0.16), residues: 1115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP A 17 HIS 0.017 0.001 HIS C 307 PHE 0.026 0.002 PHE E 394 TYR 0.053 0.002 TYR F 114 ARG 0.015 0.001 ARG E 377 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4118 Ramachandran restraints generated. 2059 Oldfield, 0 Emsley, 2059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4118 Ramachandran restraints generated. 2059 Oldfield, 0 Emsley, 2059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 232 time to evaluate : 2.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 72 MET cc_start: 0.9158 (mtm) cc_final: 0.8173 (mtm) REVERT: B 113 MET cc_start: 0.8302 (tmm) cc_final: 0.7211 (tmm) REVERT: C 66 GLU cc_start: 0.9168 (pt0) cc_final: 0.8922 (pt0) REVERT: C 103 ILE cc_start: 0.9328 (mm) cc_final: 0.9089 (mm) REVERT: C 359 ASN cc_start: 0.8382 (p0) cc_final: 0.8150 (t0) REVERT: D 305 TYR cc_start: 0.7248 (t80) cc_final: 0.6918 (t80) REVERT: E 100 MET cc_start: 0.7266 (mpp) cc_final: 0.6979 (mpp) REVERT: E 228 ASN cc_start: 0.8811 (m-40) cc_final: 0.8592 (m-40) REVERT: E 378 GLU cc_start: 0.8778 (tt0) cc_final: 0.8360 (tp30) REVERT: F 113 MET cc_start: 0.8863 (tpp) cc_final: 0.8659 (tmm) REVERT: A 14 ARG cc_start: 0.9095 (tpt90) cc_final: 0.8388 (ttp80) REVERT: A 87 TYR cc_start: 0.7956 (m-80) cc_final: 0.7737 (m-80) outliers start: 3 outliers final: 0 residues processed: 234 average time/residue: 0.3473 time to fit residues: 116.5919 Evaluate side-chains 132 residues out of total 1831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 1.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 103 optimal weight: 4.9990 chunk 58 optimal weight: 9.9990 chunk 155 optimal weight: 1.9990 chunk 127 optimal weight: 10.0000 chunk 51 optimal weight: 9.9990 chunk 187 optimal weight: 0.9980 chunk 202 optimal weight: 0.4980 chunk 166 optimal weight: 1.9990 chunk 185 optimal weight: 0.4980 chunk 63 optimal weight: 9.9990 chunk 150 optimal weight: 2.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 46 ASN ** C 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 67 GLN C 69 GLN C 104 HIS ** C 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 214 ASN C 307 HIS C 414 GLN ** C 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 431 GLN D 13 HIS ** D 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 217 GLN A 270 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.3467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 17094 Z= 0.199 Angle : 0.750 11.700 23159 Z= 0.395 Chirality : 0.047 0.261 2566 Planarity : 0.005 0.066 2994 Dihedral : 7.643 58.518 2243 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 19.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.43 % Favored : 87.57 % Rotamer: Outliers : 0.11 % Allowed : 4.34 % Favored : 95.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 2.39 % Twisted Proline : 0.00 % Twisted General : 0.40 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.17 (0.17), residues: 2059 helix: -0.56 (0.18), residues: 784 sheet: -2.27 (0.36), residues: 181 loop : -3.42 (0.16), residues: 1094 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP A 17 HIS 0.012 0.001 HIS C 307 PHE 0.018 0.001 PHE E 394 TYR 0.032 0.002 TYR F 114 ARG 0.007 0.001 ARG D 503 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4118 Ramachandran restraints generated. 2059 Oldfield, 0 Emsley, 2059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4118 Ramachandran restraints generated. 2059 Oldfield, 0 Emsley, 2059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 205 time to evaluate : 1.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 72 MET cc_start: 0.9274 (mtm) cc_final: 0.8331 (mtm) REVERT: B 113 MET cc_start: 0.7727 (tmm) cc_final: 0.7030 (tmm) REVERT: C 66 GLU cc_start: 0.9224 (pt0) cc_final: 0.8915 (pt0) REVERT: C 103 ILE cc_start: 0.9298 (mm) cc_final: 0.9076 (mm) REVERT: C 359 ASN cc_start: 0.8420 (p0) cc_final: 0.7814 (t0) REVERT: D 42 TYR cc_start: 0.8201 (t80) cc_final: 0.7677 (t80) REVERT: D 44 PHE cc_start: 0.8842 (t80) cc_final: 0.8339 (t80) REVERT: D 268 PHE cc_start: 0.8474 (t80) cc_final: 0.8153 (t80) REVERT: D 305 TYR cc_start: 0.6850 (t80) cc_final: 0.6512 (t80) REVERT: D 391 LEU cc_start: 0.7134 (mt) cc_final: 0.6925 (mt) REVERT: E 49 LEU cc_start: 0.8337 (pp) cc_final: 0.8057 (pp) REVERT: E 98 MET cc_start: 0.7738 (mtt) cc_final: 0.7476 (mtt) REVERT: E 100 MET cc_start: 0.7464 (mpp) cc_final: 0.7121 (mpp) REVERT: E 378 GLU cc_start: 0.8956 (tt0) cc_final: 0.8397 (tp30) REVERT: F 55 PHE cc_start: 0.8976 (p90) cc_final: 0.8774 (p90) REVERT: A 14 ARG cc_start: 0.9071 (tpt90) cc_final: 0.8415 (ttp80) outliers start: 2 outliers final: 0 residues processed: 206 average time/residue: 0.3263 time to fit residues: 96.8355 Evaluate side-chains 132 residues out of total 1831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 1.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 185 optimal weight: 0.0060 chunk 140 optimal weight: 6.9990 chunk 97 optimal weight: 4.9990 chunk 20 optimal weight: 10.0000 chunk 89 optimal weight: 4.9990 chunk 125 optimal weight: 0.9990 chunk 188 optimal weight: 0.1980 chunk 199 optimal weight: 1.9990 chunk 98 optimal weight: 9.9990 chunk 178 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 overall best weight: 1.0402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 5 GLN ** B 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 214 ASN ** C 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 431 GLN ** D 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 102 ASN ** A 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 270 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.3887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 17094 Z= 0.176 Angle : 0.703 10.312 23159 Z= 0.373 Chirality : 0.047 0.294 2566 Planarity : 0.005 0.060 2994 Dihedral : 7.173 54.860 2243 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 18.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.24 % Favored : 87.76 % Rotamer: Outliers : 0.11 % Allowed : 3.74 % Favored : 96.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 2.39 % Twisted Proline : 0.00 % Twisted General : 0.35 % 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: -2.88 (0.17), residues: 2059 helix: -0.24 (0.18), residues: 786 sheet: -2.14 (0.36), residues: 181 loop : -3.32 (0.16), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP A 17 HIS 0.009 0.001 HIS C 307 PHE 0.015 0.001 PHE C 140 TYR 0.029 0.001 TYR F 114 ARG 0.004 0.000 ARG C 428 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4118 Ramachandran restraints generated. 2059 Oldfield, 0 Emsley, 2059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4118 Ramachandran restraints generated. 2059 Oldfield, 0 Emsley, 2059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 195 time to evaluate : 2.079 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 72 MET cc_start: 0.9271 (mtm) cc_final: 0.8285 (mtm) REVERT: B 113 MET cc_start: 0.7651 (tmm) cc_final: 0.7285 (tmm) REVERT: C 359 ASN cc_start: 0.8372 (p0) cc_final: 0.8114 (t0) REVERT: C 390 MET cc_start: 0.9008 (ttp) cc_final: 0.8609 (ttp) REVERT: D 32 PHE cc_start: 0.7738 (m-80) cc_final: 0.7480 (m-10) REVERT: D 42 TYR cc_start: 0.8178 (t80) cc_final: 0.7650 (t80) REVERT: D 44 PHE cc_start: 0.8810 (t80) cc_final: 0.8312 (t80) REVERT: D 268 PHE cc_start: 0.8463 (t80) cc_final: 0.8066 (t80) REVERT: D 305 TYR cc_start: 0.6725 (t80) cc_final: 0.6406 (t80) REVERT: D 391 LEU cc_start: 0.7031 (mt) cc_final: 0.6821 (mt) REVERT: E 49 LEU cc_start: 0.8615 (pp) cc_final: 0.8321 (pp) REVERT: E 98 MET cc_start: 0.8078 (mtt) cc_final: 0.7829 (mtt) REVERT: E 100 MET cc_start: 0.7545 (mpp) cc_final: 0.7162 (mpp) REVERT: E 378 GLU cc_start: 0.8923 (tt0) cc_final: 0.8368 (tp30) REVERT: F 8 ILE cc_start: 0.9095 (pt) cc_final: 0.8882 (pt) REVERT: A 14 ARG cc_start: 0.9067 (tpt90) cc_final: 0.8415 (ttp80) REVERT: A 87 TYR cc_start: 0.8265 (m-80) cc_final: 0.7994 (m-80) REVERT: A 222 LYS cc_start: 0.7921 (mptt) cc_final: 0.7484 (mptt) REVERT: A 442 VAL cc_start: 0.9074 (t) cc_final: 0.8824 (t) outliers start: 2 outliers final: 0 residues processed: 196 average time/residue: 0.3087 time to fit residues: 89.1308 Evaluate side-chains 126 residues out of total 1831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 1.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 165 optimal weight: 10.0000 chunk 113 optimal weight: 0.4980 chunk 2 optimal weight: 5.9990 chunk 148 optimal weight: 10.0000 chunk 82 optimal weight: 8.9990 chunk 169 optimal weight: 0.2980 chunk 137 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 101 optimal weight: 7.9990 chunk 178 optimal weight: 4.9990 chunk 50 optimal weight: 0.8980 overall best weight: 2.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 90 HIS ** B 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 63 ASN C 135 GLN ** C 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 214 ASN C 414 GLN ** C 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 390 ASN ** E 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 102 ASN ** A 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 270 HIS A 345 ASN A 400 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.4284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 17094 Z= 0.234 Angle : 0.729 9.968 23159 Z= 0.387 Chirality : 0.047 0.301 2566 Planarity : 0.005 0.061 2994 Dihedral : 7.071 52.147 2243 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 22.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.31 % Favored : 86.69 % Rotamer: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 2.39 % Twisted Proline : 0.00 % Twisted General : 0.30 % 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: -2.68 (0.18), residues: 2059 helix: -0.10 (0.18), residues: 785 sheet: -2.06 (0.37), residues: 181 loop : -3.16 (0.17), residues: 1093 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.002 TRP A 17 HIS 0.006 0.001 HIS E 313 PHE 0.021 0.002 PHE A 337 TYR 0.025 0.002 TYR D 42 ARG 0.005 0.001 ARG A 142 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4118 Ramachandran restraints generated. 2059 Oldfield, 0 Emsley, 2059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4118 Ramachandran restraints generated. 2059 Oldfield, 0 Emsley, 2059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 177 time to evaluate : 2.093 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 72 MET cc_start: 0.9307 (mtm) cc_final: 0.8303 (mtm) REVERT: B 113 MET cc_start: 0.7692 (tmm) cc_final: 0.7261 (tmm) REVERT: C 103 ILE cc_start: 0.9249 (mm) cc_final: 0.9048 (mm) REVERT: C 359 ASN cc_start: 0.8492 (p0) cc_final: 0.8160 (t0) REVERT: C 372 ASP cc_start: 0.8437 (m-30) cc_final: 0.8179 (m-30) REVERT: C 390 MET cc_start: 0.9070 (ttp) cc_final: 0.8650 (ttp) REVERT: D 44 PHE cc_start: 0.8913 (t80) cc_final: 0.8409 (t80) REVERT: D 268 PHE cc_start: 0.8652 (t80) cc_final: 0.8313 (t80) REVERT: D 299 ILE cc_start: 0.9203 (pt) cc_final: 0.8903 (mt) REVERT: D 305 TYR cc_start: 0.6947 (t80) cc_final: 0.6549 (t80) REVERT: E 49 LEU cc_start: 0.8778 (pp) cc_final: 0.8575 (pp) REVERT: E 98 MET cc_start: 0.8350 (mtt) cc_final: 0.8119 (mtt) REVERT: E 100 MET cc_start: 0.7642 (mpp) cc_final: 0.7226 (mpp) REVERT: E 315 ILE cc_start: 0.9710 (mt) cc_final: 0.9431 (mt) REVERT: E 378 GLU cc_start: 0.8900 (tt0) cc_final: 0.8326 (tp30) REVERT: F 55 PHE cc_start: 0.9119 (p90) cc_final: 0.8862 (p90) REVERT: A 14 ARG cc_start: 0.8958 (tpt90) cc_final: 0.8048 (ttp80) REVERT: A 87 TYR cc_start: 0.8470 (m-80) cc_final: 0.8129 (m-80) REVERT: A 265 MET cc_start: 0.8765 (ptp) cc_final: 0.8448 (ptm) REVERT: A 267 MET cc_start: 0.7949 (tmm) cc_final: 0.7548 (ppp) outliers start: 0 outliers final: 0 residues processed: 177 average time/residue: 0.3326 time to fit residues: 87.3286 Evaluate side-chains 122 residues out of total 1831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 122 time to evaluate : 1.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 66 optimal weight: 5.9990 chunk 179 optimal weight: 0.4980 chunk 39 optimal weight: 3.9990 chunk 116 optimal weight: 2.9990 chunk 49 optimal weight: 0.0570 chunk 199 optimal weight: 3.9990 chunk 165 optimal weight: 0.1980 chunk 92 optimal weight: 10.0000 chunk 16 optimal weight: 10.0000 chunk 65 optimal weight: 6.9990 chunk 104 optimal weight: 0.9980 overall best weight: 0.9500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 181 HIS ** C 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 203 GLN D 390 ASN ** E 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 102 ASN ** A 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 219 HIS A 270 HIS A 345 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.4626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 17094 Z= 0.172 Angle : 0.697 11.091 23159 Z= 0.366 Chirality : 0.047 0.309 2566 Planarity : 0.004 0.055 2994 Dihedral : 6.770 47.762 2243 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 19.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.80 % Favored : 88.20 % Rotamer: Outliers : 0.05 % Allowed : 2.47 % Favored : 97.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 2.39 % Twisted Proline : 0.00 % Twisted General : 0.30 % 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 (0.18), residues: 2059 helix: 0.07 (0.19), residues: 787 sheet: -1.88 (0.38), residues: 181 loop : -3.10 (0.17), residues: 1091 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 17 HIS 0.006 0.001 HIS A 215 PHE 0.011 0.001 PHE C 440 TYR 0.023 0.001 TYR B 137 ARG 0.008 0.000 ARG A 14 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4118 Ramachandran restraints generated. 2059 Oldfield, 0 Emsley, 2059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4118 Ramachandran restraints generated. 2059 Oldfield, 0 Emsley, 2059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 184 time to evaluate : 1.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 72 MET cc_start: 0.9321 (mtm) cc_final: 0.8285 (mtm) REVERT: B 113 MET cc_start: 0.7603 (tmm) cc_final: 0.7402 (tmm) REVERT: C 103 ILE cc_start: 0.9261 (mm) cc_final: 0.9061 (mm) REVERT: C 359 ASN cc_start: 0.8401 (p0) cc_final: 0.8060 (t0) REVERT: C 372 ASP cc_start: 0.8512 (m-30) cc_final: 0.8225 (m-30) REVERT: C 390 MET cc_start: 0.9090 (ttp) cc_final: 0.8708 (ttp) REVERT: D 32 PHE cc_start: 0.7743 (m-80) cc_final: 0.7477 (m-10) REVERT: D 44 PHE cc_start: 0.8892 (t80) cc_final: 0.8290 (t80) REVERT: D 268 PHE cc_start: 0.8494 (t80) cc_final: 0.7986 (t80) REVERT: D 305 TYR cc_start: 0.6755 (t80) cc_final: 0.6276 (t80) REVERT: E 315 ILE cc_start: 0.9621 (mt) cc_final: 0.9309 (mt) REVERT: E 378 GLU cc_start: 0.8873 (tt0) cc_final: 0.8341 (tp30) REVERT: F 8 ILE cc_start: 0.9073 (pt) cc_final: 0.8779 (pt) REVERT: F 55 PHE cc_start: 0.9113 (p90) cc_final: 0.8860 (p90) REVERT: F 113 MET cc_start: 0.8146 (ppp) cc_final: 0.7914 (ppp) REVERT: A 87 TYR cc_start: 0.8382 (m-80) cc_final: 0.8059 (m-80) REVERT: A 262 LEU cc_start: 0.9513 (pp) cc_final: 0.9293 (mp) REVERT: A 265 MET cc_start: 0.8638 (ptp) cc_final: 0.8376 (ptp) REVERT: A 267 MET cc_start: 0.7857 (tmm) cc_final: 0.7622 (tmm) outliers start: 1 outliers final: 0 residues processed: 185 average time/residue: 0.3169 time to fit residues: 86.3175 Evaluate side-chains 126 residues out of total 1831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 1.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 192 optimal weight: 1.9990 chunk 22 optimal weight: 6.9990 chunk 113 optimal weight: 5.9990 chunk 145 optimal weight: 0.9990 chunk 112 optimal weight: 6.9990 chunk 167 optimal weight: 10.0000 chunk 111 optimal weight: 0.4980 chunk 198 optimal weight: 0.8980 chunk 124 optimal weight: 5.9990 chunk 121 optimal weight: 6.9990 chunk 91 optimal weight: 4.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 203 GLN D 390 ASN ** E 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 102 ASN ** A 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 270 HIS A 345 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.4909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 17094 Z= 0.208 Angle : 0.709 11.136 23159 Z= 0.373 Chirality : 0.047 0.291 2566 Planarity : 0.004 0.061 2994 Dihedral : 6.691 42.566 2243 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 20.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.31 % Favored : 86.69 % Rotamer: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 2.39 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: -2.43 (0.18), residues: 2059 helix: 0.15 (0.19), residues: 782 sheet: -1.92 (0.37), residues: 181 loop : -3.04 (0.17), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 17 HIS 0.006 0.001 HIS A 215 PHE 0.014 0.001 PHE A 277 TYR 0.021 0.002 TYR E 186 ARG 0.005 0.001 ARG D 503 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4118 Ramachandran restraints generated. 2059 Oldfield, 0 Emsley, 2059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4118 Ramachandran restraints generated. 2059 Oldfield, 0 Emsley, 2059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 173 time to evaluate : 1.877 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 72 MET cc_start: 0.9313 (mtm) cc_final: 0.8260 (mtm) REVERT: C 103 ILE cc_start: 0.9284 (mm) cc_final: 0.9081 (mm) REVERT: C 359 ASN cc_start: 0.8519 (p0) cc_final: 0.8137 (t0) REVERT: C 372 ASP cc_start: 0.8528 (m-30) cc_final: 0.8284 (m-30) REVERT: C 390 MET cc_start: 0.9046 (ttp) cc_final: 0.8731 (ttp) REVERT: D 44 PHE cc_start: 0.8885 (t80) cc_final: 0.8387 (t80) REVERT: D 268 PHE cc_start: 0.8643 (t80) cc_final: 0.8150 (t80) REVERT: D 305 TYR cc_start: 0.6846 (t80) cc_final: 0.6338 (t80) REVERT: E 49 LEU cc_start: 0.8103 (pp) cc_final: 0.7798 (pp) REVERT: E 100 MET cc_start: 0.7469 (mpp) cc_final: 0.7187 (mpp) REVERT: E 315 ILE cc_start: 0.9691 (mt) cc_final: 0.9401 (mt) REVERT: E 378 GLU cc_start: 0.8804 (tt0) cc_final: 0.8175 (tp30) REVERT: F 8 ILE cc_start: 0.9189 (pt) cc_final: 0.8956 (pt) REVERT: F 55 PHE cc_start: 0.9190 (p90) cc_final: 0.8949 (p90) REVERT: A 87 TYR cc_start: 0.8467 (m-80) cc_final: 0.8115 (m-80) REVERT: A 262 LEU cc_start: 0.9513 (pp) cc_final: 0.9264 (mp) REVERT: A 267 MET cc_start: 0.7883 (tmm) cc_final: 0.7630 (tmm) outliers start: 0 outliers final: 0 residues processed: 173 average time/residue: 0.3032 time to fit residues: 78.0567 Evaluate side-chains 115 residues out of total 1831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 1.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 122 optimal weight: 0.9990 chunk 79 optimal weight: 5.9990 chunk 118 optimal weight: 7.9990 chunk 59 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 38 optimal weight: 0.8980 chunk 126 optimal weight: 2.9990 chunk 135 optimal weight: 0.9990 chunk 98 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 156 optimal weight: 0.0770 overall best weight: 0.7542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 178 ASN ** C 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 203 GLN D 390 ASN ** E 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 102 ASN A 270 HIS A 345 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.5125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 17094 Z= 0.163 Angle : 0.701 11.266 23159 Z= 0.363 Chirality : 0.047 0.330 2566 Planarity : 0.004 0.064 2994 Dihedral : 6.494 37.297 2243 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 18.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.17 % Favored : 88.83 % Rotamer: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 2.39 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.34 (0.18), residues: 2059 helix: 0.28 (0.19), residues: 789 sheet: -1.65 (0.37), residues: 194 loop : -3.12 (0.17), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 17 HIS 0.006 0.001 HIS A 215 PHE 0.012 0.001 PHE C 440 TYR 0.029 0.001 TYR C 260 ARG 0.004 0.000 ARG E 324 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4118 Ramachandran restraints generated. 2059 Oldfield, 0 Emsley, 2059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4118 Ramachandran restraints generated. 2059 Oldfield, 0 Emsley, 2059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 176 time to evaluate : 1.972 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 72 MET cc_start: 0.9330 (mtm) cc_final: 0.8246 (mtm) REVERT: C 103 ILE cc_start: 0.9213 (mm) cc_final: 0.8983 (mm) REVERT: C 218 ARG cc_start: 0.8247 (tpm170) cc_final: 0.7857 (tpp-160) REVERT: C 359 ASN cc_start: 0.8440 (p0) cc_final: 0.8085 (t0) REVERT: C 390 MET cc_start: 0.9063 (ttp) cc_final: 0.8705 (ttp) REVERT: D 44 PHE cc_start: 0.8886 (t80) cc_final: 0.8360 (t80) REVERT: D 139 THR cc_start: 0.8234 (p) cc_final: 0.7909 (p) REVERT: D 268 PHE cc_start: 0.8511 (t80) cc_final: 0.8025 (t80) REVERT: D 305 TYR cc_start: 0.6787 (t80) cc_final: 0.6305 (t80) REVERT: E 100 MET cc_start: 0.7523 (mpp) cc_final: 0.7298 (mpp) REVERT: E 315 ILE cc_start: 0.9637 (mt) cc_final: 0.9362 (mt) REVERT: E 378 GLU cc_start: 0.8799 (tt0) cc_final: 0.8242 (tp30) REVERT: F 8 ILE cc_start: 0.9141 (pt) cc_final: 0.8907 (pt) REVERT: F 55 PHE cc_start: 0.9073 (p90) cc_final: 0.8821 (p90) REVERT: F 113 MET cc_start: 0.8099 (ppp) cc_final: 0.7834 (ppp) REVERT: A 87 TYR cc_start: 0.8310 (m-80) cc_final: 0.7983 (m-80) REVERT: A 222 LYS cc_start: 0.7610 (mptt) cc_final: 0.7307 (mptt) REVERT: A 267 MET cc_start: 0.7709 (tmm) cc_final: 0.7168 (ppp) outliers start: 0 outliers final: 0 residues processed: 176 average time/residue: 0.3174 time to fit residues: 82.6468 Evaluate side-chains 122 residues out of total 1831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 122 time to evaluate : 1.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 180 optimal weight: 0.0170 chunk 190 optimal weight: 0.9990 chunk 173 optimal weight: 0.6980 chunk 185 optimal weight: 0.0770 chunk 111 optimal weight: 9.9990 chunk 80 optimal weight: 0.0030 chunk 145 optimal weight: 0.9990 chunk 56 optimal weight: 7.9990 chunk 167 optimal weight: 10.0000 chunk 174 optimal weight: 5.9990 chunk 184 optimal weight: 2.9990 overall best weight: 0.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 414 GLN ** C 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 203 GLN D 390 ASN ** E 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 102 ASN A 270 HIS A 345 ASN A 400 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.5389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 17094 Z= 0.158 Angle : 0.704 12.029 23159 Z= 0.361 Chirality : 0.047 0.328 2566 Planarity : 0.004 0.060 2994 Dihedral : 6.232 36.705 2243 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 16.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.90 % Favored : 88.10 % Rotamer: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 2.39 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -2.23 (0.18), residues: 2059 helix: 0.35 (0.19), residues: 789 sheet: -1.23 (0.40), residues: 170 loop : -3.08 (0.16), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 17 HIS 0.006 0.001 HIS A 215 PHE 0.019 0.001 PHE A 92 TYR 0.029 0.001 TYR E 186 ARG 0.006 0.000 ARG A 503 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4118 Ramachandran restraints generated. 2059 Oldfield, 0 Emsley, 2059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4118 Ramachandran restraints generated. 2059 Oldfield, 0 Emsley, 2059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 182 time to evaluate : 2.083 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 72 MET cc_start: 0.9345 (mtm) cc_final: 0.8250 (mtm) REVERT: C 103 ILE cc_start: 0.9203 (mm) cc_final: 0.8980 (mm) REVERT: C 359 ASN cc_start: 0.8258 (p0) cc_final: 0.7997 (t0) REVERT: C 390 MET cc_start: 0.9008 (ttp) cc_final: 0.8630 (ttp) REVERT: D 32 PHE cc_start: 0.7697 (m-80) cc_final: 0.7445 (m-80) REVERT: D 44 PHE cc_start: 0.8770 (t80) cc_final: 0.8305 (t80) REVERT: D 268 PHE cc_start: 0.8473 (t80) cc_final: 0.7976 (t80) REVERT: D 305 TYR cc_start: 0.6627 (t80) cc_final: 0.6098 (t80) REVERT: E 98 MET cc_start: 0.7935 (mpp) cc_final: 0.7557 (mpp) REVERT: E 100 MET cc_start: 0.7403 (mpp) cc_final: 0.7175 (mpp) REVERT: E 315 ILE cc_start: 0.9653 (mt) cc_final: 0.9345 (mt) REVERT: E 378 GLU cc_start: 0.8789 (tt0) cc_final: 0.8203 (tp30) REVERT: F 8 ILE cc_start: 0.9187 (pt) cc_final: 0.8983 (pt) REVERT: F 55 PHE cc_start: 0.9016 (p90) cc_final: 0.8790 (p90) REVERT: F 113 MET cc_start: 0.8078 (ppp) cc_final: 0.7792 (ppp) REVERT: A 87 TYR cc_start: 0.8270 (m-80) cc_final: 0.7955 (m-80) REVERT: A 222 LYS cc_start: 0.7693 (mptt) cc_final: 0.7377 (mptt) REVERT: A 267 MET cc_start: 0.7588 (tmm) cc_final: 0.7055 (ppp) outliers start: 0 outliers final: 0 residues processed: 182 average time/residue: 0.3046 time to fit residues: 82.8643 Evaluate side-chains 117 residues out of total 1831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 1.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 121 optimal weight: 5.9990 chunk 195 optimal weight: 1.9990 chunk 119 optimal weight: 0.7980 chunk 92 optimal weight: 0.8980 chunk 136 optimal weight: 8.9990 chunk 205 optimal weight: 0.7980 chunk 188 optimal weight: 7.9990 chunk 163 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 chunk 126 optimal weight: 0.6980 chunk 100 optimal weight: 8.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 203 GLN ** D 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 102 ASN A 270 HIS A 345 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.5590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 17094 Z= 0.168 Angle : 0.709 12.997 23159 Z= 0.364 Chirality : 0.047 0.341 2566 Planarity : 0.004 0.060 2994 Dihedral : 6.131 36.360 2243 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 18.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.46 % Favored : 88.54 % Rotamer: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 2.39 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -2.14 (0.18), residues: 2059 helix: 0.43 (0.19), residues: 782 sheet: -1.13 (0.40), residues: 170 loop : -3.02 (0.16), residues: 1107 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 17 HIS 0.006 0.001 HIS A 215 PHE 0.023 0.001 PHE C 415 TYR 0.027 0.001 TYR E 186 ARG 0.005 0.000 ARG A 503 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4118 Ramachandran restraints generated. 2059 Oldfield, 0 Emsley, 2059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4118 Ramachandran restraints generated. 2059 Oldfield, 0 Emsley, 2059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 166 time to evaluate : 2.035 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 72 MET cc_start: 0.9342 (mtm) cc_final: 0.8218 (mtm) REVERT: C 103 ILE cc_start: 0.9211 (mm) cc_final: 0.8990 (mm) REVERT: C 359 ASN cc_start: 0.8328 (p0) cc_final: 0.8068 (t0) REVERT: C 390 MET cc_start: 0.8963 (ttp) cc_final: 0.8693 (ptm) REVERT: D 32 PHE cc_start: 0.7601 (m-80) cc_final: 0.7328 (m-10) REVERT: D 44 PHE cc_start: 0.8888 (t80) cc_final: 0.8359 (t80) REVERT: D 268 PHE cc_start: 0.8584 (t80) cc_final: 0.8058 (t80) REVERT: D 305 TYR cc_start: 0.6666 (t80) cc_final: 0.6178 (t80) REVERT: E 98 MET cc_start: 0.8011 (mpp) cc_final: 0.7807 (mpp) REVERT: E 100 MET cc_start: 0.7569 (mpp) cc_final: 0.7325 (mpp) REVERT: E 309 LYS cc_start: 0.9386 (mptt) cc_final: 0.8910 (mmmt) REVERT: E 315 ILE cc_start: 0.9682 (mt) cc_final: 0.9345 (mt) REVERT: E 378 GLU cc_start: 0.8868 (tt0) cc_final: 0.8341 (tp30) REVERT: F 8 ILE cc_start: 0.9162 (pt) cc_final: 0.8956 (pt) REVERT: F 55 PHE cc_start: 0.9107 (p90) cc_final: 0.8857 (p90) REVERT: F 113 MET cc_start: 0.8092 (ppp) cc_final: 0.7810 (ppp) REVERT: A 87 TYR cc_start: 0.8305 (m-80) cc_final: 0.7977 (m-80) REVERT: A 459 GLU cc_start: 0.9349 (mp0) cc_final: 0.9086 (mp0) outliers start: 0 outliers final: 0 residues processed: 166 average time/residue: 0.3174 time to fit residues: 78.1745 Evaluate side-chains 117 residues out of total 1831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 2.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 129 optimal weight: 5.9990 chunk 174 optimal weight: 9.9990 chunk 50 optimal weight: 0.9990 chunk 150 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 chunk 163 optimal weight: 0.9980 chunk 68 optimal weight: 0.9990 chunk 168 optimal weight: 0.0770 chunk 20 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 203 GLN ** D 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 102 ASN A 270 HIS A 345 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.058913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.045157 restraints weight = 124735.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.046261 restraints weight = 93512.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.047080 restraints weight = 75417.216| |-----------------------------------------------------------------------------| r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.5765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 17094 Z= 0.157 Angle : 0.698 13.355 23159 Z= 0.356 Chirality : 0.047 0.339 2566 Planarity : 0.004 0.059 2994 Dihedral : 6.009 36.450 2243 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 16.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.17 % Favored : 88.83 % Rotamer: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 2.39 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -2.04 (0.18), residues: 2059 helix: 0.51 (0.19), residues: 781 sheet: -1.03 (0.40), residues: 170 loop : -2.97 (0.17), residues: 1108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 17 HIS 0.007 0.001 HIS A 215 PHE 0.021 0.001 PHE E 342 TYR 0.028 0.001 TYR E 186 ARG 0.004 0.000 ARG A 503 =============================================================================== Job complete usr+sys time: 3166.46 seconds wall clock time: 59 minutes 5.98 seconds (3545.98 seconds total)