Starting phenix.real_space_refine on Wed Mar 4 20:55:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7btr_30183/03_2026/7btr_30183.cif Found real_map, /net/cci-nas-00/data/ceres_data/7btr_30183/03_2026/7btr_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 { model { file = "/net/cci-nas-00/data/ceres_data/7btr_30183/03_2026/7btr_30183.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7btr_30183/03_2026/7btr_30183.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7btr_30183/03_2026/7btr_30183.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7btr_30183/03_2026/7btr_30183.map" } resolution = 4.54 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.007 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. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16737 Number of models: 1 Model: "" Number of chains: 5 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: {'ASP:plan': 1, 'HIS:plan': 1, 'ARG: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: "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 Restraints were copied for chains: F Time building chain proxies: 3.89, per 1000 atoms: 0.23 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 - 3.00 Amino acid : True - 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: 1.44 Conformation dependent library (CDL) restraints added in 806.6 milliseconds 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: 0.49 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: 3.25 Time building geometry restraints manager: 1.90 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: 0.00 - 3.45: 22637 3.45 - 6.90: 445 6.90 - 10.35: 61 10.35 - 13.80: 13 13.80 - 17.25: 3 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 3.120 nonbonded pdb=" O GLY A 131 " pdb=" OH TYR A 274 " model vdw 2.214 3.040 nonbonded pdb=" OH TYR C 399 " pdb=" O LYS C 425 " model vdw 2.242 3.040 nonbonded pdb=" OD1 ASN B 136 " pdb=" OG1 THR D 396 " model vdw 2.251 3.040 nonbonded pdb=" OH TYR E 116 " pdb=" OD1 ASP E 166 " model vdw 2.266 3.040 ... (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 Time spend for trying shortcut: 0.00 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: 1.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 16.160 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.420 ------------------------------------------------------------------------------- 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= 0.340 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.012 0.001 ARG C 65 TYR 0.034 0.003 TYR F 46 PHE 0.027 0.004 PHE A 49 TRP 0.029 0.003 TRP F 23 HIS 0.011 0.002 HIS A 289 Details of bonding type rmsd covalent geometry : bond 0.00686 (17094) covalent geometry : angle 1.22874 (23159) hydrogen bonds : bond 0.17297 ( 598) hydrogen bonds : angle 8.17045 ( 1713) *********************** 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 to be fit. rotamer outliers: 18 poor density : 327 time to evaluate : 0.627 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: B 72 MET cc_start: 0.9283 (mtm) cc_final: 0.9015 (mtt) REVERT: B 152 THR cc_start: 0.8726 (m) cc_final: 0.8457 (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: 0.8209 (t0) REVERT: D 40 LEU cc_start: 0.8938 (tp) cc_final: 0.8662 (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: 0.8396 (t80) REVERT: D 48 ASN cc_start: 0.8880 (t0) cc_final: 0.8637 (m110) REVERT: D 305 TYR cc_start: 0.7394 (t80) cc_final: 0.6961 (t80) REVERT: E 228 ASN cc_start: 0.8814 (m-40) cc_final: 0.8594 (m-40) REVERT: E 297 MET cc_start: 0.8386 (ptm) cc_final: 0.7004 (ptp) REVERT: F 6 VAL cc_start: 0.9062 (m) cc_final: 0.8818 (p) REVERT: F 113 MET cc_start: 0.8998 (tpp) cc_final: 0.8645 (tmm) REVERT: F 124 THR cc_start: 0.9101 (m) cc_final: 0.8823 (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: 0.1603 time to fit residues: 78.1536 Evaluate side-chains 146 residues out of total 1831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 143 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 98 optimal weight: 0.9990 chunk 194 optimal weight: 0.7980 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 0.2980 chunk 124 optimal weight: 0.0370 chunk 103 optimal weight: 0.9980 chunk 200 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 135 GLN B 136 ASN C 42 GLN C 67 GLN C 69 GLN C 72 ASN C 120 ASN C 157 ASN C 163 GLN C 214 ASN C 221 ASN C 307 HIS ** C 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 414 GLN C 459 HIS D 219 HIS ** D 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 64 HIS ** E 180 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 379 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.059611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.045243 restraints weight = 121029.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.046409 restraints weight = 89932.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.047276 restraints weight = 71884.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.047926 restraints weight = 60573.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.048371 restraints weight = 52950.133| |-----------------------------------------------------------------------------| r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.2947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 17094 Z= 0.152 Angle : 0.793 9.602 23159 Z= 0.424 Chirality : 0.048 0.258 2566 Planarity : 0.006 0.141 2994 Dihedral : 8.151 59.160 2243 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 15.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.19 % Favored : 87.81 % Rotamer: Outliers : 0.22 % Allowed : 4.01 % Favored : 95.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 2.39 % Twisted Proline : 1.61 % Twisted General : 0.70 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.71 (0.16), residues: 2059 helix: -1.11 (0.17), residues: 782 sheet: -2.63 (0.33), residues: 197 loop : -3.63 (0.15), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 377 TYR 0.057 0.002 TYR F 114 PHE 0.021 0.002 PHE E 394 TRP 0.049 0.002 TRP A 17 HIS 0.016 0.001 HIS C 307 Details of bonding type rmsd covalent geometry : bond 0.00319 (17094) covalent geometry : angle 0.79258 (23159) hydrogen bonds : bond 0.04751 ( 598) hydrogen bonds : angle 6.21811 ( 1713) *********************** 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 251 residues out of total 1831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 247 time to evaluate : 0.626 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: 0.9236 (mtm) cc_final: 0.8325 (mtm) REVERT: B 145 ARG cc_start: 0.9127 (mpp-170) cc_final: 0.8779 (mtt-85) REVERT: C 103 ILE cc_start: 0.9244 (mm) cc_final: 0.9000 (mm) REVERT: C 359 ASN cc_start: 0.8417 (p0) cc_final: 0.8036 (t0) REVERT: D 32 PHE cc_start: 0.7770 (m-80) cc_final: 0.7559 (m-10) REVERT: D 42 TYR cc_start: 0.8359 (t80) cc_final: 0.8074 (t80) REVERT: D 44 PHE cc_start: 0.9163 (t80) cc_final: 0.8368 (t80) REVERT: D 269 LEU cc_start: 0.8662 (mt) cc_final: 0.8440 (mt) REVERT: D 305 TYR cc_start: 0.7112 (t80) cc_final: 0.6765 (t80) REVERT: E 100 MET cc_start: 0.7770 (mpp) cc_final: 0.7347 (mpp) REVERT: F 113 MET cc_start: 0.8843 (tpp) cc_final: 0.8623 (tmm) REVERT: A 14 ARG cc_start: 0.9130 (tpt90) cc_final: 0.8469 (ttp80) REVERT: A 87 TYR cc_start: 0.8317 (m-80) cc_final: 0.8041 (m-80) outliers start: 4 outliers final: 0 residues processed: 250 average time/residue: 0.1413 time to fit residues: 51.2421 Evaluate side-chains 134 residues out of total 1831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 194 optimal weight: 5.9990 chunk 7 optimal weight: 0.3980 chunk 39 optimal weight: 6.9990 chunk 76 optimal weight: 9.9990 chunk 198 optimal weight: 2.9990 chunk 178 optimal weight: 7.9990 chunk 14 optimal weight: 10.0000 chunk 63 optimal weight: 1.9990 chunk 132 optimal weight: 6.9990 chunk 153 optimal weight: 5.9990 chunk 1 optimal weight: 9.9990 overall best weight: 3.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 90 HIS ** B 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 46 ASN ** C 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 HIS ** C 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 181 HIS C 214 ASN C 402 GLN ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 13 HIS D 18 GLN ** D 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 342 HIS ** D 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 243 ASN A 270 HIS A 345 ASN A 378 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.055394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.041320 restraints weight = 131314.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.042455 restraints weight = 96375.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.043289 restraints weight = 76537.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.043905 restraints weight = 64341.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.044365 restraints weight = 56295.127| |-----------------------------------------------------------------------------| r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.3788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.104 17094 Z= 0.255 Angle : 0.827 9.735 23159 Z= 0.445 Chirality : 0.048 0.240 2566 Planarity : 0.005 0.068 2994 Dihedral : 7.958 61.268 2243 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 21.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.65 % Favored : 86.35 % Rotamer: Outliers : 0.11 % Allowed : 5.11 % Favored : 94.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 2.39 % Twisted Proline : 0.00 % Twisted General : 0.55 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.25 (0.17), residues: 2059 helix: -0.62 (0.18), residues: 777 sheet: -2.43 (0.35), residues: 181 loop : -3.43 (0.16), residues: 1101 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 43 TYR 0.031 0.002 TYR F 114 PHE 0.031 0.002 PHE A 277 TRP 0.049 0.002 TRP A 17 HIS 0.009 0.002 HIS C 307 Details of bonding type rmsd covalent geometry : bond 0.00508 (17094) covalent geometry : angle 0.82692 (23159) hydrogen bonds : bond 0.04803 ( 598) hydrogen bonds : angle 6.04097 ( 1713) *********************** 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 185 residues out of total 1831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 183 time to evaluate : 0.619 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: 0.9339 (mtm) cc_final: 0.8230 (mtm) REVERT: B 113 MET cc_start: 0.8485 (tmm) cc_final: 0.7279 (tmm) REVERT: C 60 MET cc_start: 0.9273 (mtm) cc_final: 0.9041 (mtt) REVERT: C 103 ILE cc_start: 0.9214 (mm) cc_final: 0.8966 (mm) REVERT: C 359 ASN cc_start: 0.8900 (p0) cc_final: 0.8299 (t0) REVERT: C 390 MET cc_start: 0.8790 (ttp) cc_final: 0.8075 (ptt) REVERT: D 42 TYR cc_start: 0.8396 (t80) cc_final: 0.8099 (t80) REVERT: D 44 PHE cc_start: 0.9012 (t80) cc_final: 0.8665 (t80) REVERT: D 268 PHE cc_start: 0.8895 (t80) cc_final: 0.8637 (t80) REVERT: D 269 LEU cc_start: 0.8632 (mt) cc_final: 0.8363 (mt) REVERT: D 305 TYR cc_start: 0.7326 (t80) cc_final: 0.6977 (t80) REVERT: E 100 MET cc_start: 0.7645 (mpp) cc_final: 0.7266 (mpp) REVERT: E 378 GLU cc_start: 0.9206 (tt0) cc_final: 0.8559 (tp30) REVERT: F 55 PHE cc_start: 0.9248 (p90) cc_final: 0.9019 (p90) REVERT: F 113 MET cc_start: 0.8883 (tpp) cc_final: 0.8617 (tmm) REVERT: A 14 ARG cc_start: 0.9118 (tpt90) cc_final: 0.8452 (ttp80) REVERT: A 422 PHE cc_start: 0.7434 (t80) cc_final: 0.7158 (t80) outliers start: 2 outliers final: 1 residues processed: 184 average time/residue: 0.1538 time to fit residues: 40.9500 Evaluate side-chains 114 residues out of total 1831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 113 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 44 optimal weight: 5.9990 chunk 191 optimal weight: 3.9990 chunk 124 optimal weight: 4.9990 chunk 18 optimal weight: 0.9990 chunk 169 optimal weight: 0.9980 chunk 123 optimal weight: 0.9990 chunk 11 optimal weight: 7.9990 chunk 80 optimal weight: 0.9980 chunk 47 optimal weight: 4.9990 chunk 53 optimal weight: 0.3980 chunk 154 optimal weight: 10.0000 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 163 GLN C 214 ASN C 414 GLN ** D 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 102 ASN ** A 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 345 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.058050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.043749 restraints weight = 124614.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.044869 restraints weight = 93604.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.045717 restraints weight = 75310.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.046348 restraints weight = 63656.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.046786 restraints weight = 55899.246| |-----------------------------------------------------------------------------| r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.4112 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= 0.135 Angle : 0.737 11.119 23159 Z= 0.390 Chirality : 0.048 0.329 2566 Planarity : 0.005 0.063 2994 Dihedral : 7.351 58.167 2243 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 15.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.41 % Favored : 88.59 % Rotamer: Outliers : 0.05 % Allowed : 3.68 % Favored : 96.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 2.39 % Twisted Proline : 0.00 % Twisted General : 0.40 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.88 (0.17), residues: 2059 helix: -0.24 (0.18), residues: 776 sheet: -2.19 (0.36), residues: 182 loop : -3.27 (0.16), residues: 1101 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 190 TYR 0.028 0.002 TYR D 42 PHE 0.016 0.001 PHE A 337 TRP 0.056 0.002 TRP A 17 HIS 0.009 0.001 HIS C 307 Details of bonding type rmsd covalent geometry : bond 0.00283 (17094) covalent geometry : angle 0.73710 (23159) hydrogen bonds : bond 0.03983 ( 598) hydrogen bonds : angle 5.62075 ( 1713) *********************** 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 to be fit. rotamer outliers: 1 poor density : 196 time to evaluate : 0.650 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: 0.9311 (mtm) cc_final: 0.8227 (mtm) REVERT: C 103 ILE cc_start: 0.9199 (mm) cc_final: 0.8995 (mm) REVERT: C 359 ASN cc_start: 0.8917 (p0) cc_final: 0.8234 (t0) REVERT: D 32 PHE cc_start: 0.7781 (m-80) cc_final: 0.7518 (m-10) REVERT: D 44 PHE cc_start: 0.8991 (t80) cc_final: 0.8601 (t80) REVERT: D 268 PHE cc_start: 0.8694 (t80) cc_final: 0.8327 (t80) REVERT: D 299 ILE cc_start: 0.9332 (pt) cc_final: 0.8888 (mt) REVERT: D 305 TYR cc_start: 0.6877 (t80) cc_final: 0.6564 (t80) REVERT: E 100 MET cc_start: 0.7727 (mpp) cc_final: 0.7389 (mpp) REVERT: E 315 ILE cc_start: 0.9685 (mm) cc_final: 0.9422 (mt) REVERT: E 378 GLU cc_start: 0.9219 (tt0) cc_final: 0.8672 (tp30) REVERT: F 55 PHE cc_start: 0.9262 (p90) cc_final: 0.9002 (p90) REVERT: F 113 MET cc_start: 0.8802 (tpp) cc_final: 0.8454 (tmm) REVERT: F 124 THR cc_start: 0.9185 (m) cc_final: 0.8975 (m) REVERT: A 14 ARG cc_start: 0.9109 (tpt90) cc_final: 0.8494 (ttp80) REVERT: A 87 TYR cc_start: 0.8536 (m-80) cc_final: 0.8124 (m-80) REVERT: A 222 LYS cc_start: 0.8183 (mptt) cc_final: 0.7948 (mptt) outliers start: 1 outliers final: 0 residues processed: 197 average time/residue: 0.1382 time to fit residues: 40.3823 Evaluate side-chains 127 residues out of total 1831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 200 optimal weight: 6.9990 chunk 120 optimal weight: 2.9990 chunk 42 optimal weight: 6.9990 chunk 175 optimal weight: 0.0770 chunk 121 optimal weight: 0.8980 chunk 205 optimal weight: 4.9990 chunk 179 optimal weight: 0.9990 chunk 5 optimal weight: 4.9990 chunk 56 optimal weight: 6.9990 chunk 39 optimal weight: 4.9990 chunk 18 optimal weight: 8.9990 overall best weight: 1.9944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 135 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 ** D 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 390 ASN ** 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 243 ASN A 345 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.056477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.042591 restraints weight = 126315.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.043644 restraints weight = 95631.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.044431 restraints weight = 77449.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.045024 restraints weight = 65879.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.045447 restraints weight = 58113.049| |-----------------------------------------------------------------------------| r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.4540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 17094 Z= 0.166 Angle : 0.741 10.237 23159 Z= 0.393 Chirality : 0.048 0.286 2566 Planarity : 0.005 0.062 2994 Dihedral : 7.120 55.072 2243 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 17.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.97 % Favored : 87.03 % Rotamer: Outliers : 0.05 % Allowed : 2.97 % Favored : 96.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 2.39 % Twisted Proline : 0.00 % Twisted General : 0.35 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.74 (0.17), residues: 2059 helix: -0.17 (0.18), residues: 780 sheet: -2.06 (0.37), residues: 181 loop : -3.17 (0.17), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 142 TYR 0.020 0.002 TYR F 114 PHE 0.019 0.002 PHE C 140 TRP 0.060 0.002 TRP A 17 HIS 0.008 0.001 HIS E 313 Details of bonding type rmsd covalent geometry : bond 0.00348 (17094) covalent geometry : angle 0.74122 (23159) hydrogen bonds : bond 0.03946 ( 598) hydrogen bonds : angle 5.54710 ( 1713) *********************** 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 169 residues out of total 1831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 168 time to evaluate : 0.640 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: 0.9334 (mtm) cc_final: 0.8195 (mtm) REVERT: C 103 ILE cc_start: 0.9262 (mm) cc_final: 0.9052 (mm) REVERT: C 359 ASN cc_start: 0.8890 (p0) cc_final: 0.8260 (t0) REVERT: D 32 PHE cc_start: 0.7876 (m-80) cc_final: 0.7664 (m-10) REVERT: D 44 PHE cc_start: 0.9051 (t80) cc_final: 0.8555 (t80) REVERT: D 268 PHE cc_start: 0.8837 (t80) cc_final: 0.8451 (t80) REVERT: D 299 ILE cc_start: 0.9326 (pt) cc_final: 0.8877 (mp) REVERT: D 305 TYR cc_start: 0.7003 (t80) cc_final: 0.6565 (t80) REVERT: E 100 MET cc_start: 0.7789 (mpp) cc_final: 0.7391 (mpp) REVERT: E 181 MET cc_start: 0.9294 (tmm) cc_final: 0.9084 (tmm) REVERT: E 378 GLU cc_start: 0.9218 (tt0) cc_final: 0.8527 (tp30) REVERT: F 55 PHE cc_start: 0.9393 (p90) cc_final: 0.9154 (p90) REVERT: F 113 MET cc_start: 0.8759 (tpp) cc_final: 0.8187 (tmm) REVERT: A 14 ARG cc_start: 0.9104 (tpt90) cc_final: 0.8210 (ttp80) REVERT: A 87 TYR cc_start: 0.8561 (m-80) cc_final: 0.8139 (m-80) REVERT: A 267 MET cc_start: 0.8368 (tmm) cc_final: 0.7631 (ppp) outliers start: 1 outliers final: 0 residues processed: 169 average time/residue: 0.1391 time to fit residues: 34.9918 Evaluate side-chains 117 residues out of total 1831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 114 optimal weight: 20.0000 chunk 63 optimal weight: 0.0070 chunk 185 optimal weight: 0.3980 chunk 174 optimal weight: 7.9990 chunk 26 optimal weight: 0.0980 chunk 19 optimal weight: 5.9990 chunk 101 optimal weight: 5.9990 chunk 71 optimal weight: 0.9990 chunk 189 optimal weight: 6.9990 chunk 6 optimal weight: 0.9990 chunk 1 optimal weight: 0.0470 overall best weight: 0.3098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 135 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 295 ASN ** D 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 451 HIS E 313 HIS F 107 HIS A 102 ASN A 215 HIS A 243 ASN A 345 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.058551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.044600 restraints weight = 118188.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.045672 restraints weight = 89306.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.046477 restraints weight = 72180.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.047112 restraints weight = 61273.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.047564 restraints weight = 53761.222| |-----------------------------------------------------------------------------| r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.4860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17094 Z= 0.125 Angle : 0.709 11.739 23159 Z= 0.370 Chirality : 0.048 0.310 2566 Planarity : 0.004 0.068 2994 Dihedral : 6.684 49.199 2243 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 14.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.59 % Favored : 89.41 % Rotamer: Outliers : 0.05 % Allowed : 2.53 % Favored : 97.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 2.39 % Twisted Proline : 0.00 % Twisted General : 0.30 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.57 (0.17), residues: 2059 helix: 0.07 (0.19), residues: 776 sheet: -1.79 (0.36), residues: 200 loop : -3.19 (0.16), residues: 1083 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 14 TYR 0.020 0.001 TYR D 260 PHE 0.012 0.001 PHE A 415 TRP 0.014 0.001 TRP A 17 HIS 0.008 0.001 HIS E 313 Details of bonding type rmsd covalent geometry : bond 0.00255 (17094) covalent geometry : angle 0.70913 (23159) hydrogen bonds : bond 0.03624 ( 598) hydrogen bonds : angle 5.20832 ( 1713) *********************** 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 181 residues out of total 1831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 180 time to evaluate : 0.675 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: 0.9356 (mtm) cc_final: 0.8978 (ptp) REVERT: C 103 ILE cc_start: 0.9162 (mm) cc_final: 0.8903 (mm) REVERT: C 359 ASN cc_start: 0.8956 (p0) cc_final: 0.8310 (t0) REVERT: C 372 ASP cc_start: 0.8523 (m-30) cc_final: 0.8296 (m-30) REVERT: D 32 PHE cc_start: 0.7945 (m-80) cc_final: 0.7682 (m-10) REVERT: D 44 PHE cc_start: 0.9054 (t80) cc_final: 0.8579 (t80) REVERT: D 268 PHE cc_start: 0.8696 (t80) cc_final: 0.8149 (t80) REVERT: D 299 ILE cc_start: 0.9341 (pt) cc_final: 0.8896 (mt) REVERT: D 305 TYR cc_start: 0.6669 (t80) cc_final: 0.6301 (t80) REVERT: E 49 LEU cc_start: 0.8212 (pp) cc_final: 0.7709 (pp) REVERT: E 98 MET cc_start: 0.7770 (mtt) cc_final: 0.7265 (mtt) REVERT: E 100 MET cc_start: 0.7783 (mpp) cc_final: 0.7488 (mpp) REVERT: E 181 MET cc_start: 0.9094 (tmm) cc_final: 0.8852 (ppp) REVERT: E 314 MET cc_start: 0.9331 (tmm) cc_final: 0.9076 (tmm) REVERT: E 315 ILE cc_start: 0.9715 (mm) cc_final: 0.9260 (mm) REVERT: E 378 GLU cc_start: 0.9237 (tt0) cc_final: 0.8518 (tp30) REVERT: F 55 PHE cc_start: 0.9349 (p90) cc_final: 0.9078 (p90) REVERT: F 113 MET cc_start: 0.8835 (tpp) cc_final: 0.8556 (ppp) REVERT: A 87 TYR cc_start: 0.8641 (m-80) cc_final: 0.8182 (m-80) REVERT: A 262 LEU cc_start: 0.9617 (pp) cc_final: 0.9354 (mp) outliers start: 1 outliers final: 0 residues processed: 181 average time/residue: 0.1358 time to fit residues: 36.8429 Evaluate side-chains 117 residues out of total 1831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 112 optimal weight: 9.9990 chunk 64 optimal weight: 2.9990 chunk 149 optimal weight: 3.9990 chunk 182 optimal weight: 8.9990 chunk 26 optimal weight: 4.9990 chunk 184 optimal weight: 6.9990 chunk 11 optimal weight: 2.9990 chunk 111 optimal weight: 5.9990 chunk 137 optimal weight: 7.9990 chunk 1 optimal weight: 2.9990 chunk 188 optimal weight: 0.0070 overall best weight: 2.6006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 63 ASN ** C 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 414 GLN C 419 GLN ** D 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 243 ASN A 345 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.055703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.042178 restraints weight = 127253.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.043215 restraints weight = 96550.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.043954 restraints weight = 78330.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.044577 restraints weight = 66819.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.044981 restraints weight = 58891.465| |-----------------------------------------------------------------------------| r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.5107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 17094 Z= 0.193 Angle : 0.731 10.506 23159 Z= 0.388 Chirality : 0.047 0.329 2566 Planarity : 0.004 0.064 2994 Dihedral : 6.752 45.088 2243 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 18.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.40 % Favored : 86.60 % Rotamer: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 2.39 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.44 (0.18), residues: 2059 helix: 0.14 (0.19), residues: 770 sheet: -1.61 (0.37), residues: 184 loop : -3.09 (0.17), residues: 1105 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 104 TYR 0.020 0.002 TYR E 138 PHE 0.014 0.002 PHE A 49 TRP 0.012 0.002 TRP F 23 HIS 0.006 0.001 HIS A 244 Details of bonding type rmsd covalent geometry : bond 0.00398 (17094) covalent geometry : angle 0.73143 (23159) hydrogen bonds : bond 0.03842 ( 598) hydrogen bonds : angle 5.34152 ( 1713) *********************** 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 158 residues out of total 1831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 158 time to evaluate : 0.595 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: 0.9338 (mtm) cc_final: 0.8233 (mtm) REVERT: B 113 MET cc_start: 0.9163 (mmp) cc_final: 0.8932 (tpp) REVERT: C 103 ILE cc_start: 0.9272 (mm) cc_final: 0.9042 (mm) REVERT: C 359 ASN cc_start: 0.8900 (p0) cc_final: 0.8194 (t0) REVERT: C 372 ASP cc_start: 0.8458 (m-30) cc_final: 0.8174 (m-30) REVERT: D 32 PHE cc_start: 0.8040 (m-80) cc_final: 0.7719 (m-10) REVERT: D 44 PHE cc_start: 0.9092 (t80) cc_final: 0.8615 (t80) REVERT: D 268 PHE cc_start: 0.8864 (t80) cc_final: 0.8372 (t80) REVERT: D 299 ILE cc_start: 0.9369 (pt) cc_final: 0.8889 (mp) REVERT: D 305 TYR cc_start: 0.6968 (t80) cc_final: 0.6505 (t80) REVERT: E 98 MET cc_start: 0.8028 (mtt) cc_final: 0.7642 (mtt) REVERT: E 100 MET cc_start: 0.7869 (mpp) cc_final: 0.7559 (mpp) REVERT: E 224 GLU cc_start: 0.9547 (mt-10) cc_final: 0.9286 (pm20) REVERT: E 309 LYS cc_start: 0.9436 (mptt) cc_final: 0.9120 (mmtm) REVERT: E 378 GLU cc_start: 0.9219 (tt0) cc_final: 0.8614 (tp30) REVERT: F 8 ILE cc_start: 0.9285 (pt) cc_final: 0.9020 (pt) REVERT: F 113 MET cc_start: 0.8986 (tpp) cc_final: 0.8535 (ppp) REVERT: A 87 TYR cc_start: 0.8656 (m-80) cc_final: 0.8198 (m-80) REVERT: A 267 MET cc_start: 0.8232 (tmm) cc_final: 0.7765 (ppp) outliers start: 0 outliers final: 0 residues processed: 158 average time/residue: 0.1510 time to fit residues: 35.3814 Evaluate side-chains 116 residues out of total 1831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 184 optimal weight: 0.3980 chunk 9 optimal weight: 0.0670 chunk 92 optimal weight: 5.9990 chunk 112 optimal weight: 5.9990 chunk 12 optimal weight: 9.9990 chunk 51 optimal weight: 0.7980 chunk 1 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 81 optimal weight: 10.0000 overall best weight: 1.0522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 63 ASN C 163 GLN D 151 ASN D 390 ASN ** E 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 102 ASN A 243 ASN A 345 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.057224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.043239 restraints weight = 125839.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.044359 restraints weight = 94218.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.045199 restraints weight = 75777.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.045808 restraints weight = 64111.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.046327 restraints weight = 56337.333| |-----------------------------------------------------------------------------| r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.5320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 17094 Z= 0.129 Angle : 0.720 11.115 23159 Z= 0.374 Chirality : 0.048 0.325 2566 Planarity : 0.004 0.064 2994 Dihedral : 6.565 40.392 2243 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 14.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.56 % Favored : 88.44 % Rotamer: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 2.39 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.41 (0.18), residues: 2059 helix: 0.22 (0.19), residues: 778 sheet: -1.30 (0.38), residues: 182 loop : -3.20 (0.16), residues: 1099 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 14 TYR 0.026 0.001 TYR B 120 PHE 0.015 0.001 PHE C 329 TRP 0.078 0.002 TRP A 17 HIS 0.005 0.001 HIS A 215 Details of bonding type rmsd covalent geometry : bond 0.00272 (17094) covalent geometry : angle 0.72046 (23159) hydrogen bonds : bond 0.03563 ( 598) hydrogen bonds : angle 5.14303 ( 1713) *********************** 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 169 residues out of total 1831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 169 time to evaluate : 0.612 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: B 72 MET cc_start: 0.9358 (mtm) cc_final: 0.8181 (mtm) REVERT: B 113 MET cc_start: 0.9153 (mmp) cc_final: 0.8850 (tpp) REVERT: C 103 ILE cc_start: 0.9238 (mm) cc_final: 0.9021 (mm) REVERT: C 359 ASN cc_start: 0.9026 (p0) cc_final: 0.8358 (t0) REVERT: C 390 MET cc_start: 0.8929 (ppp) cc_final: 0.8468 (ppp) REVERT: D 32 PHE cc_start: 0.7846 (m-80) cc_final: 0.7580 (m-10) REVERT: D 44 PHE cc_start: 0.9064 (t80) cc_final: 0.8562 (t80) REVERT: D 139 THR cc_start: 0.8060 (p) cc_final: 0.7771 (p) REVERT: D 268 PHE cc_start: 0.8725 (t80) cc_final: 0.8209 (t80) REVERT: D 299 ILE cc_start: 0.9357 (pt) cc_final: 0.8929 (mp) REVERT: D 305 TYR cc_start: 0.6837 (t80) cc_final: 0.6386 (t80) REVERT: E 224 GLU cc_start: 0.9517 (mt-10) cc_final: 0.9308 (pm20) REVERT: E 309 LYS cc_start: 0.9422 (mptt) cc_final: 0.9081 (mmtm) REVERT: E 378 GLU cc_start: 0.9177 (tt0) cc_final: 0.8545 (tp30) REVERT: F 8 ILE cc_start: 0.9267 (pt) cc_final: 0.9060 (pt) REVERT: F 55 PHE cc_start: 0.9372 (p90) cc_final: 0.9152 (p90) REVERT: F 113 MET cc_start: 0.8921 (tpp) cc_final: 0.8322 (tmm) REVERT: F 134 LEU cc_start: 0.9200 (tp) cc_final: 0.8954 (tp) REVERT: A 87 TYR cc_start: 0.8689 (m-80) cc_final: 0.8220 (m-80) REVERT: A 136 PHE cc_start: 0.8244 (p90) cc_final: 0.7150 (p90) REVERT: A 262 LEU cc_start: 0.9613 (pp) cc_final: 0.9339 (mp) REVERT: A 267 MET cc_start: 0.8114 (tmm) cc_final: 0.7631 (ppp) outliers start: 0 outliers final: 0 residues processed: 169 average time/residue: 0.1406 time to fit residues: 35.4232 Evaluate side-chains 118 residues out of total 1831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 75 optimal weight: 10.0000 chunk 23 optimal weight: 9.9990 chunk 157 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 chunk 68 optimal weight: 6.9990 chunk 181 optimal weight: 0.9990 chunk 90 optimal weight: 6.9990 chunk 70 optimal weight: 8.9990 chunk 132 optimal weight: 0.9980 chunk 191 optimal weight: 0.9990 chunk 7 optimal weight: 4.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 63 ASN C 163 GLN D 151 ASN ** D 390 ASN ** 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 48 ASN A 102 ASN A 243 ASN A 345 ASN ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.056940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.043362 restraints weight = 125528.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.044411 restraints weight = 95277.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.045201 restraints weight = 77503.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.045764 restraints weight = 66078.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.046259 restraints weight = 58445.657| |-----------------------------------------------------------------------------| r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.5517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 17094 Z= 0.139 Angle : 0.726 10.883 23159 Z= 0.380 Chirality : 0.048 0.342 2566 Planarity : 0.004 0.063 2994 Dihedral : 6.482 35.106 2243 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 16.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.29 % Favored : 87.71 % Rotamer: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 2.39 % Twisted Proline : 0.00 % Twisted General : 0.30 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.31 (0.18), residues: 2059 helix: 0.29 (0.19), residues: 772 sheet: -1.26 (0.38), residues: 182 loop : -3.11 (0.17), residues: 1105 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 104 TYR 0.042 0.002 TYR F 114 PHE 0.021 0.001 PHE C 329 TRP 0.081 0.002 TRP A 17 HIS 0.005 0.001 HIS D 270 Details of bonding type rmsd covalent geometry : bond 0.00296 (17094) covalent geometry : angle 0.72612 (23159) hydrogen bonds : bond 0.03672 ( 598) hydrogen bonds : angle 5.15343 ( 1713) *********************** 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 161 residues out of total 1831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 0.640 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: B 72 MET cc_start: 0.9361 (mtm) cc_final: 0.8177 (mtm) REVERT: B 113 MET cc_start: 0.9165 (mmp) cc_final: 0.8906 (tpp) REVERT: C 103 ILE cc_start: 0.9260 (mm) cc_final: 0.9039 (mm) REVERT: C 218 ARG cc_start: 0.8419 (tpm170) cc_final: 0.7962 (tpp-160) REVERT: C 359 ASN cc_start: 0.8987 (p0) cc_final: 0.8314 (t0) REVERT: C 390 MET cc_start: 0.9048 (ppp) cc_final: 0.8527 (ppp) REVERT: D 32 PHE cc_start: 0.7888 (m-80) cc_final: 0.7597 (m-10) REVERT: D 44 PHE cc_start: 0.9047 (t80) cc_final: 0.8566 (t80) REVERT: D 268 PHE cc_start: 0.8884 (t80) cc_final: 0.8385 (t80) REVERT: D 299 ILE cc_start: 0.9345 (pt) cc_final: 0.8882 (mp) REVERT: D 305 TYR cc_start: 0.6831 (t80) cc_final: 0.6340 (t80) REVERT: E 100 MET cc_start: 0.7645 (mpp) cc_final: 0.7429 (mpp) REVERT: E 309 LYS cc_start: 0.9411 (mptt) cc_final: 0.9074 (mmtm) REVERT: E 378 GLU cc_start: 0.9214 (tt0) cc_final: 0.8579 (tp30) REVERT: F 58 ASP cc_start: 0.9176 (m-30) cc_final: 0.8835 (t70) REVERT: F 113 MET cc_start: 0.8939 (tpp) cc_final: 0.8361 (tmm) REVERT: F 165 TYR cc_start: 0.5532 (m-10) cc_final: 0.5011 (m-10) REVERT: A 87 TYR cc_start: 0.8710 (m-80) cc_final: 0.8231 (m-80) REVERT: A 262 LEU cc_start: 0.9628 (pp) cc_final: 0.9396 (mp) REVERT: A 267 MET cc_start: 0.8471 (tmm) cc_final: 0.8211 (tmm) outliers start: 0 outliers final: 0 residues processed: 161 average time/residue: 0.1391 time to fit residues: 33.2526 Evaluate side-chains 111 residues out of total 1831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 179 optimal weight: 0.9980 chunk 0 optimal weight: 20.0000 chunk 53 optimal weight: 5.9990 chunk 197 optimal weight: 6.9990 chunk 95 optimal weight: 10.0000 chunk 85 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 174 optimal weight: 7.9990 chunk 45 optimal weight: 1.9990 chunk 202 optimal weight: 9.9990 chunk 36 optimal weight: 1.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 63 ASN C 163 GLN ** D 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 390 ASN ** 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 48 ASN A 243 ASN A 345 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.055915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.042279 restraints weight = 123365.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.043326 restraints weight = 93330.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.044071 restraints weight = 75621.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.044695 restraints weight = 64556.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.045127 restraints weight = 56915.184| |-----------------------------------------------------------------------------| r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.5757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 17094 Z= 0.159 Angle : 0.745 10.381 23159 Z= 0.389 Chirality : 0.048 0.347 2566 Planarity : 0.004 0.063 2994 Dihedral : 6.509 35.219 2243 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 17.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.14 % Favored : 87.86 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 2.39 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.33 (0.18), residues: 2059 helix: 0.24 (0.19), residues: 778 sheet: -1.27 (0.38), residues: 182 loop : -3.10 (0.17), residues: 1099 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 104 TYR 0.040 0.002 TYR F 114 PHE 0.023 0.001 PHE A 415 TRP 0.072 0.002 TRP A 17 HIS 0.006 0.001 HIS D 270 Details of bonding type rmsd covalent geometry : bond 0.00335 (17094) covalent geometry : angle 0.74508 (23159) hydrogen bonds : bond 0.03727 ( 598) hydrogen bonds : angle 5.17975 ( 1713) ********************** 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 150 residues out of total 1831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 150 time to evaluate : 0.605 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: 0.9353 (mtm) cc_final: 0.8111 (mtm) REVERT: B 113 MET cc_start: 0.9164 (mmp) cc_final: 0.8862 (tpp) REVERT: C 103 ILE cc_start: 0.9296 (mm) cc_final: 0.9061 (mm) REVERT: C 390 MET cc_start: 0.9029 (ppp) cc_final: 0.8551 (ppp) REVERT: D 32 PHE cc_start: 0.7746 (m-80) cc_final: 0.7497 (m-10) REVERT: D 44 PHE cc_start: 0.9027 (t80) cc_final: 0.8536 (t80) REVERT: D 268 PHE cc_start: 0.8859 (t80) cc_final: 0.8363 (t80) REVERT: D 299 ILE cc_start: 0.9371 (pt) cc_final: 0.8905 (mp) REVERT: E 100 MET cc_start: 0.7573 (mpp) cc_final: 0.7349 (mpp) REVERT: E 309 LYS cc_start: 0.9414 (mptt) cc_final: 0.9078 (mmtm) REVERT: E 378 GLU cc_start: 0.9171 (tt0) cc_final: 0.8564 (tp30) REVERT: F 8 ILE cc_start: 0.9241 (pt) cc_final: 0.9012 (pt) REVERT: F 58 ASP cc_start: 0.9204 (m-30) cc_final: 0.8889 (t70) REVERT: F 113 MET cc_start: 0.8940 (tpp) cc_final: 0.8479 (tmm) REVERT: F 165 TYR cc_start: 0.5531 (m-10) cc_final: 0.5022 (m-10) REVERT: A 87 TYR cc_start: 0.8566 (m-80) cc_final: 0.8123 (m-80) REVERT: A 267 MET cc_start: 0.8412 (tmm) cc_final: 0.8149 (tmm) outliers start: 0 outliers final: 0 residues processed: 150 average time/residue: 0.1399 time to fit residues: 31.6954 Evaluate side-chains 109 residues out of total 1831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 105 optimal weight: 0.8980 chunk 66 optimal weight: 9.9990 chunk 204 optimal weight: 0.9990 chunk 137 optimal weight: 7.9990 chunk 29 optimal weight: 10.0000 chunk 50 optimal weight: 2.9990 chunk 138 optimal weight: 2.9990 chunk 61 optimal weight: 10.0000 chunk 7 optimal weight: 8.9990 chunk 178 optimal weight: 2.9990 chunk 98 optimal weight: 8.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 63 ASN C 163 GLN C 414 GLN D 151 ASN ** D 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 64 HIS ** E 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 345 ASN ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.055373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.041941 restraints weight = 127074.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.042970 restraints weight = 96301.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.043743 restraints weight = 78267.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.044329 restraints weight = 66738.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.044743 restraints weight = 58892.119| |-----------------------------------------------------------------------------| r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.5941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 17094 Z= 0.165 Angle : 0.740 10.322 23159 Z= 0.388 Chirality : 0.048 0.333 2566 Planarity : 0.004 0.062 2994 Dihedral : 6.483 35.096 2243 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 17.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.09 % Favored : 87.91 % Rotamer: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 2.39 % Twisted Proline : 0.00 % Twisted General : 0.30 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.28 (0.18), residues: 2059 helix: 0.33 (0.19), residues: 766 sheet: -1.26 (0.38), residues: 182 loop : -3.08 (0.17), residues: 1111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 14 TYR 0.035 0.002 TYR F 114 PHE 0.019 0.002 PHE A 241 TRP 0.074 0.002 TRP A 17 HIS 0.005 0.001 HIS D 270 Details of bonding type rmsd covalent geometry : bond 0.00345 (17094) covalent geometry : angle 0.73994 (23159) hydrogen bonds : bond 0.03734 ( 598) hydrogen bonds : angle 5.18979 ( 1713) =============================================================================== Job complete usr+sys time: 2481.32 seconds wall clock time: 43 minutes 56.72 seconds (2636.72 seconds total)