Starting phenix.real_space_refine on Wed Mar 4 14:27:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6owo_20215/03_2026/6owo_20215.cif Found real_map, /net/cci-nas-00/data/ceres_data/6owo_20215/03_2026/6owo_20215.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6owo_20215/03_2026/6owo_20215.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6owo_20215/03_2026/6owo_20215.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6owo_20215/03_2026/6owo_20215.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6owo_20215/03_2026/6owo_20215.map" } resolution = 3.2 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 70 5.16 5 C 9146 2.51 5 N 2427 2.21 5 O 2632 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 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: 14276 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 569, 4505 Classifications: {'peptide': 569} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 19, 'TRANS': 549} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 4443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 559, 4443 Classifications: {'peptide': 559} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 24, 'TRANS': 534} Chain breaks: 4 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "M" Number of atoms: 3166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3166 Classifications: {'peptide': 395} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 17, 'TRANS': 377} Chain breaks: 4 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'TPO:plan-1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 11 Chain: "S" Number of atoms: 1190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1190 Classifications: {'peptide': 141} Link IDs: {'TRANS': 140} Chain: "N" Number of atoms: 972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 972 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 115} Chain breaks: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Time building chain proxies: 2.95, per 1000 atoms: 0.21 Number of scatterers: 14276 At special positions: 0 Unit cell: (102.08, 109.04, 125.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 70 16.00 P 1 15.00 O 2632 8.00 N 2427 7.00 C 9146 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: 1.22 Conformation dependent library (CDL) restraints added in 441.8 milliseconds 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3440 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 8 sheets defined 60.0% alpha, 12.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 11 through 22 removed outlier: 3.633A pdb=" N VAL A 15 " --> pdb=" O ARG A 11 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE A 16 " --> pdb=" O GLY A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 44 removed outlier: 3.630A pdb=" N GLU A 29 " --> pdb=" O SER A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 68 removed outlier: 3.740A pdb=" N TYR A 58 " --> pdb=" O SER A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 84 removed outlier: 3.523A pdb=" N SER A 84 " --> pdb=" O VAL A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 101 Processing helix chain 'A' and resid 105 through 122 removed outlier: 3.503A pdb=" N ASP A 119 " --> pdb=" O ALA A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 139 Processing helix chain 'A' and resid 140 through 148 removed outlier: 3.843A pdb=" N ALA A 146 " --> pdb=" O GLU A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 157 Processing helix chain 'A' and resid 161 through 179 Processing helix chain 'A' and resid 180 through 183 Processing helix chain 'A' and resid 188 through 193 removed outlier: 3.688A pdb=" N VAL A 193 " --> pdb=" O THR A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 198 Processing helix chain 'A' and resid 200 through 215 removed outlier: 3.594A pdb=" N SER A 209 " --> pdb=" O THR A 205 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU A 210 " --> pdb=" O ALA A 206 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR A 213 " --> pdb=" O SER A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 238 removed outlier: 3.707A pdb=" N LEU A 228 " --> pdb=" O THR A 224 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER A 231 " --> pdb=" O SER A 227 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG A 235 " --> pdb=" O SER A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 265 Processing helix chain 'A' and resid 266 through 268 No H-bonds generated for 'chain 'A' and resid 266 through 268' Processing helix chain 'A' and resid 273 through 293 removed outlier: 3.575A pdb=" N GLU A 282 " --> pdb=" O GLY A 278 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N CYS A 283 " --> pdb=" O ARG A 279 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLU A 293 " --> pdb=" O ASN A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 321 removed outlier: 3.661A pdb=" N SER A 303 " --> pdb=" O LYS A 299 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL A 309 " --> pdb=" O ALA A 305 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU A 310 " --> pdb=" O LYS A 306 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLU A 312 " --> pdb=" O ALA A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 335 Processing helix chain 'A' and resid 342 through 357 removed outlier: 3.694A pdb=" N ARG A 346 " --> pdb=" O GLU A 342 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU A 348 " --> pdb=" O ASN A 344 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR A 355 " --> pdb=" O GLU A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 367 removed outlier: 3.663A pdb=" N LYS A 367 " --> pdb=" O HIS A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 380 removed outlier: 3.528A pdb=" N ILE A 374 " --> pdb=" O ILE A 370 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N THR A 379 " --> pdb=" O ASN A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 396 Processing helix chain 'A' and resid 401 through 414 removed outlier: 3.689A pdb=" N GLU A 414 " --> pdb=" O LEU A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 435 removed outlier: 3.669A pdb=" N GLU A 433 " --> pdb=" O ALA A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 453 removed outlier: 3.714A pdb=" N TYR A 442 " --> pdb=" O ASP A 438 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N VAL A 443 " --> pdb=" O TYR A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 472 removed outlier: 3.562A pdb=" N ARG A 464 " --> pdb=" O GLU A 460 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL A 465 " --> pdb=" O VAL A 461 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ILE A 466 " --> pdb=" O TRP A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 487 removed outlier: 3.704A pdb=" N PHE A 484 " --> pdb=" O ALA A 480 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU A 485 " --> pdb=" O LYS A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 508 removed outlier: 3.617A pdb=" N TYR A 502 " --> pdb=" O LYS A 498 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE A 503 " --> pdb=" O VAL A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 512 Processing helix chain 'A' and resid 514 through 517 Processing helix chain 'A' and resid 518 through 528 Processing helix chain 'A' and resid 534 through 552 removed outlier: 3.703A pdb=" N SER A 543 " --> pdb=" O ALA A 539 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N THR A 544 " --> pdb=" O LEU A 540 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE A 546 " --> pdb=" O LEU A 542 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LYS A 547 " --> pdb=" O SER A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 564 removed outlier: 3.923A pdb=" N ASP A 561 " --> pdb=" O ALA A 557 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N VAL A 562 " --> pdb=" O THR A 558 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 570 Processing helix chain 'A' and resid 573 through 589 Processing helix chain 'B' and resid 13 through 23 removed outlier: 3.897A pdb=" N GLU B 21 " --> pdb=" O GLU B 17 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASN B 23 " --> pdb=" O LYS B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 44 removed outlier: 3.913A pdb=" N VAL B 43 " --> pdb=" O ALA B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 49 No H-bonds generated for 'chain 'B' and resid 47 through 49' Processing helix chain 'B' and resid 50 through 55 removed outlier: 3.555A pdb=" N VAL B 55 " --> pdb=" O PHE B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 58 No H-bonds generated for 'chain 'B' and resid 56 through 58' Processing helix chain 'B' and resid 62 through 80 removed outlier: 3.601A pdb=" N ASN B 75 " --> pdb=" O LEU B 71 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N TYR B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N LYS B 78 " --> pdb=" O MET B 74 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N SER B 79 " --> pdb=" O ASN B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 85 removed outlier: 3.923A pdb=" N ALA B 84 " --> pdb=" O GLN B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 95 removed outlier: 3.650A pdb=" N PHE B 91 " --> pdb=" O ALA B 87 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS B 93 " --> pdb=" O ASN B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 112 Processing helix chain 'B' and resid 115 through 121 removed outlier: 3.604A pdb=" N THR B 119 " --> pdb=" O ASP B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 130 removed outlier: 3.706A pdb=" N CYS B 129 " --> pdb=" O PRO B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 151 removed outlier: 3.698A pdb=" N VAL B 143 " --> pdb=" O LYS B 139 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ALA B 146 " --> pdb=" O ALA B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 170 removed outlier: 4.169A pdb=" N ASP B 163 " --> pdb=" O GLN B 159 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N SER B 164 " --> pdb=" O GLY B 160 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG B 166 " --> pdb=" O LEU B 162 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ALA B 170 " --> pdb=" O ARG B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 188 removed outlier: 3.847A pdb=" N VAL B 177 " --> pdb=" O ASN B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 212 removed outlier: 3.622A pdb=" N ASN B 203 " --> pdb=" O LEU B 199 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N ASN B 205 " --> pdb=" O PRO B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 227 removed outlier: 3.886A pdb=" N ILE B 220 " --> pdb=" O GLU B 216 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N PHE B 221 " --> pdb=" O TRP B 217 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N SER B 227 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 245 removed outlier: 3.507A pdb=" N CYS B 241 " --> pdb=" O ALA B 237 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N ARG B 243 " --> pdb=" O SER B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 248 No H-bonds generated for 'chain 'B' and resid 246 through 248' Processing helix chain 'B' and resid 252 through 266 Processing helix chain 'B' and resid 276 through 283 Processing helix chain 'B' and resid 284 through 290 Processing helix chain 'B' and resid 291 through 294 Processing helix chain 'B' and resid 295 through 313 removed outlier: 3.539A pdb=" N TYR B 300 " --> pdb=" O PRO B 296 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASN B 305 " --> pdb=" O VAL B 301 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU B 308 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N GLN B 311 " --> pdb=" O ASN B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 345 removed outlier: 3.945A pdb=" N GLU B 337 " --> pdb=" O TYR B 333 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASP B 340 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE B 341 " --> pdb=" O GLU B 337 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ARG B 344 " --> pdb=" O ASP B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 349 No H-bonds generated for 'chain 'B' and resid 347 through 349' Processing helix chain 'B' and resid 350 through 362 Processing helix chain 'B' and resid 366 through 384 removed outlier: 3.884A pdb=" N LYS B 372 " --> pdb=" O ASP B 368 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ARG B 375 " --> pdb=" O ARG B 371 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLY B 378 " --> pdb=" O VAL B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 400 Processing helix chain 'B' and resid 403 through 421 removed outlier: 3.724A pdb=" N GLN B 408 " --> pdb=" O ASN B 404 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N GLU B 409 " --> pdb=" O TYR B 405 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N VAL B 412 " --> pdb=" O GLN B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 428 through 433 Processing helix chain 'B' and resid 435 through 439 removed outlier: 3.580A pdb=" N SER B 438 " --> pdb=" O ASN B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 454 Processing helix chain 'B' and resid 461 through 471 removed outlier: 3.800A pdb=" N SER B 468 " --> pdb=" O GLU B 464 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N PHE B 469 " --> pdb=" O LEU B 465 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU B 470 " --> pdb=" O LEU B 466 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU B 471 " --> pdb=" O GLU B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 495 Processing helix chain 'B' and resid 499 through 512 removed outlier: 3.688A pdb=" N VAL B 503 " --> pdb=" O THR B 499 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N SER B 508 " --> pdb=" O GLN B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 516 through 533 removed outlier: 3.769A pdb=" N ARG B 522 " --> pdb=" O ASP B 518 " (cutoff:3.500A) Processing helix chain 'B' and resid 533 through 542 removed outlier: 3.866A pdb=" N GLU B 539 " --> pdb=" O VAL B 535 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 556 through 565 removed outlier: 3.807A pdb=" N CYS B 565 " --> pdb=" O ASP B 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 575 Processing helix chain 'B' and resid 577 through 581 Processing helix chain 'M' and resid 27 through 36 removed outlier: 3.515A pdb=" N PHE M 32 " --> pdb=" O ALA M 28 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ARG M 33 " --> pdb=" O VAL M 29 " (cutoff:3.500A) Processing helix chain 'M' and resid 74 through 94 removed outlier: 3.753A pdb=" N CYS M 86 " --> pdb=" O LEU M 82 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N MET M 89 " --> pdb=" O MET M 85 " (cutoff:3.500A) Processing helix chain 'M' and resid 97 through 102 Processing helix chain 'M' and resid 104 through 115 removed outlier: 3.530A pdb=" N TYR M 109 " --> pdb=" O PHE M 105 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASP M 113 " --> pdb=" O TYR M 109 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU M 114 " --> pdb=" O GLU M 110 " (cutoff:3.500A) Processing helix chain 'M' and resid 128 through 132 removed outlier: 3.521A pdb=" N THR M 131 " --> pdb=" O ALA M 128 " (cutoff:3.500A) Processing helix chain 'M' and resid 414 through 418 Processing helix chain 'S' and resid 24 through 34 Processing helix chain 'S' and resid 35 through 40 Processing helix chain 'S' and resid 79 through 95 removed outlier: 3.556A pdb=" N HIS S 85 " --> pdb=" O LEU S 81 " (cutoff:3.500A) Processing helix chain 'S' and resid 100 through 106 removed outlier: 3.544A pdb=" N VAL S 104 " --> pdb=" O GLU S 100 " (cutoff:3.500A) Processing helix chain 'S' and resid 106 through 117 removed outlier: 3.662A pdb=" N THR S 112 " --> pdb=" O TYR S 108 " (cutoff:3.500A) Processing helix chain 'S' and resid 127 through 140 removed outlier: 3.506A pdb=" N MET S 137 " --> pdb=" O LYS S 133 " (cutoff:3.500A) Processing helix chain 'N' and resid 111 through 137 removed outlier: 3.512A pdb=" N ALA N 115 " --> pdb=" O ASP N 111 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU N 122 " --> pdb=" O PHE N 118 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N TRP N 128 " --> pdb=" O ASP N 124 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'M' and resid 14 through 19 removed outlier: 7.211A pdb=" N ILE M 7 " --> pdb=" O LEU M 15 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N SER M 17 " --> pdb=" O LEU M 5 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N LEU M 5 " --> pdb=" O SER M 17 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE M 63 " --> pdb=" O ARG M 60 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'M' and resid 116 through 117 Processing sheet with id=AA3, first strand: chain 'M' and resid 245 through 248 removed outlier: 6.413A pdb=" N VAL M 200 " --> pdb=" O LEU M 274 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N ARG M 276 " --> pdb=" O GLY M 198 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N GLY M 198 " --> pdb=" O ARG M 276 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ARG M 278 " --> pdb=" O VAL M 196 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N VAL M 196 " --> pdb=" O ARG M 278 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N LEU M 173 " --> pdb=" O LYS M 420 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N VAL M 422 " --> pdb=" O LEU M 173 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N LEU M 175 " --> pdb=" O VAL M 422 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N TYR M 424 " --> pdb=" O LEU M 175 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N VAL M 177 " --> pdb=" O TYR M 424 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N GLY M 426 " --> pdb=" O VAL M 177 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N GLU M 179 " --> pdb=" O GLY M 426 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N SER M 428 " --> pdb=" O GLU M 179 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N VAL M 181 " --> pdb=" O SER M 428 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ILE M 430 " --> pdb=" O VAL M 181 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N GLY M 429 " --> pdb=" O PHE M 390 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N PHE M 390 " --> pdb=" O GLY M 429 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N TYR M 431 " --> pdb=" O MET M 388 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N SER M 387 " --> pdb=" O VAL M 322 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N VAL M 322 " --> pdb=" O SER M 387 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ASN M 389 " --> pdb=" O ILE M 320 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ILE M 320 " --> pdb=" O ASN M 389 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N LEU M 316 " --> pdb=" O ALA M 359 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ALA M 359 " --> pdb=" O LEU M 316 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N GLN M 318 " --> pdb=" O ARG M 357 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ARG M 357 " --> pdb=" O GLN M 318 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'M' and resid 262 through 265 removed outlier: 6.932A pdb=" N GLU M 211 " --> pdb=" O VAL M 406 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N VAL M 406 " --> pdb=" O GLU M 211 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N LYS M 213 " --> pdb=" O LEU M 404 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N LEU M 404 " --> pdb=" O LYS M 213 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N GLY M 215 " --> pdb=" O ARG M 402 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'M' and resid 287 through 296 removed outlier: 7.623A pdb=" N GLN M 365 " --> pdb=" O CYS M 337 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N CYS M 337 " --> pdb=" O GLN M 365 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N SER M 367 " --> pdb=" O VAL M 335 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N VAL M 335 " --> pdb=" O SER M 367 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N GLU M 369 " --> pdb=" O VAL M 333 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N VAL M 333 " --> pdb=" O GLU M 369 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N GLU M 371 " --> pdb=" O SER M 331 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'S' and resid 14 through 19 removed outlier: 6.294A pdb=" N ILE S 7 " --> pdb=" O ARG S 15 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ALA S 17 " --> pdb=" O ILE S 5 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ILE S 5 " --> pdb=" O ALA S 17 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N TRP S 19 " --> pdb=" O ARG S 3 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N ARG S 3 " --> pdb=" O TRP S 19 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N CYS S 70 " --> pdb=" O ARG S 3 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N ILE S 5 " --> pdb=" O CYS S 68 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N CYS S 68 " --> pdb=" O ILE S 5 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ILE S 7 " --> pdb=" O TYR S 66 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N TYR S 66 " --> pdb=" O ILE S 7 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG S 60 " --> pdb=" O PHE S 67 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'S' and resid 118 through 119 Processing sheet with id=AA8, first strand: chain 'N' and resid 67 through 72 removed outlier: 6.594A pdb=" N LEU N 59 " --> pdb=" O PHE N 68 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N GLN N 70 " --> pdb=" O ILE N 57 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ILE N 57 " --> pdb=" O GLN N 70 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ALA N 55 " --> pdb=" O PRO N 72 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N VAL N 54 " --> pdb=" O LYS N 51 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N TRP N 42 " --> pdb=" O HIS N 17 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N HIS N 17 " --> pdb=" O TRP N 42 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N GLY N 44 " --> pdb=" O GLU N 15 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU N 15 " --> pdb=" O GLY N 44 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ALA N 50 " --> pdb=" O VAL N 9 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N VAL N 9 " --> pdb=" O ALA N 50 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA N 103 " --> pdb=" O ILE N 95 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N PHE N 91 " --> pdb=" O LEU N 107 " (cutoff:3.500A) 735 hydrogen bonds defined for protein. 2124 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.27 Time building geometry restraints manager: 1.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4071 1.33 - 1.45: 2185 1.45 - 1.57: 8167 1.57 - 1.69: 3 1.69 - 1.81: 105 Bond restraints: 14531 Sorted by residual: bond pdb=" OG1 TPO M 156 " pdb=" P TPO M 156 " ideal model delta sigma weight residual 1.717 1.620 0.097 2.00e-02 2.50e+03 2.34e+01 bond pdb=" O1P TPO M 156 " pdb=" P TPO M 156 " ideal model delta sigma weight residual 1.525 1.612 -0.087 2.00e-02 2.50e+03 1.91e+01 bond pdb=" O2P TPO M 156 " pdb=" P TPO M 156 " ideal model delta sigma weight residual 1.528 1.602 -0.074 2.00e-02 2.50e+03 1.38e+01 bond pdb=" C PHE N 76 " pdb=" N PRO N 77 " ideal model delta sigma weight residual 1.334 1.359 -0.025 8.40e-03 1.42e+04 9.13e+00 bond pdb=" O3P TPO M 156 " pdb=" P TPO M 156 " ideal model delta sigma weight residual 1.528 1.474 0.054 2.00e-02 2.50e+03 7.25e+00 ... (remaining 14526 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.84: 19300 2.84 - 5.67: 317 5.67 - 8.51: 34 8.51 - 11.34: 9 11.34 - 14.18: 3 Bond angle restraints: 19663 Sorted by residual: angle pdb=" N VAL A 555 " pdb=" CA VAL A 555 " pdb=" C VAL A 555 " ideal model delta sigma weight residual 113.43 106.70 6.73 1.09e+00 8.42e-01 3.82e+01 angle pdb=" C ARG M 60 " pdb=" N SER M 61 " pdb=" CA SER M 61 " ideal model delta sigma weight residual 121.54 131.21 -9.67 1.91e+00 2.74e-01 2.56e+01 angle pdb=" C PHE S 52 " pdb=" N ARG S 53 " pdb=" CA ARG S 53 " ideal model delta sigma weight residual 121.54 131.10 -9.56 1.91e+00 2.74e-01 2.50e+01 angle pdb=" N PRO B 201 " pdb=" CA PRO B 201 " pdb=" C PRO B 201 " ideal model delta sigma weight residual 113.75 121.07 -7.32 1.49e+00 4.50e-01 2.41e+01 angle pdb=" C VAL N 73 " pdb=" N ASP N 74 " pdb=" CA ASP N 74 " ideal model delta sigma weight residual 121.54 130.78 -9.24 1.91e+00 2.74e-01 2.34e+01 ... (remaining 19658 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.94: 8426 14.94 - 29.88: 346 29.88 - 44.83: 101 44.83 - 59.77: 4 59.77 - 74.71: 2 Dihedral angle restraints: 8879 sinusoidal: 3602 harmonic: 5277 Sorted by residual: dihedral pdb=" CA ARG S 53 " pdb=" C ARG S 53 " pdb=" N ASN S 54 " pdb=" CA ASN S 54 " ideal model delta harmonic sigma weight residual 180.00 148.71 31.29 0 5.00e+00 4.00e-02 3.92e+01 dihedral pdb=" CA LYS B 29 " pdb=" C LYS B 29 " pdb=" N ARG B 30 " pdb=" CA ARG B 30 " ideal model delta harmonic sigma weight residual 180.00 154.15 25.85 0 5.00e+00 4.00e-02 2.67e+01 dihedral pdb=" CA ASN M 62 " pdb=" C ASN M 62 " pdb=" N ILE M 63 " pdb=" CA ILE M 63 " ideal model delta harmonic sigma weight residual -180.00 -155.06 -24.94 0 5.00e+00 4.00e-02 2.49e+01 ... (remaining 8876 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 1723 0.060 - 0.119: 476 0.119 - 0.179: 68 0.179 - 0.238: 9 0.238 - 0.298: 2 Chirality restraints: 2278 Sorted by residual: chirality pdb=" CA PRO B 201 " pdb=" N PRO B 201 " pdb=" C PRO B 201 " pdb=" CB PRO B 201 " both_signs ideal model delta sigma weight residual False 2.72 2.42 0.30 2.00e-01 2.50e+01 2.21e+00 chirality pdb=" CB ILE N 21 " pdb=" CA ILE N 21 " pdb=" CG1 ILE N 21 " pdb=" CG2 ILE N 21 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 1.96e+00 chirality pdb=" CA ASP M 282 " pdb=" N ASP M 282 " pdb=" C ASP M 282 " pdb=" CB ASP M 282 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.36e+00 ... (remaining 2275 not shown) Planarity restraints: 2496 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP M 421 " -0.026 2.00e-02 2.50e+03 2.43e-02 1.48e+01 pdb=" CG TRP M 421 " 0.064 2.00e-02 2.50e+03 pdb=" CD1 TRP M 421 " -0.031 2.00e-02 2.50e+03 pdb=" CD2 TRP M 421 " 0.005 2.00e-02 2.50e+03 pdb=" NE1 TRP M 421 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP M 421 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP M 421 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP M 421 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP M 421 " -0.009 2.00e-02 2.50e+03 pdb=" CH2 TRP M 421 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE N 21 " 0.053 5.00e-02 4.00e+02 8.02e-02 1.03e+01 pdb=" N PRO N 22 " -0.139 5.00e-02 4.00e+02 pdb=" CA PRO N 22 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO N 22 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 361 " 0.016 2.00e-02 2.50e+03 1.89e-02 7.11e+00 pdb=" CG TYR B 361 " -0.046 2.00e-02 2.50e+03 pdb=" CD1 TYR B 361 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 TYR B 361 " 0.010 2.00e-02 2.50e+03 pdb=" CE1 TYR B 361 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR B 361 " 0.005 2.00e-02 2.50e+03 pdb=" CZ TYR B 361 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 361 " 0.001 2.00e-02 2.50e+03 ... (remaining 2493 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 3751 2.79 - 3.32: 12798 3.32 - 3.84: 22718 3.84 - 4.37: 28133 4.37 - 4.90: 47315 Nonbonded interactions: 114715 Sorted by model distance: nonbonded pdb=" OH TYR A 95 " pdb=" OD2 ASP A 119 " model vdw 2.261 3.040 nonbonded pdb=" OH TYR M 20 " pdb=" O LEU M 112 " model vdw 2.266 3.040 nonbonded pdb=" OE1 GLU M 179 " pdb=" OH TYR M 277 " model vdw 2.271 3.040 nonbonded pdb=" NH1 ARG M 199 " pdb=" OE2 GLU M 273 " model vdw 2.279 3.120 nonbonded pdb=" O2P TPO M 156 " pdb=" OG SER N 87 " model vdw 2.306 3.040 ... (remaining 114710 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.040 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 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 : 0.009 0.097 14531 Z= 0.377 Angle : 0.987 14.175 19663 Z= 0.565 Chirality : 0.055 0.298 2278 Planarity : 0.007 0.080 2496 Dihedral : 9.504 74.710 5439 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.32 % Favored : 96.57 % Rotamer: Outliers : 0.25 % Allowed : 1.71 % Favored : 98.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -4.78 (0.15), residues: 1749 helix: -4.19 (0.07), residues: 973 sheet: -0.99 (0.33), residues: 235 loop : -1.53 (0.23), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG M 199 TYR 0.046 0.004 TYR B 361 PHE 0.043 0.004 PHE S 67 TRP 0.064 0.005 TRP M 421 HIS 0.008 0.002 HIS A 363 Details of bonding type rmsd covalent geometry : bond 0.00898 (14531) covalent geometry : angle 0.98723 (19663) hydrogen bonds : bond 0.29231 ( 735) hydrogen bonds : angle 9.59203 ( 2124) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 305 time to evaluate : 0.554 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 520 LEU cc_start: 0.8774 (tt) cc_final: 0.8303 (mp) REVERT: A 570 LYS cc_start: 0.8347 (mttt) cc_final: 0.8110 (tmtt) REVERT: A 585 ARG cc_start: 0.8005 (mtt-85) cc_final: 0.7724 (mtt180) REVERT: B 110 MET cc_start: 0.8984 (mtp) cc_final: 0.8727 (mtm) REVERT: B 458 ARG cc_start: 0.8333 (mmt180) cc_final: 0.7625 (ttt180) REVERT: B 467 GLU cc_start: 0.8305 (tp30) cc_final: 0.7822 (tp30) REVERT: M 218 ASP cc_start: 0.7988 (p0) cc_final: 0.7725 (p0) REVERT: N 95 ILE cc_start: 0.8705 (pp) cc_final: 0.8437 (pp) REVERT: N 137 LYS cc_start: 0.8545 (mptt) cc_final: 0.8069 (mptt) outliers start: 4 outliers final: 1 residues processed: 309 average time/residue: 0.1502 time to fit residues: 63.3184 Evaluate side-chains 158 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 157 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 248 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.4980 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.0030 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 2.9990 overall best weight: 0.6792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 ASN A 166 GLN A 194 HIS B 99 ASN B 191 HIS B 250 HIS B 252 ASN B 353 GLN B 500 GLN M 72 ASN M 135 GLN M 310 ASN S 8 GLN N 123 GLN N 125 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.108999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.088223 restraints weight = 24998.996| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 2.27 r_work: 0.2968 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2826 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.2337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14531 Z= 0.136 Angle : 0.621 11.698 19663 Z= 0.334 Chirality : 0.043 0.174 2278 Planarity : 0.005 0.067 2496 Dihedral : 5.125 31.827 1936 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.14 % Allowed : 6.52 % Favored : 92.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.52 % Twisted General : 0.00 % 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: -2.04 (0.18), residues: 1749 helix: -1.51 (0.14), residues: 993 sheet: -0.43 (0.33), residues: 242 loop : -0.99 (0.25), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG M 33 TYR 0.024 0.002 TYR A 478 PHE 0.019 0.002 PHE A 552 TRP 0.013 0.002 TRP M 353 HIS 0.005 0.001 HIS A 363 Details of bonding type rmsd covalent geometry : bond 0.00289 (14531) covalent geometry : angle 0.62104 (19663) hydrogen bonds : bond 0.04597 ( 735) hydrogen bonds : angle 5.15287 ( 2124) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 209 time to evaluate : 0.558 Fit side-chains revert: symmetry clash REVERT: A 391 ASP cc_start: 0.8474 (m-30) cc_final: 0.8257 (m-30) REVERT: A 570 LYS cc_start: 0.8510 (mttt) cc_final: 0.8048 (tmtt) REVERT: B 67 LYS cc_start: 0.9385 (OUTLIER) cc_final: 0.9020 (tttm) REVERT: B 83 MET cc_start: 0.7973 (tpp) cc_final: 0.7478 (tpp) REVERT: B 94 ASP cc_start: 0.8025 (m-30) cc_final: 0.7801 (m-30) REVERT: B 340 ASP cc_start: 0.9009 (t0) cc_final: 0.8617 (m-30) REVERT: B 458 ARG cc_start: 0.8231 (mmt180) cc_final: 0.7385 (ttt180) REVERT: B 463 ASP cc_start: 0.8457 (p0) cc_final: 0.7747 (t0) REVERT: M 167 LYS cc_start: 0.9109 (mtpp) cc_final: 0.8895 (mmtt) REVERT: M 414 SER cc_start: 0.8781 (t) cc_final: 0.8551 (p) REVERT: S 13 LYS cc_start: 0.9015 (ptmm) cc_final: 0.8713 (ptmm) REVERT: S 43 ASP cc_start: 0.8627 (p0) cc_final: 0.8416 (p0) REVERT: S 55 PHE cc_start: 0.8508 (OUTLIER) cc_final: 0.8133 (p90) outliers start: 18 outliers final: 9 residues processed: 219 average time/residue: 0.1385 time to fit residues: 42.9367 Evaluate side-chains 166 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 155 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain B residue 67 LYS Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain M residue 245 ASP Chi-restraints excluded: chain M residue 279 THR Chi-restraints excluded: chain M residue 421 TRP Chi-restraints excluded: chain S residue 22 GLN Chi-restraints excluded: chain S residue 55 PHE Chi-restraints excluded: chain N residue 21 ILE Chi-restraints excluded: chain N residue 46 LEU Chi-restraints excluded: chain N residue 79 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 103 optimal weight: 2.9990 chunk 96 optimal weight: 4.9990 chunk 32 optimal weight: 0.9980 chunk 152 optimal weight: 1.9990 chunk 132 optimal weight: 5.9990 chunk 157 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 26 optimal weight: 0.6980 chunk 47 optimal weight: 0.9990 chunk 58 optimal weight: 7.9990 chunk 125 optimal weight: 3.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 476 GLN A 560 GLN A 578 GLN ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.107138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.086012 restraints weight = 25497.082| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 2.31 r_work: 0.2921 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.2687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14531 Z= 0.163 Angle : 0.589 10.850 19663 Z= 0.310 Chirality : 0.043 0.174 2278 Planarity : 0.004 0.059 2496 Dihedral : 4.795 32.054 1936 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.71 % Allowed : 7.28 % Favored : 91.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.52 % Twisted General : 0.00 % 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: -0.62 (0.19), residues: 1749 helix: -0.13 (0.16), residues: 997 sheet: -0.25 (0.34), residues: 244 loop : -0.71 (0.26), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 110 TYR 0.025 0.002 TYR A 478 PHE 0.017 0.002 PHE S 4 TRP 0.016 0.002 TRP M 421 HIS 0.006 0.001 HIS S 85 Details of bonding type rmsd covalent geometry : bond 0.00387 (14531) covalent geometry : angle 0.58922 (19663) hydrogen bonds : bond 0.03993 ( 735) hydrogen bonds : angle 4.70923 ( 2124) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 172 time to evaluate : 0.516 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 391 ASP cc_start: 0.8160 (m-30) cc_final: 0.7940 (m-30) REVERT: A 570 LYS cc_start: 0.8516 (mttt) cc_final: 0.8024 (tmtt) REVERT: B 67 LYS cc_start: 0.9284 (OUTLIER) cc_final: 0.8893 (tttm) REVERT: B 83 MET cc_start: 0.8103 (tpp) cc_final: 0.7761 (tpp) REVERT: B 340 ASP cc_start: 0.8862 (t0) cc_final: 0.8373 (m-30) REVERT: B 458 ARG cc_start: 0.8211 (mmt180) cc_final: 0.7439 (ttt180) REVERT: B 463 ASP cc_start: 0.8290 (p0) cc_final: 0.7688 (t0) REVERT: S 13 LYS cc_start: 0.8997 (ptmm) cc_final: 0.8727 (ptmm) REVERT: S 24 ASP cc_start: 0.8596 (m-30) cc_final: 0.8369 (m-30) REVERT: S 43 ASP cc_start: 0.8572 (p0) cc_final: 0.8358 (p0) REVERT: S 61 ARG cc_start: 0.8604 (ttp-110) cc_final: 0.8183 (ttp80) REVERT: S 141 LEU cc_start: 0.8188 (tt) cc_final: 0.7981 (tp) REVERT: N 51 LYS cc_start: 0.6629 (tttp) cc_final: 0.6422 (mtpp) outliers start: 27 outliers final: 17 residues processed: 191 average time/residue: 0.1317 time to fit residues: 36.1624 Evaluate side-chains 170 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 152 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 246 ASP Chi-restraints excluded: chain A residue 462 TRP Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain B residue 67 LYS Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 404 ASN Chi-restraints excluded: chain B residue 524 TYR Chi-restraints excluded: chain M residue 22 ASP Chi-restraints excluded: chain M residue 279 THR Chi-restraints excluded: chain S residue 36 HIS Chi-restraints excluded: chain S residue 55 PHE Chi-restraints excluded: chain S residue 126 THR Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain N residue 18 VAL Chi-restraints excluded: chain N residue 49 THR Chi-restraints excluded: chain N residue 79 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 116 optimal weight: 2.9990 chunk 140 optimal weight: 0.7980 chunk 93 optimal weight: 0.9980 chunk 51 optimal weight: 0.8980 chunk 149 optimal weight: 2.9990 chunk 144 optimal weight: 3.9990 chunk 77 optimal weight: 0.0270 chunk 75 optimal weight: 0.8980 chunk 133 optimal weight: 2.9990 chunk 158 optimal weight: 0.9980 chunk 171 optimal weight: 8.9990 overall best weight: 0.7238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 HIS A 218 ASN ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.108700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.088021 restraints weight = 25112.152| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 2.25 r_work: 0.2961 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2819 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.3009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 14531 Z= 0.108 Angle : 0.531 10.666 19663 Z= 0.278 Chirality : 0.041 0.164 2278 Planarity : 0.004 0.057 2496 Dihedral : 4.497 31.654 1936 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.03 % Allowed : 8.11 % Favored : 89.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.52 % Twisted General : 0.00 % 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: 0.19 (0.20), residues: 1749 helix: 0.58 (0.17), residues: 996 sheet: 0.03 (0.35), residues: 233 loop : -0.48 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 110 TYR 0.019 0.001 TYR A 53 PHE 0.022 0.001 PHE A 552 TRP 0.011 0.001 TRP M 421 HIS 0.004 0.001 HIS S 85 Details of bonding type rmsd covalent geometry : bond 0.00247 (14531) covalent geometry : angle 0.53103 (19663) hydrogen bonds : bond 0.03247 ( 735) hydrogen bonds : angle 4.40432 ( 2124) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 181 time to evaluate : 0.563 Fit side-chains revert: symmetry clash REVERT: A 218 ASN cc_start: 0.8997 (OUTLIER) cc_final: 0.8401 (p0) REVERT: A 341 ARG cc_start: 0.8380 (mmm-85) cc_final: 0.8155 (tpt90) REVERT: A 391 ASP cc_start: 0.8284 (m-30) cc_final: 0.8056 (m-30) REVERT: A 570 LYS cc_start: 0.8607 (mttt) cc_final: 0.8010 (tmtt) REVERT: B 21 GLU cc_start: 0.8287 (pm20) cc_final: 0.7795 (pm20) REVERT: B 83 MET cc_start: 0.8090 (tpp) cc_final: 0.7513 (tpp) REVERT: B 340 ASP cc_start: 0.9003 (t0) cc_final: 0.8470 (m-30) REVERT: B 458 ARG cc_start: 0.8271 (mmt180) cc_final: 0.7448 (ttt180) REVERT: B 463 ASP cc_start: 0.8388 (p0) cc_final: 0.7740 (t70) REVERT: B 527 TRP cc_start: 0.8509 (t-100) cc_final: 0.8064 (t60) REVERT: S 13 LYS cc_start: 0.9039 (ptmm) cc_final: 0.8827 (ptmm) REVERT: S 22 GLN cc_start: 0.9049 (OUTLIER) cc_final: 0.8767 (tp40) REVERT: S 24 ASP cc_start: 0.8704 (m-30) cc_final: 0.8479 (m-30) REVERT: S 55 PHE cc_start: 0.8345 (OUTLIER) cc_final: 0.7964 (p90) REVERT: S 61 ARG cc_start: 0.8712 (ttp-110) cc_final: 0.8349 (ttp80) REVERT: S 66 TYR cc_start: 0.8917 (m-80) cc_final: 0.8697 (m-80) REVERT: N 38 ASP cc_start: 0.8324 (m-30) cc_final: 0.8073 (m-30) REVERT: N 70 GLN cc_start: 0.7990 (tt0) cc_final: 0.7783 (tt0) outliers start: 32 outliers final: 19 residues processed: 204 average time/residue: 0.1399 time to fit residues: 40.7310 Evaluate side-chains 185 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 163 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 396 MET Chi-restraints excluded: chain A residue 462 TRP Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain B residue 279 MET Chi-restraints excluded: chain B residue 524 TYR Chi-restraints excluded: chain B residue 567 ILE Chi-restraints excluded: chain M residue 22 ASP Chi-restraints excluded: chain M residue 181 VAL Chi-restraints excluded: chain M residue 245 ASP Chi-restraints excluded: chain M residue 279 THR Chi-restraints excluded: chain M residue 421 TRP Chi-restraints excluded: chain S residue 22 GLN Chi-restraints excluded: chain S residue 36 HIS Chi-restraints excluded: chain S residue 55 PHE Chi-restraints excluded: chain S residue 126 THR Chi-restraints excluded: chain N residue 18 VAL Chi-restraints excluded: chain N residue 21 ILE Chi-restraints excluded: chain N residue 37 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 39 optimal weight: 2.9990 chunk 138 optimal weight: 0.0770 chunk 116 optimal weight: 0.6980 chunk 72 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 142 optimal weight: 3.9990 chunk 53 optimal weight: 7.9990 chunk 159 optimal weight: 5.9990 chunk 135 optimal weight: 0.0070 chunk 32 optimal weight: 0.0270 chunk 96 optimal weight: 0.3980 overall best weight: 0.2414 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 HIS A 218 ASN ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 365 GLN N 75 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.110360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.089736 restraints weight = 25397.653| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 2.28 r_work: 0.2979 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2836 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.3239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 14531 Z= 0.097 Angle : 0.530 10.796 19663 Z= 0.274 Chirality : 0.041 0.215 2278 Planarity : 0.004 0.055 2496 Dihedral : 4.266 27.516 1934 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.46 % Favored : 97.48 % Rotamer: Outliers : 2.03 % Allowed : 8.11 % Favored : 89.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.68 (0.21), residues: 1749 helix: 1.02 (0.17), residues: 995 sheet: 0.15 (0.35), residues: 233 loop : -0.32 (0.28), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 110 TYR 0.017 0.001 TYR A 53 PHE 0.015 0.001 PHE S 55 TRP 0.010 0.001 TRP M 421 HIS 0.003 0.000 HIS S 85 Details of bonding type rmsd covalent geometry : bond 0.00212 (14531) covalent geometry : angle 0.53027 (19663) hydrogen bonds : bond 0.03011 ( 735) hydrogen bonds : angle 4.25461 ( 2124) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 185 time to evaluate : 0.552 Fit side-chains REVERT: A 282 GLU cc_start: 0.8334 (pm20) cc_final: 0.8009 (pm20) REVERT: A 341 ARG cc_start: 0.8382 (mmm-85) cc_final: 0.8162 (tpt90) REVERT: A 391 ASP cc_start: 0.8384 (m-30) cc_final: 0.8161 (m-30) REVERT: A 570 LYS cc_start: 0.8634 (mttt) cc_final: 0.7980 (tmtt) REVERT: B 21 GLU cc_start: 0.8187 (pm20) cc_final: 0.7677 (pm20) REVERT: B 83 MET cc_start: 0.8245 (tpp) cc_final: 0.7676 (tpp) REVERT: B 340 ASP cc_start: 0.8994 (t0) cc_final: 0.8387 (m-30) REVERT: B 458 ARG cc_start: 0.8301 (mmt180) cc_final: 0.7470 (ttt180) REVERT: B 463 ASP cc_start: 0.8286 (p0) cc_final: 0.7684 (t70) REVERT: B 527 TRP cc_start: 0.8480 (t-100) cc_final: 0.8039 (t60) REVERT: M 358 MET cc_start: 0.9200 (ttt) cc_final: 0.8724 (ttt) REVERT: S 3 ARG cc_start: 0.8058 (mtt180) cc_final: 0.7855 (mtt-85) REVERT: S 22 GLN cc_start: 0.9020 (OUTLIER) cc_final: 0.8744 (tp40) REVERT: S 24 ASP cc_start: 0.8687 (m-30) cc_final: 0.8397 (m-30) REVERT: S 55 PHE cc_start: 0.8211 (OUTLIER) cc_final: 0.7533 (p90) REVERT: S 61 ARG cc_start: 0.8654 (ttp-110) cc_final: 0.8338 (ttp80) REVERT: N 39 GLN cc_start: 0.8302 (mp10) cc_final: 0.7832 (mp10) REVERT: N 51 LYS cc_start: 0.6255 (mtpp) cc_final: 0.5979 (mmtt) REVERT: N 58 LYS cc_start: 0.8989 (mttp) cc_final: 0.8543 (mtmt) REVERT: N 134 GLU cc_start: 0.8749 (tm-30) cc_final: 0.8484 (tm-30) outliers start: 32 outliers final: 23 residues processed: 207 average time/residue: 0.1302 time to fit residues: 38.8423 Evaluate side-chains 183 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 158 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 396 MET Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 279 MET Chi-restraints excluded: chain B residue 282 LYS Chi-restraints excluded: chain B residue 524 TYR Chi-restraints excluded: chain B residue 567 ILE Chi-restraints excluded: chain M residue 22 ASP Chi-restraints excluded: chain M residue 181 VAL Chi-restraints excluded: chain M residue 245 ASP Chi-restraints excluded: chain M residue 272 PHE Chi-restraints excluded: chain M residue 279 THR Chi-restraints excluded: chain M residue 421 TRP Chi-restraints excluded: chain S residue 22 GLN Chi-restraints excluded: chain S residue 36 HIS Chi-restraints excluded: chain S residue 55 PHE Chi-restraints excluded: chain S residue 101 LEU Chi-restraints excluded: chain S residue 126 THR Chi-restraints excluded: chain N residue 18 VAL Chi-restraints excluded: chain N residue 30 TYR Chi-restraints excluded: chain N residue 37 LEU Chi-restraints excluded: chain N residue 75 GLN Chi-restraints excluded: chain N residue 83 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 135 optimal weight: 0.8980 chunk 164 optimal weight: 2.9990 chunk 96 optimal weight: 0.8980 chunk 42 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 99 optimal weight: 0.9990 chunk 3 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 123 optimal weight: 5.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 HIS A 218 ASN ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.108603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.087857 restraints weight = 25155.910| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 2.27 r_work: 0.2956 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.3298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14531 Z= 0.114 Angle : 0.529 10.493 19663 Z= 0.273 Chirality : 0.041 0.199 2278 Planarity : 0.004 0.055 2496 Dihedral : 4.202 27.775 1934 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.57 % Favored : 97.37 % Rotamer: Outliers : 2.22 % Allowed : 8.49 % Favored : 89.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.92 (0.21), residues: 1749 helix: 1.23 (0.17), residues: 997 sheet: 0.24 (0.35), residues: 233 loop : -0.26 (0.28), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG M 163 TYR 0.016 0.001 TYR A 53 PHE 0.015 0.001 PHE S 55 TRP 0.013 0.001 TRP M 421 HIS 0.004 0.001 HIS S 85 Details of bonding type rmsd covalent geometry : bond 0.00267 (14531) covalent geometry : angle 0.52915 (19663) hydrogen bonds : bond 0.03027 ( 735) hydrogen bonds : angle 4.17760 ( 2124) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 178 time to evaluate : 0.533 Fit side-chains revert: symmetry clash REVERT: A 282 GLU cc_start: 0.8202 (pm20) cc_final: 0.7889 (pm20) REVERT: A 391 ASP cc_start: 0.8072 (m-30) cc_final: 0.7834 (m-30) REVERT: A 570 LYS cc_start: 0.8502 (mttt) cc_final: 0.7940 (tmtt) REVERT: B 21 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.7609 (pm20) REVERT: B 83 MET cc_start: 0.8219 (tpp) cc_final: 0.7686 (tpp) REVERT: B 340 ASP cc_start: 0.8819 (t0) cc_final: 0.8193 (m-30) REVERT: B 458 ARG cc_start: 0.8248 (mmt180) cc_final: 0.7527 (ttt180) REVERT: B 463 ASP cc_start: 0.8187 (p0) cc_final: 0.7685 (t0) REVERT: B 527 TRP cc_start: 0.8345 (t-100) cc_final: 0.7908 (t60) REVERT: M 85 MET cc_start: 0.9018 (ttp) cc_final: 0.8484 (ttp) REVERT: M 323 ARG cc_start: 0.9024 (OUTLIER) cc_final: 0.8427 (ttm-80) REVERT: S 3 ARG cc_start: 0.7946 (mtt180) cc_final: 0.7713 (mtt-85) REVERT: S 22 GLN cc_start: 0.8855 (OUTLIER) cc_final: 0.8574 (tp40) REVERT: S 43 ASP cc_start: 0.8621 (p0) cc_final: 0.8318 (p0) REVERT: S 55 PHE cc_start: 0.8184 (OUTLIER) cc_final: 0.7317 (p90) REVERT: S 61 ARG cc_start: 0.8505 (ttp-110) cc_final: 0.8190 (ttp80) REVERT: S 93 GLU cc_start: 0.8614 (mm-30) cc_final: 0.8398 (mm-30) REVERT: N 30 TYR cc_start: 0.7027 (OUTLIER) cc_final: 0.6286 (t80) REVERT: N 34 GLU cc_start: 0.8121 (mp0) cc_final: 0.7874 (mp0) REVERT: N 39 GLN cc_start: 0.8223 (mp10) cc_final: 0.7798 (mp10) REVERT: N 45 ARG cc_start: 0.7565 (ttp-110) cc_final: 0.7196 (mtm-85) REVERT: N 58 LYS cc_start: 0.8883 (mttp) cc_final: 0.8658 (mtmm) REVERT: N 70 GLN cc_start: 0.7729 (tt0) cc_final: 0.7492 (tt0) outliers start: 35 outliers final: 23 residues processed: 200 average time/residue: 0.1242 time to fit residues: 36.0901 Evaluate side-chains 192 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 164 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 396 MET Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain B residue 21 GLU Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 253 SER Chi-restraints excluded: chain B residue 282 LYS Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 524 TYR Chi-restraints excluded: chain B residue 567 ILE Chi-restraints excluded: chain M residue 181 VAL Chi-restraints excluded: chain M residue 245 ASP Chi-restraints excluded: chain M residue 272 PHE Chi-restraints excluded: chain M residue 279 THR Chi-restraints excluded: chain M residue 323 ARG Chi-restraints excluded: chain S residue 13 LYS Chi-restraints excluded: chain S residue 22 GLN Chi-restraints excluded: chain S residue 35 VAL Chi-restraints excluded: chain S residue 36 HIS Chi-restraints excluded: chain S residue 54 ASN Chi-restraints excluded: chain S residue 55 PHE Chi-restraints excluded: chain S residue 101 LEU Chi-restraints excluded: chain S residue 126 THR Chi-restraints excluded: chain N residue 18 VAL Chi-restraints excluded: chain N residue 30 TYR Chi-restraints excluded: chain N residue 37 LEU Chi-restraints excluded: chain N residue 83 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 39 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 chunk 112 optimal weight: 0.7980 chunk 125 optimal weight: 4.9990 chunk 20 optimal weight: 0.9990 chunk 86 optimal weight: 3.9990 chunk 98 optimal weight: 0.9980 chunk 123 optimal weight: 4.9990 chunk 53 optimal weight: 0.0030 chunk 37 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 overall best weight: 0.9594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 HIS A 218 ASN B 149 HIS ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 365 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.108604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.087938 restraints weight = 25007.376| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 2.25 r_work: 0.2959 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2818 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.3371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14531 Z= 0.118 Angle : 0.532 10.354 19663 Z= 0.274 Chirality : 0.042 0.160 2278 Planarity : 0.004 0.053 2496 Dihedral : 4.177 27.530 1934 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.53 % Allowed : 8.36 % Favored : 89.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.07 (0.21), residues: 1749 helix: 1.37 (0.17), residues: 998 sheet: 0.31 (0.35), residues: 231 loop : -0.24 (0.28), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG M 163 TYR 0.015 0.001 TYR A 478 PHE 0.017 0.001 PHE A 552 TRP 0.013 0.001 TRP M 421 HIS 0.004 0.001 HIS S 85 Details of bonding type rmsd covalent geometry : bond 0.00281 (14531) covalent geometry : angle 0.53192 (19663) hydrogen bonds : bond 0.03054 ( 735) hydrogen bonds : angle 4.18302 ( 2124) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 177 time to evaluate : 0.571 Fit side-chains REVERT: A 282 GLU cc_start: 0.8394 (pm20) cc_final: 0.8098 (pm20) REVERT: A 341 ARG cc_start: 0.8333 (mmm-85) cc_final: 0.8094 (tpt90) REVERT: A 391 ASP cc_start: 0.8386 (m-30) cc_final: 0.8153 (m-30) REVERT: A 483 VAL cc_start: 0.9385 (OUTLIER) cc_final: 0.9150 (m) REVERT: A 570 LYS cc_start: 0.8669 (mttt) cc_final: 0.8073 (tmtt) REVERT: B 21 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7639 (pm20) REVERT: B 83 MET cc_start: 0.8182 (tpp) cc_final: 0.7469 (tpp) REVERT: B 340 ASP cc_start: 0.9030 (t0) cc_final: 0.8406 (m-30) REVERT: B 458 ARG cc_start: 0.8368 (mmt180) cc_final: 0.7531 (ttt180) REVERT: B 463 ASP cc_start: 0.8303 (p0) cc_final: 0.7699 (t0) REVERT: B 527 TRP cc_start: 0.8496 (t-100) cc_final: 0.8001 (t60) REVERT: M 85 MET cc_start: 0.9156 (ttp) cc_final: 0.8735 (ttp) REVERT: M 172 GLU cc_start: 0.8557 (pt0) cc_final: 0.8079 (mt-10) REVERT: M 302 GLU cc_start: 0.8296 (pm20) cc_final: 0.8015 (pm20) REVERT: M 323 ARG cc_start: 0.9196 (OUTLIER) cc_final: 0.8645 (ttm-80) REVERT: S 3 ARG cc_start: 0.8254 (mtt180) cc_final: 0.7946 (mtt-85) REVERT: S 22 GLN cc_start: 0.9007 (OUTLIER) cc_final: 0.8727 (tp40) REVERT: S 43 ASP cc_start: 0.8716 (p0) cc_final: 0.8464 (p0) REVERT: S 55 PHE cc_start: 0.8264 (OUTLIER) cc_final: 0.7414 (p90) REVERT: S 93 GLU cc_start: 0.8867 (mm-30) cc_final: 0.8664 (mm-30) REVERT: N 30 TYR cc_start: 0.7084 (OUTLIER) cc_final: 0.6479 (t80) REVERT: N 34 GLU cc_start: 0.8101 (mp0) cc_final: 0.7830 (mp0) REVERT: N 39 GLN cc_start: 0.8302 (mp10) cc_final: 0.7899 (mp10) REVERT: N 45 ARG cc_start: 0.8047 (ttp-110) cc_final: 0.7492 (mtm-85) REVERT: N 58 LYS cc_start: 0.9104 (mttp) cc_final: 0.8798 (mtmm) REVERT: N 70 GLN cc_start: 0.7865 (tt0) cc_final: 0.7643 (tt0) REVERT: N 94 ARG cc_start: 0.8310 (ttp-170) cc_final: 0.7900 (ttp-170) outliers start: 40 outliers final: 27 residues processed: 202 average time/residue: 0.1215 time to fit residues: 35.7533 Evaluate side-chains 196 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 163 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 245 GLN Chi-restraints excluded: chain A residue 396 MET Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain B residue 21 GLU Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 253 SER Chi-restraints excluded: chain B residue 279 MET Chi-restraints excluded: chain B residue 282 LYS Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 567 ILE Chi-restraints excluded: chain M residue 181 VAL Chi-restraints excluded: chain M residue 245 ASP Chi-restraints excluded: chain M residue 272 PHE Chi-restraints excluded: chain M residue 279 THR Chi-restraints excluded: chain M residue 323 ARG Chi-restraints excluded: chain S residue 13 LYS Chi-restraints excluded: chain S residue 22 GLN Chi-restraints excluded: chain S residue 35 VAL Chi-restraints excluded: chain S residue 36 HIS Chi-restraints excluded: chain S residue 54 ASN Chi-restraints excluded: chain S residue 55 PHE Chi-restraints excluded: chain S residue 101 LEU Chi-restraints excluded: chain S residue 126 THR Chi-restraints excluded: chain N residue 18 VAL Chi-restraints excluded: chain N residue 30 TYR Chi-restraints excluded: chain N residue 37 LEU Chi-restraints excluded: chain N residue 49 THR Chi-restraints excluded: chain N residue 83 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 35 optimal weight: 0.8980 chunk 29 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 72 optimal weight: 0.0770 chunk 153 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 chunk 147 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 overall best weight: 1.1942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 HIS A 218 ASN B 149 HIS ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 75 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.107489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.086887 restraints weight = 25151.671| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 2.24 r_work: 0.2937 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2795 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.3419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14531 Z= 0.134 Angle : 0.549 10.086 19663 Z= 0.283 Chirality : 0.042 0.230 2278 Planarity : 0.004 0.052 2496 Dihedral : 4.216 27.185 1934 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.52 % Favored : 97.43 % Rotamer: Outliers : 2.22 % Allowed : 9.44 % Favored : 88.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.15 (0.21), residues: 1749 helix: 1.46 (0.17), residues: 997 sheet: 0.24 (0.34), residues: 243 loop : -0.22 (0.29), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG N 45 TYR 0.016 0.001 TYR A 478 PHE 0.029 0.001 PHE N 68 TRP 0.013 0.001 TRP M 421 HIS 0.004 0.001 HIS S 85 Details of bonding type rmsd covalent geometry : bond 0.00322 (14531) covalent geometry : angle 0.54870 (19663) hydrogen bonds : bond 0.03094 ( 735) hydrogen bonds : angle 4.22498 ( 2124) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 172 time to evaluate : 0.550 Fit side-chains revert: symmetry clash REVERT: A 282 GLU cc_start: 0.8405 (pm20) cc_final: 0.8138 (pm20) REVERT: A 341 ARG cc_start: 0.8386 (mmm-85) cc_final: 0.8087 (tpt90) REVERT: A 391 ASP cc_start: 0.8409 (m-30) cc_final: 0.8171 (m-30) REVERT: A 570 LYS cc_start: 0.8668 (mttt) cc_final: 0.8070 (tmtt) REVERT: B 21 GLU cc_start: 0.8245 (OUTLIER) cc_final: 0.7673 (pm20) REVERT: B 83 MET cc_start: 0.8186 (tpp) cc_final: 0.7670 (tpp) REVERT: B 340 ASP cc_start: 0.9053 (t0) cc_final: 0.8419 (m-30) REVERT: B 458 ARG cc_start: 0.8528 (mmt180) cc_final: 0.7570 (ttt180) REVERT: B 463 ASP cc_start: 0.8307 (OUTLIER) cc_final: 0.7699 (t0) REVERT: B 527 TRP cc_start: 0.8531 (t-100) cc_final: 0.8004 (t60) REVERT: M 85 MET cc_start: 0.9224 (ttp) cc_final: 0.8832 (ttp) REVERT: M 172 GLU cc_start: 0.8623 (pt0) cc_final: 0.8142 (mt-10) REVERT: M 302 GLU cc_start: 0.8403 (pm20) cc_final: 0.8092 (pm20) REVERT: M 367 SER cc_start: 0.9287 (m) cc_final: 0.8976 (t) REVERT: S 3 ARG cc_start: 0.8339 (mtt180) cc_final: 0.8016 (mtt-85) REVERT: S 22 GLN cc_start: 0.8968 (OUTLIER) cc_final: 0.8694 (tp40) REVERT: S 43 ASP cc_start: 0.8744 (p0) cc_final: 0.8536 (p0) REVERT: S 55 PHE cc_start: 0.8328 (OUTLIER) cc_final: 0.7493 (p90) REVERT: N 30 TYR cc_start: 0.7191 (OUTLIER) cc_final: 0.6528 (t80) REVERT: N 34 GLU cc_start: 0.8150 (mp0) cc_final: 0.7892 (mp0) REVERT: N 39 GLN cc_start: 0.8329 (mp10) cc_final: 0.7947 (mp10) REVERT: N 45 ARG cc_start: 0.8155 (ttp-110) cc_final: 0.7726 (mtm-85) REVERT: N 58 LYS cc_start: 0.9195 (mttp) cc_final: 0.8821 (mtmm) outliers start: 35 outliers final: 28 residues processed: 192 average time/residue: 0.1242 time to fit residues: 34.8371 Evaluate side-chains 200 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 167 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 245 GLN Chi-restraints excluded: chain A residue 396 MET Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain B residue 21 GLU Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 253 SER Chi-restraints excluded: chain B residue 279 MET Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 463 ASP Chi-restraints excluded: chain B residue 567 ILE Chi-restraints excluded: chain M residue 181 VAL Chi-restraints excluded: chain M residue 245 ASP Chi-restraints excluded: chain M residue 272 PHE Chi-restraints excluded: chain M residue 279 THR Chi-restraints excluded: chain M residue 323 ARG Chi-restraints excluded: chain S residue 13 LYS Chi-restraints excluded: chain S residue 22 GLN Chi-restraints excluded: chain S residue 35 VAL Chi-restraints excluded: chain S residue 36 HIS Chi-restraints excluded: chain S residue 54 ASN Chi-restraints excluded: chain S residue 55 PHE Chi-restraints excluded: chain S residue 101 LEU Chi-restraints excluded: chain S residue 126 THR Chi-restraints excluded: chain N residue 18 VAL Chi-restraints excluded: chain N residue 30 TYR Chi-restraints excluded: chain N residue 37 LEU Chi-restraints excluded: chain N residue 75 GLN Chi-restraints excluded: chain N residue 83 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 39 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 130 optimal weight: 0.6980 chunk 22 optimal weight: 6.9990 chunk 111 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 170 optimal weight: 0.9990 chunk 173 optimal weight: 4.9990 chunk 100 optimal weight: 3.9990 chunk 166 optimal weight: 0.0770 overall best weight: 0.9544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 HIS A 218 ASN B 149 HIS ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 365 GLN ** N 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.108072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.086764 restraints weight = 25153.259| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 2.32 r_work: 0.2935 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.3449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14531 Z= 0.122 Angle : 0.549 9.813 19663 Z= 0.284 Chirality : 0.042 0.234 2278 Planarity : 0.004 0.052 2496 Dihedral : 4.191 29.626 1934 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.57 % Favored : 97.37 % Rotamer: Outliers : 2.22 % Allowed : 9.56 % Favored : 88.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.22 (0.21), residues: 1749 helix: 1.51 (0.17), residues: 998 sheet: 0.25 (0.35), residues: 243 loop : -0.15 (0.29), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG M 323 TYR 0.016 0.001 TYR A 478 PHE 0.026 0.001 PHE N 68 TRP 0.013 0.001 TRP M 421 HIS 0.004 0.001 HIS B 149 Details of bonding type rmsd covalent geometry : bond 0.00292 (14531) covalent geometry : angle 0.54864 (19663) hydrogen bonds : bond 0.03011 ( 735) hydrogen bonds : angle 4.19328 ( 2124) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 175 time to evaluate : 0.540 Fit side-chains REVERT: A 218 ASN cc_start: 0.8891 (OUTLIER) cc_final: 0.8442 (p0) REVERT: A 282 GLU cc_start: 0.8266 (pm20) cc_final: 0.8019 (pm20) REVERT: A 341 ARG cc_start: 0.8199 (mmm-85) cc_final: 0.7897 (tpt90) REVERT: A 391 ASP cc_start: 0.8027 (m-30) cc_final: 0.7774 (m-30) REVERT: A 483 VAL cc_start: 0.9350 (OUTLIER) cc_final: 0.9147 (m) REVERT: A 570 LYS cc_start: 0.8499 (mttt) cc_final: 0.7998 (tmtt) REVERT: B 21 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7462 (pm20) REVERT: B 83 MET cc_start: 0.8096 (tpp) cc_final: 0.7595 (tpp) REVERT: B 340 ASP cc_start: 0.8845 (t0) cc_final: 0.8197 (m-30) REVERT: B 458 ARG cc_start: 0.8441 (mmt180) cc_final: 0.7547 (ttt180) REVERT: B 463 ASP cc_start: 0.8208 (OUTLIER) cc_final: 0.7673 (t0) REVERT: B 527 TRP cc_start: 0.8446 (t-100) cc_final: 0.7920 (t60) REVERT: M 85 MET cc_start: 0.8972 (ttp) cc_final: 0.8596 (ttp) REVERT: M 172 GLU cc_start: 0.8248 (pt0) cc_final: 0.7764 (mt-10) REVERT: M 302 GLU cc_start: 0.8111 (pm20) cc_final: 0.7789 (pm20) REVERT: S 3 ARG cc_start: 0.8053 (mtt180) cc_final: 0.7730 (mtt-85) REVERT: S 22 GLN cc_start: 0.8821 (OUTLIER) cc_final: 0.8522 (tp40) REVERT: S 43 ASP cc_start: 0.8611 (p0) cc_final: 0.8401 (p0) REVERT: S 55 PHE cc_start: 0.8239 (OUTLIER) cc_final: 0.7302 (p90) REVERT: S 93 GLU cc_start: 0.8670 (mm-30) cc_final: 0.8308 (mm-30) REVERT: N 30 TYR cc_start: 0.7027 (OUTLIER) cc_final: 0.6483 (t80) REVERT: N 34 GLU cc_start: 0.8080 (mp0) cc_final: 0.7844 (mp0) REVERT: N 39 GLN cc_start: 0.8249 (mp10) cc_final: 0.7872 (mp10) REVERT: N 45 ARG cc_start: 0.8091 (ttp-110) cc_final: 0.7495 (mtm-85) REVERT: N 58 LYS cc_start: 0.9130 (mttp) cc_final: 0.8671 (mtmm) REVERT: N 74 ASP cc_start: 0.8221 (p0) cc_final: 0.7934 (t0) outliers start: 35 outliers final: 26 residues processed: 196 average time/residue: 0.1219 time to fit residues: 34.9629 Evaluate side-chains 197 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 164 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 245 GLN Chi-restraints excluded: chain A residue 396 MET Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain B residue 21 GLU Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 253 SER Chi-restraints excluded: chain B residue 279 MET Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 463 ASP Chi-restraints excluded: chain B residue 567 ILE Chi-restraints excluded: chain M residue 181 VAL Chi-restraints excluded: chain M residue 245 ASP Chi-restraints excluded: chain M residue 272 PHE Chi-restraints excluded: chain M residue 279 THR Chi-restraints excluded: chain S residue 13 LYS Chi-restraints excluded: chain S residue 22 GLN Chi-restraints excluded: chain S residue 35 VAL Chi-restraints excluded: chain S residue 36 HIS Chi-restraints excluded: chain S residue 54 ASN Chi-restraints excluded: chain S residue 55 PHE Chi-restraints excluded: chain S residue 101 LEU Chi-restraints excluded: chain S residue 126 THR Chi-restraints excluded: chain N residue 21 ILE Chi-restraints excluded: chain N residue 30 TYR Chi-restraints excluded: chain N residue 37 LEU Chi-restraints excluded: chain N residue 83 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 168 optimal weight: 0.9980 chunk 77 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 chunk 124 optimal weight: 1.9990 chunk 167 optimal weight: 2.9990 chunk 158 optimal weight: 0.8980 chunk 116 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 82 optimal weight: 0.8980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.108369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.087427 restraints weight = 25138.968| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 2.25 r_work: 0.2942 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2800 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.3482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.128 14531 Z= 0.147 Angle : 0.769 59.108 19663 Z= 0.437 Chirality : 0.043 0.472 2278 Planarity : 0.004 0.052 2496 Dihedral : 4.231 29.523 1934 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.57 % Favored : 97.31 % Rotamer: Outliers : 2.22 % Allowed : 9.44 % Favored : 88.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.22 (0.21), residues: 1749 helix: 1.51 (0.17), residues: 998 sheet: 0.26 (0.35), residues: 243 loop : -0.17 (0.29), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG N 45 TYR 0.013 0.001 TYR A 478 PHE 0.024 0.001 PHE N 68 TRP 0.012 0.001 TRP M 421 HIS 0.005 0.001 HIS S 85 Details of bonding type rmsd covalent geometry : bond 0.00339 (14531) covalent geometry : angle 0.76860 (19663) hydrogen bonds : bond 0.03012 ( 735) hydrogen bonds : angle 4.19706 ( 2124) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 165 time to evaluate : 0.588 Fit side-chains REVERT: A 218 ASN cc_start: 0.8912 (OUTLIER) cc_final: 0.8689 (p0) REVERT: A 282 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.8123 (pm20) REVERT: A 341 ARG cc_start: 0.8376 (mmm-85) cc_final: 0.8016 (tpt90) REVERT: A 391 ASP cc_start: 0.8363 (m-30) cc_final: 0.8124 (m-30) REVERT: A 483 VAL cc_start: 0.9400 (OUTLIER) cc_final: 0.9172 (m) REVERT: A 570 LYS cc_start: 0.8610 (mttt) cc_final: 0.8060 (tmtt) REVERT: B 21 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.7540 (pm20) REVERT: B 83 MET cc_start: 0.8116 (tpp) cc_final: 0.7620 (tpp) REVERT: B 340 ASP cc_start: 0.9032 (t0) cc_final: 0.8392 (m-30) REVERT: B 458 ARG cc_start: 0.8531 (mmt180) cc_final: 0.7554 (ttt180) REVERT: B 463 ASP cc_start: 0.8327 (OUTLIER) cc_final: 0.7709 (t0) REVERT: B 527 TRP cc_start: 0.8605 (t-100) cc_final: 0.8058 (t60) REVERT: M 85 MET cc_start: 0.9154 (ttp) cc_final: 0.8812 (ttp) REVERT: M 302 GLU cc_start: 0.8330 (pm20) cc_final: 0.7825 (pm20) REVERT: S 3 ARG cc_start: 0.8289 (mtt180) cc_final: 0.7965 (mtt-85) REVERT: S 22 GLN cc_start: 0.8953 (OUTLIER) cc_final: 0.8674 (tp40) REVERT: S 55 PHE cc_start: 0.8302 (OUTLIER) cc_final: 0.7369 (p90) REVERT: S 93 GLU cc_start: 0.8914 (mm-30) cc_final: 0.8575 (mm-30) REVERT: N 30 TYR cc_start: 0.7130 (OUTLIER) cc_final: 0.6554 (t80) REVERT: N 34 GLU cc_start: 0.8142 (mp0) cc_final: 0.7900 (mp0) REVERT: N 39 GLN cc_start: 0.8371 (mp10) cc_final: 0.7991 (mp10) REVERT: N 45 ARG cc_start: 0.8195 (ttp-110) cc_final: 0.7628 (mtm-85) REVERT: N 58 LYS cc_start: 0.9180 (mttp) cc_final: 0.8786 (mtmm) REVERT: N 74 ASP cc_start: 0.8375 (p0) cc_final: 0.8013 (t0) outliers start: 35 outliers final: 27 residues processed: 184 average time/residue: 0.1227 time to fit residues: 33.2136 Evaluate side-chains 197 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 162 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 245 GLN Chi-restraints excluded: chain A residue 282 GLU Chi-restraints excluded: chain A residue 396 MET Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain B residue 21 GLU Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 253 SER Chi-restraints excluded: chain B residue 279 MET Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 463 ASP Chi-restraints excluded: chain B residue 567 ILE Chi-restraints excluded: chain M residue 181 VAL Chi-restraints excluded: chain M residue 245 ASP Chi-restraints excluded: chain M residue 272 PHE Chi-restraints excluded: chain M residue 279 THR Chi-restraints excluded: chain S residue 13 LYS Chi-restraints excluded: chain S residue 22 GLN Chi-restraints excluded: chain S residue 35 VAL Chi-restraints excluded: chain S residue 36 HIS Chi-restraints excluded: chain S residue 54 ASN Chi-restraints excluded: chain S residue 55 PHE Chi-restraints excluded: chain S residue 101 LEU Chi-restraints excluded: chain S residue 126 THR Chi-restraints excluded: chain N residue 21 ILE Chi-restraints excluded: chain N residue 30 TYR Chi-restraints excluded: chain N residue 37 LEU Chi-restraints excluded: chain N residue 49 THR Chi-restraints excluded: chain N residue 83 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 8 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 129 optimal weight: 0.7980 chunk 58 optimal weight: 6.9990 chunk 1 optimal weight: 7.9990 chunk 23 optimal weight: 1.9990 chunk 80 optimal weight: 6.9990 chunk 71 optimal weight: 6.9990 chunk 116 optimal weight: 0.9990 chunk 94 optimal weight: 0.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.108074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.086741 restraints weight = 25117.535| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 2.29 r_work: 0.2942 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2799 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.3479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.126 14531 Z= 0.146 Angle : 0.769 59.200 19663 Z= 0.437 Chirality : 0.043 0.467 2278 Planarity : 0.004 0.052 2496 Dihedral : 4.231 29.522 1934 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.57 % Favored : 97.31 % Rotamer: Outliers : 2.22 % Allowed : 9.44 % Favored : 88.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.22 (0.21), residues: 1749 helix: 1.51 (0.17), residues: 998 sheet: 0.26 (0.35), residues: 243 loop : -0.17 (0.29), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG N 45 TYR 0.013 0.001 TYR A 478 PHE 0.024 0.001 PHE N 68 TRP 0.012 0.001 TRP M 421 HIS 0.005 0.001 HIS S 85 Details of bonding type rmsd covalent geometry : bond 0.00339 (14531) covalent geometry : angle 0.76861 (19663) hydrogen bonds : bond 0.03012 ( 735) hydrogen bonds : angle 4.19707 ( 2124) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3510.85 seconds wall clock time: 60 minutes 50.47 seconds (3650.47 seconds total)