Starting phenix.real_space_refine on Thu Sep 26 22:30:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6owo_20215/09_2024/6owo_20215.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6owo_20215/09_2024/6owo_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6owo_20215/09_2024/6owo_20215.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6owo_20215/09_2024/6owo_20215.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6owo_20215/09_2024/6owo_20215.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6owo_20215/09_2024/6owo_20215.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/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: 8.78, per 1000 atoms: 0.62 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: 3.82 Conformation dependent library (CDL) restraints added in 2.2 seconds 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: 1.80 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: 4.71 Time building geometry restraints manager: 4.38 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: 1.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.590 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 35.330 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.800 ------------------------------------------------------------------------------- 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= 0.569 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.78 (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 TRP 0.064 0.005 TRP M 421 HIS 0.008 0.002 HIS A 363 PHE 0.043 0.004 PHE S 67 TYR 0.046 0.004 TYR B 361 ARG 0.009 0.001 ARG M 199 *********************** 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 fitting. rotamer outliers: 4 poor density : 305 time to evaluate : 1.689 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: 0.8726 (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: 0.7825 (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: 0.3449 time to fit residues: 144.2327 Evaluate side-chains 158 residues out of total 1587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 157 time to evaluate : 1.771 ------------------------------------------------------------------------------- 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 148 optimal weight: 0.9980 chunk 133 optimal weight: 0.7980 chunk 74 optimal weight: 8.9990 chunk 45 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 137 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 83 optimal weight: 0.8980 chunk 102 optimal weight: 0.8980 chunk 159 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 A 560 GLN B 99 ASN B 191 HIS B 250 HIS B 252 ASN B 353 GLN B 500 GLN M 35 ASN M 72 ASN M 135 GLN M 310 ASN S 8 GLN N 123 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14531 Z= 0.203 Angle : 0.632 11.753 19663 Z= 0.339 Chirality : 0.043 0.185 2278 Planarity : 0.005 0.067 2496 Dihedral : 5.157 31.693 1936 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.27 % Allowed : 6.33 % Favored : 92.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.52 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.06 (0.18), residues: 1749 helix: -1.53 (0.14), residues: 993 sheet: -0.40 (0.34), residues: 241 loop : -1.01 (0.25), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP M 421 HIS 0.005 0.001 HIS A 363 PHE 0.018 0.002 PHE A 552 TYR 0.025 0.002 TYR A 478 ARG 0.012 0.001 ARG M 33 *********************** 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 222 residues out of total 1587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 202 time to evaluate : 1.622 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 570 LYS cc_start: 0.8370 (mttt) cc_final: 0.8086 (tmtt) REVERT: B 67 LYS cc_start: 0.9361 (OUTLIER) cc_final: 0.9022 (tttm) REVERT: B 83 MET cc_start: 0.8016 (tpp) cc_final: 0.7671 (tpp) REVERT: B 340 ASP cc_start: 0.8798 (t0) cc_final: 0.8424 (m-30) REVERT: B 458 ARG cc_start: 0.8337 (mmt180) cc_final: 0.7565 (ttt180) REVERT: B 463 ASP cc_start: 0.8298 (p0) cc_final: 0.7872 (t0) REVERT: S 13 LYS cc_start: 0.9084 (ptmm) cc_final: 0.8856 (ptmm) REVERT: S 43 ASP cc_start: 0.8452 (p0) cc_final: 0.8222 (p0) REVERT: S 55 PHE cc_start: 0.8451 (OUTLIER) cc_final: 0.8106 (p90) outliers start: 20 outliers final: 12 residues processed: 214 average time/residue: 0.3101 time to fit residues: 93.1485 Evaluate side-chains 161 residues out of total 1587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 147 time to evaluate : 2.001 ------------------------------------------------------------------------------- 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 35 ASN 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 S residue 126 THR Chi-restraints excluded: chain S residue 129 THR 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 88 optimal weight: 0.7980 chunk 49 optimal weight: 5.9990 chunk 133 optimal weight: 1.9990 chunk 108 optimal weight: 4.9990 chunk 44 optimal weight: 0.9990 chunk 160 optimal weight: 0.3980 chunk 172 optimal weight: 4.9990 chunk 142 optimal weight: 6.9990 chunk 158 optimal weight: 0.8980 chunk 54 optimal weight: 4.9990 chunk 128 optimal weight: 5.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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 ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.2686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14531 Z= 0.190 Angle : 0.569 10.900 19663 Z= 0.300 Chirality : 0.042 0.173 2278 Planarity : 0.004 0.060 2496 Dihedral : 4.758 32.021 1936 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.77 % Allowed : 7.47 % Favored : 90.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.52 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.19), residues: 1749 helix: -0.19 (0.16), residues: 997 sheet: -0.29 (0.33), residues: 244 loop : -0.74 (0.26), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP M 421 HIS 0.005 0.001 HIS S 85 PHE 0.015 0.001 PHE S 4 TYR 0.023 0.001 TYR A 478 ARG 0.004 0.000 ARG N 94 *********************** 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 198 residues out of total 1587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 170 time to evaluate : 1.808 Fit side-chains revert: symmetry clash REVERT: A 570 LYS cc_start: 0.8413 (mttt) cc_final: 0.8052 (tmtt) REVERT: B 67 LYS cc_start: 0.9330 (OUTLIER) cc_final: 0.8962 (tttm) REVERT: B 83 MET cc_start: 0.8197 (tpp) cc_final: 0.7972 (tpp) REVERT: B 235 ARG cc_start: 0.8503 (ptm-80) cc_final: 0.8136 (mmp80) REVERT: B 340 ASP cc_start: 0.8792 (t0) cc_final: 0.8355 (m-30) REVERT: B 458 ARG cc_start: 0.8358 (mmt180) cc_final: 0.7600 (ttt180) REVERT: B 463 ASP cc_start: 0.8331 (p0) cc_final: 0.7869 (t0) REVERT: S 43 ASP cc_start: 0.8466 (p0) cc_final: 0.8235 (p0) REVERT: S 61 ARG cc_start: 0.8601 (ttp-110) cc_final: 0.8238 (ttp80) outliers start: 28 outliers final: 19 residues processed: 190 average time/residue: 0.2989 time to fit residues: 80.9434 Evaluate side-chains 169 residues out of total 1587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 149 time to evaluate : 1.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 355 THR 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 248 LEU Chi-restraints excluded: chain B residue 524 TYR Chi-restraints excluded: chain M residue 22 ASP Chi-restraints excluded: chain M residue 35 ASN 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 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 158 optimal weight: 0.8980 chunk 120 optimal weight: 0.8980 chunk 83 optimal weight: 0.7980 chunk 17 optimal weight: 7.9990 chunk 76 optimal weight: 3.9990 chunk 107 optimal weight: 6.9990 chunk 160 optimal weight: 3.9990 chunk 170 optimal weight: 9.9990 chunk 152 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 141 optimal weight: 0.9980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 HIS A 578 GLN B 149 HIS ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.2922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14531 Z= 0.194 Angle : 0.546 10.622 19663 Z= 0.286 Chirality : 0.042 0.151 2278 Planarity : 0.004 0.057 2496 Dihedral : 4.538 31.613 1936 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.15 % Allowed : 7.60 % Favored : 90.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.52 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.20), residues: 1749 helix: 0.53 (0.17), residues: 1002 sheet: -0.10 (0.34), residues: 244 loop : -0.46 (0.28), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP M 421 HIS 0.004 0.001 HIS S 85 PHE 0.016 0.001 PHE S 4 TYR 0.018 0.001 TYR A 478 ARG 0.004 0.000 ARG M 33 *********************** 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 fitting. rotamer outliers: 34 poor density : 179 time to evaluate : 1.737 Fit side-chains REVERT: A 552 PHE cc_start: 0.8573 (m-10) cc_final: 0.8337 (m-10) REVERT: A 570 LYS cc_start: 0.8434 (mttt) cc_final: 0.7999 (tmtt) REVERT: B 21 GLU cc_start: 0.8565 (pm20) cc_final: 0.8179 (pm20) REVERT: B 83 MET cc_start: 0.8227 (tpp) cc_final: 0.7752 (tpp) REVERT: B 235 ARG cc_start: 0.8530 (ptm-80) cc_final: 0.8134 (mmp80) REVERT: B 340 ASP cc_start: 0.8794 (t0) cc_final: 0.8293 (m-30) REVERT: B 458 ARG cc_start: 0.8404 (mmt180) cc_final: 0.7631 (ttt180) REVERT: B 463 ASP cc_start: 0.8305 (p0) cc_final: 0.7867 (t0) REVERT: B 527 TRP cc_start: 0.8414 (t-100) cc_final: 0.8033 (t60) REVERT: S 21 MET cc_start: 0.8580 (ttp) cc_final: 0.8272 (ptm) REVERT: S 55 PHE cc_start: 0.8331 (OUTLIER) cc_final: 0.7985 (p90) REVERT: S 61 ARG cc_start: 0.8596 (ttp-110) cc_final: 0.8194 (ttp80) outliers start: 34 outliers final: 23 residues processed: 205 average time/residue: 0.2861 time to fit residues: 84.7913 Evaluate side-chains 183 residues out of total 1587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 159 time to evaluate : 1.947 ------------------------------------------------------------------------------- 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 246 ASP 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 248 LEU Chi-restraints excluded: chain B residue 404 ASN 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 S residue 13 LYS 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 S residue 129 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 Chi-restraints excluded: chain N residue 49 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 96 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 chunk 126 optimal weight: 5.9990 chunk 70 optimal weight: 1.9990 chunk 145 optimal weight: 4.9990 chunk 117 optimal weight: 0.9980 chunk 0 optimal weight: 7.9990 chunk 86 optimal weight: 2.9990 chunk 152 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 57 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 HIS B 149 HIS ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 365 GLN N 36 GLN ** N 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.3132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14531 Z= 0.178 Angle : 0.542 10.636 19663 Z= 0.282 Chirality : 0.042 0.220 2278 Planarity : 0.004 0.056 2496 Dihedral : 4.405 27.468 1936 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.46 % Favored : 97.48 % Rotamer: Outliers : 1.96 % Allowed : 8.49 % Favored : 89.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.20), residues: 1749 helix: 0.96 (0.17), residues: 997 sheet: 0.16 (0.36), residues: 228 loop : -0.38 (0.27), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP M 421 HIS 0.004 0.001 HIS S 85 PHE 0.015 0.001 PHE S 4 TYR 0.015 0.001 TYR A 478 ARG 0.003 0.000 ARG M 163 *********************** 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 209 residues out of total 1587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 178 time to evaluate : 1.762 Fit side-chains revert: symmetry clash REVERT: A 570 LYS cc_start: 0.8461 (mttt) cc_final: 0.8080 (tmtt) REVERT: B 21 GLU cc_start: 0.8486 (pm20) cc_final: 0.8048 (pm20) REVERT: B 83 MET cc_start: 0.8209 (tpp) cc_final: 0.7789 (tpp) REVERT: B 340 ASP cc_start: 0.8769 (t0) cc_final: 0.8230 (m-30) REVERT: B 458 ARG cc_start: 0.8392 (mmt180) cc_final: 0.7636 (ttt180) REVERT: B 463 ASP cc_start: 0.8296 (p0) cc_final: 0.7890 (t0) REVERT: B 527 TRP cc_start: 0.8449 (t-100) cc_final: 0.8046 (t60) REVERT: M 302 GLU cc_start: 0.8190 (pm20) cc_final: 0.7937 (pm20) REVERT: S 55 PHE cc_start: 0.8271 (OUTLIER) cc_final: 0.7793 (p90) REVERT: S 61 ARG cc_start: 0.8578 (ttp-110) cc_final: 0.8189 (ttp80) REVERT: S 93 GLU cc_start: 0.8565 (mm-30) cc_final: 0.8340 (mm-30) REVERT: N 39 GLN cc_start: 0.8228 (mp10) cc_final: 0.7788 (mp10) REVERT: N 134 GLU cc_start: 0.8480 (tm-30) cc_final: 0.8217 (tm-30) outliers start: 31 outliers final: 23 residues processed: 198 average time/residue: 0.2821 time to fit residues: 81.1695 Evaluate side-chains 181 residues out of total 1587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 157 time to evaluate : 1.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 246 ASP Chi-restraints excluded: chain A residue 396 MET Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 462 TRP Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain B residue 404 ASN 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 153 optimal weight: 0.7980 chunk 33 optimal weight: 3.9990 chunk 99 optimal weight: 0.5980 chunk 41 optimal weight: 0.8980 chunk 170 optimal weight: 8.9990 chunk 141 optimal weight: 0.7980 chunk 78 optimal weight: 1.9990 chunk 14 optimal weight: 6.9990 chunk 56 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 chunk 164 optimal weight: 6.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 149 HIS ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 365 GLN N 75 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.3303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14531 Z= 0.165 Angle : 0.526 10.579 19663 Z= 0.273 Chirality : 0.041 0.153 2278 Planarity : 0.004 0.056 2496 Dihedral : 4.249 27.503 1934 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.34 % Allowed : 8.49 % Favored : 89.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.21), residues: 1749 helix: 1.21 (0.17), residues: 999 sheet: 0.22 (0.35), residues: 233 loop : -0.25 (0.28), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP M 421 HIS 0.003 0.001 HIS S 85 PHE 0.017 0.001 PHE A 552 TYR 0.014 0.001 TYR A 478 ARG 0.007 0.000 ARG A 341 *********************** 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 216 residues out of total 1587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 179 time to evaluate : 1.773 Fit side-chains revert: symmetry clash REVERT: A 143 MET cc_start: 0.8567 (mtm) cc_final: 0.8300 (mtm) REVERT: A 282 GLU cc_start: 0.8214 (pm20) cc_final: 0.7998 (pm20) REVERT: A 570 LYS cc_start: 0.8460 (mttt) cc_final: 0.8071 (tmtt) REVERT: B 21 GLU cc_start: 0.8476 (OUTLIER) cc_final: 0.7999 (pm20) REVERT: B 83 MET cc_start: 0.8256 (tpp) cc_final: 0.7860 (tpp) REVERT: B 242 GLU cc_start: 0.8487 (mm-30) cc_final: 0.8279 (mm-30) REVERT: B 340 ASP cc_start: 0.8786 (t0) cc_final: 0.8234 (m-30) REVERT: B 458 ARG cc_start: 0.8436 (mmt180) cc_final: 0.7689 (ttt180) REVERT: B 463 ASP cc_start: 0.8307 (p0) cc_final: 0.7888 (t0) REVERT: B 527 TRP cc_start: 0.8489 (t-100) cc_final: 0.8035 (t60) REVERT: M 85 MET cc_start: 0.8689 (ttp) cc_final: 0.8187 (ttp) REVERT: M 302 GLU cc_start: 0.8198 (pm20) cc_final: 0.7822 (pm20) REVERT: S 43 ASP cc_start: 0.8541 (p0) cc_final: 0.8281 (p0) REVERT: S 55 PHE cc_start: 0.8153 (OUTLIER) cc_final: 0.7512 (p90) REVERT: S 61 ARG cc_start: 0.8602 (ttp-110) cc_final: 0.8376 (ttp80) REVERT: N 39 GLN cc_start: 0.8255 (mp10) cc_final: 0.7870 (mp10) REVERT: N 45 ARG cc_start: 0.7845 (ttp-110) cc_final: 0.7522 (mtm-85) outliers start: 37 outliers final: 30 residues processed: 203 average time/residue: 0.2867 time to fit residues: 84.5904 Evaluate side-chains 194 residues out of total 1587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 162 time to evaluate : 1.803 ------------------------------------------------------------------------------- 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 246 ASP 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 279 MET Chi-restraints excluded: chain B residue 282 LYS Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 404 ASN 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 S residue 13 LYS 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 57 ILE 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 75 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 19 optimal weight: 5.9990 chunk 97 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 96 optimal weight: 0.9990 chunk 143 optimal weight: 5.9990 chunk 95 optimal weight: 3.9990 chunk 169 optimal weight: 4.9990 chunk 106 optimal weight: 0.9990 chunk 103 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 104 optimal weight: 0.9980 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 149 HIS ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.3342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14531 Z= 0.202 Angle : 0.545 10.400 19663 Z= 0.282 Chirality : 0.042 0.192 2278 Planarity : 0.004 0.054 2496 Dihedral : 4.258 27.280 1934 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.53 % Allowed : 8.61 % Favored : 88.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.21), residues: 1749 helix: 1.33 (0.17), residues: 999 sheet: 0.17 (0.35), residues: 244 loop : -0.21 (0.29), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP M 421 HIS 0.004 0.001 HIS S 85 PHE 0.018 0.001 PHE A 552 TYR 0.014 0.001 TYR A 478 ARG 0.007 0.000 ARG N 45 *********************** 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 211 residues out of total 1587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 171 time to evaluate : 1.733 Fit side-chains revert: symmetry clash REVERT: A 570 LYS cc_start: 0.8471 (mttt) cc_final: 0.8078 (tmtt) REVERT: B 21 GLU cc_start: 0.8493 (OUTLIER) cc_final: 0.8006 (pm20) REVERT: B 83 MET cc_start: 0.8272 (tpp) cc_final: 0.7893 (tpp) REVERT: B 340 ASP cc_start: 0.8795 (t0) cc_final: 0.8235 (m-30) REVERT: B 458 ARG cc_start: 0.8568 (mmt180) cc_final: 0.7734 (ttt180) REVERT: B 463 ASP cc_start: 0.8313 (OUTLIER) cc_final: 0.7898 (t0) REVERT: B 527 TRP cc_start: 0.8500 (t-100) cc_final: 0.8028 (t60) REVERT: M 85 MET cc_start: 0.8713 (ttp) cc_final: 0.8253 (ttp) REVERT: M 302 GLU cc_start: 0.8192 (pm20) cc_final: 0.7956 (pm20) REVERT: S 43 ASP cc_start: 0.8529 (p0) cc_final: 0.8323 (p0) REVERT: S 55 PHE cc_start: 0.8237 (OUTLIER) cc_final: 0.7504 (p90) REVERT: S 61 ARG cc_start: 0.8585 (ttp-110) cc_final: 0.8362 (ttp80) REVERT: S 93 GLU cc_start: 0.8630 (mm-30) cc_final: 0.8304 (mm-30) REVERT: N 39 GLN cc_start: 0.8268 (mp10) cc_final: 0.7914 (mp10) REVERT: N 45 ARG cc_start: 0.8077 (ttp-110) cc_final: 0.7691 (mtm-85) outliers start: 40 outliers final: 28 residues processed: 196 average time/residue: 0.2725 time to fit residues: 78.0643 Evaluate side-chains 189 residues out of total 1587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 158 time to evaluate : 1.709 ------------------------------------------------------------------------------- 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 246 ASP Chi-restraints excluded: chain A residue 396 MET Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 462 TRP 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 298 VAL Chi-restraints excluded: chain B residue 404 ASN 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 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 S residue 129 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 67 optimal weight: 0.9980 chunk 101 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 32 optimal weight: 0.6980 chunk 107 optimal weight: 4.9990 chunk 115 optimal weight: 4.9990 chunk 83 optimal weight: 0.8980 chunk 15 optimal weight: 6.9990 chunk 133 optimal weight: 1.9990 chunk 154 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 149 HIS ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.3463 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= 0.167 Angle : 0.535 10.389 19663 Z= 0.278 Chirality : 0.042 0.223 2278 Planarity : 0.004 0.052 2496 Dihedral : 4.209 29.630 1934 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.34 % Favored : 97.60 % Rotamer: Outliers : 2.03 % Allowed : 9.12 % Favored : 88.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.21), residues: 1749 helix: 1.43 (0.17), residues: 1001 sheet: 0.22 (0.35), residues: 240 loop : -0.21 (0.29), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP M 421 HIS 0.004 0.001 HIS S 85 PHE 0.015 0.001 PHE A 552 TYR 0.012 0.001 TYR A 478 ARG 0.008 0.000 ARG A 341 *********************** 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 208 residues out of total 1587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 176 time to evaluate : 1.745 Fit side-chains revert: symmetry clash REVERT: A 570 LYS cc_start: 0.8449 (mttt) cc_final: 0.8039 (tmtt) REVERT: B 21 GLU cc_start: 0.8453 (OUTLIER) cc_final: 0.7962 (pm20) REVERT: B 83 MET cc_start: 0.8287 (tpp) cc_final: 0.7899 (tpp) REVERT: B 340 ASP cc_start: 0.8792 (t0) cc_final: 0.8225 (m-30) REVERT: B 458 ARG cc_start: 0.8572 (mmt180) cc_final: 0.7718 (ttt180) REVERT: B 463 ASP cc_start: 0.8314 (p0) cc_final: 0.7882 (t0) REVERT: B 527 TRP cc_start: 0.8495 (t-100) cc_final: 0.8012 (t60) REVERT: M 85 MET cc_start: 0.8760 (ttp) cc_final: 0.8349 (ttp) REVERT: M 172 GLU cc_start: 0.8279 (pt0) cc_final: 0.7927 (mt-10) REVERT: S 3 ARG cc_start: 0.8131 (mtt180) cc_final: 0.7876 (mtt-85) REVERT: S 55 PHE cc_start: 0.8169 (OUTLIER) cc_final: 0.7314 (p90) REVERT: S 61 ARG cc_start: 0.8571 (ttp-110) cc_final: 0.8351 (ttp80) REVERT: N 39 GLN cc_start: 0.8209 (mp10) cc_final: 0.7884 (mp10) REVERT: N 45 ARG cc_start: 0.8250 (ttp-110) cc_final: 0.7447 (mtm-85) outliers start: 32 outliers final: 27 residues processed: 197 average time/residue: 0.2798 time to fit residues: 79.3454 Evaluate side-chains 191 residues out of total 1587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 162 time to evaluate : 1.723 ------------------------------------------------------------------------------- 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 246 ASP 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 279 MET Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 404 ASN 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 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 57 ILE 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 162 optimal weight: 7.9990 chunk 148 optimal weight: 1.9990 chunk 158 optimal weight: 0.8980 chunk 95 optimal weight: 0.6980 chunk 68 optimal weight: 0.0670 chunk 124 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 142 optimal weight: 2.9990 chunk 149 optimal weight: 1.9990 chunk 157 optimal weight: 0.7980 chunk 103 optimal weight: 1.9990 overall best weight: 0.6920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 149 HIS ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 38 HIS S 8 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.3557 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= 0.159 Angle : 0.528 10.325 19663 Z= 0.273 Chirality : 0.042 0.170 2278 Planarity : 0.003 0.052 2496 Dihedral : 4.159 28.653 1934 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.34 % Allowed : 9.25 % Favored : 88.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.21), residues: 1749 helix: 1.49 (0.17), residues: 995 sheet: 0.22 (0.35), residues: 241 loop : -0.17 (0.28), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP M 421 HIS 0.004 0.001 HIS S 85 PHE 0.020 0.001 PHE A 552 TYR 0.016 0.001 TYR A 478 ARG 0.004 0.000 ARG A 123 *********************** 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 207 residues out of total 1587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 170 time to evaluate : 1.767 Fit side-chains revert: symmetry clash REVERT: A 570 LYS cc_start: 0.8421 (mttt) cc_final: 0.8036 (tmtt) REVERT: B 21 GLU cc_start: 0.8284 (OUTLIER) cc_final: 0.7811 (pm20) REVERT: B 83 MET cc_start: 0.8302 (tpp) cc_final: 0.7734 (tpp) REVERT: B 340 ASP cc_start: 0.8793 (t0) cc_final: 0.8229 (m-30) REVERT: B 458 ARG cc_start: 0.8650 (mmt180) cc_final: 0.7706 (ttt180) REVERT: B 463 ASP cc_start: 0.8316 (OUTLIER) cc_final: 0.7882 (t0) REVERT: B 527 TRP cc_start: 0.8509 (t-100) cc_final: 0.7984 (t60) REVERT: M 85 MET cc_start: 0.8751 (ttp) cc_final: 0.8357 (ttp) REVERT: M 172 GLU cc_start: 0.8254 (pt0) cc_final: 0.7906 (mt-10) REVERT: M 302 GLU cc_start: 0.8181 (pm20) cc_final: 0.7795 (pm20) REVERT: M 367 SER cc_start: 0.9175 (m) cc_final: 0.8949 (t) REVERT: S 3 ARG cc_start: 0.8105 (mtt180) cc_final: 0.7869 (mtt-85) REVERT: S 55 PHE cc_start: 0.8129 (OUTLIER) cc_final: 0.7360 (p90) REVERT: N 34 GLU cc_start: 0.8056 (mp0) cc_final: 0.7764 (mp0) REVERT: N 39 GLN cc_start: 0.8204 (mp10) cc_final: 0.7869 (mp10) REVERT: N 45 ARG cc_start: 0.8211 (ttp-110) cc_final: 0.7711 (mtm-85) outliers start: 37 outliers final: 27 residues processed: 194 average time/residue: 0.2702 time to fit residues: 76.8043 Evaluate side-chains 190 residues out of total 1587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 160 time to evaluate : 1.746 ------------------------------------------------------------------------------- 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 151 ILE 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 404 ASN Chi-restraints excluded: chain B residue 463 ASP 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 S residue 13 LYS 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 57 ILE Chi-restraints excluded: chain S residue 101 LEU Chi-restraints excluded: chain S residue 126 THR Chi-restraints excluded: chain S residue 129 THR 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 167 optimal weight: 8.9990 chunk 102 optimal weight: 0.7980 chunk 79 optimal weight: 2.9990 chunk 116 optimal weight: 0.7980 chunk 175 optimal weight: 3.9990 chunk 161 optimal weight: 3.9990 chunk 139 optimal weight: 6.9990 chunk 14 optimal weight: 7.9990 chunk 107 optimal weight: 5.9990 chunk 85 optimal weight: 0.9990 chunk 110 optimal weight: 4.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 149 HIS ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 77 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.3487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14531 Z= 0.281 Angle : 0.587 9.748 19663 Z= 0.304 Chirality : 0.044 0.171 2278 Planarity : 0.004 0.052 2496 Dihedral : 4.319 28.593 1934 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.09 % Allowed : 9.88 % Favored : 88.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.21), residues: 1749 helix: 1.39 (0.17), residues: 1001 sheet: 0.19 (0.34), residues: 240 loop : -0.24 (0.28), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP M 421 HIS 0.008 0.001 HIS S 85 PHE 0.020 0.002 PHE M 272 TYR 0.018 0.001 TYR A 478 ARG 0.007 0.001 ARG A 341 ********************** 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 194 residues out of total 1587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 161 time to evaluate : 1.740 Fit side-chains revert: symmetry clash REVERT: A 570 LYS cc_start: 0.8475 (mttt) cc_final: 0.8058 (tmtt) REVERT: B 21 GLU cc_start: 0.8454 (OUTLIER) cc_final: 0.8062 (pm20) REVERT: B 83 MET cc_start: 0.8353 (tpp) cc_final: 0.7973 (tpp) REVERT: B 458 ARG cc_start: 0.8713 (mmt180) cc_final: 0.7814 (ttt180) REVERT: B 463 ASP cc_start: 0.8326 (OUTLIER) cc_final: 0.7913 (t0) REVERT: B 527 TRP cc_start: 0.8527 (t-100) cc_final: 0.8065 (t60) REVERT: M 85 MET cc_start: 0.8765 (ttp) cc_final: 0.8393 (ttp) REVERT: M 302 GLU cc_start: 0.8244 (pm20) cc_final: 0.8033 (pm20) REVERT: S 55 PHE cc_start: 0.8386 (OUTLIER) cc_final: 0.7781 (p90) REVERT: N 39 GLN cc_start: 0.8318 (mp10) cc_final: 0.8003 (mp10) REVERT: N 45 ARG cc_start: 0.8285 (ttp-110) cc_final: 0.7755 (mtm110) outliers start: 33 outliers final: 24 residues processed: 182 average time/residue: 0.2725 time to fit residues: 72.5010 Evaluate side-chains 182 residues out of total 1587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 155 time to evaluate : 1.835 ------------------------------------------------------------------------------- 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 404 ASN Chi-restraints excluded: chain B residue 463 ASP 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 272 PHE Chi-restraints excluded: chain M residue 279 THR Chi-restraints excluded: chain S residue 13 LYS 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 77 ASN Chi-restraints excluded: chain S residue 101 LEU Chi-restraints excluded: chain S residue 126 THR Chi-restraints excluded: chain S residue 129 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 148 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 128 optimal weight: 0.3980 chunk 20 optimal weight: 0.6980 chunk 38 optimal weight: 0.7980 chunk 139 optimal weight: 0.8980 chunk 58 optimal weight: 0.0020 chunk 143 optimal weight: 4.9990 chunk 17 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 overall best weight: 0.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 149 HIS ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.106071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.084872 restraints weight = 24925.255| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 2.23 r_work: 0.2906 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2763 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.3473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.154 14531 Z= 0.292 Angle : 0.797 59.122 19663 Z= 0.459 Chirality : 0.048 1.004 2278 Planarity : 0.004 0.055 2496 Dihedral : 4.353 28.510 1934 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.84 % Allowed : 10.32 % Favored : 87.84 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.21), residues: 1749 helix: 1.39 (0.17), residues: 1002 sheet: 0.19 (0.34), residues: 240 loop : -0.23 (0.28), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP M 421 HIS 0.007 0.001 HIS S 85 PHE 0.020 0.002 PHE M 272 TYR 0.015 0.001 TYR A 478 ARG 0.003 0.000 ARG A 123 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3189.68 seconds wall clock time: 59 minutes 30.67 seconds (3570.67 seconds total)