Starting phenix.real_space_refine on Mon Mar 11 10:02:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w8s_32358/03_2024/7w8s_32358.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w8s_32358/03_2024/7w8s_32358.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w8s_32358/03_2024/7w8s_32358.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w8s_32358/03_2024/7w8s_32358.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w8s_32358/03_2024/7w8s_32358.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w8s_32358/03_2024/7w8s_32358.pdb" } resolution = 2.85 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= -0.001 sd= 0.288 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1513 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 37 5.16 5 C 4127 2.51 5 N 1079 2.21 5 O 1211 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 6455 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4899 Classifications: {'peptide': 595} Link IDs: {'PTRANS': 30, 'TRANS': 564} Chain: "B" Number of atoms: 1527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1527 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 11, 'TRANS': 181} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.05, per 1000 atoms: 0.63 Number of scatterers: 6455 At special positions: 0 Unit cell: (76.54, 91.16, 126.42, 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) Zn 1 29.99 S 37 16.00 O 1211 8.00 N 1079 7.00 C 4127 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " NAG-ASN " NAG C 1 " - " ASN A 53 " Time building additional restraints: 2.16 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 801 " pdb="ZN ZN A 801 " - pdb=" NE2 HIS A 374 " pdb="ZN ZN A 801 " - pdb=" NE2 HIS A 378 " 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1486 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 6 sheets defined 53.0% alpha, 5.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing helix chain 'A' and resid 20 through 52 removed outlier: 3.759A pdb=" N LEU A 24 " --> pdb=" O THR A 20 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU A 29 " --> pdb=" O ALA A 25 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU A 30 " --> pdb=" O LYS A 26 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LYS A 31 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N TYR A 34 " --> pdb=" O GLU A 30 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLU A 35 " --> pdb=" O LYS A 31 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLU A 38 " --> pdb=" O TYR A 34 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLN A 42 " --> pdb=" O GLU A 38 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ASN A 43 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASN A 49 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N TYR A 50 " --> pdb=" O ALA A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 77 removed outlier: 3.833A pdb=" N GLN A 60 " --> pdb=" O ASP A 56 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA A 65 " --> pdb=" O LYS A 61 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA A 67 " --> pdb=" O ASN A 63 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS A 68 " --> pdb=" O ILE A 64 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N TRP A 69 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N SER A 70 " --> pdb=" O GLY A 66 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLU A 74 " --> pdb=" O SER A 70 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLU A 75 " --> pdb=" O ALA A 71 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU A 76 " --> pdb=" O PHE A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 83 removed outlier: 3.721A pdb=" N TYR A 83 " --> pdb=" O ALA A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 88 removed outlier: 3.691A pdb=" N GLU A 87 " --> pdb=" O PRO A 84 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ILE A 88 " --> pdb=" O LEU A 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 84 through 88' Processing helix chain 'A' and resid 90 through 98 removed outlier: 3.628A pdb=" N GLN A 96 " --> pdb=" O ILE A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 108 removed outlier: 4.048A pdb=" N VAL A 107 " --> pdb=" O GLY A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 130 removed outlier: 3.548A pdb=" N ARG A 115 " --> pdb=" O ASP A 111 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASN A 117 " --> pdb=" O ARG A 113 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N SER A 124 " --> pdb=" O LEU A 120 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N THR A 125 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE A 126 " --> pdb=" O ALA A 122 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N TYR A 127 " --> pdb=" O MET A 123 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER A 128 " --> pdb=" O SER A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 155 removed outlier: 3.831A pdb=" N MET A 152 " --> pdb=" O LEU A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 172 removed outlier: 3.906A pdb=" N TRP A 163 " --> pdb=" O ASN A 159 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ALA A 164 " --> pdb=" O GLU A 160 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TRP A 165 " --> pdb=" O ARG A 161 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N TRP A 168 " --> pdb=" O ALA A 164 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ARG A 169 " --> pdb=" O TRP A 165 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU A 171 " --> pdb=" O GLY A 167 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL A 172 " --> pdb=" O TRP A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 193 removed outlier: 3.701A pdb=" N GLU A 181 " --> pdb=" O ARG A 177 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N GLU A 182 " --> pdb=" O PRO A 178 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ARG A 192 " --> pdb=" O ASN A 188 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA A 193 " --> pdb=" O GLU A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 204 removed outlier: 3.526A pdb=" N ARG A 204 " --> pdb=" O GLY A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 207 No H-bonds generated for 'chain 'A' and resid 205 through 207' Processing helix chain 'A' and resid 220 through 231 removed outlier: 3.912A pdb=" N GLU A 224 " --> pdb=" O ASN A 220 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N THR A 231 " --> pdb=" O GLU A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 252 removed outlier: 3.628A pdb=" N HIS A 239 " --> pdb=" O PRO A 235 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N ASP A 250 " --> pdb=" O ALA A 246 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ALA A 251 " --> pdb=" O LYS A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 282 removed outlier: 3.697A pdb=" N LEU A 278 " --> pdb=" O TRP A 275 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N TYR A 279 " --> pdb=" O THR A 276 " (cutoff:3.500A) Proline residue: A 280 - end of helix No H-bonds generated for 'chain 'A' and resid 275 through 282' Processing helix chain 'A' and resid 295 through 300 Processing helix chain 'A' and resid 303 through 319 removed outlier: 3.701A pdb=" N PHE A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLU A 312 " --> pdb=" O PHE A 308 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE A 314 " --> pdb=" O GLU A 310 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N PHE A 315 " --> pdb=" O ALA A 311 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER A 317 " --> pdb=" O LYS A 313 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL A 318 " --> pdb=" O PHE A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 331 removed outlier: 4.131A pdb=" N TRP A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLN A 329 " --> pdb=" O GLU A 325 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER A 331 " --> pdb=" O PHE A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 383 removed outlier: 3.571A pdb=" N ALA A 372 " --> pdb=" O ASP A 368 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N HIS A 373 " --> pdb=" O PHE A 369 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N HIS A 378 " --> pdb=" O HIS A 374 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE A 379 " --> pdb=" O GLU A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 393 removed outlier: 4.083A pdb=" N ARG A 393 " --> pdb=" O PHE A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 412 removed outlier: 3.770A pdb=" N ALA A 403 " --> pdb=" O GLY A 399 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL A 404 " --> pdb=" O PHE A 400 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLY A 405 " --> pdb=" O HIS A 401 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ILE A 407 " --> pdb=" O ALA A 403 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N SER A 409 " --> pdb=" O GLY A 405 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU A 410 " --> pdb=" O GLU A 406 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N SER A 411 " --> pdb=" O ILE A 407 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ALA A 412 " --> pdb=" O MET A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 420 removed outlier: 3.677A pdb=" N ASN A 420 " --> pdb=" O ASN A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 444 removed outlier: 3.518A pdb=" N PHE A 438 " --> pdb=" O THR A 434 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LYS A 441 " --> pdb=" O ASN A 437 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLN A 442 " --> pdb=" O PHE A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 448 No H-bonds generated for 'chain 'A' and resid 446 through 448' Processing helix chain 'A' and resid 449 through 464 removed outlier: 3.607A pdb=" N GLU A 457 " --> pdb=" O THR A 453 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS A 458 " --> pdb=" O TYR A 454 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TRP A 459 " --> pdb=" O MET A 455 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG A 460 " --> pdb=" O LEU A 456 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N MET A 462 " --> pdb=" O LYS A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 471 No H-bonds generated for 'chain 'A' and resid 469 through 471' Processing helix chain 'A' and resid 472 through 484 removed outlier: 3.733A pdb=" N LYS A 476 " --> pdb=" O GLN A 472 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N TRP A 477 " --> pdb=" O TRP A 473 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N TRP A 478 " --> pdb=" O MET A 474 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLU A 479 " --> pdb=" O GLN A 475 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N MET A 480 " --> pdb=" O LYS A 476 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS A 481 " --> pdb=" O TRP A 477 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ARG A 482 " --> pdb=" O TRP A 478 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASP A 483 " --> pdb=" O GLU A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 502 removed outlier: 3.521A pdb=" N ALA A 502 " --> pdb=" O ASP A 499 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 499 through 502' Processing helix chain 'A' and resid 503 through 508 removed outlier: 3.528A pdb=" N ALA A 507 " --> pdb=" O LEU A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 533 removed outlier: 3.715A pdb=" N THR A 517 " --> pdb=" O ILE A 513 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ARG A 518 " --> pdb=" O ARG A 514 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N THR A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ILE A 520 " --> pdb=" O TYR A 516 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLN A 524 " --> pdb=" O ILE A 520 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE A 525 " --> pdb=" O TYR A 521 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N CYS A 530 " --> pdb=" O GLN A 526 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N GLN A 531 " --> pdb=" O GLU A 527 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ILE A 532 " --> pdb=" O ALA A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 removed outlier: 3.572A pdb=" N LYS A 541 " --> pdb=" O PRO A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 559 removed outlier: 3.559A pdb=" N GLN A 552 " --> pdb=" O ARG A 548 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LYS A 553 " --> pdb=" O GLU A 549 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU A 554 " --> pdb=" O ALA A 550 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLU A 556 " --> pdb=" O GLN A 552 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N SER A 559 " --> pdb=" O HIS A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 572 removed outlier: 3.829A pdb=" N GLU A 571 " --> pdb=" O THR A 567 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ARG A 572 " --> pdb=" O PHE A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 588 removed outlier: 3.537A pdb=" N TYR A 587 " --> pdb=" O PRO A 583 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N PHE A 588 " --> pdb=" O LEU A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 599 removed outlier: 3.511A pdb=" N TRP A 594 " --> pdb=" O PRO A 590 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU A 597 " --> pdb=" O THR A 593 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 364 through 370 removed outlier: 4.291A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 502 through 505 Processing sheet with id=AA1, first strand: chain 'A' and resid 132 through 133 Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 263 removed outlier: 6.090A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 347 through 350 Processing sheet with id=AA4, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.061A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N TYR B 396 " --> pdb=" O SER B 514 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA B 435 " --> pdb=" O THR B 376 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N THR B 376 " --> pdb=" O ALA B 435 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 452 through 453 Processing sheet with id=AA6, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.637A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) 179 hydrogen bonds defined for protein. 501 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: 1.58 Time building geometry restraints manager: 2.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2071 1.35 - 1.46: 1709 1.46 - 1.58: 2803 1.58 - 1.70: 0 1.70 - 1.82: 58 Bond restraints: 6641 Sorted by residual: bond pdb=" C1 NAG C 2 " pdb=" O5 NAG C 2 " ideal model delta sigma weight residual 1.406 1.445 -0.039 2.00e-02 2.50e+03 3.80e+00 bond pdb=" C1 NAG C 1 " pdb=" O5 NAG C 1 " ideal model delta sigma weight residual 1.406 1.445 -0.039 2.00e-02 2.50e+03 3.78e+00 bond pdb=" C GLU A 145 " pdb=" N PRO A 146 " ideal model delta sigma weight residual 1.334 1.372 -0.038 2.34e-02 1.83e+03 2.69e+00 bond pdb=" C LYS A 234 " pdb=" N PRO A 235 " ideal model delta sigma weight residual 1.335 1.352 -0.017 1.28e-02 6.10e+03 1.75e+00 bond pdb=" C TYR A 279 " pdb=" N PRO A 280 " ideal model delta sigma weight residual 1.337 1.351 -0.014 1.11e-02 8.12e+03 1.66e+00 ... (remaining 6636 not shown) Histogram of bond angle deviations from ideal: 100.41 - 107.14: 235 107.14 - 113.86: 3426 113.86 - 120.59: 2780 120.59 - 127.32: 2495 127.32 - 134.04: 87 Bond angle restraints: 9023 Sorted by residual: angle pdb=" C ILE A 233 " pdb=" N LYS A 234 " pdb=" CA LYS A 234 " ideal model delta sigma weight residual 120.09 124.32 -4.23 1.25e+00 6.40e-01 1.15e+01 angle pdb=" N ARG A 582 " pdb=" CA ARG A 582 " pdb=" C ARG A 582 " ideal model delta sigma weight residual 109.81 116.21 -6.40 2.21e+00 2.05e-01 8.38e+00 angle pdb=" N ASP A 499 " pdb=" CA ASP A 499 " pdb=" C ASP A 499 " ideal model delta sigma weight residual 109.81 115.94 -6.13 2.21e+00 2.05e-01 7.70e+00 angle pdb=" CA ARG A 582 " pdb=" C ARG A 582 " pdb=" N PRO A 583 " ideal model delta sigma weight residual 118.44 122.79 -4.35 1.59e+00 3.96e-01 7.47e+00 angle pdb=" CA LEU A 450 " pdb=" C LEU A 450 " pdb=" N PRO A 451 " ideal model delta sigma weight residual 118.44 122.34 -3.90 1.59e+00 3.96e-01 6.03e+00 ... (remaining 9018 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 3712 17.84 - 35.68: 205 35.68 - 53.52: 31 53.52 - 71.36: 5 71.36 - 89.20: 2 Dihedral angle restraints: 3955 sinusoidal: 1639 harmonic: 2316 Sorted by residual: dihedral pdb=" CA CYS B 336 " pdb=" CB CYS B 336 " pdb=" SG CYS B 336 " pdb=" SG CYS B 361 " ideal model delta sinusoidal sigma weight residual 79.00 22.27 56.73 1 2.00e+01 2.50e-03 1.08e+01 dihedral pdb=" CA TYR A 497 " pdb=" C TYR A 497 " pdb=" N CYS A 498 " pdb=" CA CYS A 498 " ideal model delta harmonic sigma weight residual 180.00 164.65 15.35 0 5.00e+00 4.00e-02 9.42e+00 dihedral pdb=" N LEU A 570 " pdb=" CA LEU A 570 " pdb=" CB LEU A 570 " pdb=" CG LEU A 570 " ideal model delta sinusoidal sigma weight residual -180.00 -125.17 -54.83 3 1.50e+01 4.44e-03 9.31e+00 ... (remaining 3952 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 536 0.033 - 0.065: 294 0.065 - 0.098: 59 0.098 - 0.131: 39 0.131 - 0.163: 7 Chirality restraints: 935 Sorted by residual: chirality pdb=" CA GLU A 145 " pdb=" N GLU A 145 " pdb=" C GLU A 145 " pdb=" CB GLU A 145 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.68e-01 chirality pdb=" CA TYR A 279 " pdb=" N TYR A 279 " pdb=" C TYR A 279 " pdb=" CB TYR A 279 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.55e-01 chirality pdb=" CA ARG A 177 " pdb=" N ARG A 177 " pdb=" C ARG A 177 " pdb=" CB ARG A 177 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.99e-01 ... (remaining 932 not shown) Planarity restraints: 1173 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 582 " -0.042 5.00e-02 4.00e+02 6.36e-02 6.47e+00 pdb=" N PRO A 583 " 0.110 5.00e-02 4.00e+02 pdb=" CA PRO A 583 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 583 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS B 336 " 0.036 5.00e-02 4.00e+02 5.44e-02 4.73e+00 pdb=" N PRO B 337 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO B 337 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 337 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 520 " 0.034 5.00e-02 4.00e+02 5.09e-02 4.14e+00 pdb=" N PRO B 521 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO B 521 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 521 " 0.028 5.00e-02 4.00e+02 ... (remaining 1170 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 40 2.66 - 3.22: 5074 3.22 - 3.78: 8522 3.78 - 4.34: 12521 4.34 - 4.90: 20834 Nonbonded interactions: 46991 Sorted by model distance: nonbonded pdb=" OE1 GLU A 402 " pdb="ZN ZN A 801 " model vdw 2.102 2.230 nonbonded pdb=" OH TYR A 183 " pdb=" OD1 ASP A 509 " model vdw 2.307 2.440 nonbonded pdb=" O THR A 125 " pdb=" OG1 THR A 129 " model vdw 2.316 2.440 nonbonded pdb=" OH TYR A 217 " pdb=" OD2 ASP A 225 " model vdw 2.374 2.440 nonbonded pdb=" OG SER A 170 " pdb=" OE1 GLU A 171 " model vdw 2.388 2.440 ... (remaining 46986 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 1.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.000 Extract box with map and model: 7.350 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 21.660 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 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:11.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 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 : 0.003 0.047 6641 Z= 0.193 Angle : 0.597 7.497 9023 Z= 0.321 Chirality : 0.045 0.163 935 Planarity : 0.007 0.064 1172 Dihedral : 11.074 89.201 2448 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 0.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 3.48 % Allowed : 3.77 % Favored : 92.75 % 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: -4.03 (0.24), residues: 784 helix: -4.51 (0.10), residues: 307 sheet: 1.25 (0.91), residues: 41 loop : -1.60 (0.26), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 163 HIS 0.006 0.001 HIS A 241 PHE 0.014 0.001 PHE B 453 TYR 0.021 0.001 TYR A 385 ARG 0.002 0.000 ARG B 509 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 107 time to evaluate : 0.807 Fit side-chains REVERT: A 89 GLN cc_start: 0.6046 (mp10) cc_final: 0.5703 (mp10) REVERT: A 92 ILE cc_start: 0.6990 (mm) cc_final: 0.6764 (mp) REVERT: A 383 MET cc_start: 0.8283 (mtp) cc_final: 0.7935 (mtm) REVERT: A 580 ASP cc_start: 0.7721 (t0) cc_final: 0.7240 (t0) REVERT: B 356 LYS cc_start: 0.7695 (ttmt) cc_final: 0.6962 (tttp) outliers start: 24 outliers final: 5 residues processed: 124 average time/residue: 1.2393 time to fit residues: 161.2874 Evaluate side-chains 87 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 82 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 395 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 32 optimal weight: 8.9990 chunk 20 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 61 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 37 optimal weight: 0.0010 chunk 45 optimal weight: 0.0070 chunk 70 optimal weight: 4.9990 overall best weight: 1.1808 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 ASN A 420 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.1627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6641 Z= 0.208 Angle : 0.583 6.359 9023 Z= 0.310 Chirality : 0.043 0.132 935 Planarity : 0.006 0.044 1172 Dihedral : 5.368 48.566 914 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 1.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.61 % Allowed : 9.86 % Favored : 87.54 % 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: -3.11 (0.25), residues: 784 helix: -2.81 (0.20), residues: 343 sheet: 1.66 (1.00), residues: 36 loop : -1.66 (0.27), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 163 HIS 0.008 0.001 HIS A 241 PHE 0.018 0.002 PHE A 28 TYR 0.020 0.002 TYR A 385 ARG 0.003 0.000 ARG B 408 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 77 time to evaluate : 0.707 Fit side-chains REVERT: A 89 GLN cc_start: 0.5884 (mp10) cc_final: 0.5558 (mp10) REVERT: A 323 MET cc_start: 0.8467 (mmp) cc_final: 0.8170 (mmt) REVERT: A 383 MET cc_start: 0.8176 (mtp) cc_final: 0.7972 (mtm) REVERT: A 580 ASP cc_start: 0.7584 (t0) cc_final: 0.7202 (t0) REVERT: B 395 VAL cc_start: 0.7469 (OUTLIER) cc_final: 0.7178 (t) outliers start: 18 outliers final: 9 residues processed: 91 average time/residue: 1.1135 time to fit residues: 107.3384 Evaluate side-chains 81 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 71 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 503 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 39 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 chunk 58 optimal weight: 0.0980 chunk 48 optimal weight: 0.2980 chunk 19 optimal weight: 4.9990 chunk 70 optimal weight: 4.9990 chunk 76 optimal weight: 6.9990 chunk 63 optimal weight: 4.9990 chunk 24 optimal weight: 0.7980 chunk 56 optimal weight: 0.8980 chunk 53 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN A 322 ASN A 401 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 6641 Z= 0.139 Angle : 0.473 4.785 9023 Z= 0.249 Chirality : 0.041 0.132 935 Planarity : 0.004 0.040 1172 Dihedral : 4.839 42.784 913 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 1.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.61 % Allowed : 10.58 % Favored : 86.81 % 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: -2.38 (0.27), residues: 784 helix: -1.87 (0.25), residues: 345 sheet: 1.41 (1.01), residues: 36 loop : -1.54 (0.27), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 163 HIS 0.006 0.001 HIS A 241 PHE 0.015 0.001 PHE B 377 TYR 0.012 0.001 TYR A 385 ARG 0.001 0.000 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 75 time to evaluate : 0.804 Fit side-chains REVERT: A 89 GLN cc_start: 0.5800 (mp10) cc_final: 0.5511 (mp10) REVERT: A 323 MET cc_start: 0.8406 (mmp) cc_final: 0.8053 (mmt) REVERT: B 395 VAL cc_start: 0.7507 (OUTLIER) cc_final: 0.7266 (t) outliers start: 18 outliers final: 11 residues processed: 86 average time/residue: 1.2052 time to fit residues: 109.4569 Evaluate side-chains 83 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 71 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 483 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 36 optimal weight: 0.8980 chunk 7 optimal weight: 0.0980 chunk 33 optimal weight: 0.0870 chunk 47 optimal weight: 3.9990 chunk 71 optimal weight: 0.0670 chunk 75 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 67 optimal weight: 0.6980 chunk 20 optimal weight: 4.9990 chunk 62 optimal weight: 10.0000 chunk 42 optimal weight: 2.9990 overall best weight: 0.3696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 ASN A 586 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.2183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6641 Z= 0.114 Angle : 0.427 4.806 9023 Z= 0.223 Chirality : 0.040 0.134 935 Planarity : 0.004 0.039 1172 Dihedral : 4.347 33.204 913 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 2.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.46 % Allowed : 11.59 % Favored : 85.94 % 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: -1.79 (0.28), residues: 784 helix: -1.18 (0.27), residues: 345 sheet: 1.32 (0.99), residues: 36 loop : -1.38 (0.28), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 163 HIS 0.004 0.001 HIS A 241 PHE 0.010 0.001 PHE A 28 TYR 0.009 0.001 TYR B 396 ARG 0.001 0.000 ARG A 548 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 79 time to evaluate : 0.799 Fit side-chains REVERT: A 89 GLN cc_start: 0.5684 (mp10) cc_final: 0.5380 (mp10) REVERT: A 233 ILE cc_start: 0.7424 (OUTLIER) cc_final: 0.7174 (pt) REVERT: B 465 GLU cc_start: 0.7749 (tt0) cc_final: 0.7222 (tm-30) REVERT: B 513 LEU cc_start: 0.7989 (mt) cc_final: 0.7725 (mp) outliers start: 17 outliers final: 8 residues processed: 90 average time/residue: 1.2041 time to fit residues: 113.9264 Evaluate side-chains 78 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 69 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 503 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 1 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 64 optimal weight: 10.0000 chunk 52 optimal weight: 0.7980 chunk 0 optimal weight: 0.5980 chunk 38 optimal weight: 0.3980 chunk 67 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 6641 Z= 0.140 Angle : 0.465 4.796 9023 Z= 0.242 Chirality : 0.041 0.131 935 Planarity : 0.004 0.038 1172 Dihedral : 4.156 30.959 912 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 1.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.75 % Allowed : 12.61 % Favored : 84.64 % 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: -1.52 (0.28), residues: 784 helix: -0.80 (0.28), residues: 344 sheet: 1.41 (1.00), residues: 36 loop : -1.40 (0.27), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 163 HIS 0.006 0.001 HIS A 241 PHE 0.015 0.001 PHE A 28 TYR 0.014 0.001 TYR A 385 ARG 0.002 0.000 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 70 time to evaluate : 0.858 Fit side-chains REVERT: A 89 GLN cc_start: 0.5783 (mp10) cc_final: 0.5480 (mp10) REVERT: A 323 MET cc_start: 0.8360 (mmp) cc_final: 0.7968 (mmt) REVERT: B 465 GLU cc_start: 0.7698 (tt0) cc_final: 0.7149 (tm-30) outliers start: 19 outliers final: 14 residues processed: 83 average time/residue: 1.3785 time to fit residues: 120.6075 Evaluate side-chains 82 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 68 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 522 GLN Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 503 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 44 optimal weight: 0.9980 chunk 18 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 chunk 34 optimal weight: 5.9990 chunk 6 optimal weight: 0.5980 chunk 24 optimal weight: 5.9990 chunk 39 optimal weight: 0.4980 chunk 72 optimal weight: 3.9990 chunk 8 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6641 Z= 0.272 Angle : 0.628 7.790 9023 Z= 0.329 Chirality : 0.046 0.131 935 Planarity : 0.005 0.040 1172 Dihedral : 4.704 37.405 911 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 3.77 % Allowed : 12.32 % Favored : 83.91 % 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: -1.87 (0.27), residues: 784 helix: -0.96 (0.28), residues: 337 sheet: 1.37 (0.99), residues: 36 loop : -1.73 (0.26), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 163 HIS 0.011 0.002 HIS A 241 PHE 0.021 0.002 PHE A 28 TYR 0.022 0.002 TYR A 385 ARG 0.004 0.001 ARG B 509 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 68 time to evaluate : 0.933 Fit side-chains REVERT: A 89 GLN cc_start: 0.5867 (mp10) cc_final: 0.5508 (mp10) REVERT: A 323 MET cc_start: 0.8394 (mmp) cc_final: 0.8132 (mmp) REVERT: B 465 GLU cc_start: 0.7685 (tt0) cc_final: 0.7073 (tm-30) outliers start: 26 outliers final: 17 residues processed: 88 average time/residue: 1.2482 time to fit residues: 115.5879 Evaluate side-chains 85 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 68 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 522 GLN Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 503 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 55 optimal weight: 0.1980 chunk 42 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 47 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 46 optimal weight: 0.6980 chunk 30 optimal weight: 0.2980 chunk 44 optimal weight: 0.5980 chunk 22 optimal weight: 2.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 ASN A 401 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.2348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.074 6641 Z= 0.156 Angle : 0.517 19.410 9023 Z= 0.268 Chirality : 0.043 0.291 935 Planarity : 0.004 0.038 1172 Dihedral : 4.284 31.681 911 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 2.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.17 % Allowed : 14.06 % Favored : 83.77 % 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: -1.51 (0.28), residues: 784 helix: -0.58 (0.29), residues: 338 sheet: 1.34 (0.98), residues: 36 loop : -1.58 (0.26), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 163 HIS 0.005 0.001 HIS A 241 PHE 0.011 0.001 PHE A 28 TYR 0.010 0.001 TYR B 495 ARG 0.001 0.000 ARG A 192 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 74 time to evaluate : 0.781 Fit side-chains REVERT: A 89 GLN cc_start: 0.5726 (mp10) cc_final: 0.5413 (mp10) REVERT: A 121 ASN cc_start: 0.7528 (m-40) cc_final: 0.7319 (t0) REVERT: A 323 MET cc_start: 0.8370 (mmp) cc_final: 0.8040 (mmp) REVERT: B 465 GLU cc_start: 0.7704 (tt0) cc_final: 0.7104 (tm-30) REVERT: B 513 LEU cc_start: 0.7970 (mt) cc_final: 0.7739 (mp) outliers start: 15 outliers final: 12 residues processed: 86 average time/residue: 1.2789 time to fit residues: 115.7316 Evaluate side-chains 81 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 69 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 483 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 14 optimal weight: 2.9990 chunk 47 optimal weight: 0.6980 chunk 51 optimal weight: 0.0770 chunk 37 optimal weight: 0.0030 chunk 7 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 chunk 72 optimal weight: 3.9990 chunk 65 optimal weight: 0.8980 chunk 70 optimal weight: 0.0470 chunk 42 optimal weight: 2.9990 overall best weight: 0.3446 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.2462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 6641 Z= 0.131 Angle : 0.483 18.977 9023 Z= 0.248 Chirality : 0.041 0.261 935 Planarity : 0.004 0.038 1172 Dihedral : 3.933 32.156 911 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 2.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.74 % Allowed : 15.07 % Favored : 83.19 % 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 (0.29), residues: 784 helix: -0.17 (0.29), residues: 339 sheet: 1.74 (1.00), residues: 36 loop : -1.40 (0.27), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 163 HIS 0.004 0.001 HIS A 241 PHE 0.010 0.001 PHE B 377 TYR 0.009 0.001 TYR B 351 ARG 0.002 0.000 ARG A 548 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 70 time to evaluate : 0.764 Fit side-chains REVERT: A 89 GLN cc_start: 0.5747 (mp10) cc_final: 0.5421 (mp10) REVERT: B 465 GLU cc_start: 0.7698 (tt0) cc_final: 0.7092 (tm-30) REVERT: B 513 LEU cc_start: 0.7991 (mt) cc_final: 0.7780 (mp) outliers start: 12 outliers final: 10 residues processed: 80 average time/residue: 1.4234 time to fit residues: 119.7983 Evaluate side-chains 76 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 66 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 503 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 30 optimal weight: 2.9990 chunk 55 optimal weight: 0.3980 chunk 21 optimal weight: 0.0370 chunk 63 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 45 optimal weight: 0.4980 chunk 35 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 ASN A 194 ASN A 322 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.2488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 6641 Z= 0.135 Angle : 0.490 18.242 9023 Z= 0.252 Chirality : 0.042 0.241 935 Planarity : 0.004 0.037 1172 Dihedral : 3.902 31.815 911 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 2.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.88 % Allowed : 15.22 % Favored : 82.90 % 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: -0.97 (0.29), residues: 784 helix: -0.04 (0.29), residues: 338 sheet: 1.64 (0.98), residues: 36 loop : -1.39 (0.27), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 163 HIS 0.005 0.001 HIS A 241 PHE 0.012 0.001 PHE A 28 TYR 0.010 0.001 TYR A 385 ARG 0.001 0.000 ARG B 509 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 67 time to evaluate : 0.784 Fit side-chains REVERT: A 89 GLN cc_start: 0.5755 (mp10) cc_final: 0.5436 (mp10) REVERT: B 465 GLU cc_start: 0.7682 (tt0) cc_final: 0.7105 (tm-30) REVERT: B 513 LEU cc_start: 0.7972 (mt) cc_final: 0.7763 (mp) outliers start: 13 outliers final: 10 residues processed: 78 average time/residue: 1.2779 time to fit residues: 104.7738 Evaluate side-chains 78 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 68 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 503 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 77 optimal weight: 0.9990 chunk 71 optimal weight: 0.1980 chunk 61 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 37 optimal weight: 0.0370 chunk 49 optimal weight: 4.9990 chunk 65 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 9 optimal weight: 0.6980 overall best weight: 0.4658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 ASN A 322 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.2551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 6641 Z= 0.132 Angle : 0.480 17.603 9023 Z= 0.247 Chirality : 0.041 0.231 935 Planarity : 0.004 0.037 1172 Dihedral : 3.830 32.004 911 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 2.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.88 % Allowed : 15.07 % Favored : 83.04 % 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: -0.82 (0.29), residues: 784 helix: 0.14 (0.30), residues: 335 sheet: 1.53 (1.01), residues: 35 loop : -1.32 (0.27), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 163 HIS 0.005 0.001 HIS A 241 PHE 0.011 0.001 PHE A 28 TYR 0.009 0.001 TYR A 385 ARG 0.001 0.000 ARG A 273 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 69 time to evaluate : 0.695 Fit side-chains REVERT: A 89 GLN cc_start: 0.5747 (mp10) cc_final: 0.5432 (mp10) REVERT: B 465 GLU cc_start: 0.7680 (tt0) cc_final: 0.7105 (tm-30) REVERT: B 513 LEU cc_start: 0.7979 (mt) cc_final: 0.7752 (mp) outliers start: 13 outliers final: 11 residues processed: 81 average time/residue: 1.1994 time to fit residues: 102.3875 Evaluate side-chains 78 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 67 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 503 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 0.9980 chunk 61 optimal weight: 7.9990 chunk 25 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 54 optimal weight: 0.8980 chunk 3 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 chunk 70 optimal weight: 0.0060 chunk 41 optimal weight: 1.9990 overall best weight: 0.9800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 ASN A 322 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.164287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.135554 restraints weight = 6903.596| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 1.75 r_work: 0.3477 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3383 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 6641 Z= 0.185 Angle : 0.547 17.498 9023 Z= 0.284 Chirality : 0.044 0.239 935 Planarity : 0.004 0.037 1172 Dihedral : 4.150 30.208 911 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.03 % Allowed : 15.07 % Favored : 82.90 % 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: -1.01 (0.29), residues: 784 helix: -0.05 (0.29), residues: 336 sheet: 1.53 (1.01), residues: 35 loop : -1.41 (0.27), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 163 HIS 0.007 0.001 HIS A 241 PHE 0.016 0.001 PHE A 28 TYR 0.015 0.001 TYR A 385 ARG 0.002 0.000 ARG B 509 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2771.08 seconds wall clock time: 49 minutes 43.42 seconds (2983.42 seconds total)