Starting phenix.real_space_refine on Sun Nov 17 11:43:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fx4_29523/11_2024/8fx4_29523.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fx4_29523/11_2024/8fx4_29523.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fx4_29523/11_2024/8fx4_29523.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fx4_29523/11_2024/8fx4_29523.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fx4_29523/11_2024/8fx4_29523.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fx4_29523/11_2024/8fx4_29523.cif" } resolution = 3.9 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= 0.002 sd= 0.034 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 6 5.49 5 S 68 5.16 5 C 8530 2.51 5 N 2271 2.21 5 O 2599 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 13474 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 623, 5039 Classifications: {'peptide': 623} Link IDs: {'PTRANS': 17, 'TRANS': 605} Chain breaks: 1 Chain: "B" Number of atoms: 5011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 619, 5011 Classifications: {'peptide': 619} Link IDs: {'PTRANS': 17, 'TRANS': 601} Chain breaks: 2 Chain: "C" Number of atoms: 1699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1699 Classifications: {'peptide': 200} Link IDs: {'PTRANS': 4, 'TRANS': 195} Chain breaks: 5 Chain: "D" Number of atoms: 1663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1663 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 8, 'TRANS': 194} Chain breaks: 1 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.88, per 1000 atoms: 0.58 Number of scatterers: 13474 At special positions: 0 Unit cell: (99.4671, 130.806, 138.981, 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 68 16.00 P 6 15.00 O 2599 8.00 N 2271 7.00 C 8530 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: 3.13 Conformation dependent library (CDL) restraints added in 1.7 seconds 3238 Ramachandran restraints generated. 1619 Oldfield, 0 Emsley, 1619 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3146 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 14 sheets defined 47.3% alpha, 10.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.51 Creating SS restraints... Processing helix chain 'A' and resid 21 through 31 Processing helix chain 'A' and resid 37 through 61 removed outlier: 4.228A pdb=" N ARG A 41 " --> pdb=" O GLU A 37 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU A 43 " --> pdb=" O PHE A 39 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N SER A 48 " --> pdb=" O ILE A 44 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASP A 49 " --> pdb=" O SER A 45 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N ALA A 50 " --> pdb=" O ASN A 46 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N THR A 60 " --> pdb=" O TYR A 56 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ASP A 61 " --> pdb=" O GLU A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 67 removed outlier: 3.591A pdb=" N ASP A 66 " --> pdb=" O SER A 63 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N SER A 67 " --> pdb=" O LYS A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 101 Processing helix chain 'A' and resid 108 through 117 removed outlier: 3.731A pdb=" N ALA A 112 " --> pdb=" O SER A 108 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU A 117 " --> pdb=" O PHE A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 138 Processing helix chain 'A' and resid 188 through 193 removed outlier: 4.263A pdb=" N GLU A 191 " --> pdb=" O ASP A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 203 removed outlier: 4.219A pdb=" N VAL A 198 " --> pdb=" O GLU A 194 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LYS A 199 " --> pdb=" O GLU A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 309 Processing helix chain 'A' and resid 400 through 420 removed outlier: 4.326A pdb=" N ILE A 404 " --> pdb=" O ILE A 400 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N ARG A 405 " --> pdb=" O LEU A 401 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N LYS A 406 " --> pdb=" O LYS A 402 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ASN A 407 " --> pdb=" O VAL A 403 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LYS A 410 " --> pdb=" O LYS A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 444 removed outlier: 6.552A pdb=" N LYS A 435 " --> pdb=" O GLU A 431 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N ASN A 436 " --> pdb=" O ALA A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 452 Processing helix chain 'A' and resid 469 through 475 Processing helix chain 'A' and resid 490 through 496 removed outlier: 3.885A pdb=" N VAL A 494 " --> pdb=" O SER A 490 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ASN A 496 " --> pdb=" O GLU A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 507 Processing helix chain 'A' and resid 515 through 525 removed outlier: 3.884A pdb=" N GLN A 523 " --> pdb=" O GLU A 519 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N GLN A 524 " --> pdb=" O TYR A 520 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU A 525 " --> pdb=" O CYS A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 570 removed outlier: 3.729A pdb=" N LYS A 550 " --> pdb=" O ASP A 546 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLU A 561 " --> pdb=" O LYS A 557 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N ASN A 562 " --> pdb=" O ALA A 558 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N LEU A 563 " --> pdb=" O LYS A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 607 Processing helix chain 'A' and resid 615 through 621 Processing helix chain 'A' and resid 632 through 645 Processing helix chain 'A' and resid 649 through 667 removed outlier: 3.959A pdb=" N GLY A 667 " --> pdb=" O LEU A 663 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 688 removed outlier: 4.502A pdb=" N HIS A 676 " --> pdb=" O ASP A 672 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 31 removed outlier: 3.699A pdb=" N SER B 26 " --> pdb=" O ALA B 22 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ILE B 29 " --> pdb=" O MET B 25 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N THR B 31 " --> pdb=" O LEU B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 61 removed outlier: 3.758A pdb=" N LEU B 59 " --> pdb=" O ARG B 55 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N THR B 60 " --> pdb=" O TYR B 56 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ASP B 61 " --> pdb=" O GLU B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 66 Processing helix chain 'B' and resid 94 through 101 removed outlier: 3.724A pdb=" N ASN B 100 " --> pdb=" O ALA B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 117 removed outlier: 4.041A pdb=" N ALA B 112 " --> pdb=" O SER B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 140 removed outlier: 3.879A pdb=" N VAL B 139 " --> pdb=" O ALA B 136 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ALA B 140 " --> pdb=" O TYR B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 193 removed outlier: 3.584A pdb=" N TYR B 192 " --> pdb=" O GLN B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 206 removed outlier: 3.604A pdb=" N VAL B 198 " --> pdb=" O GLU B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 310 Processing helix chain 'B' and resid 371 through 375 Processing helix chain 'B' and resid 398 through 419 removed outlier: 3.714A pdb=" N LYS B 402 " --> pdb=" O SER B 398 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL B 403 " --> pdb=" O LYS B 399 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ILE B 404 " --> pdb=" O ILE B 400 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ARG B 405 " --> pdb=" O LEU B 401 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LYS B 406 " --> pdb=" O LYS B 402 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N LYS B 410 " --> pdb=" O LYS B 406 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N LYS B 411 " --> pdb=" O ASN B 407 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU B 415 " --> pdb=" O LYS B 411 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N PHE B 416 " --> pdb=" O CYS B 412 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N SER B 417 " --> pdb=" O LEU B 413 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU B 418 " --> pdb=" O GLU B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 444 removed outlier: 3.889A pdb=" N TYR B 426 " --> pdb=" O ASP B 422 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ALA B 432 " --> pdb=" O LYS B 428 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N PHE B 433 " --> pdb=" O PHE B 429 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N LYS B 435 " --> pdb=" O GLU B 431 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N ASN B 436 " --> pdb=" O ALA B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 452 Processing helix chain 'B' and resid 469 through 474 Processing helix chain 'B' and resid 490 through 496 removed outlier: 3.579A pdb=" N VAL B 494 " --> pdb=" O SER B 490 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASN B 496 " --> pdb=" O GLU B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 501 through 506 Processing helix chain 'B' and resid 517 through 525 removed outlier: 3.621A pdb=" N CYS B 521 " --> pdb=" O ILE B 517 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLN B 523 " --> pdb=" O GLU B 519 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLN B 524 " --> pdb=" O TYR B 520 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 558 removed outlier: 3.731A pdb=" N ALA B 558 " --> pdb=" O GLU B 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 572 removed outlier: 3.520A pdb=" N LYS B 565 " --> pdb=" O GLU B 561 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N MET B 567 " --> pdb=" O LEU B 563 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N LYS B 568 " --> pdb=" O CYS B 564 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLU B 569 " --> pdb=" O LYS B 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 599 through 609 Processing helix chain 'B' and resid 632 through 645 removed outlier: 3.879A pdb=" N GLU B 636 " --> pdb=" O HIS B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 648 through 665 removed outlier: 3.949A pdb=" N LYS B 652 " --> pdb=" O ASP B 648 " (cutoff:3.500A) Processing helix chain 'B' and resid 672 through 689 removed outlier: 4.318A pdb=" N HIS B 676 " --> pdb=" O ASP B 672 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLY B 689 " --> pdb=" O LYS B 685 " (cutoff:3.500A) Processing helix chain 'C' and resid 24 through 58 removed outlier: 3.886A pdb=" N ARG C 30 " --> pdb=" O ALA C 26 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N CYS C 54 " --> pdb=" O LEU C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 113 Processing helix chain 'C' and resid 143 through 160 removed outlier: 3.665A pdb=" N PHE C 152 " --> pdb=" O LYS C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 183 Processing helix chain 'C' and resid 184 through 199 Processing helix chain 'C' and resid 207 through 228 Processing helix chain 'C' and resid 230 through 234 removed outlier: 3.606A pdb=" N ALA C 233 " --> pdb=" O ASP C 230 " (cutoff:3.500A) Processing helix chain 'C' and resid 235 through 243 removed outlier: 3.814A pdb=" N PHE C 239 " --> pdb=" O PHE C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 266 Processing helix chain 'D' and resid 547 through 551 Processing helix chain 'D' and resid 564 through 582 Processing helix chain 'D' and resid 625 through 631 removed outlier: 3.523A pdb=" N LEU D 629 " --> pdb=" O ALA D 625 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLN D 631 " --> pdb=" O GLU D 627 " (cutoff:3.500A) Processing helix chain 'D' and resid 635 through 653 Processing helix chain 'D' and resid 664 through 674 Processing helix chain 'D' and resid 694 through 704 Processing helix chain 'D' and resid 714 through 729 removed outlier: 4.386A pdb=" N ILE D 718 " --> pdb=" O ASP D 714 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 13 through 15 removed outlier: 4.539A pdb=" N GLU A 13 " --> pdb=" O VAL B 167 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N VAL B 167 " --> pdb=" O GLU A 13 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N PHE A 15 " --> pdb=" O PHE B 165 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N PHE B 165 " --> pdb=" O PHE A 15 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N GLU B 153 " --> pdb=" O HIS B 149 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N HIS B 149 " --> pdb=" O GLU B 153 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N ILE B 73 " --> pdb=" O THR B 214 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N ILE B 213 " --> pdb=" O LEU B 282 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU B 215 " --> pdb=" O GLU B 280 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N GLU B 280 " --> pdb=" O LEU B 215 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 18 through 19 removed outlier: 7.359A pdb=" N GLN A 18 " --> pdb=" O ILE B 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 73 through 78 removed outlier: 3.793A pdb=" N LYS A 142 " --> pdb=" O HIS A 184 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N PHE A 165 " --> pdb=" O PHE B 15 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N PHE B 15 " --> pdb=" O PHE A 165 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 104 through 105 Processing sheet with id=AA5, first strand: chain 'A' and resid 317 through 323 removed outlier: 4.357A pdb=" N ALA A 317 " --> pdb=" O ILE A 335 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N LYS A 354 " --> pdb=" O GLY A 379 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N VAL A 381 " --> pdb=" O LYS A 354 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N TYR A 356 " --> pdb=" O VAL A 381 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N SER A 383 " --> pdb=" O TYR A 356 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N ILE A 353 " --> pdb=" O ASP A 364 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N ASP A 364 " --> pdb=" O ILE A 353 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N LEU A 355 " --> pdb=" O ILE A 362 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 456 through 457 Processing sheet with id=AA7, first strand: chain 'A' and resid 483 through 485 removed outlier: 5.957A pdb=" N ILE A 483 " --> pdb=" O VAL A 534 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 578 through 579 removed outlier: 3.562A pdb=" N ILE A 628 " --> pdb=" O THR A 579 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 361 through 363 removed outlier: 5.891A pdb=" N PHE B 361 " --> pdb=" O VAL B 357 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N VAL B 357 " --> pdb=" O PHE B 361 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N MET B 363 " --> pdb=" O LEU B 355 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LYS B 354 " --> pdb=" O GLY B 379 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N PHE B 329 " --> pdb=" O VAL B 323 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N VAL B 318 " --> pdb=" O SER C 128 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N SER C 128 " --> pdb=" O VAL B 318 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N HIS B 320 " --> pdb=" O SER C 126 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N SER C 126 " --> pdb=" O HIS B 320 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N SER B 322 " --> pdb=" O GLY C 124 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 456 through 457 Processing sheet with id=AB2, first strand: chain 'B' and resid 482 through 483 Processing sheet with id=AB3, first strand: chain 'B' and resid 486 through 487 removed outlier: 6.815A pdb=" N ILE B 486 " --> pdb=" O MET B 513 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'B' and resid 577 through 580 removed outlier: 4.367A pdb=" N LYS B 577 " --> pdb=" O LYS B 624 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU B 626 " --> pdb=" O LYS B 577 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N THR B 579 " --> pdb=" O LEU B 626 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N CYS B 590 " --> pdb=" O GLU B 627 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 597 through 599 574 hydrogen bonds defined for protein. 1617 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: 4.15 Time building geometry restraints manager: 3.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4377 1.34 - 1.46: 2243 1.46 - 1.58: 6962 1.58 - 1.70: 12 1.70 - 1.82: 114 Bond restraints: 13708 Sorted by residual: bond pdb=" CB PRO A 79 " pdb=" CG PRO A 79 " ideal model delta sigma weight residual 1.492 1.667 -0.175 5.00e-02 4.00e+02 1.22e+01 bond pdb=" CA ASN A 582 " pdb=" CB ASN A 582 " ideal model delta sigma weight residual 1.536 1.634 -0.098 4.10e-02 5.95e+02 5.71e+00 bond pdb=" CB GLN B 397 " pdb=" CG GLN B 397 " ideal model delta sigma weight residual 1.520 1.572 -0.052 3.00e-02 1.11e+03 3.00e+00 bond pdb=" N PRO A 79 " pdb=" CD PRO A 79 " ideal model delta sigma weight residual 1.473 1.495 -0.022 1.40e-02 5.10e+03 2.49e+00 bond pdb=" CA ASN A 46 " pdb=" C ASN A 46 " ideal model delta sigma weight residual 1.522 1.544 -0.021 1.37e-02 5.33e+03 2.46e+00 ... (remaining 13703 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.92: 18099 2.92 - 5.85: 271 5.85 - 8.77: 47 8.77 - 11.69: 13 11.69 - 14.62: 3 Bond angle restraints: 18433 Sorted by residual: angle pdb=" CA PRO A 79 " pdb=" N PRO A 79 " pdb=" CD PRO A 79 " ideal model delta sigma weight residual 112.00 97.38 14.62 1.40e+00 5.10e-01 1.09e+02 angle pdb=" CA GLN B 397 " pdb=" CB GLN B 397 " pdb=" CG GLN B 397 " ideal model delta sigma weight residual 114.10 125.22 -11.12 2.00e+00 2.50e-01 3.09e+01 angle pdb=" CA GLN C 44 " pdb=" CB GLN C 44 " pdb=" CG GLN C 44 " ideal model delta sigma weight residual 114.10 123.20 -9.10 2.00e+00 2.50e-01 2.07e+01 angle pdb=" CA LYS B 557 " pdb=" CB LYS B 557 " pdb=" CG LYS B 557 " ideal model delta sigma weight residual 114.10 123.18 -9.08 2.00e+00 2.50e-01 2.06e+01 angle pdb=" C LYS B 552 " pdb=" N MET B 553 " pdb=" CA MET B 553 " ideal model delta sigma weight residual 121.14 113.29 7.85 1.75e+00 3.27e-01 2.01e+01 ... (remaining 18428 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 7047 17.93 - 35.86: 1084 35.86 - 53.78: 276 53.78 - 71.71: 49 71.71 - 89.64: 22 Dihedral angle restraints: 8478 sinusoidal: 3640 harmonic: 4838 Sorted by residual: dihedral pdb=" CA GLU C 16 " pdb=" C GLU C 16 " pdb=" N ASP C 17 " pdb=" CA ASP C 17 " ideal model delta harmonic sigma weight residual -180.00 -158.71 -21.29 0 5.00e+00 4.00e-02 1.81e+01 dihedral pdb=" CA ALA D 632 " pdb=" C ALA D 632 " pdb=" N ASN D 633 " pdb=" CA ASN D 633 " ideal model delta harmonic sigma weight residual 180.00 158.73 21.27 0 5.00e+00 4.00e-02 1.81e+01 dihedral pdb=" CA LYS B 477 " pdb=" C LYS B 477 " pdb=" N GLU B 478 " pdb=" CA GLU B 478 " ideal model delta harmonic sigma weight residual 180.00 159.26 20.74 0 5.00e+00 4.00e-02 1.72e+01 ... (remaining 8475 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 1777 0.069 - 0.139: 238 0.139 - 0.208: 11 0.208 - 0.278: 3 0.278 - 0.347: 1 Chirality restraints: 2030 Sorted by residual: chirality pdb=" CA PRO A 79 " pdb=" N PRO A 79 " pdb=" C PRO A 79 " pdb=" CB PRO A 79 " both_signs ideal model delta sigma weight residual False 2.72 2.37 0.35 2.00e-01 2.50e+01 3.01e+00 chirality pdb=" CB ILE D 607 " pdb=" CA ILE D 607 " pdb=" CG1 ILE D 607 " pdb=" CG2 ILE D 607 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" CB VAL A 656 " pdb=" CA VAL A 656 " pdb=" CG1 VAL A 656 " pdb=" CG2 VAL A 656 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.34e+00 ... (remaining 2027 not shown) Planarity restraints: 2345 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 78 " 0.061 5.00e-02 4.00e+02 8.36e-02 1.12e+01 pdb=" N PRO A 79 " -0.144 5.00e-02 4.00e+02 pdb=" CA PRO A 79 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 79 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 370 " -0.038 5.00e-02 4.00e+02 5.87e-02 5.51e+00 pdb=" N PRO B 371 " 0.102 5.00e-02 4.00e+02 pdb=" CA PRO B 371 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 371 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 623 " -0.019 2.00e-02 2.50e+03 1.45e-02 5.29e+00 pdb=" CG TRP D 623 " 0.038 2.00e-02 2.50e+03 pdb=" CD1 TRP D 623 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP D 623 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP D 623 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP D 623 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP D 623 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 623 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 623 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP D 623 " -0.009 2.00e-02 2.50e+03 ... (remaining 2342 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 351 2.67 - 3.23: 13395 3.23 - 3.79: 19965 3.79 - 4.34: 24887 4.34 - 4.90: 39435 Nonbonded interactions: 98033 Sorted by model distance: nonbonded pdb=" O ARG B 55 " pdb=" OG SER B 58 " model vdw 2.117 3.040 nonbonded pdb=" OD1 ASP B 546 " pdb=" N GLU B 547 " model vdw 2.155 3.120 nonbonded pdb=" O GLY B 132 " pdb=" OG SER B 135 " model vdw 2.201 3.040 nonbonded pdb=" OD1 ASN C 116 " pdb=" OG1 THR C 119 " model vdw 2.206 3.040 nonbonded pdb=" O VAL D 672 " pdb=" OG SER D 675 " model vdw 2.217 3.040 ... (remaining 98028 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 12 through 218 or resid 278 through 613 or resid 617 throu \ gh 690 or resid 801)) selection = (chain 'B' and (resid 12 through 218 or resid 278 through 690 or resid 801)) } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.480 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 30.610 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7093 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 : 0.004 0.175 13708 Z= 0.244 Angle : 0.915 14.618 18433 Z= 0.490 Chirality : 0.046 0.347 2030 Planarity : 0.004 0.084 2345 Dihedral : 18.476 89.640 5332 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.43 % Allowed : 7.66 % Favored : 91.91 % Rotamer: Outliers : 0.80 % Allowed : 33.00 % Favored : 66.20 % 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: -1.50 (0.21), residues: 1619 helix: 0.35 (0.20), residues: 678 sheet: 0.51 (0.42), residues: 181 loop : -2.77 (0.20), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP D 623 HIS 0.007 0.001 HIS A 149 PHE 0.016 0.001 PHE A 39 TYR 0.021 0.001 TYR A 430 ARG 0.006 0.001 ARG B 475 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3238 Ramachandran restraints generated. 1619 Oldfield, 0 Emsley, 1619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3238 Ramachandran restraints generated. 1619 Oldfield, 0 Emsley, 1619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 421 time to evaluate : 1.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 LYS cc_start: 0.8484 (mtpt) cc_final: 0.8221 (mtpp) REVERT: A 430 TYR cc_start: 0.7491 (t80) cc_final: 0.7214 (t80) REVERT: A 481 LYS cc_start: 0.8836 (mmtt) cc_final: 0.8632 (mmtt) REVERT: A 501 GLU cc_start: 0.7593 (mp0) cc_final: 0.7364 (mp0) REVERT: A 509 GLU cc_start: 0.6405 (tp30) cc_final: 0.5402 (tp30) REVERT: A 551 LYS cc_start: 0.7642 (ptpp) cc_final: 0.7439 (pttm) REVERT: B 57 GLU cc_start: 0.7862 (tp30) cc_final: 0.7506 (tp30) REVERT: B 279 GLN cc_start: 0.7070 (OUTLIER) cc_final: 0.6632 (mm-40) REVERT: B 280 GLU cc_start: 0.7697 (pt0) cc_final: 0.6946 (tm-30) REVERT: B 300 GLU cc_start: 0.7555 (mp0) cc_final: 0.7264 (mp0) REVERT: B 304 PHE cc_start: 0.8536 (t80) cc_final: 0.8127 (t80) REVERT: B 312 TRP cc_start: 0.7418 (p-90) cc_final: 0.7136 (p-90) REVERT: B 393 GLU cc_start: 0.7260 (mp0) cc_final: 0.6909 (mp0) REVERT: B 395 LEU cc_start: 0.8045 (tp) cc_final: 0.7720 (tt) REVERT: B 471 GLU cc_start: 0.7123 (tm-30) cc_final: 0.6813 (tm-30) REVERT: B 476 MET cc_start: 0.6600 (mmm) cc_final: 0.6071 (mmm) REVERT: B 553 MET cc_start: 0.7549 (ppp) cc_final: 0.7228 (ppp) REVERT: B 559 LYS cc_start: 0.7841 (ttpp) cc_final: 0.7577 (ttpp) REVERT: B 627 GLU cc_start: 0.7885 (mm-30) cc_final: 0.7392 (mm-30) REVERT: C 20 HIS cc_start: 0.7635 (t-90) cc_final: 0.7363 (t70) REVERT: C 29 PHE cc_start: 0.7187 (m-10) cc_final: 0.6975 (m-80) REVERT: C 36 ARG cc_start: 0.7606 (ttp-170) cc_final: 0.6894 (tmm-80) REVERT: D 627 GLU cc_start: 0.7252 (pp20) cc_final: 0.7026 (pp20) outliers start: 12 outliers final: 8 residues processed: 424 average time/residue: 0.3424 time to fit residues: 198.1058 Evaluate side-chains 412 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 403 time to evaluate : 1.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 196 ARG Chi-restraints excluded: chain A residue 397 GLN Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 519 GLU Chi-restraints excluded: chain B residue 279 GLN Chi-restraints excluded: chain B residue 632 HIS Chi-restraints excluded: chain D residue 634 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 137 optimal weight: 8.9990 chunk 123 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 83 optimal weight: 8.9990 chunk 66 optimal weight: 0.9980 chunk 127 optimal weight: 10.0000 chunk 49 optimal weight: 2.9990 chunk 77 optimal weight: 0.0970 chunk 95 optimal weight: 2.9990 chunk 148 optimal weight: 0.0970 overall best weight: 0.5976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 458 HIS B 150 ASN B 396 GLN ** C 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7099 moved from start: 0.1125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 13708 Z= 0.183 Angle : 0.682 9.825 18433 Z= 0.361 Chirality : 0.044 0.182 2030 Planarity : 0.004 0.059 2345 Dihedral : 7.578 87.234 1867 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.41 % Favored : 92.28 % Rotamer: Outliers : 3.95 % Allowed : 27.51 % Favored : 68.54 % 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: -1.29 (0.21), residues: 1619 helix: 0.55 (0.20), residues: 694 sheet: 0.38 (0.40), residues: 192 loop : -2.71 (0.22), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP D 623 HIS 0.006 0.001 HIS A 149 PHE 0.024 0.001 PHE C 125 TYR 0.028 0.001 TYR B 305 ARG 0.006 0.000 ARG A 338 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3238 Ramachandran restraints generated. 1619 Oldfield, 0 Emsley, 1619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3238 Ramachandran restraints generated. 1619 Oldfield, 0 Emsley, 1619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 487 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 428 time to evaluate : 1.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 LYS cc_start: 0.8482 (mtpt) cc_final: 0.8045 (mtpp) REVERT: A 80 GLN cc_start: 0.7885 (mp10) cc_final: 0.7658 (mp10) REVERT: A 153 GLU cc_start: 0.7537 (mp0) cc_final: 0.7223 (mp0) REVERT: A 195 GLU cc_start: 0.7690 (tp30) cc_final: 0.7293 (tp30) REVERT: A 300 GLU cc_start: 0.7048 (pp20) cc_final: 0.6528 (pt0) REVERT: A 303 GLU cc_start: 0.7274 (pp20) cc_final: 0.6929 (pp20) REVERT: A 364 ASP cc_start: 0.7588 (p0) cc_final: 0.7382 (p0) REVERT: A 397 GLN cc_start: 0.7398 (tt0) cc_final: 0.6551 (tm-30) REVERT: A 400 ILE cc_start: 0.8724 (mm) cc_final: 0.8136 (mm) REVERT: A 449 ARG cc_start: 0.8309 (mmm-85) cc_final: 0.7740 (tpp80) REVERT: A 481 LYS cc_start: 0.8760 (mmtt) cc_final: 0.8470 (mmtt) REVERT: A 501 GLU cc_start: 0.7623 (mp0) cc_final: 0.7169 (mp0) REVERT: A 509 GLU cc_start: 0.6914 (tp30) cc_final: 0.6453 (tp30) REVERT: A 526 LYS cc_start: 0.7634 (pptt) cc_final: 0.7254 (pptt) REVERT: A 527 GLU cc_start: 0.6947 (mt-10) cc_final: 0.6036 (mt-10) REVERT: A 553 MET cc_start: 0.7339 (mmm) cc_final: 0.7127 (mmm) REVERT: B 55 ARG cc_start: 0.8336 (ttt180) cc_final: 0.7431 (ttp-170) REVERT: B 101 ASN cc_start: 0.8116 (t0) cc_final: 0.7631 (t0) REVERT: B 154 GLN cc_start: 0.7397 (mm-40) cc_final: 0.7048 (mm-40) REVERT: B 279 GLN cc_start: 0.7194 (OUTLIER) cc_final: 0.6888 (mm110) REVERT: B 294 ASP cc_start: 0.7918 (t0) cc_final: 0.7470 (t0) REVERT: B 312 TRP cc_start: 0.7455 (p-90) cc_final: 0.7134 (p-90) REVERT: B 356 TYR cc_start: 0.8325 (m-80) cc_final: 0.7824 (m-80) REVERT: B 359 ARG cc_start: 0.8020 (mpp80) cc_final: 0.7637 (mpp80) REVERT: B 424 GLU cc_start: 0.6995 (pm20) cc_final: 0.6777 (pm20) REVERT: B 426 TYR cc_start: 0.8389 (t80) cc_final: 0.8139 (t80) REVERT: B 427 LYS cc_start: 0.8797 (mttt) cc_final: 0.8473 (mtmm) REVERT: B 493 GLN cc_start: 0.8448 (OUTLIER) cc_final: 0.7969 (tp40) REVERT: B 513 MET cc_start: 0.6583 (mmt) cc_final: 0.6300 (mmt) REVERT: B 559 LYS cc_start: 0.7907 (ttpp) cc_final: 0.7438 (ttpp) REVERT: B 627 GLU cc_start: 0.7791 (mm-30) cc_final: 0.7191 (mm-30) REVERT: C 16 GLU cc_start: 0.6981 (pp20) cc_final: 0.6779 (tm-30) REVERT: C 29 PHE cc_start: 0.7115 (m-10) cc_final: 0.6898 (m-80) REVERT: C 30 ARG cc_start: 0.6900 (mtm180) cc_final: 0.6566 (mtm-85) REVERT: C 31 TRP cc_start: 0.8599 (m-10) cc_final: 0.7908 (m100) REVERT: C 107 ARG cc_start: 0.7773 (mtt-85) cc_final: 0.7480 (mtt-85) REVERT: D 582 HIS cc_start: 0.6208 (OUTLIER) cc_final: 0.5957 (t-90) REVERT: D 585 LYS cc_start: 0.7692 (mmmm) cc_final: 0.7437 (mmmm) REVERT: D 627 GLU cc_start: 0.7271 (pp20) cc_final: 0.7034 (pp20) REVERT: D 724 LYS cc_start: 0.8413 (tmmt) cc_final: 0.8167 (tmmt) outliers start: 59 outliers final: 34 residues processed: 463 average time/residue: 0.3184 time to fit residues: 199.5751 Evaluate side-chains 444 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 407 time to evaluate : 1.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 283 ASN Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 683 MET Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 279 GLN Chi-restraints excluded: chain B residue 284 LYS Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 571 LEU Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 632 HIS Chi-restraints excluded: chain C residue 23 ILE Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain D residue 534 ILE Chi-restraints excluded: chain D residue 582 HIS Chi-restraints excluded: chain D residue 586 THR Chi-restraints excluded: chain D residue 588 VAL Chi-restraints excluded: chain D residue 598 VAL Chi-restraints excluded: chain D residue 634 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 82 optimal weight: 0.0170 chunk 45 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 148 optimal weight: 1.9990 chunk 160 optimal weight: 4.9990 chunk 132 optimal weight: 2.9990 chunk 147 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 118 optimal weight: 0.6980 overall best weight: 0.9424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7125 moved from start: 0.1551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13708 Z= 0.197 Angle : 0.666 11.123 18433 Z= 0.350 Chirality : 0.044 0.194 2030 Planarity : 0.004 0.053 2345 Dihedral : 6.931 87.226 1854 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.78 % Favored : 91.97 % Rotamer: Outliers : 5.82 % Allowed : 28.31 % Favored : 65.86 % 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: -1.20 (0.21), residues: 1619 helix: 0.68 (0.20), residues: 695 sheet: 0.51 (0.42), residues: 174 loop : -2.69 (0.21), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 289 HIS 0.006 0.001 HIS B 320 PHE 0.024 0.001 PHE A 361 TYR 0.015 0.001 TYR B 305 ARG 0.009 0.000 ARG A 338 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3238 Ramachandran restraints generated. 1619 Oldfield, 0 Emsley, 1619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3238 Ramachandran restraints generated. 1619 Oldfield, 0 Emsley, 1619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 508 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 421 time to evaluate : 1.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 GLN cc_start: 0.7893 (mp10) cc_final: 0.7665 (mp10) REVERT: A 107 LYS cc_start: 0.7800 (tppp) cc_final: 0.7371 (tptp) REVERT: A 195 GLU cc_start: 0.7624 (tp30) cc_final: 0.7162 (tp30) REVERT: A 199 LYS cc_start: 0.8676 (pttm) cc_final: 0.8295 (pttm) REVERT: A 300 GLU cc_start: 0.7067 (pp20) cc_final: 0.6736 (pp20) REVERT: A 303 GLU cc_start: 0.7331 (pp20) cc_final: 0.6906 (pp20) REVERT: A 324 GLU cc_start: 0.6748 (OUTLIER) cc_final: 0.6455 (tm-30) REVERT: A 328 GLU cc_start: 0.7171 (mp0) cc_final: 0.6772 (mp0) REVERT: A 397 GLN cc_start: 0.7329 (tt0) cc_final: 0.6595 (tm-30) REVERT: A 400 ILE cc_start: 0.8747 (mm) cc_final: 0.8361 (mm) REVERT: A 449 ARG cc_start: 0.8353 (mmm-85) cc_final: 0.7770 (tpp80) REVERT: A 481 LYS cc_start: 0.8787 (mmtt) cc_final: 0.8529 (mmtt) REVERT: A 509 GLU cc_start: 0.6681 (tp30) cc_final: 0.6362 (tp30) REVERT: A 526 LYS cc_start: 0.7612 (pptt) cc_final: 0.7245 (pptt) REVERT: A 527 GLU cc_start: 0.7007 (mt-10) cc_final: 0.6006 (mt-10) REVERT: A 553 MET cc_start: 0.7442 (mmm) cc_final: 0.7096 (mmp) REVERT: B 55 ARG cc_start: 0.8375 (ttt180) cc_final: 0.7452 (ttp-170) REVERT: B 82 ARG cc_start: 0.8110 (mtp180) cc_final: 0.7897 (mtp180) REVERT: B 95 LYS cc_start: 0.8503 (tttt) cc_final: 0.8252 (ttmm) REVERT: B 101 ASN cc_start: 0.8086 (t0) cc_final: 0.7557 (t0) REVERT: B 128 GLN cc_start: 0.7651 (OUTLIER) cc_final: 0.7085 (mp-120) REVERT: B 154 GLN cc_start: 0.7432 (mm-40) cc_final: 0.7081 (mm-40) REVERT: B 279 GLN cc_start: 0.7188 (OUTLIER) cc_final: 0.6818 (mm110) REVERT: B 294 ASP cc_start: 0.7952 (t0) cc_final: 0.7554 (t0) REVERT: B 312 TRP cc_start: 0.7461 (p-90) cc_final: 0.7126 (p-90) REVERT: B 395 LEU cc_start: 0.8085 (tp) cc_final: 0.7766 (tt) REVERT: B 476 MET cc_start: 0.6378 (mmm) cc_final: 0.5836 (mmm) REVERT: B 481 LYS cc_start: 0.8560 (mmtt) cc_final: 0.8328 (mmtt) REVERT: B 493 GLN cc_start: 0.8444 (OUTLIER) cc_final: 0.8014 (mm-40) REVERT: B 513 MET cc_start: 0.6559 (mmt) cc_final: 0.6054 (mmt) REVERT: B 559 LYS cc_start: 0.7887 (ttpp) cc_final: 0.7426 (ttpt) REVERT: B 569 GLU cc_start: 0.7708 (pm20) cc_final: 0.7390 (pm20) REVERT: B 572 ASP cc_start: 0.6914 (OUTLIER) cc_final: 0.6570 (p0) REVERT: C 8 ASP cc_start: 0.6922 (m-30) cc_final: 0.6682 (m-30) REVERT: C 29 PHE cc_start: 0.7149 (m-10) cc_final: 0.6808 (m-80) REVERT: C 30 ARG cc_start: 0.6894 (mtm180) cc_final: 0.6643 (mtm-85) REVERT: C 31 TRP cc_start: 0.8637 (OUTLIER) cc_final: 0.7615 (m-90) REVERT: C 36 ARG cc_start: 0.7291 (ttp-170) cc_final: 0.6949 (ttm170) REVERT: C 38 GLU cc_start: 0.7569 (pt0) cc_final: 0.7276 (pt0) REVERT: C 40 MET cc_start: 0.7536 (tpt) cc_final: 0.7304 (tpt) REVERT: C 46 GLU cc_start: 0.7166 (OUTLIER) cc_final: 0.6840 (mm-30) REVERT: C 104 GLU cc_start: 0.8002 (mm-30) cc_final: 0.7566 (mm-30) REVERT: C 107 ARG cc_start: 0.7834 (mtt-85) cc_final: 0.7589 (mtt-85) REVERT: D 582 HIS cc_start: 0.6317 (OUTLIER) cc_final: 0.6029 (t-90) REVERT: D 585 LYS cc_start: 0.7659 (mmmm) cc_final: 0.7430 (mmmm) REVERT: D 674 ASN cc_start: 0.7454 (OUTLIER) cc_final: 0.7210 (t0) REVERT: D 724 LYS cc_start: 0.8449 (tmmt) cc_final: 0.8057 (tmmt) outliers start: 87 outliers final: 55 residues processed: 467 average time/residue: 0.3100 time to fit residues: 197.2816 Evaluate side-chains 473 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 409 time to evaluate : 1.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 366 CYS Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 521 CYS Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 617 MET Chi-restraints excluded: chain A residue 632 HIS Chi-restraints excluded: chain A residue 683 MET Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 128 GLN Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 279 GLN Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 394 MET Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 406 LYS Chi-restraints excluded: chain B residue 459 THR Chi-restraints excluded: chain B residue 466 MET Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 497 SER Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain B residue 571 LEU Chi-restraints excluded: chain B residue 572 ASP Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 592 VAL Chi-restraints excluded: chain B residue 605 ILE Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 617 MET Chi-restraints excluded: chain B residue 632 HIS Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain C residue 23 ILE Chi-restraints excluded: chain C residue 31 TRP Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain D residue 534 ILE Chi-restraints excluded: chain D residue 571 LEU Chi-restraints excluded: chain D residue 582 HIS Chi-restraints excluded: chain D residue 586 THR Chi-restraints excluded: chain D residue 588 VAL Chi-restraints excluded: chain D residue 598 VAL Chi-restraints excluded: chain D residue 634 ILE Chi-restraints excluded: chain D residue 652 LEU Chi-restraints excluded: chain D residue 674 ASN Chi-restraints excluded: chain D residue 708 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 146 optimal weight: 4.9990 chunk 111 optimal weight: 0.5980 chunk 76 optimal weight: 0.9980 chunk 16 optimal weight: 7.9990 chunk 70 optimal weight: 1.9990 chunk 99 optimal weight: 4.9990 chunk 148 optimal weight: 4.9990 chunk 157 optimal weight: 1.9990 chunk 77 optimal weight: 0.7980 chunk 141 optimal weight: 5.9990 chunk 42 optimal weight: 0.0470 overall best weight: 0.8880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 GLN B 352 ASN ** C 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7127 moved from start: 0.1762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13708 Z= 0.195 Angle : 0.669 11.253 18433 Z= 0.350 Chirality : 0.044 0.187 2030 Planarity : 0.004 0.050 2345 Dihedral : 6.784 87.699 1854 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.09 % Favored : 91.72 % Rotamer: Outliers : 5.56 % Allowed : 27.84 % Favored : 66.60 % 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: -1.14 (0.21), residues: 1619 helix: 0.73 (0.20), residues: 696 sheet: 0.44 (0.41), residues: 181 loop : -2.67 (0.22), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 289 HIS 0.005 0.001 HIS B 320 PHE 0.015 0.001 PHE A 329 TYR 0.017 0.001 TYR B 305 ARG 0.011 0.001 ARG A 338 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3238 Ramachandran restraints generated. 1619 Oldfield, 0 Emsley, 1619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3238 Ramachandran restraints generated. 1619 Oldfield, 0 Emsley, 1619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 413 time to evaluate : 1.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 GLN cc_start: 0.7893 (mp10) cc_final: 0.7665 (mp10) REVERT: A 107 LYS cc_start: 0.7803 (tppp) cc_final: 0.7380 (tptp) REVERT: A 195 GLU cc_start: 0.7619 (tp30) cc_final: 0.6326 (tp30) REVERT: A 199 LYS cc_start: 0.8703 (pttm) cc_final: 0.7904 (pttm) REVERT: A 300 GLU cc_start: 0.7061 (pp20) cc_final: 0.6695 (pp20) REVERT: A 303 GLU cc_start: 0.7459 (pp20) cc_final: 0.7163 (pp20) REVERT: A 397 GLN cc_start: 0.7275 (tt0) cc_final: 0.6523 (tm-30) REVERT: A 400 ILE cc_start: 0.8750 (mm) cc_final: 0.8378 (mm) REVERT: A 449 ARG cc_start: 0.8348 (mmm-85) cc_final: 0.7732 (tpp80) REVERT: A 481 LYS cc_start: 0.8752 (mmtt) cc_final: 0.8381 (mmtt) REVERT: A 509 GLU cc_start: 0.6411 (tp30) cc_final: 0.6209 (tp30) REVERT: A 526 LYS cc_start: 0.7648 (pptt) cc_final: 0.7440 (pptt) REVERT: A 527 GLU cc_start: 0.7041 (mt-10) cc_final: 0.5990 (mt-10) REVERT: A 553 MET cc_start: 0.7552 (mmm) cc_final: 0.7128 (mmp) REVERT: B 55 ARG cc_start: 0.8269 (ttt180) cc_final: 0.7490 (ttp-170) REVERT: B 95 LYS cc_start: 0.8538 (tttt) cc_final: 0.8283 (ttmm) REVERT: B 101 ASN cc_start: 0.8087 (t0) cc_final: 0.7539 (t0) REVERT: B 128 GLN cc_start: 0.7664 (OUTLIER) cc_final: 0.7089 (mp-120) REVERT: B 154 GLN cc_start: 0.7411 (mm-40) cc_final: 0.7026 (mm-40) REVERT: B 279 GLN cc_start: 0.7205 (OUTLIER) cc_final: 0.6860 (mm110) REVERT: B 294 ASP cc_start: 0.7938 (t0) cc_final: 0.7537 (t0) REVERT: B 312 TRP cc_start: 0.7429 (p-90) cc_final: 0.7111 (p-90) REVERT: B 376 PHE cc_start: 0.8753 (p90) cc_final: 0.7976 (p90) REVERT: B 395 LEU cc_start: 0.8077 (tp) cc_final: 0.7751 (tt) REVERT: B 410 LYS cc_start: 0.8073 (tttt) cc_final: 0.7834 (tmmt) REVERT: B 476 MET cc_start: 0.6464 (mmm) cc_final: 0.6012 (mmm) REVERT: B 481 LYS cc_start: 0.8596 (mmtt) cc_final: 0.8394 (mmtt) REVERT: B 493 GLN cc_start: 0.8466 (OUTLIER) cc_final: 0.8110 (mm-40) REVERT: B 513 MET cc_start: 0.6705 (mmt) cc_final: 0.6441 (mmt) REVERT: B 559 LYS cc_start: 0.7855 (ttpp) cc_final: 0.7322 (ttpt) REVERT: B 569 GLU cc_start: 0.7683 (pm20) cc_final: 0.7450 (pm20) REVERT: B 572 ASP cc_start: 0.6925 (OUTLIER) cc_final: 0.6635 (p0) REVERT: B 606 MET cc_start: 0.7329 (mmm) cc_final: 0.7101 (mmm) REVERT: B 683 MET cc_start: 0.7938 (mmm) cc_final: 0.7727 (mmm) REVERT: C 8 ASP cc_start: 0.6925 (m-30) cc_final: 0.6679 (m-30) REVERT: C 29 PHE cc_start: 0.7173 (m-10) cc_final: 0.6894 (m-80) REVERT: C 31 TRP cc_start: 0.8646 (OUTLIER) cc_final: 0.7662 (m-90) REVERT: C 36 ARG cc_start: 0.7288 (ttp-170) cc_final: 0.6919 (ttm170) REVERT: C 40 MET cc_start: 0.7504 (tpt) cc_final: 0.7229 (tpt) REVERT: C 107 ARG cc_start: 0.7911 (mtt-85) cc_final: 0.7498 (mtt-85) REVERT: D 529 LYS cc_start: 0.5957 (OUTLIER) cc_final: 0.5743 (ptmm) REVERT: D 582 HIS cc_start: 0.6390 (OUTLIER) cc_final: 0.6099 (t-90) REVERT: D 585 LYS cc_start: 0.7606 (mmmm) cc_final: 0.7388 (mmmm) REVERT: D 674 ASN cc_start: 0.7453 (OUTLIER) cc_final: 0.7190 (t0) REVERT: D 724 LYS cc_start: 0.8470 (tmmt) cc_final: 0.8045 (tmmt) outliers start: 83 outliers final: 54 residues processed: 458 average time/residue: 0.3150 time to fit residues: 197.8216 Evaluate side-chains 467 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 405 time to evaluate : 1.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 283 ASN Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 366 CYS Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 468 SER Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 620 MET Chi-restraints excluded: chain A residue 634 ILE Chi-restraints excluded: chain A residue 683 MET Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 128 GLN Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 279 GLN Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 370 ILE Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 394 MET Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 406 LYS Chi-restraints excluded: chain B residue 459 THR Chi-restraints excluded: chain B residue 466 MET Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain B residue 572 ASP Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 592 VAL Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 632 HIS Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain C residue 23 ILE Chi-restraints excluded: chain C residue 31 TRP Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain D residue 529 LYS Chi-restraints excluded: chain D residue 534 ILE Chi-restraints excluded: chain D residue 571 LEU Chi-restraints excluded: chain D residue 582 HIS Chi-restraints excluded: chain D residue 586 THR Chi-restraints excluded: chain D residue 588 VAL Chi-restraints excluded: chain D residue 598 VAL Chi-restraints excluded: chain D residue 605 VAL Chi-restraints excluded: chain D residue 634 ILE Chi-restraints excluded: chain D residue 654 LYS Chi-restraints excluded: chain D residue 674 ASN Chi-restraints excluded: chain D residue 708 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 131 optimal weight: 0.8980 chunk 89 optimal weight: 3.9990 chunk 2 optimal weight: 0.2980 chunk 117 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 134 optimal weight: 10.0000 chunk 108 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 80 optimal weight: 0.8980 chunk 141 optimal weight: 4.9990 chunk 39 optimal weight: 0.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 GLN ** C 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7153 moved from start: 0.1954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13708 Z= 0.225 Angle : 0.692 11.416 18433 Z= 0.362 Chirality : 0.045 0.173 2030 Planarity : 0.004 0.048 2345 Dihedral : 6.805 84.856 1854 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.08 % Favored : 90.74 % Rotamer: Outliers : 6.16 % Allowed : 28.85 % Favored : 64.99 % 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: -1.14 (0.21), residues: 1619 helix: 0.72 (0.20), residues: 699 sheet: 0.55 (0.43), residues: 167 loop : -2.64 (0.21), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 289 HIS 0.006 0.001 HIS B 320 PHE 0.019 0.001 PHE A 329 TYR 0.021 0.002 TYR A 305 ARG 0.009 0.001 ARG A 506 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3238 Ramachandran restraints generated. 1619 Oldfield, 0 Emsley, 1619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3238 Ramachandran restraints generated. 1619 Oldfield, 0 Emsley, 1619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 516 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 424 time to evaluate : 1.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 ARG cc_start: 0.8553 (OUTLIER) cc_final: 0.8211 (tmm-80) REVERT: A 72 LYS cc_start: 0.7440 (OUTLIER) cc_final: 0.6611 (pttm) REVERT: A 80 GLN cc_start: 0.7931 (mp10) cc_final: 0.7711 (mp10) REVERT: A 107 LYS cc_start: 0.7838 (tppp) cc_final: 0.7413 (tptp) REVERT: A 115 GLU cc_start: 0.7840 (tp30) cc_final: 0.7513 (tp30) REVERT: A 189 GLN cc_start: 0.8536 (OUTLIER) cc_final: 0.8309 (mm110) REVERT: A 195 GLU cc_start: 0.7687 (tp30) cc_final: 0.6253 (tp30) REVERT: A 199 LYS cc_start: 0.8722 (pttm) cc_final: 0.7680 (pttm) REVERT: A 300 GLU cc_start: 0.7099 (pp20) cc_final: 0.6724 (pp20) REVERT: A 303 GLU cc_start: 0.7484 (pp20) cc_final: 0.7147 (pp20) REVERT: A 359 ARG cc_start: 0.8529 (mpp80) cc_final: 0.8186 (mpp80) REVERT: A 397 GLN cc_start: 0.7360 (tt0) cc_final: 0.6511 (tm-30) REVERT: A 400 ILE cc_start: 0.8758 (mm) cc_final: 0.8447 (mm) REVERT: A 449 ARG cc_start: 0.8323 (mmm-85) cc_final: 0.8112 (mtp85) REVERT: A 492 GLU cc_start: 0.7695 (mp0) cc_final: 0.7405 (mm-30) REVERT: A 501 GLU cc_start: 0.7603 (mp0) cc_final: 0.7305 (mp0) REVERT: A 509 GLU cc_start: 0.5981 (tp30) cc_final: 0.5739 (tp30) REVERT: A 526 LYS cc_start: 0.7693 (pptt) cc_final: 0.7489 (pptt) REVERT: A 527 GLU cc_start: 0.7011 (mt-10) cc_final: 0.5994 (mm-30) REVERT: A 553 MET cc_start: 0.7541 (mmm) cc_final: 0.7340 (mmp) REVERT: A 582 ASN cc_start: 0.8045 (p0) cc_final: 0.7744 (p0) REVERT: A 599 THR cc_start: 0.6962 (OUTLIER) cc_final: 0.6603 (t) REVERT: B 101 ASN cc_start: 0.8066 (t0) cc_final: 0.7544 (t0) REVERT: B 128 GLN cc_start: 0.7683 (OUTLIER) cc_final: 0.7081 (mp-120) REVERT: B 154 GLN cc_start: 0.7266 (mm-40) cc_final: 0.6883 (mm-40) REVERT: B 279 GLN cc_start: 0.7304 (OUTLIER) cc_final: 0.7003 (mm-40) REVERT: B 294 ASP cc_start: 0.7915 (t0) cc_final: 0.7537 (t0) REVERT: B 300 GLU cc_start: 0.7560 (mp0) cc_final: 0.7336 (mp0) REVERT: B 312 TRP cc_start: 0.7492 (p-90) cc_final: 0.7187 (p-90) REVERT: B 329 PHE cc_start: 0.8479 (p90) cc_final: 0.7880 (p90) REVERT: B 352 ASN cc_start: 0.8300 (m-40) cc_final: 0.7994 (m-40) REVERT: B 376 PHE cc_start: 0.8686 (p90) cc_final: 0.8133 (p90) REVERT: B 395 LEU cc_start: 0.8155 (tp) cc_final: 0.7919 (tt) REVERT: B 410 LYS cc_start: 0.8122 (tttt) cc_final: 0.7891 (tmmt) REVERT: B 471 GLU cc_start: 0.7988 (mm-30) cc_final: 0.7758 (mp0) REVERT: B 476 MET cc_start: 0.6485 (mmm) cc_final: 0.6062 (mmm) REVERT: B 493 GLN cc_start: 0.8478 (OUTLIER) cc_final: 0.8142 (mm-40) REVERT: B 513 MET cc_start: 0.6808 (mmt) cc_final: 0.6504 (mmt) REVERT: B 559 LYS cc_start: 0.7903 (ttpp) cc_final: 0.7374 (ttpp) REVERT: B 569 GLU cc_start: 0.7740 (pm20) cc_final: 0.7523 (pm20) REVERT: B 683 MET cc_start: 0.7986 (mmm) cc_final: 0.7761 (mmm) REVERT: C 30 ARG cc_start: 0.7024 (mtm180) cc_final: 0.6804 (mtm-85) REVERT: C 31 TRP cc_start: 0.8660 (OUTLIER) cc_final: 0.7583 (m-90) REVERT: C 36 ARG cc_start: 0.7292 (ttp-170) cc_final: 0.6922 (ttm170) REVERT: C 40 MET cc_start: 0.7506 (tpt) cc_final: 0.7213 (tpt) REVERT: C 107 ARG cc_start: 0.7986 (mtt-85) cc_final: 0.7586 (mtt-85) REVERT: D 529 LYS cc_start: 0.6006 (OUTLIER) cc_final: 0.5785 (ptmm) REVERT: D 582 HIS cc_start: 0.6373 (OUTLIER) cc_final: 0.6132 (t-90) REVERT: D 585 LYS cc_start: 0.7590 (mmmm) cc_final: 0.7390 (mmmm) REVERT: D 674 ASN cc_start: 0.7552 (OUTLIER) cc_final: 0.7308 (t0) REVERT: D 724 LYS cc_start: 0.8472 (tmmt) cc_final: 0.7995 (tmmt) outliers start: 92 outliers final: 62 residues processed: 477 average time/residue: 0.3186 time to fit residues: 206.6117 Evaluate side-chains 495 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 422 time to evaluate : 1.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ARG Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 72 LYS Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 189 GLN Chi-restraints excluded: chain A residue 283 ASN Chi-restraints excluded: chain A residue 307 SER Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 366 CYS Chi-restraints excluded: chain A residue 399 LYS Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 468 SER Chi-restraints excluded: chain A residue 470 SER Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 521 CYS Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 570 ILE Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 634 ILE Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 128 GLN Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 279 GLN Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 370 ILE Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 394 MET Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 406 LYS Chi-restraints excluded: chain B residue 459 THR Chi-restraints excluded: chain B residue 466 MET Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 497 SER Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 592 VAL Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 617 MET Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 23 ILE Chi-restraints excluded: chain C residue 31 TRP Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain D residue 529 LYS Chi-restraints excluded: chain D residue 534 ILE Chi-restraints excluded: chain D residue 571 LEU Chi-restraints excluded: chain D residue 582 HIS Chi-restraints excluded: chain D residue 586 THR Chi-restraints excluded: chain D residue 588 VAL Chi-restraints excluded: chain D residue 598 VAL Chi-restraints excluded: chain D residue 605 VAL Chi-restraints excluded: chain D residue 634 ILE Chi-restraints excluded: chain D residue 652 LEU Chi-restraints excluded: chain D residue 674 ASN Chi-restraints excluded: chain D residue 686 PHE Chi-restraints excluded: chain D residue 708 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 53 optimal weight: 0.9980 chunk 141 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 92 optimal weight: 0.0060 chunk 38 optimal weight: 0.1980 chunk 157 optimal weight: 9.9990 chunk 130 optimal weight: 3.9990 chunk 73 optimal weight: 0.0030 chunk 13 optimal weight: 8.9990 chunk 52 optimal weight: 0.9980 chunk 82 optimal weight: 1.9990 overall best weight: 0.4406 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 632 HIS ** C 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7104 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13708 Z= 0.181 Angle : 0.679 12.217 18433 Z= 0.349 Chirality : 0.043 0.193 2030 Planarity : 0.004 0.048 2345 Dihedral : 6.588 85.665 1852 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.35 % Favored : 92.46 % Rotamer: Outliers : 4.82 % Allowed : 30.25 % Favored : 64.93 % 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: 1619 helix: 0.79 (0.20), residues: 706 sheet: 0.44 (0.40), residues: 192 loop : -2.63 (0.22), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 623 HIS 0.004 0.001 HIS A 149 PHE 0.030 0.001 PHE A 361 TYR 0.026 0.001 TYR B 305 ARG 0.012 0.000 ARG A 338 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3238 Ramachandran restraints generated. 1619 Oldfield, 0 Emsley, 1619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3238 Ramachandran restraints generated. 1619 Oldfield, 0 Emsley, 1619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 504 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 432 time to evaluate : 1.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 MET cc_start: 0.7881 (mpp) cc_final: 0.7473 (mpp) REVERT: A 107 LYS cc_start: 0.7818 (tppp) cc_final: 0.7451 (tptp) REVERT: A 189 GLN cc_start: 0.8561 (OUTLIER) cc_final: 0.8225 (mm110) REVERT: A 199 LYS cc_start: 0.8699 (pttm) cc_final: 0.8245 (ptpp) REVERT: A 300 GLU cc_start: 0.7002 (pp20) cc_final: 0.6650 (pp20) REVERT: A 301 TYR cc_start: 0.8413 (OUTLIER) cc_final: 0.7791 (t80) REVERT: A 303 GLU cc_start: 0.7446 (pp20) cc_final: 0.7086 (pp20) REVERT: A 330 ARG cc_start: 0.7348 (OUTLIER) cc_final: 0.6675 (mtm-85) REVERT: A 397 GLN cc_start: 0.7255 (tt0) cc_final: 0.6434 (tm-30) REVERT: A 400 ILE cc_start: 0.8753 (mm) cc_final: 0.8396 (mm) REVERT: A 449 ARG cc_start: 0.8278 (mmm-85) cc_final: 0.8074 (mtp85) REVERT: A 492 GLU cc_start: 0.7649 (mp0) cc_final: 0.7399 (mm-30) REVERT: A 501 GLU cc_start: 0.7399 (mp0) cc_final: 0.7157 (mp0) REVERT: A 509 GLU cc_start: 0.6103 (tp30) cc_final: 0.5892 (tp30) REVERT: A 527 GLU cc_start: 0.7051 (mt-10) cc_final: 0.5938 (mm-30) REVERT: A 553 MET cc_start: 0.7533 (mmm) cc_final: 0.7274 (mmp) REVERT: A 582 ASN cc_start: 0.8019 (p0) cc_final: 0.7733 (p0) REVERT: B 55 ARG cc_start: 0.8238 (ttt180) cc_final: 0.7475 (ttp-170) REVERT: B 95 LYS cc_start: 0.8512 (tttt) cc_final: 0.8219 (ttmm) REVERT: B 128 GLN cc_start: 0.7670 (OUTLIER) cc_final: 0.7086 (mp-120) REVERT: B 154 GLN cc_start: 0.7223 (mm-40) cc_final: 0.6825 (mm-40) REVERT: B 279 GLN cc_start: 0.7307 (OUTLIER) cc_final: 0.7005 (mm-40) REVERT: B 294 ASP cc_start: 0.7944 (t0) cc_final: 0.7555 (t0) REVERT: B 312 TRP cc_start: 0.7403 (p-90) cc_final: 0.7056 (p-90) REVERT: B 352 ASN cc_start: 0.8312 (m-40) cc_final: 0.7958 (m-40) REVERT: B 376 PHE cc_start: 0.8634 (p90) cc_final: 0.8146 (p90) REVERT: B 395 LEU cc_start: 0.8049 (tp) cc_final: 0.7709 (tt) REVERT: B 410 LYS cc_start: 0.8116 (tttt) cc_final: 0.7851 (ttmt) REVERT: B 427 LYS cc_start: 0.8794 (mtmt) cc_final: 0.8426 (mtmm) REVERT: B 471 GLU cc_start: 0.7913 (mm-30) cc_final: 0.7691 (mp0) REVERT: B 481 LYS cc_start: 0.8579 (mmtt) cc_final: 0.8368 (mmtt) REVERT: B 493 GLN cc_start: 0.8419 (OUTLIER) cc_final: 0.8082 (mm-40) REVERT: B 514 THR cc_start: 0.7424 (OUTLIER) cc_final: 0.7098 (p) REVERT: B 548 GLU cc_start: 0.8061 (pm20) cc_final: 0.7614 (pm20) REVERT: B 559 LYS cc_start: 0.7758 (ttpp) cc_final: 0.7412 (ttpp) REVERT: B 572 ASP cc_start: 0.7026 (OUTLIER) cc_final: 0.6712 (p0) REVERT: B 683 MET cc_start: 0.7940 (mmm) cc_final: 0.7674 (mmm) REVERT: C 8 ASP cc_start: 0.6878 (m-30) cc_final: 0.6621 (m-30) REVERT: C 31 TRP cc_start: 0.8650 (OUTLIER) cc_final: 0.7712 (m-10) REVERT: C 40 MET cc_start: 0.7431 (tpt) cc_final: 0.7122 (tpt) REVERT: C 46 GLU cc_start: 0.7185 (OUTLIER) cc_final: 0.6608 (mt-10) REVERT: C 107 ARG cc_start: 0.8025 (mtt-85) cc_final: 0.7647 (mtt-85) REVERT: C 133 LYS cc_start: 0.6546 (ttpt) cc_final: 0.6235 (mmtm) REVERT: D 529 LYS cc_start: 0.6031 (OUTLIER) cc_final: 0.5773 (ptmm) REVERT: D 578 MET cc_start: 0.7401 (mmm) cc_final: 0.7039 (mmm) REVERT: D 606 LYS cc_start: 0.7066 (mmmt) cc_final: 0.6669 (mmmt) REVERT: D 674 ASN cc_start: 0.7528 (OUTLIER) cc_final: 0.7278 (t0) REVERT: D 724 LYS cc_start: 0.8546 (tmmt) cc_final: 0.8146 (tmmt) outliers start: 72 outliers final: 45 residues processed: 474 average time/residue: 0.3182 time to fit residues: 204.4029 Evaluate side-chains 472 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 415 time to evaluate : 1.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 189 GLN Chi-restraints excluded: chain A residue 301 TYR Chi-restraints excluded: chain A residue 307 SER Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 330 ARG Chi-restraints excluded: chain A residue 366 CYS Chi-restraints excluded: chain A residue 399 LYS Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 570 ILE Chi-restraints excluded: chain A residue 574 LYS Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 683 MET Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 114 MET Chi-restraints excluded: chain B residue 128 GLN Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 279 GLN Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 370 ILE Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 459 THR Chi-restraints excluded: chain B residue 466 MET Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain B residue 497 SER Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain B residue 572 ASP Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 592 VAL Chi-restraints excluded: chain B residue 594 SER Chi-restraints excluded: chain B residue 617 MET Chi-restraints excluded: chain B residue 632 HIS Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain C residue 23 ILE Chi-restraints excluded: chain C residue 31 TRP Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain D residue 529 LYS Chi-restraints excluded: chain D residue 534 ILE Chi-restraints excluded: chain D residue 586 THR Chi-restraints excluded: chain D residue 588 VAL Chi-restraints excluded: chain D residue 605 VAL Chi-restraints excluded: chain D residue 634 ILE Chi-restraints excluded: chain D residue 652 LEU Chi-restraints excluded: chain D residue 674 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 152 optimal weight: 0.8980 chunk 17 optimal weight: 0.1980 chunk 89 optimal weight: 0.5980 chunk 115 optimal weight: 0.9980 chunk 132 optimal weight: 7.9990 chunk 88 optimal weight: 2.9990 chunk 157 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 chunk 95 optimal weight: 0.7980 chunk 72 optimal weight: 5.9990 chunk 97 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7111 moved from start: 0.2255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13708 Z= 0.192 Angle : 0.715 11.467 18433 Z= 0.366 Chirality : 0.044 0.187 2030 Planarity : 0.004 0.048 2345 Dihedral : 6.550 85.443 1852 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.60 % Favored : 92.22 % Rotamer: Outliers : 4.89 % Allowed : 30.66 % Favored : 64.46 % 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: -1.05 (0.21), residues: 1619 helix: 0.74 (0.20), residues: 707 sheet: 0.48 (0.40), residues: 192 loop : -2.63 (0.22), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 289 HIS 0.011 0.001 HIS B 632 PHE 0.036 0.001 PHE C 29 TYR 0.025 0.001 TYR B 305 ARG 0.014 0.000 ARG A 338 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3238 Ramachandran restraints generated. 1619 Oldfield, 0 Emsley, 1619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3238 Ramachandran restraints generated. 1619 Oldfield, 0 Emsley, 1619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 420 time to evaluate : 1.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 ARG cc_start: 0.8509 (OUTLIER) cc_final: 0.8171 (tmm-80) REVERT: A 93 MET cc_start: 0.7904 (mpp) cc_final: 0.7459 (mpp) REVERT: A 107 LYS cc_start: 0.7839 (tppp) cc_final: 0.7477 (tptp) REVERT: A 199 LYS cc_start: 0.8576 (pttm) cc_final: 0.7923 (pttm) REVERT: A 300 GLU cc_start: 0.7055 (pp20) cc_final: 0.6715 (pp20) REVERT: A 301 TYR cc_start: 0.8387 (OUTLIER) cc_final: 0.7782 (t80) REVERT: A 303 GLU cc_start: 0.7499 (pp20) cc_final: 0.7112 (pp20) REVERT: A 397 GLN cc_start: 0.7255 (tt0) cc_final: 0.6439 (tm-30) REVERT: A 400 ILE cc_start: 0.8757 (mm) cc_final: 0.8431 (mm) REVERT: A 449 ARG cc_start: 0.8305 (mmm-85) cc_final: 0.8096 (mtp85) REVERT: A 487 THR cc_start: 0.8049 (OUTLIER) cc_final: 0.7607 (p) REVERT: A 492 GLU cc_start: 0.7657 (mp0) cc_final: 0.7421 (mm-30) REVERT: A 501 GLU cc_start: 0.7588 (mp0) cc_final: 0.7358 (mp0) REVERT: A 553 MET cc_start: 0.7521 (mmm) cc_final: 0.7279 (mmp) REVERT: A 567 MET cc_start: 0.5838 (mmt) cc_final: 0.5507 (tpp) REVERT: A 582 ASN cc_start: 0.8045 (p0) cc_final: 0.7784 (p0) REVERT: A 599 THR cc_start: 0.6780 (OUTLIER) cc_final: 0.6426 (t) REVERT: A 607 LYS cc_start: 0.8529 (ttmt) cc_final: 0.8081 (mtpt) REVERT: B 55 ARG cc_start: 0.8253 (ttt180) cc_final: 0.7474 (ttp-170) REVERT: B 95 LYS cc_start: 0.8513 (tttt) cc_final: 0.8221 (ttmm) REVERT: B 101 ASN cc_start: 0.8069 (t0) cc_final: 0.7532 (t0) REVERT: B 128 GLN cc_start: 0.7683 (OUTLIER) cc_final: 0.7074 (mp-120) REVERT: B 142 LYS cc_start: 0.8374 (mttt) cc_final: 0.7758 (mtmm) REVERT: B 154 GLN cc_start: 0.7199 (mm-40) cc_final: 0.6766 (mm-40) REVERT: B 279 GLN cc_start: 0.7321 (OUTLIER) cc_final: 0.6936 (tp40) REVERT: B 294 ASP cc_start: 0.7929 (t0) cc_final: 0.7546 (t0) REVERT: B 312 TRP cc_start: 0.7410 (p-90) cc_final: 0.7057 (p-90) REVERT: B 352 ASN cc_start: 0.8244 (m-40) cc_final: 0.7932 (m-40) REVERT: B 376 PHE cc_start: 0.8583 (p90) cc_final: 0.8124 (p90) REVERT: B 395 LEU cc_start: 0.8058 (tp) cc_final: 0.7725 (tt) REVERT: B 410 LYS cc_start: 0.8139 (tttt) cc_final: 0.7876 (ttmt) REVERT: B 427 LYS cc_start: 0.8796 (mtmt) cc_final: 0.8438 (mtmm) REVERT: B 471 GLU cc_start: 0.7919 (mm-30) cc_final: 0.7699 (mp0) REVERT: B 493 GLN cc_start: 0.8424 (OUTLIER) cc_final: 0.8091 (mm-40) REVERT: B 513 MET cc_start: 0.6647 (mmt) cc_final: 0.6096 (mmt) REVERT: B 514 THR cc_start: 0.7370 (OUTLIER) cc_final: 0.7010 (p) REVERT: B 559 LYS cc_start: 0.7802 (ttpp) cc_final: 0.7365 (ttpp) REVERT: B 572 ASP cc_start: 0.7034 (OUTLIER) cc_final: 0.6767 (p0) REVERT: B 612 ARG cc_start: 0.8213 (mmm-85) cc_final: 0.7878 (mmm-85) REVERT: B 683 MET cc_start: 0.7957 (mmm) cc_final: 0.7677 (mmm) REVERT: C 8 ASP cc_start: 0.6877 (m-30) cc_final: 0.6628 (m-30) REVERT: C 31 TRP cc_start: 0.8666 (OUTLIER) cc_final: 0.7665 (m-10) REVERT: C 36 ARG cc_start: 0.7218 (ttp-170) cc_final: 0.6999 (ttm170) REVERT: C 40 MET cc_start: 0.7461 (tpt) cc_final: 0.7163 (tpt) REVERT: C 46 GLU cc_start: 0.7194 (OUTLIER) cc_final: 0.6613 (mt-10) REVERT: C 107 ARG cc_start: 0.7979 (mtt-85) cc_final: 0.7579 (mtt-85) REVERT: D 578 MET cc_start: 0.7399 (mmm) cc_final: 0.7065 (mmm) REVERT: D 674 ASN cc_start: 0.7587 (OUTLIER) cc_final: 0.7342 (t0) REVERT: D 724 LYS cc_start: 0.8549 (tmmt) cc_final: 0.8140 (tmmt) outliers start: 73 outliers final: 49 residues processed: 462 average time/residue: 0.3092 time to fit residues: 194.5020 Evaluate side-chains 482 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 421 time to evaluate : 1.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ARG Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 301 TYR Chi-restraints excluded: chain A residue 307 SER Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 366 CYS Chi-restraints excluded: chain A residue 399 LYS Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 468 SER Chi-restraints excluded: chain A residue 487 THR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 518 ASP Chi-restraints excluded: chain A residue 521 CYS Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 574 LYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 634 ILE Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 128 GLN Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 279 GLN Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 370 ILE Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 394 MET Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 459 THR Chi-restraints excluded: chain B residue 466 MET Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain B residue 497 SER Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain B residue 572 ASP Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 592 VAL Chi-restraints excluded: chain B residue 617 MET Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain C residue 23 ILE Chi-restraints excluded: chain C residue 31 TRP Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain D residue 534 ILE Chi-restraints excluded: chain D residue 571 LEU Chi-restraints excluded: chain D residue 586 THR Chi-restraints excluded: chain D residue 588 VAL Chi-restraints excluded: chain D residue 605 VAL Chi-restraints excluded: chain D residue 634 ILE Chi-restraints excluded: chain D residue 652 LEU Chi-restraints excluded: chain D residue 674 ASN Chi-restraints excluded: chain D residue 708 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 62 optimal weight: 2.9990 chunk 93 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 99 optimal weight: 4.9990 chunk 107 optimal weight: 0.0270 chunk 77 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 123 optimal weight: 0.9980 chunk 142 optimal weight: 0.0970 chunk 150 optimal weight: 0.2980 overall best weight: 0.4636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 GLN ** C 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 674 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7091 moved from start: 0.2401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13708 Z= 0.195 Angle : 0.726 12.758 18433 Z= 0.371 Chirality : 0.044 0.179 2030 Planarity : 0.004 0.048 2345 Dihedral : 6.511 85.672 1852 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.54 % Favored : 92.28 % Rotamer: Outliers : 4.75 % Allowed : 30.39 % Favored : 64.86 % 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: -0.99 (0.21), residues: 1619 helix: 0.77 (0.20), residues: 707 sheet: 0.49 (0.40), residues: 193 loop : -2.57 (0.22), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 623 HIS 0.004 0.001 HIS A 149 PHE 0.048 0.001 PHE C 29 TYR 0.026 0.001 TYR A 305 ARG 0.019 0.001 ARG A 338 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3238 Ramachandran restraints generated. 1619 Oldfield, 0 Emsley, 1619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3238 Ramachandran restraints generated. 1619 Oldfield, 0 Emsley, 1619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 417 time to evaluate : 1.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 ARG cc_start: 0.8464 (OUTLIER) cc_final: 0.8207 (tmm-80) REVERT: A 72 LYS cc_start: 0.7314 (OUTLIER) cc_final: 0.6223 (ptpp) REVERT: A 93 MET cc_start: 0.7890 (mpp) cc_final: 0.7429 (mpp) REVERT: A 107 LYS cc_start: 0.7848 (tppp) cc_final: 0.7486 (tptp) REVERT: A 195 GLU cc_start: 0.7426 (tp30) cc_final: 0.6500 (tp30) REVERT: A 199 LYS cc_start: 0.8669 (pttm) cc_final: 0.8189 (pttm) REVERT: A 300 GLU cc_start: 0.6996 (pp20) cc_final: 0.6659 (pp20) REVERT: A 301 TYR cc_start: 0.8390 (OUTLIER) cc_final: 0.7780 (t80) REVERT: A 303 GLU cc_start: 0.7496 (pp20) cc_final: 0.7105 (pp20) REVERT: A 330 ARG cc_start: 0.7349 (OUTLIER) cc_final: 0.6675 (mtm-85) REVERT: A 397 GLN cc_start: 0.7180 (tt0) cc_final: 0.6392 (tm-30) REVERT: A 400 ILE cc_start: 0.8769 (mm) cc_final: 0.8446 (mm) REVERT: A 414 GLU cc_start: 0.7441 (tp30) cc_final: 0.7227 (tp30) REVERT: A 424 GLU cc_start: 0.7504 (pm20) cc_final: 0.7113 (pm20) REVERT: A 449 ARG cc_start: 0.8283 (mmm-85) cc_final: 0.8064 (mtp85) REVERT: A 450 ARG cc_start: 0.8358 (ttm-80) cc_final: 0.7960 (mmp80) REVERT: A 487 THR cc_start: 0.8033 (OUTLIER) cc_final: 0.7554 (p) REVERT: A 492 GLU cc_start: 0.7635 (mp0) cc_final: 0.7375 (mm-30) REVERT: A 553 MET cc_start: 0.7493 (mmm) cc_final: 0.7264 (mmp) REVERT: A 567 MET cc_start: 0.5839 (mmt) cc_final: 0.5493 (tpp) REVERT: A 582 ASN cc_start: 0.8045 (p0) cc_final: 0.7765 (p0) REVERT: A 607 LYS cc_start: 0.8513 (ttmt) cc_final: 0.8034 (mtpt) REVERT: B 55 ARG cc_start: 0.8240 (ttt180) cc_final: 0.7506 (ttp-170) REVERT: B 57 GLU cc_start: 0.7776 (tp30) cc_final: 0.7486 (tp30) REVERT: B 95 LYS cc_start: 0.8500 (tttt) cc_final: 0.8191 (ttmm) REVERT: B 128 GLN cc_start: 0.7680 (OUTLIER) cc_final: 0.7094 (mp-120) REVERT: B 142 LYS cc_start: 0.8338 (mttt) cc_final: 0.7763 (mtmm) REVERT: B 154 GLN cc_start: 0.7173 (mm-40) cc_final: 0.6721 (mm-40) REVERT: B 279 GLN cc_start: 0.7350 (OUTLIER) cc_final: 0.7021 (mm110) REVERT: B 294 ASP cc_start: 0.7957 (t0) cc_final: 0.7556 (t0) REVERT: B 312 TRP cc_start: 0.7396 (p-90) cc_final: 0.7025 (p-90) REVERT: B 344 PHE cc_start: 0.7520 (m-80) cc_final: 0.7277 (m-80) REVERT: B 352 ASN cc_start: 0.8330 (m-40) cc_final: 0.8000 (m-40) REVERT: B 376 PHE cc_start: 0.8578 (p90) cc_final: 0.8145 (p90) REVERT: B 410 LYS cc_start: 0.8117 (tttt) cc_final: 0.7877 (ttmt) REVERT: B 427 LYS cc_start: 0.8767 (mtmt) cc_final: 0.8442 (mtmm) REVERT: B 461 GLN cc_start: 0.8320 (mm-40) cc_final: 0.8022 (mm-40) REVERT: B 481 LYS cc_start: 0.8566 (mmtt) cc_final: 0.8345 (mmtt) REVERT: B 493 GLN cc_start: 0.8409 (OUTLIER) cc_final: 0.8099 (mm-40) REVERT: B 513 MET cc_start: 0.6627 (mmt) cc_final: 0.6050 (mmt) REVERT: B 514 THR cc_start: 0.7321 (OUTLIER) cc_final: 0.6946 (p) REVERT: B 559 LYS cc_start: 0.7785 (ttpp) cc_final: 0.7372 (ttpp) REVERT: B 572 ASP cc_start: 0.6962 (OUTLIER) cc_final: 0.6695 (p0) REVERT: B 683 MET cc_start: 0.7941 (mmm) cc_final: 0.7654 (mmm) REVERT: C 8 ASP cc_start: 0.6884 (m-30) cc_final: 0.6597 (m-30) REVERT: C 14 ASP cc_start: 0.7346 (p0) cc_final: 0.6887 (p0) REVERT: C 31 TRP cc_start: 0.8637 (OUTLIER) cc_final: 0.7711 (m-10) REVERT: C 40 MET cc_start: 0.7414 (tpt) cc_final: 0.7070 (tpt) REVERT: C 46 GLU cc_start: 0.7172 (OUTLIER) cc_final: 0.6558 (mt-10) REVERT: C 48 GLU cc_start: 0.7640 (mm-30) cc_final: 0.7178 (mm-30) REVERT: C 107 ARG cc_start: 0.7969 (mtt-85) cc_final: 0.7430 (mtt-85) REVERT: C 111 LYS cc_start: 0.8239 (mmmm) cc_final: 0.7914 (mttt) REVERT: C 118 ASP cc_start: 0.6231 (t0) cc_final: 0.5973 (t0) REVERT: D 529 LYS cc_start: 0.6049 (OUTLIER) cc_final: 0.5790 (ptmm) REVERT: D 578 MET cc_start: 0.7403 (mmm) cc_final: 0.7057 (mmm) REVERT: D 724 LYS cc_start: 0.8493 (tmmt) cc_final: 0.8117 (tmmt) outliers start: 71 outliers final: 50 residues processed: 461 average time/residue: 0.3231 time to fit residues: 201.9788 Evaluate side-chains 470 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 407 time to evaluate : 1.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ARG Chi-restraints excluded: chain A residue 72 LYS Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 301 TYR Chi-restraints excluded: chain A residue 307 SER Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 330 ARG Chi-restraints excluded: chain A residue 366 CYS Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 399 LYS Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 468 SER Chi-restraints excluded: chain A residue 487 THR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 518 ASP Chi-restraints excluded: chain A residue 521 CYS Chi-restraints excluded: chain A residue 570 ILE Chi-restraints excluded: chain A residue 574 LYS Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 634 ILE Chi-restraints excluded: chain A residue 683 MET Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 128 GLN Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 279 GLN Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 370 ILE Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 406 LYS Chi-restraints excluded: chain B residue 459 THR Chi-restraints excluded: chain B residue 466 MET Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain B residue 497 SER Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain B residue 572 ASP Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 592 VAL Chi-restraints excluded: chain B residue 617 MET Chi-restraints excluded: chain C residue 23 ILE Chi-restraints excluded: chain C residue 31 TRP Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain D residue 529 LYS Chi-restraints excluded: chain D residue 534 ILE Chi-restraints excluded: chain D residue 571 LEU Chi-restraints excluded: chain D residue 586 THR Chi-restraints excluded: chain D residue 588 VAL Chi-restraints excluded: chain D residue 605 VAL Chi-restraints excluded: chain D residue 634 ILE Chi-restraints excluded: chain D residue 652 LEU Chi-restraints excluded: chain D residue 708 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 137 optimal weight: 8.9990 chunk 146 optimal weight: 3.9990 chunk 150 optimal weight: 0.9980 chunk 88 optimal weight: 0.6980 chunk 63 optimal weight: 3.9990 chunk 114 optimal weight: 0.5980 chunk 44 optimal weight: 2.9990 chunk 132 optimal weight: 3.9990 chunk 138 optimal weight: 9.9990 chunk 145 optimal weight: 0.0020 chunk 96 optimal weight: 0.5980 overall best weight: 0.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 218 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7096 moved from start: 0.2494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13708 Z= 0.202 Angle : 0.758 13.820 18433 Z= 0.385 Chirality : 0.045 0.224 2030 Planarity : 0.004 0.048 2345 Dihedral : 6.531 85.343 1852 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.66 % Favored : 92.16 % Rotamer: Outliers : 4.82 % Allowed : 31.12 % Favored : 64.06 % 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: -0.97 (0.21), residues: 1619 helix: 0.75 (0.20), residues: 709 sheet: 0.56 (0.40), residues: 194 loop : -2.55 (0.22), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 289 HIS 0.004 0.001 HIS A 149 PHE 0.026 0.001 PHE B 304 TYR 0.025 0.001 TYR D 658 ARG 0.023 0.001 ARG A 338 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3238 Ramachandran restraints generated. 1619 Oldfield, 0 Emsley, 1619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3238 Ramachandran restraints generated. 1619 Oldfield, 0 Emsley, 1619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 413 time to evaluate : 1.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 ARG cc_start: 0.8471 (OUTLIER) cc_final: 0.8151 (tmm-80) REVERT: A 72 LYS cc_start: 0.7328 (OUTLIER) cc_final: 0.6550 (mtmm) REVERT: A 93 MET cc_start: 0.7874 (mpp) cc_final: 0.7408 (mpp) REVERT: A 107 LYS cc_start: 0.7857 (tppp) cc_final: 0.7503 (tptp) REVERT: A 195 GLU cc_start: 0.7432 (tp30) cc_final: 0.7067 (tp30) REVERT: A 199 LYS cc_start: 0.8675 (pttm) cc_final: 0.8114 (pttm) REVERT: A 300 GLU cc_start: 0.6989 (pp20) cc_final: 0.6672 (pp20) REVERT: A 301 TYR cc_start: 0.8400 (OUTLIER) cc_final: 0.7776 (t80) REVERT: A 303 GLU cc_start: 0.7506 (pp20) cc_final: 0.7102 (pp20) REVERT: A 330 ARG cc_start: 0.7362 (OUTLIER) cc_final: 0.6695 (mtm-85) REVERT: A 338 ARG cc_start: 0.7941 (mmp80) cc_final: 0.7481 (mmp80) REVERT: A 366 CYS cc_start: 0.7804 (OUTLIER) cc_final: 0.7522 (p) REVERT: A 397 GLN cc_start: 0.7164 (tt0) cc_final: 0.6400 (tm-30) REVERT: A 400 ILE cc_start: 0.8755 (mm) cc_final: 0.8481 (mm) REVERT: A 449 ARG cc_start: 0.8245 (mmm-85) cc_final: 0.8042 (mtp85) REVERT: A 471 GLU cc_start: 0.7578 (mp0) cc_final: 0.7372 (mp0) REVERT: A 481 LYS cc_start: 0.8695 (mmtt) cc_final: 0.8345 (mmtm) REVERT: A 487 THR cc_start: 0.8009 (OUTLIER) cc_final: 0.7563 (p) REVERT: A 492 GLU cc_start: 0.7642 (mp0) cc_final: 0.7381 (mm-30) REVERT: A 509 GLU cc_start: 0.7528 (tm-30) cc_final: 0.7010 (tm-30) REVERT: A 528 PHE cc_start: 0.8547 (t80) cc_final: 0.8124 (t80) REVERT: A 553 MET cc_start: 0.7488 (mmm) cc_final: 0.7250 (mmp) REVERT: A 567 MET cc_start: 0.5851 (mmt) cc_final: 0.5507 (tpp) REVERT: A 582 ASN cc_start: 0.8031 (p0) cc_final: 0.7776 (p0) REVERT: A 599 THR cc_start: 0.6665 (OUTLIER) cc_final: 0.6286 (t) REVERT: A 668 PHE cc_start: 0.8147 (m-80) cc_final: 0.7920 (m-80) REVERT: B 57 GLU cc_start: 0.7791 (tp30) cc_final: 0.7496 (tp30) REVERT: B 128 GLN cc_start: 0.7681 (OUTLIER) cc_final: 0.7087 (mp-120) REVERT: B 142 LYS cc_start: 0.8327 (mttt) cc_final: 0.7717 (mtmm) REVERT: B 154 GLN cc_start: 0.7148 (mm-40) cc_final: 0.6710 (mm-40) REVERT: B 279 GLN cc_start: 0.7350 (OUTLIER) cc_final: 0.7036 (mm110) REVERT: B 294 ASP cc_start: 0.7951 (t0) cc_final: 0.7575 (t0) REVERT: B 300 GLU cc_start: 0.7289 (mp0) cc_final: 0.6845 (pm20) REVERT: B 312 TRP cc_start: 0.7414 (p-90) cc_final: 0.7040 (p-90) REVERT: B 352 ASN cc_start: 0.8313 (m-40) cc_final: 0.8008 (m-40) REVERT: B 376 PHE cc_start: 0.8568 (p90) cc_final: 0.8202 (p90) REVERT: B 395 LEU cc_start: 0.8053 (tp) cc_final: 0.7717 (tt) REVERT: B 410 LYS cc_start: 0.8122 (tttt) cc_final: 0.7894 (ttmt) REVERT: B 427 LYS cc_start: 0.8756 (mtmt) cc_final: 0.8475 (mtmm) REVERT: B 481 LYS cc_start: 0.8572 (mmtt) cc_final: 0.8346 (mmtt) REVERT: B 492 GLU cc_start: 0.7776 (pm20) cc_final: 0.7303 (pm20) REVERT: B 493 GLN cc_start: 0.8479 (OUTLIER) cc_final: 0.8016 (mm-40) REVERT: B 513 MET cc_start: 0.6664 (mmt) cc_final: 0.6072 (mmt) REVERT: B 514 THR cc_start: 0.7263 (OUTLIER) cc_final: 0.6898 (p) REVERT: B 519 GLU cc_start: 0.6856 (tm-30) cc_final: 0.6522 (tm-30) REVERT: B 559 LYS cc_start: 0.7825 (ttpp) cc_final: 0.7540 (ttpp) REVERT: B 572 ASP cc_start: 0.6980 (OUTLIER) cc_final: 0.6722 (p0) REVERT: B 683 MET cc_start: 0.7929 (mmm) cc_final: 0.7652 (mmm) REVERT: C 8 ASP cc_start: 0.6878 (m-30) cc_final: 0.6591 (m-30) REVERT: C 14 ASP cc_start: 0.7308 (p0) cc_final: 0.6694 (p0) REVERT: C 29 PHE cc_start: 0.7282 (m-10) cc_final: 0.7030 (m-10) REVERT: C 31 TRP cc_start: 0.8664 (OUTLIER) cc_final: 0.7697 (m-10) REVERT: C 40 MET cc_start: 0.7416 (tpt) cc_final: 0.7053 (tpt) REVERT: C 46 GLU cc_start: 0.7179 (OUTLIER) cc_final: 0.6629 (mt-10) REVERT: C 107 ARG cc_start: 0.7963 (mtt-85) cc_final: 0.7588 (mtt-85) REVERT: C 111 LYS cc_start: 0.8230 (mmmm) cc_final: 0.7942 (mttt) REVERT: C 118 ASP cc_start: 0.6224 (t0) cc_final: 0.5962 (t0) REVERT: D 529 LYS cc_start: 0.6084 (OUTLIER) cc_final: 0.5778 (ptmm) REVERT: D 578 MET cc_start: 0.7420 (mmm) cc_final: 0.7105 (mmm) REVERT: D 724 LYS cc_start: 0.8493 (tmmt) cc_final: 0.8127 (tmmt) outliers start: 72 outliers final: 52 residues processed: 453 average time/residue: 0.3085 time to fit residues: 190.3030 Evaluate side-chains 479 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 412 time to evaluate : 1.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ARG Chi-restraints excluded: chain A residue 72 LYS Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 301 TYR Chi-restraints excluded: chain A residue 307 SER Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 330 ARG Chi-restraints excluded: chain A residue 366 CYS Chi-restraints excluded: chain A residue 399 LYS Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 468 SER Chi-restraints excluded: chain A residue 487 THR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 521 CYS Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 574 LYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 623 LYS Chi-restraints excluded: chain A residue 634 ILE Chi-restraints excluded: chain A residue 683 MET Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 128 GLN Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 279 GLN Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 370 ILE Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 406 LYS Chi-restraints excluded: chain B residue 459 THR Chi-restraints excluded: chain B residue 466 MET Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain B residue 497 SER Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain B residue 572 ASP Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 592 VAL Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 617 MET Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain C residue 23 ILE Chi-restraints excluded: chain C residue 31 TRP Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain D residue 529 LYS Chi-restraints excluded: chain D residue 534 ILE Chi-restraints excluded: chain D residue 571 LEU Chi-restraints excluded: chain D residue 586 THR Chi-restraints excluded: chain D residue 588 VAL Chi-restraints excluded: chain D residue 605 VAL Chi-restraints excluded: chain D residue 634 ILE Chi-restraints excluded: chain D residue 652 LEU Chi-restraints excluded: chain D residue 708 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 154 optimal weight: 0.8980 chunk 94 optimal weight: 0.0010 chunk 73 optimal weight: 2.9990 chunk 107 optimal weight: 5.9990 chunk 162 optimal weight: 0.9980 chunk 149 optimal weight: 2.9990 chunk 129 optimal weight: 10.0000 chunk 13 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 overall best weight: 1.1790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 189 GLN B 632 HIS ** C 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7142 moved from start: 0.2611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13708 Z= 0.246 Angle : 0.801 13.588 18433 Z= 0.411 Chirality : 0.046 0.206 2030 Planarity : 0.004 0.053 2345 Dihedral : 6.796 85.010 1852 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.51 % Favored : 90.30 % Rotamer: Outliers : 4.95 % Allowed : 31.59 % Favored : 63.45 % 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: -1.06 (0.21), residues: 1619 helix: 0.66 (0.20), residues: 709 sheet: 0.59 (0.42), residues: 177 loop : -2.54 (0.22), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 289 HIS 0.007 0.001 HIS B 320 PHE 0.030 0.002 PHE B 304 TYR 0.034 0.002 TYR D 658 ARG 0.021 0.001 ARG A 338 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3238 Ramachandran restraints generated. 1619 Oldfield, 0 Emsley, 1619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3238 Ramachandran restraints generated. 1619 Oldfield, 0 Emsley, 1619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 491 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 417 time to evaluate : 2.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 LYS cc_start: 0.7416 (OUTLIER) cc_final: 0.6590 (pttm) REVERT: A 93 MET cc_start: 0.7907 (mpp) cc_final: 0.7437 (mpp) REVERT: A 107 LYS cc_start: 0.7819 (tppp) cc_final: 0.7460 (tptp) REVERT: A 195 GLU cc_start: 0.7857 (tp30) cc_final: 0.7264 (tp30) REVERT: A 300 GLU cc_start: 0.7070 (pp20) cc_final: 0.6470 (pt0) REVERT: A 301 TYR cc_start: 0.8478 (OUTLIER) cc_final: 0.7824 (t80) REVERT: A 303 GLU cc_start: 0.7535 (pp20) cc_final: 0.7127 (pp20) REVERT: A 338 ARG cc_start: 0.7991 (mmp80) cc_final: 0.7429 (mmp80) REVERT: A 359 ARG cc_start: 0.8494 (mpp80) cc_final: 0.8126 (mpp80) REVERT: A 366 CYS cc_start: 0.7860 (OUTLIER) cc_final: 0.7451 (p) REVERT: A 397 GLN cc_start: 0.7291 (tt0) cc_final: 0.6515 (tm-30) REVERT: A 400 ILE cc_start: 0.8763 (mm) cc_final: 0.8521 (mm) REVERT: A 414 GLU cc_start: 0.7461 (tp30) cc_final: 0.7252 (tp30) REVERT: A 449 ARG cc_start: 0.8290 (mmm-85) cc_final: 0.8067 (mtp85) REVERT: A 476 MET cc_start: 0.7586 (tpp) cc_final: 0.6865 (tpp) REVERT: A 487 THR cc_start: 0.8055 (OUTLIER) cc_final: 0.7767 (p) REVERT: A 492 GLU cc_start: 0.7686 (mp0) cc_final: 0.7437 (mm-30) REVERT: A 551 LYS cc_start: 0.8217 (pttm) cc_final: 0.7862 (pttm) REVERT: A 553 MET cc_start: 0.7510 (mmm) cc_final: 0.7262 (mmp) REVERT: A 582 ASN cc_start: 0.8059 (p0) cc_final: 0.7753 (p0) REVERT: A 599 THR cc_start: 0.6737 (OUTLIER) cc_final: 0.6333 (t) REVERT: A 640 GLN cc_start: 0.8018 (pp30) cc_final: 0.7568 (pp30) REVERT: B 101 ASN cc_start: 0.8061 (t0) cc_final: 0.7546 (t0) REVERT: B 128 GLN cc_start: 0.7686 (OUTLIER) cc_final: 0.7080 (mp-120) REVERT: B 142 LYS cc_start: 0.8317 (mttt) cc_final: 0.7745 (mtmm) REVERT: B 154 GLN cc_start: 0.7111 (mm-40) cc_final: 0.6675 (mm-40) REVERT: B 279 GLN cc_start: 0.7332 (OUTLIER) cc_final: 0.7006 (tp40) REVERT: B 294 ASP cc_start: 0.7966 (t0) cc_final: 0.7573 (t0) REVERT: B 295 ASP cc_start: 0.8198 (m-30) cc_final: 0.7951 (p0) REVERT: B 300 GLU cc_start: 0.7320 (mp0) cc_final: 0.6926 (pm20) REVERT: B 312 TRP cc_start: 0.7474 (p-90) cc_final: 0.7121 (p-90) REVERT: B 329 PHE cc_start: 0.8455 (p90) cc_final: 0.7901 (p90) REVERT: B 352 ASN cc_start: 0.8337 (m-40) cc_final: 0.7979 (m-40) REVERT: B 376 PHE cc_start: 0.8577 (p90) cc_final: 0.8153 (p90) REVERT: B 395 LEU cc_start: 0.8166 (tp) cc_final: 0.7918 (tt) REVERT: B 410 LYS cc_start: 0.8181 (tttt) cc_final: 0.7918 (ttmt) REVERT: B 461 GLN cc_start: 0.8354 (mm-40) cc_final: 0.8048 (mm-40) REVERT: B 481 LYS cc_start: 0.8663 (mmtt) cc_final: 0.8373 (mmtt) REVERT: B 492 GLU cc_start: 0.7796 (pm20) cc_final: 0.7331 (pm20) REVERT: B 493 GLN cc_start: 0.8503 (OUTLIER) cc_final: 0.8050 (mm-40) REVERT: B 513 MET cc_start: 0.6604 (mmt) cc_final: 0.6020 (mmt) REVERT: B 514 THR cc_start: 0.7385 (OUTLIER) cc_final: 0.7054 (p) REVERT: B 559 LYS cc_start: 0.7942 (ttpp) cc_final: 0.7537 (ttpt) REVERT: B 569 GLU cc_start: 0.7658 (pm20) cc_final: 0.7152 (pm20) REVERT: B 572 ASP cc_start: 0.6977 (OUTLIER) cc_final: 0.6708 (p0) REVERT: B 683 MET cc_start: 0.7987 (mmm) cc_final: 0.7735 (mmm) REVERT: C 8 ASP cc_start: 0.7009 (m-30) cc_final: 0.6707 (m-30) REVERT: C 14 ASP cc_start: 0.7308 (p0) cc_final: 0.6769 (p0) REVERT: C 31 TRP cc_start: 0.8665 (OUTLIER) cc_final: 0.7637 (m-10) REVERT: C 40 MET cc_start: 0.7450 (tpt) cc_final: 0.7111 (tpt) REVERT: C 46 GLU cc_start: 0.7229 (OUTLIER) cc_final: 0.6645 (mt-10) REVERT: C 48 GLU cc_start: 0.7649 (mm-30) cc_final: 0.7207 (mm-30) REVERT: C 107 ARG cc_start: 0.7970 (mtt-85) cc_final: 0.7426 (mtt-85) REVERT: C 111 LYS cc_start: 0.8251 (mmmm) cc_final: 0.7958 (mttt) REVERT: C 118 ASP cc_start: 0.6902 (t0) cc_final: 0.6535 (t0) REVERT: D 529 LYS cc_start: 0.6085 (OUTLIER) cc_final: 0.5808 (ptmm) REVERT: D 578 MET cc_start: 0.7444 (mmm) cc_final: 0.7233 (mmm) REVERT: D 724 LYS cc_start: 0.8540 (tmmt) cc_final: 0.8177 (tmmt) outliers start: 74 outliers final: 57 residues processed: 458 average time/residue: 0.3335 time to fit residues: 210.4329 Evaluate side-chains 484 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 414 time to evaluate : 1.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LYS Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 283 ASN Chi-restraints excluded: chain A residue 301 TYR Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 350 LYS Chi-restraints excluded: chain A residue 366 CYS Chi-restraints excluded: chain A residue 399 LYS Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 468 SER Chi-restraints excluded: chain A residue 487 THR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 521 CYS Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 574 LYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 623 LYS Chi-restraints excluded: chain A residue 632 HIS Chi-restraints excluded: chain A residue 634 ILE Chi-restraints excluded: chain A residue 683 MET Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 128 GLN Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 189 GLN Chi-restraints excluded: chain B residue 279 GLN Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 370 ILE Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 406 LYS Chi-restraints excluded: chain B residue 459 THR Chi-restraints excluded: chain B residue 466 MET Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 497 SER Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain B residue 572 ASP Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 592 VAL Chi-restraints excluded: chain B residue 617 MET Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 632 HIS Chi-restraints excluded: chain C residue 23 ILE Chi-restraints excluded: chain C residue 31 TRP Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain D residue 529 LYS Chi-restraints excluded: chain D residue 534 ILE Chi-restraints excluded: chain D residue 571 LEU Chi-restraints excluded: chain D residue 586 THR Chi-restraints excluded: chain D residue 588 VAL Chi-restraints excluded: chain D residue 605 VAL Chi-restraints excluded: chain D residue 622 LEU Chi-restraints excluded: chain D residue 634 ILE Chi-restraints excluded: chain D residue 652 LEU Chi-restraints excluded: chain D residue 708 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 137 optimal weight: 20.0000 chunk 39 optimal weight: 0.9990 chunk 119 optimal weight: 6.9990 chunk 19 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 129 optimal weight: 8.9990 chunk 54 optimal weight: 6.9990 chunk 132 optimal weight: 6.9990 chunk 16 optimal weight: 7.9990 chunk 23 optimal weight: 1.9990 chunk 113 optimal weight: 0.9980 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 30 ASN ** B 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 632 HIS ** C 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.141719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.112988 restraints weight = 24828.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.116847 restraints weight = 13490.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.119454 restraints weight = 8550.049| |-----------------------------------------------------------------------------| r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7236 moved from start: 0.2717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 13708 Z= 0.359 Angle : 0.860 13.310 18433 Z= 0.450 Chirality : 0.050 0.223 2030 Planarity : 0.005 0.055 2345 Dihedral : 7.082 84.787 1852 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.19 % Allowed : 10.07 % Favored : 89.75 % Rotamer: Outliers : 4.69 % Allowed : 31.79 % Favored : 63.52 % 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: -1.36 (0.21), residues: 1619 helix: 0.40 (0.20), residues: 706 sheet: 0.34 (0.42), residues: 180 loop : -2.66 (0.22), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 289 HIS 0.010 0.001 HIS B 320 PHE 0.035 0.002 PHE A 39 TYR 0.035 0.002 TYR D 658 ARG 0.021 0.001 ARG A 338 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3716.69 seconds wall clock time: 68 minutes 13.60 seconds (4093.60 seconds total)