Starting phenix.real_space_refine on Fri Jun 27 15:18:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ffw_29069/06_2025/8ffw_29069_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ffw_29069/06_2025/8ffw_29069.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ffw_29069/06_2025/8ffw_29069.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ffw_29069/06_2025/8ffw_29069.map" model { file = "/net/cci-nas-00/data/ceres_data/8ffw_29069/06_2025/8ffw_29069_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ffw_29069/06_2025/8ffw_29069_trim.cif" } resolution = 3.23 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= 0.003 sd= 0.033 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: 8 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 85 5.16 5 C 9984 2.51 5 N 2637 2.21 5 O 3040 1.98 5 F 1 1.80 5 H 15742 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 92 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 31497 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 10279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 630, 10279 Classifications: {'peptide': 630} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 614} Chain breaks: 1 Chain: "B" Number of atoms: 10442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 641, 10442 Classifications: {'peptide': 641} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 624} Chain breaks: 2 Chain: "C" Number of atoms: 4235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 4235 Classifications: {'peptide': 259} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 247} Chain: "D" Number of atoms: 6449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 409, 6449 Classifications: {'peptide': 409} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 396} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'DEX': 1} Classifications: {'undetermined': 1} Time building chain proxies: 15.77, per 1000 atoms: 0.50 Number of scatterers: 31497 At special positions: 0 Unit cell: (141.95, 129.425, 121.075, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 85 16.00 P 6 15.00 Mg 2 11.99 F 1 9.00 O 3040 8.00 N 2637 7.00 C 9984 6.00 H 15742 1.00 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: 8.83 Conformation dependent library (CDL) restraints added in 2.5 seconds 3850 Ramachandran restraints generated. 1925 Oldfield, 0 Emsley, 1925 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3666 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 14 sheets defined 49.8% alpha, 13.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.05 Creating SS restraints... Processing helix chain 'A' and resid 25 through 36 Processing helix chain 'A' and resid 42 through 63 removed outlier: 3.616A pdb=" N ARG A 46 " --> pdb=" O GLU A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 65 No H-bonds generated for 'chain 'A' and resid 64 through 65' Processing helix chain 'A' and resid 66 through 71 Processing helix chain 'A' and resid 99 through 108 Processing helix chain 'A' and resid 113 through 121 Processing helix chain 'A' and resid 137 through 143 Processing helix chain 'A' and resid 195 through 198 Processing helix chain 'A' and resid 199 through 212 removed outlier: 3.909A pdb=" N GLN A 212 " --> pdb=" O LYS A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 299 Processing helix chain 'A' and resid 300 through 304 Processing helix chain 'A' and resid 305 through 318 Processing helix chain 'A' and resid 374 through 378 Processing helix chain 'A' and resid 379 through 383 Processing helix chain 'A' and resid 406 through 428 Processing helix chain 'A' and resid 430 through 451 removed outlier: 3.759A pdb=" N GLN A 440 " --> pdb=" O LYS A 436 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N LYS A 443 " --> pdb=" O GLU A 439 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N ASN A 444 " --> pdb=" O GLN A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 454 No H-bonds generated for 'chain 'A' and resid 452 through 454' Processing helix chain 'A' and resid 455 through 460 Processing helix chain 'A' and resid 461 through 463 No H-bonds generated for 'chain 'A' and resid 461 through 463' Processing helix chain 'A' and resid 476 through 483 Processing helix chain 'A' and resid 498 through 504 removed outlier: 3.659A pdb=" N VAL A 502 " --> pdb=" O THR A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 507 No H-bonds generated for 'chain 'A' and resid 505 through 507' Processing helix chain 'A' and resid 508 through 514 Processing helix chain 'A' and resid 525 through 530 removed outlier: 3.744A pdb=" N CYS A 529 " --> pdb=" O ILE A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 578 removed outlier: 4.867A pdb=" N ASN A 570 " --> pdb=" O THR A 566 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N LEU A 571 " --> pdb=" O LYS A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 615 Processing helix chain 'A' and resid 621 through 629 removed outlier: 4.326A pdb=" N MET A 625 " --> pdb=" O ASP A 621 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 653 Processing helix chain 'A' and resid 656 through 674 Processing helix chain 'A' and resid 681 through 696 removed outlier: 3.505A pdb=" N ALA A 685 " --> pdb=" O PRO A 681 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 37 removed outlier: 3.807A pdb=" N PHE B 37 " --> pdb=" O ILE B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 63 removed outlier: 4.186A pdb=" N ARG B 46 " --> pdb=" O GLU B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 65 No H-bonds generated for 'chain 'B' and resid 64 through 65' Processing helix chain 'B' and resid 66 through 71 Processing helix chain 'B' and resid 99 through 108 Processing helix chain 'B' and resid 113 through 121 Processing helix chain 'B' and resid 136 through 143 Processing helix chain 'B' and resid 194 through 198 Processing helix chain 'B' and resid 199 through 211 Processing helix chain 'B' and resid 300 through 304 removed outlier: 3.681A pdb=" N ASP B 303 " --> pdb=" O ASN B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 318 Processing helix chain 'B' and resid 374 through 378 removed outlier: 3.600A pdb=" N ILE B 378 " --> pdb=" O GLU B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 383 Processing helix chain 'B' and resid 406 through 428 removed outlier: 3.548A pdb=" N LYS B 410 " --> pdb=" O SER B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 452 removed outlier: 3.584A pdb=" N GLN B 440 " --> pdb=" O LYS B 436 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N LYS B 443 " --> pdb=" O GLU B 439 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N ASN B 444 " --> pdb=" O GLN B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 460 Processing helix chain 'B' and resid 477 through 482 Processing helix chain 'B' and resid 498 through 504 Processing helix chain 'B' and resid 505 through 507 No H-bonds generated for 'chain 'B' and resid 505 through 507' Processing helix chain 'B' and resid 508 through 514 Processing helix chain 'B' and resid 525 through 533 removed outlier: 4.091A pdb=" N GLN B 531 " --> pdb=" O GLU B 527 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLN B 532 " --> pdb=" O TYR B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 554 through 565 Processing helix chain 'B' and resid 568 through 579 Processing helix chain 'B' and resid 609 through 616 Processing helix chain 'B' and resid 621 through 627 Processing helix chain 'B' and resid 640 through 653 Processing helix chain 'B' and resid 656 through 674 Processing helix chain 'B' and resid 680 through 696 removed outlier: 3.981A pdb=" N HIS B 684 " --> pdb=" O ASP B 680 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N ASN B 686 " --> pdb=" O GLN B 682 " (cutoff:3.500A) Processing helix chain 'B' and resid 724 through 729 Processing helix chain 'C' and resid 531 through 540 Processing helix chain 'C' and resid 555 through 580 Processing helix chain 'C' and resid 583 through 587 Processing helix chain 'C' and resid 588 through 616 removed outlier: 4.849A pdb=" N MET C 601 " --> pdb=" O GLN C 597 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N SER C 602 " --> pdb=" O TYR C 598 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 634 Processing helix chain 'C' and resid 636 through 656 removed outlier: 5.393A pdb=" N LYS C 644 " --> pdb=" O TYR C 640 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N HIS C 645 " --> pdb=" O ASP C 641 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N TYR C 648 " --> pdb=" O LYS C 644 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL C 649 " --> pdb=" O HIS C 645 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER C 650 " --> pdb=" O MET C 646 " (cutoff:3.500A) Processing helix chain 'C' and resid 659 through 672 Processing helix chain 'C' and resid 682 through 706 removed outlier: 5.272A pdb=" N GLU C 688 " --> pdb=" O GLU C 684 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ARG C 704 " --> pdb=" O ALA C 700 " (cutoff:3.500A) Processing helix chain 'C' and resid 708 through 742 removed outlier: 3.799A pdb=" N LEU C 721 " --> pdb=" O GLN C 717 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU C 722 " --> pdb=" O LEU C 718 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N HIS C 726 " --> pdb=" O LEU C 722 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N GLU C 727 " --> pdb=" O ASP C 723 " (cutoff:3.500A) Processing helix chain 'C' and resid 750 through 766 Proline residue: C 762 - end of helix Processing helix chain 'D' and resid 14 through 18 Processing helix chain 'D' and resid 19 through 21 No H-bonds generated for 'chain 'D' and resid 19 through 21' Processing helix chain 'D' and resid 69 through 74 Processing helix chain 'D' and resid 87 through 95 removed outlier: 3.808A pdb=" N GLY D 93 " --> pdb=" O ALA D 89 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA D 95 " --> pdb=" O ASP D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 112 Processing helix chain 'D' and resid 191 through 196 Processing helix chain 'D' and resid 201 through 206 Processing helix chain 'D' and resid 260 through 281 Processing helix chain 'D' and resid 283 through 299 Processing helix chain 'D' and resid 308 through 331 removed outlier: 3.661A pdb=" N SER D 312 " --> pdb=" O GLU D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 334 through 347 Processing helix chain 'D' and resid 350 through 363 Processing helix chain 'D' and resid 366 through 381 Processing helix chain 'D' and resid 384 through 410 removed outlier: 3.608A pdb=" N ARG D 388 " --> pdb=" O ASN D 384 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 420 Processing sheet with id=AA1, first strand: chain 'A' and resid 18 through 21 removed outlier: 3.538A pdb=" N LYS B 147 " --> pdb=" O HIS B 189 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N GLU B 223 " --> pdb=" O PRO B 82 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ILE B 218 " --> pdb=" O LEU B 290 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 284 through 289 removed outlier: 6.611A pdb=" N GLU A 223 " --> pdb=" O PRO A 82 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 109 through 110 Processing sheet with id=AA4, first strand: chain 'A' and resid 323 through 332 removed outlier: 6.659A pdb=" N VAL A 343 " --> pdb=" O LEU A 324 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N VAL A 326 " --> pdb=" O LEU A 341 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N LEU A 341 " --> pdb=" O VAL A 326 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N HIS A 328 " --> pdb=" O ALA A 339 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ALA A 339 " --> pdb=" O HIS A 328 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N SER A 330 " --> pdb=" O PHE A 337 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N PHE A 337 " --> pdb=" O SER A 330 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N VAL A 365 " --> pdb=" O PHE A 369 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N PHE A 369 " --> pdb=" O VAL A 365 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 466 through 467 removed outlier: 4.450A pdb=" N TYR A 466 " --> pdb=" O TYR A 520 " (cutoff:3.500A) removed outlier: 9.242A pdb=" N ILE A 519 " --> pdb=" O HIS A 490 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N TYR A 492 " --> pdb=" O ILE A 519 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N MET A 521 " --> pdb=" O TYR A 492 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ILE A 494 " --> pdb=" O MET A 521 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N ILE A 491 " --> pdb=" O VAL A 542 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 586 through 588 Processing sheet with id=AA7, first strand: chain 'B' and resid 323 through 331 removed outlier: 6.674A pdb=" N VAL B 343 " --> pdb=" O LEU B 324 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N VAL B 326 " --> pdb=" O LEU B 341 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N LEU B 341 " --> pdb=" O VAL B 326 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N HIS B 328 " --> pdb=" O ALA B 339 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ALA B 339 " --> pdb=" O HIS B 328 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N SER B 330 " --> pdb=" O PHE B 337 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N PHE B 337 " --> pdb=" O SER B 330 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N VAL B 365 " --> pdb=" O PHE B 369 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N PHE B 369 " --> pdb=" O VAL B 365 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 475 through 476 removed outlier: 4.316A pdb=" N TYR B 466 " --> pdb=" O TYR B 520 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N TYR B 492 " --> pdb=" O ILE B 519 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N MET B 521 " --> pdb=" O TYR B 492 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N ILE B 494 " --> pdb=" O MET B 521 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILE B 491 " --> pdb=" O VAL B 542 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 585 through 588 removed outlier: 6.622A pdb=" N LYS B 585 " --> pdb=" O LEU B 634 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N ILE B 636 " --> pdb=" O LYS B 585 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N VAL B 587 " --> pdb=" O ILE B 636 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 621 through 624 removed outlier: 6.288A pdb=" N LEU C 627 " --> pdb=" O PHE C 623 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 674 through 676 Processing sheet with id=AB3, first strand: chain 'D' and resid 23 through 25 Processing sheet with id=AB4, first strand: chain 'D' and resid 39 through 40 removed outlier: 3.738A pdb=" N ARG D 39 " --> pdb=" O ILE D 102 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 148 through 154 removed outlier: 6.520A pdb=" N GLN D 214 " --> pdb=" O LYS D 153 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N LEU D 247 " --> pdb=" O HIS D 171 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N HIS D 171 " --> pdb=" O LEU D 247 " (cutoff:3.500A) 783 hydrogen bonds defined for protein. 2148 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: 13.17 Time building geometry restraints manager: 10.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.95 - 1.13: 15714 1.13 - 1.31: 3005 1.31 - 1.49: 6725 1.49 - 1.66: 6187 1.66 - 1.84: 141 Bond restraints: 31772 Sorted by residual: bond pdb=" C4 ATP A 801 " pdb=" C5 ATP A 801 " ideal model delta sigma weight residual 1.388 1.495 -0.107 1.00e-02 1.00e+04 1.14e+02 bond pdb=" C5 ATP B 801 " pdb=" C6 ATP B 801 " ideal model delta sigma weight residual 1.409 1.515 -0.106 1.00e-02 1.00e+04 1.13e+02 bond pdb=" C5 ATP A 801 " pdb=" C6 ATP A 801 " ideal model delta sigma weight residual 1.409 1.515 -0.106 1.00e-02 1.00e+04 1.12e+02 bond pdb=" C4 ATP B 801 " pdb=" C5 ATP B 801 " ideal model delta sigma weight residual 1.388 1.494 -0.106 1.00e-02 1.00e+04 1.12e+02 bond pdb=" CB HIS D 71 " pdb=" CG HIS D 71 " ideal model delta sigma weight residual 1.497 1.351 0.146 1.40e-02 5.10e+03 1.08e+02 ... (remaining 31767 not shown) Histogram of bond angle deviations from ideal: 0.00 - 10.31: 57493 10.31 - 20.62: 56 20.62 - 30.93: 3 30.93 - 41.24: 11 41.24 - 51.55: 7 Bond angle restraints: 57570 Sorted by residual: angle pdb=" C TYR A 528 " pdb=" N CYS A 529 " pdb=" CA CYS A 529 " ideal model delta sigma weight residual 120.44 154.74 -34.30 1.36e+00 5.41e-01 6.36e+02 angle pdb=" C MET D 48 " pdb=" N ILE D 49 " pdb=" CA ILE D 49 " ideal model delta sigma weight residual 122.90 153.13 -30.23 1.28e+00 6.10e-01 5.58e+02 angle pdb=" C MET B 484 " pdb=" N LYS B 485 " pdb=" CA LYS B 485 " ideal model delta sigma weight residual 120.94 153.36 -32.42 1.57e+00 4.06e-01 4.26e+02 angle pdb=" C THR B 594 " pdb=" N SER B 595 " pdb=" CA SER B 595 " ideal model delta sigma weight residual 120.49 149.48 -28.99 1.42e+00 4.96e-01 4.17e+02 angle pdb=" PB ATP B 801 " pdb=" O3B ATP B 801 " pdb=" PG ATP B 801 " ideal model delta sigma weight residual 139.87 120.06 19.81 1.00e+00 1.00e+00 3.92e+02 ... (remaining 57565 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 14179 17.88 - 35.76: 434 35.76 - 53.64: 194 53.64 - 71.52: 58 71.52 - 89.40: 16 Dihedral angle restraints: 14881 sinusoidal: 8302 harmonic: 6579 Sorted by residual: dihedral pdb=" CA ASP B 472 " pdb=" C ASP B 472 " pdb=" N GLU B 473 " pdb=" CA GLU B 473 " ideal model delta harmonic sigma weight residual 180.00 150.02 29.98 0 5.00e+00 4.00e-02 3.60e+01 dihedral pdb=" CA PHE A 437 " pdb=" C PHE A 437 " pdb=" N TYR A 438 " pdb=" CA TYR A 438 " ideal model delta harmonic sigma weight residual 180.00 -155.87 -24.13 0 5.00e+00 4.00e-02 2.33e+01 dihedral pdb=" CA TYR B 480 " pdb=" C TYR B 480 " pdb=" N CYS B 481 " pdb=" CA CYS B 481 " ideal model delta harmonic sigma weight residual 180.00 -156.55 -23.45 0 5.00e+00 4.00e-02 2.20e+01 ... (remaining 14878 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.181: 2203 0.181 - 0.362: 172 0.362 - 0.543: 3 0.543 - 0.724: 0 0.724 - 0.905: 1 Chirality restraints: 2379 Sorted by residual: chirality pdb=" C8 DEX C 801 " pdb=" C14 DEX C 801 " pdb=" C7 DEX C 801 " pdb=" C9 DEX C 801 " both_signs ideal model delta sigma weight residual False 2.68 1.78 0.91 2.00e-01 2.50e+01 2.05e+01 chirality pdb=" CB ILE B 378 " pdb=" CA ILE B 378 " pdb=" CG1 ILE B 378 " pdb=" CG2 ILE B 378 " both_signs ideal model delta sigma weight residual False 2.64 2.13 0.51 2.00e-01 2.50e+01 6.50e+00 chirality pdb=" CG LEU D 128 " pdb=" CB LEU D 128 " pdb=" CD1 LEU D 128 " pdb=" CD2 LEU D 128 " both_signs ideal model delta sigma weight residual False -2.59 -2.09 -0.50 2.00e-01 2.50e+01 6.16e+00 ... (remaining 2376 not shown) Planarity restraints: 4627 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 578 " -0.082 2.00e-02 2.50e+03 1.57e-01 2.47e+02 pdb=" N LEU A 579 " 0.270 2.00e-02 2.50e+03 pdb=" CA LEU A 579 " -0.070 2.00e-02 2.50e+03 pdb=" H LEU A 579 " -0.118 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 36 " -0.081 2.00e-02 2.50e+03 1.57e-01 2.46e+02 pdb=" N PHE A 37 " 0.270 2.00e-02 2.50e+03 pdb=" CA PHE A 37 " -0.073 2.00e-02 2.50e+03 pdb=" H PHE A 37 " -0.117 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 168 " -0.087 2.00e-02 2.50e+03 1.56e-01 2.42e+02 pdb=" N SER A 169 " 0.268 2.00e-02 2.50e+03 pdb=" CA SER A 169 " -0.073 2.00e-02 2.50e+03 pdb=" H SER A 169 " -0.109 2.00e-02 2.50e+03 ... (remaining 4624 not shown) Histogram of nonbonded interaction distances: 1.20 - 1.88: 367 1.88 - 2.56: 31302 2.56 - 3.24: 99843 3.24 - 3.92: 126698 3.92 - 4.60: 198418 Nonbonded interactions: 456628 Sorted by model distance: nonbonded pdb=" H ASP A 639 " pdb=" H HIS A 640 " model vdw 1.200 2.100 nonbonded pdb=" H VAL A 544 " pdb=" H THR A 545 " model vdw 1.200 2.100 nonbonded pdb=" H PHE B 384 " pdb=" H ILE B 385 " model vdw 1.221 2.100 nonbonded pdb=" H ILE A 43 " pdb=" H PHE A 44 " model vdw 1.223 2.100 nonbonded pdb=" H TYR C 613 " pdb=" H ARG C 614 " model vdw 1.228 2.100 ... (remaining 456623 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' selection = (chain 'B' and (resid 15 through 701 or resid 801 through 802)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.270 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: 0.570 Extract box with map and model: 1.350 Check model and map are aligned: 0.240 Set scattering table: 0.300 Process input model: 69.360 Find NCS groups from input model: 0.760 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 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 : 0.024 0.174 16030 Z= 1.347 Angle : 1.946 34.304 21578 Z= 1.325 Chirality : 0.103 0.905 2379 Planarity : 0.016 0.149 2749 Dihedral : 11.357 89.400 6286 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 1.30 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.40 % Favored : 98.55 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 3.70 % 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: 0.37 (0.18), residues: 1925 helix: -0.24 (0.16), residues: 841 sheet: 1.37 (0.32), residues: 273 loop : 0.64 (0.22), residues: 811 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.068 0.012 TRP C 712 HIS 0.012 0.003 HIS D 104 PHE 0.044 0.007 PHE B 337 TYR 0.088 0.010 TYR D 333 ARG 0.007 0.001 ARG A 591 Details of bonding type rmsd hydrogen bonds : bond 0.17587 ( 783) hydrogen bonds : angle 7.23724 ( 2148) covalent geometry : bond 0.02447 (16030) covalent geometry : angle 1.94625 (21578) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3850 Ramachandran restraints generated. 1925 Oldfield, 0 Emsley, 1925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3850 Ramachandran restraints generated. 1925 Oldfield, 0 Emsley, 1925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 180 time to evaluate : 2.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 219 THR cc_start: 0.8592 (m) cc_final: 0.8342 (p) REVERT: A 371 MET cc_start: 0.6443 (ttt) cc_final: 0.6168 (ttp) REVERT: C 742 ASP cc_start: 0.9241 (t0) cc_final: 0.9015 (p0) outliers start: 0 outliers final: 0 residues processed: 180 average time/residue: 0.7854 time to fit residues: 201.5845 Evaluate side-chains 108 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 2.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 162 optimal weight: 9.9990 chunk 145 optimal weight: 6.9990 chunk 80 optimal weight: 1.9990 chunk 49 optimal weight: 5.9990 chunk 98 optimal weight: 0.9980 chunk 77 optimal weight: 5.9990 chunk 150 optimal weight: 7.9990 chunk 58 optimal weight: 5.9990 chunk 91 optimal weight: 5.9990 chunk 112 optimal weight: 5.9990 chunk 174 optimal weight: 10.0000 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 531 GLN B 633 HIS ** C 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 586 ASN C 734 ASN ** D 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 210 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.093214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.059270 restraints weight = 146304.636| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 4.04 r_work: 0.3081 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 16030 Z= 0.284 Angle : 0.797 22.135 21578 Z= 0.459 Chirality : 0.045 0.180 2379 Planarity : 0.005 0.052 2749 Dihedral : 7.762 80.789 2244 Min Nonbonded Distance : 1.623 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 0.52 % Allowed : 3.01 % Favored : 96.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.46 (0.19), residues: 1925 helix: 0.44 (0.17), residues: 841 sheet: 0.82 (0.32), residues: 263 loop : 0.17 (0.22), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP C 600 HIS 0.006 0.002 HIS A 77 PHE 0.021 0.002 PHE C 606 TYR 0.025 0.002 TYR B 465 ARG 0.003 0.001 ARG D 222 Details of bonding type rmsd hydrogen bonds : bond 0.06757 ( 783) hydrogen bonds : angle 5.69807 ( 2148) covalent geometry : bond 0.00615 (16030) covalent geometry : angle 0.79721 (21578) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3850 Ramachandran restraints generated. 1925 Oldfield, 0 Emsley, 1925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3850 Ramachandran restraints generated. 1925 Oldfield, 0 Emsley, 1925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 118 time to evaluate : 4.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 371 MET cc_start: 0.6019 (ttt) cc_final: 0.5615 (ttp) REVERT: B 654 LYS cc_start: 0.9240 (mttt) cc_final: 0.8755 (mmtm) REVERT: C 588 HIS cc_start: 0.8381 (t-90) cc_final: 0.8142 (t-90) REVERT: C 601 MET cc_start: 0.8989 (mmm) cc_final: 0.8533 (mmm) REVERT: C 646 MET cc_start: 0.7844 (ptt) cc_final: 0.6836 (ptt) REVERT: C 690 ARG cc_start: 0.9192 (mtp180) cc_final: 0.8795 (mmm-85) REVERT: C 742 ASP cc_start: 0.9351 (t0) cc_final: 0.9083 (p0) outliers start: 9 outliers final: 8 residues processed: 125 average time/residue: 0.9771 time to fit residues: 179.1355 Evaluate side-chains 110 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 102 time to evaluate : 4.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 MET Chi-restraints excluded: chain A residue 581 LYS Chi-restraints excluded: chain A residue 601 THR Chi-restraints excluded: chain B residue 453 SER Chi-restraints excluded: chain C residue 709 SER Chi-restraints excluded: chain C residue 715 PHE Chi-restraints excluded: chain C residue 774 PHE Chi-restraints excluded: chain D residue 299 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 97 optimal weight: 0.6980 chunk 27 optimal weight: 0.0570 chunk 190 optimal weight: 2.9990 chunk 30 optimal weight: 0.4980 chunk 16 optimal weight: 5.9990 chunk 142 optimal weight: 9.9990 chunk 164 optimal weight: 30.0000 chunk 64 optimal weight: 1.9990 chunk 145 optimal weight: 9.9990 chunk 20 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 overall best weight: 1.2502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 633 HIS C 564 ASN C 734 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.095151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.061433 restraints weight = 145142.964| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 4.05 r_work: 0.3139 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.3056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 16030 Z= 0.143 Angle : 0.634 21.064 21578 Z= 0.362 Chirality : 0.040 0.165 2379 Planarity : 0.004 0.042 2749 Dihedral : 7.132 87.896 2244 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 0.64 % Allowed : 3.76 % Favored : 95.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.73 (0.19), residues: 1925 helix: 0.96 (0.17), residues: 842 sheet: 0.55 (0.31), residues: 264 loop : 0.11 (0.22), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 600 HIS 0.003 0.001 HIS D 104 PHE 0.024 0.001 PHE C 606 TYR 0.018 0.002 TYR D 218 ARG 0.003 0.000 ARG D 406 Details of bonding type rmsd hydrogen bonds : bond 0.05195 ( 783) hydrogen bonds : angle 5.03911 ( 2148) covalent geometry : bond 0.00296 (16030) covalent geometry : angle 0.63384 (21578) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3850 Ramachandran restraints generated. 1925 Oldfield, 0 Emsley, 1925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3850 Ramachandran restraints generated. 1925 Oldfield, 0 Emsley, 1925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 119 time to evaluate : 2.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 610 MET cc_start: 0.8798 (tpp) cc_final: 0.7845 (tpp) REVERT: B 654 LYS cc_start: 0.9095 (mttt) cc_final: 0.8570 (mmtm) REVERT: C 601 MET cc_start: 0.9105 (mmm) cc_final: 0.8789 (mmm) REVERT: C 646 MET cc_start: 0.6987 (ptt) cc_final: 0.6647 (ptt) REVERT: C 666 MET cc_start: 0.9229 (mtm) cc_final: 0.8693 (tpt) REVERT: C 690 ARG cc_start: 0.9158 (mtp180) cc_final: 0.8781 (mmm-85) REVERT: C 742 ASP cc_start: 0.9340 (t0) cc_final: 0.9056 (p0) outliers start: 11 outliers final: 8 residues processed: 127 average time/residue: 0.7681 time to fit residues: 138.3307 Evaluate side-chains 111 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 103 time to evaluate : 2.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 581 LYS Chi-restraints excluded: chain B residue 193 ASP Chi-restraints excluded: chain B residue 453 SER Chi-restraints excluded: chain B residue 581 LYS Chi-restraints excluded: chain C residue 715 PHE Chi-restraints excluded: chain C residue 774 PHE Chi-restraints excluded: chain D residue 299 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 96 optimal weight: 0.9980 chunk 46 optimal weight: 4.9990 chunk 92 optimal weight: 0.6980 chunk 125 optimal weight: 5.9990 chunk 135 optimal weight: 9.9990 chunk 79 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 147 optimal weight: 9.9990 chunk 19 optimal weight: 3.9990 chunk 93 optimal weight: 0.5980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 633 HIS C 734 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.095223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.060825 restraints weight = 147598.551| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 4.12 r_work: 0.3136 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.3451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 16030 Z= 0.110 Angle : 0.578 20.857 21578 Z= 0.325 Chirality : 0.039 0.151 2379 Planarity : 0.003 0.040 2749 Dihedral : 6.667 88.716 2244 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 0.46 % Allowed : 4.39 % Favored : 95.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 0.87 (0.19), residues: 1925 helix: 1.30 (0.18), residues: 842 sheet: 0.27 (0.30), residues: 275 loop : 0.05 (0.23), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 162 HIS 0.003 0.001 HIS D 104 PHE 0.016 0.001 PHE C 606 TYR 0.014 0.001 TYR D 218 ARG 0.005 0.000 ARG C 558 Details of bonding type rmsd hydrogen bonds : bond 0.04398 ( 783) hydrogen bonds : angle 4.72646 ( 2148) covalent geometry : bond 0.00227 (16030) covalent geometry : angle 0.57809 (21578) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3850 Ramachandran restraints generated. 1925 Oldfield, 0 Emsley, 1925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3850 Ramachandran restraints generated. 1925 Oldfield, 0 Emsley, 1925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 109 time to evaluate : 2.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 628 MET cc_start: 0.3917 (ttm) cc_final: 0.3643 (ttm) REVERT: B 577 ASP cc_start: 0.9446 (t0) cc_final: 0.9077 (m-30) REVERT: B 654 LYS cc_start: 0.9064 (mttt) cc_final: 0.8549 (mmtm) REVERT: C 531 THR cc_start: 0.5920 (m) cc_final: 0.5570 (m) REVERT: C 593 MET cc_start: 0.9095 (mmm) cc_final: 0.8887 (mmp) REVERT: C 601 MET cc_start: 0.9172 (mmm) cc_final: 0.8743 (mmm) REVERT: C 646 MET cc_start: 0.7013 (ptt) cc_final: 0.6667 (ptt) REVERT: C 666 MET cc_start: 0.9206 (mtm) cc_final: 0.8648 (tpt) REVERT: C 690 ARG cc_start: 0.9169 (mtp180) cc_final: 0.8955 (mmm-85) REVERT: C 742 ASP cc_start: 0.9314 (t0) cc_final: 0.9017 (p0) outliers start: 8 outliers final: 6 residues processed: 116 average time/residue: 0.7727 time to fit residues: 127.5859 Evaluate side-chains 109 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 103 time to evaluate : 2.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain C residue 709 SER Chi-restraints excluded: chain C residue 715 PHE Chi-restraints excluded: chain C residue 774 PHE Chi-restraints excluded: chain D residue 218 TYR Chi-restraints excluded: chain D residue 299 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 135 optimal weight: 10.0000 chunk 105 optimal weight: 4.9990 chunk 175 optimal weight: 9.9990 chunk 187 optimal weight: 10.0000 chunk 103 optimal weight: 1.9990 chunk 168 optimal weight: 5.9990 chunk 55 optimal weight: 10.0000 chunk 97 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 147 optimal weight: 9.9990 chunk 104 optimal weight: 0.8980 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 633 HIS C 734 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.093967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.060245 restraints weight = 145254.089| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 3.96 r_work: 0.3097 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.3664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 16030 Z= 0.172 Angle : 0.586 20.727 21578 Z= 0.333 Chirality : 0.039 0.147 2379 Planarity : 0.003 0.041 2749 Dihedral : 6.547 83.063 2244 Min Nonbonded Distance : 1.734 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.58 % Allowed : 4.80 % Favored : 94.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 0.83 (0.19), residues: 1925 helix: 1.40 (0.18), residues: 844 sheet: -0.03 (0.31), residues: 274 loop : -0.03 (0.23), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 162 HIS 0.004 0.001 HIS A 450 PHE 0.013 0.001 PHE C 606 TYR 0.017 0.002 TYR B 465 ARG 0.007 0.000 ARG C 558 Details of bonding type rmsd hydrogen bonds : bond 0.04506 ( 783) hydrogen bonds : angle 4.71368 ( 2148) covalent geometry : bond 0.00371 (16030) covalent geometry : angle 0.58586 (21578) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3850 Ramachandran restraints generated. 1925 Oldfield, 0 Emsley, 1925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3850 Ramachandran restraints generated. 1925 Oldfield, 0 Emsley, 1925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 104 time to evaluate : 2.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 484 MET cc_start: 0.4784 (mtm) cc_final: 0.4563 (mtm) REVERT: A 610 MET cc_start: 0.8487 (tpp) cc_final: 0.7869 (tpp) REVERT: B 628 MET cc_start: 0.8125 (mmm) cc_final: 0.7807 (mmm) REVERT: B 654 LYS cc_start: 0.9102 (mttt) cc_final: 0.8590 (mmtm) REVERT: C 588 HIS cc_start: 0.8407 (t-90) cc_final: 0.8129 (t-90) REVERT: C 601 MET cc_start: 0.9214 (mmm) cc_final: 0.8796 (mmm) REVERT: C 646 MET cc_start: 0.7083 (ptt) cc_final: 0.6716 (ptt) REVERT: C 666 MET cc_start: 0.9220 (mtm) cc_final: 0.8683 (tpt) REVERT: C 690 ARG cc_start: 0.9202 (mtp180) cc_final: 0.8974 (mmm-85) outliers start: 10 outliers final: 7 residues processed: 112 average time/residue: 0.7900 time to fit residues: 127.7784 Evaluate side-chains 106 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 99 time to evaluate : 2.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain B residue 193 ASP Chi-restraints excluded: chain B residue 581 LYS Chi-restraints excluded: chain C residue 715 PHE Chi-restraints excluded: chain C residue 774 PHE Chi-restraints excluded: chain D residue 218 TYR Chi-restraints excluded: chain D residue 299 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 22 optimal weight: 0.8980 chunk 107 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 154 optimal weight: 30.0000 chunk 0 optimal weight: 5.9990 chunk 176 optimal weight: 9.9990 chunk 84 optimal weight: 0.6980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 633 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.094489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.060639 restraints weight = 146059.081| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 3.99 r_work: 0.3111 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.3856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16030 Z= 0.121 Angle : 0.555 20.682 21578 Z= 0.313 Chirality : 0.038 0.144 2379 Planarity : 0.003 0.040 2749 Dihedral : 6.342 79.483 2244 Min Nonbonded Distance : 1.744 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 0.64 % Allowed : 5.14 % Favored : 94.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 0.92 (0.20), residues: 1925 helix: 1.56 (0.18), residues: 844 sheet: -0.02 (0.31), residues: 274 loop : -0.08 (0.23), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 162 HIS 0.003 0.001 HIS D 104 PHE 0.010 0.001 PHE D 181 TYR 0.013 0.001 TYR A 434 ARG 0.005 0.000 ARG C 558 Details of bonding type rmsd hydrogen bonds : bond 0.04115 ( 783) hydrogen bonds : angle 4.56398 ( 2148) covalent geometry : bond 0.00257 (16030) covalent geometry : angle 0.55463 (21578) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3850 Ramachandran restraints generated. 1925 Oldfield, 0 Emsley, 1925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3850 Ramachandran restraints generated. 1925 Oldfield, 0 Emsley, 1925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 103 time to evaluate : 2.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 484 MET cc_start: 0.4462 (mtm) cc_final: 0.4251 (mtm) REVERT: A 610 MET cc_start: 0.8455 (tpp) cc_final: 0.7939 (tpp) REVERT: B 130 MET cc_start: 0.9030 (mmt) cc_final: 0.7922 (mmt) REVERT: B 577 ASP cc_start: 0.9423 (t0) cc_final: 0.9033 (m-30) REVERT: B 628 MET cc_start: 0.8102 (mmm) cc_final: 0.7746 (mmm) REVERT: B 654 LYS cc_start: 0.9060 (mttt) cc_final: 0.8525 (mmtm) REVERT: C 588 HIS cc_start: 0.8344 (t-90) cc_final: 0.8085 (t-90) REVERT: C 601 MET cc_start: 0.9264 (mmm) cc_final: 0.8900 (mmm) REVERT: C 646 MET cc_start: 0.7031 (ptt) cc_final: 0.6713 (ptt) REVERT: C 666 MET cc_start: 0.9193 (mtm) cc_final: 0.8625 (tpt) REVERT: C 690 ARG cc_start: 0.9168 (mtp180) cc_final: 0.8944 (mmm-85) REVERT: C 745 MET cc_start: 0.6746 (mpp) cc_final: 0.6473 (mpp) REVERT: D 30 ASP cc_start: 0.7968 (t0) cc_final: 0.7263 (p0) outliers start: 11 outliers final: 9 residues processed: 111 average time/residue: 0.7981 time to fit residues: 125.2405 Evaluate side-chains 114 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 105 time to evaluate : 2.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 402 MET Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain B residue 633 HIS Chi-restraints excluded: chain C residue 613 TYR Chi-restraints excluded: chain C residue 709 SER Chi-restraints excluded: chain C residue 715 PHE Chi-restraints excluded: chain C residue 774 PHE Chi-restraints excluded: chain D residue 218 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 186 optimal weight: 10.0000 chunk 129 optimal weight: 9.9990 chunk 35 optimal weight: 4.9990 chunk 137 optimal weight: 20.0000 chunk 61 optimal weight: 3.9990 chunk 111 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 78 optimal weight: 7.9990 chunk 15 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 490 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 633 HIS C 527 GLN C 734 ASN D 322 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.093222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.059352 restraints weight = 147502.205| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 3.98 r_work: 0.3063 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.3983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 16030 Z= 0.217 Angle : 0.598 20.598 21578 Z= 0.338 Chirality : 0.040 0.143 2379 Planarity : 0.003 0.038 2749 Dihedral : 6.390 76.136 2244 Min Nonbonded Distance : 1.675 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.21 % Allowed : 4.74 % Favored : 94.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 0.71 (0.19), residues: 1925 helix: 1.43 (0.18), residues: 845 sheet: -0.12 (0.31), residues: 278 loop : -0.25 (0.22), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 162 HIS 0.008 0.001 HIS B 633 PHE 0.011 0.001 PHE A 342 TYR 0.018 0.002 TYR A 434 ARG 0.004 0.000 ARG C 558 Details of bonding type rmsd hydrogen bonds : bond 0.04465 ( 783) hydrogen bonds : angle 4.69900 ( 2148) covalent geometry : bond 0.00478 (16030) covalent geometry : angle 0.59806 (21578) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3850 Ramachandran restraints generated. 1925 Oldfield, 0 Emsley, 1925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3850 Ramachandran restraints generated. 1925 Oldfield, 0 Emsley, 1925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 101 time to evaluate : 2.734 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 484 MET cc_start: 0.5047 (mtm) cc_final: 0.4829 (mtm) REVERT: B 40 ASN cc_start: 0.8964 (m-40) cc_final: 0.8744 (m110) REVERT: B 625 MET cc_start: 0.9268 (mtt) cc_final: 0.8915 (mmt) REVERT: B 628 MET cc_start: 0.8160 (mmm) cc_final: 0.7787 (mmm) REVERT: B 654 LYS cc_start: 0.9148 (mttt) cc_final: 0.8652 (mmtm) REVERT: C 588 HIS cc_start: 0.8395 (t-90) cc_final: 0.8118 (t-90) REVERT: C 601 MET cc_start: 0.9272 (mmm) cc_final: 0.8934 (mmm) REVERT: C 646 MET cc_start: 0.7141 (ptt) cc_final: 0.6791 (ptt) REVERT: C 666 MET cc_start: 0.9213 (mtm) cc_final: 0.8666 (tpt) REVERT: C 690 ARG cc_start: 0.9215 (mtp180) cc_final: 0.8962 (mmm-85) REVERT: D 30 ASP cc_start: 0.8006 (t0) cc_final: 0.7292 (p0) REVERT: D 322 ASN cc_start: 0.8952 (OUTLIER) cc_final: 0.8486 (t0) outliers start: 21 outliers final: 14 residues processed: 116 average time/residue: 0.8381 time to fit residues: 140.9355 Evaluate side-chains 112 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 97 time to evaluate : 3.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 PHE Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 402 MET Chi-restraints excluded: chain A residue 581 LYS Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain B residue 359 ASN Chi-restraints excluded: chain B residue 378 ILE Chi-restraints excluded: chain B residue 633 HIS Chi-restraints excluded: chain C residue 613 TYR Chi-restraints excluded: chain C residue 709 SER Chi-restraints excluded: chain C residue 715 PHE Chi-restraints excluded: chain C residue 774 PHE Chi-restraints excluded: chain D residue 218 TYR Chi-restraints excluded: chain D residue 300 MET Chi-restraints excluded: chain D residue 322 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 189 optimal weight: 20.0000 chunk 142 optimal weight: 10.0000 chunk 137 optimal weight: 20.0000 chunk 191 optimal weight: 6.9990 chunk 83 optimal weight: 0.9980 chunk 145 optimal weight: 10.0000 chunk 106 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 70 optimal weight: 0.0270 chunk 128 optimal weight: 5.9990 overall best weight: 2.4044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 490 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 633 HIS C 734 ASN ** D 322 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 = 0.4077 r_free = 0.4077 target = 0.093483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.059675 restraints weight = 146672.739| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 3.97 r_work: 0.3081 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.4109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 16030 Z= 0.166 Angle : 0.583 20.606 21578 Z= 0.329 Chirality : 0.039 0.154 2379 Planarity : 0.003 0.038 2749 Dihedral : 6.368 73.578 2244 Min Nonbonded Distance : 1.708 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.16 % Allowed : 4.91 % Favored : 93.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 0.73 (0.19), residues: 1925 helix: 1.51 (0.18), residues: 838 sheet: -0.24 (0.31), residues: 280 loop : -0.25 (0.22), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 162 HIS 0.011 0.001 HIS B 633 PHE 0.010 0.001 PHE D 320 TYR 0.016 0.001 TYR A 434 ARG 0.013 0.000 ARG B 727 Details of bonding type rmsd hydrogen bonds : bond 0.04313 ( 783) hydrogen bonds : angle 4.63881 ( 2148) covalent geometry : bond 0.00362 (16030) covalent geometry : angle 0.58315 (21578) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3850 Ramachandran restraints generated. 1925 Oldfield, 0 Emsley, 1925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3850 Ramachandran restraints generated. 1925 Oldfield, 0 Emsley, 1925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 98 time to evaluate : 2.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 484 MET cc_start: 0.4977 (mtm) cc_final: 0.4776 (mtm) REVERT: B 40 ASN cc_start: 0.8919 (m-40) cc_final: 0.8686 (m110) REVERT: B 130 MET cc_start: 0.9002 (mmt) cc_final: 0.7970 (mmt) REVERT: B 577 ASP cc_start: 0.9413 (t0) cc_final: 0.9086 (m-30) REVERT: B 625 MET cc_start: 0.9282 (mtt) cc_final: 0.8920 (mmt) REVERT: B 628 MET cc_start: 0.8222 (mmm) cc_final: 0.7817 (mmm) REVERT: B 654 LYS cc_start: 0.9157 (mttt) cc_final: 0.8646 (mmtm) REVERT: C 588 HIS cc_start: 0.8483 (t-90) cc_final: 0.8196 (t-90) REVERT: C 601 MET cc_start: 0.9244 (mmm) cc_final: 0.8938 (mmm) REVERT: C 646 MET cc_start: 0.7210 (ptt) cc_final: 0.6846 (ptt) REVERT: C 666 MET cc_start: 0.9185 (mtm) cc_final: 0.8633 (tpt) REVERT: C 690 ARG cc_start: 0.9240 (mtp180) cc_final: 0.8728 (mmm-85) REVERT: D 30 ASP cc_start: 0.7965 (t0) cc_final: 0.7262 (p0) outliers start: 20 outliers final: 17 residues processed: 112 average time/residue: 0.7244 time to fit residues: 117.6422 Evaluate side-chains 115 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 98 time to evaluate : 2.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 PHE Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 402 MET Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 581 LYS Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain B residue 193 ASP Chi-restraints excluded: chain B residue 359 ASN Chi-restraints excluded: chain B residue 378 ILE Chi-restraints excluded: chain B residue 547 GLU Chi-restraints excluded: chain B residue 562 GLU Chi-restraints excluded: chain B residue 571 LEU Chi-restraints excluded: chain C residue 613 TYR Chi-restraints excluded: chain C residue 709 SER Chi-restraints excluded: chain C residue 715 PHE Chi-restraints excluded: chain C residue 774 PHE Chi-restraints excluded: chain D residue 218 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 42 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 178 optimal weight: 10.0000 chunk 91 optimal weight: 3.9990 chunk 191 optimal weight: 5.9990 chunk 123 optimal weight: 3.9990 chunk 46 optimal weight: 4.9990 chunk 57 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 174 optimal weight: 20.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 212 GLN B 194 GLN ** B 490 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 322 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 = 0.4046 r_free = 0.4046 target = 0.092307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.058272 restraints weight = 147877.246| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 4.00 r_work: 0.3037 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.4228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 16030 Z= 0.227 Angle : 0.608 20.567 21578 Z= 0.344 Chirality : 0.040 0.144 2379 Planarity : 0.004 0.039 2749 Dihedral : 6.471 69.585 2244 Min Nonbonded Distance : 1.667 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 0.92 % Allowed : 4.97 % Favored : 94.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 0.57 (0.19), residues: 1925 helix: 1.38 (0.18), residues: 840 sheet: -0.31 (0.31), residues: 277 loop : -0.34 (0.23), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 162 HIS 0.005 0.001 HIS A 450 PHE 0.013 0.001 PHE A 342 TYR 0.020 0.002 TYR A 434 ARG 0.007 0.000 ARG B 727 Details of bonding type rmsd hydrogen bonds : bond 0.04539 ( 783) hydrogen bonds : angle 4.74192 ( 2148) covalent geometry : bond 0.00496 (16030) covalent geometry : angle 0.60803 (21578) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3850 Ramachandran restraints generated. 1925 Oldfield, 0 Emsley, 1925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3850 Ramachandran restraints generated. 1925 Oldfield, 0 Emsley, 1925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 99 time to evaluate : 2.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 40 ASN cc_start: 0.8911 (m-40) cc_final: 0.8692 (m110) REVERT: B 625 MET cc_start: 0.9245 (mtt) cc_final: 0.8949 (mmt) REVERT: B 628 MET cc_start: 0.8229 (mmm) cc_final: 0.7966 (mmm) REVERT: B 654 LYS cc_start: 0.9195 (mttt) cc_final: 0.8687 (mmtm) REVERT: C 588 HIS cc_start: 0.8558 (t-90) cc_final: 0.8270 (t-90) REVERT: C 601 MET cc_start: 0.9297 (mmm) cc_final: 0.9012 (mmm) REVERT: C 646 MET cc_start: 0.7317 (ptt) cc_final: 0.6953 (ptt) REVERT: C 666 MET cc_start: 0.9204 (mtm) cc_final: 0.8645 (tpt) REVERT: C 690 ARG cc_start: 0.9217 (mtp180) cc_final: 0.8699 (mmm-85) REVERT: D 30 ASP cc_start: 0.8019 (t0) cc_final: 0.7319 (p0) outliers start: 16 outliers final: 15 residues processed: 111 average time/residue: 0.7429 time to fit residues: 119.6926 Evaluate side-chains 114 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 99 time to evaluate : 2.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 PHE Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 402 MET Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 581 LYS Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain B residue 193 ASP Chi-restraints excluded: chain B residue 378 ILE Chi-restraints excluded: chain B residue 562 GLU Chi-restraints excluded: chain B residue 571 LEU Chi-restraints excluded: chain C residue 613 TYR Chi-restraints excluded: chain C residue 709 SER Chi-restraints excluded: chain C residue 715 PHE Chi-restraints excluded: chain C residue 774 PHE Chi-restraints excluded: chain D residue 218 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 104 optimal weight: 4.9990 chunk 156 optimal weight: 20.0000 chunk 101 optimal weight: 0.8980 chunk 4 optimal weight: 0.7980 chunk 31 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 182 optimal weight: 10.0000 chunk 166 optimal weight: 20.0000 chunk 143 optimal weight: 10.0000 chunk 70 optimal weight: 0.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 734 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.093735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.059751 restraints weight = 145561.245| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 3.99 r_work: 0.3092 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.4335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 16030 Z= 0.106 Angle : 0.554 20.502 21578 Z= 0.310 Chirality : 0.039 0.142 2379 Planarity : 0.003 0.038 2749 Dihedral : 6.222 73.553 2244 Min Nonbonded Distance : 1.754 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.64 % Allowed : 5.38 % Favored : 93.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 0.85 (0.20), residues: 1925 helix: 1.67 (0.18), residues: 845 sheet: -0.25 (0.31), residues: 274 loop : -0.25 (0.23), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 162 HIS 0.003 0.001 HIS A 323 PHE 0.011 0.001 PHE D 181 TYR 0.012 0.001 TYR B 434 ARG 0.008 0.000 ARG B 727 Details of bonding type rmsd hydrogen bonds : bond 0.03925 ( 783) hydrogen bonds : angle 4.49197 ( 2148) covalent geometry : bond 0.00223 (16030) covalent geometry : angle 0.55446 (21578) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3850 Ramachandran restraints generated. 1925 Oldfield, 0 Emsley, 1925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3850 Ramachandran restraints generated. 1925 Oldfield, 0 Emsley, 1925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 104 time to evaluate : 2.914 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 40 ASN cc_start: 0.8856 (m-40) cc_final: 0.8619 (m110) REVERT: B 130 MET cc_start: 0.8898 (mmt) cc_final: 0.7921 (mmt) REVERT: B 577 ASP cc_start: 0.9448 (t0) cc_final: 0.9070 (m-30) REVERT: B 625 MET cc_start: 0.9177 (mtt) cc_final: 0.8796 (mmt) REVERT: B 628 MET cc_start: 0.8304 (mmm) cc_final: 0.8052 (mmm) REVERT: B 654 LYS cc_start: 0.9141 (mttt) cc_final: 0.8602 (mmtm) REVERT: C 588 HIS cc_start: 0.8560 (t-90) cc_final: 0.8276 (t-90) REVERT: C 601 MET cc_start: 0.9289 (mmm) cc_final: 0.9049 (mmm) REVERT: C 646 MET cc_start: 0.7271 (ptt) cc_final: 0.6928 (ptt) REVERT: C 666 MET cc_start: 0.9194 (mtm) cc_final: 0.8624 (tpt) REVERT: C 690 ARG cc_start: 0.9179 (mtp180) cc_final: 0.8641 (mmm-85) REVERT: C 742 ASP cc_start: 0.9251 (t0) cc_final: 0.9009 (p0) REVERT: D 30 ASP cc_start: 0.7941 (t0) cc_final: 0.7251 (p0) outliers start: 11 outliers final: 11 residues processed: 111 average time/residue: 0.8197 time to fit residues: 133.0425 Evaluate side-chains 109 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 98 time to evaluate : 2.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 402 MET Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain B residue 378 ILE Chi-restraints excluded: chain B residue 571 LEU Chi-restraints excluded: chain C residue 613 TYR Chi-restraints excluded: chain C residue 709 SER Chi-restraints excluded: chain C residue 715 PHE Chi-restraints excluded: chain C residue 774 PHE Chi-restraints excluded: chain D residue 218 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 168 optimal weight: 9.9990 chunk 27 optimal weight: 0.7980 chunk 184 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 142 optimal weight: 9.9990 chunk 101 optimal weight: 0.9990 chunk 141 optimal weight: 0.9990 chunk 71 optimal weight: 5.9990 chunk 116 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 404 GLN B 532 GLN C 734 ASN D 365 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.094728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.061160 restraints weight = 145170.963| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 3.97 r_work: 0.3108 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.4471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 16030 Z= 0.100 Angle : 0.541 20.492 21578 Z= 0.303 Chirality : 0.038 0.142 2379 Planarity : 0.003 0.038 2749 Dihedral : 5.886 72.114 2244 Min Nonbonded Distance : 1.749 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 0.46 % Allowed : 5.78 % Favored : 93.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 1.04 (0.20), residues: 1925 helix: 1.88 (0.18), residues: 846 sheet: -0.23 (0.31), residues: 274 loop : -0.20 (0.23), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 162 HIS 0.003 0.001 HIS A 323 PHE 0.011 0.001 PHE D 181 TYR 0.013 0.001 TYR C 735 ARG 0.007 0.000 ARG B 727 Details of bonding type rmsd hydrogen bonds : bond 0.03629 ( 783) hydrogen bonds : angle 4.34932 ( 2148) covalent geometry : bond 0.00211 (16030) covalent geometry : angle 0.54056 (21578) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18454.58 seconds wall clock time: 319 minutes 52.18 seconds (19192.18 seconds total)