Starting phenix.real_space_refine on Tue Aug 26 00:26:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ffw_29069/08_2025/8ffw_29069_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ffw_29069/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8ffw_29069/08_2025/8ffw_29069_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ffw_29069/08_2025/8ffw_29069_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ffw_29069/08_2025/8ffw_29069.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ffw_29069/08_2025/8ffw_29069.map" } resolution = 3.23 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 6.09, per 1000 atoms: 0.19 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: 3.15 Conformation dependent library (CDL) restraints added in 897.7 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.96 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: 8.28 Time building geometry restraints manager: 4.32 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: 3.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.210 Extract box with map and model: 0.590 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 32.440 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.350 ------------------------------------------------------------------------------- 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 : 1.24 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.007 0.001 ARG A 591 TYR 0.088 0.010 TYR D 333 PHE 0.044 0.007 PHE B 337 TRP 0.068 0.012 TRP C 712 HIS 0.012 0.003 HIS D 104 Details of bonding type rmsd covalent geometry : bond 0.02447 (16030) covalent geometry : angle 1.94625 (21578) hydrogen bonds : bond 0.17587 ( 783) hydrogen bonds : angle 7.23724 ( 2148) *********************** 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 : 0.888 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: 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: 0.3780 time to fit residues: 95.8744 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 : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 9.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- 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 586 ASN C 734 ASN ** D 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.096188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.062398 restraints weight = 144569.506| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 4.09 r_work: 0.3176 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.2338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 16030 Z= 0.163 Angle : 0.750 22.229 21578 Z= 0.432 Chirality : 0.043 0.186 2379 Planarity : 0.004 0.054 2749 Dihedral : 7.838 88.379 2244 Min Nonbonded Distance : 1.752 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 0.23 % Allowed : 3.06 % Favored : 96.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.74 (0.19), residues: 1925 helix: 0.60 (0.17), residues: 841 sheet: 1.18 (0.32), residues: 252 loop : 0.35 (0.22), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 612 TYR 0.027 0.002 TYR D 218 PHE 0.023 0.002 PHE C 606 TRP 0.024 0.002 TRP C 600 HIS 0.005 0.001 HIS C 645 Details of bonding type rmsd covalent geometry : bond 0.00327 (16030) covalent geometry : angle 0.74960 (21578) hydrogen bonds : bond 0.06854 ( 783) hydrogen bonds : angle 5.55874 ( 2148) *********************** 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 138 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 134 time to evaluate : 1.031 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 358 LYS cc_start: 0.7278 (tttt) cc_final: 0.7077 (ptmm) REVERT: B 577 ASP cc_start: 0.9463 (t0) cc_final: 0.9142 (m-30) REVERT: B 654 LYS cc_start: 0.9185 (mttt) cc_final: 0.8668 (mmtm) REVERT: C 588 HIS cc_start: 0.8334 (t-90) cc_final: 0.8117 (t-90) REVERT: C 601 MET cc_start: 0.8920 (mmm) cc_final: 0.8456 (mmm) REVERT: C 646 MET cc_start: 0.7826 (ptt) cc_final: 0.6807 (ptt) REVERT: C 690 ARG cc_start: 0.9094 (mtp180) cc_final: 0.8589 (mmm-85) REVERT: C 742 ASP cc_start: 0.9372 (t0) cc_final: 0.9113 (p0) outliers start: 4 outliers final: 4 residues processed: 137 average time/residue: 0.3926 time to fit residues: 75.2374 Evaluate side-chains 109 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 105 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 94 optimal weight: 1.9990 chunk 84 optimal weight: 6.9990 chunk 13 optimal weight: 3.9990 chunk 105 optimal weight: 4.9990 chunk 81 optimal weight: 3.9990 chunk 149 optimal weight: 7.9990 chunk 154 optimal weight: 20.0000 chunk 95 optimal weight: 2.9990 chunk 133 optimal weight: 3.9990 chunk 171 optimal weight: 30.0000 chunk 55 optimal weight: 9.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 212 GLN B 531 GLN C 734 ASN D 210 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.093791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.060047 restraints weight = 146752.895| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 4.01 r_work: 0.3070 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.3075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 16030 Z= 0.238 Angle : 0.689 21.205 21578 Z= 0.396 Chirality : 0.041 0.161 2379 Planarity : 0.004 0.059 2749 Dihedral : 7.149 86.555 2244 Min Nonbonded Distance : 1.693 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 0.81 % Allowed : 3.93 % Favored : 95.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.65 (0.19), residues: 1925 helix: 0.91 (0.17), residues: 839 sheet: 0.53 (0.31), residues: 253 loop : 0.05 (0.22), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 727 TYR 0.027 0.002 TYR B 465 PHE 0.023 0.002 PHE C 606 TRP 0.018 0.002 TRP C 600 HIS 0.005 0.001 HIS A 450 Details of bonding type rmsd covalent geometry : bond 0.00508 (16030) covalent geometry : angle 0.68904 (21578) hydrogen bonds : bond 0.05622 ( 783) hydrogen bonds : angle 5.17809 ( 2148) *********************** 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 123 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 109 time to evaluate : 0.881 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: B 654 LYS cc_start: 0.9151 (mttt) cc_final: 0.8657 (mmtm) REVERT: C 601 MET cc_start: 0.9150 (mmm) cc_final: 0.8820 (mmm) REVERT: C 646 MET cc_start: 0.7097 (ptt) cc_final: 0.6731 (ptt) REVERT: C 666 MET cc_start: 0.9116 (mtp) cc_final: 0.8650 (tpt) REVERT: C 690 ARG cc_start: 0.9187 (mtp180) cc_final: 0.8828 (mmm-85) REVERT: C 742 ASP cc_start: 0.9319 (t0) cc_final: 0.9013 (p0) outliers start: 14 outliers final: 11 residues processed: 121 average time/residue: 0.3799 time to fit residues: 64.8145 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 : 0.924 ------------------------------------------------------------------------------- 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 581 LYS Chi-restraints excluded: chain A residue 601 THR Chi-restraints excluded: chain B residue 193 ASP Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 665 LEU 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 166 optimal weight: 30.0000 chunk 3 optimal weight: 0.9980 chunk 104 optimal weight: 6.9990 chunk 91 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 chunk 147 optimal weight: 10.0000 chunk 21 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 117 optimal weight: 4.9990 chunk 96 optimal weight: 4.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 532 GLN C 734 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.093286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.059361 restraints weight = 146733.520| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 4.02 r_work: 0.3068 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.3446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 16030 Z= 0.200 Angle : 0.626 20.864 21578 Z= 0.356 Chirality : 0.040 0.149 2379 Planarity : 0.004 0.041 2749 Dihedral : 7.032 89.554 2244 Min Nonbonded Distance : 1.712 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.75 % Allowed : 4.51 % Favored : 94.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.67 (0.19), residues: 1925 helix: 1.11 (0.18), residues: 841 sheet: 0.35 (0.31), residues: 260 loop : -0.10 (0.22), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 558 TYR 0.019 0.002 TYR A 434 PHE 0.017 0.001 PHE C 606 TRP 0.012 0.002 TRP B 162 HIS 0.005 0.001 HIS A 450 Details of bonding type rmsd covalent geometry : bond 0.00434 (16030) covalent geometry : angle 0.62569 (21578) hydrogen bonds : bond 0.05076 ( 783) hydrogen bonds : angle 4.97161 ( 2148) *********************** 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 118 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 105 time to evaluate : 0.847 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: B 654 LYS cc_start: 0.9131 (mttt) cc_final: 0.8646 (mmtm) REVERT: C 593 MET cc_start: 0.9084 (mmm) cc_final: 0.8866 (mmp) REVERT: C 601 MET cc_start: 0.9185 (mmm) cc_final: 0.8751 (mmm) REVERT: C 646 MET cc_start: 0.7127 (ptt) cc_final: 0.6758 (ptt) REVERT: C 666 MET cc_start: 0.9148 (mtp) cc_final: 0.8674 (tpt) REVERT: C 690 ARG cc_start: 0.9214 (mtp180) cc_final: 0.8672 (mmm-85) REVERT: C 742 ASP cc_start: 0.9297 (t0) cc_final: 0.9006 (p0) outliers start: 13 outliers final: 11 residues processed: 115 average time/residue: 0.3278 time to fit residues: 54.2753 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 : 0.811 ------------------------------------------------------------------------------- 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 581 LYS Chi-restraints excluded: chain B residue 193 ASP Chi-restraints excluded: chain B residue 581 LYS Chi-restraints excluded: chain B residue 665 LEU Chi-restraints excluded: chain B residue 692 ILE 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 184 optimal weight: 7.9990 chunk 42 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 176 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 127 optimal weight: 9.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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 404 GLN C 734 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.093166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.059455 restraints weight = 147002.017| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 3.98 r_work: 0.3068 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.3780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 16030 Z= 0.192 Angle : 0.604 20.820 21578 Z= 0.343 Chirality : 0.040 0.147 2379 Planarity : 0.003 0.041 2749 Dihedral : 6.804 86.873 2244 Min Nonbonded Distance : 1.698 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.27 % Allowed : 4.51 % Favored : 94.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.58 (0.19), residues: 1925 helix: 1.20 (0.18), residues: 842 sheet: -0.06 (0.30), residues: 280 loop : -0.21 (0.23), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 591 TYR 0.018 0.002 TYR A 434 PHE 0.014 0.001 PHE C 606 TRP 0.012 0.002 TRP A 162 HIS 0.006 0.001 HIS A 450 Details of bonding type rmsd covalent geometry : bond 0.00417 (16030) covalent geometry : angle 0.60430 (21578) hydrogen bonds : bond 0.04722 ( 783) hydrogen bonds : angle 4.83236 ( 2148) *********************** 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 125 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 103 time to evaluate : 0.722 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 625 MET cc_start: 0.9153 (mpp) cc_final: 0.8937 (mmt) REVERT: B 654 LYS cc_start: 0.9123 (mttt) cc_final: 0.8631 (mmtm) REVERT: C 601 MET cc_start: 0.9284 (mmm) cc_final: 0.8923 (mmm) REVERT: C 646 MET cc_start: 0.7155 (ptt) cc_final: 0.6934 (ptt) REVERT: C 666 MET cc_start: 0.9144 (mtp) cc_final: 0.8702 (tpt) REVERT: C 690 ARG cc_start: 0.9182 (mtp180) cc_final: 0.8940 (mmm-85) outliers start: 22 outliers final: 18 residues processed: 121 average time/residue: 0.2809 time to fit residues: 49.3575 Evaluate side-chains 116 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 98 time to evaluate : 0.750 ------------------------------------------------------------------------------- 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 601 THR Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain A residue 628 MET Chi-restraints excluded: chain B residue 193 ASP Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 562 GLU Chi-restraints excluded: chain B residue 665 LEU Chi-restraints excluded: chain B residue 692 ILE 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 299 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 19 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 47 optimal weight: 0.5980 chunk 134 optimal weight: 10.0000 chunk 132 optimal weight: 10.0000 chunk 42 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 117 optimal weight: 4.9990 chunk 168 optimal weight: 10.0000 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 404 GLN 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 = 0.093628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.059921 restraints weight = 145749.053| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 3.96 r_work: 0.3085 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.3967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16030 Z= 0.130 Angle : 0.570 20.777 21578 Z= 0.322 Chirality : 0.039 0.148 2379 Planarity : 0.003 0.040 2749 Dihedral : 6.559 83.495 2244 Min Nonbonded Distance : 1.736 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 0.98 % Allowed : 4.91 % Favored : 94.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.72 (0.19), residues: 1925 helix: 1.45 (0.18), residues: 835 sheet: -0.19 (0.30), residues: 277 loop : -0.21 (0.22), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 558 TYR 0.020 0.001 TYR A 466 PHE 0.012 0.001 PHE C 606 TRP 0.016 0.002 TRP D 90 HIS 0.004 0.001 HIS D 104 Details of bonding type rmsd covalent geometry : bond 0.00278 (16030) covalent geometry : angle 0.57045 (21578) hydrogen bonds : bond 0.04306 ( 783) hydrogen bonds : angle 4.67547 ( 2148) *********************** 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 119 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 102 time to evaluate : 0.553 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: A 610 MET cc_start: 0.8717 (tpp) cc_final: 0.7891 (tpp) REVERT: B 577 ASP cc_start: 0.9458 (t0) cc_final: 0.9107 (m-30) REVERT: B 625 MET cc_start: 0.9108 (mpp) cc_final: 0.8878 (mmt) REVERT: B 654 LYS cc_start: 0.9091 (mttt) cc_final: 0.8599 (mmtm) REVERT: C 601 MET cc_start: 0.9254 (mmm) cc_final: 0.8913 (mmm) REVERT: C 646 MET cc_start: 0.7168 (ptt) cc_final: 0.6787 (ptt) REVERT: C 666 MET cc_start: 0.9104 (mtp) cc_final: 0.8652 (tpt) REVERT: C 690 ARG cc_start: 0.9211 (mtp180) cc_final: 0.8961 (mmm-85) REVERT: C 745 MET cc_start: 0.6762 (mpp) cc_final: 0.6473 (mpp) outliers start: 17 outliers final: 15 residues processed: 114 average time/residue: 0.2973 time to fit residues: 48.0439 Evaluate side-chains 113 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 98 time to evaluate : 0.692 ------------------------------------------------------------------------------- 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 581 LYS Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain B residue 193 ASP Chi-restraints excluded: chain B residue 484 MET Chi-restraints excluded: chain B residue 571 LEU Chi-restraints excluded: chain B residue 627 TYR Chi-restraints excluded: chain B residue 665 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 Chi-restraints excluded: chain D residue 299 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 70 optimal weight: 4.9990 chunk 142 optimal weight: 9.9990 chunk 79 optimal weight: 5.9990 chunk 120 optimal weight: 4.9990 chunk 157 optimal weight: 0.4980 chunk 78 optimal weight: 7.9990 chunk 154 optimal weight: 30.0000 chunk 60 optimal weight: 3.9990 chunk 169 optimal weight: 8.9990 chunk 17 optimal weight: 0.5980 chunk 25 optimal weight: 0.3980 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 GLN B 404 GLN C 734 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.093467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.059682 restraints weight = 146821.479| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 3.97 r_work: 0.3065 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.4126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16030 Z= 0.152 Angle : 0.570 20.661 21578 Z= 0.322 Chirality : 0.039 0.147 2379 Planarity : 0.003 0.048 2749 Dihedral : 6.406 79.095 2244 Min Nonbonded Distance : 1.716 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.10 % Allowed : 4.97 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.72 (0.19), residues: 1925 helix: 1.50 (0.18), residues: 836 sheet: -0.29 (0.31), residues: 277 loop : -0.23 (0.23), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 558 TYR 0.015 0.001 TYR A 434 PHE 0.010 0.001 PHE D 181 TRP 0.015 0.002 TRP D 90 HIS 0.004 0.001 HIS A 450 Details of bonding type rmsd covalent geometry : bond 0.00328 (16030) covalent geometry : angle 0.56972 (21578) hydrogen bonds : bond 0.04250 ( 783) hydrogen bonds : angle 4.62126 ( 2148) *********************** 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 119 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 100 time to evaluate : 0.825 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: A 610 MET cc_start: 0.8638 (tpp) cc_final: 0.8183 (tpp) REVERT: B 573 LYS cc_start: 0.9774 (mmmm) cc_final: 0.9399 (mmmm) REVERT: B 577 ASP cc_start: 0.9438 (t0) cc_final: 0.9111 (m-30) REVERT: B 625 MET cc_start: 0.9151 (mpp) cc_final: 0.8922 (mmt) REVERT: B 654 LYS cc_start: 0.9100 (mttt) cc_final: 0.8603 (mmtm) REVERT: C 601 MET cc_start: 0.9263 (mmm) cc_final: 0.8957 (mmm) REVERT: C 646 MET cc_start: 0.7133 (ptt) cc_final: 0.6752 (ptt) REVERT: C 666 MET cc_start: 0.9097 (mtp) cc_final: 0.8655 (tpt) outliers start: 19 outliers final: 18 residues processed: 116 average time/residue: 0.3147 time to fit residues: 52.0943 Evaluate side-chains 116 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 98 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 GLN 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 601 THR 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 B residue 665 LEU Chi-restraints excluded: chain C residue 613 TYR Chi-restraints excluded: chain C residue 684 GLU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 156 optimal weight: 20.0000 chunk 86 optimal weight: 0.8980 chunk 152 optimal weight: 20.0000 chunk 56 optimal weight: 2.9990 chunk 103 optimal weight: 0.3980 chunk 84 optimal weight: 0.7980 chunk 70 optimal weight: 4.9990 chunk 117 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 404 GLN C 734 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.094252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.060310 restraints weight = 144270.221| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 3.96 r_work: 0.3091 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 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 : 0.002 0.044 16030 Z= 0.100 Angle : 0.549 20.579 21578 Z= 0.307 Chirality : 0.038 0.140 2379 Planarity : 0.003 0.039 2749 Dihedral : 6.253 75.894 2244 Min Nonbonded Distance : 1.755 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.69 % Allowed : 5.61 % Favored : 93.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.87 (0.20), residues: 1925 helix: 1.65 (0.18), residues: 843 sheet: -0.24 (0.31), residues: 274 loop : -0.19 (0.23), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 558 TYR 0.012 0.001 TYR C 735 PHE 0.011 0.001 PHE D 181 TRP 0.013 0.001 TRP A 162 HIS 0.003 0.001 HIS A 323 Details of bonding type rmsd covalent geometry : bond 0.00208 (16030) covalent geometry : angle 0.54936 (21578) hydrogen bonds : bond 0.03910 ( 783) hydrogen bonds : angle 4.46287 ( 2148) *********************** 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 115 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 103 time to evaluate : 0.898 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: A 610 MET cc_start: 0.8630 (tpp) cc_final: 0.8158 (tpp) REVERT: B 573 LYS cc_start: 0.9766 (mmmm) cc_final: 0.9376 (mmmm) REVERT: B 577 ASP cc_start: 0.9406 (t0) cc_final: 0.9076 (m-30) REVERT: B 625 MET cc_start: 0.9122 (mpp) cc_final: 0.8882 (mmt) REVERT: B 654 LYS cc_start: 0.9066 (mttt) cc_final: 0.8523 (mmtm) REVERT: C 588 HIS cc_start: 0.8449 (t-90) cc_final: 0.8196 (t-90) REVERT: C 601 MET cc_start: 0.9297 (mmm) cc_final: 0.9048 (mmm) REVERT: C 646 MET cc_start: 0.7175 (ptt) cc_final: 0.6811 (ptt) REVERT: C 666 MET cc_start: 0.9099 (mtp) cc_final: 0.8639 (tpt) REVERT: D 30 ASP cc_start: 0.7968 (t0) cc_final: 0.7262 (p0) outliers start: 12 outliers final: 10 residues processed: 112 average time/residue: 0.3633 time to fit residues: 57.7062 Evaluate side-chains 110 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 100 time to evaluate : 0.931 ------------------------------------------------------------------------------- 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 B residue 571 LEU Chi-restraints excluded: chain B residue 665 LEU Chi-restraints excluded: chain C residue 560 MET 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 D residue 218 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 147 optimal weight: 8.9990 chunk 24 optimal weight: 5.9990 chunk 126 optimal weight: 0.9990 chunk 100 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 chunk 183 optimal weight: 9.9990 chunk 34 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 chunk 78 optimal weight: 7.9990 chunk 116 optimal weight: 2.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 212 GLN B 404 GLN C 527 GLN C 734 ASN D 322 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.093431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.059417 restraints weight = 146206.059| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 4.00 r_work: 0.3069 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.4364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 16030 Z= 0.154 Angle : 0.568 20.492 21578 Z= 0.320 Chirality : 0.039 0.142 2379 Planarity : 0.003 0.043 2749 Dihedral : 6.230 71.258 2244 Min Nonbonded Distance : 1.704 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 0.87 % Allowed : 5.43 % Favored : 93.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.80 (0.20), residues: 1925 helix: 1.63 (0.18), residues: 843 sheet: -0.35 (0.30), residues: 275 loop : -0.25 (0.23), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 558 TYR 0.016 0.001 TYR A 434 PHE 0.013 0.001 PHE B 337 TRP 0.010 0.001 TRP A 162 HIS 0.004 0.001 HIS A 450 Details of bonding type rmsd covalent geometry : bond 0.00335 (16030) covalent geometry : angle 0.56806 (21578) hydrogen bonds : bond 0.04121 ( 783) hydrogen bonds : angle 4.51435 ( 2148) *********************** 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: 15 poor density : 100 time to evaluate : 0.911 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: A 610 MET cc_start: 0.8739 (tpp) cc_final: 0.8245 (tpp) REVERT: B 573 LYS cc_start: 0.9759 (mmmm) cc_final: 0.9384 (mmmm) REVERT: B 577 ASP cc_start: 0.9398 (t0) cc_final: 0.9073 (m-30) REVERT: B 625 MET cc_start: 0.9166 (mpp) cc_final: 0.8863 (mmt) REVERT: B 654 LYS cc_start: 0.9130 (mttt) cc_final: 0.8624 (mmtm) REVERT: C 601 MET cc_start: 0.9268 (mmm) cc_final: 0.9001 (mmm) REVERT: C 646 MET cc_start: 0.7169 (ptt) cc_final: 0.6793 (ptt) REVERT: C 666 MET cc_start: 0.9102 (mtp) cc_final: 0.8647 (tpt) REVERT: D 30 ASP cc_start: 0.7762 (t0) cc_final: 0.7077 (p0) REVERT: D 322 ASN cc_start: 0.9034 (OUTLIER) cc_final: 0.8494 (t0) outliers start: 15 outliers final: 10 residues processed: 112 average time/residue: 0.3235 time to fit residues: 51.7886 Evaluate side-chains 107 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 96 time to evaluate : 0.850 ------------------------------------------------------------------------------- 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 B residue 571 LEU Chi-restraints excluded: chain B residue 665 LEU Chi-restraints excluded: chain C residue 613 TYR Chi-restraints excluded: chain C residue 684 GLU Chi-restraints excluded: chain C residue 709 SER Chi-restraints excluded: chain C residue 715 PHE Chi-restraints excluded: chain D residue 218 TYR Chi-restraints excluded: chain D residue 322 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 161 optimal weight: 40.0000 chunk 165 optimal weight: 9.9990 chunk 117 optimal weight: 4.9990 chunk 152 optimal weight: 20.0000 chunk 127 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 126 optimal weight: 20.0000 chunk 45 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 chunk 28 optimal weight: 10.0000 chunk 119 optimal weight: 2.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 404 GLN C 734 ASN D 322 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.093434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.059637 restraints weight = 146102.109| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 3.97 r_work: 0.3072 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.4439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16030 Z= 0.143 Angle : 0.569 20.462 21578 Z= 0.318 Chirality : 0.039 0.140 2379 Planarity : 0.003 0.038 2749 Dihedral : 6.254 73.245 2244 Min Nonbonded Distance : 1.720 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 0.69 % Allowed : 5.55 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.81 (0.20), residues: 1925 helix: 1.67 (0.18), residues: 843 sheet: -0.36 (0.30), residues: 275 loop : -0.26 (0.23), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 558 TYR 0.014 0.001 TYR A 434 PHE 0.012 0.001 PHE D 320 TRP 0.011 0.001 TRP A 162 HIS 0.007 0.001 HIS C 588 Details of bonding type rmsd covalent geometry : bond 0.00312 (16030) covalent geometry : angle 0.56912 (21578) hydrogen bonds : bond 0.04064 ( 783) hydrogen bonds : angle 4.49211 ( 2148) ********************** 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 109 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 97 time to evaluate : 0.836 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 610 MET cc_start: 0.8745 (tpp) cc_final: 0.8172 (tpp) REVERT: B 573 LYS cc_start: 0.9761 (mmmm) cc_final: 0.9374 (mmmm) REVERT: B 577 ASP cc_start: 0.9392 (t0) cc_final: 0.9065 (m-30) REVERT: B 625 MET cc_start: 0.9164 (mpp) cc_final: 0.8862 (mmt) REVERT: B 654 LYS cc_start: 0.9143 (mttt) cc_final: 0.8614 (mmtm) REVERT: C 601 MET cc_start: 0.9274 (mmm) cc_final: 0.9011 (mmm) REVERT: C 646 MET cc_start: 0.7217 (ptt) cc_final: 0.6846 (ptt) REVERT: C 666 MET cc_start: 0.9099 (mtp) cc_final: 0.8640 (tpt) REVERT: C 742 ASP cc_start: 0.9245 (t0) cc_final: 0.9006 (p0) REVERT: D 30 ASP cc_start: 0.7754 (t0) cc_final: 0.7081 (p0) outliers start: 12 outliers final: 11 residues processed: 106 average time/residue: 0.3237 time to fit residues: 48.9265 Evaluate side-chains 107 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 96 time to evaluate : 0.619 ------------------------------------------------------------------------------- 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 B residue 571 LEU Chi-restraints excluded: chain B residue 581 LYS Chi-restraints excluded: chain B residue 665 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 D residue 218 TYR Chi-restraints excluded: chain D residue 322 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 169 optimal weight: 30.0000 chunk 135 optimal weight: 0.8980 chunk 160 optimal weight: 7.9990 chunk 79 optimal weight: 0.0270 chunk 27 optimal weight: 0.6980 chunk 136 optimal weight: 6.9990 chunk 4 optimal weight: 5.9990 chunk 163 optimal weight: 40.0000 chunk 191 optimal weight: 7.9990 chunk 97 optimal weight: 2.9990 chunk 95 optimal weight: 0.0970 overall best weight: 0.9438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 404 GLN D 322 ASN D 365 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.094156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.060397 restraints weight = 145952.982| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 3.98 r_work: 0.3093 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.4507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 16030 Z= 0.104 Angle : 0.555 20.462 21578 Z= 0.309 Chirality : 0.038 0.142 2379 Planarity : 0.003 0.038 2749 Dihedral : 6.133 75.123 2244 Min Nonbonded Distance : 1.749 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 0.58 % Allowed : 5.66 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.93 (0.20), residues: 1925 helix: 1.78 (0.18), residues: 844 sheet: -0.29 (0.30), residues: 274 loop : -0.22 (0.23), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 558 TYR 0.012 0.001 TYR B 434 PHE 0.014 0.001 PHE D 320 TRP 0.013 0.001 TRP A 162 HIS 0.003 0.001 HIS C 588 Details of bonding type rmsd covalent geometry : bond 0.00222 (16030) covalent geometry : angle 0.55486 (21578) hydrogen bonds : bond 0.03848 ( 783) hydrogen bonds : angle 4.38975 ( 2148) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8138.77 seconds wall clock time: 138 minutes 37.99 seconds (8317.99 seconds total)