Starting phenix.real_space_refine on Fri Jun 13 09:55:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hwc_35053/06_2025/8hwc_35053.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hwc_35053/06_2025/8hwc_35053.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hwc_35053/06_2025/8hwc_35053.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hwc_35053/06_2025/8hwc_35053.map" model { file = "/net/cci-nas-00/data/ceres_data/8hwc_35053/06_2025/8hwc_35053.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hwc_35053/06_2025/8hwc_35053.cif" } resolution = 3.3 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= 0.005 sd= 0.081 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: 4 Type Number sf(0) Gaussians S 84 5.16 5 C 9564 2.51 5 N 2541 2.21 5 O 2754 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 14943 Number of models: 1 Model: "" Number of chains: 6 Chain: "E" Number of atoms: 2313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2313 Classifications: {'peptide': 284} Link IDs: {'PTRANS': 10, 'TRANS': 273} Chain breaks: 5 Chain: "F" Number of atoms: 2514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2514 Classifications: {'peptide': 308} Link IDs: {'PTRANS': 13, 'TRANS': 294} Chain breaks: 4 Chain: "D" Number of atoms: 2178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2178 Classifications: {'peptide': 266} Link IDs: {'PTRANS': 10, 'TRANS': 255} Chain breaks: 6 Chain: "C" Number of atoms: 2283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2283 Classifications: {'peptide': 280} Link IDs: {'PTRANS': 10, 'TRANS': 269} Chain breaks: 5 Chain: "B" Number of atoms: 2610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2610 Classifications: {'peptide': 320} Link IDs: {'PTRANS': 13, 'TRANS': 306} Chain breaks: 4 Chain: "A" Number of atoms: 3045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 3045 Classifications: {'peptide': 378} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 18, 'TRANS': 359} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Time building chain proxies: 10.25, per 1000 atoms: 0.69 Number of scatterers: 14943 At special positions: 0 Unit cell: (101.835, 136.875, 135.78, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 84 16.00 O 2754 8.00 N 2541 7.00 C 9564 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.89 Conformation dependent library (CDL) restraints added in 2.2 seconds 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3518 Finding SS restraints... Secondary structure from input PDB file: 79 helices and 23 sheets defined 41.4% alpha, 7.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.62 Creating SS restraints... Processing helix chain 'E' and resid 324 through 336 removed outlier: 3.635A pdb=" N ALA E 330 " --> pdb=" O LEU E 326 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR E 336 " --> pdb=" O ARG E 332 " (cutoff:3.500A) Processing helix chain 'E' and resid 363 through 371 removed outlier: 3.916A pdb=" N LEU E 367 " --> pdb=" O LEU E 363 " (cutoff:3.500A) Processing helix chain 'E' and resid 372 through 374 No H-bonds generated for 'chain 'E' and resid 372 through 374' Processing helix chain 'E' and resid 376 through 381 Processing helix chain 'E' and resid 387 through 400 removed outlier: 3.711A pdb=" N THR E 391 " --> pdb=" O ARG E 387 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N VAL E 392 " --> pdb=" O LYS E 388 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLU E 393 " --> pdb=" O ARG E 389 " (cutoff:3.500A) Processing helix chain 'E' and resid 430 through 435 removed outlier: 4.318A pdb=" N LYS E 435 " --> pdb=" O ASP E 432 " (cutoff:3.500A) Processing helix chain 'E' and resid 455 through 469 removed outlier: 3.605A pdb=" N GLU E 459 " --> pdb=" O SER E 455 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N ILE E 464 " --> pdb=" O GLU E 460 " (cutoff:3.500A) Processing helix chain 'E' and resid 476 through 488 Processing helix chain 'E' and resid 508 through 521 Processing helix chain 'E' and resid 571 through 577 Processing helix chain 'E' and resid 617 through 621 removed outlier: 3.562A pdb=" N ARG E 620 " --> pdb=" O LEU E 617 " (cutoff:3.500A) Processing helix chain 'E' and resid 664 through 680 Processing helix chain 'F' and resid 324 through 336 removed outlier: 3.589A pdb=" N ASN F 328 " --> pdb=" O ASN F 324 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA F 330 " --> pdb=" O LEU F 326 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N THR F 336 " --> pdb=" O ARG F 332 " (cutoff:3.500A) Processing helix chain 'F' and resid 363 through 371 removed outlier: 3.871A pdb=" N LEU F 367 " --> pdb=" O LEU F 363 " (cutoff:3.500A) Processing helix chain 'F' and resid 372 through 374 No H-bonds generated for 'chain 'F' and resid 372 through 374' Processing helix chain 'F' and resid 376 through 381 Processing helix chain 'F' and resid 385 through 398 removed outlier: 3.674A pdb=" N LYS F 390 " --> pdb=" O PRO F 386 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N THR F 391 " --> pdb=" O ARG F 387 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N VAL F 392 " --> pdb=" O LYS F 388 " (cutoff:3.500A) Processing helix chain 'F' and resid 429 through 435 removed outlier: 4.393A pdb=" N ASP F 432 " --> pdb=" O SER F 429 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N LYS F 435 " --> pdb=" O ASP F 432 " (cutoff:3.500A) Processing helix chain 'F' and resid 456 through 469 removed outlier: 3.662A pdb=" N GLU F 460 " --> pdb=" O PRO F 456 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N ILE F 464 " --> pdb=" O GLU F 460 " (cutoff:3.500A) Processing helix chain 'F' and resid 476 through 488 Processing helix chain 'F' and resid 508 through 521 Processing helix chain 'F' and resid 572 through 577 Processing helix chain 'F' and resid 617 through 621 removed outlier: 3.922A pdb=" N ILE F 621 " --> pdb=" O MET F 618 " (cutoff:3.500A) Processing helix chain 'F' and resid 656 through 661 Processing helix chain 'F' and resid 664 through 680 Processing helix chain 'D' and resid 324 through 336 removed outlier: 3.669A pdb=" N ASN D 328 " --> pdb=" O ASN D 324 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ALA D 330 " --> pdb=" O LEU D 326 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR D 336 " --> pdb=" O ARG D 332 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 371 removed outlier: 4.038A pdb=" N LEU D 367 " --> pdb=" O LEU D 363 " (cutoff:3.500A) Processing helix chain 'D' and resid 376 through 381 Processing helix chain 'D' and resid 387 through 400 removed outlier: 3.594A pdb=" N THR D 391 " --> pdb=" O ARG D 387 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N VAL D 392 " --> pdb=" O LYS D 388 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLU D 393 " --> pdb=" O ARG D 389 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 434 Processing helix chain 'D' and resid 455 through 469 removed outlier: 3.764A pdb=" N GLU D 459 " --> pdb=" O SER D 455 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ILE D 464 " --> pdb=" O GLU D 460 " (cutoff:3.500A) Processing helix chain 'D' and resid 476 through 488 Processing helix chain 'D' and resid 510 through 521 Processing helix chain 'D' and resid 574 through 578 removed outlier: 3.610A pdb=" N LEU D 577 " --> pdb=" O ILE D 574 " (cutoff:3.500A) Processing helix chain 'D' and resid 617 through 621 removed outlier: 4.062A pdb=" N ILE D 621 " --> pdb=" O MET D 618 " (cutoff:3.500A) Processing helix chain 'D' and resid 657 through 661 Processing helix chain 'D' and resid 664 through 680 Processing helix chain 'C' and resid 324 through 336 removed outlier: 3.513A pdb=" N ASN C 328 " --> pdb=" O ASN C 324 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ALA C 330 " --> pdb=" O LEU C 326 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR C 336 " --> pdb=" O ARG C 332 " (cutoff:3.500A) Processing helix chain 'C' and resid 363 through 371 removed outlier: 3.736A pdb=" N LEU C 367 " --> pdb=" O LEU C 363 " (cutoff:3.500A) Processing helix chain 'C' and resid 376 through 381 Processing helix chain 'C' and resid 390 through 398 Processing helix chain 'C' and resid 455 through 469 removed outlier: 4.071A pdb=" N GLU C 459 " --> pdb=" O SER C 455 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ILE C 464 " --> pdb=" O GLU C 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 488 Processing helix chain 'C' and resid 489 through 491 No H-bonds generated for 'chain 'C' and resid 489 through 491' Processing helix chain 'C' and resid 508 through 521 Processing helix chain 'C' and resid 617 through 621 removed outlier: 3.758A pdb=" N ILE C 621 " --> pdb=" O MET C 618 " (cutoff:3.500A) Processing helix chain 'C' and resid 656 through 661 Processing helix chain 'C' and resid 664 through 680 Processing helix chain 'B' and resid 324 through 336 removed outlier: 3.618A pdb=" N ASN B 328 " --> pdb=" O ASN B 324 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N THR B 336 " --> pdb=" O ARG B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 371 removed outlier: 3.931A pdb=" N LEU B 367 " --> pdb=" O LEU B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 374 No H-bonds generated for 'chain 'B' and resid 372 through 374' Processing helix chain 'B' and resid 376 through 381 Processing helix chain 'B' and resid 387 through 398 removed outlier: 3.867A pdb=" N THR B 391 " --> pdb=" O ARG B 387 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N VAL B 392 " --> pdb=" O LYS B 388 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLU B 393 " --> pdb=" O ARG B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 435 removed outlier: 4.358A pdb=" N LYS B 435 " --> pdb=" O ASP B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 469 removed outlier: 3.609A pdb=" N GLU B 459 " --> pdb=" O SER B 455 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ILE B 464 " --> pdb=" O GLU B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 488 Processing helix chain 'B' and resid 508 through 521 Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 544 through 548 removed outlier: 3.649A pdb=" N HIS B 548 " --> pdb=" O ALA B 545 " (cutoff:3.500A) Processing helix chain 'B' and resid 571 through 577 removed outlier: 3.839A pdb=" N LYS B 575 " --> pdb=" O SER B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 617 through 621 removed outlier: 3.773A pdb=" N ILE B 621 " --> pdb=" O MET B 618 " (cutoff:3.500A) Processing helix chain 'B' and resid 656 through 661 Processing helix chain 'B' and resid 664 through 680 Processing helix chain 'A' and resid 324 through 336 removed outlier: 3.779A pdb=" N ALA A 330 " --> pdb=" O LEU A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 371 removed outlier: 4.002A pdb=" N LEU A 367 " --> pdb=" O LEU A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 374 No H-bonds generated for 'chain 'A' and resid 372 through 374' Processing helix chain 'A' and resid 376 through 381 Processing helix chain 'A' and resid 386 through 398 removed outlier: 3.664A pdb=" N LYS A 390 " --> pdb=" O PRO A 386 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N THR A 391 " --> pdb=" O ARG A 387 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL A 392 " --> pdb=" O LYS A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 435 removed outlier: 4.179A pdb=" N ASP A 432 " --> pdb=" O SER A 429 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N LYS A 435 " --> pdb=" O ASP A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 469 removed outlier: 3.644A pdb=" N GLU A 459 " --> pdb=" O SER A 455 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ILE A 464 " --> pdb=" O GLU A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 488 Processing helix chain 'A' and resid 508 through 521 Processing helix chain 'A' and resid 530 through 534 removed outlier: 3.664A pdb=" N ASP A 534 " --> pdb=" O ILE A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 546 Processing helix chain 'A' and resid 570 through 577 Processing helix chain 'A' and resid 617 through 621 removed outlier: 3.625A pdb=" N ILE A 621 " --> pdb=" O MET A 618 " (cutoff:3.500A) Processing helix chain 'A' and resid 635 through 639 Processing helix chain 'A' and resid 654 through 661 Processing helix chain 'A' and resid 664 through 680 Processing sheet with id=AA1, first strand: chain 'E' and resid 339 through 341 Processing sheet with id=AA2, first strand: chain 'E' and resid 412 through 415 Processing sheet with id=AA3, first strand: chain 'E' and resid 500 through 503 removed outlier: 6.213A pdb=" N PHE E 500 " --> pdb=" O VAL E 624 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N PHE E 626 " --> pdb=" O PHE E 500 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N PHE E 502 " --> pdb=" O PHE E 626 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'E' and resid 553 through 555 removed outlier: 6.425A pdb=" N VAL E 553 " --> pdb=" O ILE E 601 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'F' and resid 339 through 341 Processing sheet with id=AA6, first strand: chain 'F' and resid 412 through 415 Processing sheet with id=AA7, first strand: chain 'F' and resid 500 through 503 removed outlier: 6.320A pdb=" N PHE F 500 " --> pdb=" O VAL F 624 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N PHE F 626 " --> pdb=" O PHE F 500 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N PHE F 502 " --> pdb=" O PHE F 626 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'F' and resid 525 through 526 removed outlier: 6.794A pdb=" N VAL F 525 " --> pdb=" O PHE F 554 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N VAL F 553 " --> pdb=" O ILE F 601 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'D' and resid 339 through 341 Processing sheet with id=AB1, first strand: chain 'D' and resid 412 through 415 Processing sheet with id=AB2, first strand: chain 'C' and resid 339 through 341 Processing sheet with id=AB3, first strand: chain 'C' and resid 412 through 415 Processing sheet with id=AB4, first strand: chain 'C' and resid 500 through 503 removed outlier: 5.956A pdb=" N PHE C 500 " --> pdb=" O VAL C 624 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N PHE C 626 " --> pdb=" O PHE C 500 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N PHE C 502 " --> pdb=" O PHE C 626 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'C' and resid 552 through 553 removed outlier: 3.825A pdb=" N VAL C 553 " --> pdb=" O THR C 599 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'B' and resid 339 through 341 Processing sheet with id=AB7, first strand: chain 'B' and resid 412 through 415 Processing sheet with id=AB8, first strand: chain 'B' and resid 500 through 502 removed outlier: 6.172A pdb=" N PHE B 500 " --> pdb=" O VAL B 624 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'B' and resid 525 through 526 removed outlier: 6.444A pdb=" N VAL B 525 " --> pdb=" O PHE B 554 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N VAL B 553 " --> pdb=" O ILE B 601 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'A' and resid 340 through 341 Processing sheet with id=AC2, first strand: chain 'A' and resid 412 through 415 Processing sheet with id=AC3, first strand: chain 'A' and resid 500 through 502 removed outlier: 5.845A pdb=" N PHE A 500 " --> pdb=" O VAL A 624 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'A' and resid 525 through 526 removed outlier: 6.939A pdb=" N VAL A 525 " --> pdb=" O PHE A 554 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N VAL A 553 " --> pdb=" O ILE A 601 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'A' and resid 628 through 630 removed outlier: 5.749A pdb=" N HIS A 629 " --> pdb=" O LYS A 649 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 474 hydrogen bonds defined for protein. 1323 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: 5.26 Time building geometry restraints manager: 4.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4657 1.34 - 1.46: 2156 1.46 - 1.58: 8284 1.58 - 1.70: 1 1.70 - 1.81: 126 Bond restraints: 15224 Sorted by residual: bond pdb=" CB PRO B 690 " pdb=" CG PRO B 690 " ideal model delta sigma weight residual 1.492 1.617 -0.125 5.00e-02 4.00e+02 6.28e+00 bond pdb=" C LEU A 558 " pdb=" N PRO A 559 " ideal model delta sigma weight residual 1.330 1.361 -0.031 1.25e-02 6.40e+03 6.07e+00 bond pdb=" N ASP B 402 " pdb=" CA ASP B 402 " ideal model delta sigma weight residual 1.453 1.483 -0.030 1.22e-02 6.72e+03 5.91e+00 bond pdb=" N THR D 449 " pdb=" CA THR D 449 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.19e-02 7.06e+03 5.42e+00 bond pdb=" N LEU F 515 " pdb=" CA LEU F 515 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.21e-02 6.83e+03 5.23e+00 ... (remaining 15219 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.76: 20075 1.76 - 3.52: 366 3.52 - 5.27: 38 5.27 - 7.03: 19 7.03 - 8.79: 8 Bond angle restraints: 20506 Sorted by residual: angle pdb=" N ILE A 544 " pdb=" CA ILE A 544 " pdb=" C ILE A 544 " ideal model delta sigma weight residual 113.42 106.79 6.63 1.17e+00 7.31e-01 3.22e+01 angle pdb=" N TRP C 675 " pdb=" CA TRP C 675 " pdb=" CB TRP C 675 " ideal model delta sigma weight residual 109.94 102.38 7.56 1.49e+00 4.50e-01 2.57e+01 angle pdb=" CA PRO B 690 " pdb=" N PRO B 690 " pdb=" CD PRO B 690 " ideal model delta sigma weight residual 112.00 105.65 6.35 1.40e+00 5.10e-01 2.05e+01 angle pdb=" C LYS C 674 " pdb=" N TRP C 675 " pdb=" CA TRP C 675 " ideal model delta sigma weight residual 120.54 125.53 -4.99 1.35e+00 5.49e-01 1.37e+01 angle pdb=" CA MET B 462 " pdb=" CB MET B 462 " pdb=" CG MET B 462 " ideal model delta sigma weight residual 114.10 121.32 -7.22 2.00e+00 2.50e-01 1.30e+01 ... (remaining 20501 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 7953 17.95 - 35.91: 1084 35.91 - 53.86: 215 53.86 - 71.81: 34 71.81 - 89.77: 13 Dihedral angle restraints: 9299 sinusoidal: 3909 harmonic: 5390 Sorted by residual: dihedral pdb=" CA LYS D 677 " pdb=" C LYS D 677 " pdb=" N LYS D 678 " pdb=" CA LYS D 678 " ideal model delta harmonic sigma weight residual 180.00 154.38 25.62 0 5.00e+00 4.00e-02 2.63e+01 dihedral pdb=" CA ASN B 594 " pdb=" CB ASN B 594 " pdb=" CG ASN B 594 " pdb=" OD1 ASN B 594 " ideal model delta sinusoidal sigma weight residual -90.00 -160.39 70.39 2 2.00e+01 2.50e-03 1.06e+01 dihedral pdb=" CB GLU C 405 " pdb=" CG GLU C 405 " pdb=" CD GLU C 405 " pdb=" OE1 GLU C 405 " ideal model delta sinusoidal sigma weight residual 0.00 -89.77 89.77 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 9296 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1935 0.056 - 0.111: 347 0.111 - 0.167: 31 0.167 - 0.223: 2 0.223 - 0.279: 1 Chirality restraints: 2316 Sorted by residual: chirality pdb=" CB ILE A 583 " pdb=" CA ILE A 583 " pdb=" CG1 ILE A 583 " pdb=" CG2 ILE A 583 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.28 2.00e-01 2.50e+01 1.94e+00 chirality pdb=" CG LEU A 461 " pdb=" CB LEU A 461 " pdb=" CD1 LEU A 461 " pdb=" CD2 LEU A 461 " both_signs ideal model delta sigma weight residual False -2.59 -2.81 0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CA LEU A 515 " pdb=" N LEU A 515 " pdb=" C LEU A 515 " pdb=" CB LEU A 515 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.42e-01 ... (remaining 2313 not shown) Planarity restraints: 2583 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 675 " -0.051 2.00e-02 2.50e+03 4.78e-02 5.72e+01 pdb=" CG TRP C 675 " 0.125 2.00e-02 2.50e+03 pdb=" CD1 TRP C 675 " -0.065 2.00e-02 2.50e+03 pdb=" CD2 TRP C 675 " 0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP C 675 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TRP C 675 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP C 675 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 675 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 675 " -0.015 2.00e-02 2.50e+03 pdb=" CH2 TRP C 675 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE D 681 " -0.049 5.00e-02 4.00e+02 7.40e-02 8.77e+00 pdb=" N PRO D 682 " 0.128 5.00e-02 4.00e+02 pdb=" CA PRO D 682 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO D 682 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU B 361 " -0.048 5.00e-02 4.00e+02 7.18e-02 8.26e+00 pdb=" N PRO B 362 " 0.124 5.00e-02 4.00e+02 pdb=" CA PRO B 362 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO B 362 " -0.039 5.00e-02 4.00e+02 ... (remaining 2580 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 3127 2.78 - 3.31: 14135 3.31 - 3.84: 23657 3.84 - 4.37: 27458 4.37 - 4.90: 47541 Nonbonded interactions: 115918 Sorted by model distance: nonbonded pdb=" N GLN E 660 " pdb=" OE1 GLN E 660 " model vdw 2.245 3.120 nonbonded pdb=" OD2 ASP F 346 " pdb=" OG SER F 359 " model vdw 2.254 3.040 nonbonded pdb=" OD2 ASP E 398 " pdb=" NH1 ARG D 389 " model vdw 2.254 3.120 nonbonded pdb=" O THR A 406 " pdb=" NH1 ARG A 595 " model vdw 2.256 3.120 nonbonded pdb=" OG1 THR C 342 " pdb=" O ASP C 346 " model vdw 2.258 3.040 ... (remaining 115913 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 'B' and (resid 323 through 525 or resid 543 through 554 or resid 573 thro \ ugh 602 or resid 617 through 626 or resid 656 through 688)) selection = (chain 'C' and (resid 323 through 593 or resid 595 through 626 or resid 656 thro \ ugh 688)) selection = (chain 'E' and (resid 323 through 525 or resid 543 through 554 or resid 573 thro \ ugh 602 or resid 617 through 688)) selection = (chain 'F' and (resid 323 through 525 or resid 543 through 554 or resid 573 thro \ ugh 602 or resid 617 through 626 or resid 656 through 688)) } 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: 17.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.640 Check model and map are aligned: 0.110 Set scattering table: 0.170 Process input model: 38.380 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.125 15224 Z= 0.144 Angle : 0.603 8.790 20506 Z= 0.334 Chirality : 0.042 0.279 2316 Planarity : 0.005 0.074 2583 Dihedral : 16.491 89.765 5781 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 0.30 % Allowed : 24.91 % Favored : 74.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.21), residues: 1776 helix: -0.35 (0.20), residues: 699 sheet: -1.51 (0.34), residues: 251 loop : -1.79 (0.23), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.125 0.003 TRP C 675 HIS 0.003 0.001 HIS E 548 PHE 0.013 0.001 PHE A 357 TYR 0.017 0.001 TYR C 482 ARG 0.009 0.000 ARG A 625 Details of bonding type rmsd hydrogen bonds : bond 0.13317 ( 474) hydrogen bonds : angle 5.73867 ( 1323) covalent geometry : bond 0.00312 (15224) covalent geometry : angle 0.60287 (20506) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 177 time to evaluate : 1.654 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 449 THR cc_start: 0.6113 (OUTLIER) cc_final: 0.5769 (p) outliers start: 5 outliers final: 1 residues processed: 181 average time/residue: 0.2212 time to fit residues: 63.9088 Evaluate side-chains 169 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 167 time to evaluate : 1.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 449 THR Chi-restraints excluded: chain D residue 478 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 152 optimal weight: 4.9990 chunk 137 optimal weight: 5.9990 chunk 76 optimal weight: 5.9990 chunk 46 optimal weight: 9.9990 chunk 92 optimal weight: 3.9990 chunk 73 optimal weight: 5.9990 chunk 141 optimal weight: 7.9990 chunk 54 optimal weight: 8.9990 chunk 86 optimal weight: 0.7980 chunk 105 optimal weight: 9.9990 chunk 164 optimal weight: 0.1980 overall best weight: 3.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 478 ASN D 660 GLN B 478 ASN B 660 GLN A 478 ASN A 597 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.212419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.155609 restraints weight = 18552.406| |-----------------------------------------------------------------------------| r_work (start): 0.3795 rms_B_bonded: 3.45 r_work: 0.3088 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.1291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 15224 Z= 0.297 Angle : 0.658 9.649 20506 Z= 0.333 Chirality : 0.047 0.197 2316 Planarity : 0.005 0.057 2583 Dihedral : 4.497 24.666 1977 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.94 % Favored : 92.06 % Rotamer: Outliers : 3.20 % Allowed : 24.20 % Favored : 72.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.96 (0.20), residues: 1776 helix: -0.48 (0.20), residues: 687 sheet: -1.68 (0.32), residues: 267 loop : -1.83 (0.22), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.069 0.003 TRP C 675 HIS 0.005 0.001 HIS E 347 PHE 0.018 0.002 PHE A 357 TYR 0.016 0.001 TYR F 482 ARG 0.005 0.001 ARG A 514 Details of bonding type rmsd hydrogen bonds : bond 0.04761 ( 474) hydrogen bonds : angle 5.15581 ( 1323) covalent geometry : bond 0.00748 (15224) covalent geometry : angle 0.65813 (20506) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 177 time to evaluate : 2.009 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 346 ASP cc_start: 0.8116 (m-30) cc_final: 0.7794 (m-30) REVERT: E 477 LYS cc_start: 0.7816 (tmmt) cc_final: 0.7531 (mptt) REVERT: F 497 CYS cc_start: 0.7630 (OUTLIER) cc_final: 0.7043 (m) REVERT: D 436 TYR cc_start: 0.8178 (OUTLIER) cc_final: 0.7907 (m-80) REVERT: D 600 ILE cc_start: 0.8462 (OUTLIER) cc_final: 0.7753 (pt) REVERT: D 679 TYR cc_start: 0.7633 (m-10) cc_final: 0.7398 (m-10) REVERT: D 681 ILE cc_start: 0.8911 (OUTLIER) cc_final: 0.8572 (mp) REVERT: B 618 MET cc_start: 0.8208 (OUTLIER) cc_final: 0.7840 (mtt) REVERT: A 351 ILE cc_start: 0.7796 (OUTLIER) cc_final: 0.7312 (mt) REVERT: A 372 ARG cc_start: 0.8997 (OUTLIER) cc_final: 0.7801 (ptt-90) REVERT: A 469 GLN cc_start: 0.7677 (mm-40) cc_final: 0.7035 (mm-40) REVERT: A 478 ASN cc_start: 0.8137 (OUTLIER) cc_final: 0.7527 (t0) REVERT: A 515 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8781 (mp) REVERT: A 529 GLN cc_start: 0.7345 (mp10) cc_final: 0.6787 (mp10) REVERT: A 600 ILE cc_start: 0.9134 (OUTLIER) cc_final: 0.8903 (mm) outliers start: 54 outliers final: 21 residues processed: 222 average time/residue: 0.2454 time to fit residues: 85.0181 Evaluate side-chains 191 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 160 time to evaluate : 1.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 413 LEU Chi-restraints excluded: chain E residue 450 LYS Chi-restraints excluded: chain E residue 491 CYS Chi-restraints excluded: chain E residue 507 THR Chi-restraints excluded: chain F residue 357 PHE Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain F residue 497 CYS Chi-restraints excluded: chain F residue 498 LEU Chi-restraints excluded: chain F residue 549 LEU Chi-restraints excluded: chain F residue 600 ILE Chi-restraints excluded: chain D residue 436 TYR Chi-restraints excluded: chain D residue 511 THR Chi-restraints excluded: chain D residue 581 CYS Chi-restraints excluded: chain D residue 600 ILE Chi-restraints excluded: chain D residue 681 ILE Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 436 TYR Chi-restraints excluded: chain C residue 507 THR Chi-restraints excluded: chain C residue 596 ASN Chi-restraints excluded: chain B residue 351 ILE Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain B residue 618 MET Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 372 ARG Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain A residue 478 ASN Chi-restraints excluded: chain A residue 501 PHE Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 600 ILE Chi-restraints excluded: chain A residue 603 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 170 optimal weight: 0.0980 chunk 155 optimal weight: 2.9990 chunk 20 optimal weight: 9.9990 chunk 139 optimal weight: 1.9990 chunk 163 optimal weight: 1.9990 chunk 147 optimal weight: 0.9980 chunk 171 optimal weight: 5.9990 chunk 132 optimal weight: 0.8980 chunk 54 optimal weight: 9.9990 chunk 72 optimal weight: 6.9990 chunk 79 optimal weight: 10.0000 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 660 GLN A 478 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.215308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.158690 restraints weight = 18553.588| |-----------------------------------------------------------------------------| r_work (start): 0.3831 rms_B_bonded: 3.50 r_work: 0.3134 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.1336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15224 Z= 0.137 Angle : 0.541 10.186 20506 Z= 0.273 Chirality : 0.042 0.294 2316 Planarity : 0.004 0.051 2583 Dihedral : 4.024 24.837 1974 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 2.25 % Allowed : 24.44 % Favored : 73.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.20), residues: 1776 helix: -0.27 (0.20), residues: 692 sheet: -1.71 (0.33), residues: 254 loop : -1.73 (0.23), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.002 TRP C 675 HIS 0.002 0.001 HIS E 548 PHE 0.019 0.001 PHE B 543 TYR 0.017 0.001 TYR C 676 ARG 0.004 0.000 ARG A 595 Details of bonding type rmsd hydrogen bonds : bond 0.03243 ( 474) hydrogen bonds : angle 4.70006 ( 1323) covalent geometry : bond 0.00339 (15224) covalent geometry : angle 0.54099 (20506) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 177 time to evaluate : 1.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 346 ASP cc_start: 0.7971 (m-30) cc_final: 0.7711 (m-30) REVERT: E 477 LYS cc_start: 0.7789 (tmmt) cc_final: 0.7515 (mptt) REVERT: F 497 CYS cc_start: 0.7725 (OUTLIER) cc_final: 0.6846 (m) REVERT: D 436 TYR cc_start: 0.8078 (OUTLIER) cc_final: 0.7732 (m-80) REVERT: D 679 TYR cc_start: 0.7604 (m-10) cc_final: 0.7230 (m-10) REVERT: C 497 CYS cc_start: 0.7609 (OUTLIER) cc_final: 0.6853 (m) REVERT: C 579 GLU cc_start: 0.8246 (pt0) cc_final: 0.7696 (pt0) REVERT: B 618 MET cc_start: 0.8118 (mtm) cc_final: 0.7787 (mtt) REVERT: A 344 ARG cc_start: 0.7518 (mtp85) cc_final: 0.7061 (mtm-85) REVERT: A 458 MET cc_start: 0.8218 (tpt) cc_final: 0.7491 (tpt) REVERT: A 462 MET cc_start: 0.8621 (mmm) cc_final: 0.7952 (mmm) REVERT: A 469 GLN cc_start: 0.7716 (mm-40) cc_final: 0.7137 (mm-40) REVERT: A 478 ASN cc_start: 0.8093 (OUTLIER) cc_final: 0.7522 (t0) REVERT: A 529 GLN cc_start: 0.7343 (mp10) cc_final: 0.6912 (mp10) outliers start: 38 outliers final: 19 residues processed: 203 average time/residue: 0.2739 time to fit residues: 87.2640 Evaluate side-chains 185 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 162 time to evaluate : 1.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 450 LYS Chi-restraints excluded: chain E residue 491 CYS Chi-restraints excluded: chain E residue 507 THR Chi-restraints excluded: chain E residue 669 LEU Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 357 PHE Chi-restraints excluded: chain F residue 497 CYS Chi-restraints excluded: chain F residue 549 LEU Chi-restraints excluded: chain F residue 600 ILE Chi-restraints excluded: chain D residue 436 TYR Chi-restraints excluded: chain D residue 491 CYS Chi-restraints excluded: chain D residue 543 PHE Chi-restraints excluded: chain D residue 581 CYS Chi-restraints excluded: chain C residue 436 TYR Chi-restraints excluded: chain C residue 497 CYS Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain B residue 505 THR Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 478 ASN Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 585 ARG Chi-restraints excluded: chain A residue 603 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 2 optimal weight: 0.1980 chunk 17 optimal weight: 20.0000 chunk 15 optimal weight: 5.9990 chunk 171 optimal weight: 3.9990 chunk 118 optimal weight: 0.0970 chunk 30 optimal weight: 2.9990 chunk 147 optimal weight: 0.5980 chunk 123 optimal weight: 0.5980 chunk 46 optimal weight: 8.9990 chunk 5 optimal weight: 0.7980 chunk 117 optimal weight: 0.0270 overall best weight: 0.3036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 478 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.218152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.162962 restraints weight = 18512.474| |-----------------------------------------------------------------------------| r_work (start): 0.3881 rms_B_bonded: 3.53 r_work: 0.3190 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.1485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 15224 Z= 0.087 Angle : 0.493 9.495 20506 Z= 0.250 Chirality : 0.041 0.236 2316 Planarity : 0.004 0.051 2583 Dihedral : 3.604 24.693 1974 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 1.78 % Allowed : 24.38 % Favored : 73.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.21), residues: 1776 helix: -0.11 (0.20), residues: 717 sheet: -1.66 (0.32), residues: 274 loop : -1.52 (0.24), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.002 TRP C 675 HIS 0.001 0.000 HIS B 680 PHE 0.008 0.001 PHE E 357 TYR 0.013 0.001 TYR A 482 ARG 0.003 0.000 ARG A 514 Details of bonding type rmsd hydrogen bonds : bond 0.02476 ( 474) hydrogen bonds : angle 4.33555 ( 1323) covalent geometry : bond 0.00197 (15224) covalent geometry : angle 0.49285 (20506) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 190 time to evaluate : 1.840 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 477 LYS cc_start: 0.7925 (tmmt) cc_final: 0.7606 (mptt) REVERT: E 526 GLU cc_start: 0.5574 (tp30) cc_final: 0.4617 (mm-30) REVERT: E 664 TYR cc_start: 0.6867 (m-80) cc_final: 0.6123 (m-80) REVERT: F 497 CYS cc_start: 0.7556 (OUTLIER) cc_final: 0.6674 (m) REVERT: D 436 TYR cc_start: 0.7958 (OUTLIER) cc_final: 0.7544 (m-80) REVERT: D 679 TYR cc_start: 0.7696 (m-10) cc_final: 0.7333 (m-10) REVERT: C 344 ARG cc_start: 0.8290 (mtp85) cc_final: 0.8083 (mtp85) REVERT: C 497 CYS cc_start: 0.7472 (OUTLIER) cc_final: 0.6780 (m) REVERT: C 579 GLU cc_start: 0.8234 (pt0) cc_final: 0.7726 (pt0) REVERT: B 351 ILE cc_start: 0.8238 (OUTLIER) cc_final: 0.7758 (mt) REVERT: B 454 ASP cc_start: 0.8044 (t0) cc_final: 0.7504 (p0) REVERT: B 618 MET cc_start: 0.7934 (mtm) cc_final: 0.7627 (mtt) REVERT: A 344 ARG cc_start: 0.7472 (mtp85) cc_final: 0.6914 (mtm-85) REVERT: A 462 MET cc_start: 0.8633 (mmm) cc_final: 0.8371 (mmm) REVERT: A 466 ASN cc_start: 0.8810 (m-40) cc_final: 0.8263 (m-40) REVERT: A 469 GLN cc_start: 0.7674 (mm-40) cc_final: 0.7227 (mm-40) REVERT: A 478 ASN cc_start: 0.8150 (OUTLIER) cc_final: 0.7500 (t0) REVERT: A 497 CYS cc_start: 0.8388 (OUTLIER) cc_final: 0.7763 (m) REVERT: A 529 GLN cc_start: 0.7367 (mp10) cc_final: 0.6945 (mp10) outliers start: 30 outliers final: 13 residues processed: 212 average time/residue: 0.2392 time to fit residues: 78.4209 Evaluate side-chains 194 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 175 time to evaluate : 1.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 543 PHE Chi-restraints excluded: chain E residue 669 LEU Chi-restraints excluded: chain F residue 471 LEU Chi-restraints excluded: chain F residue 497 CYS Chi-restraints excluded: chain D residue 436 TYR Chi-restraints excluded: chain D residue 543 PHE Chi-restraints excluded: chain D residue 600 ILE Chi-restraints excluded: chain D residue 624 VAL Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 436 TYR Chi-restraints excluded: chain C residue 490 LEU Chi-restraints excluded: chain C residue 497 CYS Chi-restraints excluded: chain C residue 507 THR Chi-restraints excluded: chain B residue 351 ILE Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain A residue 478 ASN Chi-restraints excluded: chain A residue 497 CYS Chi-restraints excluded: chain A residue 585 ARG Chi-restraints excluded: chain A residue 603 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 64 optimal weight: 0.0040 chunk 163 optimal weight: 5.9990 chunk 177 optimal weight: 6.9990 chunk 50 optimal weight: 8.9990 chunk 122 optimal weight: 4.9990 chunk 88 optimal weight: 0.6980 chunk 113 optimal weight: 0.6980 chunk 97 optimal weight: 9.9990 chunk 6 optimal weight: 1.9990 chunk 68 optimal weight: 5.9990 chunk 142 optimal weight: 2.9990 overall best weight: 1.2796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 548 HIS A 478 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.214942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.154967 restraints weight = 18386.419| |-----------------------------------------------------------------------------| r_work (start): 0.3807 rms_B_bonded: 3.30 r_work: 0.3158 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.1598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15224 Z= 0.137 Angle : 0.540 16.352 20506 Z= 0.269 Chirality : 0.042 0.201 2316 Planarity : 0.004 0.051 2583 Dihedral : 3.785 24.552 1974 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 2.66 % Allowed : 23.96 % Favored : 73.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.21), residues: 1776 helix: -0.21 (0.20), residues: 723 sheet: -1.62 (0.33), residues: 270 loop : -1.56 (0.24), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.067 0.002 TRP C 675 HIS 0.003 0.001 HIS B 347 PHE 0.009 0.001 PHE A 357 TYR 0.016 0.001 TYR A 482 ARG 0.003 0.000 ARG A 595 Details of bonding type rmsd hydrogen bonds : bond 0.03155 ( 474) hydrogen bonds : angle 4.45867 ( 1323) covalent geometry : bond 0.00340 (15224) covalent geometry : angle 0.54033 (20506) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 175 time to evaluate : 2.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 664 TYR cc_start: 0.6849 (m-80) cc_final: 0.6095 (m-80) REVERT: F 497 CYS cc_start: 0.7630 (OUTLIER) cc_final: 0.6764 (m) REVERT: F 675 TRP cc_start: 0.8658 (m-10) cc_final: 0.8256 (m-10) REVERT: D 436 TYR cc_start: 0.8026 (OUTLIER) cc_final: 0.7669 (m-80) REVERT: D 679 TYR cc_start: 0.7648 (m-10) cc_final: 0.7286 (m-10) REVERT: C 497 CYS cc_start: 0.7516 (OUTLIER) cc_final: 0.6864 (m) REVERT: B 454 ASP cc_start: 0.8033 (t0) cc_final: 0.7500 (p0) REVERT: B 618 MET cc_start: 0.7993 (mtm) cc_final: 0.7647 (mtt) REVERT: A 344 ARG cc_start: 0.7557 (mtp85) cc_final: 0.6967 (mtm-85) REVERT: A 458 MET cc_start: 0.8222 (tpt) cc_final: 0.7518 (tpt) REVERT: A 462 MET cc_start: 0.8658 (mmm) cc_final: 0.7979 (mmm) REVERT: A 469 GLN cc_start: 0.7755 (mm-40) cc_final: 0.7370 (mm-40) REVERT: A 478 ASN cc_start: 0.8059 (OUTLIER) cc_final: 0.7456 (t0) REVERT: A 497 CYS cc_start: 0.8279 (OUTLIER) cc_final: 0.7664 (m) REVERT: A 529 GLN cc_start: 0.7315 (mp10) cc_final: 0.6837 (mp10) outliers start: 45 outliers final: 23 residues processed: 209 average time/residue: 0.2334 time to fit residues: 77.4101 Evaluate side-chains 192 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 164 time to evaluate : 1.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 450 LYS Chi-restraints excluded: chain E residue 491 CYS Chi-restraints excluded: chain E residue 507 THR Chi-restraints excluded: chain E residue 543 PHE Chi-restraints excluded: chain E residue 669 LEU Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 357 PHE Chi-restraints excluded: chain F residue 471 LEU Chi-restraints excluded: chain F residue 497 CYS Chi-restraints excluded: chain D residue 436 TYR Chi-restraints excluded: chain D residue 491 CYS Chi-restraints excluded: chain D residue 543 PHE Chi-restraints excluded: chain D residue 581 CYS Chi-restraints excluded: chain D residue 600 ILE Chi-restraints excluded: chain D residue 624 VAL Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 436 TYR Chi-restraints excluded: chain C residue 497 CYS Chi-restraints excluded: chain C residue 507 THR Chi-restraints excluded: chain C residue 596 ASN Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 351 ILE Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 478 ASN Chi-restraints excluded: chain A residue 497 CYS Chi-restraints excluded: chain A residue 585 ARG Chi-restraints excluded: chain A residue 603 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 107 optimal weight: 10.0000 chunk 125 optimal weight: 5.9990 chunk 9 optimal weight: 0.9980 chunk 97 optimal weight: 20.0000 chunk 76 optimal weight: 10.0000 chunk 145 optimal weight: 0.9990 chunk 133 optimal weight: 2.9990 chunk 161 optimal weight: 8.9990 chunk 81 optimal weight: 0.7980 chunk 103 optimal weight: 1.9990 chunk 21 optimal weight: 9.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 478 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.214477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.153252 restraints weight = 18275.313| |-----------------------------------------------------------------------------| r_work (start): 0.3788 rms_B_bonded: 3.33 r_work: 0.3149 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.1758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 15224 Z= 0.159 Angle : 0.565 17.492 20506 Z= 0.279 Chirality : 0.042 0.179 2316 Planarity : 0.004 0.051 2583 Dihedral : 3.898 30.143 1974 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 2.60 % Allowed : 23.96 % Favored : 73.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.21), residues: 1776 helix: -0.20 (0.20), residues: 712 sheet: -1.64 (0.32), residues: 270 loop : -1.54 (0.24), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.071 0.003 TRP C 675 HIS 0.002 0.001 HIS B 347 PHE 0.011 0.001 PHE A 357 TYR 0.016 0.001 TYR A 482 ARG 0.003 0.000 ARG A 595 Details of bonding type rmsd hydrogen bonds : bond 0.03351 ( 474) hydrogen bonds : angle 4.51019 ( 1323) covalent geometry : bond 0.00396 (15224) covalent geometry : angle 0.56548 (20506) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 174 time to evaluate : 1.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 501 PHE cc_start: 0.8350 (OUTLIER) cc_final: 0.7743 (m-10) REVERT: E 664 TYR cc_start: 0.6850 (m-80) cc_final: 0.6122 (m-80) REVERT: F 497 CYS cc_start: 0.7725 (OUTLIER) cc_final: 0.6910 (m) REVERT: F 675 TRP cc_start: 0.8598 (m-10) cc_final: 0.8218 (m-10) REVERT: D 436 TYR cc_start: 0.8070 (OUTLIER) cc_final: 0.7716 (m-80) REVERT: D 679 TYR cc_start: 0.7692 (m-10) cc_final: 0.7492 (m-10) REVERT: C 458 MET cc_start: 0.8095 (ppp) cc_final: 0.7768 (mtm) REVERT: C 497 CYS cc_start: 0.7493 (OUTLIER) cc_final: 0.6733 (m) REVERT: B 454 ASP cc_start: 0.8075 (t0) cc_final: 0.7535 (p0) REVERT: B 618 MET cc_start: 0.7968 (mtm) cc_final: 0.7633 (mtt) REVERT: B 699 TYR cc_start: 0.6820 (m-80) cc_final: 0.6503 (m-80) REVERT: A 344 ARG cc_start: 0.7589 (mtp85) cc_final: 0.7013 (mtm-85) REVERT: A 469 GLN cc_start: 0.7817 (mm-40) cc_final: 0.7455 (mm-40) REVERT: A 478 ASN cc_start: 0.8124 (OUTLIER) cc_final: 0.7586 (t0) REVERT: A 497 CYS cc_start: 0.8337 (OUTLIER) cc_final: 0.7732 (m) REVERT: A 529 GLN cc_start: 0.7287 (mp10) cc_final: 0.6774 (mp10) outliers start: 44 outliers final: 29 residues processed: 205 average time/residue: 0.2193 time to fit residues: 71.9581 Evaluate side-chains 204 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 169 time to evaluate : 1.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 450 LYS Chi-restraints excluded: chain E residue 491 CYS Chi-restraints excluded: chain E residue 501 PHE Chi-restraints excluded: chain E residue 507 THR Chi-restraints excluded: chain E residue 543 PHE Chi-restraints excluded: chain E residue 552 SER Chi-restraints excluded: chain E residue 669 LEU Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 357 PHE Chi-restraints excluded: chain F residue 471 LEU Chi-restraints excluded: chain F residue 497 CYS Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 436 TYR Chi-restraints excluded: chain D residue 491 CYS Chi-restraints excluded: chain D residue 543 PHE Chi-restraints excluded: chain D residue 581 CYS Chi-restraints excluded: chain D residue 600 ILE Chi-restraints excluded: chain D residue 624 VAL Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 436 TYR Chi-restraints excluded: chain C residue 497 CYS Chi-restraints excluded: chain C residue 507 THR Chi-restraints excluded: chain C residue 596 ASN Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 351 ILE Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain B residue 505 THR Chi-restraints excluded: chain B residue 511 THR Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 478 ASN Chi-restraints excluded: chain A residue 497 CYS Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 603 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 121 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 chunk 80 optimal weight: 8.9990 chunk 106 optimal weight: 6.9990 chunk 93 optimal weight: 2.9990 chunk 134 optimal weight: 9.9990 chunk 10 optimal weight: 10.0000 chunk 9 optimal weight: 1.9990 chunk 145 optimal weight: 0.0770 chunk 139 optimal weight: 0.5980 chunk 54 optimal weight: 9.9990 overall best weight: 1.9344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 466 ASN ** E 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 660 GLN A 478 ASN A 594 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.214309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.159879 restraints weight = 18651.819| |-----------------------------------------------------------------------------| r_work (start): 0.3847 rms_B_bonded: 3.40 r_work: 0.3117 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 15224 Z= 0.189 Angle : 0.591 18.316 20506 Z= 0.290 Chirality : 0.043 0.168 2316 Planarity : 0.004 0.050 2583 Dihedral : 4.051 29.394 1974 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 2.84 % Allowed : 23.85 % Favored : 73.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.21), residues: 1776 helix: -0.21 (0.20), residues: 700 sheet: -1.68 (0.32), residues: 270 loop : -1.52 (0.23), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.003 TRP C 675 HIS 0.003 0.001 HIS B 347 PHE 0.013 0.001 PHE A 357 TYR 0.018 0.001 TYR A 482 ARG 0.003 0.000 ARG F 514 Details of bonding type rmsd hydrogen bonds : bond 0.03586 ( 474) hydrogen bonds : angle 4.61984 ( 1323) covalent geometry : bond 0.00475 (15224) covalent geometry : angle 0.59061 (20506) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 173 time to evaluate : 1.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 346 ASP cc_start: 0.8185 (m-30) cc_final: 0.7985 (m-30) REVERT: E 501 PHE cc_start: 0.8373 (OUTLIER) cc_final: 0.7751 (m-10) REVERT: E 664 TYR cc_start: 0.6866 (m-80) cc_final: 0.6140 (m-80) REVERT: F 497 CYS cc_start: 0.7855 (OUTLIER) cc_final: 0.7026 (m) REVERT: F 675 TRP cc_start: 0.8654 (m-10) cc_final: 0.8234 (m-10) REVERT: D 436 TYR cc_start: 0.8175 (OUTLIER) cc_final: 0.7864 (m-80) REVERT: D 679 TYR cc_start: 0.7759 (m-10) cc_final: 0.7330 (m-10) REVERT: C 469 GLN cc_start: 0.7407 (tp40) cc_final: 0.6722 (tt0) REVERT: C 497 CYS cc_start: 0.7565 (OUTLIER) cc_final: 0.6827 (m) REVERT: B 454 ASP cc_start: 0.8133 (t0) cc_final: 0.7568 (p0) REVERT: B 612 ARG cc_start: 0.7738 (ttp80) cc_final: 0.6923 (ttp80) REVERT: B 618 MET cc_start: 0.7971 (mtm) cc_final: 0.7636 (mtt) REVERT: B 699 TYR cc_start: 0.6835 (m-80) cc_final: 0.6528 (m-80) REVERT: A 372 ARG cc_start: 0.9006 (OUTLIER) cc_final: 0.8388 (ptt-90) REVERT: A 469 GLN cc_start: 0.7804 (mm-40) cc_final: 0.7354 (mm-40) REVERT: A 478 ASN cc_start: 0.8214 (OUTLIER) cc_final: 0.7704 (t0) REVERT: A 497 CYS cc_start: 0.8338 (OUTLIER) cc_final: 0.7688 (m) REVERT: A 529 GLN cc_start: 0.7218 (mp10) cc_final: 0.6634 (mp10) outliers start: 48 outliers final: 34 residues processed: 210 average time/residue: 0.2278 time to fit residues: 75.5749 Evaluate side-chains 214 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 173 time to evaluate : 1.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 450 LYS Chi-restraints excluded: chain E residue 491 CYS Chi-restraints excluded: chain E residue 501 PHE Chi-restraints excluded: chain E residue 507 THR Chi-restraints excluded: chain E residue 543 PHE Chi-restraints excluded: chain E residue 552 SER Chi-restraints excluded: chain E residue 669 LEU Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 357 PHE Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain F residue 408 THR Chi-restraints excluded: chain F residue 471 LEU Chi-restraints excluded: chain F residue 497 CYS Chi-restraints excluded: chain F residue 549 LEU Chi-restraints excluded: chain F residue 600 ILE Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 436 TYR Chi-restraints excluded: chain D residue 491 CYS Chi-restraints excluded: chain D residue 543 PHE Chi-restraints excluded: chain D residue 581 CYS Chi-restraints excluded: chain D residue 600 ILE Chi-restraints excluded: chain D residue 624 VAL Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 436 TYR Chi-restraints excluded: chain C residue 497 CYS Chi-restraints excluded: chain C residue 507 THR Chi-restraints excluded: chain C residue 596 ASN Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 351 ILE Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain B residue 505 THR Chi-restraints excluded: chain B residue 511 THR Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 372 ARG Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 478 ASN Chi-restraints excluded: chain A residue 497 CYS Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 603 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 125 optimal weight: 5.9990 chunk 44 optimal weight: 3.9990 chunk 145 optimal weight: 0.0470 chunk 59 optimal weight: 2.9990 chunk 136 optimal weight: 0.6980 chunk 163 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 97 optimal weight: 6.9990 chunk 41 optimal weight: 5.9990 chunk 22 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 overall best weight: 1.1282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 478 ASN A 594 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.215860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.157328 restraints weight = 18490.421| |-----------------------------------------------------------------------------| r_work (start): 0.3816 rms_B_bonded: 3.41 r_work: 0.3151 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15224 Z= 0.129 Angle : 0.560 18.912 20506 Z= 0.275 Chirality : 0.042 0.172 2316 Planarity : 0.004 0.050 2583 Dihedral : 3.903 29.118 1974 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 2.54 % Allowed : 23.91 % Favored : 73.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.21), residues: 1776 helix: -0.18 (0.20), residues: 705 sheet: -1.68 (0.32), residues: 275 loop : -1.49 (0.23), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.080 0.002 TRP C 675 HIS 0.002 0.001 HIS B 347 PHE 0.009 0.001 PHE E 427 TYR 0.015 0.001 TYR A 482 ARG 0.003 0.000 ARG F 514 Details of bonding type rmsd hydrogen bonds : bond 0.03121 ( 474) hydrogen bonds : angle 4.46314 ( 1323) covalent geometry : bond 0.00316 (15224) covalent geometry : angle 0.56049 (20506) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 182 time to evaluate : 1.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 501 PHE cc_start: 0.8335 (OUTLIER) cc_final: 0.7732 (m-10) REVERT: E 553 VAL cc_start: 0.8324 (t) cc_final: 0.8079 (m) REVERT: E 664 TYR cc_start: 0.6859 (m-80) cc_final: 0.6153 (m-80) REVERT: F 497 CYS cc_start: 0.7661 (OUTLIER) cc_final: 0.6917 (m) REVERT: F 675 TRP cc_start: 0.8640 (m-10) cc_final: 0.8294 (m-10) REVERT: D 436 TYR cc_start: 0.8129 (OUTLIER) cc_final: 0.7813 (m-80) REVERT: D 600 ILE cc_start: 0.8360 (OUTLIER) cc_final: 0.7374 (pt) REVERT: D 679 TYR cc_start: 0.7737 (m-10) cc_final: 0.7316 (m-10) REVERT: C 469 GLN cc_start: 0.7414 (tp40) cc_final: 0.6733 (tt0) REVERT: C 497 CYS cc_start: 0.7591 (OUTLIER) cc_final: 0.6836 (m) REVERT: B 454 ASP cc_start: 0.8256 (t0) cc_final: 0.7753 (p0) REVERT: B 618 MET cc_start: 0.7896 (mtm) cc_final: 0.7580 (mtt) REVERT: B 699 TYR cc_start: 0.6779 (m-80) cc_final: 0.6466 (m-80) REVERT: A 344 ARG cc_start: 0.7583 (mtp85) cc_final: 0.7294 (mtp180) REVERT: A 372 ARG cc_start: 0.8968 (OUTLIER) cc_final: 0.8064 (ptt-90) REVERT: A 469 GLN cc_start: 0.7802 (mm-40) cc_final: 0.7264 (mm-40) REVERT: A 478 ASN cc_start: 0.7992 (OUTLIER) cc_final: 0.7483 (t0) REVERT: A 497 CYS cc_start: 0.8316 (OUTLIER) cc_final: 0.7711 (m) REVERT: A 529 GLN cc_start: 0.7177 (mp10) cc_final: 0.6593 (mp10) REVERT: A 684 MET cc_start: 0.8263 (tmm) cc_final: 0.7830 (tmm) outliers start: 43 outliers final: 29 residues processed: 217 average time/residue: 0.2300 time to fit residues: 78.9701 Evaluate side-chains 211 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 174 time to evaluate : 1.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 450 LYS Chi-restraints excluded: chain E residue 491 CYS Chi-restraints excluded: chain E residue 501 PHE Chi-restraints excluded: chain E residue 507 THR Chi-restraints excluded: chain E residue 543 PHE Chi-restraints excluded: chain E residue 552 SER Chi-restraints excluded: chain E residue 669 LEU Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 357 PHE Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain F residue 408 THR Chi-restraints excluded: chain F residue 471 LEU Chi-restraints excluded: chain F residue 497 CYS Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 436 TYR Chi-restraints excluded: chain D residue 491 CYS Chi-restraints excluded: chain D residue 543 PHE Chi-restraints excluded: chain D residue 600 ILE Chi-restraints excluded: chain D residue 624 VAL Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 357 PHE Chi-restraints excluded: chain C residue 436 TYR Chi-restraints excluded: chain C residue 497 CYS Chi-restraints excluded: chain C residue 507 THR Chi-restraints excluded: chain C residue 596 ASN Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 351 ILE Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain B residue 511 THR Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 372 ARG Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 478 ASN Chi-restraints excluded: chain A residue 497 CYS Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 603 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 167 optimal weight: 7.9990 chunk 42 optimal weight: 3.9990 chunk 150 optimal weight: 0.4980 chunk 98 optimal weight: 10.0000 chunk 144 optimal weight: 0.7980 chunk 86 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 25 optimal weight: 5.9990 chunk 110 optimal weight: 0.9980 chunk 147 optimal weight: 3.9990 chunk 107 optimal weight: 20.0000 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 478 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.216329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.159368 restraints weight = 18551.859| |-----------------------------------------------------------------------------| r_work (start): 0.3841 rms_B_bonded: 3.52 r_work: 0.3148 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15224 Z= 0.124 Angle : 0.564 19.285 20506 Z= 0.276 Chirality : 0.042 0.157 2316 Planarity : 0.004 0.050 2583 Dihedral : 3.840 28.956 1974 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 2.37 % Allowed : 24.08 % Favored : 73.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.21), residues: 1776 helix: -0.14 (0.20), residues: 706 sheet: -1.66 (0.32), residues: 275 loop : -1.46 (0.24), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.074 0.002 TRP C 675 HIS 0.002 0.001 HIS B 347 PHE 0.011 0.001 PHE F 554 TYR 0.018 0.001 TYR A 482 ARG 0.003 0.000 ARG A 585 Details of bonding type rmsd hydrogen bonds : bond 0.03062 ( 474) hydrogen bonds : angle 4.40664 ( 1323) covalent geometry : bond 0.00305 (15224) covalent geometry : angle 0.56445 (20506) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 179 time to evaluate : 1.886 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 501 PHE cc_start: 0.8333 (OUTLIER) cc_final: 0.7726 (m-10) REVERT: E 553 VAL cc_start: 0.8369 (t) cc_final: 0.8129 (m) REVERT: E 664 TYR cc_start: 0.6855 (m-80) cc_final: 0.6162 (m-80) REVERT: F 497 CYS cc_start: 0.7685 (OUTLIER) cc_final: 0.6938 (m) REVERT: F 675 TRP cc_start: 0.8610 (m-10) cc_final: 0.8213 (m-10) REVERT: D 436 TYR cc_start: 0.8124 (OUTLIER) cc_final: 0.7806 (m-80) REVERT: D 600 ILE cc_start: 0.8333 (OUTLIER) cc_final: 0.7363 (pt) REVERT: D 679 TYR cc_start: 0.7708 (m-10) cc_final: 0.7310 (m-10) REVERT: C 469 GLN cc_start: 0.7414 (tp40) cc_final: 0.6752 (tt0) REVERT: C 497 CYS cc_start: 0.7364 (OUTLIER) cc_final: 0.6616 (m) REVERT: C 683 ILE cc_start: 0.8659 (OUTLIER) cc_final: 0.8455 (mm) REVERT: B 351 ILE cc_start: 0.8288 (OUTLIER) cc_final: 0.7802 (mt) REVERT: B 454 ASP cc_start: 0.8262 (t0) cc_final: 0.7774 (p0) REVERT: B 458 MET cc_start: 0.8274 (tpt) cc_final: 0.7899 (mmm) REVERT: B 612 ARG cc_start: 0.7755 (ttp80) cc_final: 0.7029 (ttp80) REVERT: B 618 MET cc_start: 0.7868 (mtm) cc_final: 0.7585 (mtt) REVERT: B 699 TYR cc_start: 0.6729 (m-80) cc_final: 0.6458 (m-80) REVERT: A 344 ARG cc_start: 0.7581 (mtp85) cc_final: 0.7011 (mtm-85) REVERT: A 372 ARG cc_start: 0.8962 (OUTLIER) cc_final: 0.7839 (ptt-90) REVERT: A 469 GLN cc_start: 0.7811 (mm-40) cc_final: 0.7321 (mm-40) REVERT: A 478 ASN cc_start: 0.8102 (OUTLIER) cc_final: 0.7744 (t0) REVERT: A 497 CYS cc_start: 0.8321 (OUTLIER) cc_final: 0.7721 (m) REVERT: A 529 GLN cc_start: 0.7174 (mp10) cc_final: 0.6596 (mp10) REVERT: A 684 MET cc_start: 0.8303 (tmm) cc_final: 0.8073 (tmm) outliers start: 40 outliers final: 28 residues processed: 210 average time/residue: 0.2306 time to fit residues: 76.1255 Evaluate side-chains 215 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 177 time to evaluate : 1.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 450 LYS Chi-restraints excluded: chain E residue 491 CYS Chi-restraints excluded: chain E residue 501 PHE Chi-restraints excluded: chain E residue 507 THR Chi-restraints excluded: chain E residue 543 PHE Chi-restraints excluded: chain E residue 552 SER Chi-restraints excluded: chain E residue 669 LEU Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 357 PHE Chi-restraints excluded: chain F residue 408 THR Chi-restraints excluded: chain F residue 471 LEU Chi-restraints excluded: chain F residue 497 CYS Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 436 TYR Chi-restraints excluded: chain D residue 543 PHE Chi-restraints excluded: chain D residue 581 CYS Chi-restraints excluded: chain D residue 600 ILE Chi-restraints excluded: chain D residue 624 VAL Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 357 PHE Chi-restraints excluded: chain C residue 436 TYR Chi-restraints excluded: chain C residue 497 CYS Chi-restraints excluded: chain C residue 507 THR Chi-restraints excluded: chain C residue 596 ASN Chi-restraints excluded: chain C residue 683 ILE Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 351 ILE Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain B residue 511 THR Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 372 ARG Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 478 ASN Chi-restraints excluded: chain A residue 497 CYS Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 603 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 39 optimal weight: 4.9990 chunk 173 optimal weight: 2.9990 chunk 134 optimal weight: 9.9990 chunk 100 optimal weight: 6.9990 chunk 87 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 95 optimal weight: 0.9990 chunk 105 optimal weight: 6.9990 chunk 148 optimal weight: 0.5980 chunk 146 optimal weight: 2.9990 chunk 176 optimal weight: 0.0980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 478 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.216578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.158470 restraints weight = 18684.583| |-----------------------------------------------------------------------------| r_work (start): 0.3828 rms_B_bonded: 3.44 r_work: 0.3166 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.2122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15224 Z= 0.116 Angle : 0.559 19.710 20506 Z= 0.272 Chirality : 0.041 0.153 2316 Planarity : 0.004 0.050 2583 Dihedral : 3.779 28.900 1974 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 2.25 % Allowed : 24.20 % Favored : 73.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.21), residues: 1776 helix: -0.09 (0.20), residues: 705 sheet: -1.62 (0.32), residues: 275 loop : -1.43 (0.24), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.071 0.002 TRP C 675 HIS 0.002 0.001 HIS B 347 PHE 0.009 0.001 PHE F 554 TYR 0.020 0.001 TYR A 482 ARG 0.004 0.000 ARG F 514 Details of bonding type rmsd hydrogen bonds : bond 0.02966 ( 474) hydrogen bonds : angle 4.36838 ( 1323) covalent geometry : bond 0.00283 (15224) covalent geometry : angle 0.55906 (20506) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 180 time to evaluate : 1.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 501 PHE cc_start: 0.8323 (OUTLIER) cc_final: 0.7793 (m-10) REVERT: E 553 VAL cc_start: 0.8364 (t) cc_final: 0.8125 (m) REVERT: E 664 TYR cc_start: 0.6875 (m-80) cc_final: 0.6189 (m-80) REVERT: F 497 CYS cc_start: 0.7716 (OUTLIER) cc_final: 0.6952 (m) REVERT: F 675 TRP cc_start: 0.8567 (m-10) cc_final: 0.8094 (m-10) REVERT: D 436 TYR cc_start: 0.8062 (OUTLIER) cc_final: 0.7679 (m-80) REVERT: D 600 ILE cc_start: 0.8316 (OUTLIER) cc_final: 0.7344 (pt) REVERT: D 679 TYR cc_start: 0.7722 (m-10) cc_final: 0.7319 (m-10) REVERT: C 469 GLN cc_start: 0.7423 (tp40) cc_final: 0.6788 (tt0) REVERT: C 497 CYS cc_start: 0.7382 (OUTLIER) cc_final: 0.6588 (m) REVERT: B 351 ILE cc_start: 0.8261 (OUTLIER) cc_final: 0.7781 (mt) REVERT: B 454 ASP cc_start: 0.8241 (t0) cc_final: 0.7776 (p0) REVERT: B 612 ARG cc_start: 0.7749 (ttp80) cc_final: 0.6970 (ttp80) REVERT: B 618 MET cc_start: 0.7881 (mtm) cc_final: 0.7593 (mtt) REVERT: B 699 TYR cc_start: 0.6957 (m-80) cc_final: 0.6622 (m-80) REVERT: A 344 ARG cc_start: 0.7598 (mtp85) cc_final: 0.7028 (mtm-85) REVERT: A 372 ARG cc_start: 0.8949 (OUTLIER) cc_final: 0.7845 (ptt-90) REVERT: A 462 MET cc_start: 0.8635 (mmm) cc_final: 0.7976 (mmm) REVERT: A 469 GLN cc_start: 0.7800 (mm-40) cc_final: 0.7328 (mm-40) REVERT: A 478 ASN cc_start: 0.8029 (OUTLIER) cc_final: 0.7620 (t0) REVERT: A 497 CYS cc_start: 0.8116 (OUTLIER) cc_final: 0.7566 (m) REVERT: A 529 GLN cc_start: 0.7153 (mp10) cc_final: 0.6551 (mp10) REVERT: A 532 LEU cc_start: 0.7978 (mm) cc_final: 0.7684 (tt) outliers start: 38 outliers final: 29 residues processed: 209 average time/residue: 0.2268 time to fit residues: 74.8865 Evaluate side-chains 215 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 177 time to evaluate : 1.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 450 LYS Chi-restraints excluded: chain E residue 491 CYS Chi-restraints excluded: chain E residue 501 PHE Chi-restraints excluded: chain E residue 507 THR Chi-restraints excluded: chain E residue 543 PHE Chi-restraints excluded: chain E residue 552 SER Chi-restraints excluded: chain E residue 669 LEU Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 357 PHE Chi-restraints excluded: chain F residue 408 THR Chi-restraints excluded: chain F residue 471 LEU Chi-restraints excluded: chain F residue 497 CYS Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 436 TYR Chi-restraints excluded: chain D residue 543 PHE Chi-restraints excluded: chain D residue 581 CYS Chi-restraints excluded: chain D residue 600 ILE Chi-restraints excluded: chain D residue 624 VAL Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 357 PHE Chi-restraints excluded: chain C residue 436 TYR Chi-restraints excluded: chain C residue 497 CYS Chi-restraints excluded: chain C residue 507 THR Chi-restraints excluded: chain C residue 596 ASN Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 351 ILE Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain B residue 511 THR Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 372 ARG Chi-restraints excluded: chain A residue 478 ASN Chi-restraints excluded: chain A residue 497 CYS Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 603 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 118 optimal weight: 0.9990 chunk 96 optimal weight: 4.9990 chunk 47 optimal weight: 0.9990 chunk 66 optimal weight: 4.9990 chunk 0 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 99 optimal weight: 30.0000 chunk 50 optimal weight: 9.9990 chunk 4 optimal weight: 0.6980 chunk 35 optimal weight: 0.5980 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 478 ASN A 594 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.215992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.159480 restraints weight = 18775.588| |-----------------------------------------------------------------------------| r_work (start): 0.3836 rms_B_bonded: 3.48 r_work: 0.3130 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15224 Z= 0.138 Angle : 0.573 19.415 20506 Z= 0.278 Chirality : 0.042 0.159 2316 Planarity : 0.004 0.050 2583 Dihedral : 3.851 28.901 1974 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 2.49 % Allowed : 24.26 % Favored : 73.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.21), residues: 1776 helix: -0.12 (0.20), residues: 706 sheet: -1.58 (0.32), residues: 272 loop : -1.41 (0.24), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.069 0.002 TRP C 675 HIS 0.002 0.001 HIS B 347 PHE 0.009 0.001 PHE E 427 TYR 0.020 0.001 TYR A 482 ARG 0.007 0.000 ARG F 514 Details of bonding type rmsd hydrogen bonds : bond 0.03137 ( 474) hydrogen bonds : angle 4.41464 ( 1323) covalent geometry : bond 0.00342 (15224) covalent geometry : angle 0.57265 (20506) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8317.34 seconds wall clock time: 145 minutes 46.91 seconds (8746.91 seconds total)