Starting phenix.real_space_refine on Sat Aug 23 21:45:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hwc_35053/08_2025/8hwc_35053.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hwc_35053/08_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_35053/08_2025/8hwc_35053.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hwc_35053/08_2025/8hwc_35053.map" model { file = "/net/cci-nas-00/data/ceres_data/8hwc_35053/08_2025/8hwc_35053.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hwc_35053/08_2025/8hwc_35053.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 3.64, per 1000 atoms: 0.24 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: 1.29 Conformation dependent library (CDL) restraints added in 659.3 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.48 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: 2.07 Time building geometry restraints manager: 1.76 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: 1.480 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: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 13.560 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.080 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -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 ARG 0.009 0.000 ARG A 625 TYR 0.017 0.001 TYR C 482 PHE 0.013 0.001 PHE A 357 TRP 0.125 0.003 TRP C 675 HIS 0.003 0.001 HIS E 548 Details of bonding type rmsd covalent geometry : bond 0.00312 (15224) covalent geometry : angle 0.60287 (20506) hydrogen bonds : bond 0.13317 ( 474) hydrogen bonds : angle 5.73867 ( 1323) *********************** 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 : 0.638 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: 0.0992 time to fit residues: 28.9502 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 : 0.632 ------------------------------------------------------------------------------- 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 98 optimal weight: 30.0000 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 0.0370 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 1.9990 overall best weight: 2.1864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 478 ASN B 660 GLN A 478 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.213520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.155337 restraints weight = 18305.475| |-----------------------------------------------------------------------------| r_work (start): 0.3809 rms_B_bonded: 3.52 r_work: 0.3109 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.1013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 15224 Z= 0.212 Angle : 0.584 8.970 20506 Z= 0.297 Chirality : 0.044 0.195 2316 Planarity : 0.005 0.054 2583 Dihedral : 4.187 24.742 1977 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.81 (0.20), residues: 1776 helix: -0.30 (0.20), residues: 689 sheet: -1.63 (0.33), residues: 257 loop : -1.79 (0.22), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 514 TYR 0.014 0.001 TYR A 482 PHE 0.013 0.001 PHE A 357 TRP 0.069 0.003 TRP C 675 HIS 0.004 0.001 HIS E 347 Details of bonding type rmsd covalent geometry : bond 0.00533 (15224) covalent geometry : angle 0.58430 (20506) hydrogen bonds : bond 0.04058 ( 474) hydrogen bonds : angle 4.94386 ( 1323) *********************** 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 217 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 175 time to evaluate : 0.621 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 477 LYS cc_start: 0.7846 (tmmt) cc_final: 0.7533 (mptt) REVERT: F 351 ILE cc_start: 0.8099 (OUTLIER) cc_final: 0.7745 (mt) REVERT: F 497 CYS cc_start: 0.7526 (OUTLIER) cc_final: 0.6901 (m) REVERT: D 436 TYR cc_start: 0.8055 (OUTLIER) cc_final: 0.7700 (m-80) REVERT: D 679 TYR cc_start: 0.7605 (m-10) cc_final: 0.7307 (m-10) REVERT: C 360 GLU cc_start: 0.6997 (pm20) cc_final: 0.6766 (pm20) REVERT: B 458 MET cc_start: 0.8030 (mmm) cc_final: 0.7538 (tpt) REVERT: B 618 MET cc_start: 0.8153 (mtm) cc_final: 0.7788 (mtt) REVERT: A 469 GLN cc_start: 0.7574 (mm-40) cc_final: 0.6934 (mm-40) REVERT: A 478 ASN cc_start: 0.8191 (OUTLIER) cc_final: 0.7616 (t0) REVERT: A 515 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8761 (mp) REVERT: A 529 GLN cc_start: 0.7279 (mp10) cc_final: 0.6861 (mp10) outliers start: 42 outliers final: 15 residues processed: 208 average time/residue: 0.1038 time to fit residues: 34.5798 Evaluate side-chains 183 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 163 time to evaluate : 0.612 ------------------------------------------------------------------------------- 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 F residue 351 ILE 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 D residue 436 TYR Chi-restraints excluded: chain D residue 511 THR Chi-restraints excluded: chain D residue 581 CYS 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 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 382 GLU Chi-restraints excluded: chain A residue 478 ASN Chi-restraints excluded: chain A residue 515 LEU 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 156 optimal weight: 3.9990 chunk 108 optimal weight: 5.9990 chunk 158 optimal weight: 0.7980 chunk 116 optimal weight: 0.5980 chunk 89 optimal weight: 2.9990 chunk 137 optimal weight: 10.0000 chunk 139 optimal weight: 5.9990 chunk 138 optimal weight: 3.9990 chunk 75 optimal weight: 20.0000 chunk 143 optimal weight: 0.6980 chunk 110 optimal weight: 6.9990 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 478 ASN B 660 GLN A 478 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.214591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.158516 restraints weight = 18775.272| |-----------------------------------------------------------------------------| r_work (start): 0.3827 rms_B_bonded: 3.58 r_work: 0.3112 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.1286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 15224 Z= 0.180 Angle : 0.565 10.215 20506 Z= 0.284 Chirality : 0.043 0.303 2316 Planarity : 0.004 0.051 2583 Dihedral : 4.071 24.865 1974 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 2.31 % Allowed : 23.85 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.76 (0.20), residues: 1776 helix: -0.32 (0.20), residues: 699 sheet: -1.57 (0.34), residues: 244 loop : -1.74 (0.22), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 595 TYR 0.018 0.001 TYR A 664 PHE 0.014 0.001 PHE B 543 TRP 0.060 0.002 TRP C 675 HIS 0.003 0.001 HIS E 548 Details of bonding type rmsd covalent geometry : bond 0.00453 (15224) covalent geometry : angle 0.56487 (20506) hydrogen bonds : bond 0.03625 ( 474) hydrogen bonds : angle 4.76586 ( 1323) *********************** 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 216 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 177 time to evaluate : 0.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 346 ASP cc_start: 0.8061 (m-30) cc_final: 0.7803 (m-30) REVERT: E 477 LYS cc_start: 0.7805 (tmmt) cc_final: 0.7521 (mptt) REVERT: F 372 ARG cc_start: 0.9072 (OUTLIER) cc_final: 0.8782 (ptt-90) REVERT: F 497 CYS cc_start: 0.7613 (OUTLIER) cc_final: 0.6899 (m) REVERT: D 436 TYR cc_start: 0.8084 (OUTLIER) cc_final: 0.7734 (m-80) REVERT: D 600 ILE cc_start: 0.8502 (OUTLIER) cc_final: 0.7778 (pt) REVERT: D 679 TYR cc_start: 0.7599 (m-10) cc_final: 0.7232 (m-10) REVERT: C 497 CYS cc_start: 0.7525 (OUTLIER) cc_final: 0.6795 (m) REVERT: B 618 MET cc_start: 0.8078 (mtm) cc_final: 0.7712 (mtt) REVERT: A 372 ARG cc_start: 0.8934 (OUTLIER) cc_final: 0.8312 (ptt-90) REVERT: A 469 GLN cc_start: 0.7740 (mm-40) cc_final: 0.7181 (mm-40) REVERT: A 478 ASN cc_start: 0.8191 (OUTLIER) cc_final: 0.7515 (t0) REVERT: A 529 GLN cc_start: 0.7351 (mp10) cc_final: 0.6901 (mp10) outliers start: 39 outliers final: 22 residues processed: 205 average time/residue: 0.0999 time to fit residues: 32.8210 Evaluate side-chains 193 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 164 time to evaluate : 0.608 ------------------------------------------------------------------------------- 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 F residue 339 VAL Chi-restraints excluded: chain F residue 357 PHE Chi-restraints excluded: chain F residue 372 ARG Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain F residue 497 CYS Chi-restraints excluded: chain F residue 549 LEU 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 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 C residue 596 ASN 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 372 ARG Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 478 ASN Chi-restraints excluded: chain A residue 501 PHE Chi-restraints excluded: chain A residue 530 THR 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 101 optimal weight: 0.9980 chunk 166 optimal weight: 3.9990 chunk 74 optimal weight: 0.9990 chunk 19 optimal weight: 4.9990 chunk 48 optimal weight: 10.0000 chunk 45 optimal weight: 7.9990 chunk 129 optimal weight: 6.9990 chunk 100 optimal weight: 5.9990 chunk 118 optimal weight: 0.7980 chunk 36 optimal weight: 5.9990 chunk 169 optimal weight: 0.8980 overall best weight: 1.5384 ------------------------------------------------------------------------------- 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 = 0.4398 r_free = 0.4398 target = 0.214885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.161767 restraints weight = 18665.864| |-----------------------------------------------------------------------------| r_work (start): 0.3867 rms_B_bonded: 3.41 r_work: 0.3134 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.1442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15224 Z= 0.158 Angle : 0.547 10.196 20506 Z= 0.274 Chirality : 0.042 0.242 2316 Planarity : 0.004 0.051 2583 Dihedral : 3.988 24.757 1974 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 3.02 % Allowed : 23.79 % Favored : 73.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.70 (0.21), residues: 1776 helix: -0.25 (0.20), residues: 700 sheet: -1.65 (0.33), residues: 255 loop : -1.68 (0.23), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 612 TYR 0.014 0.001 TYR A 664 PHE 0.010 0.001 PHE A 357 TRP 0.061 0.002 TRP C 675 HIS 0.002 0.001 HIS E 347 Details of bonding type rmsd covalent geometry : bond 0.00395 (15224) covalent geometry : angle 0.54663 (20506) hydrogen bonds : bond 0.03350 ( 474) hydrogen bonds : angle 4.63710 ( 1323) *********************** 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 231 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 180 time to evaluate : 0.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 346 ASP cc_start: 0.8056 (m-30) cc_final: 0.7767 (m-30) REVERT: E 377 LYS cc_start: 0.8281 (OUTLIER) cc_final: 0.8071 (mmmm) REVERT: F 372 ARG cc_start: 0.9072 (OUTLIER) cc_final: 0.8817 (ptt-90) REVERT: F 497 CYS cc_start: 0.7672 (OUTLIER) cc_final: 0.6942 (m) REVERT: D 436 TYR cc_start: 0.8088 (OUTLIER) cc_final: 0.7733 (m-80) REVERT: D 600 ILE cc_start: 0.8444 (OUTLIER) cc_final: 0.7712 (pt) REVERT: D 679 TYR cc_start: 0.7642 (m-10) cc_final: 0.7225 (m-10) REVERT: C 497 CYS cc_start: 0.7597 (OUTLIER) cc_final: 0.6859 (m) REVERT: C 579 GLU cc_start: 0.8170 (pt0) cc_final: 0.7629 (pt0) REVERT: B 454 ASP cc_start: 0.8040 (t0) cc_final: 0.7472 (p0) REVERT: B 618 MET cc_start: 0.7955 (mtm) cc_final: 0.7614 (mtt) REVERT: A 372 ARG cc_start: 0.8950 (OUTLIER) cc_final: 0.8365 (ptt-90) REVERT: A 458 MET cc_start: 0.8181 (tpt) cc_final: 0.7455 (tpt) REVERT: A 462 MET cc_start: 0.8599 (mmm) cc_final: 0.7928 (mmm) REVERT: A 469 GLN cc_start: 0.7851 (mm-40) cc_final: 0.7375 (mm-40) REVERT: A 478 ASN cc_start: 0.8133 (OUTLIER) cc_final: 0.7480 (t0) REVERT: A 497 CYS cc_start: 0.8410 (OUTLIER) cc_final: 0.7770 (m) REVERT: A 514 ARG cc_start: 0.8211 (ptp90) cc_final: 0.7933 (ptp90) REVERT: A 529 GLN cc_start: 0.7407 (mp10) cc_final: 0.6913 (mp10) REVERT: A 600 ILE cc_start: 0.9209 (OUTLIER) cc_final: 0.8952 (mm) outliers start: 51 outliers final: 24 residues processed: 220 average time/residue: 0.1044 time to fit residues: 35.8523 Evaluate side-chains 201 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 167 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 377 LYS 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 F residue 339 VAL Chi-restraints excluded: chain F residue 357 PHE Chi-restraints excluded: chain F residue 372 ARG Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain F residue 471 LEU 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 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 596 ASN 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 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 585 ARG Chi-restraints excluded: chain A residue 600 ILE 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 61 optimal weight: 2.9990 chunk 2 optimal weight: 0.0010 chunk 49 optimal weight: 6.9990 chunk 4 optimal weight: 0.7980 chunk 147 optimal weight: 2.9990 chunk 116 optimal weight: 0.6980 chunk 151 optimal weight: 0.5980 chunk 1 optimal weight: 0.1980 chunk 98 optimal weight: 10.0000 chunk 79 optimal weight: 10.0000 chunk 176 optimal weight: 10.0000 overall best weight: 0.4586 ------------------------------------------------------------------------------- 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 A 594 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.217518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.164527 restraints weight = 18669.389| |-----------------------------------------------------------------------------| r_work (start): 0.3893 rms_B_bonded: 3.40 r_work: 0.3171 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.1552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 15224 Z= 0.091 Angle : 0.512 15.701 20506 Z= 0.255 Chirality : 0.041 0.198 2316 Planarity : 0.004 0.051 2583 Dihedral : 3.688 29.569 1974 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 2.72 % Allowed : 23.73 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.52 (0.21), residues: 1776 helix: -0.13 (0.20), residues: 718 sheet: -1.58 (0.33), residues: 259 loop : -1.57 (0.23), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 612 TYR 0.014 0.001 TYR A 482 PHE 0.008 0.001 PHE E 357 TRP 0.065 0.002 TRP C 675 HIS 0.003 0.000 HIS A 680 Details of bonding type rmsd covalent geometry : bond 0.00212 (15224) covalent geometry : angle 0.51247 (20506) hydrogen bonds : bond 0.02593 ( 474) hydrogen bonds : angle 4.34858 ( 1323) *********************** 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 229 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 183 time to evaluate : 0.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 346 ASP cc_start: 0.7993 (m-30) cc_final: 0.7788 (m-30) REVERT: E 382 GLU cc_start: 0.8524 (pt0) cc_final: 0.8324 (pt0) REVERT: E 664 TYR cc_start: 0.6801 (m-80) cc_final: 0.6044 (m-80) REVERT: F 343 GLU cc_start: 0.7610 (OUTLIER) cc_final: 0.7041 (mp0) REVERT: F 372 ARG cc_start: 0.9051 (OUTLIER) cc_final: 0.8743 (ptt-90) REVERT: F 497 CYS cc_start: 0.7656 (OUTLIER) cc_final: 0.6769 (m) REVERT: D 436 TYR cc_start: 0.7967 (OUTLIER) cc_final: 0.7550 (m-80) REVERT: D 679 TYR cc_start: 0.7600 (m-10) cc_final: 0.7253 (m-10) REVERT: C 497 CYS cc_start: 0.7488 (OUTLIER) cc_final: 0.6808 (m) REVERT: C 579 GLU cc_start: 0.8096 (pt0) cc_final: 0.7630 (pt0) REVERT: B 351 ILE cc_start: 0.8164 (OUTLIER) cc_final: 0.7678 (mt) REVERT: B 454 ASP cc_start: 0.8014 (t0) cc_final: 0.7506 (p0) REVERT: B 618 MET cc_start: 0.7872 (mtm) cc_final: 0.7599 (mtt) REVERT: B 699 TYR cc_start: 0.6727 (m-80) cc_final: 0.6406 (m-80) REVERT: A 344 ARG cc_start: 0.7540 (mtp85) cc_final: 0.6963 (mtm-85) REVERT: A 469 GLN cc_start: 0.7770 (mm-40) cc_final: 0.7322 (mm-40) REVERT: A 478 ASN cc_start: 0.8093 (OUTLIER) cc_final: 0.7506 (t0) REVERT: A 497 CYS cc_start: 0.8370 (OUTLIER) cc_final: 0.7751 (m) REVERT: A 529 GLN cc_start: 0.7299 (mp10) cc_final: 0.6828 (mp10) outliers start: 46 outliers final: 20 residues processed: 219 average time/residue: 0.1097 time to fit residues: 37.5991 Evaluate side-chains 201 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 173 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 552 SER Chi-restraints excluded: chain E residue 669 LEU Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 343 GLU Chi-restraints excluded: chain F residue 357 PHE Chi-restraints excluded: chain F residue 372 ARG Chi-restraints excluded: chain F residue 471 LEU Chi-restraints excluded: chain F residue 497 CYS Chi-restraints excluded: chain F residue 498 LEU 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 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 B residue 511 THR 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 79 optimal weight: 9.9990 chunk 143 optimal weight: 0.9980 chunk 83 optimal weight: 10.0000 chunk 122 optimal weight: 4.9990 chunk 33 optimal weight: 0.7980 chunk 2 optimal weight: 3.9990 chunk 91 optimal weight: 0.9990 chunk 36 optimal weight: 4.9990 chunk 169 optimal weight: 10.0000 chunk 140 optimal weight: 7.9990 chunk 94 optimal weight: 10.0000 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 594 ASN B 660 GLN A 478 ASN ** A 593 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 594 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.213576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.156023 restraints weight = 18635.526| |-----------------------------------------------------------------------------| r_work (start): 0.3800 rms_B_bonded: 3.57 r_work: 0.3099 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 15224 Z= 0.224 Angle : 0.620 17.544 20506 Z= 0.306 Chirality : 0.044 0.183 2316 Planarity : 0.004 0.050 2583 Dihedral : 4.109 28.941 1974 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 3.25 % Allowed : 23.25 % Favored : 73.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.67 (0.20), residues: 1776 helix: -0.26 (0.20), residues: 694 sheet: -1.72 (0.32), residues: 270 loop : -1.57 (0.23), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 332 TYR 0.019 0.001 TYR A 482 PHE 0.016 0.001 PHE A 357 TRP 0.073 0.003 TRP C 675 HIS 0.003 0.001 HIS A 347 Details of bonding type rmsd covalent geometry : bond 0.00564 (15224) covalent geometry : angle 0.62036 (20506) hydrogen bonds : bond 0.03955 ( 474) hydrogen bonds : angle 4.69720 ( 1323) *********************** 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 234 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 179 time to evaluate : 0.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 346 ASP cc_start: 0.8038 (m-30) cc_final: 0.7730 (m-30) REVERT: E 477 LYS cc_start: 0.7911 (tmmt) cc_final: 0.7626 (mptt) REVERT: E 501 PHE cc_start: 0.8405 (OUTLIER) cc_final: 0.7739 (m-10) REVERT: E 664 TYR cc_start: 0.6910 (m-80) cc_final: 0.6166 (m-80) REVERT: F 483 GLU cc_start: 0.8692 (mt-10) cc_final: 0.8241 (mt-10) REVERT: F 497 CYS cc_start: 0.7705 (OUTLIER) cc_final: 0.7017 (m) REVERT: F 675 TRP cc_start: 0.8734 (m-10) cc_final: 0.8443 (m-10) REVERT: D 436 TYR cc_start: 0.8145 (OUTLIER) cc_final: 0.7792 (m-80) REVERT: D 679 TYR cc_start: 0.7720 (m-10) cc_final: 0.7339 (m-10) REVERT: C 469 GLN cc_start: 0.7385 (tp40) cc_final: 0.6711 (tt0) REVERT: C 497 CYS cc_start: 0.7531 (OUTLIER) cc_final: 0.6771 (m) REVERT: C 579 GLU cc_start: 0.8112 (pt0) cc_final: 0.7601 (pt0) REVERT: B 454 ASP cc_start: 0.8100 (t0) cc_final: 0.7521 (p0) REVERT: B 618 MET cc_start: 0.8007 (mtm) cc_final: 0.7664 (mtt) REVERT: B 699 TYR cc_start: 0.6810 (m-80) cc_final: 0.6499 (m-80) REVERT: A 372 ARG cc_start: 0.9002 (OUTLIER) cc_final: 0.8419 (ptt-90) REVERT: A 469 GLN cc_start: 0.7860 (mm-40) cc_final: 0.7420 (mm-40) REVERT: A 478 ASN cc_start: 0.7975 (OUTLIER) cc_final: 0.7347 (t0) REVERT: A 497 CYS cc_start: 0.8477 (OUTLIER) cc_final: 0.7877 (m) REVERT: A 529 GLN cc_start: 0.7307 (mp10) cc_final: 0.6732 (mp10) REVERT: A 600 ILE cc_start: 0.9230 (OUTLIER) cc_final: 0.8959 (mm) outliers start: 55 outliers final: 32 residues processed: 222 average time/residue: 0.1131 time to fit residues: 39.2676 Evaluate side-chains 214 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 174 time to evaluate : 0.608 ------------------------------------------------------------------------------- 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 552 SER 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 471 LEU Chi-restraints excluded: chain F residue 497 CYS Chi-restraints excluded: chain F residue 498 LEU Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 436 TYR Chi-restraints excluded: chain D residue 511 THR 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 511 THR Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 372 ARG Chi-restraints excluded: chain A residue 436 TYR Chi-restraints excluded: chain A residue 478 ASN Chi-restraints excluded: chain A residue 497 CYS Chi-restraints excluded: chain A residue 501 PHE Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 585 ARG Chi-restraints excluded: chain A residue 594 ASN Chi-restraints excluded: chain A residue 600 ILE 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 17 optimal weight: 8.9990 chunk 110 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 49 optimal weight: 0.0970 chunk 175 optimal weight: 7.9990 chunk 111 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 167 optimal weight: 4.9990 chunk 61 optimal weight: 0.8980 chunk 100 optimal weight: 0.9990 chunk 123 optimal weight: 2.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 660 GLN B 660 GLN A 478 ASN A 594 ASN A 597 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.214697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.157244 restraints weight = 18479.395| |-----------------------------------------------------------------------------| r_work (start): 0.3817 rms_B_bonded: 3.52 r_work: 0.3120 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.1884 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= 0.163 Angle : 0.583 18.452 20506 Z= 0.287 Chirality : 0.043 0.169 2316 Planarity : 0.004 0.050 2583 Dihedral : 4.028 28.610 1974 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.67 (0.21), residues: 1776 helix: -0.28 (0.20), residues: 705 sheet: -1.73 (0.32), residues: 275 loop : -1.55 (0.23), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 514 TYR 0.016 0.001 TYR A 482 PHE 0.011 0.001 PHE A 357 TRP 0.082 0.003 TRP C 675 HIS 0.002 0.001 HIS E 347 Details of bonding type rmsd covalent geometry : bond 0.00405 (15224) covalent geometry : angle 0.58287 (20506) hydrogen bonds : bond 0.03436 ( 474) hydrogen bonds : angle 4.57374 ( 1323) *********************** 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 222 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 177 time to evaluate : 0.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 346 ASP cc_start: 0.8035 (m-30) cc_final: 0.7791 (m-30) REVERT: E 477 LYS cc_start: 0.7871 (tmmt) cc_final: 0.7605 (mptt) REVERT: E 501 PHE cc_start: 0.8393 (OUTLIER) cc_final: 0.7747 (m-10) REVERT: E 664 TYR cc_start: 0.6926 (m-80) cc_final: 0.6180 (m-80) REVERT: F 483 GLU cc_start: 0.8671 (mt-10) cc_final: 0.8369 (mt-10) REVERT: F 497 CYS cc_start: 0.7834 (OUTLIER) cc_final: 0.6995 (m) REVERT: D 436 TYR cc_start: 0.8153 (OUTLIER) cc_final: 0.7826 (m-80) REVERT: D 679 TYR cc_start: 0.7736 (m-10) cc_final: 0.7328 (m-10) REVERT: C 469 GLN cc_start: 0.7400 (tp40) cc_final: 0.6685 (tt0) REVERT: C 497 CYS cc_start: 0.7573 (OUTLIER) cc_final: 0.6806 (m) REVERT: C 683 ILE cc_start: 0.8745 (OUTLIER) cc_final: 0.8473 (mm) REVERT: B 454 ASP cc_start: 0.8169 (t0) cc_final: 0.7603 (p0) REVERT: B 618 MET cc_start: 0.8005 (mtm) cc_final: 0.7684 (mtt) REVERT: B 699 TYR cc_start: 0.6824 (m-80) cc_final: 0.6521 (m-80) REVERT: A 372 ARG cc_start: 0.8985 (OUTLIER) cc_final: 0.8499 (ptt-90) REVERT: A 469 GLN cc_start: 0.7858 (mm-40) cc_final: 0.7325 (mm-40) REVERT: A 478 ASN cc_start: 0.8009 (OUTLIER) cc_final: 0.7546 (t0) REVERT: A 497 CYS cc_start: 0.8439 (OUTLIER) cc_final: 0.7812 (m) REVERT: A 529 GLN cc_start: 0.7187 (mp10) cc_final: 0.6515 (mp10) REVERT: A 600 ILE cc_start: 0.9192 (OUTLIER) cc_final: 0.8921 (mm) outliers start: 45 outliers final: 31 residues processed: 213 average time/residue: 0.1142 time to fit residues: 38.0900 Evaluate side-chains 214 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 174 time to evaluate : 0.621 ------------------------------------------------------------------------------- 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 552 SER 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 498 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 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 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 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 436 TYR 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 594 ASN Chi-restraints excluded: chain A residue 600 ILE 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 127 optimal weight: 5.9990 chunk 28 optimal weight: 0.7980 chunk 62 optimal weight: 0.5980 chunk 134 optimal weight: 9.9990 chunk 59 optimal weight: 0.9990 chunk 111 optimal weight: 4.9990 chunk 5 optimal weight: 0.3980 chunk 89 optimal weight: 2.9990 chunk 53 optimal weight: 20.0000 chunk 176 optimal weight: 6.9990 chunk 66 optimal weight: 3.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 466 ASN B 660 GLN A 478 ASN ** A 593 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 594 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4406 r_free = 0.4406 target = 0.215643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.157606 restraints weight = 18663.500| |-----------------------------------------------------------------------------| r_work (start): 0.3820 rms_B_bonded: 3.44 r_work: 0.3144 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15224 Z= 0.131 Angle : 0.565 18.893 20506 Z= 0.277 Chirality : 0.042 0.172 2316 Planarity : 0.004 0.050 2583 Dihedral : 3.911 28.430 1974 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 2.90 % Allowed : 23.73 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.61 (0.21), residues: 1776 helix: -0.23 (0.20), residues: 711 sheet: -1.71 (0.32), residues: 275 loop : -1.52 (0.23), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 514 TYR 0.016 0.001 TYR A 482 PHE 0.011 0.001 PHE F 554 TRP 0.075 0.003 TRP C 675 HIS 0.011 0.001 HIS E 548 Details of bonding type rmsd covalent geometry : bond 0.00323 (15224) covalent geometry : angle 0.56488 (20506) hydrogen bonds : bond 0.03148 ( 474) hydrogen bonds : angle 4.46923 ( 1323) *********************** 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: 49 poor density : 176 time to evaluate : 0.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 346 ASP cc_start: 0.8040 (m-30) cc_final: 0.7817 (m-30) REVERT: E 501 PHE cc_start: 0.8370 (OUTLIER) cc_final: 0.7733 (m-10) REVERT: E 664 TYR cc_start: 0.6888 (m-80) cc_final: 0.6174 (m-80) REVERT: F 483 GLU cc_start: 0.8747 (mt-10) cc_final: 0.8332 (mt-10) REVERT: F 497 CYS cc_start: 0.7806 (OUTLIER) cc_final: 0.6952 (m) REVERT: F 675 TRP cc_start: 0.8724 (m-10) cc_final: 0.8517 (m-10) REVERT: D 436 TYR cc_start: 0.8068 (OUTLIER) cc_final: 0.7737 (m-80) REVERT: D 679 TYR cc_start: 0.7694 (m-10) cc_final: 0.7305 (m-10) REVERT: C 469 GLN cc_start: 0.7403 (tp40) cc_final: 0.6710 (tt0) REVERT: C 497 CYS cc_start: 0.7534 (OUTLIER) cc_final: 0.6799 (m) REVERT: C 683 ILE cc_start: 0.8669 (OUTLIER) cc_final: 0.8459 (mm) REVERT: B 454 ASP cc_start: 0.8261 (t0) cc_final: 0.7735 (p0) REVERT: B 612 ARG cc_start: 0.7725 (ttp80) cc_final: 0.6952 (ttp80) REVERT: B 618 MET cc_start: 0.7929 (mtm) cc_final: 0.7623 (mtt) REVERT: B 699 TYR cc_start: 0.6810 (m-80) cc_final: 0.6487 (m-80) REVERT: A 372 ARG cc_start: 0.8957 (OUTLIER) cc_final: 0.8040 (ptt-90) REVERT: A 469 GLN cc_start: 0.7818 (mm-40) cc_final: 0.7315 (mm-40) REVERT: A 478 ASN cc_start: 0.8058 (OUTLIER) cc_final: 0.7650 (t0) REVERT: A 497 CYS cc_start: 0.8400 (OUTLIER) cc_final: 0.7754 (m) REVERT: A 529 GLN cc_start: 0.7098 (mp10) cc_final: 0.6393 (mp10) REVERT: A 532 LEU cc_start: 0.7913 (mm) cc_final: 0.7621 (tt) outliers start: 49 outliers final: 36 residues processed: 215 average time/residue: 0.1101 time to fit residues: 37.3200 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 : 0.663 ------------------------------------------------------------------------------- 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 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 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 482 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 370 SER 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 436 TYR 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 603 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 152 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 148 optimal weight: 0.0570 chunk 40 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 91 optimal weight: 0.5980 chunk 8 optimal weight: 2.9990 chunk 79 optimal weight: 9.9990 chunk 81 optimal weight: 7.9990 chunk 173 optimal weight: 8.9990 overall best weight: 1.1304 ------------------------------------------------------------------------------- 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 ** A 593 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 594 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.216056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.158556 restraints weight = 18581.577| |-----------------------------------------------------------------------------| r_work (start): 0.3831 rms_B_bonded: 3.45 r_work: 0.3155 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15224 Z= 0.129 Angle : 0.568 19.344 20506 Z= 0.278 Chirality : 0.042 0.168 2316 Planarity : 0.004 0.050 2583 Dihedral : 3.861 28.410 1974 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 2.72 % Allowed : 24.02 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.57 (0.21), residues: 1776 helix: -0.20 (0.20), residues: 711 sheet: -1.69 (0.32), residues: 275 loop : -1.49 (0.23), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 514 TYR 0.021 0.001 TYR A 482 PHE 0.009 0.001 PHE F 554 TRP 0.069 0.002 TRP C 675 HIS 0.003 0.001 HIS E 548 Details of bonding type rmsd covalent geometry : bond 0.00318 (15224) covalent geometry : angle 0.56815 (20506) hydrogen bonds : bond 0.03103 ( 474) hydrogen bonds : angle 4.44163 ( 1323) *********************** 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 221 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 175 time to evaluate : 0.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 346 ASP cc_start: 0.8022 (m-30) cc_final: 0.7798 (m-30) REVERT: E 382 GLU cc_start: 0.8662 (pt0) cc_final: 0.8418 (pt0) REVERT: E 501 PHE cc_start: 0.8342 (OUTLIER) cc_final: 0.7721 (m-10) REVERT: E 553 VAL cc_start: 0.8315 (t) cc_final: 0.8081 (m) REVERT: E 664 TYR cc_start: 0.6885 (m-80) cc_final: 0.6174 (m-80) REVERT: F 483 GLU cc_start: 0.8724 (mt-10) cc_final: 0.8315 (mt-10) REVERT: F 497 CYS cc_start: 0.7834 (OUTLIER) cc_final: 0.6985 (m) REVERT: D 436 TYR cc_start: 0.8053 (OUTLIER) cc_final: 0.7720 (m-80) REVERT: D 600 ILE cc_start: 0.8358 (OUTLIER) cc_final: 0.7381 (pt) REVERT: D 679 TYR cc_start: 0.7686 (m-10) cc_final: 0.7284 (m-10) REVERT: C 469 GLN cc_start: 0.7390 (tp40) cc_final: 0.6709 (tt0) REVERT: C 497 CYS cc_start: 0.7501 (OUTLIER) cc_final: 0.6745 (m) REVERT: C 679 TYR cc_start: 0.7474 (m-10) cc_final: 0.7204 (m-10) REVERT: B 454 ASP cc_start: 0.8248 (t0) cc_final: 0.7756 (p0) REVERT: B 612 ARG cc_start: 0.7736 (ttp80) cc_final: 0.6977 (ttp80) REVERT: B 618 MET cc_start: 0.7906 (mtm) cc_final: 0.7603 (mtt) REVERT: B 699 TYR cc_start: 0.6745 (m-80) cc_final: 0.6432 (m-80) REVERT: A 344 ARG cc_start: 0.7331 (mtp180) cc_final: 0.6615 (mtm-85) REVERT: A 372 ARG cc_start: 0.8950 (OUTLIER) cc_final: 0.8028 (ptt-90) REVERT: A 478 ASN cc_start: 0.8077 (OUTLIER) cc_final: 0.7787 (p0) REVERT: A 497 CYS cc_start: 0.8373 (OUTLIER) cc_final: 0.7790 (m) REVERT: A 529 GLN cc_start: 0.7083 (mp10) cc_final: 0.6372 (mp10) REVERT: A 532 LEU cc_start: 0.7836 (mm) cc_final: 0.7544 (tt) REVERT: A 600 ILE cc_start: 0.9160 (OUTLIER) cc_final: 0.8890 (mm) REVERT: A 684 MET cc_start: 0.8246 (tmm) cc_final: 0.7954 (tmm) outliers start: 46 outliers final: 35 residues processed: 213 average time/residue: 0.1085 time to fit residues: 36.6238 Evaluate side-chains 212 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 168 time to evaluate : 0.608 ------------------------------------------------------------------------------- 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 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 498 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 511 THR 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 482 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 370 SER 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 436 TYR 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 600 ILE 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 78 optimal weight: 10.0000 chunk 107 optimal weight: 0.8980 chunk 175 optimal weight: 9.9990 chunk 162 optimal weight: 20.0000 chunk 157 optimal weight: 6.9990 chunk 161 optimal weight: 3.9990 chunk 9 optimal weight: 0.8980 chunk 142 optimal weight: 5.9990 chunk 54 optimal weight: 9.9990 chunk 29 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 478 ASN ** A 593 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 594 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.213711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.155728 restraints weight = 18743.924| |-----------------------------------------------------------------------------| r_work (start): 0.3802 rms_B_bonded: 3.41 r_work: 0.3122 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.2203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 15224 Z= 0.209 Angle : 0.636 19.682 20506 Z= 0.311 Chirality : 0.044 0.167 2316 Planarity : 0.004 0.050 2583 Dihedral : 4.145 28.348 1974 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.15 % Favored : 92.85 % Rotamer: Outliers : 3.08 % Allowed : 23.67 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.70 (0.20), residues: 1776 helix: -0.35 (0.20), residues: 701 sheet: -1.72 (0.32), residues: 275 loop : -1.52 (0.23), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 514 TYR 0.020 0.001 TYR C 679 PHE 0.015 0.001 PHE A 357 TRP 0.099 0.004 TRP C 675 HIS 0.003 0.001 HIS E 548 Details of bonding type rmsd covalent geometry : bond 0.00526 (15224) covalent geometry : angle 0.63552 (20506) hydrogen bonds : bond 0.03920 ( 474) hydrogen bonds : angle 4.70216 ( 1323) ********************** 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 228 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 176 time to evaluate : 0.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 346 ASP cc_start: 0.8013 (m-30) cc_final: 0.7772 (m-30) REVERT: E 501 PHE cc_start: 0.8388 (OUTLIER) cc_final: 0.7730 (m-10) REVERT: E 553 VAL cc_start: 0.8349 (t) cc_final: 0.8110 (m) REVERT: E 664 TYR cc_start: 0.6919 (m-80) cc_final: 0.6204 (m-80) REVERT: F 483 GLU cc_start: 0.8647 (mt-10) cc_final: 0.8241 (mt-10) REVERT: F 497 CYS cc_start: 0.8064 (OUTLIER) cc_final: 0.7229 (m) REVERT: D 436 TYR cc_start: 0.8198 (OUTLIER) cc_final: 0.7879 (m-80) REVERT: D 679 TYR cc_start: 0.7718 (m-10) cc_final: 0.7294 (m-10) REVERT: C 469 GLN cc_start: 0.7405 (tp40) cc_final: 0.6730 (tt0) REVERT: C 497 CYS cc_start: 0.7323 (OUTLIER) cc_final: 0.6572 (m) REVERT: B 454 ASP cc_start: 0.8261 (t0) cc_final: 0.7622 (p0) REVERT: B 612 ARG cc_start: 0.7659 (ttp80) cc_final: 0.6919 (ttp80) REVERT: B 618 MET cc_start: 0.7963 (mtm) cc_final: 0.7631 (mtt) REVERT: B 699 TYR cc_start: 0.6893 (m-80) cc_final: 0.6616 (m-80) REVERT: A 372 ARG cc_start: 0.8999 (OUTLIER) cc_final: 0.7956 (ptt-90) REVERT: A 478 ASN cc_start: 0.8005 (OUTLIER) cc_final: 0.7529 (t0) REVERT: A 497 CYS cc_start: 0.8429 (OUTLIER) cc_final: 0.7807 (m) REVERT: A 529 GLN cc_start: 0.7090 (mp10) cc_final: 0.6398 (mp10) REVERT: A 532 LEU cc_start: 0.7873 (mm) cc_final: 0.7559 (tt) REVERT: A 600 ILE cc_start: 0.9198 (OUTLIER) cc_final: 0.8928 (mm) REVERT: A 684 MET cc_start: 0.8219 (tmm) cc_final: 0.7931 (tmm) outliers start: 52 outliers final: 38 residues processed: 217 average time/residue: 0.1067 time to fit residues: 36.9867 Evaluate side-chains 220 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 174 time to evaluate : 0.632 ------------------------------------------------------------------------------- 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 552 SER 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 498 LEU 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 511 THR Chi-restraints excluded: chain D residue 543 PHE Chi-restraints excluded: chain D residue 581 CYS Chi-restraints excluded: chain D residue 596 ASN 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 482 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 370 SER 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 436 TYR 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 600 ILE 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 30 optimal weight: 0.8980 chunk 84 optimal weight: 0.6980 chunk 116 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 chunk 110 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 160 optimal weight: 0.6980 chunk 141 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 478 ASN ** A 593 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 594 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4415 r_free = 0.4415 target = 0.216534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.158937 restraints weight = 18628.371| |-----------------------------------------------------------------------------| r_work (start): 0.3835 rms_B_bonded: 3.43 r_work: 0.3170 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15224 Z= 0.110 Angle : 0.579 19.608 20506 Z= 0.283 Chirality : 0.042 0.194 2316 Planarity : 0.004 0.050 2583 Dihedral : 3.835 28.308 1974 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.57 % Favored : 94.37 % Rotamer: Outliers : 2.43 % Allowed : 24.50 % Favored : 73.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.55 (0.21), residues: 1776 helix: -0.24 (0.20), residues: 709 sheet: -1.60 (0.32), residues: 272 loop : -1.45 (0.23), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 514 TYR 0.019 0.001 TYR A 482 PHE 0.011 0.001 PHE B 543 TRP 0.095 0.003 TRP C 675 HIS 0.002 0.001 HIS E 548 Details of bonding type rmsd covalent geometry : bond 0.00265 (15224) covalent geometry : angle 0.57904 (20506) hydrogen bonds : bond 0.02954 ( 474) hydrogen bonds : angle 4.41898 ( 1323) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3823.70 seconds wall clock time: 66 minutes 27.12 seconds (3987.12 seconds total)