Starting phenix.real_space_refine on Sun Dec 29 06:51:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8f75_28895/12_2024/8f75_28895.cif Found real_map, /net/cci-nas-00/data/ceres_data/8f75_28895/12_2024/8f75_28895.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8f75_28895/12_2024/8f75_28895.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8f75_28895/12_2024/8f75_28895.map" model { file = "/net/cci-nas-00/data/ceres_data/8f75_28895/12_2024/8f75_28895.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8f75_28895/12_2024/8f75_28895.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.044 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 32 5.16 5 C 6369 2.51 5 N 1713 2.21 5 O 1785 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 9899 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 407, 3321 Classifications: {'peptide': 407} Link IDs: {'PTRANS': 18, 'TRANS': 388} Chain: "B" Number of atoms: 3321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 407, 3321 Classifications: {'peptide': 407} Link IDs: {'PTRANS': 18, 'TRANS': 388} Chain: "F" Number of atoms: 3257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 404, 3257 Classifications: {'peptide': 404} Link IDs: {'PTRANS': 17, 'TRANS': 386} Time building chain proxies: 7.75, per 1000 atoms: 0.78 Number of scatterers: 9899 At special positions: 0 Unit cell: (128.904, 112.136, 91.176, 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 32 16.00 O 1785 8.00 N 1713 7.00 C 6369 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: 2.54 Conformation dependent library (CDL) restraints added in 1.3 seconds 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2364 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 9 sheets defined 33.3% alpha, 12.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.25 Creating SS restraints... Processing helix chain 'A' and resid 402 through 411 Processing helix chain 'A' and resid 412 through 420 Processing helix chain 'A' and resid 439 through 444 removed outlier: 3.637A pdb=" N PHE A 443 " --> pdb=" O PRO A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 467 removed outlier: 3.528A pdb=" N ILE A 465 " --> pdb=" O PRO A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 495 Processing helix chain 'A' and resid 536 through 542 removed outlier: 3.888A pdb=" N GLY A 539 " --> pdb=" O VAL A 536 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ARG A 541 " --> pdb=" O ASP A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 566 removed outlier: 3.695A pdb=" N THR A 563 " --> pdb=" O PRO A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 590 removed outlier: 3.910A pdb=" N LYS A 588 " --> pdb=" O ASN A 585 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LYS A 589 " --> pdb=" O SER A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 613 Processing helix chain 'A' and resid 629 through 638 removed outlier: 3.954A pdb=" N ILE A 633 " --> pdb=" O GLU A 630 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLN A 636 " --> pdb=" O ILE A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 661 Processing helix chain 'A' and resid 680 through 684 removed outlier: 3.606A pdb=" N CYS A 684 " --> pdb=" O LEU A 681 " (cutoff:3.500A) Processing helix chain 'A' and resid 701 through 706 Processing helix chain 'A' and resid 724 through 730 removed outlier: 3.645A pdb=" N CYS A 730 " --> pdb=" O LEU A 727 " (cutoff:3.500A) Processing helix chain 'A' and resid 747 through 753 removed outlier: 3.549A pdb=" N VAL A 750 " --> pdb=" O PRO A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 770 through 776 removed outlier: 3.656A pdb=" N CYS A 776 " --> pdb=" O LEU A 773 " (cutoff:3.500A) Processing helix chain 'A' and resid 787 through 793 Processing helix chain 'A' and resid 795 through 808 Processing helix chain 'B' and resid 403 through 411 Processing helix chain 'B' and resid 412 through 420 Processing helix chain 'B' and resid 440 through 445 Processing helix chain 'B' and resid 462 through 468 Processing helix chain 'B' and resid 484 through 495 removed outlier: 3.648A pdb=" N GLU B 493 " --> pdb=" O ALA B 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 503 through 508 removed outlier: 3.877A pdb=" N GLU B 507 " --> pdb=" O ASP B 504 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE B 508 " --> pdb=" O ILE B 505 " (cutoff:3.500A) Processing helix chain 'B' and resid 559 through 566 Processing helix chain 'B' and resid 567 through 569 No H-bonds generated for 'chain 'B' and resid 567 through 569' Processing helix chain 'B' and resid 586 through 590 removed outlier: 4.012A pdb=" N LYS B 589 " --> pdb=" O SER B 586 " (cutoff:3.500A) Processing helix chain 'B' and resid 609 through 613 removed outlier: 3.513A pdb=" N LEU B 613 " --> pdb=" O ILE B 610 " (cutoff:3.500A) Processing helix chain 'B' and resid 633 through 638 removed outlier: 3.757A pdb=" N HIS B 637 " --> pdb=" O SER B 634 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 661 removed outlier: 3.718A pdb=" N ILE B 658 " --> pdb=" O PRO B 655 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU B 661 " --> pdb=" O ILE B 658 " (cutoff:3.500A) Processing helix chain 'B' and resid 679 through 684 removed outlier: 3.866A pdb=" N CYS B 684 " --> pdb=" O LEU B 681 " (cutoff:3.500A) Processing helix chain 'B' and resid 701 through 705 removed outlier: 3.619A pdb=" N ILE B 704 " --> pdb=" O PRO B 701 " (cutoff:3.500A) Processing helix chain 'B' and resid 724 through 729 Processing helix chain 'B' and resid 747 through 752 removed outlier: 3.637A pdb=" N VAL B 750 " --> pdb=" O PRO B 747 " (cutoff:3.500A) Processing helix chain 'B' and resid 770 through 776 removed outlier: 3.510A pdb=" N CYS B 776 " --> pdb=" O LEU B 773 " (cutoff:3.500A) Processing helix chain 'B' and resid 787 through 792 Processing helix chain 'B' and resid 795 through 808 Processing helix chain 'F' and resid 401 through 409 Processing helix chain 'F' and resid 410 through 418 Processing helix chain 'F' and resid 460 through 466 removed outlier: 3.649A pdb=" N ILE F 463 " --> pdb=" O PRO F 460 " (cutoff:3.500A) Processing helix chain 'F' and resid 482 through 493 Processing helix chain 'F' and resid 502 through 506 Processing helix chain 'F' and resid 508 through 513 removed outlier: 3.711A pdb=" N TYR F 511 " --> pdb=" O PRO F 508 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LEU F 513 " --> pdb=" O MET F 510 " (cutoff:3.500A) Processing helix chain 'F' and resid 534 through 540 removed outlier: 4.042A pdb=" N ARG F 539 " --> pdb=" O GLU F 536 " (cutoff:3.500A) Processing helix chain 'F' and resid 557 through 563 removed outlier: 3.574A pdb=" N VAL F 561 " --> pdb=" O PRO F 557 " (cutoff:3.500A) Processing helix chain 'F' and resid 582 through 587 Processing helix chain 'F' and resid 605 through 610 Processing helix chain 'F' and resid 629 through 636 removed outlier: 4.564A pdb=" N GLN F 634 " --> pdb=" O VAL F 631 " (cutoff:3.500A) Processing helix chain 'F' and resid 653 through 659 removed outlier: 3.797A pdb=" N ILE F 656 " --> pdb=" O PRO F 653 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU F 659 " --> pdb=" O ILE F 656 " (cutoff:3.500A) Processing helix chain 'F' and resid 676 through 682 removed outlier: 3.939A pdb=" N PHE F 680 " --> pdb=" O PRO F 676 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N CYS F 682 " --> pdb=" O HIS F 678 " (cutoff:3.500A) Processing helix chain 'F' and resid 699 through 705 removed outlier: 3.537A pdb=" N ILE F 702 " --> pdb=" O PRO F 699 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLY F 703 " --> pdb=" O PRO F 700 " (cutoff:3.500A) Processing helix chain 'F' and resid 724 through 728 Processing helix chain 'F' and resid 768 through 774 removed outlier: 3.696A pdb=" N CYS F 774 " --> pdb=" O LEU F 771 " (cutoff:3.500A) Processing helix chain 'F' and resid 785 through 791 Processing helix chain 'F' and resid 793 through 802 removed outlier: 3.838A pdb=" N MET F 800 " --> pdb=" O VAL F 796 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 421 through 422 removed outlier: 6.378A pdb=" N LEU A 428 " --> pdb=" O VAL A 450 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N LYS A 452 " --> pdb=" O LEU A 428 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N LEU A 430 " --> pdb=" O LYS A 452 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N GLU A 454 " --> pdb=" O LEU A 430 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N LEU A 432 " --> pdb=" O GLU A 454 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N LEU A 451 " --> pdb=" O TRP A 475 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N TYR A 477 " --> pdb=" O LEU A 451 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N LEU A 453 " --> pdb=" O TYR A 477 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N LEU A 572 " --> pdb=" O GLU A 597 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ILE A 599 " --> pdb=" O LEU A 572 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N ILE A 574 " --> pdb=" O ILE A 599 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N LEU A 596 " --> pdb=" O ASP A 620 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N ILE A 619 " --> pdb=" O LYS A 645 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 459 through 461 removed outlier: 6.352A pdb=" N VAL A 459 " --> pdb=" O LYS A 482 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 666 through 668 removed outlier: 3.660A pdb=" N ASP A 691 " --> pdb=" O LEU A 667 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 759 through 760 removed outlier: 6.342A pdb=" N ILE A 759 " --> pdb=" O VAL A 785 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 421 through 422 removed outlier: 6.517A pdb=" N LEU B 428 " --> pdb=" O VAL B 450 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N LYS B 452 " --> pdb=" O LEU B 428 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N LEU B 430 " --> pdb=" O LYS B 452 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N GLU B 454 " --> pdb=" O LEU B 430 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LEU B 432 " --> pdb=" O GLU B 454 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N LEU B 451 " --> pdb=" O TRP B 475 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N TYR B 477 " --> pdb=" O LEU B 451 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N LEU B 453 " --> pdb=" O TYR B 477 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS B 501 " --> pdb=" O LEU B 476 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N LEU B 498 " --> pdb=" O HIS B 522 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N THR B 524 " --> pdb=" O LEU B 498 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ILE B 500 " --> pdb=" O THR B 524 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N SER B 573 " --> pdb=" O LEU B 549 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N LEU B 644 " --> pdb=" O TYR B 668 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N LEU B 667 " --> pdb=" O ASP B 691 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 459 through 461 Processing sheet with id=AA7, first strand: chain 'B' and resid 712 through 714 removed outlier: 7.029A pdb=" N LEU B 713 " --> pdb=" O HIS B 737 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 419 through 420 removed outlier: 6.080A pdb=" N LEU F 426 " --> pdb=" O SER F 448 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N LYS F 450 " --> pdb=" O LEU F 426 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N LEU F 428 " --> pdb=" O LYS F 450 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N GLU F 452 " --> pdb=" O LEU F 428 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N LEU F 430 " --> pdb=" O GLU F 452 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N LEU F 449 " --> pdb=" O CYS F 473 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N HIS F 475 " --> pdb=" O LEU F 449 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N LEU F 451 " --> pdb=" O HIS F 475 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N LEU F 472 " --> pdb=" O SER F 497 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N LYS F 499 " --> pdb=" O LEU F 472 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N LEU F 474 " --> pdb=" O LYS F 499 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N MET F 570 " --> pdb=" O GLU F 595 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N VAL F 597 " --> pdb=" O MET F 570 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N VAL F 572 " --> pdb=" O VAL F 597 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N LEU F 617 " --> pdb=" O LYS F 643 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LYS F 735 " --> pdb=" O PHE F 711 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASP F 758 " --> pdb=" O LEU F 734 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N LEU F 757 " --> pdb=" O VAL F 783 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 457 through 459 removed outlier: 5.735A pdb=" N VAL F 457 " --> pdb=" O LYS F 480 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 242 hydrogen bonds defined for protein. 513 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: 3.12 Time building geometry restraints manager: 2.76 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: 3157 1.34 - 1.46: 1064 1.46 - 1.57: 5806 1.57 - 1.69: 0 1.69 - 1.81: 44 Bond restraints: 10071 Sorted by residual: bond pdb=" N THR B 412 " pdb=" CA THR B 412 " ideal model delta sigma weight residual 1.453 1.489 -0.037 1.31e-02 5.83e+03 7.89e+00 bond pdb=" N ARG B 688 " pdb=" CA ARG B 688 " ideal model delta sigma weight residual 1.457 1.490 -0.032 1.17e-02 7.31e+03 7.65e+00 bond pdb=" N ILE A 606 " pdb=" CA ILE A 606 " ideal model delta sigma weight residual 1.461 1.495 -0.034 1.23e-02 6.61e+03 7.57e+00 bond pdb=" N HIS A 608 " pdb=" CA HIS A 608 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.32e-02 5.74e+03 6.44e+00 bond pdb=" N ASP B 414 " pdb=" CA ASP B 414 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.21e-02 6.83e+03 6.37e+00 ... (remaining 10066 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.94: 13156 1.94 - 3.88: 402 3.88 - 5.83: 56 5.83 - 7.77: 21 7.77 - 9.71: 7 Bond angle restraints: 13642 Sorted by residual: angle pdb=" N ARG B 685 " pdb=" CA ARG B 685 " pdb=" C ARG B 685 " ideal model delta sigma weight residual 113.16 122.65 -9.49 1.24e+00 6.50e-01 5.86e+01 angle pdb=" CA LYS F 555 " pdb=" CB LYS F 555 " pdb=" CG LYS F 555 " ideal model delta sigma weight residual 114.10 122.85 -8.75 2.00e+00 2.50e-01 1.91e+01 angle pdb=" N ILE F 713 " pdb=" CA ILE F 713 " pdb=" C ILE F 713 " ideal model delta sigma weight residual 112.17 108.07 4.10 9.50e-01 1.11e+00 1.87e+01 angle pdb=" CA LEU B 687 " pdb=" C LEU B 687 " pdb=" O LEU B 687 " ideal model delta sigma weight residual 122.64 117.83 4.81 1.25e+00 6.40e-01 1.48e+01 angle pdb=" CA VAL B 715 " pdb=" CB VAL B 715 " pdb=" CG1 VAL B 715 " ideal model delta sigma weight residual 110.40 116.86 -6.46 1.70e+00 3.46e-01 1.44e+01 ... (remaining 13637 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 5500 17.82 - 35.63: 576 35.63 - 53.45: 148 53.45 - 71.26: 22 71.26 - 89.08: 4 Dihedral angle restraints: 6250 sinusoidal: 2646 harmonic: 3604 Sorted by residual: dihedral pdb=" CA ASP B 703 " pdb=" C ASP B 703 " pdb=" N ILE B 704 " pdb=" CA ILE B 704 " ideal model delta harmonic sigma weight residual 180.00 159.64 20.36 0 5.00e+00 4.00e-02 1.66e+01 dihedral pdb=" CA PRO B 747 " pdb=" C PRO B 747 " pdb=" N SER B 748 " pdb=" CA SER B 748 " ideal model delta harmonic sigma weight residual 180.00 -160.78 -19.22 0 5.00e+00 4.00e-02 1.48e+01 dihedral pdb=" CA LYS A 552 " pdb=" C LYS A 552 " pdb=" N SER A 553 " pdb=" CA SER A 553 " ideal model delta harmonic sigma weight residual -180.00 -161.93 -18.07 0 5.00e+00 4.00e-02 1.31e+01 ... (remaining 6247 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1299 0.055 - 0.111: 279 0.111 - 0.166: 46 0.166 - 0.222: 5 0.222 - 0.277: 4 Chirality restraints: 1633 Sorted by residual: chirality pdb=" CB ILE B 677 " pdb=" CA ILE B 677 " pdb=" CG1 ILE B 677 " pdb=" CG2 ILE B 677 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" CB ILE B 456 " pdb=" CA ILE B 456 " pdb=" CG1 ILE B 456 " pdb=" CG2 ILE B 456 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.53e+00 chirality pdb=" CA ILE A 606 " pdb=" N ILE A 606 " pdb=" C ILE A 606 " pdb=" CB ILE A 606 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.24 2.00e-01 2.50e+01 1.45e+00 ... (remaining 1630 not shown) Planarity restraints: 1715 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 795 " -0.047 5.00e-02 4.00e+02 7.19e-02 8.27e+00 pdb=" N PRO A 796 " 0.124 5.00e-02 4.00e+02 pdb=" CA PRO A 796 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 796 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 438 " -0.040 5.00e-02 4.00e+02 6.00e-02 5.76e+00 pdb=" N PRO B 439 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO B 439 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 439 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 475 " -0.009 2.00e-02 2.50e+03 1.44e-02 5.17e+00 pdb=" CG TRP A 475 " 0.033 2.00e-02 2.50e+03 pdb=" CD1 TRP A 475 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 TRP A 475 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 475 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 TRP A 475 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A 475 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 475 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 475 " -0.010 2.00e-02 2.50e+03 pdb=" CH2 TRP A 475 " 0.004 2.00e-02 2.50e+03 ... (remaining 1712 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2062 2.79 - 3.31: 9318 3.31 - 3.84: 16982 3.84 - 4.37: 21247 4.37 - 4.90: 33546 Nonbonded interactions: 83155 Sorted by model distance: nonbonded pdb=" O ILE F 556 " pdb=" ND2 ASN F 584 " model vdw 2.258 3.120 nonbonded pdb=" O TRP A 411 " pdb=" OG1 THR A 441 " model vdw 2.271 3.040 nonbonded pdb=" O GLN A 560 " pdb=" OG1 THR A 563 " model vdw 2.278 3.040 nonbonded pdb=" O GLU F 790 " pdb=" NH2 ARG F 797 " model vdw 2.310 3.120 nonbonded pdb=" NH1 ARG B 749 " pdb=" OE1 GLU B 752 " model vdw 2.313 3.120 ... (remaining 83150 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 11.800 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: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 25.340 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6913 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 10071 Z= 0.258 Angle : 0.804 9.710 13642 Z= 0.453 Chirality : 0.049 0.277 1633 Planarity : 0.006 0.072 1715 Dihedral : 15.362 89.081 3886 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 0.62 % Allowed : 19.24 % Favored : 80.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.96 (0.23), residues: 1212 helix: -2.75 (0.23), residues: 369 sheet: -2.58 (0.37), residues: 182 loop : -1.19 (0.24), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP A 475 HIS 0.009 0.001 HIS B 499 PHE 0.029 0.002 PHE F 609 TYR 0.017 0.001 TYR F 756 ARG 0.006 0.001 ARG B 749 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 385 time to evaluate : 1.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 430 LEU cc_start: 0.8195 (tp) cc_final: 0.7310 (mt) REVERT: A 448 LEU cc_start: 0.8331 (tp) cc_final: 0.7879 (tp) REVERT: A 471 LEU cc_start: 0.8452 (tt) cc_final: 0.8162 (tp) REVERT: A 546 LEU cc_start: 0.8464 (tp) cc_final: 0.8127 (tp) REVERT: A 569 LEU cc_start: 0.8404 (mt) cc_final: 0.8129 (mt) REVERT: A 572 LEU cc_start: 0.8994 (tp) cc_final: 0.8558 (tp) REVERT: A 611 PHE cc_start: 0.7456 (OUTLIER) cc_final: 0.6730 (m-80) REVERT: A 621 LEU cc_start: 0.8903 (mt) cc_final: 0.8654 (mt) REVERT: A 623 ASP cc_start: 0.8758 (t0) cc_final: 0.8031 (t70) REVERT: A 643 CYS cc_start: 0.7469 (t) cc_final: 0.7090 (m) REVERT: A 710 LEU cc_start: 0.9117 (tp) cc_final: 0.8611 (mt) REVERT: A 720 ILE cc_start: 0.9366 (mt) cc_final: 0.9148 (mm) REVERT: A 736 LEU cc_start: 0.9170 (mt) cc_final: 0.8951 (mt) REVERT: A 794 LEU cc_start: 0.9110 (mt) cc_final: 0.8784 (mt) REVERT: A 799 LYS cc_start: 0.9261 (mtmt) cc_final: 0.9034 (ttmt) REVERT: B 443 PHE cc_start: 0.7575 (m-10) cc_final: 0.7304 (m-80) REVERT: B 475 TRP cc_start: 0.8269 (m-10) cc_final: 0.7400 (m-10) REVERT: B 513 TYR cc_start: 0.6183 (m-80) cc_final: 0.5371 (m-10) REVERT: B 549 LEU cc_start: 0.9121 (tp) cc_final: 0.8833 (tp) REVERT: F 458 MET cc_start: 0.7017 (tpt) cc_final: 0.6781 (tpt) REVERT: F 505 GLU cc_start: 0.7582 (mt-10) cc_final: 0.6343 (mm-30) REVERT: F 516 LEU cc_start: 0.8752 (mt) cc_final: 0.8371 (tp) REVERT: F 550 LYS cc_start: 0.9181 (tmtt) cc_final: 0.8804 (mppt) REVERT: F 581 MET cc_start: 0.7455 (tpp) cc_final: 0.7084 (tpp) REVERT: F 583 ASN cc_start: 0.8785 (m-40) cc_final: 0.8530 (p0) REVERT: F 594 LEU cc_start: 0.8165 (tp) cc_final: 0.7671 (tp) REVERT: F 612 LEU cc_start: 0.7415 (mt) cc_final: 0.6945 (pp) REVERT: F 623 ASN cc_start: 0.7476 (m-40) cc_final: 0.6586 (p0) REVERT: F 642 LEU cc_start: 0.7566 (tp) cc_final: 0.7240 (tp) REVERT: F 644 LEU cc_start: 0.9414 (mt) cc_final: 0.9202 (tt) REVERT: F 701 GLU cc_start: 0.7745 (mm-30) cc_final: 0.7095 (tp30) REVERT: F 704 VAL cc_start: 0.7392 (t) cc_final: 0.6964 (t) REVERT: F 777 LEU cc_start: 0.8244 (tp) cc_final: 0.8037 (tt) outliers start: 7 outliers final: 0 residues processed: 389 average time/residue: 0.2748 time to fit residues: 140.2077 Evaluate side-chains 228 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 227 time to evaluate : 1.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 611 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 101 optimal weight: 5.9990 chunk 90 optimal weight: 3.9990 chunk 50 optimal weight: 0.0770 chunk 31 optimal weight: 10.0000 chunk 61 optimal weight: 5.9990 chunk 48 optimal weight: 0.0170 chunk 94 optimal weight: 6.9990 chunk 36 optimal weight: 0.0000 chunk 57 optimal weight: 10.0000 chunk 70 optimal weight: 4.9990 chunk 108 optimal weight: 10.0000 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 418 GLN ** A 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 592 ASN A 636 GLN A 637 HIS A 755 ASN B 409 ASN B 478 HIS B 575 ASN ** B 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 758 GLN F 515 ASN F 606 HIS F 635 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7185 moved from start: 0.3993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10071 Z= 0.263 Angle : 0.782 12.130 13642 Z= 0.389 Chirality : 0.046 0.206 1633 Planarity : 0.006 0.052 1715 Dihedral : 5.166 22.823 1305 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 21.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 5.18 % Allowed : 22.76 % Favored : 72.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.70 (0.24), residues: 1212 helix: -2.33 (0.25), residues: 368 sheet: -2.55 (0.37), residues: 179 loop : -1.13 (0.25), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 475 HIS 0.007 0.001 HIS A 694 PHE 0.020 0.002 PHE B 682 TYR 0.021 0.002 TYR A 689 ARG 0.010 0.001 ARG A 640 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 225 time to evaluate : 1.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 441 THR cc_start: 0.7844 (OUTLIER) cc_final: 0.7635 (m) REVERT: A 496 ARG cc_start: 0.8299 (mmt90) cc_final: 0.7886 (mmt-90) REVERT: A 560 GLN cc_start: 0.5667 (pm20) cc_final: 0.5397 (pp30) REVERT: A 645 LYS cc_start: 0.8730 (mttt) cc_final: 0.8464 (mtpt) REVERT: A 710 LEU cc_start: 0.9116 (tp) cc_final: 0.8372 (mt) REVERT: A 712 ASN cc_start: 0.8764 (m-40) cc_final: 0.8466 (t0) REVERT: A 732 LYS cc_start: 0.8869 (OUTLIER) cc_final: 0.8542 (mmtm) REVERT: A 736 LEU cc_start: 0.9198 (mt) cc_final: 0.8889 (mp) REVERT: A 737 HIS cc_start: 0.8782 (m170) cc_final: 0.8377 (m-70) REVERT: A 791 PHE cc_start: 0.7394 (t80) cc_final: 0.6887 (t80) REVERT: A 802 LEU cc_start: 0.8941 (tp) cc_final: 0.8352 (tp) REVERT: B 434 MET cc_start: 0.7534 (tmm) cc_final: 0.6751 (tmm) REVERT: B 477 TYR cc_start: 0.6959 (m-10) cc_final: 0.6619 (m-10) REVERT: B 543 LEU cc_start: 0.6891 (mp) cc_final: 0.6654 (tp) REVERT: B 575 ASN cc_start: 0.7840 (OUTLIER) cc_final: 0.7482 (m-40) REVERT: B 599 ILE cc_start: 0.8618 (mm) cc_final: 0.8133 (mp) REVERT: B 620 ASP cc_start: 0.6987 (t0) cc_final: 0.6143 (m-30) REVERT: B 621 LEU cc_start: 0.8480 (mt) cc_final: 0.8106 (mt) REVERT: B 687 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8327 (tp) REVERT: F 516 LEU cc_start: 0.8868 (mt) cc_final: 0.8187 (tp) REVERT: F 521 LEU cc_start: 0.9070 (mt) cc_final: 0.8844 (mt) REVERT: F 541 LEU cc_start: 0.4935 (mt) cc_final: 0.4442 (mt) REVERT: F 550 LYS cc_start: 0.9270 (tmtt) cc_final: 0.8835 (mptt) REVERT: F 588 MET cc_start: 0.8273 (mmm) cc_final: 0.7607 (mmm) REVERT: F 591 LEU cc_start: 0.7136 (mm) cc_final: 0.5439 (tp) REVERT: F 611 LEU cc_start: 0.7299 (mm) cc_final: 0.6714 (mm) REVERT: F 612 LEU cc_start: 0.7642 (mt) cc_final: 0.7385 (pp) REVERT: F 665 LEU cc_start: 0.8112 (tp) cc_final: 0.7898 (mt) REVERT: F 680 PHE cc_start: 0.6488 (OUTLIER) cc_final: 0.5091 (m-80) REVERT: F 687 TYR cc_start: 0.7114 (t80) cc_final: 0.6798 (t80) REVERT: F 688 LEU cc_start: 0.9350 (mt) cc_final: 0.9129 (mt) REVERT: F 701 GLU cc_start: 0.8075 (mm-30) cc_final: 0.7530 (tp30) REVERT: F 704 VAL cc_start: 0.7248 (t) cc_final: 0.6664 (t) outliers start: 59 outliers final: 23 residues processed: 265 average time/residue: 0.2432 time to fit residues: 87.8598 Evaluate side-chains 213 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 185 time to evaluate : 1.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 609 SER Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 732 LYS Chi-restraints excluded: chain A residue 784 LEU Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 458 ASP Chi-restraints excluded: chain B residue 476 LEU Chi-restraints excluded: chain B residue 562 VAL Chi-restraints excluded: chain B residue 572 LEU Chi-restraints excluded: chain B residue 575 ASN Chi-restraints excluded: chain B residue 619 ILE Chi-restraints excluded: chain B residue 683 TYR Chi-restraints excluded: chain B residue 687 LEU Chi-restraints excluded: chain B residue 723 LEU Chi-restraints excluded: chain B residue 754 THR Chi-restraints excluded: chain B residue 758 GLN Chi-restraints excluded: chain F residue 451 LEU Chi-restraints excluded: chain F residue 560 VAL Chi-restraints excluded: chain F residue 563 VAL Chi-restraints excluded: chain F residue 593 GLU Chi-restraints excluded: chain F residue 606 HIS Chi-restraints excluded: chain F residue 680 PHE Chi-restraints excluded: chain F residue 689 ASP Chi-restraints excluded: chain F residue 734 LEU Chi-restraints excluded: chain F residue 743 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 60 optimal weight: 0.0050 chunk 33 optimal weight: 7.9990 chunk 90 optimal weight: 0.8980 chunk 74 optimal weight: 20.0000 chunk 30 optimal weight: 0.6980 chunk 109 optimal weight: 4.9990 chunk 117 optimal weight: 9.9990 chunk 97 optimal weight: 9.9990 chunk 108 optimal weight: 3.9990 chunk 37 optimal weight: 0.1980 chunk 87 optimal weight: 8.9990 overall best weight: 1.1596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 575 ASN B 614 HIS ** B 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 758 GLN F 606 HIS ** F 716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7230 moved from start: 0.4810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10071 Z= 0.210 Angle : 0.735 16.980 13642 Z= 0.359 Chirality : 0.045 0.218 1633 Planarity : 0.005 0.049 1715 Dihedral : 4.955 20.567 1303 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 22.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 4.57 % Allowed : 23.64 % Favored : 71.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.62 (0.24), residues: 1212 helix: -2.21 (0.25), residues: 371 sheet: -2.31 (0.38), residues: 183 loop : -1.16 (0.25), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 645 HIS 0.005 0.001 HIS A 694 PHE 0.029 0.002 PHE B 635 TYR 0.018 0.001 TYR B 653 ARG 0.010 0.001 ARG F 603 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 194 time to evaluate : 1.056 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 433 PHE cc_start: 0.8608 (t80) cc_final: 0.8265 (t80) REVERT: A 496 ARG cc_start: 0.8421 (mmt90) cc_final: 0.8020 (mmt-90) REVERT: A 645 LYS cc_start: 0.8834 (mttt) cc_final: 0.8543 (mtpt) REVERT: A 648 TYR cc_start: 0.7854 (OUTLIER) cc_final: 0.7610 (m-10) REVERT: A 710 LEU cc_start: 0.9019 (tp) cc_final: 0.8418 (mt) REVERT: A 712 ASN cc_start: 0.8682 (m-40) cc_final: 0.8389 (t0) REVERT: A 736 LEU cc_start: 0.9194 (mt) cc_final: 0.8606 (mt) REVERT: A 791 PHE cc_start: 0.7169 (t80) cc_final: 0.6942 (t80) REVERT: A 802 LEU cc_start: 0.8738 (tp) cc_final: 0.8513 (tp) REVERT: B 403 ARG cc_start: 0.5434 (OUTLIER) cc_final: 0.4826 (ptt-90) REVERT: B 433 PHE cc_start: 0.7591 (t80) cc_final: 0.7374 (t80) REVERT: B 434 MET cc_start: 0.7614 (OUTLIER) cc_final: 0.6421 (tmm) REVERT: B 684 CYS cc_start: 0.5358 (OUTLIER) cc_final: 0.3551 (m) REVERT: B 749 ARG cc_start: 0.4182 (OUTLIER) cc_final: 0.3850 (ttp80) REVERT: B 761 LEU cc_start: 0.6875 (mt) cc_final: 0.6321 (mt) REVERT: B 762 ARG cc_start: 0.7496 (mmp-170) cc_final: 0.7294 (mmp-170) REVERT: F 458 MET cc_start: 0.7248 (tpp) cc_final: 0.7003 (tpt) REVERT: F 516 LEU cc_start: 0.8853 (mt) cc_final: 0.8103 (tp) REVERT: F 541 LEU cc_start: 0.4969 (mt) cc_final: 0.4489 (mt) REVERT: F 550 LYS cc_start: 0.9298 (tmtt) cc_final: 0.8904 (tptp) REVERT: F 588 MET cc_start: 0.8359 (mmm) cc_final: 0.7774 (mmm) REVERT: F 591 LEU cc_start: 0.7107 (mm) cc_final: 0.5499 (tp) REVERT: F 611 LEU cc_start: 0.7523 (mm) cc_final: 0.6800 (mt) REVERT: F 612 LEU cc_start: 0.7428 (mt) cc_final: 0.7163 (pp) REVERT: F 687 TYR cc_start: 0.7441 (t80) cc_final: 0.7154 (t80) REVERT: F 688 LEU cc_start: 0.9351 (mt) cc_final: 0.9145 (mt) REVERT: F 701 GLU cc_start: 0.8143 (mm-30) cc_final: 0.7457 (tp30) outliers start: 52 outliers final: 28 residues processed: 231 average time/residue: 0.2448 time to fit residues: 79.4472 Evaluate side-chains 206 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 173 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 609 SER Chi-restraints excluded: chain A residue 648 TYR Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 784 LEU Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 434 MET Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 458 ASP Chi-restraints excluded: chain B residue 476 LEU Chi-restraints excluded: chain B residue 562 VAL Chi-restraints excluded: chain B residue 614 HIS Chi-restraints excluded: chain B residue 619 ILE Chi-restraints excluded: chain B residue 683 TYR Chi-restraints excluded: chain B residue 684 CYS Chi-restraints excluded: chain B residue 723 LEU Chi-restraints excluded: chain B residue 749 ARG Chi-restraints excluded: chain B residue 754 THR Chi-restraints excluded: chain F residue 451 LEU Chi-restraints excluded: chain F residue 496 LEU Chi-restraints excluded: chain F residue 560 VAL Chi-restraints excluded: chain F residue 563 VAL Chi-restraints excluded: chain F residue 606 HIS Chi-restraints excluded: chain F residue 627 ILE Chi-restraints excluded: chain F residue 689 ASP Chi-restraints excluded: chain F residue 734 LEU Chi-restraints excluded: chain F residue 743 VAL Chi-restraints excluded: chain F residue 783 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 107 optimal weight: 0.9990 chunk 82 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 52 optimal weight: 7.9990 chunk 73 optimal weight: 7.9990 chunk 109 optimal weight: 4.9990 chunk 115 optimal weight: 10.0000 chunk 57 optimal weight: 5.9990 chunk 103 optimal weight: 0.1980 chunk 31 optimal weight: 9.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 418 GLN ** A 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 554 ASN ** A 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 431 HIS ** B 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 614 HIS ** B 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 709 ASN ** B 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 606 HIS ** F 716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7296 moved from start: 0.5344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10071 Z= 0.219 Angle : 0.710 12.177 13642 Z= 0.345 Chirality : 0.045 0.210 1633 Planarity : 0.005 0.064 1715 Dihedral : 4.948 20.231 1303 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 21.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 4.92 % Allowed : 24.17 % Favored : 70.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.46 (0.25), residues: 1212 helix: -2.03 (0.26), residues: 363 sheet: -2.40 (0.37), residues: 201 loop : -0.99 (0.26), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 475 HIS 0.024 0.002 HIS B 614 PHE 0.020 0.002 PHE B 635 TYR 0.020 0.002 TYR B 653 ARG 0.006 0.001 ARG B 749 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 176 time to evaluate : 1.166 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 415 LYS cc_start: 0.8609 (ttpt) cc_final: 0.8387 (tptt) REVERT: A 433 PHE cc_start: 0.8609 (t80) cc_final: 0.8346 (t80) REVERT: A 471 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.8228 (tp) REVERT: A 496 ARG cc_start: 0.8494 (mmt90) cc_final: 0.8022 (mmt-90) REVERT: A 648 TYR cc_start: 0.7929 (OUTLIER) cc_final: 0.7613 (m-10) REVERT: A 710 LEU cc_start: 0.8969 (tp) cc_final: 0.8402 (mt) REVERT: A 802 LEU cc_start: 0.8743 (tp) cc_final: 0.8527 (tp) REVERT: B 403 ARG cc_start: 0.4969 (OUTLIER) cc_final: 0.3788 (ptt-90) REVERT: B 410 GLU cc_start: 0.8543 (mm-30) cc_final: 0.8289 (mm-30) REVERT: B 433 PHE cc_start: 0.7800 (t80) cc_final: 0.7516 (t80) REVERT: B 434 MET cc_start: 0.7670 (OUTLIER) cc_final: 0.6587 (tmm) REVERT: B 477 TYR cc_start: 0.7059 (m-10) cc_final: 0.6767 (m-10) REVERT: B 550 ARG cc_start: 0.8431 (ttt-90) cc_final: 0.8142 (ttt-90) REVERT: B 551 LEU cc_start: 0.7932 (tp) cc_final: 0.7432 (tp) REVERT: B 687 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8465 (tp) REVERT: B 700 LEU cc_start: 0.5192 (tt) cc_final: 0.4091 (tp) REVERT: B 749 ARG cc_start: 0.4188 (OUTLIER) cc_final: 0.3962 (ttp80) REVERT: F 516 LEU cc_start: 0.8880 (mt) cc_final: 0.8177 (tp) REVERT: F 541 LEU cc_start: 0.4979 (mt) cc_final: 0.4517 (mt) REVERT: F 550 LYS cc_start: 0.9322 (tmtt) cc_final: 0.8963 (tptp) REVERT: F 588 MET cc_start: 0.8251 (mmm) cc_final: 0.7713 (mmm) REVERT: F 591 LEU cc_start: 0.6979 (mm) cc_final: 0.5337 (tp) REVERT: F 611 LEU cc_start: 0.7725 (mm) cc_final: 0.6866 (mt) REVERT: F 612 LEU cc_start: 0.7433 (mt) cc_final: 0.7151 (pp) REVERT: F 645 TRP cc_start: 0.7240 (p90) cc_final: 0.6675 (p90) REVERT: F 688 LEU cc_start: 0.9367 (mt) cc_final: 0.9163 (mt) REVERT: F 701 GLU cc_start: 0.8238 (mm-30) cc_final: 0.7496 (tp30) outliers start: 56 outliers final: 30 residues processed: 215 average time/residue: 0.2378 time to fit residues: 70.4055 Evaluate side-chains 195 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 159 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 609 SER Chi-restraints excluded: chain A residue 648 TYR Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 434 MET Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 458 ASP Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 562 VAL Chi-restraints excluded: chain B residue 596 LEU Chi-restraints excluded: chain B residue 614 HIS Chi-restraints excluded: chain B residue 619 ILE Chi-restraints excluded: chain B residue 654 ILE Chi-restraints excluded: chain B residue 683 TYR Chi-restraints excluded: chain B residue 687 LEU Chi-restraints excluded: chain B residue 723 LEU Chi-restraints excluded: chain B residue 733 LEU Chi-restraints excluded: chain B residue 746 LEU Chi-restraints excluded: chain B residue 749 ARG Chi-restraints excluded: chain B residue 754 THR Chi-restraints excluded: chain F residue 451 LEU Chi-restraints excluded: chain F residue 496 LEU Chi-restraints excluded: chain F residue 560 VAL Chi-restraints excluded: chain F residue 606 HIS Chi-restraints excluded: chain F residue 627 ILE Chi-restraints excluded: chain F residue 689 ASP Chi-restraints excluded: chain F residue 734 LEU Chi-restraints excluded: chain F residue 743 VAL Chi-restraints excluded: chain F residue 783 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 96 optimal weight: 10.0000 chunk 65 optimal weight: 4.9990 chunk 1 optimal weight: 5.9990 chunk 86 optimal weight: 0.8980 chunk 47 optimal weight: 0.9990 chunk 98 optimal weight: 0.5980 chunk 80 optimal weight: 5.9990 chunk 0 optimal weight: 3.9990 chunk 59 optimal weight: 10.0000 chunk 104 optimal weight: 7.9990 chunk 29 optimal weight: 3.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 614 HIS ** B 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 696 ASN ** B 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 606 HIS ** F 670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 moved from start: 0.5802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10071 Z= 0.243 Angle : 0.715 11.817 13642 Z= 0.345 Chirality : 0.045 0.283 1633 Planarity : 0.005 0.056 1715 Dihedral : 4.961 21.057 1303 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 22.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 5.36 % Allowed : 24.43 % Favored : 70.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.48 (0.25), residues: 1212 helix: -2.02 (0.26), residues: 371 sheet: -2.43 (0.36), residues: 210 loop : -0.97 (0.26), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 475 HIS 0.018 0.001 HIS B 614 PHE 0.019 0.002 PHE B 635 TYR 0.026 0.002 TYR F 687 ARG 0.007 0.001 ARG B 749 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 162 time to evaluate : 1.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 415 LYS cc_start: 0.8600 (ttpt) cc_final: 0.8390 (tptt) REVERT: A 433 PHE cc_start: 0.8726 (t80) cc_final: 0.8490 (t80) REVERT: A 496 ARG cc_start: 0.8529 (mmt90) cc_final: 0.8048 (mmt-90) REVERT: A 648 TYR cc_start: 0.7992 (OUTLIER) cc_final: 0.7750 (m-10) REVERT: A 710 LEU cc_start: 0.8985 (tp) cc_final: 0.8402 (mt) REVERT: A 734 ARG cc_start: 0.9062 (mmm-85) cc_final: 0.8833 (mmm-85) REVERT: A 791 PHE cc_start: 0.6768 (t80) cc_final: 0.6350 (t80) REVERT: B 403 ARG cc_start: 0.5254 (OUTLIER) cc_final: 0.3653 (ptt-90) REVERT: B 434 MET cc_start: 0.7852 (OUTLIER) cc_final: 0.6893 (tmm) REVERT: B 453 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8242 (mm) REVERT: B 550 ARG cc_start: 0.8370 (ttt-90) cc_final: 0.7909 (tpt-90) REVERT: B 551 LEU cc_start: 0.8123 (tp) cc_final: 0.7555 (tp) REVERT: B 749 ARG cc_start: 0.4240 (OUTLIER) cc_final: 0.3567 (tmt170) REVERT: B 761 LEU cc_start: 0.6697 (mt) cc_final: 0.6362 (mt) REVERT: B 762 ARG cc_start: 0.7687 (mmp-170) cc_final: 0.7486 (mmp-170) REVERT: F 458 MET cc_start: 0.6813 (tpt) cc_final: 0.6558 (tpt) REVERT: F 495 VAL cc_start: 0.7993 (OUTLIER) cc_final: 0.7670 (t) REVERT: F 550 LYS cc_start: 0.9341 (tmtt) cc_final: 0.8987 (tptp) REVERT: F 611 LEU cc_start: 0.7778 (mm) cc_final: 0.7250 (mp) REVERT: F 627 ILE cc_start: 0.6218 (OUTLIER) cc_final: 0.5904 (mt) REVERT: F 687 TYR cc_start: 0.7439 (t80) cc_final: 0.7117 (t80) REVERT: F 688 LEU cc_start: 0.9425 (mt) cc_final: 0.9176 (mt) REVERT: F 701 GLU cc_start: 0.8353 (mm-30) cc_final: 0.7624 (tp30) outliers start: 61 outliers final: 34 residues processed: 205 average time/residue: 0.2452 time to fit residues: 69.5167 Evaluate side-chains 185 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 144 time to evaluate : 1.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 609 SER Chi-restraints excluded: chain A residue 648 TYR Chi-restraints excluded: chain A residue 654 ILE Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 698 THR Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 784 LEU Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 434 MET Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain B residue 458 ASP Chi-restraints excluded: chain B residue 537 ILE Chi-restraints excluded: chain B residue 562 VAL Chi-restraints excluded: chain B residue 596 LEU Chi-restraints excluded: chain B residue 614 HIS Chi-restraints excluded: chain B residue 619 ILE Chi-restraints excluded: chain B residue 654 ILE Chi-restraints excluded: chain B residue 683 TYR Chi-restraints excluded: chain B residue 733 LEU Chi-restraints excluded: chain B residue 746 LEU Chi-restraints excluded: chain B residue 749 ARG Chi-restraints excluded: chain B residue 754 THR Chi-restraints excluded: chain F residue 449 LEU Chi-restraints excluded: chain F residue 451 LEU Chi-restraints excluded: chain F residue 495 VAL Chi-restraints excluded: chain F residue 496 LEU Chi-restraints excluded: chain F residue 560 VAL Chi-restraints excluded: chain F residue 606 HIS Chi-restraints excluded: chain F residue 627 ILE Chi-restraints excluded: chain F residue 672 VAL Chi-restraints excluded: chain F residue 677 SER Chi-restraints excluded: chain F residue 689 ASP Chi-restraints excluded: chain F residue 734 LEU Chi-restraints excluded: chain F residue 743 VAL Chi-restraints excluded: chain F residue 783 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 39 optimal weight: 0.9980 chunk 104 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 chunk 68 optimal weight: 8.9990 chunk 28 optimal weight: 5.9990 chunk 116 optimal weight: 0.9980 chunk 96 optimal weight: 3.9990 chunk 53 optimal weight: 0.0970 chunk 9 optimal weight: 0.2980 chunk 38 optimal weight: 0.0770 chunk 60 optimal weight: 5.9990 overall best weight: 0.4736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 606 HIS ** F 716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7313 moved from start: 0.5965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10071 Z= 0.176 Angle : 0.714 11.438 13642 Z= 0.338 Chirality : 0.045 0.244 1633 Planarity : 0.005 0.052 1715 Dihedral : 4.846 21.141 1303 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 18.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 3.95 % Allowed : 26.45 % Favored : 69.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.52 (0.24), residues: 1212 helix: -1.98 (0.26), residues: 378 sheet: -2.29 (0.38), residues: 201 loop : -1.12 (0.25), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 475 HIS 0.013 0.001 HIS B 614 PHE 0.016 0.002 PHE B 635 TYR 0.011 0.001 TYR F 687 ARG 0.007 0.000 ARG B 749 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 162 time to evaluate : 1.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 415 LYS cc_start: 0.8659 (ttpt) cc_final: 0.8437 (tptt) REVERT: A 433 PHE cc_start: 0.8672 (t80) cc_final: 0.8438 (t80) REVERT: A 441 THR cc_start: 0.8072 (OUTLIER) cc_final: 0.7859 (m) REVERT: A 471 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8328 (tp) REVERT: A 496 ARG cc_start: 0.8562 (mmt90) cc_final: 0.8078 (mmt-90) REVERT: A 546 LEU cc_start: 0.9177 (OUTLIER) cc_final: 0.8965 (tp) REVERT: A 620 ASP cc_start: 0.8409 (t0) cc_final: 0.7951 (m-30) REVERT: A 648 TYR cc_start: 0.8014 (OUTLIER) cc_final: 0.7797 (m-10) REVERT: A 710 LEU cc_start: 0.8985 (tp) cc_final: 0.8246 (mt) REVERT: B 403 ARG cc_start: 0.5325 (OUTLIER) cc_final: 0.3974 (ptt-90) REVERT: B 434 MET cc_start: 0.7704 (OUTLIER) cc_final: 0.6738 (tmm) REVERT: B 551 LEU cc_start: 0.8081 (tp) cc_final: 0.7577 (tp) REVERT: B 741 ASN cc_start: 0.7652 (m-40) cc_final: 0.6713 (m110) REVERT: B 749 ARG cc_start: 0.4223 (OUTLIER) cc_final: 0.3710 (tmt170) REVERT: F 458 MET cc_start: 0.6850 (tpt) cc_final: 0.6615 (tpt) REVERT: F 495 VAL cc_start: 0.7928 (OUTLIER) cc_final: 0.7607 (t) REVERT: F 529 ILE cc_start: 0.6564 (OUTLIER) cc_final: 0.6319 (tt) REVERT: F 550 LYS cc_start: 0.9351 (tmtt) cc_final: 0.9013 (tptp) REVERT: F 611 LEU cc_start: 0.7600 (mm) cc_final: 0.7146 (mm) REVERT: F 627 ILE cc_start: 0.6239 (OUTLIER) cc_final: 0.5956 (mt) REVERT: F 687 TYR cc_start: 0.7519 (t80) cc_final: 0.7131 (t80) REVERT: F 701 GLU cc_start: 0.8312 (mm-30) cc_final: 0.7607 (tp30) outliers start: 45 outliers final: 24 residues processed: 195 average time/residue: 0.2568 time to fit residues: 69.7972 Evaluate side-chains 180 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 146 time to evaluate : 1.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 609 SER Chi-restraints excluded: chain A residue 648 TYR Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 426 ASP Chi-restraints excluded: chain B residue 434 MET Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 562 VAL Chi-restraints excluded: chain B residue 596 LEU Chi-restraints excluded: chain B residue 614 HIS Chi-restraints excluded: chain B residue 619 ILE Chi-restraints excluded: chain B residue 677 ILE Chi-restraints excluded: chain B residue 683 TYR Chi-restraints excluded: chain B residue 733 LEU Chi-restraints excluded: chain B residue 749 ARG Chi-restraints excluded: chain B residue 754 THR Chi-restraints excluded: chain F residue 451 LEU Chi-restraints excluded: chain F residue 495 VAL Chi-restraints excluded: chain F residue 496 LEU Chi-restraints excluded: chain F residue 516 LEU Chi-restraints excluded: chain F residue 529 ILE Chi-restraints excluded: chain F residue 606 HIS Chi-restraints excluded: chain F residue 627 ILE Chi-restraints excluded: chain F residue 689 ASP Chi-restraints excluded: chain F residue 734 LEU Chi-restraints excluded: chain F residue 783 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 111 optimal weight: 4.9990 chunk 13 optimal weight: 7.9990 chunk 66 optimal weight: 9.9990 chunk 84 optimal weight: 10.0000 chunk 65 optimal weight: 0.6980 chunk 97 optimal weight: 7.9990 chunk 64 optimal weight: 3.9990 chunk 115 optimal weight: 9.9990 chunk 72 optimal weight: 0.9980 chunk 70 optimal weight: 7.9990 chunk 53 optimal weight: 0.4980 overall best weight: 2.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 737 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 592 ASN ** B 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 606 HIS ** F 670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.6413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 10071 Z= 0.259 Angle : 0.743 11.504 13642 Z= 0.355 Chirality : 0.046 0.388 1633 Planarity : 0.005 0.053 1715 Dihedral : 4.971 21.604 1303 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 23.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 4.57 % Allowed : 26.89 % Favored : 68.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.63 (0.24), residues: 1212 helix: -2.12 (0.25), residues: 387 sheet: -2.30 (0.37), residues: 210 loop : -1.12 (0.25), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP F 645 HIS 0.007 0.001 HIS B 522 PHE 0.017 0.002 PHE B 635 TYR 0.012 0.002 TYR F 710 ARG 0.007 0.001 ARG B 749 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 155 time to evaluate : 1.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 415 LYS cc_start: 0.8645 (ttpt) cc_final: 0.8442 (tptt) REVERT: A 433 PHE cc_start: 0.8814 (t80) cc_final: 0.8609 (t80) REVERT: A 496 ARG cc_start: 0.8608 (mmt90) cc_final: 0.8091 (mmt-90) REVERT: A 620 ASP cc_start: 0.8447 (t0) cc_final: 0.7957 (m-30) REVERT: A 648 TYR cc_start: 0.8035 (OUTLIER) cc_final: 0.7758 (m-10) REVERT: A 710 LEU cc_start: 0.8953 (tp) cc_final: 0.8415 (mt) REVERT: A 734 ARG cc_start: 0.8973 (mmm-85) cc_final: 0.8529 (mmm-85) REVERT: B 403 ARG cc_start: 0.5501 (OUTLIER) cc_final: 0.3894 (ptt-90) REVERT: B 434 MET cc_start: 0.7964 (OUTLIER) cc_final: 0.7190 (tmm) REVERT: B 453 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8468 (mm) REVERT: B 475 TRP cc_start: 0.7832 (m-10) cc_final: 0.7608 (m100) REVERT: B 596 LEU cc_start: 0.8226 (OUTLIER) cc_final: 0.7896 (mt) REVERT: B 710 LEU cc_start: 0.8684 (OUTLIER) cc_final: 0.8050 (mm) REVERT: B 749 ARG cc_start: 0.4451 (OUTLIER) cc_final: 0.4129 (ttp80) REVERT: F 495 VAL cc_start: 0.7912 (OUTLIER) cc_final: 0.7573 (t) REVERT: F 529 ILE cc_start: 0.6600 (OUTLIER) cc_final: 0.6330 (tt) REVERT: F 550 LYS cc_start: 0.9394 (tmtt) cc_final: 0.9084 (tptp) REVERT: F 611 LEU cc_start: 0.7676 (mm) cc_final: 0.7005 (mt) REVERT: F 687 TYR cc_start: 0.7715 (t80) cc_final: 0.7412 (t80) REVERT: F 701 GLU cc_start: 0.8441 (mm-30) cc_final: 0.7648 (tp30) outliers start: 52 outliers final: 31 residues processed: 196 average time/residue: 0.2239 time to fit residues: 61.1590 Evaluate side-chains 185 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 145 time to evaluate : 1.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 609 SER Chi-restraints excluded: chain A residue 648 TYR Chi-restraints excluded: chain A residue 654 ILE Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 698 THR Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 426 ASP Chi-restraints excluded: chain B residue 434 MET Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain B residue 537 ILE Chi-restraints excluded: chain B residue 562 VAL Chi-restraints excluded: chain B residue 596 LEU Chi-restraints excluded: chain B residue 614 HIS Chi-restraints excluded: chain B residue 619 ILE Chi-restraints excluded: chain B residue 650 HIS Chi-restraints excluded: chain B residue 677 ILE Chi-restraints excluded: chain B residue 683 TYR Chi-restraints excluded: chain B residue 710 LEU Chi-restraints excluded: chain B residue 733 LEU Chi-restraints excluded: chain B residue 746 LEU Chi-restraints excluded: chain B residue 749 ARG Chi-restraints excluded: chain B residue 754 THR Chi-restraints excluded: chain F residue 451 LEU Chi-restraints excluded: chain F residue 462 THR Chi-restraints excluded: chain F residue 495 VAL Chi-restraints excluded: chain F residue 496 LEU Chi-restraints excluded: chain F residue 513 LEU Chi-restraints excluded: chain F residue 516 LEU Chi-restraints excluded: chain F residue 529 ILE Chi-restraints excluded: chain F residue 606 HIS Chi-restraints excluded: chain F residue 627 ILE Chi-restraints excluded: chain F residue 672 VAL Chi-restraints excluded: chain F residue 689 ASP Chi-restraints excluded: chain F residue 743 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 71 optimal weight: 0.9980 chunk 46 optimal weight: 0.6980 chunk 69 optimal weight: 2.9990 chunk 34 optimal weight: 9.9990 chunk 22 optimal weight: 2.9990 chunk 73 optimal weight: 0.7980 chunk 78 optimal weight: 0.0000 chunk 57 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 90 optimal weight: 0.5980 chunk 105 optimal weight: 6.9990 overall best weight: 0.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 755 ASN ** A 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 606 HIS ** F 716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 0.6512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10071 Z= 0.182 Angle : 0.742 10.949 13642 Z= 0.347 Chirality : 0.047 0.358 1633 Planarity : 0.005 0.052 1715 Dihedral : 4.871 19.571 1303 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 18.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 3.16 % Allowed : 28.47 % Favored : 68.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.64 (0.24), residues: 1212 helix: -2.09 (0.25), residues: 389 sheet: -2.27 (0.38), residues: 199 loop : -1.21 (0.25), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP F 645 HIS 0.008 0.001 HIS B 522 PHE 0.014 0.002 PHE B 635 TYR 0.010 0.001 TYR F 710 ARG 0.006 0.001 ARG B 749 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 158 time to evaluate : 1.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 415 LYS cc_start: 0.8645 (ttpt) cc_final: 0.8444 (tptt) REVERT: A 433 PHE cc_start: 0.8803 (t80) cc_final: 0.8574 (t80) REVERT: A 496 ARG cc_start: 0.8617 (mmt90) cc_final: 0.8230 (mmt-90) REVERT: A 572 LEU cc_start: 0.8532 (mt) cc_final: 0.8330 (mt) REVERT: A 620 ASP cc_start: 0.8363 (t0) cc_final: 0.7968 (m-30) REVERT: A 648 TYR cc_start: 0.8050 (OUTLIER) cc_final: 0.7810 (m-10) REVERT: A 710 LEU cc_start: 0.8891 (tp) cc_final: 0.8378 (mt) REVERT: A 734 ARG cc_start: 0.9001 (mmm-85) cc_final: 0.8759 (mmm-85) REVERT: B 403 ARG cc_start: 0.5196 (OUTLIER) cc_final: 0.3971 (ptt-90) REVERT: B 433 PHE cc_start: 0.7632 (t80) cc_final: 0.7403 (t80) REVERT: B 434 MET cc_start: 0.7902 (OUTLIER) cc_final: 0.6891 (tmm) REVERT: B 453 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8459 (mm) REVERT: B 596 LEU cc_start: 0.8167 (tp) cc_final: 0.7895 (mt) REVERT: B 710 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8114 (mm) REVERT: B 741 ASN cc_start: 0.7734 (m-40) cc_final: 0.6809 (m110) REVERT: B 749 ARG cc_start: 0.4673 (OUTLIER) cc_final: 0.4194 (ttp80) REVERT: F 458 MET cc_start: 0.6748 (tpt) cc_final: 0.6534 (tpt) REVERT: F 495 VAL cc_start: 0.7782 (OUTLIER) cc_final: 0.7426 (t) REVERT: F 529 ILE cc_start: 0.6559 (OUTLIER) cc_final: 0.6226 (tt) REVERT: F 550 LYS cc_start: 0.9390 (tmtt) cc_final: 0.9112 (tptp) REVERT: F 588 MET cc_start: 0.7631 (mmm) cc_final: 0.7413 (mmm) REVERT: F 611 LEU cc_start: 0.7596 (mm) cc_final: 0.6936 (mp) REVERT: F 612 LEU cc_start: 0.7144 (mt) cc_final: 0.6721 (pp) REVERT: F 680 PHE cc_start: 0.6798 (OUTLIER) cc_final: 0.5844 (m-80) REVERT: F 701 GLU cc_start: 0.8424 (mm-30) cc_final: 0.7640 (tp30) outliers start: 36 outliers final: 25 residues processed: 185 average time/residue: 0.2348 time to fit residues: 60.1760 Evaluate side-chains 185 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 151 time to evaluate : 1.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 609 SER Chi-restraints excluded: chain A residue 648 TYR Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 426 ASP Chi-restraints excluded: chain B residue 434 MET Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain B residue 476 LEU Chi-restraints excluded: chain B residue 562 VAL Chi-restraints excluded: chain B residue 614 HIS Chi-restraints excluded: chain B residue 619 ILE Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain B residue 677 ILE Chi-restraints excluded: chain B residue 683 TYR Chi-restraints excluded: chain B residue 710 LEU Chi-restraints excluded: chain B residue 733 LEU Chi-restraints excluded: chain B residue 749 ARG Chi-restraints excluded: chain B residue 754 THR Chi-restraints excluded: chain F residue 451 LEU Chi-restraints excluded: chain F residue 462 THR Chi-restraints excluded: chain F residue 495 VAL Chi-restraints excluded: chain F residue 496 LEU Chi-restraints excluded: chain F residue 513 LEU Chi-restraints excluded: chain F residue 516 LEU Chi-restraints excluded: chain F residue 529 ILE Chi-restraints excluded: chain F residue 606 HIS Chi-restraints excluded: chain F residue 627 ILE Chi-restraints excluded: chain F residue 672 VAL Chi-restraints excluded: chain F residue 680 PHE Chi-restraints excluded: chain F residue 689 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 110 optimal weight: 0.0270 chunk 101 optimal weight: 8.9990 chunk 107 optimal weight: 6.9990 chunk 64 optimal weight: 0.6980 chunk 46 optimal weight: 0.9980 chunk 84 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 97 optimal weight: 1.9990 chunk 70 optimal weight: 20.0000 chunk 113 optimal weight: 9.9990 chunk 69 optimal weight: 0.8980 overall best weight: 0.9240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 568 HIS A 608 HIS ** A 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 606 HIS ** F 716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 moved from start: 0.6688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10071 Z= 0.190 Angle : 0.725 10.199 13642 Z= 0.344 Chirality : 0.046 0.345 1633 Planarity : 0.005 0.050 1715 Dihedral : 4.822 19.645 1303 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 18.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 3.25 % Allowed : 28.38 % Favored : 68.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.71 (0.24), residues: 1212 helix: -2.09 (0.25), residues: 396 sheet: -2.30 (0.37), residues: 212 loop : -1.24 (0.25), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 475 HIS 0.007 0.001 HIS B 522 PHE 0.013 0.001 PHE B 635 TYR 0.036 0.002 TYR F 687 ARG 0.008 0.001 ARG A 765 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 148 time to evaluate : 1.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 415 LYS cc_start: 0.8605 (ttpt) cc_final: 0.8394 (tptt) REVERT: A 471 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8381 (tp) REVERT: A 496 ARG cc_start: 0.8655 (mmt90) cc_final: 0.8304 (mpt180) REVERT: A 572 LEU cc_start: 0.8492 (mt) cc_final: 0.8248 (mt) REVERT: A 620 ASP cc_start: 0.8323 (t0) cc_final: 0.7905 (m-30) REVERT: A 648 TYR cc_start: 0.8077 (OUTLIER) cc_final: 0.7823 (m-10) REVERT: A 710 LEU cc_start: 0.8931 (tp) cc_final: 0.8322 (mp) REVERT: A 734 ARG cc_start: 0.9029 (mmm-85) cc_final: 0.8792 (mmm-85) REVERT: B 403 ARG cc_start: 0.5230 (OUTLIER) cc_final: 0.3852 (ptt-90) REVERT: B 433 PHE cc_start: 0.7749 (t80) cc_final: 0.7521 (t80) REVERT: B 434 MET cc_start: 0.7806 (OUTLIER) cc_final: 0.6864 (tmm) REVERT: B 453 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8456 (mm) REVERT: B 475 TRP cc_start: 0.7849 (m100) cc_final: 0.7253 (m-10) REVERT: B 596 LEU cc_start: 0.8094 (OUTLIER) cc_final: 0.7812 (mt) REVERT: B 710 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8331 (mm) REVERT: B 741 ASN cc_start: 0.7769 (m-40) cc_final: 0.6888 (m110) REVERT: F 458 MET cc_start: 0.6764 (tpt) cc_final: 0.6555 (tpt) REVERT: F 495 VAL cc_start: 0.7840 (OUTLIER) cc_final: 0.7519 (t) REVERT: F 529 ILE cc_start: 0.6549 (OUTLIER) cc_final: 0.6231 (tt) REVERT: F 550 LYS cc_start: 0.9411 (tmtt) cc_final: 0.9149 (tptp) REVERT: F 611 LEU cc_start: 0.7687 (mm) cc_final: 0.6789 (mt) REVERT: F 612 LEU cc_start: 0.7078 (mt) cc_final: 0.6760 (pp) REVERT: F 680 PHE cc_start: 0.6876 (OUTLIER) cc_final: 0.5883 (m-80) REVERT: F 701 GLU cc_start: 0.8452 (mm-30) cc_final: 0.7658 (tp30) outliers start: 37 outliers final: 23 residues processed: 177 average time/residue: 0.2792 time to fit residues: 68.9248 Evaluate side-chains 176 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 143 time to evaluate : 1.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 609 SER Chi-restraints excluded: chain A residue 648 TYR Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 426 ASP Chi-restraints excluded: chain B residue 434 MET Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain B residue 476 LEU Chi-restraints excluded: chain B residue 562 VAL Chi-restraints excluded: chain B residue 596 LEU Chi-restraints excluded: chain B residue 619 ILE Chi-restraints excluded: chain B residue 677 ILE Chi-restraints excluded: chain B residue 683 TYR Chi-restraints excluded: chain B residue 710 LEU Chi-restraints excluded: chain B residue 733 LEU Chi-restraints excluded: chain B residue 754 THR Chi-restraints excluded: chain F residue 451 LEU Chi-restraints excluded: chain F residue 462 THR Chi-restraints excluded: chain F residue 495 VAL Chi-restraints excluded: chain F residue 496 LEU Chi-restraints excluded: chain F residue 516 LEU Chi-restraints excluded: chain F residue 529 ILE Chi-restraints excluded: chain F residue 606 HIS Chi-restraints excluded: chain F residue 627 ILE Chi-restraints excluded: chain F residue 672 VAL Chi-restraints excluded: chain F residue 680 PHE Chi-restraints excluded: chain F residue 689 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 54 optimal weight: 7.9990 chunk 79 optimal weight: 0.9980 chunk 119 optimal weight: 0.0060 chunk 110 optimal weight: 0.0570 chunk 95 optimal weight: 0.8980 chunk 9 optimal weight: 4.9990 chunk 73 optimal weight: 0.7980 chunk 58 optimal weight: 6.9990 chunk 75 optimal weight: 5.9990 chunk 101 optimal weight: 0.9990 chunk 29 optimal weight: 9.9990 overall best weight: 0.5514 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 418 GLN ** A 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 606 HIS ** F 716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7353 moved from start: 0.6833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10071 Z= 0.179 Angle : 0.746 9.816 13642 Z= 0.349 Chirality : 0.046 0.307 1633 Planarity : 0.005 0.050 1715 Dihedral : 4.813 22.865 1303 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 17.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 3.08 % Allowed : 28.91 % Favored : 68.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.59 (0.24), residues: 1212 helix: -2.05 (0.25), residues: 389 sheet: -2.23 (0.37), residues: 213 loop : -1.15 (0.25), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 475 HIS 0.009 0.001 HIS B 522 PHE 0.032 0.002 PHE A 433 TYR 0.042 0.002 TYR B 477 ARG 0.009 0.000 ARG A 801 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 150 time to evaluate : 1.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 415 LYS cc_start: 0.8602 (ttpt) cc_final: 0.8386 (tptt) REVERT: A 433 PHE cc_start: 0.8621 (t80) cc_final: 0.8406 (t80) REVERT: A 496 ARG cc_start: 0.8657 (mmt90) cc_final: 0.8302 (mpt180) REVERT: A 572 LEU cc_start: 0.8498 (mt) cc_final: 0.8283 (mt) REVERT: A 648 TYR cc_start: 0.8075 (OUTLIER) cc_final: 0.7811 (m-10) REVERT: A 710 LEU cc_start: 0.8894 (tp) cc_final: 0.8434 (mt) REVERT: A 734 ARG cc_start: 0.9078 (mmm-85) cc_final: 0.8877 (mmm-85) REVERT: B 403 ARG cc_start: 0.5437 (OUTLIER) cc_final: 0.4196 (ptt-90) REVERT: B 433 PHE cc_start: 0.7726 (t80) cc_final: 0.7493 (t80) REVERT: B 434 MET cc_start: 0.7800 (OUTLIER) cc_final: 0.6980 (tmm) REVERT: B 453 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8544 (mm) REVERT: B 475 TRP cc_start: 0.7791 (m100) cc_final: 0.7432 (m-10) REVERT: B 550 ARG cc_start: 0.7511 (tmt-80) cc_final: 0.7166 (tpt90) REVERT: B 596 LEU cc_start: 0.8191 (OUTLIER) cc_final: 0.7927 (mt) REVERT: B 710 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8373 (mm) REVERT: B 741 ASN cc_start: 0.7695 (m-40) cc_final: 0.6834 (m110) REVERT: F 495 VAL cc_start: 0.7824 (OUTLIER) cc_final: 0.7499 (t) REVERT: F 529 ILE cc_start: 0.6664 (OUTLIER) cc_final: 0.6366 (tt) REVERT: F 550 LYS cc_start: 0.9438 (tmtt) cc_final: 0.9176 (tptp) REVERT: F 611 LEU cc_start: 0.7654 (mm) cc_final: 0.6743 (mt) REVERT: F 612 LEU cc_start: 0.7040 (mt) cc_final: 0.6769 (pp) REVERT: F 701 GLU cc_start: 0.8453 (mm-30) cc_final: 0.7626 (tp30) outliers start: 35 outliers final: 23 residues processed: 177 average time/residue: 0.2287 time to fit residues: 57.1809 Evaluate side-chains 173 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 142 time to evaluate : 1.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 609 SER Chi-restraints excluded: chain A residue 648 TYR Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 426 ASP Chi-restraints excluded: chain B residue 434 MET Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain B residue 476 LEU Chi-restraints excluded: chain B residue 562 VAL Chi-restraints excluded: chain B residue 596 LEU Chi-restraints excluded: chain B residue 616 LEU Chi-restraints excluded: chain B residue 619 ILE Chi-restraints excluded: chain B residue 677 ILE Chi-restraints excluded: chain B residue 683 TYR Chi-restraints excluded: chain B residue 710 LEU Chi-restraints excluded: chain B residue 733 LEU Chi-restraints excluded: chain B residue 754 THR Chi-restraints excluded: chain F residue 451 LEU Chi-restraints excluded: chain F residue 462 THR Chi-restraints excluded: chain F residue 495 VAL Chi-restraints excluded: chain F residue 496 LEU Chi-restraints excluded: chain F residue 516 LEU Chi-restraints excluded: chain F residue 529 ILE Chi-restraints excluded: chain F residue 606 HIS Chi-restraints excluded: chain F residue 627 ILE Chi-restraints excluded: chain F residue 672 VAL Chi-restraints excluded: chain F residue 689 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 87 optimal weight: 0.8980 chunk 14 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 95 optimal weight: 0.8980 chunk 39 optimal weight: 0.7980 chunk 97 optimal weight: 0.9980 chunk 12 optimal weight: 4.9990 chunk 17 optimal weight: 7.9990 chunk 83 optimal weight: 3.9990 chunk 5 optimal weight: 0.0030 chunk 68 optimal weight: 4.9990 overall best weight: 0.7190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 418 GLN ** A 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 614 HIS ** B 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 711 GLN F 598 HIS F 606 HIS ** F 716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.082808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.071933 restraints weight = 68607.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.072323 restraints weight = 45269.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.072403 restraints weight = 38263.547| |-----------------------------------------------------------------------------| r_work (final): 0.3876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7204 moved from start: 0.6996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10071 Z= 0.184 Angle : 0.754 10.827 13642 Z= 0.355 Chirality : 0.046 0.334 1633 Planarity : 0.005 0.073 1715 Dihedral : 4.807 21.715 1303 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 17.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 2.99 % Allowed : 29.17 % Favored : 67.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.65 (0.24), residues: 1212 helix: -2.13 (0.25), residues: 396 sheet: -2.21 (0.38), residues: 212 loop : -1.15 (0.25), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP B 475 HIS 0.007 0.001 HIS B 522 PHE 0.055 0.002 PHE A 433 TYR 0.046 0.002 TYR F 687 ARG 0.011 0.001 ARG B 804 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2634.30 seconds wall clock time: 49 minutes 1.20 seconds (2941.20 seconds total)