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/8dra_27675/12_2024/8dra_27675.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dra_27675/12_2024/8dra_27675.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dra_27675/12_2024/8dra_27675.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dra_27675/12_2024/8dra_27675.map" model { file = "/net/cci-nas-00/data/ceres_data/8dra_27675/12_2024/8dra_27675.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dra_27675/12_2024/8dra_27675.cif" } resolution = 3.98 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= 0.001 sd= 0.045 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 18 residue(s): 0.04s 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: 7.13, per 1000 atoms: 0.72 Number of scatterers: 9899 At special positions: 0 Unit cell: (119.472, 114.232, 92.224, 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: 2.46 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 33.2% alpha, 12.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.22 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: 3.527A 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: 3.889A pdb=" N GLY A 539 " --> pdb=" O VAL A 536 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG A 541 " --> pdb=" O ASP A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 566 removed outlier: 3.694A pdb=" N THR A 563 " --> pdb=" O PRO A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 590 removed outlier: 3.911A 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: 3.644A 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: 3.655A 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 419 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: 3.647A pdb=" N GLU B 493 " --> pdb=" O ALA B 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 503 through 508 removed outlier: 3.878A pdb=" N GLU B 507 " --> pdb=" O ASP B 504 " (cutoff:3.500A) removed outlier: 3.581A 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: 4.011A pdb=" N LYS B 589 " --> pdb=" O SER B 586 " (cutoff:3.500A) Processing helix chain 'B' and resid 609 through 613 removed outlier: 3.512A pdb=" N LEU B 613 " --> pdb=" O ILE B 610 " (cutoff:3.500A) Processing helix chain 'B' and resid 633 through 638 removed outlier: 3.756A 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: 3.538A 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: 3.638A 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: 3.710A pdb=" N TYR F 511 " --> pdb=" O PRO F 508 " (cutoff:3.500A) removed outlier: 3.860A 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: 3.573A 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: 3.938A pdb=" N PHE F 680 " --> pdb=" O PRO F 676 " (cutoff:3.500A) removed outlier: 4.093A 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: 4.000A 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: 3.839A 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: 6.379A 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: 6.795A 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: 5.947A pdb=" N ILE A 574 " --> pdb=" O ILE A 599 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N LEU A 596 " --> pdb=" O ASP A 620 " (cutoff:3.500A) removed outlier: 7.038A 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: 6.351A 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: 6.341A 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 420 through 422 removed outlier: 6.518A 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: 6.978A 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: 6.900A pdb=" N LEU B 451 " --> pdb=" O TRP B 475 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N TYR B 477 " --> pdb=" O LEU B 451 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N LEU B 453 " --> pdb=" O TYR B 477 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N LEU B 474 " --> pdb=" O HIS B 499 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N LYS B 501 " --> pdb=" O LEU B 474 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N LEU B 476 " --> pdb=" O LYS B 501 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N LEU B 498 " --> pdb=" O HIS B 522 " (cutoff:3.500A) removed outlier: 8.185A pdb=" N THR B 524 " --> pdb=" O LEU B 498 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ILE B 500 " --> pdb=" O THR B 524 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N SER B 573 " --> pdb=" O LEU B 549 " (cutoff:3.500A) removed outlier: 6.833A 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: 7.164A 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: 7.106A pdb=" N HIS F 475 " --> pdb=" O LEU F 449 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N LEU F 451 " --> pdb=" O HIS F 475 " (cutoff:3.500A) removed outlier: 6.664A 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: 6.886A 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: 3.892A 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 238 hydrogen bonds defined for protein. 504 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.92 Time building geometry restraints manager: 2.73 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: 3172 1.34 - 1.46: 1052 1.46 - 1.57: 5803 1.57 - 1.69: 0 1.69 - 1.81: 44 Bond restraints: 10071 Sorted by residual: bond pdb=" N ASP F 540 " pdb=" CA ASP F 540 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.23e-02 6.61e+03 5.56e+00 bond pdb=" N ASN F 456 " pdb=" CA ASN F 456 " ideal model delta sigma weight residual 1.457 1.480 -0.022 1.29e-02 6.01e+03 3.03e+00 bond pdb=" CB TRP B 411 " pdb=" CG TRP B 411 " ideal model delta sigma weight residual 1.498 1.538 -0.040 3.10e-02 1.04e+03 1.70e+00 bond pdb=" CB PRO F 507 " pdb=" CG PRO F 507 " ideal model delta sigma weight residual 1.492 1.556 -0.064 5.00e-02 4.00e+02 1.65e+00 bond pdb=" C PRO A 607 " pdb=" O PRO A 607 " ideal model delta sigma weight residual 1.235 1.219 0.016 1.30e-02 5.92e+03 1.52e+00 ... (remaining 10066 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.96: 13252 1.96 - 3.91: 310 3.91 - 5.87: 55 5.87 - 7.82: 18 7.82 - 9.78: 7 Bond angle restraints: 13642 Sorted by residual: angle pdb=" CA LYS F 555 " pdb=" CB LYS F 555 " pdb=" CG LYS F 555 " ideal model delta sigma weight residual 114.10 122.88 -8.78 2.00e+00 2.50e-01 1.93e+01 angle pdb=" N ILE F 713 " pdb=" CA ILE F 713 " pdb=" C ILE F 713 " ideal model delta sigma weight residual 112.17 108.09 4.08 9.50e-01 1.11e+00 1.85e+01 angle pdb=" CA VAL B 715 " pdb=" CB VAL B 715 " pdb=" CG1 VAL B 715 " ideal model delta sigma weight residual 110.40 116.85 -6.45 1.70e+00 3.46e-01 1.44e+01 angle pdb=" C SER B 553 " pdb=" N ASN B 554 " pdb=" CA ASN B 554 " ideal model delta sigma weight residual 121.54 128.42 -6.88 1.91e+00 2.74e-01 1.30e+01 angle pdb=" CA MET F 581 " pdb=" CB MET F 581 " pdb=" CG MET F 581 " ideal model delta sigma weight residual 114.10 121.28 -7.18 2.00e+00 2.50e-01 1.29e+01 ... (remaining 13637 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 5469 17.83 - 35.65: 595 35.65 - 53.48: 157 53.48 - 71.30: 24 71.30 - 89.13: 5 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 180.00 159.66 20.34 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 -160.82 -19.18 0 5.00e+00 4.00e-02 1.47e+01 dihedral pdb=" CA GLN B 758 " pdb=" C GLN B 758 " pdb=" N ILE B 759 " pdb=" CA ILE B 759 " 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 - 0.056: 1325 0.056 - 0.111: 267 0.111 - 0.167: 34 0.167 - 0.222: 5 0.222 - 0.278: 2 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 1.93e+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 1.55e+00 chirality pdb=" CA ASN F 456 " pdb=" N ASN F 456 " pdb=" C ASN F 456 " pdb=" CB ASN F 456 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.98e-01 ... (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 7.16e-02 8.20e+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 6.03e-02 5.81e+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 1.45e-02 5.27e+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: 2095 2.79 - 3.31: 9310 3.31 - 3.84: 17119 3.84 - 4.37: 21342 4.37 - 4.90: 33726 Nonbonded interactions: 83592 Sorted by model distance: nonbonded pdb=" O ILE F 556 " pdb=" ND2 ASN F 584 " model vdw 2.257 3.120 nonbonded pdb=" O TRP A 411 " pdb=" OG1 THR A 441 " model vdw 2.272 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 2.309 3.120 nonbonded pdb=" NH1 ARG B 749 " pdb=" OE1 GLU B 752 " model vdw 2.313 3.120 ... (remaining 83587 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: 7.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.560 Check model and map are aligned: 0.240 Set scattering table: 0.110 Process input model: 25.740 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.040 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7014 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 10071 Z= 0.218 Angle : 0.766 9.779 13642 Z= 0.399 Chirality : 0.046 0.278 1633 Planarity : 0.006 0.072 1715 Dihedral : 15.743 89.126 3886 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 0.35 % Allowed : 21.09 % Favored : 78.56 % 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: -3.01 (0.23), residues: 1212 helix: -2.86 (0.22), residues: 369 sheet: -2.58 (0.37), residues: 182 loop : -1.18 (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 0.016 0.001 TYR F 756 ARG 0.006 0.000 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 381 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 377 time to evaluate : 1.091 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: A 447 GLU cc_start: 0.8049 (pm20) cc_final: 0.7523 (pm20) REVERT: A 534 TYR cc_start: 0.7233 (m-80) cc_final: 0.6984 (m-10) REVERT: A 540 LEU cc_start: 0.9316 (mt) cc_final: 0.9112 (mt) REVERT: A 616 LEU cc_start: 0.7902 (mt) cc_final: 0.7360 (mt) REVERT: A 624 ASN cc_start: 0.8522 (m-40) cc_final: 0.8190 (m-40) REVERT: A 626 LEU cc_start: 0.8220 (mt) cc_final: 0.7558 (mp) REVERT: A 682 PHE cc_start: 0.8523 (m-10) cc_final: 0.8263 (m-80) REVERT: B 503 THR cc_start: 0.8813 (m) cc_final: 0.8599 (p) REVERT: B 570 GLN cc_start: 0.7773 (mt0) cc_final: 0.7380 (mm110) REVERT: B 623 ASP cc_start: 0.7996 (t0) cc_final: 0.7507 (t0) REVERT: B 637 HIS cc_start: 0.7817 (m90) cc_final: 0.6765 (t-90) REVERT: B 644 LEU cc_start: 0.8857 (pt) cc_final: 0.8576 (tp) REVERT: B 648 TYR cc_start: 0.8373 (m-80) cc_final: 0.8084 (m-10) REVERT: B 664 LEU cc_start: 0.9077 (tp) cc_final: 0.8836 (tp) REVERT: B 682 PHE cc_start: 0.8600 (m-80) cc_final: 0.8219 (m-80) REVERT: F 428 LEU cc_start: 0.9160 (mt) cc_final: 0.8958 (mt) REVERT: F 476 GLN cc_start: 0.7831 (mp-120) cc_final: 0.6511 (mm-40) REVERT: F 490 LYS cc_start: 0.9409 (tttt) cc_final: 0.9146 (ttpp) REVERT: F 504 ARG cc_start: 0.8292 (tpt170) cc_final: 0.8074 (tpt90) REVERT: F 545 LYS cc_start: 0.8834 (ptpt) cc_final: 0.8508 (mmmt) REVERT: F 567 LEU cc_start: 0.7844 (tp) cc_final: 0.7428 (tp) REVERT: F 637 ARG cc_start: 0.7585 (ptp90) cc_final: 0.7343 (ptp90) REVERT: F 777 LEU cc_start: 0.7998 (tp) cc_final: 0.7533 (tp) outliers start: 4 outliers final: 0 residues processed: 378 average time/residue: 0.2569 time to fit residues: 128.9347 Evaluate side-chains 218 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 218 time to evaluate : 1.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 101 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 chunk 50 optimal weight: 10.0000 chunk 31 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 chunk 48 optimal weight: 0.0040 chunk 94 optimal weight: 0.8980 chunk 36 optimal weight: 6.9990 chunk 57 optimal weight: 0.7980 chunk 70 optimal weight: 8.9990 chunk 108 optimal weight: 0.9990 overall best weight: 1.1396 ------------------------------------------------------------------------------- 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 478 HIS B 650 HIS F 402 GLN ** F 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 558 GLN F 635 HIS F 693 ASN ** 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: 0.7148 moved from start: 0.2903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10071 Z= 0.242 Angle : 0.738 8.784 13642 Z= 0.360 Chirality : 0.047 0.367 1633 Planarity : 0.005 0.073 1715 Dihedral : 5.034 23.773 1303 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 18.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 3.51 % Allowed : 24.87 % Favored : 71.62 % 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: -2.75 (0.23), residues: 1212 helix: -2.51 (0.24), residues: 360 sheet: -2.71 (0.35), residues: 191 loop : -1.00 (0.25), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 647 HIS 0.004 0.001 HIS B 499 PHE 0.020 0.002 PHE F 609 TYR 0.021 0.002 TYR F 646 ARG 0.008 0.001 ARG B 749 *********************** 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 261 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 221 time to evaluate : 1.267 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: A 447 GLU cc_start: 0.8024 (pm20) cc_final: 0.7606 (pm20) REVERT: A 451 LEU cc_start: 0.8171 (OUTLIER) cc_final: 0.7897 (pt) REVERT: A 534 TYR cc_start: 0.7345 (m-80) cc_final: 0.6836 (m-10) REVERT: B 545 ARG cc_start: 0.8324 (mtm180) cc_final: 0.7938 (ttm-80) REVERT: B 614 HIS cc_start: 0.6607 (OUTLIER) cc_final: 0.6362 (t70) REVERT: B 644 LEU cc_start: 0.8784 (pt) cc_final: 0.8526 (tp) REVERT: F 452 GLU cc_start: 0.8072 (tt0) cc_final: 0.7635 (tt0) REVERT: F 504 ARG cc_start: 0.8420 (tpt170) cc_final: 0.8041 (tpt90) REVERT: F 567 LEU cc_start: 0.7854 (tp) cc_final: 0.7173 (tp) REVERT: F 570 MET cc_start: 0.8333 (tmm) cc_final: 0.7947 (tpp) REVERT: F 581 MET cc_start: 0.7028 (tpp) cc_final: 0.6780 (tpp) REVERT: F 599 CYS cc_start: 0.8968 (m) cc_final: 0.8703 (m) REVERT: F 628 GLU cc_start: 0.7370 (tp30) cc_final: 0.7098 (mm-30) REVERT: F 637 ARG cc_start: 0.7858 (ptp90) cc_final: 0.7576 (ptp90) REVERT: F 638 LYS cc_start: 0.7143 (mttt) cc_final: 0.6696 (ptmt) REVERT: F 686 ARG cc_start: 0.7827 (OUTLIER) cc_final: 0.7131 (ptp-170) outliers start: 40 outliers final: 18 residues processed: 247 average time/residue: 0.2229 time to fit residues: 77.1348 Evaluate side-chains 208 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 187 time to evaluate : 1.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 778 LEU Chi-restraints excluded: chain A residue 788 GLU Chi-restraints excluded: chain B residue 614 HIS Chi-restraints excluded: chain B residue 744 GLN Chi-restraints excluded: chain F residue 510 MET Chi-restraints excluded: chain F residue 541 LEU Chi-restraints excluded: chain F residue 627 ILE Chi-restraints excluded: chain F residue 645 TRP Chi-restraints excluded: chain F residue 652 ILE Chi-restraints excluded: chain F residue 679 LEU Chi-restraints excluded: chain F residue 686 ARG Chi-restraints excluded: chain F residue 694 ASP Chi-restraints excluded: chain F residue 708 LEU Chi-restraints excluded: chain F residue 753 PHE Chi-restraints excluded: chain F residue 757 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 60 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 90 optimal weight: 5.9990 chunk 74 optimal weight: 0.2980 chunk 30 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 117 optimal weight: 9.9990 chunk 97 optimal weight: 7.9990 chunk 108 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 overall best weight: 2.0588 ------------------------------------------------------------------------------- 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 467 GLN ** B 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 532 ASN F 584 ASN ** 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: 0.7240 moved from start: 0.3714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 10071 Z= 0.304 Angle : 0.717 10.047 13642 Z= 0.353 Chirality : 0.047 0.303 1633 Planarity : 0.005 0.049 1715 Dihedral : 5.140 22.398 1303 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 20.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 5.45 % Allowed : 25.13 % Favored : 69.42 % 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: -2.52 (0.24), residues: 360 sheet: -2.56 (0.36), residues: 193 loop : -0.99 (0.25), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 475 HIS 0.004 0.001 HIS A 431 PHE 0.020 0.002 PHE F 609 TYR 0.015 0.002 TYR F 756 ARG 0.007 0.001 ARG B 749 *********************** 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 247 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 185 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 447 GLU cc_start: 0.8160 (pm20) cc_final: 0.7789 (pm20) REVERT: A 451 LEU cc_start: 0.8196 (OUTLIER) cc_final: 0.7789 (pt) REVERT: A 454 GLU cc_start: 0.8359 (tt0) cc_final: 0.7735 (tt0) REVERT: A 520 GLU cc_start: 0.8059 (mp0) cc_final: 0.7750 (mp0) REVERT: B 438 ILE cc_start: 0.8983 (OUTLIER) cc_final: 0.8683 (mp) REVERT: B 550 ARG cc_start: 0.8717 (mtt90) cc_final: 0.8118 (mtt-85) REVERT: B 614 HIS cc_start: 0.6915 (OUTLIER) cc_final: 0.6579 (t70) REVERT: B 700 LEU cc_start: 0.7169 (OUTLIER) cc_final: 0.6892 (tt) REVERT: B 720 ILE cc_start: 0.7839 (mm) cc_final: 0.7618 (mm) REVERT: F 452 GLU cc_start: 0.8016 (tt0) cc_final: 0.7735 (tt0) REVERT: F 504 ARG cc_start: 0.8442 (tpt170) cc_final: 0.7955 (tpt90) REVERT: F 570 MET cc_start: 0.8530 (tmm) cc_final: 0.8220 (tmm) REVERT: F 588 MET cc_start: 0.7727 (mmm) cc_final: 0.7484 (mmm) REVERT: F 599 CYS cc_start: 0.9009 (m) cc_final: 0.8720 (m) REVERT: F 600 ASP cc_start: 0.7657 (t0) cc_final: 0.7419 (m-30) REVERT: F 617 LEU cc_start: 0.8637 (OUTLIER) cc_final: 0.8307 (mt) REVERT: F 638 LYS cc_start: 0.7379 (mttt) cc_final: 0.6901 (ptmt) REVERT: F 643 LYS cc_start: 0.8081 (mttt) cc_final: 0.7659 (mttm) REVERT: F 686 ARG cc_start: 0.7674 (OUTLIER) cc_final: 0.7041 (ptp-170) REVERT: F 711 PHE cc_start: 0.8351 (t80) cc_final: 0.8034 (t80) outliers start: 62 outliers final: 38 residues processed: 227 average time/residue: 0.2011 time to fit residues: 66.2585 Evaluate side-chains 208 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 164 time to evaluate : 1.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 465 ILE Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 568 HIS Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain A residue 609 SER Chi-restraints excluded: chain A residue 611 PHE Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 778 LEU Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 788 GLU Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 613 LEU Chi-restraints excluded: chain B residue 614 HIS Chi-restraints excluded: chain B residue 687 LEU Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain F residue 449 LEU Chi-restraints excluded: chain F residue 476 GLN Chi-restraints excluded: chain F residue 510 MET Chi-restraints excluded: chain F residue 617 LEU Chi-restraints excluded: chain F residue 627 ILE Chi-restraints excluded: chain F residue 645 TRP Chi-restraints excluded: chain F residue 652 ILE Chi-restraints excluded: chain F residue 679 LEU Chi-restraints excluded: chain F residue 686 ARG Chi-restraints excluded: chain F residue 694 ASP Chi-restraints excluded: chain F residue 697 PHE Chi-restraints excluded: chain F residue 705 LEU Chi-restraints excluded: chain F residue 708 LEU Chi-restraints excluded: chain F residue 753 PHE Chi-restraints excluded: chain F residue 757 LEU Chi-restraints excluded: chain F residue 774 CYS Chi-restraints excluded: chain F residue 789 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 107 optimal weight: 2.9990 chunk 82 optimal weight: 6.9990 chunk 56 optimal weight: 10.0000 chunk 12 optimal weight: 0.8980 chunk 52 optimal weight: 8.9990 chunk 73 optimal weight: 6.9990 chunk 109 optimal weight: 0.9980 chunk 115 optimal weight: 4.9990 chunk 57 optimal weight: 9.9990 chunk 103 optimal weight: 0.9990 chunk 31 optimal weight: 5.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- 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 625 ASN ** B 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 598 HIS ** F 716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7287 moved from start: 0.4367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 10071 Z= 0.313 Angle : 0.716 11.525 13642 Z= 0.353 Chirality : 0.047 0.262 1633 Planarity : 0.005 0.052 1715 Dihedral : 5.124 20.658 1303 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 21.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 5.54 % Allowed : 25.04 % Favored : 69.42 % 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: -2.78 (0.24), residues: 1212 helix: -2.53 (0.25), residues: 360 sheet: -2.59 (0.36), residues: 194 loop : -1.07 (0.25), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP F 645 HIS 0.005 0.001 HIS B 499 PHE 0.023 0.002 PHE F 609 TYR 0.016 0.002 TYR F 646 ARG 0.011 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 236 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 173 time to evaluate : 1.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 447 GLU cc_start: 0.8237 (pm20) cc_final: 0.7963 (pm20) REVERT: A 520 GLU cc_start: 0.8010 (mp0) cc_final: 0.7701 (mp0) REVERT: A 626 LEU cc_start: 0.8640 (mt) cc_final: 0.8138 (mt) REVERT: A 674 ILE cc_start: 0.9448 (mt) cc_final: 0.9240 (mm) REVERT: B 443 PHE cc_start: 0.7978 (m-10) cc_final: 0.6948 (m-10) REVERT: B 473 GLU cc_start: 0.7536 (tt0) cc_final: 0.7330 (tt0) REVERT: B 550 ARG cc_start: 0.8777 (mtt90) cc_final: 0.8169 (mtt-85) REVERT: B 614 HIS cc_start: 0.6930 (OUTLIER) cc_final: 0.6534 (t70) REVERT: B 644 LEU cc_start: 0.9007 (pt) cc_final: 0.8716 (tp) REVERT: B 668 TYR cc_start: 0.8313 (m-10) cc_final: 0.7567 (m-10) REVERT: B 700 LEU cc_start: 0.7068 (OUTLIER) cc_final: 0.6813 (tt) REVERT: B 728 PHE cc_start: 0.6020 (m-10) cc_final: 0.5413 (m-80) REVERT: B 738 LEU cc_start: 0.8554 (mt) cc_final: 0.7972 (pt) REVERT: B 754 THR cc_start: 0.5666 (OUTLIER) cc_final: 0.5330 (p) REVERT: F 450 LYS cc_start: 0.7842 (OUTLIER) cc_final: 0.7570 (tptp) REVERT: F 452 GLU cc_start: 0.8131 (tt0) cc_final: 0.7819 (tt0) REVERT: F 504 ARG cc_start: 0.8395 (tpt170) cc_final: 0.8008 (tpt90) REVERT: F 545 LYS cc_start: 0.8789 (ptpt) cc_final: 0.8383 (mmmt) REVERT: F 570 MET cc_start: 0.8581 (tmm) cc_final: 0.8364 (tmm) REVERT: F 599 CYS cc_start: 0.9005 (m) cc_final: 0.8700 (m) REVERT: F 611 LEU cc_start: 0.8563 (mm) cc_final: 0.8299 (mm) REVERT: F 617 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8392 (mt) REVERT: F 638 LYS cc_start: 0.7506 (mttt) cc_final: 0.7050 (ptmt) REVERT: F 643 LYS cc_start: 0.8138 (mttt) cc_final: 0.7703 (mttm) REVERT: F 686 ARG cc_start: 0.7553 (OUTLIER) cc_final: 0.6978 (ptp-170) REVERT: F 756 TYR cc_start: 0.7293 (t80) cc_final: 0.6553 (t80) outliers start: 63 outliers final: 34 residues processed: 216 average time/residue: 0.1963 time to fit residues: 61.8147 Evaluate side-chains 194 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 154 time to evaluate : 1.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 465 ILE Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 568 HIS Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain A residue 609 SER Chi-restraints excluded: chain A residue 611 PHE Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 778 LEU Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 788 GLU Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 614 HIS Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 754 THR Chi-restraints excluded: chain F residue 450 LYS Chi-restraints excluded: chain F residue 476 GLN Chi-restraints excluded: chain F residue 496 LEU Chi-restraints excluded: chain F residue 510 MET Chi-restraints excluded: chain F residue 538 LEU Chi-restraints excluded: chain F residue 541 LEU Chi-restraints excluded: chain F residue 617 LEU Chi-restraints excluded: chain F residue 627 ILE Chi-restraints excluded: chain F residue 645 TRP Chi-restraints excluded: chain F residue 652 ILE Chi-restraints excluded: chain F residue 686 ARG Chi-restraints excluded: chain F residue 694 ASP Chi-restraints excluded: chain F residue 697 PHE Chi-restraints excluded: chain F residue 719 GLU Chi-restraints excluded: chain F residue 753 PHE Chi-restraints excluded: chain F residue 789 PHE 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: 8.9990 chunk 1 optimal weight: 0.5980 chunk 86 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 80 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 chunk 104 optimal weight: 6.9990 chunk 29 optimal weight: 0.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- 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 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 431 HIS ** B 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 694 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7304 moved from start: 0.4854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 10071 Z= 0.299 Angle : 0.717 12.119 13642 Z= 0.348 Chirality : 0.046 0.215 1633 Planarity : 0.005 0.048 1715 Dihedral : 5.139 21.341 1303 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 21.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 5.62 % Allowed : 26.27 % Favored : 68.10 % 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: -2.83 (0.24), residues: 1212 helix: -2.62 (0.24), residues: 367 sheet: -2.73 (0.35), residues: 206 loop : -0.95 (0.25), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 647 HIS 0.007 0.001 HIS F 655 PHE 0.027 0.002 PHE B 443 TYR 0.021 0.002 TYR F 726 ARG 0.004 0.001 ARG B 765 *********************** 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 220 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 156 time to evaluate : 1.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 447 GLU cc_start: 0.8227 (pm20) cc_final: 0.7966 (pm20) REVERT: A 520 GLU cc_start: 0.8034 (mp0) cc_final: 0.7735 (mp0) REVERT: B 426 ASP cc_start: 0.8685 (m-30) cc_final: 0.8163 (t70) REVERT: B 473 GLU cc_start: 0.7611 (tt0) cc_final: 0.7403 (tt0) REVERT: B 550 ARG cc_start: 0.8780 (mtt90) cc_final: 0.8063 (mtt-85) REVERT: B 644 LEU cc_start: 0.8942 (pt) cc_final: 0.8564 (tp) REVERT: B 664 LEU cc_start: 0.9022 (OUTLIER) cc_final: 0.8717 (tt) REVERT: B 668 TYR cc_start: 0.8253 (m-10) cc_final: 0.7782 (m-10) REVERT: B 673 LYS cc_start: 0.8185 (OUTLIER) cc_final: 0.7739 (tptp) REVERT: B 700 LEU cc_start: 0.7018 (OUTLIER) cc_final: 0.6752 (tt) REVERT: B 754 THR cc_start: 0.5679 (OUTLIER) cc_final: 0.5384 (p) REVERT: F 450 LYS cc_start: 0.7776 (OUTLIER) cc_final: 0.7498 (tptp) REVERT: F 452 GLU cc_start: 0.8038 (tt0) cc_final: 0.7597 (tt0) REVERT: F 499 LYS cc_start: 0.7926 (tptp) cc_final: 0.7583 (tptp) REVERT: F 504 ARG cc_start: 0.8395 (tpt90) cc_final: 0.7950 (tpt90) REVERT: F 545 LYS cc_start: 0.8792 (ptpt) cc_final: 0.8411 (mmmt) REVERT: F 599 CYS cc_start: 0.9042 (m) cc_final: 0.8781 (m) REVERT: F 611 LEU cc_start: 0.8556 (mm) cc_final: 0.8285 (mm) REVERT: F 617 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8283 (mt) REVERT: F 638 LYS cc_start: 0.7565 (mttt) cc_final: 0.7121 (ptmt) REVERT: F 643 LYS cc_start: 0.8124 (mttt) cc_final: 0.7727 (mttm) REVERT: F 686 ARG cc_start: 0.7446 (OUTLIER) cc_final: 0.6909 (ptp-170) REVERT: F 727 PHE cc_start: 0.8538 (t80) cc_final: 0.8146 (m-80) REVERT: F 756 TYR cc_start: 0.7454 (t80) cc_final: 0.6896 (t80) outliers start: 64 outliers final: 41 residues processed: 196 average time/residue: 0.2060 time to fit residues: 58.1876 Evaluate side-chains 197 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 149 time to evaluate : 1.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 465 ILE Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 534 TYR Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain A residue 609 SER Chi-restraints excluded: chain A residue 611 PHE Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 713 LEU Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 778 LEU Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 788 GLU Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 591 VAL Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain B residue 673 LYS Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 754 THR Chi-restraints excluded: chain B residue 756 LEU Chi-restraints excluded: chain F residue 449 LEU Chi-restraints excluded: chain F residue 450 LYS Chi-restraints excluded: chain F residue 476 GLN Chi-restraints excluded: chain F residue 510 MET Chi-restraints excluded: chain F residue 541 LEU Chi-restraints excluded: chain F residue 617 LEU Chi-restraints excluded: chain F residue 645 TRP Chi-restraints excluded: chain F residue 686 ARG Chi-restraints excluded: chain F residue 694 ASP Chi-restraints excluded: chain F residue 697 PHE Chi-restraints excluded: chain F residue 708 LEU Chi-restraints excluded: chain F residue 753 PHE Chi-restraints excluded: chain F residue 784 VAL Chi-restraints excluded: chain F residue 789 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 39 optimal weight: 0.7980 chunk 104 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 68 optimal weight: 10.0000 chunk 28 optimal weight: 0.9980 chunk 116 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 53 optimal weight: 7.9990 chunk 9 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 60 optimal weight: 0.0050 overall best weight: 0.9598 ------------------------------------------------------------------------------- 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 554 ASN A 755 ASN ** A 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7281 moved from start: 0.5000 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= 0.196 Angle : 0.658 11.466 13642 Z= 0.316 Chirality : 0.044 0.214 1633 Planarity : 0.004 0.046 1715 Dihedral : 4.892 20.368 1303 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 18.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 4.57 % Allowed : 27.24 % Favored : 68.19 % 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 (0.24), residues: 1212 helix: -2.66 (0.23), residues: 389 sheet: -2.66 (0.36), residues: 209 loop : -1.04 (0.26), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 647 HIS 0.004 0.001 HIS B 499 PHE 0.021 0.001 PHE F 609 TYR 0.013 0.002 TYR B 689 ARG 0.006 0.001 ARG A 419 *********************** 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 225 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 173 time to evaluate : 1.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 447 GLU cc_start: 0.8255 (pm20) cc_final: 0.7916 (pm20) REVERT: A 520 GLU cc_start: 0.8005 (mp0) cc_final: 0.7686 (mp0) REVERT: A 591 VAL cc_start: 0.7848 (OUTLIER) cc_final: 0.7646 (t) REVERT: A 626 LEU cc_start: 0.8873 (mt) cc_final: 0.8506 (mt) REVERT: B 426 ASP cc_start: 0.8637 (m-30) cc_final: 0.8126 (t70) REVERT: B 550 ARG cc_start: 0.8761 (mtt90) cc_final: 0.8139 (mtt-85) REVERT: B 590 MET cc_start: 0.7920 (mpp) cc_final: 0.7369 (mmm) REVERT: B 614 HIS cc_start: 0.6828 (OUTLIER) cc_final: 0.6501 (t70) REVERT: B 644 LEU cc_start: 0.8888 (pt) cc_final: 0.8517 (tp) REVERT: B 664 LEU cc_start: 0.8988 (OUTLIER) cc_final: 0.8684 (tt) REVERT: B 668 TYR cc_start: 0.8316 (m-10) cc_final: 0.7917 (m-10) REVERT: B 673 LYS cc_start: 0.8161 (OUTLIER) cc_final: 0.7704 (tptp) REVERT: B 728 PHE cc_start: 0.5884 (m-10) cc_final: 0.5337 (m-80) REVERT: B 754 THR cc_start: 0.5737 (OUTLIER) cc_final: 0.5466 (p) REVERT: B 760 GLU cc_start: 0.8176 (mm-30) cc_final: 0.7972 (mm-30) REVERT: F 450 LYS cc_start: 0.7786 (OUTLIER) cc_final: 0.7519 (tptp) REVERT: F 499 LYS cc_start: 0.7883 (tptp) cc_final: 0.7556 (tptp) REVERT: F 504 ARG cc_start: 0.8408 (tpt90) cc_final: 0.7937 (tpt90) REVERT: F 545 LYS cc_start: 0.8801 (ptpt) cc_final: 0.8486 (mmmt) REVERT: F 588 MET cc_start: 0.7592 (mmm) cc_final: 0.7221 (mmm) REVERT: F 599 CYS cc_start: 0.8970 (m) cc_final: 0.8709 (m) REVERT: F 611 LEU cc_start: 0.8698 (mm) cc_final: 0.8427 (mm) REVERT: F 617 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8356 (mt) REVERT: F 628 GLU cc_start: 0.7368 (tp30) cc_final: 0.7053 (tm-30) REVERT: F 638 LYS cc_start: 0.7501 (mttt) cc_final: 0.7096 (ptmt) REVERT: F 643 LYS cc_start: 0.8117 (mttt) cc_final: 0.7723 (mttm) REVERT: F 686 ARG cc_start: 0.7319 (OUTLIER) cc_final: 0.6976 (ptp-170) REVERT: F 727 PHE cc_start: 0.8493 (t80) cc_final: 0.8147 (m-80) REVERT: F 756 TYR cc_start: 0.7526 (t80) cc_final: 0.6954 (t80) outliers start: 52 outliers final: 30 residues processed: 205 average time/residue: 0.2072 time to fit residues: 61.3480 Evaluate side-chains 196 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 158 time to evaluate : 1.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 534 TYR Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain A residue 609 SER Chi-restraints excluded: chain A residue 611 PHE Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 778 LEU Chi-restraints excluded: chain A residue 784 LEU Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 788 GLU Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 614 HIS Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain B residue 673 LYS Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 754 THR Chi-restraints excluded: chain B residue 756 LEU Chi-restraints excluded: chain F residue 449 LEU Chi-restraints excluded: chain F residue 450 LYS Chi-restraints excluded: chain F residue 476 GLN Chi-restraints excluded: chain F residue 617 LEU Chi-restraints excluded: chain F residue 633 PHE Chi-restraints excluded: chain F residue 686 ARG Chi-restraints excluded: chain F residue 694 ASP Chi-restraints excluded: chain F residue 697 PHE Chi-restraints excluded: chain F residue 753 PHE Chi-restraints excluded: chain F residue 789 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 111 optimal weight: 2.9990 chunk 13 optimal weight: 0.5980 chunk 66 optimal weight: 5.9990 chunk 84 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 97 optimal weight: 0.0670 chunk 64 optimal weight: 0.9990 chunk 115 optimal weight: 10.0000 chunk 72 optimal weight: 6.9990 chunk 70 optimal weight: 5.9990 chunk 53 optimal weight: 8.9990 overall best weight: 1.3324 ------------------------------------------------------------------------------- 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 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 694 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 moved from start: 0.5223 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= 0.219 Angle : 0.656 11.432 13642 Z= 0.315 Chirality : 0.045 0.205 1633 Planarity : 0.004 0.045 1715 Dihedral : 4.831 18.587 1303 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 18.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 5.54 % Allowed : 26.98 % Favored : 67.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.88 (0.24), residues: 1212 helix: -2.64 (0.23), residues: 383 sheet: -2.54 (0.36), residues: 203 loop : -1.04 (0.25), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 647 HIS 0.005 0.001 HIS F 669 PHE 0.025 0.002 PHE B 443 TYR 0.013 0.002 TYR A 534 ARG 0.004 0.001 ARG A 419 *********************** 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 222 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 159 time to evaluate : 1.212 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 447 GLU cc_start: 0.8256 (pm20) cc_final: 0.7924 (pm20) REVERT: A 520 GLU cc_start: 0.8008 (mp0) cc_final: 0.7679 (mp0) REVERT: A 591 VAL cc_start: 0.7906 (OUTLIER) cc_final: 0.7625 (t) REVERT: A 626 LEU cc_start: 0.8984 (mt) cc_final: 0.8615 (mt) REVERT: B 426 ASP cc_start: 0.8666 (m-30) cc_final: 0.8128 (t70) REVERT: B 545 ARG cc_start: 0.8286 (mtt180) cc_final: 0.7799 (ttm-80) REVERT: B 550 ARG cc_start: 0.8757 (mtt90) cc_final: 0.8114 (mtt-85) REVERT: B 572 LEU cc_start: 0.7521 (mt) cc_final: 0.7311 (mt) REVERT: B 590 MET cc_start: 0.7931 (mpp) cc_final: 0.7562 (mmm) REVERT: B 614 HIS cc_start: 0.6878 (OUTLIER) cc_final: 0.6541 (t70) REVERT: B 644 LEU cc_start: 0.8887 (pt) cc_final: 0.8539 (tp) REVERT: B 668 TYR cc_start: 0.8312 (m-10) cc_final: 0.7866 (m-10) REVERT: B 673 LYS cc_start: 0.8156 (OUTLIER) cc_final: 0.7687 (tptp) REVERT: B 754 THR cc_start: 0.5659 (OUTLIER) cc_final: 0.5409 (p) REVERT: B 760 GLU cc_start: 0.8297 (mm-30) cc_final: 0.8058 (mm-30) REVERT: F 469 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8445 (mm) REVERT: F 499 LYS cc_start: 0.7949 (tptp) cc_final: 0.7342 (tptp) REVERT: F 504 ARG cc_start: 0.8504 (tpt90) cc_final: 0.7999 (tpt90) REVERT: F 545 LYS cc_start: 0.8774 (ptpt) cc_final: 0.8454 (mmmt) REVERT: F 588 MET cc_start: 0.7764 (mmm) cc_final: 0.7435 (mmm) REVERT: F 599 CYS cc_start: 0.9010 (m) cc_final: 0.8744 (m) REVERT: F 611 LEU cc_start: 0.8739 (mm) cc_final: 0.8485 (mm) REVERT: F 617 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8260 (mt) REVERT: F 643 LYS cc_start: 0.8110 (mttt) cc_final: 0.7124 (mttm) REVERT: F 645 TRP cc_start: 0.6752 (OUTLIER) cc_final: 0.5542 (p90) REVERT: F 686 ARG cc_start: 0.7233 (OUTLIER) cc_final: 0.6971 (ptp-170) REVERT: F 693 ASN cc_start: 0.7544 (m-40) cc_final: 0.7283 (m-40) REVERT: F 727 PHE cc_start: 0.8503 (t80) cc_final: 0.8147 (m-80) REVERT: F 752 LEU cc_start: 0.7870 (tt) cc_final: 0.7583 (mm) outliers start: 63 outliers final: 39 residues processed: 198 average time/residue: 0.2039 time to fit residues: 58.2857 Evaluate side-chains 203 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 156 time to evaluate : 1.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 534 TYR Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain A residue 609 SER Chi-restraints excluded: chain A residue 611 PHE Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 778 LEU Chi-restraints excluded: chain A residue 784 LEU Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 788 GLU Chi-restraints excluded: chain A residue 791 PHE Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain B residue 436 SER Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 473 GLU Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 614 HIS Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 673 LYS Chi-restraints excluded: chain B residue 683 TYR Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 754 THR Chi-restraints excluded: chain B residue 756 LEU Chi-restraints excluded: chain F residue 449 LEU Chi-restraints excluded: chain F residue 469 LEU Chi-restraints excluded: chain F residue 476 GLN Chi-restraints excluded: chain F residue 617 LEU Chi-restraints excluded: chain F residue 633 PHE Chi-restraints excluded: chain F residue 645 TRP Chi-restraints excluded: chain F residue 686 ARG Chi-restraints excluded: chain F residue 694 ASP Chi-restraints excluded: chain F residue 697 PHE Chi-restraints excluded: chain F residue 708 LEU Chi-restraints excluded: chain F residue 753 PHE Chi-restraints excluded: chain F residue 784 VAL Chi-restraints excluded: chain F residue 789 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 71 optimal weight: 0.9990 chunk 46 optimal weight: 0.2980 chunk 69 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 73 optimal weight: 5.9990 chunk 78 optimal weight: 10.0000 chunk 57 optimal weight: 0.9980 chunk 10 optimal weight: 0.0470 chunk 90 optimal weight: 6.9990 chunk 105 optimal weight: 3.9990 overall best weight: 0.6478 ------------------------------------------------------------------------------- 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 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 431 HIS B 478 HIS ** B 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7272 moved from start: 0.5387 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= 0.170 Angle : 0.645 11.355 13642 Z= 0.305 Chirality : 0.044 0.199 1633 Planarity : 0.004 0.045 1715 Dihedral : 4.628 18.531 1303 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 16.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 3.34 % Allowed : 29.26 % Favored : 67.40 % 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: -2.89 (0.23), residues: 1212 helix: -2.63 (0.23), residues: 392 sheet: -2.46 (0.37), residues: 196 loop : -1.08 (0.25), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 647 HIS 0.008 0.001 HIS A 608 PHE 0.016 0.001 PHE F 609 TYR 0.012 0.001 TYR A 534 ARG 0.004 0.000 ARG A 419 *********************** 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 211 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 173 time to evaluate : 1.444 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: A 447 GLU cc_start: 0.8143 (pm20) cc_final: 0.7791 (pm20) REVERT: A 520 GLU cc_start: 0.7999 (mp0) cc_final: 0.7673 (mp0) REVERT: A 626 LEU cc_start: 0.8977 (mt) cc_final: 0.8603 (mt) REVERT: B 426 ASP cc_start: 0.8656 (m-30) cc_final: 0.8091 (t70) REVERT: B 545 ARG cc_start: 0.8250 (mtt180) cc_final: 0.7779 (ttm-80) REVERT: B 550 ARG cc_start: 0.8686 (mtt90) cc_final: 0.8057 (mtt-85) REVERT: B 572 LEU cc_start: 0.7492 (mt) cc_final: 0.7279 (mt) REVERT: B 590 MET cc_start: 0.7922 (mpp) cc_final: 0.7564 (mmm) REVERT: B 614 HIS cc_start: 0.6682 (OUTLIER) cc_final: 0.6406 (t70) REVERT: B 644 LEU cc_start: 0.8841 (pt) cc_final: 0.8490 (tp) REVERT: B 728 PHE cc_start: 0.5533 (m-10) cc_final: 0.5126 (m-80) REVERT: B 754 THR cc_start: 0.5636 (OUTLIER) cc_final: 0.5399 (p) REVERT: F 452 GLU cc_start: 0.7992 (tt0) cc_final: 0.7562 (tt0) REVERT: F 469 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.8405 (mm) REVERT: F 476 GLN cc_start: 0.7662 (OUTLIER) cc_final: 0.6280 (mm-40) REVERT: F 504 ARG cc_start: 0.8515 (tpt90) cc_final: 0.7996 (tpt90) REVERT: F 541 LEU cc_start: 0.8692 (mp) cc_final: 0.8153 (mp) REVERT: F 556 ILE cc_start: 0.8041 (OUTLIER) cc_final: 0.7690 (tp) REVERT: F 581 MET cc_start: 0.7245 (tpt) cc_final: 0.6957 (tpt) REVERT: F 588 MET cc_start: 0.7757 (mmm) cc_final: 0.7412 (mmm) REVERT: F 598 HIS cc_start: 0.8770 (t-170) cc_final: 0.8294 (t70) REVERT: F 599 CYS cc_start: 0.8951 (m) cc_final: 0.8495 (m) REVERT: F 611 LEU cc_start: 0.8737 (mm) cc_final: 0.8499 (mm) REVERT: F 617 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8273 (mt) REVERT: F 693 ASN cc_start: 0.7306 (m-40) cc_final: 0.7048 (m110) REVERT: F 727 PHE cc_start: 0.8475 (t80) cc_final: 0.8139 (m-80) REVERT: F 752 LEU cc_start: 0.7900 (tt) cc_final: 0.7596 (mm) outliers start: 38 outliers final: 25 residues processed: 196 average time/residue: 0.2122 time to fit residues: 59.3503 Evaluate side-chains 194 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 163 time to evaluate : 1.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain A residue 609 SER Chi-restraints excluded: chain A residue 611 PHE Chi-restraints excluded: chain A residue 713 LEU Chi-restraints excluded: chain A residue 778 LEU Chi-restraints excluded: chain A residue 784 LEU Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 788 GLU Chi-restraints excluded: chain B residue 436 SER Chi-restraints excluded: chain B residue 614 HIS Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 754 THR Chi-restraints excluded: chain B residue 756 LEU Chi-restraints excluded: chain F residue 449 LEU Chi-restraints excluded: chain F residue 469 LEU Chi-restraints excluded: chain F residue 476 GLN Chi-restraints excluded: chain F residue 556 ILE Chi-restraints excluded: chain F residue 617 LEU Chi-restraints excluded: chain F residue 627 ILE Chi-restraints excluded: chain F residue 633 PHE Chi-restraints excluded: chain F residue 694 ASP Chi-restraints excluded: chain F residue 697 PHE Chi-restraints excluded: chain F residue 753 PHE Chi-restraints excluded: chain F residue 784 VAL Chi-restraints excluded: chain F residue 789 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 110 optimal weight: 0.4980 chunk 101 optimal weight: 4.9990 chunk 107 optimal weight: 0.9990 chunk 64 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 chunk 84 optimal weight: 0.6980 chunk 33 optimal weight: 5.9990 chunk 97 optimal weight: 3.9990 chunk 70 optimal weight: 8.9990 chunk 113 optimal weight: 1.9990 chunk 69 optimal weight: 6.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- 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 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 431 HIS ** B 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 694 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7283 moved from start: 0.5524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10071 Z= 0.179 Angle : 0.651 11.144 13642 Z= 0.306 Chirality : 0.044 0.192 1633 Planarity : 0.004 0.044 1715 Dihedral : 4.556 19.021 1303 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 17.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 3.78 % Allowed : 28.73 % Favored : 67.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.81 (0.24), residues: 1212 helix: -2.58 (0.23), residues: 392 sheet: -2.47 (0.36), residues: 206 loop : -0.96 (0.26), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP F 645 HIS 0.007 0.001 HIS A 608 PHE 0.030 0.001 PHE B 443 TYR 0.011 0.001 TYR F 511 ARG 0.004 0.000 ARG B 801 *********************** 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 212 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 169 time to evaluate : 1.275 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 447 GLU cc_start: 0.8170 (pm20) cc_final: 0.7778 (pm20) REVERT: A 520 GLU cc_start: 0.8043 (mp0) cc_final: 0.7695 (mp0) REVERT: A 591 VAL cc_start: 0.8051 (OUTLIER) cc_final: 0.7742 (t) REVERT: A 626 LEU cc_start: 0.8936 (mt) cc_final: 0.8544 (mt) REVERT: B 426 ASP cc_start: 0.8670 (m-30) cc_final: 0.8106 (t70) REVERT: B 545 ARG cc_start: 0.8238 (mtt180) cc_final: 0.7779 (ttm-80) REVERT: B 550 ARG cc_start: 0.8675 (mtt90) cc_final: 0.8062 (mtt-85) REVERT: B 572 LEU cc_start: 0.7608 (mt) cc_final: 0.7361 (mt) REVERT: B 590 MET cc_start: 0.7920 (mpp) cc_final: 0.7577 (mmm) REVERT: B 614 HIS cc_start: 0.6661 (OUTLIER) cc_final: 0.6336 (t70) REVERT: B 644 LEU cc_start: 0.8840 (pt) cc_final: 0.8418 (tp) REVERT: B 673 LYS cc_start: 0.8134 (OUTLIER) cc_final: 0.7634 (tptp) REVERT: B 754 THR cc_start: 0.5587 (OUTLIER) cc_final: 0.5383 (p) REVERT: F 452 GLU cc_start: 0.8006 (tt0) cc_final: 0.7585 (tt0) REVERT: F 469 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8416 (mm) REVERT: F 504 ARG cc_start: 0.8481 (tpt90) cc_final: 0.7930 (tpt90) REVERT: F 556 ILE cc_start: 0.8013 (mp) cc_final: 0.7694 (tp) REVERT: F 581 MET cc_start: 0.7039 (tpt) cc_final: 0.6760 (tpt) REVERT: F 588 MET cc_start: 0.7749 (mmm) cc_final: 0.7416 (mmm) REVERT: F 598 HIS cc_start: 0.8714 (t-170) cc_final: 0.8264 (t70) REVERT: F 599 CYS cc_start: 0.8962 (m) cc_final: 0.8501 (m) REVERT: F 617 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.7860 (mt) REVERT: F 620 LYS cc_start: 0.6892 (mmmt) cc_final: 0.6398 (tppt) REVERT: F 646 TYR cc_start: 0.7236 (m-80) cc_final: 0.6886 (m-10) REVERT: F 693 ASN cc_start: 0.7392 (m-40) cc_final: 0.7148 (m110) REVERT: F 727 PHE cc_start: 0.8464 (t80) cc_final: 0.8134 (m-80) REVERT: F 752 LEU cc_start: 0.7868 (tt) cc_final: 0.7573 (mm) outliers start: 43 outliers final: 32 residues processed: 195 average time/residue: 0.2254 time to fit residues: 63.3684 Evaluate side-chains 203 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 165 time to evaluate : 1.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain A residue 609 SER Chi-restraints excluded: chain A residue 611 PHE Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 713 LEU Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 778 LEU Chi-restraints excluded: chain A residue 784 LEU Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 788 GLU Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain B residue 436 SER Chi-restraints excluded: chain B residue 613 LEU Chi-restraints excluded: chain B residue 614 HIS Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 673 LYS Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 743 LEU Chi-restraints excluded: chain B residue 754 THR Chi-restraints excluded: chain B residue 756 LEU Chi-restraints excluded: chain F residue 449 LEU Chi-restraints excluded: chain F residue 469 LEU Chi-restraints excluded: chain F residue 476 GLN Chi-restraints excluded: chain F residue 617 LEU Chi-restraints excluded: chain F residue 627 ILE Chi-restraints excluded: chain F residue 694 ASP Chi-restraints excluded: chain F residue 697 PHE Chi-restraints excluded: chain F residue 705 LEU Chi-restraints excluded: chain F residue 753 PHE Chi-restraints excluded: chain F residue 784 VAL Chi-restraints excluded: chain F residue 789 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 54 optimal weight: 2.9990 chunk 79 optimal weight: 0.0010 chunk 119 optimal weight: 0.1980 chunk 110 optimal weight: 0.9980 chunk 95 optimal weight: 10.0000 chunk 9 optimal weight: 0.9980 chunk 73 optimal weight: 10.0000 chunk 58 optimal weight: 8.9990 chunk 75 optimal weight: 0.7980 chunk 101 optimal weight: 5.9990 chunk 29 optimal weight: 0.0470 overall best weight: 0.4084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 431 HIS A 764 ASN B 431 HIS ** B 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 584 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: 0.7263 moved from start: 0.5632 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= 0.171 Angle : 0.680 13.416 13642 Z= 0.313 Chirality : 0.044 0.190 1633 Planarity : 0.004 0.044 1715 Dihedral : 4.507 20.224 1303 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 16.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 3.16 % Allowed : 29.44 % Favored : 67.40 % 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: -2.50 (0.24), residues: 386 sheet: -2.35 (0.36), residues: 202 loop : -0.96 (0.25), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP F 645 HIS 0.007 0.001 HIS A 608 PHE 0.013 0.001 PHE F 609 TYR 0.011 0.001 TYR F 710 ARG 0.010 0.000 ARG B 749 ********************** 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 211 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 175 time to evaluate : 1.266 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: A 447 GLU cc_start: 0.8127 (pm20) cc_final: 0.7828 (pm20) REVERT: A 520 GLU cc_start: 0.8013 (mp0) cc_final: 0.7641 (mp0) REVERT: A 591 VAL cc_start: 0.8022 (OUTLIER) cc_final: 0.7698 (t) REVERT: A 626 LEU cc_start: 0.8938 (mt) cc_final: 0.8552 (mt) REVERT: B 426 ASP cc_start: 0.8630 (m-30) cc_final: 0.8046 (t70) REVERT: B 545 ARG cc_start: 0.8172 (mtt180) cc_final: 0.7720 (ttm-80) REVERT: B 550 ARG cc_start: 0.8666 (mtt90) cc_final: 0.8061 (mtt-85) REVERT: B 572 LEU cc_start: 0.7619 (mt) cc_final: 0.7387 (mt) REVERT: B 590 MET cc_start: 0.7903 (mpp) cc_final: 0.7522 (mmm) REVERT: B 614 HIS cc_start: 0.6611 (OUTLIER) cc_final: 0.6330 (t70) REVERT: B 644 LEU cc_start: 0.8688 (pt) cc_final: 0.8315 (tp) REVERT: B 673 LYS cc_start: 0.8106 (OUTLIER) cc_final: 0.7592 (tptp) REVERT: F 452 GLU cc_start: 0.7983 (tt0) cc_final: 0.7580 (tt0) REVERT: F 469 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8350 (mm) REVERT: F 476 GLN cc_start: 0.7325 (OUTLIER) cc_final: 0.6964 (mm-40) REVERT: F 504 ARG cc_start: 0.8490 (tpt90) cc_final: 0.7946 (tpt90) REVERT: F 556 ILE cc_start: 0.8041 (mp) cc_final: 0.7719 (tp) REVERT: F 581 MET cc_start: 0.7167 (tpt) cc_final: 0.6910 (tpt) REVERT: F 588 MET cc_start: 0.7681 (mmm) cc_final: 0.7366 (mmm) REVERT: F 598 HIS cc_start: 0.8730 (t-170) cc_final: 0.8317 (t70) REVERT: F 599 CYS cc_start: 0.8942 (m) cc_final: 0.8482 (m) REVERT: F 617 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.7897 (mt) REVERT: F 620 LYS cc_start: 0.6888 (mmmt) cc_final: 0.6292 (tppt) REVERT: F 646 TYR cc_start: 0.7136 (m-80) cc_final: 0.6782 (m-10) REVERT: F 727 PHE cc_start: 0.8460 (t80) cc_final: 0.8133 (m-80) REVERT: F 752 LEU cc_start: 0.7902 (tt) cc_final: 0.7609 (mm) outliers start: 36 outliers final: 27 residues processed: 199 average time/residue: 0.2400 time to fit residues: 66.6458 Evaluate side-chains 195 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 162 time to evaluate : 1.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain A residue 609 SER Chi-restraints excluded: chain A residue 611 PHE Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 713 LEU Chi-restraints excluded: chain A residue 778 LEU Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 788 GLU Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain B residue 436 SER Chi-restraints excluded: chain B residue 613 LEU Chi-restraints excluded: chain B residue 614 HIS Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 673 LYS Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 756 LEU Chi-restraints excluded: chain F residue 449 LEU Chi-restraints excluded: chain F residue 469 LEU Chi-restraints excluded: chain F residue 476 GLN Chi-restraints excluded: chain F residue 617 LEU Chi-restraints excluded: chain F residue 627 ILE Chi-restraints excluded: chain F residue 694 ASP Chi-restraints excluded: chain F residue 697 PHE Chi-restraints excluded: chain F residue 708 LEU Chi-restraints excluded: chain F residue 753 PHE Chi-restraints excluded: chain F residue 784 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 87 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 chunk 26 optimal weight: 0.7980 chunk 95 optimal weight: 9.9990 chunk 39 optimal weight: 0.5980 chunk 97 optimal weight: 8.9990 chunk 12 optimal weight: 2.9990 chunk 17 optimal weight: 7.9990 chunk 83 optimal weight: 8.9990 chunk 5 optimal weight: 0.0570 chunk 68 optimal weight: 5.9990 overall best weight: 1.0300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 431 HIS ** B 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 694 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.113268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.095391 restraints weight = 35124.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.094544 restraints weight = 27572.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.095381 restraints weight = 22752.419| |-----------------------------------------------------------------------------| r_work (final): 0.3784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.5821 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= 0.201 Angle : 0.680 12.666 13642 Z= 0.315 Chirality : 0.044 0.191 1633 Planarity : 0.004 0.044 1715 Dihedral : 4.517 20.139 1303 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 17.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 3.25 % Allowed : 29.61 % Favored : 67.14 % 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: -2.68 (0.24), residues: 1212 helix: -2.51 (0.24), residues: 386 sheet: -2.26 (0.37), residues: 201 loop : -0.96 (0.25), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP F 645 HIS 0.007 0.001 HIS A 608 PHE 0.039 0.002 PHE B 443 TYR 0.014 0.002 TYR B 477 ARG 0.005 0.000 ARG B 749 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2486.85 seconds wall clock time: 46 minutes 30.44 seconds (2790.44 seconds total)