Starting phenix.real_space_refine on Sun May 3 12:31:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jrg_61754/05_2026/9jrg_61754.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jrg_61754/05_2026/9jrg_61754.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.63 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jrg_61754/05_2026/9jrg_61754.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jrg_61754/05_2026/9jrg_61754.map" model { file = "/net/cci-nas-00/data/ceres_data/9jrg_61754/05_2026/9jrg_61754.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jrg_61754/05_2026/9jrg_61754.cif" } resolution = 3.63 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.099 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 60 5.16 5 C 8268 2.51 5 N 2151 2.21 5 O 2375 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 33 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12854 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 409, 3184 Classifications: {'peptide': 409} Link IDs: {'PTRANS': 12, 'TRANS': 396} Chain breaks: 1 Chain: "B" Number of atoms: 3226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 413, 3226 Classifications: {'peptide': 413} Link IDs: {'PTRANS': 12, 'TRANS': 400} Chain breaks: 1 Chain: "C" Number of atoms: 3199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 412, 3199 Classifications: {'peptide': 412} Link IDs: {'PTRANS': 12, 'TRANS': 399} Chain breaks: 1 Chain: "D" Number of atoms: 3245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 3245 Classifications: {'peptide': 415} Link IDs: {'PTRANS': 12, 'TRANS': 402} Chain breaks: 1 Time building chain proxies: 3.02, per 1000 atoms: 0.23 Number of scatterers: 12854 At special positions: 0 Unit cell: (137.28, 115.2, 135.36, 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 60 16.00 O 2375 8.00 N 2151 7.00 C 8268 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 757 " - pdb=" SG CYS A 812 " distance=2.03 Simple disulfide: pdb=" SG CYS B 756 " - pdb=" SG CYS B 811 " distance=2.03 Simple disulfide: pdb=" SG CYS C 756 " - pdb=" SG CYS C 811 " distance=2.03 Simple disulfide: pdb=" SG CYS D 756 " - pdb=" SG CYS D 811 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.03 Conformation dependent library (CDL) restraints added in 557.2 milliseconds 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3058 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 17 sheets defined 53.2% alpha, 9.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'A' and resid 467 through 480 removed outlier: 3.596A pdb=" N LEU A 472 " --> pdb=" O SER A 468 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA A 478 " --> pdb=" O ALA A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 511 removed outlier: 3.675A pdb=" N GLU A 508 " --> pdb=" O GLY A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 529 removed outlier: 3.928A pdb=" N SER A 529 " --> pdb=" O PRO A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 588 removed outlier: 3.715A pdb=" N ALA A 568 " --> pdb=" O PHE A 564 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ILE A 574 " --> pdb=" O ILE A 570 " (cutoff:3.500A) Proline residue: A 575 - end of helix removed outlier: 3.513A pdb=" N GLY A 578 " --> pdb=" O ILE A 574 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU A 580 " --> pdb=" O VAL A 576 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE A 581 " --> pdb=" O VAL A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 618 removed outlier: 3.767A pdb=" N TRP A 611 " --> pdb=" O HIS A 607 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL A 613 " --> pdb=" O ALA A 609 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA A 616 " --> pdb=" O ILE A 612 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N PHE A 617 " --> pdb=" O VAL A 613 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 662 removed outlier: 3.701A pdb=" N MET A 635 " --> pdb=" O MET A 631 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLY A 636 " --> pdb=" O ARG A 632 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER A 637 " --> pdb=" O ILE A 633 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N TRP A 638 " --> pdb=" O VAL A 634 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE A 644 " --> pdb=" O LEU A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 668 through 675 removed outlier: 3.680A pdb=" N GLN A 675 " --> pdb=" O ASP A 671 " (cutoff:3.500A) Processing helix chain 'A' and resid 689 through 696 Processing helix chain 'A' and resid 705 through 714 Processing helix chain 'A' and resid 715 through 718 Processing helix chain 'A' and resid 725 through 734 removed outlier: 3.720A pdb=" N LYS A 734 " --> pdb=" O ILE A 730 " (cutoff:3.500A) Processing helix chain 'A' and resid 744 through 754 removed outlier: 3.560A pdb=" N TYR A 749 " --> pdb=" O ALA A 745 " (cutoff:3.500A) Processing helix chain 'A' and resid 780 through 795 removed outlier: 4.454A pdb=" N LEU A 784 " --> pdb=" O PRO A 780 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER A 786 " --> pdb=" O ARG A 782 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLN A 787 " --> pdb=" O ASP A 783 " (cutoff:3.500A) Processing helix chain 'A' and resid 796 through 806 removed outlier: 3.548A pdb=" N LYS A 804 " --> pdb=" O VAL A 800 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N TRP A 805 " --> pdb=" O LEU A 801 " (cutoff:3.500A) Processing helix chain 'A' and resid 813 through 819 removed outlier: 4.104A pdb=" N HIS A 817 " --> pdb=" O ASP A 813 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER A 819 " --> pdb=" O THR A 815 " (cutoff:3.500A) Processing helix chain 'A' and resid 832 through 853 removed outlier: 4.072A pdb=" N CYS A 847 " --> pdb=" O LEU A 843 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N LEU A 848 " --> pdb=" O LEU A 844 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL A 849 " --> pdb=" O LEU A 845 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA A 850 " --> pdb=" O ALA A 846 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 437 removed outlier: 3.788A pdb=" N GLY B 436 " --> pdb=" O SER B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 479 Processing helix chain 'B' and resid 496 through 500 removed outlier: 3.659A pdb=" N THR B 499 " --> pdb=" O LEU B 496 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N SER B 500 " --> pdb=" O HIS B 497 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 496 through 500' Processing helix chain 'B' and resid 502 through 510 Processing helix chain 'B' and resid 523 through 530 removed outlier: 3.951A pdb=" N VAL B 529 " --> pdb=" O GLU B 525 " (cutoff:3.500A) Processing helix chain 'B' and resid 562 through 588 removed outlier: 3.727A pdb=" N ILE B 573 " --> pdb=" O ILE B 569 " (cutoff:3.500A) Proline residue: B 574 - end of helix removed outlier: 3.871A pdb=" N ALA B 588 " --> pdb=" O ASN B 584 " (cutoff:3.500A) Processing helix chain 'B' and resid 605 through 617 Processing helix chain 'B' and resid 627 through 658 removed outlier: 3.814A pdb=" N ILE B 632 " --> pdb=" O VAL B 628 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N VAL B 633 " --> pdb=" O ALA B 629 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N MET B 634 " --> pdb=" O MET B 630 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL B 658 " --> pdb=" O ALA B 654 " (cutoff:3.500A) Processing helix chain 'B' and resid 667 through 674 Processing helix chain 'B' and resid 685 through 696 removed outlier: 3.600A pdb=" N GLU B 689 " --> pdb=" O SER B 685 " (cutoff:3.500A) Processing helix chain 'B' and resid 702 through 713 Processing helix chain 'B' and resid 724 through 735 removed outlier: 4.037A pdb=" N GLY B 728 " --> pdb=" O ASN B 724 " (cutoff:3.500A) Processing helix chain 'B' and resid 743 through 753 Processing helix chain 'B' and resid 780 through 795 Processing helix chain 'B' and resid 795 through 805 removed outlier: 3.528A pdb=" N LYS B 803 " --> pdb=" O VAL B 799 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N TRP B 804 " --> pdb=" O LEU B 800 " (cutoff:3.500A) Processing helix chain 'B' and resid 812 through 818 removed outlier: 3.786A pdb=" N HIS B 816 " --> pdb=" O ASP B 812 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N SER B 817 " --> pdb=" O LEU B 813 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N SER B 818 " --> pdb=" O THR B 814 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 812 through 818' Processing helix chain 'B' and resid 827 through 854 removed outlier: 5.260A pdb=" N GLY B 833 " --> pdb=" O HIS B 829 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N VAL B 834 " --> pdb=" O SER B 830 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N PHE B 835 " --> pdb=" O PHE B 831 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA B 849 " --> pdb=" O ALA B 845 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N ALA B 850 " --> pdb=" O CYS B 846 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N LEU B 851 " --> pdb=" O LEU B 847 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N GLU B 852 " --> pdb=" O VAL B 848 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N TRP B 854 " --> pdb=" O ALA B 850 " (cutoff:3.500A) Processing helix chain 'C' and resid 431 through 435 Processing helix chain 'C' and resid 466 through 479 Processing helix chain 'C' and resid 503 through 510 Processing helix chain 'C' and resid 523 through 528 removed outlier: 4.006A pdb=" N SER C 528 " --> pdb=" O PRO C 524 " (cutoff:3.500A) Processing helix chain 'C' and resid 555 through 559 Processing helix chain 'C' and resid 562 through 588 removed outlier: 4.107A pdb=" N ILE C 573 " --> pdb=" O ILE C 569 " (cutoff:3.500A) Proline residue: C 574 - end of helix removed outlier: 3.506A pdb=" N LEU C 579 " --> pdb=" O VAL C 575 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ALA C 588 " --> pdb=" O ASN C 584 " (cutoff:3.500A) Processing helix chain 'C' and resid 604 through 617 Processing helix chain 'C' and resid 627 through 662 removed outlier: 3.524A pdb=" N ARG C 631 " --> pdb=" O SER C 627 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N THR C 649 " --> pdb=" O CYS C 645 " (cutoff:3.500A) Processing helix chain 'C' and resid 667 through 674 Processing helix chain 'C' and resid 685 through 696 Processing helix chain 'C' and resid 703 through 713 Processing helix chain 'C' and resid 724 through 734 removed outlier: 3.708A pdb=" N LYS C 734 " --> pdb=" O ARG C 730 " (cutoff:3.500A) Processing helix chain 'C' and resid 743 through 752 Processing helix chain 'C' and resid 780 through 795 removed outlier: 3.632A pdb=" N LEU C 791 " --> pdb=" O ARG C 787 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLN C 792 " --> pdb=" O ILE C 788 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASP C 793 " --> pdb=" O LEU C 789 " (cutoff:3.500A) Processing helix chain 'C' and resid 795 through 805 Processing helix chain 'C' and resid 813 through 818 Processing helix chain 'C' and resid 832 through 844 Processing helix chain 'C' and resid 844 through 851 removed outlier: 3.714A pdb=" N VAL C 848 " --> pdb=" O LEU C 844 " (cutoff:3.500A) Processing helix chain 'D' and resid 465 through 478 Processing helix chain 'D' and resid 502 through 510 Processing helix chain 'D' and resid 523 through 530 removed outlier: 3.560A pdb=" N VAL D 529 " --> pdb=" O GLU D 525 " (cutoff:3.500A) Processing helix chain 'D' and resid 555 through 559 removed outlier: 3.595A pdb=" N PHE D 558 " --> pdb=" O PHE D 555 " (cutoff:3.500A) Processing helix chain 'D' and resid 562 through 588 removed outlier: 3.742A pdb=" N ILE D 573 " --> pdb=" O ILE D 569 " (cutoff:3.500A) Proline residue: D 574 - end of helix Processing helix chain 'D' and resid 605 through 617 Processing helix chain 'D' and resid 627 through 657 removed outlier: 3.947A pdb=" N TRP D 637 " --> pdb=" O VAL D 633 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N TRP D 638 " --> pdb=" O MET D 634 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N LEU D 639 " --> pdb=" O GLY D 635 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N PHE D 640 " --> pdb=" O SER D 636 " (cutoff:3.500A) Processing helix chain 'D' and resid 667 through 674 removed outlier: 3.511A pdb=" N GLN D 674 " --> pdb=" O ASP D 670 " (cutoff:3.500A) Processing helix chain 'D' and resid 685 through 696 removed outlier: 3.637A pdb=" N GLU D 689 " --> pdb=" O SER D 685 " (cutoff:3.500A) Processing helix chain 'D' and resid 703 through 713 Processing helix chain 'D' and resid 724 through 735 removed outlier: 3.529A pdb=" N GLY D 735 " --> pdb=" O LYS D 731 " (cutoff:3.500A) Processing helix chain 'D' and resid 743 through 751 Processing helix chain 'D' and resid 780 through 794 Processing helix chain 'D' and resid 795 through 805 Processing helix chain 'D' and resid 831 through 859 removed outlier: 3.681A pdb=" N PHE D 835 " --> pdb=" O PHE D 831 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 481 through 487 removed outlier: 3.544A pdb=" N LEU A 516 " --> pdb=" O LYS A 441 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE A 518 " --> pdb=" O VAL A 443 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N SER A 519 " --> pdb=" O GLY A 772 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N GLY A 772 " --> pdb=" O SER A 519 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N TYR A 771 " --> pdb=" O ARG A 536 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ARG A 536 " --> pdb=" O TYR A 771 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N ILE A 773 " --> pdb=" O SER A 534 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 451 through 453 removed outlier: 3.675A pdb=" N MET A 452 " --> pdb=" O LYS A 465 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYS A 465 " --> pdb=" O MET A 452 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 495 through 496 removed outlier: 3.945A pdb=" N ASN A 503 " --> pdb=" O HIS A 495 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 680 through 681 removed outlier: 6.453A pdb=" N GLY A 681 " --> pdb=" O LEU A 741 " (cutoff:3.500A) removed outlier: 8.942A pdb=" N ASP A 743 " --> pdb=" O GLY A 681 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 438 through 443 Processing sheet with id=AA6, first strand: chain 'B' and resid 515 through 521 removed outlier: 8.041A pdb=" N SER B 518 " --> pdb=" O ALA B 773 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ALA B 773 " --> pdb=" O SER B 518 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ILE B 520 " --> pdb=" O GLY B 771 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LYS B 768 " --> pdb=" O TYR B 539 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 679 through 680 removed outlier: 7.418A pdb=" N GLY B 680 " --> pdb=" O LEU B 740 " (cutoff:3.500A) removed outlier: 10.032A pdb=" N ASP B 742 " --> pdb=" O GLY B 680 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N TRP B 741 " --> pdb=" O GLY B 542 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 480 through 486 removed outlier: 3.566A pdb=" N TYR C 485 " --> pdb=" O VAL C 441 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N THR C 443 " --> pdb=" O TYR C 485 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 450 through 452 Processing sheet with id=AB1, first strand: chain 'C' and resid 537 through 539 removed outlier: 4.354A pdb=" N MET C 537 " --> pdb=" O TYR C 770 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N TYR C 770 " --> pdb=" O MET C 537 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LYS C 768 " --> pdb=" O TYR C 539 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 679 through 680 removed outlier: 6.799A pdb=" N GLY C 680 " --> pdb=" O LEU C 740 " (cutoff:3.500A) removed outlier: 9.199A pdb=" N ASP C 742 " --> pdb=" O GLY C 680 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N TRP C 741 " --> pdb=" O GLY C 542 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 482 through 486 removed outlier: 5.966A pdb=" N LEU D 439 " --> pdb=" O GLU D 483 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N TYR D 485 " --> pdb=" O LEU D 439 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N VAL D 441 " --> pdb=" O TYR D 485 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LEU D 515 " --> pdb=" O LYS D 440 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL D 442 " --> pdb=" O LEU D 515 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'D' and resid 451 through 456 removed outlier: 5.599A pdb=" N ALA D 453 " --> pdb=" O LYS D 464 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N LYS D 464 " --> pdb=" O ALA D 453 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N ASN D 455 " --> pdb=" O ARG D 462 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG D 462 " --> pdb=" O ASN D 455 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'D' and resid 537 through 539 removed outlier: 4.481A pdb=" N MET D 537 " --> pdb=" O TYR D 770 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LYS D 768 " --> pdb=" O TYR D 539 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 741 through 742 removed outlier: 3.566A pdb=" N TRP D 741 " --> pdb=" O GLY D 542 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 658 through 659 removed outlier: 3.622A pdb=" N GLN D 820 " --> pdb=" O SER D 659 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 678 through 680 removed outlier: 6.425A pdb=" N SER D 678 " --> pdb=" O ALA D 738 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 587 hydrogen bonds defined for protein. 1731 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: 1.94 Time building geometry restraints manager: 1.40 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: 4093 1.34 - 1.46: 3113 1.46 - 1.58: 5840 1.58 - 1.70: 0 1.70 - 1.82: 92 Bond restraints: 13138 Sorted by residual: bond pdb=" N ARG A 513 " pdb=" CA ARG A 513 " ideal model delta sigma weight residual 1.457 1.478 -0.021 1.29e-02 6.01e+03 2.57e+00 bond pdb=" C GLN B 459 " pdb=" N PRO B 460 " ideal model delta sigma weight residual 1.334 1.349 -0.015 1.11e-02 8.12e+03 1.82e+00 bond pdb=" N ASN D 736 " pdb=" CA ASN D 736 " ideal model delta sigma weight residual 1.457 1.475 -0.017 1.29e-02 6.01e+03 1.77e+00 bond pdb=" C ASN C 697 " pdb=" O ASN C 697 " ideal model delta sigma weight residual 1.249 1.238 0.010 8.50e-03 1.38e+04 1.51e+00 bond pdb=" C GLU B 447 " pdb=" N PRO B 448 " ideal model delta sigma weight residual 1.336 1.350 -0.014 1.20e-02 6.94e+03 1.35e+00 ... (remaining 13133 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.29: 17209 1.29 - 2.58: 475 2.58 - 3.86: 102 3.86 - 5.15: 30 5.15 - 6.44: 8 Bond angle restraints: 17824 Sorted by residual: angle pdb=" C ARG A 513 " pdb=" CA ARG A 513 " pdb=" CB ARG A 513 " ideal model delta sigma weight residual 110.42 116.86 -6.44 1.99e+00 2.53e-01 1.05e+01 angle pdb=" CA ARG B 710 " pdb=" CB ARG B 710 " pdb=" CG ARG B 710 " ideal model delta sigma weight residual 114.10 120.06 -5.96 2.00e+00 2.50e-01 8.88e+00 angle pdb=" C LYS A 552 " pdb=" CA LYS A 552 " pdb=" CB LYS A 552 " ideal model delta sigma weight residual 110.42 115.71 -5.29 1.99e+00 2.53e-01 7.07e+00 angle pdb=" C GLY D 735 " pdb=" N ASN D 736 " pdb=" CA ASN D 736 " ideal model delta sigma weight residual 121.54 126.39 -4.85 1.91e+00 2.74e-01 6.45e+00 angle pdb=" CA TRP A 742 " pdb=" CB TRP A 742 " pdb=" CG TRP A 742 " ideal model delta sigma weight residual 113.60 118.18 -4.58 1.90e+00 2.77e-01 5.82e+00 ... (remaining 17819 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.30: 7055 16.30 - 32.61: 526 32.61 - 48.91: 129 48.91 - 65.21: 22 65.21 - 81.51: 8 Dihedral angle restraints: 7740 sinusoidal: 2981 harmonic: 4759 Sorted by residual: dihedral pdb=" CB CYS B 756 " pdb=" SG CYS B 756 " pdb=" SG CYS B 811 " pdb=" CB CYS B 811 " ideal model delta sinusoidal sigma weight residual 93.00 160.23 -67.23 1 1.00e+01 1.00e-02 5.88e+01 dihedral pdb=" CB CYS C 756 " pdb=" SG CYS C 756 " pdb=" SG CYS C 811 " pdb=" CB CYS C 811 " ideal model delta sinusoidal sigma weight residual 93.00 157.50 -64.50 1 1.00e+01 1.00e-02 5.47e+01 dihedral pdb=" CA ILE A 518 " pdb=" C ILE A 518 " pdb=" N SER A 519 " pdb=" CA SER A 519 " ideal model delta harmonic sigma weight residual -180.00 -159.22 -20.78 0 5.00e+00 4.00e-02 1.73e+01 ... (remaining 7737 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1462 0.036 - 0.072: 403 0.072 - 0.108: 128 0.108 - 0.144: 29 0.144 - 0.180: 3 Chirality restraints: 2025 Sorted by residual: chirality pdb=" CG LEU D 434 " pdb=" CB LEU D 434 " pdb=" CD1 LEU D 434 " pdb=" CD2 LEU D 434 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 8.08e-01 chirality pdb=" CA ARG B 787 " pdb=" N ARG B 787 " pdb=" C ARG B 787 " pdb=" CB ARG B 787 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.76e-01 chirality pdb=" CA ASN D 736 " pdb=" N ASN D 736 " pdb=" C ASN D 736 " pdb=" CB ASN D 736 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.43e-01 ... (remaining 2022 not shown) Planarity restraints: 2237 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 742 " -0.026 2.00e-02 2.50e+03 2.37e-02 1.40e+01 pdb=" CG TRP A 742 " 0.064 2.00e-02 2.50e+03 pdb=" CD1 TRP A 742 " -0.029 2.00e-02 2.50e+03 pdb=" CD2 TRP A 742 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 742 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 742 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 742 " -0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 742 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 742 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A 742 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN D 724 " 0.036 5.00e-02 4.00e+02 5.44e-02 4.73e+00 pdb=" N PRO D 725 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO D 725 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO D 725 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU B 447 " -0.031 5.00e-02 4.00e+02 4.65e-02 3.47e+00 pdb=" N PRO B 448 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO B 448 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 448 " -0.026 5.00e-02 4.00e+02 ... (remaining 2234 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 476 2.72 - 3.27: 13328 3.27 - 3.81: 20307 3.81 - 4.36: 23811 4.36 - 4.90: 39881 Nonbonded interactions: 97803 Sorted by model distance: nonbonded pdb=" NZ LYS B 440 " pdb=" O ARG B 512 " model vdw 2.177 3.120 nonbonded pdb=" OD2 ASP B 469 " pdb=" NE1 TRP B 804 " model vdw 2.219 3.120 nonbonded pdb=" O THR C 814 " pdb=" OG SER C 818 " model vdw 2.238 3.040 nonbonded pdb=" OG1 THR C 523 " pdb=" OE1 GLU C 525 " model vdw 2.266 3.040 nonbonded pdb=" NH1 ARG D 692 " pdb=" OG1 THR D 696 " model vdw 2.276 3.120 ... (remaining 97798 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' and resid 431 through 853) selection = (chain 'B' and resid 430 through 852) selection = (chain 'C' and (resid 430 through 588 or resid 604 through 852)) selection = (chain 'D' and resid 430 through 852) } 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: 2.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.510 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6363 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 : 0.002 0.033 13142 Z= 0.118 Angle : 0.557 6.439 17832 Z= 0.310 Chirality : 0.039 0.180 2025 Planarity : 0.004 0.054 2237 Dihedral : 12.504 81.514 4670 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 0.00 % Allowed : 0.07 % Favored : 99.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.20), residues: 1633 helix: 0.75 (0.18), residues: 806 sheet: -0.35 (0.50), residues: 100 loop : -1.53 (0.20), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 787 TYR 0.015 0.001 TYR A 691 PHE 0.019 0.001 PHE A 582 TRP 0.064 0.001 TRP A 742 HIS 0.003 0.000 HIS B 816 Details of bonding type rmsd covalent geometry : bond 0.00219 (13138) covalent geometry : angle 0.55682 (17824) SS BOND : bond 0.00182 ( 4) SS BOND : angle 0.65030 ( 8) hydrogen bonds : bond 0.21458 ( 587) hydrogen bonds : angle 6.48674 ( 1731) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 347 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 505 MET cc_start: 0.6071 (mmm) cc_final: 0.5545 (mtp) REVERT: A 619 GLN cc_start: 0.6197 (mm-40) cc_final: 0.5543 (tm-30) REVERT: A 742 TRP cc_start: 0.6027 (t-100) cc_final: 0.5584 (t-100) REVERT: B 535 ARG cc_start: 0.7298 (mtp180) cc_final: 0.4851 (ttp80) REVERT: B 649 THR cc_start: 0.8225 (t) cc_final: 0.6993 (p) REVERT: C 661 MET cc_start: 0.6977 (ttm) cc_final: 0.6764 (ttp) REVERT: C 724 ASN cc_start: 0.8182 (m-40) cc_final: 0.7316 (m110) REVERT: C 787 ARG cc_start: 0.7598 (mmt90) cc_final: 0.7236 (tpp80) outliers start: 0 outliers final: 0 residues processed: 347 average time/residue: 0.1326 time to fit residues: 63.4433 Evaluate side-chains 187 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 187 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 20.0000 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 2.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 620 GLN ** B 674 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 720 ASN B 802 GLN B 829 HIS C 459 GLN C 502 ASN C 584 ASN C 829 HIS D 495 GLN D 587 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4506 r_free = 0.4506 target = 0.219744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.184805 restraints weight = 17455.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.182048 restraints weight = 25776.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.179278 restraints weight = 21667.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.179166 restraints weight = 21275.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.178568 restraints weight = 19993.827| |-----------------------------------------------------------------------------| r_work (final): 0.4129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6845 moved from start: 0.3272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.073 13142 Z= 0.270 Angle : 0.727 7.221 17832 Z= 0.394 Chirality : 0.048 0.190 2025 Planarity : 0.005 0.049 2237 Dihedral : 4.556 21.876 1770 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.46 % Allowed : 11.28 % Favored : 86.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.19), residues: 1633 helix: 0.31 (0.17), residues: 849 sheet: -0.36 (0.48), residues: 111 loop : -1.67 (0.21), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 660 TYR 0.041 0.003 TYR A 691 PHE 0.023 0.002 PHE D 561 TRP 0.029 0.003 TRP D 804 HIS 0.008 0.001 HIS C 829 Details of bonding type rmsd covalent geometry : bond 0.00652 (13138) covalent geometry : angle 0.72683 (17824) SS BOND : bond 0.00226 ( 4) SS BOND : angle 0.44398 ( 8) hydrogen bonds : bond 0.06709 ( 587) hydrogen bonds : angle 5.23135 ( 1731) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 204 time to evaluate : 0.499 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 505 MET cc_start: 0.6350 (mmm) cc_final: 0.5995 (mtp) REVERT: A 619 GLN cc_start: 0.7038 (mm-40) cc_final: 0.5932 (tm-30) REVERT: A 730 ILE cc_start: 0.5951 (pt) cc_final: 0.5649 (mt) REVERT: C 430 MET cc_start: 0.5790 (ppp) cc_final: 0.5148 (mtt) REVERT: D 430 MET cc_start: 0.6620 (ppp) cc_final: 0.5559 (ttt) REVERT: D 445 LEU cc_start: 0.7751 (mt) cc_final: 0.7431 (mp) outliers start: 34 outliers final: 21 residues processed: 227 average time/residue: 0.1160 time to fit residues: 38.0284 Evaluate side-chains 182 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 161 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 620 GLN Chi-restraints excluded: chain A residue 728 GLU Chi-restraints excluded: chain A residue 759 VAL Chi-restraints excluded: chain A residue 767 SER Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 802 GLN Chi-restraints excluded: chain C residue 507 GLU Chi-restraints excluded: chain C residue 530 VAL Chi-restraints excluded: chain C residue 541 VAL Chi-restraints excluded: chain C residue 579 LEU Chi-restraints excluded: chain C residue 662 ASP Chi-restraints excluded: chain C residue 842 LEU Chi-restraints excluded: chain D residue 441 VAL Chi-restraints excluded: chain D residue 509 ILE Chi-restraints excluded: chain D residue 569 ILE Chi-restraints excluded: chain D residue 582 VAL Chi-restraints excluded: chain D residue 628 VAL Chi-restraints excluded: chain D residue 830 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 62 optimal weight: 1.9990 chunk 101 optimal weight: 0.5980 chunk 33 optimal weight: 4.9990 chunk 66 optimal weight: 0.7980 chunk 144 optimal weight: 1.9990 chunk 135 optimal weight: 0.4980 chunk 121 optimal weight: 7.9990 chunk 48 optimal weight: 0.0070 chunk 68 optimal weight: 0.6980 chunk 79 optimal weight: 0.7980 chunk 53 optimal weight: 0.8980 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 620 GLN A 808 HIS B 829 HIS C 584 ASN D 495 GLN D 587 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4546 r_free = 0.4546 target = 0.224526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.190020 restraints weight = 17577.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.179603 restraints weight = 26488.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.178180 restraints weight = 24091.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.178199 restraints weight = 24860.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.179254 restraints weight = 19383.221| |-----------------------------------------------------------------------------| r_work (final): 0.4100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6849 moved from start: 0.3563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13142 Z= 0.126 Angle : 0.561 8.413 17832 Z= 0.300 Chirality : 0.041 0.146 2025 Planarity : 0.004 0.043 2237 Dihedral : 4.210 19.447 1770 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.17 % Allowed : 14.32 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.20), residues: 1633 helix: 0.69 (0.18), residues: 845 sheet: -0.12 (0.50), residues: 111 loop : -1.58 (0.21), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 667 TYR 0.030 0.001 TYR C 485 PHE 0.021 0.001 PHE D 480 TRP 0.047 0.002 TRP B 804 HIS 0.003 0.001 HIS A 808 Details of bonding type rmsd covalent geometry : bond 0.00277 (13138) covalent geometry : angle 0.56092 (17824) SS BOND : bond 0.00117 ( 4) SS BOND : angle 0.26449 ( 8) hydrogen bonds : bond 0.04646 ( 587) hydrogen bonds : angle 4.67804 ( 1731) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 184 time to evaluate : 0.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 505 MET cc_start: 0.6139 (mmm) cc_final: 0.5694 (mtp) REVERT: A 698 ASN cc_start: 0.6383 (t0) cc_final: 0.5851 (p0) REVERT: B 649 THR cc_start: 0.8428 (t) cc_final: 0.7484 (p) REVERT: B 812 ASP cc_start: 0.4698 (t70) cc_final: 0.4479 (t70) REVERT: D 451 MET cc_start: 0.5638 (ptt) cc_final: 0.5359 (ptt) REVERT: D 724 ASN cc_start: 0.6140 (t0) cc_final: 0.5896 (t0) outliers start: 30 outliers final: 17 residues processed: 197 average time/residue: 0.1059 time to fit residues: 31.4017 Evaluate side-chains 177 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 160 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 486 TYR Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 759 VAL Chi-restraints excluded: chain A residue 767 SER Chi-restraints excluded: chain A residue 783 ASP Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 494 HIS Chi-restraints excluded: chain B residue 661 MET Chi-restraints excluded: chain B residue 672 SER Chi-restraints excluded: chain B residue 797 LEU Chi-restraints excluded: chain C residue 441 VAL Chi-restraints excluded: chain C residue 507 GLU Chi-restraints excluded: chain C residue 530 VAL Chi-restraints excluded: chain C residue 579 LEU Chi-restraints excluded: chain D residue 441 VAL Chi-restraints excluded: chain D residue 760 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 68 optimal weight: 0.3980 chunk 58 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 15 optimal weight: 6.9990 chunk 65 optimal weight: 10.0000 chunk 35 optimal weight: 6.9990 chunk 140 optimal weight: 3.9990 chunk 125 optimal weight: 8.9990 chunk 143 optimal weight: 2.9990 overall best weight: 2.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 620 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 808 HIS D 495 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4479 r_free = 0.4479 target = 0.217027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.181540 restraints weight = 17582.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.173441 restraints weight = 25511.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.170109 restraints weight = 26395.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.169933 restraints weight = 24665.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.169630 restraints weight = 21571.723| |-----------------------------------------------------------------------------| r_work (final): 0.4038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6992 moved from start: 0.4263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 13142 Z= 0.244 Angle : 0.668 8.588 17832 Z= 0.360 Chirality : 0.046 0.165 2025 Planarity : 0.004 0.059 2237 Dihedral : 4.637 22.517 1770 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 3.04 % Allowed : 16.12 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.20), residues: 1633 helix: 0.26 (0.17), residues: 856 sheet: -0.27 (0.50), residues: 111 loop : -1.66 (0.21), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 811 TYR 0.024 0.003 TYR C 536 PHE 0.026 0.002 PHE B 784 TRP 0.038 0.002 TRP B 804 HIS 0.006 0.001 HIS D 807 Details of bonding type rmsd covalent geometry : bond 0.00589 (13138) covalent geometry : angle 0.66832 (17824) SS BOND : bond 0.00227 ( 4) SS BOND : angle 0.42145 ( 8) hydrogen bonds : bond 0.06255 ( 587) hydrogen bonds : angle 4.91879 ( 1731) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 158 time to evaluate : 0.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 505 MET cc_start: 0.6608 (mmm) cc_final: 0.6282 (mtp) REVERT: A 556 PHE cc_start: 0.7828 (m-80) cc_final: 0.7610 (m-80) REVERT: A 692 PHE cc_start: 0.6905 (t80) cc_final: 0.6544 (t80) REVERT: A 693 ARG cc_start: 0.7049 (tpm170) cc_final: 0.6708 (tpp-160) REVERT: B 486 GLN cc_start: 0.7636 (OUTLIER) cc_final: 0.7178 (mm-40) REVERT: C 661 MET cc_start: 0.6715 (ttm) cc_final: 0.6487 (ttm) REVERT: C 707 GLU cc_start: 0.7489 (OUTLIER) cc_final: 0.7177 (tm-30) REVERT: C 720 ASN cc_start: 0.5412 (p0) cc_final: 0.4951 (m-40) REVERT: C 787 ARG cc_start: 0.7597 (mmt90) cc_final: 0.7284 (tpp80) REVERT: D 445 LEU cc_start: 0.7571 (mt) cc_final: 0.7230 (mp) REVERT: D 451 MET cc_start: 0.6248 (ptt) cc_final: 0.5581 (ptt) outliers start: 42 outliers final: 28 residues processed: 183 average time/residue: 0.1058 time to fit residues: 28.9494 Evaluate side-chains 171 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 141 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain A residue 486 TYR Chi-restraints excluded: chain A residue 515 ASP Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 659 VAL Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 759 VAL Chi-restraints excluded: chain A residue 767 SER Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 486 GLN Chi-restraints excluded: chain B residue 494 HIS Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain B residue 672 SER Chi-restraints excluded: chain B residue 797 LEU Chi-restraints excluded: chain C residue 507 GLU Chi-restraints excluded: chain C residue 530 VAL Chi-restraints excluded: chain C residue 541 VAL Chi-restraints excluded: chain C residue 579 LEU Chi-restraints excluded: chain C residue 687 VAL Chi-restraints excluded: chain C residue 707 GLU Chi-restraints excluded: chain C residue 747 GLU Chi-restraints excluded: chain C residue 842 LEU Chi-restraints excluded: chain D residue 441 VAL Chi-restraints excluded: chain D residue 609 ILE Chi-restraints excluded: chain D residue 681 THR Chi-restraints excluded: chain D residue 760 VAL Chi-restraints excluded: chain D residue 830 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 162 optimal weight: 0.8980 chunk 111 optimal weight: 0.5980 chunk 60 optimal weight: 0.5980 chunk 101 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 82 optimal weight: 0.7980 chunk 78 optimal weight: 0.9980 chunk 80 optimal weight: 0.6980 chunk 36 optimal weight: 0.9980 chunk 114 optimal weight: 1.9990 chunk 151 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 588 GLN ** A 620 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 808 HIS D 495 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4520 r_free = 0.4520 target = 0.221876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.187564 restraints weight = 17526.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.179368 restraints weight = 26057.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.178630 restraints weight = 24193.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.178293 restraints weight = 23011.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.178616 restraints weight = 19153.452| |-----------------------------------------------------------------------------| r_work (final): 0.4122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6844 moved from start: 0.4340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13142 Z= 0.124 Angle : 0.541 7.940 17832 Z= 0.286 Chirality : 0.041 0.142 2025 Planarity : 0.003 0.040 2237 Dihedral : 4.267 20.672 1770 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.02 % Allowed : 18.66 % Favored : 79.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.20), residues: 1633 helix: 0.72 (0.18), residues: 846 sheet: -0.15 (0.54), residues: 103 loop : -1.59 (0.21), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 787 TYR 0.013 0.001 TYR B 679 PHE 0.015 0.001 PHE B 784 TRP 0.027 0.002 TRP B 804 HIS 0.003 0.001 HIS C 829 Details of bonding type rmsd covalent geometry : bond 0.00284 (13138) covalent geometry : angle 0.54060 (17824) SS BOND : bond 0.00112 ( 4) SS BOND : angle 0.40681 ( 8) hydrogen bonds : bond 0.04406 ( 587) hydrogen bonds : angle 4.49149 ( 1731) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 165 time to evaluate : 0.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 505 MET cc_start: 0.6609 (mmm) cc_final: 0.6272 (mtp) REVERT: A 547 LYS cc_start: 0.6435 (tptm) cc_final: 0.5357 (ptmt) REVERT: A 556 PHE cc_start: 0.7819 (m-80) cc_final: 0.7605 (m-80) REVERT: A 587 ILE cc_start: 0.8516 (mm) cc_final: 0.8275 (tt) REVERT: A 672 LEU cc_start: 0.7767 (tp) cc_final: 0.7524 (tt) REVERT: A 697 THR cc_start: 0.6958 (OUTLIER) cc_final: 0.6454 (m) REVERT: B 486 GLN cc_start: 0.7408 (OUTLIER) cc_final: 0.7101 (mm-40) REVERT: B 649 THR cc_start: 0.8795 (t) cc_final: 0.7913 (p) REVERT: C 689 GLU cc_start: 0.6728 (OUTLIER) cc_final: 0.6043 (tp30) REVERT: C 707 GLU cc_start: 0.7640 (OUTLIER) cc_final: 0.7320 (tm-30) REVERT: C 787 ARG cc_start: 0.7439 (mmt90) cc_final: 0.7156 (tpp80) REVERT: D 445 LEU cc_start: 0.7658 (mt) cc_final: 0.7289 (mp) REVERT: D 451 MET cc_start: 0.6245 (ptt) cc_final: 0.5635 (ptt) REVERT: D 724 ASN cc_start: 0.6396 (t0) cc_final: 0.6183 (t0) outliers start: 28 outliers final: 20 residues processed: 179 average time/residue: 0.1059 time to fit residues: 28.3351 Evaluate side-chains 178 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 154 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain A residue 659 VAL Chi-restraints excluded: chain A residue 697 THR Chi-restraints excluded: chain A residue 759 VAL Chi-restraints excluded: chain A residue 767 SER Chi-restraints excluded: chain A residue 783 ASP Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain B residue 486 GLN Chi-restraints excluded: chain B residue 494 HIS Chi-restraints excluded: chain B residue 672 SER Chi-restraints excluded: chain B residue 797 LEU Chi-restraints excluded: chain C residue 507 GLU Chi-restraints excluded: chain C residue 530 VAL Chi-restraints excluded: chain C residue 579 LEU Chi-restraints excluded: chain C residue 625 VAL Chi-restraints excluded: chain C residue 689 GLU Chi-restraints excluded: chain C residue 707 GLU Chi-restraints excluded: chain C residue 747 GLU Chi-restraints excluded: chain C residue 842 LEU Chi-restraints excluded: chain D residue 441 VAL Chi-restraints excluded: chain D residue 495 GLN Chi-restraints excluded: chain D residue 514 ASP Chi-restraints excluded: chain D residue 609 ILE Chi-restraints excluded: chain D residue 760 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 152 optimal weight: 3.9990 chunk 75 optimal weight: 0.0970 chunk 52 optimal weight: 0.5980 chunk 154 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 127 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 155 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 148 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 620 GLN A 808 HIS ** B 619 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 776 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4535 r_free = 0.4535 target = 0.223062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.191277 restraints weight = 17356.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.178292 restraints weight = 23344.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.177850 restraints weight = 25530.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.178974 restraints weight = 25058.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.178775 restraints weight = 19500.018| |-----------------------------------------------------------------------------| r_work (final): 0.4115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6879 moved from start: 0.4501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13142 Z= 0.126 Angle : 0.540 8.622 17832 Z= 0.285 Chirality : 0.041 0.140 2025 Planarity : 0.004 0.052 2237 Dihedral : 4.143 19.233 1770 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.39 % Allowed : 18.73 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.20), residues: 1633 helix: 0.91 (0.18), residues: 844 sheet: -0.09 (0.55), residues: 103 loop : -1.58 (0.21), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 811 TYR 0.018 0.001 TYR B 679 PHE 0.019 0.001 PHE A 692 TRP 0.045 0.002 TRP D 804 HIS 0.003 0.001 HIS B 816 Details of bonding type rmsd covalent geometry : bond 0.00291 (13138) covalent geometry : angle 0.53979 (17824) SS BOND : bond 0.00150 ( 4) SS BOND : angle 0.24045 ( 8) hydrogen bonds : bond 0.04288 ( 587) hydrogen bonds : angle 4.41740 ( 1731) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 163 time to evaluate : 0.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 505 MET cc_start: 0.6603 (mmm) cc_final: 0.6278 (mtp) REVERT: A 516 LEU cc_start: 0.8383 (OUTLIER) cc_final: 0.7786 (pt) REVERT: A 556 PHE cc_start: 0.7834 (m-80) cc_final: 0.7619 (m-80) REVERT: A 587 ILE cc_start: 0.8459 (mm) cc_final: 0.8242 (tt) REVERT: A 672 LEU cc_start: 0.7679 (tp) cc_final: 0.7436 (tt) REVERT: A 690 GLU cc_start: 0.7370 (mp0) cc_final: 0.7075 (tp30) REVERT: B 486 GLN cc_start: 0.7402 (OUTLIER) cc_final: 0.7142 (mm-40) REVERT: B 504 MET cc_start: 0.4687 (mmt) cc_final: 0.4370 (mmt) REVERT: B 649 THR cc_start: 0.8816 (t) cc_final: 0.7699 (p) REVERT: C 689 GLU cc_start: 0.6797 (OUTLIER) cc_final: 0.6074 (tp30) REVERT: C 707 GLU cc_start: 0.7675 (OUTLIER) cc_final: 0.7350 (tm-30) REVERT: C 720 ASN cc_start: 0.5182 (p0) cc_final: 0.4388 (m-40) REVERT: C 787 ARG cc_start: 0.7401 (mmt90) cc_final: 0.7133 (tpp80) REVERT: D 430 MET cc_start: 0.5094 (OUTLIER) cc_final: 0.4852 (ttt) REVERT: D 445 LEU cc_start: 0.7610 (mt) cc_final: 0.7282 (mp) REVERT: D 451 MET cc_start: 0.6321 (ptt) cc_final: 0.5443 (ptt) REVERT: D 724 ASN cc_start: 0.6424 (t0) cc_final: 0.6172 (t0) outliers start: 33 outliers final: 22 residues processed: 182 average time/residue: 0.1019 time to fit residues: 27.9182 Evaluate side-chains 182 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 155 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 620 GLN Chi-restraints excluded: chain A residue 659 VAL Chi-restraints excluded: chain A residue 759 VAL Chi-restraints excluded: chain A residue 767 SER Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 486 GLN Chi-restraints excluded: chain B residue 494 HIS Chi-restraints excluded: chain B residue 687 VAL Chi-restraints excluded: chain B residue 797 LEU Chi-restraints excluded: chain C residue 507 GLU Chi-restraints excluded: chain C residue 530 VAL Chi-restraints excluded: chain C residue 579 LEU Chi-restraints excluded: chain C residue 625 VAL Chi-restraints excluded: chain C residue 689 GLU Chi-restraints excluded: chain C residue 707 GLU Chi-restraints excluded: chain C residue 747 GLU Chi-restraints excluded: chain C residue 842 LEU Chi-restraints excluded: chain D residue 430 MET Chi-restraints excluded: chain D residue 441 VAL Chi-restraints excluded: chain D residue 514 ASP Chi-restraints excluded: chain D residue 609 ILE Chi-restraints excluded: chain D residue 760 VAL Chi-restraints excluded: chain D residue 783 LEU Chi-restraints excluded: chain D residue 830 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 125 optimal weight: 0.8980 chunk 131 optimal weight: 0.3980 chunk 116 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 79 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 156 optimal weight: 0.0670 chunk 66 optimal weight: 5.9990 chunk 104 optimal weight: 0.9980 chunk 136 optimal weight: 0.8980 chunk 97 optimal weight: 6.9990 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 620 GLN ** B 619 GLN ** 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 = 0.4530 r_free = 0.4530 target = 0.222615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.187852 restraints weight = 17400.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.177588 restraints weight = 23133.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.174697 restraints weight = 24273.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.176175 restraints weight = 21732.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.174948 restraints weight = 17825.663| |-----------------------------------------------------------------------------| r_work (final): 0.4087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6900 moved from start: 0.4650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13142 Z= 0.120 Angle : 0.549 11.061 17832 Z= 0.284 Chirality : 0.041 0.220 2025 Planarity : 0.004 0.071 2237 Dihedral : 4.053 19.212 1770 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.31 % Allowed : 19.60 % Favored : 78.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.20), residues: 1633 helix: 1.02 (0.18), residues: 842 sheet: -0.07 (0.55), residues: 103 loop : -1.55 (0.21), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 811 TYR 0.020 0.001 TYR D 679 PHE 0.014 0.001 PHE A 692 TRP 0.035 0.001 TRP A 710 HIS 0.005 0.001 HIS B 816 Details of bonding type rmsd covalent geometry : bond 0.00276 (13138) covalent geometry : angle 0.54922 (17824) SS BOND : bond 0.00174 ( 4) SS BOND : angle 0.27085 ( 8) hydrogen bonds : bond 0.04048 ( 587) hydrogen bonds : angle 4.36590 ( 1731) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 160 time to evaluate : 0.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 505 MET cc_start: 0.6593 (OUTLIER) cc_final: 0.6323 (mtp) REVERT: A 516 LEU cc_start: 0.8386 (OUTLIER) cc_final: 0.7780 (pt) REVERT: A 556 PHE cc_start: 0.7842 (m-80) cc_final: 0.7601 (m-80) REVERT: A 587 ILE cc_start: 0.8624 (mm) cc_final: 0.8419 (tt) REVERT: A 693 ARG cc_start: 0.6911 (tpm170) cc_final: 0.6665 (tpp-160) REVERT: B 486 GLN cc_start: 0.7314 (OUTLIER) cc_final: 0.7096 (mm-40) REVERT: B 504 MET cc_start: 0.4669 (mmt) cc_final: 0.4315 (mmt) REVERT: B 527 GLU cc_start: 0.8082 (tm-30) cc_final: 0.7771 (tm-30) REVERT: B 649 THR cc_start: 0.8741 (t) cc_final: 0.7618 (p) REVERT: B 828 LEU cc_start: 0.7870 (OUTLIER) cc_final: 0.7637 (tt) REVERT: C 689 GLU cc_start: 0.6814 (OUTLIER) cc_final: 0.6095 (tp30) REVERT: C 707 GLU cc_start: 0.7699 (OUTLIER) cc_final: 0.7375 (tm-30) REVERT: C 720 ASN cc_start: 0.4903 (p0) cc_final: 0.4424 (m-40) REVERT: C 787 ARG cc_start: 0.7410 (mmt90) cc_final: 0.7113 (tpp80) REVERT: D 445 LEU cc_start: 0.7590 (mt) cc_final: 0.7265 (mp) REVERT: D 451 MET cc_start: 0.6178 (ptt) cc_final: 0.5306 (ptt) REVERT: D 724 ASN cc_start: 0.6320 (t0) cc_final: 0.6083 (t0) REVERT: D 792 GLN cc_start: 0.7296 (tp-100) cc_final: 0.6783 (mt0) outliers start: 32 outliers final: 18 residues processed: 178 average time/residue: 0.1058 time to fit residues: 28.0553 Evaluate side-chains 178 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 154 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain A residue 505 MET Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 620 GLN Chi-restraints excluded: chain A residue 659 VAL Chi-restraints excluded: chain A residue 759 VAL Chi-restraints excluded: chain A residue 767 SER Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 486 GLN Chi-restraints excluded: chain B residue 494 HIS Chi-restraints excluded: chain B residue 687 VAL Chi-restraints excluded: chain B residue 797 LEU Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain C residue 530 VAL Chi-restraints excluded: chain C residue 579 LEU Chi-restraints excluded: chain C residue 625 VAL Chi-restraints excluded: chain C residue 689 GLU Chi-restraints excluded: chain C residue 707 GLU Chi-restraints excluded: chain C residue 747 GLU Chi-restraints excluded: chain C residue 842 LEU Chi-restraints excluded: chain D residue 441 VAL Chi-restraints excluded: chain D residue 760 VAL Chi-restraints excluded: chain D residue 783 LEU Chi-restraints excluded: chain D residue 830 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 74 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 22 optimal weight: 5.9990 chunk 31 optimal weight: 0.5980 chunk 97 optimal weight: 5.9990 chunk 64 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 76 optimal weight: 7.9990 chunk 159 optimal weight: 2.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 620 GLN ** B 619 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 495 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4501 r_free = 0.4501 target = 0.218841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.182676 restraints weight = 17381.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.171536 restraints weight = 24949.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.169683 restraints weight = 24332.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.170006 restraints weight = 25247.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.170626 restraints weight = 19143.974| |-----------------------------------------------------------------------------| r_work (final): 0.4019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7027 moved from start: 0.4932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 13142 Z= 0.204 Angle : 0.629 9.863 17832 Z= 0.332 Chirality : 0.044 0.251 2025 Planarity : 0.004 0.045 2237 Dihedral : 4.380 21.148 1770 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.96 % Allowed : 19.16 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.20), residues: 1633 helix: 0.67 (0.17), residues: 851 sheet: -0.29 (0.52), residues: 111 loop : -1.72 (0.21), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 811 TYR 0.025 0.002 TYR B 679 PHE 0.024 0.002 PHE A 692 TRP 0.038 0.002 TRP A 710 HIS 0.004 0.001 HIS B 816 Details of bonding type rmsd covalent geometry : bond 0.00498 (13138) covalent geometry : angle 0.62954 (17824) SS BOND : bond 0.00197 ( 4) SS BOND : angle 0.30296 ( 8) hydrogen bonds : bond 0.05499 ( 587) hydrogen bonds : angle 4.64476 ( 1731) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 154 time to evaluate : 0.476 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 505 MET cc_start: 0.6760 (OUTLIER) cc_final: 0.6493 (mtp) REVERT: A 516 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.7919 (pt) REVERT: A 547 LYS cc_start: 0.6488 (tptm) cc_final: 0.5419 (ptmt) REVERT: A 556 PHE cc_start: 0.7891 (m-80) cc_final: 0.7682 (m-80) REVERT: A 587 ILE cc_start: 0.8740 (mm) cc_final: 0.8474 (tt) REVERT: A 690 GLU cc_start: 0.7190 (mp0) cc_final: 0.6747 (tp30) REVERT: A 693 ARG cc_start: 0.6991 (tpm170) cc_final: 0.6685 (tpp-160) REVERT: B 486 GLN cc_start: 0.7646 (OUTLIER) cc_final: 0.7289 (mm-40) REVERT: B 504 MET cc_start: 0.4657 (mmt) cc_final: 0.4374 (mmt) REVERT: B 579 LEU cc_start: 0.7701 (OUTLIER) cc_final: 0.7318 (tt) REVERT: B 587 GLN cc_start: 0.6375 (tp40) cc_final: 0.5588 (pt0) REVERT: C 430 MET cc_start: 0.5935 (ppp) cc_final: 0.5719 (ppp) REVERT: C 689 GLU cc_start: 0.6834 (OUTLIER) cc_final: 0.6106 (tp30) REVERT: C 707 GLU cc_start: 0.7803 (OUTLIER) cc_final: 0.7577 (tm-30) REVERT: C 787 ARG cc_start: 0.7443 (mmt90) cc_final: 0.7171 (tpp80) REVERT: D 445 LEU cc_start: 0.7582 (mt) cc_final: 0.7253 (mp) REVERT: D 451 MET cc_start: 0.6283 (ptt) cc_final: 0.5298 (ptt) REVERT: D 792 GLN cc_start: 0.7292 (tp-100) cc_final: 0.6884 (mt0) outliers start: 41 outliers final: 23 residues processed: 181 average time/residue: 0.1078 time to fit residues: 28.8829 Evaluate side-chains 173 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 144 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain A residue 505 MET Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 620 GLN Chi-restraints excluded: chain A residue 659 VAL Chi-restraints excluded: chain A residue 668 THR Chi-restraints excluded: chain A residue 691 TYR Chi-restraints excluded: chain A residue 759 VAL Chi-restraints excluded: chain A residue 767 SER Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 486 GLN Chi-restraints excluded: chain B residue 494 HIS Chi-restraints excluded: chain B residue 579 LEU Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain B residue 687 VAL Chi-restraints excluded: chain B residue 797 LEU Chi-restraints excluded: chain C residue 530 VAL Chi-restraints excluded: chain C residue 579 LEU Chi-restraints excluded: chain C residue 625 VAL Chi-restraints excluded: chain C residue 689 GLU Chi-restraints excluded: chain C residue 707 GLU Chi-restraints excluded: chain C residue 747 GLU Chi-restraints excluded: chain C residue 842 LEU Chi-restraints excluded: chain D residue 441 VAL Chi-restraints excluded: chain D residue 495 GLN Chi-restraints excluded: chain D residue 760 VAL Chi-restraints excluded: chain D residue 783 LEU Chi-restraints excluded: chain D residue 830 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 134 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 chunk 121 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 39 optimal weight: 3.9990 chunk 140 optimal weight: 1.9990 chunk 31 optimal weight: 6.9990 chunk 116 optimal weight: 2.9990 chunk 75 optimal weight: 7.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 585 ASN A 620 GLN ** B 619 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4509 r_free = 0.4509 target = 0.219786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.183582 restraints weight = 17494.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.169564 restraints weight = 25692.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.168801 restraints weight = 25287.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.168150 restraints weight = 24491.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.168854 restraints weight = 19760.616| |-----------------------------------------------------------------------------| r_work (final): 0.3991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7068 moved from start: 0.5074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13142 Z= 0.174 Angle : 0.618 8.727 17832 Z= 0.324 Chirality : 0.044 0.246 2025 Planarity : 0.004 0.081 2237 Dihedral : 4.357 21.317 1770 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.39 % Allowed : 19.81 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.20), residues: 1633 helix: 0.68 (0.17), residues: 853 sheet: -0.28 (0.54), residues: 101 loop : -1.72 (0.21), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 811 TYR 0.033 0.002 TYR D 679 PHE 0.022 0.002 PHE A 582 TRP 0.060 0.002 TRP B 804 HIS 0.006 0.001 HIS A 607 Details of bonding type rmsd covalent geometry : bond 0.00420 (13138) covalent geometry : angle 0.61854 (17824) SS BOND : bond 0.00204 ( 4) SS BOND : angle 0.37426 ( 8) hydrogen bonds : bond 0.05088 ( 587) hydrogen bonds : angle 4.64254 ( 1731) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 158 time to evaluate : 0.421 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 505 MET cc_start: 0.6712 (OUTLIER) cc_final: 0.6436 (mtp) REVERT: A 516 LEU cc_start: 0.8506 (OUTLIER) cc_final: 0.7889 (pt) REVERT: A 587 ILE cc_start: 0.8759 (mm) cc_final: 0.8462 (tt) REVERT: A 690 GLU cc_start: 0.7272 (mp0) cc_final: 0.6654 (tp30) REVERT: A 693 ARG cc_start: 0.7123 (tpm170) cc_final: 0.6763 (tpp-160) REVERT: B 451 MET cc_start: 0.6454 (pmm) cc_final: 0.6127 (pmm) REVERT: B 486 GLN cc_start: 0.7570 (OUTLIER) cc_final: 0.7251 (mm-40) REVERT: B 504 MET cc_start: 0.4626 (mmt) cc_final: 0.4319 (mmt) REVERT: B 579 LEU cc_start: 0.7699 (OUTLIER) cc_final: 0.7297 (tt) REVERT: B 587 GLN cc_start: 0.6494 (tp40) cc_final: 0.5592 (pt0) REVERT: B 649 THR cc_start: 0.8794 (OUTLIER) cc_final: 0.8097 (p) REVERT: C 586 ILE cc_start: 0.8777 (mm) cc_final: 0.8396 (tt) REVERT: C 634 MET cc_start: 0.8539 (mmm) cc_final: 0.8143 (mmt) REVERT: C 689 GLU cc_start: 0.7025 (OUTLIER) cc_final: 0.6047 (tp30) REVERT: C 707 GLU cc_start: 0.8107 (OUTLIER) cc_final: 0.7854 (tm-30) REVERT: C 787 ARG cc_start: 0.7423 (mmt90) cc_final: 0.7184 (tpp80) REVERT: D 445 LEU cc_start: 0.7564 (mt) cc_final: 0.7235 (mp) REVERT: D 451 MET cc_start: 0.6172 (ptt) cc_final: 0.5280 (ptt) REVERT: D 683 ARG cc_start: 0.5680 (tpm170) cc_final: 0.4172 (ptp-170) REVERT: D 792 GLN cc_start: 0.7232 (tp-100) cc_final: 0.6824 (mt0) outliers start: 33 outliers final: 25 residues processed: 175 average time/residue: 0.1107 time to fit residues: 28.5209 Evaluate side-chains 179 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 147 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain A residue 505 MET Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 610 ILE Chi-restraints excluded: chain A residue 620 GLN Chi-restraints excluded: chain A residue 659 VAL Chi-restraints excluded: chain A residue 668 THR Chi-restraints excluded: chain A residue 691 TYR Chi-restraints excluded: chain A residue 759 VAL Chi-restraints excluded: chain A residue 767 SER Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 486 GLN Chi-restraints excluded: chain B residue 494 HIS Chi-restraints excluded: chain B residue 579 LEU Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain B residue 687 VAL Chi-restraints excluded: chain B residue 797 LEU Chi-restraints excluded: chain C residue 530 VAL Chi-restraints excluded: chain C residue 579 LEU Chi-restraints excluded: chain C residue 625 VAL Chi-restraints excluded: chain C residue 687 VAL Chi-restraints excluded: chain C residue 689 GLU Chi-restraints excluded: chain C residue 707 GLU Chi-restraints excluded: chain C residue 720 ASN Chi-restraints excluded: chain C residue 747 GLU Chi-restraints excluded: chain C residue 842 LEU Chi-restraints excluded: chain D residue 441 VAL Chi-restraints excluded: chain D residue 760 VAL Chi-restraints excluded: chain D residue 783 LEU Chi-restraints excluded: chain D residue 830 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 111 optimal weight: 0.9990 chunk 65 optimal weight: 8.9990 chunk 152 optimal weight: 3.9990 chunk 57 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 chunk 151 optimal weight: 0.9980 chunk 55 optimal weight: 4.9990 chunk 52 optimal weight: 0.0870 chunk 35 optimal weight: 0.4980 chunk 133 optimal weight: 1.9990 chunk 53 optimal weight: 0.2980 overall best weight: 0.5760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 620 GLN ** B 619 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 495 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4538 r_free = 0.4538 target = 0.223416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.182269 restraints weight = 17447.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.178040 restraints weight = 26300.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.175340 restraints weight = 21401.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.173738 restraints weight = 22197.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.174624 restraints weight = 18680.892| |-----------------------------------------------------------------------------| r_work (final): 0.4066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6931 moved from start: 0.5129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13142 Z= 0.120 Angle : 0.575 9.398 17832 Z= 0.298 Chirality : 0.041 0.240 2025 Planarity : 0.004 0.057 2237 Dihedral : 4.097 19.903 1770 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.95 % Allowed : 20.32 % Favored : 77.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.20), residues: 1633 helix: 1.00 (0.18), residues: 850 sheet: -0.02 (0.56), residues: 98 loop : -1.68 (0.21), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 811 TYR 0.022 0.001 TYR D 679 PHE 0.016 0.001 PHE A 582 TRP 0.043 0.002 TRP A 710 HIS 0.005 0.001 HIS A 607 Details of bonding type rmsd covalent geometry : bond 0.00274 (13138) covalent geometry : angle 0.57472 (17824) SS BOND : bond 0.00160 ( 4) SS BOND : angle 0.34424 ( 8) hydrogen bonds : bond 0.04032 ( 587) hydrogen bonds : angle 4.42707 ( 1731) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 163 time to evaluate : 0.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 505 MET cc_start: 0.6643 (OUTLIER) cc_final: 0.6366 (mtp) REVERT: A 693 ARG cc_start: 0.6953 (tpm170) cc_final: 0.6684 (tpp-160) REVERT: B 486 GLN cc_start: 0.7350 (OUTLIER) cc_final: 0.7132 (mm-40) REVERT: B 504 MET cc_start: 0.4652 (mmt) cc_final: 0.4353 (mmt) REVERT: B 579 LEU cc_start: 0.7733 (OUTLIER) cc_final: 0.7387 (tt) REVERT: B 587 GLN cc_start: 0.6224 (tp40) cc_final: 0.5433 (pt0) REVERT: B 649 THR cc_start: 0.8881 (t) cc_final: 0.7729 (p) REVERT: C 586 ILE cc_start: 0.8782 (mm) cc_final: 0.8408 (tt) REVERT: C 689 GLU cc_start: 0.6874 (OUTLIER) cc_final: 0.6046 (tp30) REVERT: C 707 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.7585 (tm-30) REVERT: C 787 ARG cc_start: 0.7420 (mmt90) cc_final: 0.7108 (tpp80) REVERT: D 451 MET cc_start: 0.6114 (ptt) cc_final: 0.5280 (ptt) REVERT: D 683 ARG cc_start: 0.5428 (tpm170) cc_final: 0.4064 (ptp-170) REVERT: D 724 ASN cc_start: 0.6461 (t0) cc_final: 0.6179 (t0) outliers start: 27 outliers final: 20 residues processed: 177 average time/residue: 0.1091 time to fit residues: 28.5674 Evaluate side-chains 177 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 152 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain A residue 505 MET Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 659 VAL Chi-restraints excluded: chain A residue 668 THR Chi-restraints excluded: chain A residue 691 TYR Chi-restraints excluded: chain A residue 759 VAL Chi-restraints excluded: chain A residue 767 SER Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 486 GLN Chi-restraints excluded: chain B residue 494 HIS Chi-restraints excluded: chain B residue 579 LEU Chi-restraints excluded: chain B residue 687 VAL Chi-restraints excluded: chain B residue 797 LEU Chi-restraints excluded: chain C residue 530 VAL Chi-restraints excluded: chain C residue 579 LEU Chi-restraints excluded: chain C residue 625 VAL Chi-restraints excluded: chain C residue 689 GLU Chi-restraints excluded: chain C residue 707 GLU Chi-restraints excluded: chain C residue 747 GLU Chi-restraints excluded: chain D residue 441 VAL Chi-restraints excluded: chain D residue 495 GLN Chi-restraints excluded: chain D residue 760 VAL Chi-restraints excluded: chain D residue 783 LEU Chi-restraints excluded: chain D residue 830 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 107 optimal weight: 6.9990 chunk 120 optimal weight: 0.6980 chunk 94 optimal weight: 0.9980 chunk 46 optimal weight: 9.9990 chunk 44 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 129 optimal weight: 4.9990 chunk 2 optimal weight: 0.7980 chunk 84 optimal weight: 0.7980 chunk 85 optimal weight: 0.7980 chunk 12 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 620 GLN ** B 619 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 701 GLN D 495 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4531 r_free = 0.4531 target = 0.222524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.182955 restraints weight = 17454.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.171814 restraints weight = 24652.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.168465 restraints weight = 20845.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.169581 restraints weight = 19634.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.168570 restraints weight = 17172.357| |-----------------------------------------------------------------------------| r_work (final): 0.4006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7035 moved from start: 0.5180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13142 Z= 0.130 Angle : 0.575 10.009 17832 Z= 0.297 Chirality : 0.042 0.226 2025 Planarity : 0.004 0.080 2237 Dihedral : 4.065 20.089 1770 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.39 % Allowed : 20.17 % Favored : 77.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.20), residues: 1633 helix: 1.03 (0.18), residues: 850 sheet: 0.02 (0.56), residues: 98 loop : -1.66 (0.21), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 684 TYR 0.021 0.001 TYR D 679 PHE 0.013 0.001 PHE A 641 TRP 0.041 0.002 TRP A 710 HIS 0.005 0.001 HIS A 607 Details of bonding type rmsd covalent geometry : bond 0.00305 (13138) covalent geometry : angle 0.57497 (17824) SS BOND : bond 0.00118 ( 4) SS BOND : angle 0.46078 ( 8) hydrogen bonds : bond 0.04258 ( 587) hydrogen bonds : angle 4.39057 ( 1731) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2268.23 seconds wall clock time: 39 minutes 56.64 seconds (2396.64 seconds total)