Starting phenix.real_space_refine on Sun May 3 09:32:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mzr_48766/05_2026/9mzr_48766.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mzr_48766/05_2026/9mzr_48766.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9mzr_48766/05_2026/9mzr_48766.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mzr_48766/05_2026/9mzr_48766.map" model { file = "/net/cci-nas-00/data/ceres_data/9mzr_48766/05_2026/9mzr_48766.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mzr_48766/05_2026/9mzr_48766.cif" } resolution = 3.93 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= 0.001 sd= 0.031 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: 5 Type Number sf(0) Gaussians S 72 5.16 5 C 7723 2.51 5 N 1917 2.21 5 O 2211 1.98 5 F 4 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 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: 11927 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2991 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 378, 2984 Classifications: {'peptide': 378} Link IDs: {'PTRANS': 14, 'TRANS': 363} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 378, 2984 Classifications: {'peptide': 378} Link IDs: {'PTRANS': 14, 'TRANS': 363} Chain breaks: 1 bond proxies already assigned to first conformer: 3040 Chain: "B" Number of atoms: 2938 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 372, 2935 Classifications: {'peptide': 372} Link IDs: {'PTRANS': 12, 'TRANS': 359} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 372, 2935 Classifications: {'peptide': 372} Link IDs: {'PTRANS': 12, 'TRANS': 359} Chain breaks: 1 bond proxies already assigned to first conformer: 2993 Chain: "C" Number of atoms: 2980 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 377, 2973 Classifications: {'peptide': 377} Link IDs: {'PTRANS': 14, 'TRANS': 362} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 377, 2973 Classifications: {'peptide': 377} Link IDs: {'PTRANS': 14, 'TRANS': 362} Chain breaks: 1 bond proxies already assigned to first conformer: 3028 Chain: "D" Number of atoms: 2914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2914 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 13, 'TRANS': 356} Chain breaks: 1 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'2J9': 2} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1} Link IDs: {None: 2} Chain: "B" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'2J9': 2} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1} Link IDs: {None: 2} Chain: "D" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Time building chain proxies: 5.01, per 1000 atoms: 0.42 Number of scatterers: 11927 At special positions: 0 Unit cell: (102.82, 132.5, 128.26, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 72 16.00 F 4 9.00 O 2211 8.00 N 1917 7.00 C 7723 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 676 " - pdb=" SG CYS B 802 " distance=2.03 Simple disulfide: pdb=" SG CYS A 750 " - pdb=" SG CYS A 804 " distance=2.03 Simple disulfide: pdb=" SG CYS B 750 " - pdb=" SG CYS B 804 " distance=2.03 Simple disulfide: pdb=" SG CYS C 676 " - pdb=" SG CYS D 802 " distance=2.03 Simple disulfide: pdb=" SG CYS C 750 " - pdb=" SG CYS C 804 " distance=2.03 Simple disulfide: pdb=" SG CYS D 750 " - pdb=" SG CYS D 804 " 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: 0.94 Conformation dependent library (CDL) restraints added in 693.3 milliseconds 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2772 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 18 sheets defined 50.1% alpha, 9.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 455 through 457 No H-bonds generated for 'chain 'A' and resid 455 through 457' Processing helix chain 'A' and resid 461 through 474 removed outlier: 3.543A pdb=" N LEU A 467 " --> pdb=" O CYS A 463 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR A 472 " --> pdb=" O ARG A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 505 Processing helix chain 'A' and resid 520 through 527 removed outlier: 4.011A pdb=" N VAL A 526 " --> pdb=" O VAL A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 553 through 557 removed outlier: 3.587A pdb=" N LEU A 556 " --> pdb=" O PHE A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 582 removed outlier: 3.554A pdb=" N TRP A 564 " --> pdb=" O SER A 560 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N MET A 565 " --> pdb=" O PRO A 561 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TYR A 566 " --> pdb=" O ASP A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 659 removed outlier: 4.066A pdb=" N TRP A 641 " --> pdb=" O GLY A 637 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ILE A 648 " --> pdb=" O THR A 644 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER A 649 " --> pdb=" O LEU A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 696 removed outlier: 3.698A pdb=" N THR A 692 " --> pdb=" O GLY A 688 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N PHE A 694 " --> pdb=" O THR A 690 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LYS A 696 " --> pdb=" O THR A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 703 through 705 No H-bonds generated for 'chain 'A' and resid 703 through 705' Processing helix chain 'A' and resid 706 through 712 removed outlier: 3.774A pdb=" N SER A 711 " --> pdb=" O ALA A 707 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ARG A 712 " --> pdb=" O PHE A 708 " (cutoff:3.500A) Processing helix chain 'A' and resid 720 through 731 Processing helix chain 'A' and resid 738 through 749 removed outlier: 3.873A pdb=" N GLU A 743 " --> pdb=" O SER A 739 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N PHE A 744 " --> pdb=" O THR A 740 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N VAL A 745 " --> pdb=" O THR A 741 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N GLN A 747 " --> pdb=" O GLU A 743 " (cutoff:3.500A) Processing helix chain 'A' and resid 776 through 788 removed outlier: 3.853A pdb=" N ALA A 781 " --> pdb=" O LYS A 777 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLN A 786 " --> pdb=" O ILE A 782 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU A 787 " --> pdb=" O LEU A 783 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 798 removed outlier: 3.602A pdb=" N LYS A 795 " --> pdb=" O LEU A 791 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N GLU A 796 " --> pdb=" O HIS A 792 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N TRP A 798 " --> pdb=" O MET A 794 " (cutoff:3.500A) Processing helix chain 'A' and resid 820 through 836 removed outlier: 4.076A pdb=" N PHE A 824 " --> pdb=" O ILE A 820 " (cutoff:3.500A) Processing helix chain 'A' and resid 837 through 845 Processing helix chain 'B' and resid 455 through 459 removed outlier: 4.387A pdb=" N PHE B 459 " --> pdb=" O ASN B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 471 removed outlier: 3.591A pdb=" N SER B 471 " --> pdb=" O LEU B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 500 through 505 removed outlier: 3.653A pdb=" N GLU B 504 " --> pdb=" O GLY B 500 " (cutoff:3.500A) Processing helix chain 'B' and resid 520 through 525 Processing helix chain 'B' and resid 560 through 584 removed outlier: 3.541A pdb=" N LEU B 568 " --> pdb=" O TRP B 564 " (cutoff:3.500A) Processing helix chain 'B' and resid 634 through 657 removed outlier: 4.030A pdb=" N TRP B 641 " --> pdb=" O GLY B 637 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ILE B 648 " --> pdb=" O THR B 644 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ALA B 657 " --> pdb=" O ALA B 653 " (cutoff:3.500A) Processing helix chain 'B' and resid 672 through 677 removed outlier: 3.650A pdb=" N CYS B 676 " --> pdb=" O ASP B 672 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLN B 677 " --> pdb=" O ASP B 673 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 672 through 677' Processing helix chain 'B' and resid 688 through 696 removed outlier: 3.959A pdb=" N THR B 692 " --> pdb=" O GLY B 688 " (cutoff:3.500A) Processing helix chain 'B' and resid 699 through 712 removed outlier: 3.513A pdb=" N LYS B 704 " --> pdb=" O SER B 700 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N MET B 709 " --> pdb=" O MET B 705 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N SER B 711 " --> pdb=" O ALA B 707 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ARG B 712 " --> pdb=" O PHE B 708 " (cutoff:3.500A) Processing helix chain 'B' and resid 720 through 730 removed outlier: 3.567A pdb=" N LEU B 729 " --> pdb=" O ILE B 725 " (cutoff:3.500A) Processing helix chain 'B' and resid 739 through 746 removed outlier: 3.533A pdb=" N PHE B 744 " --> pdb=" O THR B 740 " (cutoff:3.500A) Processing helix chain 'B' and resid 773 through 788 removed outlier: 3.728A pdb=" N LYS B 777 " --> pdb=" O PRO B 773 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ILE B 780 " --> pdb=" O ASP B 776 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU B 785 " --> pdb=" O ALA B 781 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLN B 786 " --> pdb=" O ILE B 782 " (cutoff:3.500A) Processing helix chain 'B' and resid 790 through 799 removed outlier: 3.505A pdb=" N TRP B 798 " --> pdb=" O MET B 794 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 845 removed outlier: 6.289A pdb=" N GLY B 822 " --> pdb=" O GLN B 818 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ILE B 823 " --> pdb=" O ASN B 819 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N PHE B 824 " --> pdb=" O ILE B 820 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE B 825 " --> pdb=" O GLY B 821 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU B 827 " --> pdb=" O ILE B 823 " (cutoff:3.500A) Processing helix chain 'C' and resid 461 through 474 Processing helix chain 'C' and resid 500 through 507 removed outlier: 3.636A pdb=" N ASP C 507 " --> pdb=" O ARG C 503 " (cutoff:3.500A) Processing helix chain 'C' and resid 520 through 527 removed outlier: 4.192A pdb=" N VAL C 526 " --> pdb=" O VAL C 522 " (cutoff:3.500A) Processing helix chain 'C' and resid 553 through 557 Processing helix chain 'C' and resid 562 through 585 removed outlier: 3.560A pdb=" N TYR C 566 " --> pdb=" O ASP C 562 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 662 removed outlier: 3.583A pdb=" N VAL C 636 " --> pdb=" O SER C 632 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLY C 637 " --> pdb=" O THR C 633 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N TRP C 641 " --> pdb=" O GLY C 637 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE C 648 " --> pdb=" O THR C 644 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU C 659 " --> pdb=" O LEU C 655 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N THR C 660 " --> pdb=" O ALA C 656 " (cutoff:3.500A) Processing helix chain 'C' and resid 670 through 675 removed outlier: 3.696A pdb=" N ALA C 675 " --> pdb=" O ALA C 671 " (cutoff:3.500A) Processing helix chain 'C' and resid 688 through 696 removed outlier: 3.839A pdb=" N THR C 692 " --> pdb=" O GLY C 688 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N PHE C 694 " --> pdb=" O THR C 690 " (cutoff:3.500A) Processing helix chain 'C' and resid 701 through 706 removed outlier: 3.622A pdb=" N TRP C 706 " --> pdb=" O TYR C 702 " (cutoff:3.500A) Processing helix chain 'C' and resid 706 through 712 removed outlier: 4.115A pdb=" N ARG C 712 " --> pdb=" O PHE C 708 " (cutoff:3.500A) Processing helix chain 'C' and resid 720 through 727 Processing helix chain 'C' and resid 738 through 746 removed outlier: 3.757A pdb=" N PHE C 744 " --> pdb=" O THR C 740 " (cutoff:3.500A) Processing helix chain 'C' and resid 773 through 788 removed outlier: 3.811A pdb=" N LYS C 777 " --> pdb=" O PRO C 773 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLN C 784 " --> pdb=" O ILE C 780 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLU C 787 " --> pdb=" O LEU C 783 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLU C 788 " --> pdb=" O GLN C 784 " (cutoff:3.500A) Processing helix chain 'C' and resid 789 through 799 removed outlier: 3.643A pdb=" N TRP C 798 " --> pdb=" O MET C 794 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 848 removed outlier: 6.574A pdb=" N GLY C 822 " --> pdb=" O GLN C 818 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N ILE C 823 " --> pdb=" O ASN C 819 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N PHE C 824 " --> pdb=" O ILE C 820 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLY C 840 " --> pdb=" O PHE C 836 " (cutoff:3.500A) Processing helix chain 'D' and resid 454 through 457 removed outlier: 4.077A pdb=" N ASP D 457 " --> pdb=" O TYR D 454 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 454 through 457' Processing helix chain 'D' and resid 461 through 474 removed outlier: 3.591A pdb=" N GLU D 469 " --> pdb=" O ASP D 465 " (cutoff:3.500A) Processing helix chain 'D' and resid 500 through 507 removed outlier: 3.924A pdb=" N GLU D 504 " --> pdb=" O GLY D 500 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ASP D 507 " --> pdb=" O ARG D 503 " (cutoff:3.500A) Processing helix chain 'D' and resid 520 through 525 removed outlier: 3.521A pdb=" N LYS D 525 " --> pdb=" O TYR D 521 " (cutoff:3.500A) Processing helix chain 'D' and resid 560 through 581 Processing helix chain 'D' and resid 630 through 659 removed outlier: 3.692A pdb=" N VAL D 636 " --> pdb=" O SER D 632 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N TRP D 641 " --> pdb=" O GLY D 637 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ILE D 648 " --> pdb=" O THR D 644 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ALA D 657 " --> pdb=" O ALA D 653 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU D 659 " --> pdb=" O LEU D 655 " (cutoff:3.500A) Processing helix chain 'D' and resid 671 through 676 Processing helix chain 'D' and resid 688 through 697 removed outlier: 3.672A pdb=" N PHE D 694 " --> pdb=" O THR D 690 " (cutoff:3.500A) Processing helix chain 'D' and resid 699 through 712 removed outlier: 3.606A pdb=" N MET D 705 " --> pdb=" O THR D 701 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N PHE D 708 " --> pdb=" O LYS D 704 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N MET D 709 " --> pdb=" O MET D 705 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N SER D 711 " --> pdb=" O ALA D 707 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ARG D 712 " --> pdb=" O PHE D 708 " (cutoff:3.500A) Processing helix chain 'D' and resid 720 through 730 Processing helix chain 'D' and resid 739 through 749 removed outlier: 3.706A pdb=" N PHE D 744 " --> pdb=" O THR D 740 " (cutoff:3.500A) Processing helix chain 'D' and resid 773 through 788 removed outlier: 3.999A pdb=" N LYS D 777 " --> pdb=" O PRO D 773 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ILE D 780 " --> pdb=" O ASP D 776 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEU D 783 " --> pdb=" O THR D 779 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N GLN D 784 " --> pdb=" O ILE D 780 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU D 785 " --> pdb=" O ALA D 781 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N GLN D 786 " --> pdb=" O ILE D 782 " (cutoff:3.500A) Processing helix chain 'D' and resid 790 through 799 Processing helix chain 'D' and resid 816 through 821 Processing helix chain 'D' and resid 821 through 845 removed outlier: 3.768A pdb=" N ILE D 825 " --> pdb=" O GLY D 821 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 433 through 437 Processing sheet with id=AA2, first strand: chain 'A' and resid 445 through 446 Processing sheet with id=AA3, first strand: chain 'A' and resid 513 through 514 Processing sheet with id=AA4, first strand: chain 'A' and resid 541 through 543 removed outlier: 3.707A pdb=" N TYR A 542 " --> pdb=" O THR A 753 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 681 through 683 removed outlier: 6.387A pdb=" N GLU A 681 " --> pdb=" O ALA A 734 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 433 through 437 removed outlier: 7.491A pdb=" N LEU B 433 " --> pdb=" O GLU B 479 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N ARG B 481 " --> pdb=" O LEU B 433 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N VAL B 435 " --> pdb=" O ARG B 481 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 513 through 518 removed outlier: 4.849A pdb=" N ALA B 515 " --> pdb=" O GLY B 765 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N GLY B 765 " --> pdb=" O ALA B 515 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N LEU B 517 " --> pdb=" O GLY B 763 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N GLY B 763 " --> pdb=" O LEU B 517 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N GLY B 683 " --> pdb=" O LEU B 736 " (cutoff:3.500A) removed outlier: 9.220A pdb=" N GLU B 738 " --> pdb=" O GLY B 683 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 513 through 518 removed outlier: 4.849A pdb=" N ALA B 515 " --> pdb=" O GLY B 765 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N GLY B 765 " --> pdb=" O ALA B 515 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N LEU B 517 " --> pdb=" O GLY B 763 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N GLY B 763 " --> pdb=" O LEU B 517 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N TYR B 542 " --> pdb=" O THR B 753 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N THR B 753 " --> pdb=" O TYR B 542 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 432 through 435 Processing sheet with id=AB1, first strand: chain 'C' and resid 445 through 446 removed outlier: 3.718A pdb=" N LEU C 445 " --> pdb=" O GLU C 460 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 513 through 514 Processing sheet with id=AB3, first strand: chain 'C' and resid 541 through 543 removed outlier: 3.947A pdb=" N TYR C 542 " --> pdb=" O THR C 753 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N THR C 753 " --> pdb=" O TYR C 542 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'C' and resid 682 through 683 Processing sheet with id=AB5, first strand: chain 'D' and resid 435 through 436 Processing sheet with id=AB6, first strand: chain 'D' and resid 445 through 446 Processing sheet with id=AB7, first strand: chain 'D' and resid 528 through 529 Processing sheet with id=AB8, first strand: chain 'D' and resid 717 through 718 removed outlier: 7.358A pdb=" N VAL D 718 " --> pdb=" O TYR D 682 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ALA D 684 " --> pdb=" O VAL D 718 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N VAL D 685 " --> pdb=" O LEU D 736 " (cutoff:3.500A) removed outlier: 10.130A pdb=" N GLU D 738 " --> pdb=" O VAL D 685 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N MET D 737 " --> pdb=" O SER D 539 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ILE D 540 " --> pdb=" O ILE D 755 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE D 755 " --> pdb=" O ILE D 540 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N TYR D 542 " --> pdb=" O THR D 753 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N THR D 753 " --> pdb=" O TYR D 542 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 717 through 718 removed outlier: 7.358A pdb=" N VAL D 718 " --> pdb=" O TYR D 682 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ALA D 684 " --> pdb=" O VAL D 718 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N VAL D 685 " --> pdb=" O LEU D 736 " (cutoff:3.500A) removed outlier: 10.130A pdb=" N GLU D 738 " --> pdb=" O VAL D 685 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N MET D 737 " --> pdb=" O SER D 539 " (cutoff:3.500A) 468 hydrogen bonds defined for protein. 1354 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: 1.83 Time building geometry restraints manager: 1.20 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: 3715 1.34 - 1.46: 2920 1.46 - 1.58: 5434 1.58 - 1.70: 4 1.70 - 1.82: 116 Bond restraints: 12189 Sorted by residual: bond pdb=" CB ARG D 800 " pdb=" CG ARG D 800 " ideal model delta sigma weight residual 1.520 1.563 -0.043 3.00e-02 1.11e+03 2.08e+00 bond pdb=" N ASP D 687 " pdb=" CA ASP D 687 " ideal model delta sigma weight residual 1.457 1.475 -0.018 1.29e-02 6.01e+03 1.91e+00 bond pdb=" CA ARG C 727 " pdb=" CB ARG C 727 " ideal model delta sigma weight residual 1.524 1.541 -0.017 1.31e-02 5.83e+03 1.70e+00 bond pdb=" CG ARG D 800 " pdb=" CD ARG D 800 " ideal model delta sigma weight residual 1.520 1.556 -0.036 3.00e-02 1.11e+03 1.45e+00 bond pdb=" CB ASP C 493 " pdb=" CG ASP C 493 " ideal model delta sigma weight residual 1.516 1.544 -0.028 2.50e-02 1.60e+03 1.27e+00 ... (remaining 12184 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.37: 16345 2.37 - 4.75: 141 4.75 - 7.12: 16 7.12 - 9.49: 4 9.49 - 11.86: 3 Bond angle restraints: 16509 Sorted by residual: angle pdb=" N VAL C 728 " pdb=" CA VAL C 728 " pdb=" C VAL C 728 " ideal model delta sigma weight residual 112.12 108.31 3.81 8.40e-01 1.42e+00 2.06e+01 angle pdb=" CA ARG D 800 " pdb=" CB ARG D 800 " pdb=" CG ARG D 800 " ideal model delta sigma weight residual 114.10 122.54 -8.44 2.00e+00 2.50e-01 1.78e+01 angle pdb=" CA ARG C 727 " pdb=" CB ARG C 727 " pdb=" CG ARG C 727 " ideal model delta sigma weight residual 114.10 122.30 -8.20 2.00e+00 2.50e-01 1.68e+01 angle pdb=" CA LEU D 445 " pdb=" CB LEU D 445 " pdb=" CG LEU D 445 " ideal model delta sigma weight residual 116.30 128.16 -11.86 3.50e+00 8.16e-02 1.15e+01 angle pdb=" CB MET D 770 " pdb=" CG MET D 770 " pdb=" SD MET D 770 " ideal model delta sigma weight residual 112.70 122.23 -9.53 3.00e+00 1.11e-01 1.01e+01 ... (remaining 16504 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.18: 6755 28.18 - 56.36: 457 56.36 - 84.53: 31 84.53 - 112.71: 5 112.71 - 140.89: 3 Dihedral angle restraints: 7251 sinusoidal: 2915 harmonic: 4336 Sorted by residual: dihedral pdb=" CB CYS D 750 " pdb=" SG CYS D 750 " pdb=" SG CYS D 804 " pdb=" CB CYS D 804 " ideal model delta sinusoidal sigma weight residual 93.00 179.53 -86.53 1 1.00e+01 1.00e-02 9.02e+01 dihedral pdb=" CB CYS B 750 " pdb=" SG CYS B 750 " pdb=" SG CYS B 804 " pdb=" CB CYS B 804 " ideal model delta sinusoidal sigma weight residual -86.00 -168.01 82.01 1 1.00e+01 1.00e-02 8.27e+01 dihedral pdb=" CB CYS A 750 " pdb=" SG CYS A 750 " pdb=" SG CYS A 804 " pdb=" CB CYS A 804 " ideal model delta sinusoidal sigma weight residual -86.00 -164.67 78.67 1 1.00e+01 1.00e-02 7.71e+01 ... (remaining 7248 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1214 0.033 - 0.065: 473 0.065 - 0.098: 121 0.098 - 0.130: 45 0.130 - 0.163: 7 Chirality restraints: 1860 Sorted by residual: chirality pdb=" CA TRP A 798 " pdb=" N TRP A 798 " pdb=" C TRP A 798 " pdb=" CB TRP A 798 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.64e-01 chirality pdb=" CA ASP D 687 " pdb=" N ASP D 687 " pdb=" C ASP D 687 " pdb=" CB ASP D 687 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.12e-01 chirality pdb=" CA ILE C 438 " pdb=" N ILE C 438 " pdb=" C ILE C 438 " pdb=" CB ILE C 438 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.80e-01 ... (remaining 1857 not shown) Planarity restraints: 2053 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU D 441 " 0.042 5.00e-02 4.00e+02 6.36e-02 6.46e+00 pdb=" N PRO D 442 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO D 442 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO D 442 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 441 " 0.038 5.00e-02 4.00e+02 5.82e-02 5.41e+00 pdb=" N PRO A 442 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO A 442 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 442 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 798 " -0.021 2.00e-02 2.50e+03 1.38e-02 4.77e+00 pdb=" CG TRP A 798 " 0.036 2.00e-02 2.50e+03 pdb=" CD1 TRP A 798 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 TRP A 798 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP A 798 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 798 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 798 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 798 " -0.006 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 798 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 798 " -0.002 2.00e-02 2.50e+03 ... (remaining 2050 not shown) Histogram of nonbonded interaction distances: 2.50 - 2.98: 5855 2.98 - 3.46: 12493 3.46 - 3.94: 18635 3.94 - 4.42: 21168 4.42 - 4.90: 32967 Nonbonded interactions: 91118 Sorted by model distance: nonbonded pdb=" O GLU D 686 " pdb=" OD1 ASP D 687 " model vdw 2.498 3.040 nonbonded pdb=" O ASP B 465 " pdb=" OD1 ASP B 465 " model vdw 2.535 3.040 nonbonded pdb=" C THR A 535 " pdb=" OG1ATHR A 535 " model vdw 2.535 2.616 nonbonded pdb=" C THR A 535 " pdb=" OG1BTHR A 535 " model vdw 2.535 2.616 nonbonded pdb=" C THR C 535 " pdb=" OG1BTHR C 535 " model vdw 2.563 2.616 ... (remaining 91113 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 433 through 470 or resid 472 through 534 or resid 536 thro \ ugh 583 or resid 629 through 845 or resid 1003)) selection = (chain 'B' and (resid 433 through 470 or resid 472 through 534 or resid 536 thro \ ugh 583 or resid 629 through 845 or resid 1001)) selection = (chain 'C' and (resid 433 through 470 or resid 472 through 534 or resid 536 thro \ ugh 583 or resid 629 through 845 or resid 1003)) selection = (chain 'D' and (resid 433 through 470 or resid 472 through 534 or resid 536 thro \ ugh 583 or resid 629 through 845 or resid 1001)) } 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=0.38 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: 2.210 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: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 14.260 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7265 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12195 Z= 0.112 Angle : 0.568 11.865 16521 Z= 0.286 Chirality : 0.039 0.163 1860 Planarity : 0.004 0.064 2053 Dihedral : 17.436 140.890 4461 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 2.63 % Allowed : 25.19 % Favored : 72.18 % 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: -1.23 (0.21), residues: 1486 helix: -0.25 (0.20), residues: 647 sheet: -0.30 (0.85), residues: 36 loop : -1.31 (0.22), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 800 TYR 0.011 0.001 TYR B 488 PHE 0.021 0.001 PHE D 658 TRP 0.036 0.002 TRP A 798 HIS 0.001 0.000 HIS D 508 Details of bonding type rmsd covalent geometry : bond 0.00257 (12189) covalent geometry : angle 0.56783 (16509) SS BOND : bond 0.00080 ( 6) SS BOND : angle 0.56056 ( 12) hydrogen bonds : bond 0.22505 ( 459) hydrogen bonds : angle 8.52390 ( 1354) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 207 time to evaluate : 0.467 Fit side-chains revert: symmetry clash REVERT: A 536 LEU cc_start: 0.8887 (tp) cc_final: 0.8576 (tp) REVERT: A 565 MET cc_start: 0.8005 (mmp) cc_final: 0.7752 (mmp) REVERT: B 507 ASP cc_start: 0.7355 (m-30) cc_final: 0.6772 (t0) REVERT: B 564 TRP cc_start: 0.8173 (m100) cc_final: 0.7790 (m100) REVERT: B 571 TYR cc_start: 0.8328 (t80) cc_final: 0.7743 (t80) REVERT: B 784 GLN cc_start: 0.7839 (mm-40) cc_final: 0.7489 (mm-40) REVERT: C 434 ILE cc_start: 0.8286 (mt) cc_final: 0.7922 (mt) REVERT: C 439 LEU cc_start: 0.7430 (tp) cc_final: 0.7074 (pp) REVERT: C 502 VAL cc_start: 0.6827 (t) cc_final: 0.6415 (t) REVERT: C 531 LYS cc_start: 0.8889 (OUTLIER) cc_final: 0.7684 (ttmm) REVERT: C 709 MET cc_start: 0.7368 (mmt) cc_final: 0.6858 (mmm) REVERT: C 815 LEU cc_start: 0.9102 (mt) cc_final: 0.8787 (mt) REVERT: D 491 GLN cc_start: 0.6774 (tp40) cc_final: 0.6493 (tp-100) REVERT: D 526 VAL cc_start: 0.9048 (m) cc_final: 0.8634 (t) REVERT: D 571 TYR cc_start: 0.8082 (t80) cc_final: 0.7732 (t80) REVERT: D 631 LEU cc_start: 0.7531 (tt) cc_final: 0.7264 (tt) REVERT: D 764 TYR cc_start: 0.7836 (m-80) cc_final: 0.7461 (m-10) REVERT: D 796 GLU cc_start: 0.6779 (tp30) cc_final: 0.6560 (tp30) outliers start: 28 outliers final: 25 residues processed: 225 average time/residue: 0.0839 time to fit residues: 29.8082 Evaluate side-chains 225 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 199 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 531 LYS Chi-restraints excluded: chain A residue 566 TYR Chi-restraints excluded: chain A residue 576 CYS Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain B residue 520 THR Chi-restraints excluded: chain B residue 666 SER Chi-restraints excluded: chain C residue 531 LYS Chi-restraints excluded: chain C residue 538 ILE Chi-restraints excluded: chain C residue 556 LEU Chi-restraints excluded: chain C residue 566 TYR Chi-restraints excluded: chain C residue 576 CYS Chi-restraints excluded: chain C residue 691 MET Chi-restraints excluded: chain C residue 783 LEU Chi-restraints excluded: chain D residue 494 VAL Chi-restraints excluded: chain D residue 520 THR Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain D residue 636 VAL Chi-restraints excluded: chain D residue 661 VAL Chi-restraints excluded: chain D residue 742 ILE Chi-restraints excluded: chain D residue 817 VAL Chi-restraints excluded: chain D residue 831 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.0570 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 0.6980 chunk 55 optimal weight: 3.9990 overall best weight: 1.1502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 677 GLN ** B 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 784 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 = 0.4472 r_free = 0.4472 target = 0.210992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.187657 restraints weight = 44617.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.191292 restraints weight = 48779.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.194496 restraints weight = 15482.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.196936 restraints weight = 8490.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.196900 restraints weight = 6099.440| |-----------------------------------------------------------------------------| r_work (final): 0.4295 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4295 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4295 r_free = 0.4295 target_work(ls_wunit_k1) = 0.193 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4295 r_free = 0.4295 target_work(ls_wunit_k1) = 0.193 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4295 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 moved from start: 0.1080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12195 Z= 0.169 Angle : 0.576 13.398 16521 Z= 0.294 Chirality : 0.041 0.174 1860 Planarity : 0.004 0.043 2053 Dihedral : 9.168 140.837 1704 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 4.10 % Allowed : 23.42 % Favored : 72.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.22), residues: 1486 helix: 0.22 (0.20), residues: 677 sheet: 0.02 (0.85), residues: 34 loop : -1.41 (0.22), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 543 TYR 0.017 0.001 TYR C 521 PHE 0.015 0.001 PHE C 744 TRP 0.049 0.002 TRP A 798 HIS 0.003 0.001 HIS D 792 Details of bonding type rmsd covalent geometry : bond 0.00396 (12189) covalent geometry : angle 0.57627 (16509) SS BOND : bond 0.00125 ( 6) SS BOND : angle 0.70771 ( 12) hydrogen bonds : bond 0.04263 ( 459) hydrogen bonds : angle 5.04968 ( 1354) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 217 time to evaluate : 0.461 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 536 LEU cc_start: 0.9128 (tp) cc_final: 0.8832 (tp) REVERT: A 726 GLN cc_start: 0.7990 (mm110) cc_final: 0.7738 (mm-40) REVERT: A 736 LEU cc_start: 0.8301 (OUTLIER) cc_final: 0.8055 (mp) REVERT: B 507 ASP cc_start: 0.7214 (m-30) cc_final: 0.6773 (t0) REVERT: B 564 TRP cc_start: 0.8185 (m100) cc_final: 0.7950 (m100) REVERT: B 571 TYR cc_start: 0.8448 (t80) cc_final: 0.8051 (t80) REVERT: B 784 GLN cc_start: 0.7680 (mm-40) cc_final: 0.6980 (mm-40) REVERT: B 831 LEU cc_start: 0.8334 (mm) cc_final: 0.7773 (tt) REVERT: C 434 ILE cc_start: 0.8348 (mt) cc_final: 0.8057 (mt) REVERT: C 465 ASP cc_start: 0.8152 (t70) cc_final: 0.7944 (t0) REVERT: C 502 VAL cc_start: 0.6748 (t) cc_final: 0.6353 (t) REVERT: C 531 LYS cc_start: 0.8962 (OUTLIER) cc_final: 0.7684 (mptt) REVERT: C 705 MET cc_start: 0.8448 (mmm) cc_final: 0.8178 (mmt) REVERT: C 815 LEU cc_start: 0.9179 (mt) cc_final: 0.8759 (mt) REVERT: D 442 PRO cc_start: 0.8235 (Cg_endo) cc_final: 0.7985 (Cg_exo) REVERT: D 491 GLN cc_start: 0.6811 (tp40) cc_final: 0.6548 (tp-100) REVERT: D 526 VAL cc_start: 0.9025 (m) cc_final: 0.8586 (t) REVERT: D 569 LEU cc_start: 0.7083 (OUTLIER) cc_final: 0.6686 (mt) REVERT: D 571 TYR cc_start: 0.8225 (t80) cc_final: 0.7753 (t80) REVERT: D 735 PHE cc_start: 0.6668 (OUTLIER) cc_final: 0.6182 (t80) outliers start: 47 outliers final: 33 residues processed: 249 average time/residue: 0.0816 time to fit residues: 32.3043 Evaluate side-chains 245 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 208 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 531 LYS Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 566 TYR Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain A residue 804 CYS Chi-restraints excluded: chain B residue 520 THR Chi-restraints excluded: chain B residue 658 PHE Chi-restraints excluded: chain B residue 718 VAL Chi-restraints excluded: chain C residue 531 LYS Chi-restraints excluded: chain C residue 538 ILE Chi-restraints excluded: chain C residue 566 TYR Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 749 ASN Chi-restraints excluded: chain C residue 783 LEU Chi-restraints excluded: chain C residue 843 LEU Chi-restraints excluded: chain C residue 844 TYR Chi-restraints excluded: chain D residue 436 THR Chi-restraints excluded: chain D residue 494 VAL Chi-restraints excluded: chain D residue 520 THR Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 661 VAL Chi-restraints excluded: chain D residue 691 MET Chi-restraints excluded: chain D residue 718 VAL Chi-restraints excluded: chain D residue 735 PHE Chi-restraints excluded: chain D residue 742 ILE Chi-restraints excluded: chain D residue 831 LEU Chi-restraints excluded: chain D residue 835 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 70 optimal weight: 0.0980 chunk 74 optimal weight: 5.9990 chunk 134 optimal weight: 5.9990 chunk 143 optimal weight: 0.6980 chunk 69 optimal weight: 1.9990 chunk 140 optimal weight: 0.8980 chunk 120 optimal weight: 0.9990 chunk 101 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 86 optimal weight: 0.0770 chunk 96 optimal weight: 2.9990 overall best weight: 0.5540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4505 r_free = 0.4505 target = 0.214770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.185866 restraints weight = 27573.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.191822 restraints weight = 37174.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.194225 restraints weight = 15481.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.196565 restraints weight = 10995.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.197231 restraints weight = 8952.002| |-----------------------------------------------------------------------------| r_work (final): 0.4303 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4304 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4304 r_free = 0.4304 target_work(ls_wunit_k1) = 0.194 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4304 r_free = 0.4304 target_work(ls_wunit_k1) = 0.194 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4304 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 moved from start: 0.1259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12195 Z= 0.114 Angle : 0.539 14.085 16521 Z= 0.273 Chirality : 0.040 0.156 1860 Planarity : 0.004 0.045 2053 Dihedral : 8.867 140.780 1694 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 4.33 % Allowed : 23.65 % Favored : 72.02 % 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: -0.74 (0.22), residues: 1486 helix: 0.44 (0.21), residues: 681 sheet: -0.05 (0.81), residues: 36 loop : -1.40 (0.22), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 800 TYR 0.020 0.001 TYR C 521 PHE 0.014 0.001 PHE D 658 TRP 0.037 0.001 TRP A 798 HIS 0.001 0.000 HIS D 792 Details of bonding type rmsd covalent geometry : bond 0.00262 (12189) covalent geometry : angle 0.53888 (16509) SS BOND : bond 0.00088 ( 6) SS BOND : angle 0.68694 ( 12) hydrogen bonds : bond 0.03435 ( 459) hydrogen bonds : angle 4.50622 ( 1354) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 213 time to evaluate : 0.524 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 536 LEU cc_start: 0.8982 (tp) cc_final: 0.8702 (tp) REVERT: A 726 GLN cc_start: 0.8040 (mm110) cc_final: 0.7820 (mm-40) REVERT: B 507 ASP cc_start: 0.7372 (m-30) cc_final: 0.6823 (t0) REVERT: B 564 TRP cc_start: 0.8155 (m100) cc_final: 0.7920 (m100) REVERT: C 434 ILE cc_start: 0.8380 (mt) cc_final: 0.8127 (mt) REVERT: C 465 ASP cc_start: 0.8166 (t70) cc_final: 0.7850 (t0) REVERT: C 521 TYR cc_start: 0.6403 (t80) cc_final: 0.6161 (t80) REVERT: C 531 LYS cc_start: 0.8838 (OUTLIER) cc_final: 0.7515 (mptt) REVERT: C 709 MET cc_start: 0.7496 (mmt) cc_final: 0.7060 (mmm) REVERT: C 815 LEU cc_start: 0.9116 (mt) cc_final: 0.8693 (mt) REVERT: D 438 ILE cc_start: 0.6864 (tp) cc_final: 0.6644 (tp) REVERT: D 442 PRO cc_start: 0.8260 (Cg_endo) cc_final: 0.7989 (Cg_exo) REVERT: D 491 GLN cc_start: 0.6926 (tp40) cc_final: 0.6523 (tp40) REVERT: D 571 TYR cc_start: 0.8298 (t80) cc_final: 0.7842 (t80) outliers start: 50 outliers final: 31 residues processed: 244 average time/residue: 0.0938 time to fit residues: 35.4288 Evaluate side-chains 236 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 204 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 441 GLU Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 531 LYS Chi-restraints excluded: chain A residue 566 TYR Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain A residue 804 CYS Chi-restraints excluded: chain B residue 520 THR Chi-restraints excluded: chain B residue 658 PHE Chi-restraints excluded: chain B residue 666 SER Chi-restraints excluded: chain C residue 531 LYS Chi-restraints excluded: chain C residue 566 TYR Chi-restraints excluded: chain C residue 576 CYS Chi-restraints excluded: chain C residue 658 PHE Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 729 LEU Chi-restraints excluded: chain C residue 783 LEU Chi-restraints excluded: chain C residue 837 VAL Chi-restraints excluded: chain C residue 843 LEU Chi-restraints excluded: chain C residue 844 TYR Chi-restraints excluded: chain D residue 436 THR Chi-restraints excluded: chain D residue 494 VAL Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain D residue 661 VAL Chi-restraints excluded: chain D residue 691 MET Chi-restraints excluded: chain D residue 709 MET Chi-restraints excluded: chain D residue 742 ILE Chi-restraints excluded: chain D residue 831 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 125 optimal weight: 6.9990 chunk 48 optimal weight: 0.9980 chunk 36 optimal weight: 0.1980 chunk 105 optimal weight: 0.9980 chunk 87 optimal weight: 0.8980 chunk 90 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 chunk 137 optimal weight: 0.9980 chunk 98 optimal weight: 5.9990 chunk 58 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4492 r_free = 0.4492 target = 0.213143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.189054 restraints weight = 47036.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.192648 restraints weight = 50802.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.196735 restraints weight = 16628.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.197771 restraints weight = 8179.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.198273 restraints weight = 6663.495| |-----------------------------------------------------------------------------| r_work (final): 0.4305 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4306 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4306 r_free = 0.4306 target_work(ls_wunit_k1) = 0.195 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4306 r_free = 0.4306 target_work(ls_wunit_k1) = 0.195 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4306 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 moved from start: 0.1486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12195 Z= 0.134 Angle : 0.552 14.303 16521 Z= 0.279 Chirality : 0.040 0.146 1860 Planarity : 0.004 0.047 2053 Dihedral : 8.732 140.928 1689 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 4.56 % Allowed : 23.80 % Favored : 71.64 % 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: -0.71 (0.22), residues: 1486 helix: 0.53 (0.21), residues: 677 sheet: 0.03 (0.82), residues: 36 loop : -1.45 (0.22), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 800 TYR 0.030 0.001 TYR A 542 PHE 0.019 0.001 PHE B 579 TRP 0.042 0.002 TRP C 798 HIS 0.001 0.000 HIS D 792 Details of bonding type rmsd covalent geometry : bond 0.00317 (12189) covalent geometry : angle 0.55033 (16509) SS BOND : bond 0.00151 ( 6) SS BOND : angle 1.88171 ( 12) hydrogen bonds : bond 0.03254 ( 459) hydrogen bonds : angle 4.43459 ( 1354) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 210 time to evaluate : 0.466 Fit side-chains revert: symmetry clash REVERT: A 536 LEU cc_start: 0.9087 (tp) cc_final: 0.8810 (tp) REVERT: A 726 GLN cc_start: 0.8031 (mm110) cc_final: 0.7829 (mm-40) REVERT: B 445 LEU cc_start: 0.6761 (OUTLIER) cc_final: 0.6465 (tt) REVERT: B 507 ASP cc_start: 0.7291 (m-30) cc_final: 0.6768 (t0) REVERT: B 564 TRP cc_start: 0.8070 (m100) cc_final: 0.7798 (m100) REVERT: B 571 TYR cc_start: 0.7950 (t80) cc_final: 0.7561 (t80) REVERT: B 579 PHE cc_start: 0.7842 (t80) cc_final: 0.7252 (t80) REVERT: B 709 MET cc_start: 0.7508 (OUTLIER) cc_final: 0.7304 (pmm) REVERT: C 434 ILE cc_start: 0.8380 (mt) cc_final: 0.8145 (mt) REVERT: C 502 VAL cc_start: 0.6841 (t) cc_final: 0.6481 (t) REVERT: C 531 LYS cc_start: 0.8858 (OUTLIER) cc_final: 0.7480 (mptt) REVERT: C 709 MET cc_start: 0.7324 (mmt) cc_final: 0.6800 (mmt) REVERT: C 815 LEU cc_start: 0.9113 (mt) cc_final: 0.8676 (mt) REVERT: D 438 ILE cc_start: 0.6929 (tp) cc_final: 0.6708 (tp) REVERT: D 491 GLN cc_start: 0.6908 (tp40) cc_final: 0.6562 (tp40) REVERT: D 571 TYR cc_start: 0.8323 (t80) cc_final: 0.7848 (t80) REVERT: D 800 ARG cc_start: 0.7942 (tpm170) cc_final: 0.7693 (tpm170) outliers start: 53 outliers final: 41 residues processed: 240 average time/residue: 0.0869 time to fit residues: 33.0186 Evaluate side-chains 248 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 204 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 441 GLU Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 531 LYS Chi-restraints excluded: chain A residue 566 TYR Chi-restraints excluded: chain A residue 576 CYS Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain A residue 797 LYS Chi-restraints excluded: chain A residue 804 CYS Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 520 THR Chi-restraints excluded: chain B residue 658 PHE Chi-restraints excluded: chain B residue 666 SER Chi-restraints excluded: chain B residue 709 MET Chi-restraints excluded: chain C residue 531 LYS Chi-restraints excluded: chain C residue 566 TYR Chi-restraints excluded: chain C residue 576 CYS Chi-restraints excluded: chain C residue 658 PHE Chi-restraints excluded: chain C residue 691 MET Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 729 LEU Chi-restraints excluded: chain C residue 737 MET Chi-restraints excluded: chain C residue 783 LEU Chi-restraints excluded: chain C residue 843 LEU Chi-restraints excluded: chain C residue 844 TYR Chi-restraints excluded: chain D residue 436 THR Chi-restraints excluded: chain D residue 494 VAL Chi-restraints excluded: chain D residue 520 THR Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 661 VAL Chi-restraints excluded: chain D residue 669 ASP Chi-restraints excluded: chain D residue 691 MET Chi-restraints excluded: chain D residue 709 MET Chi-restraints excluded: chain D residue 717 LEU Chi-restraints excluded: chain D residue 742 ILE Chi-restraints excluded: chain D residue 785 LEU Chi-restraints excluded: chain D residue 817 VAL Chi-restraints excluded: chain D residue 831 LEU Chi-restraints excluded: chain D residue 844 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 64 optimal weight: 0.0980 chunk 38 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 75 optimal weight: 0.6980 chunk 61 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 101 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 146 optimal weight: 2.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4478 r_free = 0.4478 target = 0.211621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.187633 restraints weight = 38840.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.191145 restraints weight = 45621.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.194677 restraints weight = 16144.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.196603 restraints weight = 9026.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.196869 restraints weight = 6563.514| |-----------------------------------------------------------------------------| r_work (final): 0.4297 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4300 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4300 r_free = 0.4300 target_work(ls_wunit_k1) = 0.194 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4300 r_free = 0.4300 target_work(ls_wunit_k1) = 0.194 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.4300 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.1651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 12195 Z= 0.145 Angle : 0.557 14.647 16521 Z= 0.282 Chirality : 0.040 0.151 1860 Planarity : 0.004 0.049 2053 Dihedral : 8.786 140.903 1689 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 4.64 % Allowed : 24.19 % Favored : 71.17 % 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: -0.73 (0.22), residues: 1486 helix: 0.52 (0.21), residues: 680 sheet: 0.30 (0.84), residues: 34 loop : -1.47 (0.22), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 800 TYR 0.021 0.001 TYR A 542 PHE 0.017 0.001 PHE B 579 TRP 0.035 0.002 TRP C 798 HIS 0.001 0.000 HIS D 792 Details of bonding type rmsd covalent geometry : bond 0.00342 (12189) covalent geometry : angle 0.55634 (16509) SS BOND : bond 0.00136 ( 6) SS BOND : angle 1.31633 ( 12) hydrogen bonds : bond 0.03187 ( 459) hydrogen bonds : angle 4.39638 ( 1354) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 206 time to evaluate : 0.452 Fit side-chains revert: symmetry clash REVERT: A 536 LEU cc_start: 0.9139 (tp) cc_final: 0.8876 (tp) REVERT: A 726 GLN cc_start: 0.8061 (mm110) cc_final: 0.7838 (mm-40) REVERT: B 507 ASP cc_start: 0.7301 (m-30) cc_final: 0.6764 (t0) REVERT: B 564 TRP cc_start: 0.8048 (m100) cc_final: 0.7758 (m100) REVERT: B 571 TYR cc_start: 0.7985 (t80) cc_final: 0.7655 (t80) REVERT: B 579 PHE cc_start: 0.7857 (t80) cc_final: 0.7263 (t80) REVERT: B 709 MET cc_start: 0.7531 (OUTLIER) cc_final: 0.7312 (pmm) REVERT: C 434 ILE cc_start: 0.8411 (mt) cc_final: 0.8166 (mt) REVERT: C 502 VAL cc_start: 0.6839 (t) cc_final: 0.6478 (t) REVERT: C 531 LYS cc_start: 0.8889 (OUTLIER) cc_final: 0.7578 (mptt) REVERT: C 709 MET cc_start: 0.7476 (mmt) cc_final: 0.6973 (mmt) REVERT: C 815 LEU cc_start: 0.9156 (mt) cc_final: 0.8719 (mt) REVERT: D 438 ILE cc_start: 0.7065 (tp) cc_final: 0.6815 (tp) REVERT: D 491 GLN cc_start: 0.6820 (tp40) cc_final: 0.6519 (tp40) REVERT: D 571 TYR cc_start: 0.8310 (t80) cc_final: 0.7844 (t80) REVERT: D 800 ARG cc_start: 0.7825 (tpm170) cc_final: 0.7550 (tpm170) outliers start: 54 outliers final: 43 residues processed: 239 average time/residue: 0.0849 time to fit residues: 32.2003 Evaluate side-chains 250 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 205 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 441 GLU Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 531 LYS Chi-restraints excluded: chain A residue 566 TYR Chi-restraints excluded: chain A residue 576 CYS Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain A residue 804 CYS Chi-restraints excluded: chain B residue 520 THR Chi-restraints excluded: chain B residue 658 PHE Chi-restraints excluded: chain B residue 666 SER Chi-restraints excluded: chain B residue 709 MET Chi-restraints excluded: chain B residue 742 ILE Chi-restraints excluded: chain C residue 531 LYS Chi-restraints excluded: chain C residue 566 TYR Chi-restraints excluded: chain C residue 576 CYS Chi-restraints excluded: chain C residue 658 PHE Chi-restraints excluded: chain C residue 691 MET Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 729 LEU Chi-restraints excluded: chain C residue 737 MET Chi-restraints excluded: chain C residue 783 LEU Chi-restraints excluded: chain C residue 804 CYS Chi-restraints excluded: chain C residue 843 LEU Chi-restraints excluded: chain C residue 844 TYR Chi-restraints excluded: chain D residue 436 THR Chi-restraints excluded: chain D residue 494 VAL Chi-restraints excluded: chain D residue 520 THR Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 661 VAL Chi-restraints excluded: chain D residue 669 ASP Chi-restraints excluded: chain D residue 691 MET Chi-restraints excluded: chain D residue 709 MET Chi-restraints excluded: chain D residue 717 LEU Chi-restraints excluded: chain D residue 742 ILE Chi-restraints excluded: chain D residue 785 LEU Chi-restraints excluded: chain D residue 817 VAL Chi-restraints excluded: chain D residue 831 LEU Chi-restraints excluded: chain D residue 844 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 83 optimal weight: 0.2980 chunk 111 optimal weight: 0.6980 chunk 78 optimal weight: 3.9990 chunk 90 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 101 optimal weight: 3.9990 chunk 128 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 76 optimal weight: 0.7980 chunk 25 optimal weight: 0.6980 chunk 108 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4492 r_free = 0.4492 target = 0.213230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.189010 restraints weight = 41406.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.192644 restraints weight = 46995.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.196708 restraints weight = 16397.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.198769 restraints weight = 8514.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.198972 restraints weight = 6244.041| |-----------------------------------------------------------------------------| r_work (final): 0.4317 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4317 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4317 r_free = 0.4317 target_work(ls_wunit_k1) = 0.196 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4317 r_free = 0.4317 target_work(ls_wunit_k1) = 0.196 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.4317 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7272 moved from start: 0.1725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12195 Z= 0.123 Angle : 0.556 15.182 16521 Z= 0.275 Chirality : 0.040 0.151 1860 Planarity : 0.003 0.052 2053 Dihedral : 8.710 140.935 1689 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 3.94 % Allowed : 25.50 % Favored : 70.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.71 (0.22), residues: 1486 helix: 0.53 (0.21), residues: 681 sheet: 0.05 (0.83), residues: 36 loop : -1.46 (0.22), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 800 TYR 0.015 0.001 TYR D 443 PHE 0.017 0.001 PHE D 579 TRP 0.029 0.002 TRP C 798 HIS 0.001 0.000 HIS A 792 Details of bonding type rmsd covalent geometry : bond 0.00289 (12189) covalent geometry : angle 0.55537 (16509) SS BOND : bond 0.00098 ( 6) SS BOND : angle 0.99357 ( 12) hydrogen bonds : bond 0.02980 ( 459) hydrogen bonds : angle 4.26637 ( 1354) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 211 time to evaluate : 0.426 Fit side-chains revert: symmetry clash REVERT: A 536 LEU cc_start: 0.9092 (tp) cc_final: 0.8848 (tp) REVERT: A 726 GLN cc_start: 0.8059 (mm110) cc_final: 0.7820 (mm-40) REVERT: B 507 ASP cc_start: 0.7242 (m-30) cc_final: 0.6722 (t0) REVERT: B 571 TYR cc_start: 0.7979 (t80) cc_final: 0.7703 (t80) REVERT: B 579 PHE cc_start: 0.7847 (t80) cc_final: 0.7244 (t80) REVERT: C 434 ILE cc_start: 0.8372 (mt) cc_final: 0.8128 (mt) REVERT: C 531 LYS cc_start: 0.8823 (OUTLIER) cc_final: 0.7450 (mptt) REVERT: C 709 MET cc_start: 0.7473 (mmt) cc_final: 0.6954 (mmt) REVERT: C 815 LEU cc_start: 0.9142 (mt) cc_final: 0.8921 (mt) REVERT: D 491 GLN cc_start: 0.6882 (tp40) cc_final: 0.6615 (tp40) REVERT: D 571 TYR cc_start: 0.8300 (t80) cc_final: 0.7839 (t80) REVERT: D 669 ASP cc_start: 0.7570 (OUTLIER) cc_final: 0.7186 (m-30) REVERT: D 770 MET cc_start: 0.7747 (tpp) cc_final: 0.7460 (tpp) outliers start: 45 outliers final: 38 residues processed: 237 average time/residue: 0.0803 time to fit residues: 30.3061 Evaluate side-chains 238 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 198 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 441 GLU Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 531 LYS Chi-restraints excluded: chain A residue 566 TYR Chi-restraints excluded: chain A residue 576 CYS Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain A residue 804 CYS Chi-restraints excluded: chain B residue 520 THR Chi-restraints excluded: chain B residue 658 PHE Chi-restraints excluded: chain B residue 666 SER Chi-restraints excluded: chain B residue 718 VAL Chi-restraints excluded: chain C residue 531 LYS Chi-restraints excluded: chain C residue 566 TYR Chi-restraints excluded: chain C residue 576 CYS Chi-restraints excluded: chain C residue 658 PHE Chi-restraints excluded: chain C residue 691 MET Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 729 LEU Chi-restraints excluded: chain C residue 737 MET Chi-restraints excluded: chain C residue 783 LEU Chi-restraints excluded: chain C residue 804 CYS Chi-restraints excluded: chain C residue 843 LEU Chi-restraints excluded: chain C residue 844 TYR Chi-restraints excluded: chain D residue 436 THR Chi-restraints excluded: chain D residue 494 VAL Chi-restraints excluded: chain D residue 520 THR Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain D residue 661 VAL Chi-restraints excluded: chain D residue 669 ASP Chi-restraints excluded: chain D residue 691 MET Chi-restraints excluded: chain D residue 709 MET Chi-restraints excluded: chain D residue 717 LEU Chi-restraints excluded: chain D residue 742 ILE Chi-restraints excluded: chain D residue 785 LEU Chi-restraints excluded: chain D residue 817 VAL Chi-restraints excluded: chain D residue 844 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 11 optimal weight: 0.8980 chunk 24 optimal weight: 6.9990 chunk 143 optimal weight: 0.9990 chunk 80 optimal weight: 9.9990 chunk 138 optimal weight: 4.9990 chunk 54 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 41 optimal weight: 0.4980 chunk 36 optimal weight: 0.0270 chunk 82 optimal weight: 0.9990 overall best weight: 0.6640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4495 r_free = 0.4495 target = 0.213544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.186289 restraints weight = 33704.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.191628 restraints weight = 42241.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.194515 restraints weight = 15501.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.196888 restraints weight = 10115.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.199413 restraints weight = 7238.509| |-----------------------------------------------------------------------------| r_work (final): 0.4322 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4324 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4324 r_free = 0.4324 target_work(ls_wunit_k1) = 0.196 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4324 r_free = 0.4324 target_work(ls_wunit_k1) = 0.196 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4324 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7269 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12195 Z= 0.123 Angle : 0.564 15.408 16521 Z= 0.279 Chirality : 0.040 0.157 1860 Planarity : 0.004 0.053 2053 Dihedral : 8.595 140.972 1685 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 4.40 % Allowed : 25.35 % Favored : 70.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.22), residues: 1486 helix: 0.57 (0.21), residues: 681 sheet: 0.14 (0.83), residues: 36 loop : -1.43 (0.22), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 800 TYR 0.016 0.001 TYR B 443 PHE 0.018 0.001 PHE D 658 TRP 0.032 0.002 TRP C 798 HIS 0.001 0.000 HIS A 792 Details of bonding type rmsd covalent geometry : bond 0.00291 (12189) covalent geometry : angle 0.56305 (16509) SS BOND : bond 0.00108 ( 6) SS BOND : angle 1.01801 ( 12) hydrogen bonds : bond 0.02900 ( 459) hydrogen bonds : angle 4.21488 ( 1354) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 201 time to evaluate : 0.396 Fit side-chains revert: symmetry clash REVERT: A 483 VAL cc_start: 0.8898 (OUTLIER) cc_final: 0.8661 (m) REVERT: A 536 LEU cc_start: 0.9097 (tp) cc_final: 0.8853 (tp) REVERT: A 726 GLN cc_start: 0.8103 (mm110) cc_final: 0.7868 (mm-40) REVERT: B 507 ASP cc_start: 0.7175 (m-30) cc_final: 0.6678 (t0) REVERT: B 571 TYR cc_start: 0.8027 (t80) cc_final: 0.7763 (t80) REVERT: B 579 PHE cc_start: 0.7787 (t80) cc_final: 0.7179 (t80) REVERT: B 709 MET cc_start: 0.7372 (OUTLIER) cc_final: 0.6959 (ptp) REVERT: C 434 ILE cc_start: 0.8388 (mt) cc_final: 0.8147 (mt) REVERT: C 502 VAL cc_start: 0.7017 (t) cc_final: 0.6658 (t) REVERT: C 531 LYS cc_start: 0.8820 (OUTLIER) cc_final: 0.7497 (mptt) REVERT: C 709 MET cc_start: 0.7400 (mmt) cc_final: 0.6911 (mmt) REVERT: C 815 LEU cc_start: 0.9183 (mt) cc_final: 0.8805 (mt) REVERT: D 442 PRO cc_start: 0.8226 (Cg_endo) cc_final: 0.7958 (Cg_exo) REVERT: D 491 GLN cc_start: 0.6841 (tp40) cc_final: 0.6594 (tp40) REVERT: D 571 TYR cc_start: 0.8305 (t80) cc_final: 0.7839 (t80) REVERT: D 669 ASP cc_start: 0.7574 (OUTLIER) cc_final: 0.7194 (m-30) outliers start: 51 outliers final: 41 residues processed: 234 average time/residue: 0.0821 time to fit residues: 30.5601 Evaluate side-chains 245 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 200 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 441 GLU Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 531 LYS Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 566 TYR Chi-restraints excluded: chain A residue 576 CYS Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain A residue 804 CYS Chi-restraints excluded: chain B residue 520 THR Chi-restraints excluded: chain B residue 658 PHE Chi-restraints excluded: chain B residue 666 SER Chi-restraints excluded: chain B residue 709 MET Chi-restraints excluded: chain B residue 718 VAL Chi-restraints excluded: chain B residue 742 ILE Chi-restraints excluded: chain C residue 531 LYS Chi-restraints excluded: chain C residue 566 TYR Chi-restraints excluded: chain C residue 658 PHE Chi-restraints excluded: chain C residue 691 MET Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 729 LEU Chi-restraints excluded: chain C residue 737 MET Chi-restraints excluded: chain C residue 783 LEU Chi-restraints excluded: chain C residue 804 CYS Chi-restraints excluded: chain C residue 833 LEU Chi-restraints excluded: chain C residue 843 LEU Chi-restraints excluded: chain C residue 844 TYR Chi-restraints excluded: chain D residue 436 THR Chi-restraints excluded: chain D residue 494 VAL Chi-restraints excluded: chain D residue 520 THR Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 661 VAL Chi-restraints excluded: chain D residue 669 ASP Chi-restraints excluded: chain D residue 691 MET Chi-restraints excluded: chain D residue 709 MET Chi-restraints excluded: chain D residue 717 LEU Chi-restraints excluded: chain D residue 742 ILE Chi-restraints excluded: chain D residue 785 LEU Chi-restraints excluded: chain D residue 817 VAL Chi-restraints excluded: chain D residue 844 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 120 optimal weight: 2.9990 chunk 114 optimal weight: 0.9980 chunk 122 optimal weight: 1.9990 chunk 95 optimal weight: 0.6980 chunk 88 optimal weight: 2.9990 chunk 139 optimal weight: 0.9980 chunk 132 optimal weight: 0.8980 chunk 107 optimal weight: 9.9990 chunk 8 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 102 optimal weight: 0.0770 overall best weight: 0.7338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4491 r_free = 0.4491 target = 0.213092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.189415 restraints weight = 40874.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.193039 restraints weight = 46316.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.196873 restraints weight = 16026.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.198825 restraints weight = 8423.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.198970 restraints weight = 6239.148| |-----------------------------------------------------------------------------| r_work (final): 0.4318 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4318 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4318 r_free = 0.4318 target_work(ls_wunit_k1) = 0.196 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4318 r_free = 0.4318 target_work(ls_wunit_k1) = 0.196 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4318 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12195 Z= 0.128 Angle : 0.567 15.542 16521 Z= 0.281 Chirality : 0.040 0.232 1860 Planarity : 0.004 0.055 2053 Dihedral : 8.633 140.972 1685 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 4.25 % Allowed : 25.66 % Favored : 70.09 % 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: -0.66 (0.22), residues: 1486 helix: 0.57 (0.21), residues: 683 sheet: 0.40 (0.86), residues: 34 loop : -1.44 (0.22), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 800 TYR 0.016 0.001 TYR B 443 PHE 0.021 0.001 PHE D 658 TRP 0.034 0.002 TRP A 798 HIS 0.001 0.000 HIS A 508 Details of bonding type rmsd covalent geometry : bond 0.00306 (12189) covalent geometry : angle 0.56699 (16509) SS BOND : bond 0.00113 ( 6) SS BOND : angle 0.89293 ( 12) hydrogen bonds : bond 0.02893 ( 459) hydrogen bonds : angle 4.20044 ( 1354) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 202 time to evaluate : 0.447 Fit side-chains revert: symmetry clash REVERT: A 483 VAL cc_start: 0.8898 (OUTLIER) cc_final: 0.8661 (m) REVERT: A 536 LEU cc_start: 0.9108 (tp) cc_final: 0.8878 (tp) REVERT: A 726 GLN cc_start: 0.8110 (mm110) cc_final: 0.7879 (mm-40) REVERT: B 507 ASP cc_start: 0.7226 (m-30) cc_final: 0.6702 (t0) REVERT: B 571 TYR cc_start: 0.8036 (t80) cc_final: 0.7780 (t80) REVERT: B 579 PHE cc_start: 0.7749 (t80) cc_final: 0.7207 (t80) REVERT: B 709 MET cc_start: 0.7430 (OUTLIER) cc_final: 0.7051 (ptp) REVERT: C 434 ILE cc_start: 0.8402 (mt) cc_final: 0.8164 (mt) REVERT: C 502 VAL cc_start: 0.6974 (t) cc_final: 0.6611 (t) REVERT: C 531 LYS cc_start: 0.8823 (OUTLIER) cc_final: 0.7601 (mptt) REVERT: C 682 TYR cc_start: 0.7659 (p90) cc_final: 0.6840 (p90) REVERT: C 709 MET cc_start: 0.7371 (mmt) cc_final: 0.6864 (mmt) REVERT: C 815 LEU cc_start: 0.9200 (mt) cc_final: 0.8825 (mt) REVERT: D 442 PRO cc_start: 0.8227 (Cg_endo) cc_final: 0.7921 (Cg_exo) REVERT: D 491 GLN cc_start: 0.6857 (tp40) cc_final: 0.6623 (tp40) REVERT: D 669 ASP cc_start: 0.7565 (OUTLIER) cc_final: 0.7197 (m-30) outliers start: 49 outliers final: 42 residues processed: 233 average time/residue: 0.0919 time to fit residues: 33.6630 Evaluate side-chains 244 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 198 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 441 GLU Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 531 LYS Chi-restraints excluded: chain A residue 566 TYR Chi-restraints excluded: chain A residue 576 CYS Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain A residue 804 CYS Chi-restraints excluded: chain B residue 520 THR Chi-restraints excluded: chain B residue 658 PHE Chi-restraints excluded: chain B residue 666 SER Chi-restraints excluded: chain B residue 709 MET Chi-restraints excluded: chain B residue 718 VAL Chi-restraints excluded: chain B residue 742 ILE Chi-restraints excluded: chain C residue 531 LYS Chi-restraints excluded: chain C residue 556 LEU Chi-restraints excluded: chain C residue 566 TYR Chi-restraints excluded: chain C residue 581 ILE Chi-restraints excluded: chain C residue 658 PHE Chi-restraints excluded: chain C residue 691 MET Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 729 LEU Chi-restraints excluded: chain C residue 737 MET Chi-restraints excluded: chain C residue 783 LEU Chi-restraints excluded: chain C residue 804 CYS Chi-restraints excluded: chain C residue 843 LEU Chi-restraints excluded: chain C residue 844 TYR Chi-restraints excluded: chain D residue 436 THR Chi-restraints excluded: chain D residue 494 VAL Chi-restraints excluded: chain D residue 520 THR Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 661 VAL Chi-restraints excluded: chain D residue 669 ASP Chi-restraints excluded: chain D residue 691 MET Chi-restraints excluded: chain D residue 709 MET Chi-restraints excluded: chain D residue 717 LEU Chi-restraints excluded: chain D residue 742 ILE Chi-restraints excluded: chain D residue 785 LEU Chi-restraints excluded: chain D residue 817 VAL Chi-restraints excluded: chain D residue 844 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 95 optimal weight: 1.9990 chunk 109 optimal weight: 0.6980 chunk 143 optimal weight: 0.6980 chunk 80 optimal weight: 10.0000 chunk 67 optimal weight: 0.7980 chunk 78 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 chunk 16 optimal weight: 6.9990 chunk 21 optimal weight: 0.0030 chunk 72 optimal weight: 0.9990 chunk 85 optimal weight: 0.8980 overall best weight: 0.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4498 r_free = 0.4498 target = 0.213908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.190381 restraints weight = 38963.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.193880 restraints weight = 46144.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.197174 restraints weight = 16372.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.199808 restraints weight = 9221.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.199992 restraints weight = 6159.815| |-----------------------------------------------------------------------------| r_work (final): 0.4324 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4326 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4326 r_free = 0.4326 target_work(ls_wunit_k1) = 0.197 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4326 r_free = 0.4326 target_work(ls_wunit_k1) = 0.197 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4326 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12195 Z= 0.120 Angle : 0.574 15.781 16521 Z= 0.281 Chirality : 0.040 0.214 1860 Planarity : 0.004 0.056 2053 Dihedral : 8.599 140.955 1685 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 4.25 % Allowed : 25.73 % Favored : 70.02 % 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: -0.65 (0.22), residues: 1486 helix: 0.61 (0.21), residues: 682 sheet: 0.18 (0.84), residues: 36 loop : -1.45 (0.22), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 748 TYR 0.015 0.001 TYR B 443 PHE 0.020 0.001 PHE D 658 TRP 0.035 0.002 TRP A 798 HIS 0.001 0.000 HIS A 792 Details of bonding type rmsd covalent geometry : bond 0.00286 (12189) covalent geometry : angle 0.57392 (16509) SS BOND : bond 0.00080 ( 6) SS BOND : angle 0.77922 ( 12) hydrogen bonds : bond 0.02824 ( 459) hydrogen bonds : angle 4.16385 ( 1354) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 208 time to evaluate : 0.499 Fit side-chains revert: symmetry clash REVERT: A 483 VAL cc_start: 0.8903 (OUTLIER) cc_final: 0.8665 (m) REVERT: A 536 LEU cc_start: 0.9053 (tp) cc_final: 0.8814 (tp) REVERT: A 726 GLN cc_start: 0.8107 (mm110) cc_final: 0.7879 (mm-40) REVERT: B 507 ASP cc_start: 0.7192 (m-30) cc_final: 0.6678 (t0) REVERT: B 571 TYR cc_start: 0.8037 (t80) cc_final: 0.7754 (t80) REVERT: B 579 PHE cc_start: 0.7752 (t80) cc_final: 0.7208 (t80) REVERT: B 709 MET cc_start: 0.7367 (OUTLIER) cc_final: 0.6829 (ptp) REVERT: B 831 LEU cc_start: 0.8262 (OUTLIER) cc_final: 0.7747 (tt) REVERT: C 439 LEU cc_start: 0.7542 (tp) cc_final: 0.7009 (pp) REVERT: C 502 VAL cc_start: 0.6944 (t) cc_final: 0.6585 (t) REVERT: C 531 LYS cc_start: 0.8802 (OUTLIER) cc_final: 0.7595 (mptt) REVERT: C 682 TYR cc_start: 0.7611 (p90) cc_final: 0.6965 (p90) REVERT: C 709 MET cc_start: 0.7279 (mmt) cc_final: 0.6786 (mmt) REVERT: C 815 LEU cc_start: 0.9205 (mt) cc_final: 0.8828 (mt) REVERT: D 442 PRO cc_start: 0.8248 (Cg_endo) cc_final: 0.7993 (Cg_exo) REVERT: D 491 GLN cc_start: 0.6873 (tp40) cc_final: 0.6631 (tp40) REVERT: D 669 ASP cc_start: 0.7610 (OUTLIER) cc_final: 0.7239 (m-30) REVERT: D 770 MET cc_start: 0.7699 (tpp) cc_final: 0.7424 (tpp) outliers start: 49 outliers final: 43 residues processed: 238 average time/residue: 0.0809 time to fit residues: 30.5231 Evaluate side-chains 252 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 204 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 441 GLU Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 531 LYS Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 566 TYR Chi-restraints excluded: chain A residue 576 CYS Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain A residue 804 CYS Chi-restraints excluded: chain B residue 520 THR Chi-restraints excluded: chain B residue 658 PHE Chi-restraints excluded: chain B residue 666 SER Chi-restraints excluded: chain B residue 709 MET Chi-restraints excluded: chain B residue 718 VAL Chi-restraints excluded: chain B residue 742 ILE Chi-restraints excluded: chain B residue 831 LEU Chi-restraints excluded: chain C residue 531 LYS Chi-restraints excluded: chain C residue 556 LEU Chi-restraints excluded: chain C residue 566 TYR Chi-restraints excluded: chain C residue 581 ILE Chi-restraints excluded: chain C residue 658 PHE Chi-restraints excluded: chain C residue 691 MET Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 729 LEU Chi-restraints excluded: chain C residue 737 MET Chi-restraints excluded: chain C residue 783 LEU Chi-restraints excluded: chain C residue 804 CYS Chi-restraints excluded: chain C residue 843 LEU Chi-restraints excluded: chain C residue 844 TYR Chi-restraints excluded: chain D residue 436 THR Chi-restraints excluded: chain D residue 485 ASP Chi-restraints excluded: chain D residue 494 VAL Chi-restraints excluded: chain D residue 520 THR Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 661 VAL Chi-restraints excluded: chain D residue 669 ASP Chi-restraints excluded: chain D residue 691 MET Chi-restraints excluded: chain D residue 709 MET Chi-restraints excluded: chain D residue 717 LEU Chi-restraints excluded: chain D residue 785 LEU Chi-restraints excluded: chain D residue 817 VAL Chi-restraints excluded: chain D residue 844 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 14 optimal weight: 0.7980 chunk 52 optimal weight: 0.8980 chunk 138 optimal weight: 5.9990 chunk 59 optimal weight: 3.9990 chunk 23 optimal weight: 8.9990 chunk 9 optimal weight: 2.9990 chunk 76 optimal weight: 0.6980 chunk 33 optimal weight: 3.9990 chunk 69 optimal weight: 0.8980 chunk 105 optimal weight: 0.9980 chunk 103 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4485 r_free = 0.4485 target = 0.212500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.188711 restraints weight = 44800.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.192212 restraints weight = 48859.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.196445 restraints weight = 16412.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.198288 restraints weight = 7973.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.198425 restraints weight = 6119.052| |-----------------------------------------------------------------------------| r_work (final): 0.4306 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4309 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4309 r_free = 0.4309 target_work(ls_wunit_k1) = 0.195 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4309 r_free = 0.4309 target_work(ls_wunit_k1) = 0.195 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4309 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7287 moved from start: 0.1977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12195 Z= 0.137 Angle : 0.589 15.633 16521 Z= 0.290 Chirality : 0.041 0.210 1860 Planarity : 0.004 0.057 2053 Dihedral : 8.569 140.927 1683 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 4.25 % Allowed : 25.97 % Favored : 69.78 % 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: -0.62 (0.22), residues: 1486 helix: 0.63 (0.21), residues: 682 sheet: 0.41 (0.87), residues: 34 loop : -1.46 (0.22), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 800 TYR 0.016 0.001 TYR B 443 PHE 0.022 0.001 PHE D 658 TRP 0.034 0.002 TRP C 798 HIS 0.001 0.000 HIS A 792 Details of bonding type rmsd covalent geometry : bond 0.00329 (12189) covalent geometry : angle 0.58891 (16509) SS BOND : bond 0.00105 ( 6) SS BOND : angle 0.75076 ( 12) hydrogen bonds : bond 0.02867 ( 459) hydrogen bonds : angle 4.20729 ( 1354) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 204 time to evaluate : 0.452 Fit side-chains revert: symmetry clash REVERT: A 536 LEU cc_start: 0.9113 (tp) cc_final: 0.8865 (tp) REVERT: A 726 GLN cc_start: 0.8108 (mm110) cc_final: 0.7871 (mm-40) REVERT: B 507 ASP cc_start: 0.7178 (m-30) cc_final: 0.6662 (t0) REVERT: B 571 TYR cc_start: 0.8048 (t80) cc_final: 0.7784 (t80) REVERT: B 579 PHE cc_start: 0.7753 (t80) cc_final: 0.7214 (t80) REVERT: B 709 MET cc_start: 0.7248 (OUTLIER) cc_final: 0.6651 (ptp) REVERT: B 831 LEU cc_start: 0.8259 (OUTLIER) cc_final: 0.7714 (tt) REVERT: C 439 LEU cc_start: 0.7569 (tp) cc_final: 0.7033 (pp) REVERT: C 502 VAL cc_start: 0.6975 (t) cc_final: 0.6591 (t) REVERT: C 531 LYS cc_start: 0.8841 (OUTLIER) cc_final: 0.7608 (mptt) REVERT: C 682 TYR cc_start: 0.7516 (p90) cc_final: 0.7020 (p90) REVERT: C 709 MET cc_start: 0.7286 (mmt) cc_final: 0.6795 (mmt) REVERT: C 815 LEU cc_start: 0.9221 (mt) cc_final: 0.8870 (mt) REVERT: D 442 PRO cc_start: 0.8202 (Cg_endo) cc_final: 0.7969 (Cg_exo) REVERT: D 491 GLN cc_start: 0.6889 (tp40) cc_final: 0.6646 (tp40) REVERT: D 764 TYR cc_start: 0.7910 (m-10) cc_final: 0.7541 (m-10) REVERT: D 770 MET cc_start: 0.7751 (tpp) cc_final: 0.7497 (tpp) outliers start: 49 outliers final: 44 residues processed: 234 average time/residue: 0.0862 time to fit residues: 31.7367 Evaluate side-chains 248 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 201 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 441 GLU Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 531 LYS Chi-restraints excluded: chain A residue 566 TYR Chi-restraints excluded: chain A residue 576 CYS Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain A residue 804 CYS Chi-restraints excluded: chain B residue 520 THR Chi-restraints excluded: chain B residue 658 PHE Chi-restraints excluded: chain B residue 666 SER Chi-restraints excluded: chain B residue 709 MET Chi-restraints excluded: chain B residue 718 VAL Chi-restraints excluded: chain B residue 742 ILE Chi-restraints excluded: chain B residue 831 LEU Chi-restraints excluded: chain C residue 531 LYS Chi-restraints excluded: chain C residue 556 LEU Chi-restraints excluded: chain C residue 566 TYR Chi-restraints excluded: chain C residue 581 ILE Chi-restraints excluded: chain C residue 658 PHE Chi-restraints excluded: chain C residue 691 MET Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 729 LEU Chi-restraints excluded: chain C residue 737 MET Chi-restraints excluded: chain C residue 783 LEU Chi-restraints excluded: chain C residue 804 CYS Chi-restraints excluded: chain C residue 843 LEU Chi-restraints excluded: chain C residue 844 TYR Chi-restraints excluded: chain D residue 436 THR Chi-restraints excluded: chain D residue 485 ASP Chi-restraints excluded: chain D residue 494 VAL Chi-restraints excluded: chain D residue 520 THR Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 661 VAL Chi-restraints excluded: chain D residue 691 MET Chi-restraints excluded: chain D residue 709 MET Chi-restraints excluded: chain D residue 717 LEU Chi-restraints excluded: chain D residue 742 ILE Chi-restraints excluded: chain D residue 785 LEU Chi-restraints excluded: chain D residue 817 VAL Chi-restraints excluded: chain D residue 844 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 112 optimal weight: 2.9990 chunk 85 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 140 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 121 optimal weight: 0.3980 chunk 119 optimal weight: 0.8980 chunk 124 optimal weight: 0.6980 chunk 63 optimal weight: 1.9990 chunk 26 optimal weight: 0.0060 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4498 r_free = 0.4498 target = 0.213955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.189816 restraints weight = 38091.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.193341 restraints weight = 46182.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.196740 restraints weight = 17018.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.199570 restraints weight = 9654.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.199749 restraints weight = 6372.101| |-----------------------------------------------------------------------------| r_work (final): 0.4326 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4325 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4325 r_free = 0.4325 target_work(ls_wunit_k1) = 0.197 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4325 r_free = 0.4325 target_work(ls_wunit_k1) = 0.197 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4325 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7261 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12195 Z= 0.123 Angle : 0.587 15.706 16521 Z= 0.289 Chirality : 0.040 0.204 1860 Planarity : 0.004 0.058 2053 Dihedral : 8.526 140.960 1683 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 4.25 % Allowed : 25.81 % Favored : 69.94 % 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: -0.61 (0.22), residues: 1486 helix: 0.65 (0.21), residues: 682 sheet: 0.20 (0.85), residues: 36 loop : -1.45 (0.22), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 800 TYR 0.015 0.001 TYR B 443 PHE 0.022 0.001 PHE D 658 TRP 0.038 0.002 TRP A 798 HIS 0.001 0.000 HIS B 792 Details of bonding type rmsd covalent geometry : bond 0.00294 (12189) covalent geometry : angle 0.58680 (16509) SS BOND : bond 0.00093 ( 6) SS BOND : angle 0.69053 ( 12) hydrogen bonds : bond 0.02827 ( 459) hydrogen bonds : angle 4.18951 ( 1354) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1829.38 seconds wall clock time: 32 minutes 32.06 seconds (1952.06 seconds total)