Starting phenix.real_space_refine on Sat Oct 24 01:02:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9oeh_70399/10_2026/9oeh_70399.cif Found real_map, /net/cci-nas-00/data/ceres_data/9oeh_70399/10_2026/9oeh_70399.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.67 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9oeh_70399/10_2026/9oeh_70399.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9oeh_70399/10_2026/9oeh_70399.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9oeh_70399/10_2026/9oeh_70399.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9oeh_70399/10_2026/9oeh_70399.map" } resolution = 3.67 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= 0.017 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: 6 Type Number sf(0) Gaussians Br 2 7.06 5 P 2 5.49 5 S 68 5.16 5 C 7367 2.51 5 N 1946 2.21 5 O 2104 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11489 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 2826 Classifications: {'peptide': 396} Incomplete info: {'truncation_to_alanine': 98} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 380} Chain breaks: 5 Unresolved non-hydrogen bonds: 328 Unresolved non-hydrogen angles: 408 Unresolved non-hydrogen dihedrals: 264 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'ASP:plan': 6, 'ASN:plan1': 6, 'ARG:plan': 7, 'GLU:plan': 12, 'PHE:plan': 5, 'GLN:plan1': 4, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 179 Chain: "C" Number of atoms: 2783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 393, 2783 Classifications: {'peptide': 393} Incomplete info: {'truncation_to_alanine': 103} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 378} Chain breaks: 5 Unresolved non-hydrogen bonds: 351 Unresolved non-hydrogen angles: 436 Unresolved non-hydrogen dihedrals: 282 Unresolved non-hydrogen chiralities: 31 Planarities with less than four sites: {'ASP:plan': 7, 'ASN:plan1': 5, 'ARG:plan': 9, 'GLU:plan': 12, 'GLN:plan1': 5, 'PHE:plan': 5, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 193 Chain: "B" Number of atoms: 2848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 2848 Classifications: {'peptide': 401} Incomplete info: {'truncation_to_alanine': 97} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 381} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 340 Unresolved non-hydrogen angles: 429 Unresolved non-hydrogen dihedrals: 284 Unresolved non-hydrogen chiralities: 35 Planarities with less than four sites: {'ASP:plan': 7, 'GLU:plan': 6, 'ARG:plan': 5, 'ASN:plan1': 3, 'PHE:plan': 6, 'TYR:plan': 3, 'TRP:plan': 1, 'HIS:plan': 2, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 163 Chain: "D" Number of atoms: 2850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 2850 Classifications: {'peptide': 401} Incomplete info: {'truncation_to_alanine': 98} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 381} Chain breaks: 4 Unresolved non-hydrogen bonds: 339 Unresolved non-hydrogen angles: 428 Unresolved non-hydrogen dihedrals: 286 Unresolved non-hydrogen chiralities: 33 Planarities with less than four sites: {'ASP:plan': 7, 'GLU:plan': 7, 'ASN:plan1': 3, 'ARG:plan': 6, 'PHE:plan': 6, 'TRP:plan': 2, 'TYR:plan': 2, 'HIS:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 170 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 49 Unusual residues: {'J86': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 49 Unusual residues: {'J86': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.96, per 1000 atoms: 0.26 Number of scatterers: 11489 At special positions: 0 Unit cell: (104.681, 132.539, 118.188, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Br 2 34.99 S 68 16.00 P 2 15.00 O 2104 8.00 N 1946 7.00 C 7367 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 420 " - pdb=" SG CYS A 454 " distance=2.03 Simple disulfide: pdb=" SG CYS A 436 " - pdb=" SG CYS A 455 " distance=2.03 Simple disulfide: pdb=" SG CYS A 744 " - pdb=" SG CYS A 798 " distance=2.03 Simple disulfide: pdb=" SG CYS C 420 " - pdb=" SG CYS C 454 " distance=2.03 Simple disulfide: pdb=" SG CYS C 436 " - pdb=" SG CYS C 455 " distance=2.03 Simple disulfide: pdb=" SG CYS C 744 " - pdb=" SG CYS C 798 " distance=2.03 Simple disulfide: pdb=" SG CYS B 537 " - pdb=" SG CYS B 575 " distance=2.03 Simple disulfide: pdb=" SG CYS B 543 " - pdb=" SG CYS B 576 " distance=2.03 Simple disulfide: pdb=" SG CYS B 859 " - pdb=" SG CYS B 913 " distance=2.03 Simple disulfide: pdb=" SG CYS D 537 " - pdb=" SG CYS D 575 " distance=2.03 Simple disulfide: pdb=" SG CYS D 543 " - pdb=" SG CYS D 576 " distance=2.03 Simple disulfide: pdb=" SG CYS D 859 " - pdb=" SG CYS D 913 " 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 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG A 902 " - " ASN A 771 " " NAG B1001 " - " ASN B 886 " " NAG C 901 " - " ASN C 471 " " NAG C 902 " - " ASN C 771 " " NAG D1001 " - " ASN D 886 " " NAG E 1 " - " ASN B 549 " " NAG F 1 " - " ASN D 549 " Time building additional restraints: 0.68 Conformation dependent library (CDL) restraints added in 489.6 milliseconds 3094 Ramachandran restraints generated. 1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2966 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 15 sheets defined 49.5% alpha, 12.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 458 through 471 Processing helix chain 'A' and resid 499 through 507 Processing helix chain 'A' and resid 520 through 527 Processing helix chain 'A' and resid 559 through 580 Processing helix chain 'A' and resid 605 through 615 Processing helix chain 'A' and resid 627 through 658 Processing helix chain 'A' and resid 669 through 674 Processing helix chain 'A' and resid 687 through 696 Processing helix chain 'A' and resid 699 through 707 Processing helix chain 'A' and resid 713 through 723 Processing helix chain 'A' and resid 733 through 743 Processing helix chain 'A' and resid 768 through 782 Processing helix chain 'A' and resid 783 through 793 Processing helix chain 'A' and resid 813 through 830 removed outlier: 3.764A pdb=" N PHE A 817 " --> pdb=" O MET A 813 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU A 819 " --> pdb=" O GLY A 815 " (cutoff:3.500A) Processing helix chain 'C' and resid 457 through 471 Processing helix chain 'C' and resid 499 through 507 Processing helix chain 'C' and resid 520 through 527 Processing helix chain 'C' and resid 561 through 580 Processing helix chain 'C' and resid 605 through 615 Processing helix chain 'C' and resid 626 through 658 Processing helix chain 'C' and resid 669 through 674 Processing helix chain 'C' and resid 687 through 696 removed outlier: 3.501A pdb=" N GLN C 696 " --> pdb=" O TYR C 692 " (cutoff:3.500A) Processing helix chain 'C' and resid 699 through 707 Processing helix chain 'C' and resid 713 through 723 Processing helix chain 'C' and resid 733 through 743 Processing helix chain 'C' and resid 768 through 782 Processing helix chain 'C' and resid 783 through 793 Processing helix chain 'C' and resid 817 through 830 Processing helix chain 'B' and resid 550 through 563 Processing helix chain 'B' and resid 569 through 571 No H-bonds generated for 'chain 'B' and resid 569 through 571' Processing helix chain 'B' and resid 578 through 592 Processing helix chain 'B' and resid 614 through 622 Processing helix chain 'B' and resid 635 through 642 removed outlier: 3.867A pdb=" N VAL B 641 " --> pdb=" O ALA B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 674 through 695 removed outlier: 3.726A pdb=" N LEU B 694 " --> pdb=" O ILE B 690 " (cutoff:3.500A) Processing helix chain 'B' and resid 716 through 729 Processing helix chain 'B' and resid 740 through 770 removed outlier: 3.527A pdb=" N PHE B 744 " --> pdb=" O TRP B 740 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL B 769 " --> pdb=" O ALA B 765 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLY B 770 " --> pdb=" O ALA B 766 " (cutoff:3.500A) Processing helix chain 'B' and resid 782 through 787 removed outlier: 3.674A pdb=" N HIS B 786 " --> pdb=" O ASP B 782 " (cutoff:3.500A) Processing helix chain 'B' and resid 800 through 810 Processing helix chain 'B' and resid 810 through 818 Processing helix chain 'B' and resid 824 through 834 Processing helix chain 'B' and resid 846 through 856 removed outlier: 3.789A pdb=" N TYR B 851 " --> pdb=" O ALA B 847 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ASP B 856 " --> pdb=" O GLU B 852 " (cutoff:3.500A) Processing helix chain 'B' and resid 882 through 898 removed outlier: 4.664A pdb=" N ASN B 886 " --> pdb=" O PRO B 882 " (cutoff:3.500A) Processing helix chain 'B' and resid 898 through 908 Processing helix chain 'B' and resid 931 through 948 removed outlier: 3.962A pdb=" N PHE B 935 " --> pdb=" O PHE B 931 " (cutoff:3.500A) Processing helix chain 'D' and resid 550 through 563 Processing helix chain 'D' and resid 569 through 571 No H-bonds generated for 'chain 'D' and resid 569 through 571' Processing helix chain 'D' and resid 578 through 592 Processing helix chain 'D' and resid 614 through 623 Processing helix chain 'D' and resid 635 through 642 Processing helix chain 'D' and resid 674 through 695 removed outlier: 3.773A pdb=" N GLY D 680 " --> pdb=" O THR D 676 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU D 694 " --> pdb=" O ILE D 690 " (cutoff:3.500A) Processing helix chain 'D' and resid 716 through 728 Processing helix chain 'D' and resid 741 through 770 Processing helix chain 'D' and resid 782 through 787 removed outlier: 3.801A pdb=" N HIS D 786 " --> pdb=" O ASP D 782 " (cutoff:3.500A) Processing helix chain 'D' and resid 800 through 810 Processing helix chain 'D' and resid 810 through 818 Processing helix chain 'D' and resid 824 through 834 removed outlier: 3.557A pdb=" N GLY D 828 " --> pdb=" O ALA D 824 " (cutoff:3.500A) Processing helix chain 'D' and resid 846 through 856 removed outlier: 3.606A pdb=" N TYR D 851 " --> pdb=" O ALA D 847 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ASP D 856 " --> pdb=" O GLU D 852 " (cutoff:3.500A) Processing helix chain 'D' and resid 883 through 898 Processing helix chain 'D' and resid 898 through 908 Processing helix chain 'D' and resid 931 through 948 removed outlier: 3.885A pdb=" N PHE D 935 " --> pdb=" O PHE D 931 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 475 through 478 removed outlier: 6.329A pdb=" N ILE A 400 " --> pdb=" O HIS A 477 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL A 401 " --> pdb=" O MET A 512 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 409 through 411 removed outlier: 3.697A pdb=" N GLY A 438 " --> pdb=" O VAL A 451 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 487 through 489 Processing sheet with id=AA4, first strand: chain 'A' and resid 681 through 682 removed outlier: 6.657A pdb=" N ALA A 682 " --> pdb=" O ILE A 730 " (cutoff:3.500A) removed outlier: 9.064A pdb=" N ASP A 732 " --> pdb=" O ALA A 682 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N LEU A 538 " --> pdb=" O PHE A 754 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N PHE A 754 " --> pdb=" O LEU A 538 " (cutoff:3.500A) removed outlier: 8.845A pdb=" N ILE A 540 " --> pdb=" O LEU A 752 " (cutoff:3.500A) removed outlier: 8.834A pdb=" N LEU A 752 " --> pdb=" O ILE A 540 " (cutoff:3.500A) removed outlier: 9.816A pdb=" N VAL A 542 " --> pdb=" O GLY A 750 " (cutoff:3.500A) removed outlier: 9.506A pdb=" N GLY A 750 " --> pdb=" O VAL A 542 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 475 through 478 removed outlier: 6.023A pdb=" N ILE C 400 " --> pdb=" O HIS C 477 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL C 401 " --> pdb=" O MET C 512 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 410 through 412 Processing sheet with id=AA7, first strand: chain 'C' and resid 487 through 489 removed outlier: 3.507A pdb=" N GLU C 497 " --> pdb=" O GLU C 488 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 681 through 682 removed outlier: 6.528A pdb=" N ALA C 682 " --> pdb=" O ILE C 730 " (cutoff:3.500A) removed outlier: 9.089A pdb=" N ASP C 732 " --> pdb=" O ALA C 682 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N LEU C 538 " --> pdb=" O GLU C 751 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N GLU C 751 " --> pdb=" O LEU C 538 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE C 540 " --> pdb=" O THR C 749 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 594 through 599 removed outlier: 3.550A pdb=" N ASP B 596 " --> pdb=" O LEU B 515 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL B 517 " --> pdb=" O ASP B 596 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N THR B 630 " --> pdb=" O GLY B 874 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N GLY B 874 " --> pdb=" O THR B 630 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N PHE B 632 " --> pdb=" O GLY B 872 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N GLY B 872 " --> pdb=" O PHE B 632 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE B 655 " --> pdb=" O VAL B 864 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N LYS B 866 " --> pdb=" O LEU B 653 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N LEU B 653 " --> pdb=" O LYS B 866 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N PHE B 868 " --> pdb=" O THR B 651 " (cutoff:3.500A) removed outlier: 8.369A pdb=" N THR B 651 " --> pdb=" O PHE B 868 " (cutoff:3.500A) removed outlier: 10.395A pdb=" N ILE B 870 " --> pdb=" O PHE B 649 " (cutoff:3.500A) removed outlier: 11.562A pdb=" N PHE B 649 " --> pdb=" O ILE B 870 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N GLY B 795 " --> pdb=" O ILE B 843 " (cutoff:3.500A) removed outlier: 8.954A pdb=" N ASP B 845 " --> pdb=" O GLY B 795 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 529 through 530 Processing sheet with id=AB2, first strand: chain 'B' and resid 608 through 609 removed outlier: 3.761A pdb=" N LYS B 609 " --> pdb=" O HIS B 612 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 517 through 519 Processing sheet with id=AB4, first strand: chain 'D' and resid 529 through 530 Processing sheet with id=AB5, first strand: chain 'D' and resid 608 through 609 removed outlier: 3.582A pdb=" N LYS D 609 " --> pdb=" O HIS D 612 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 628 through 633 removed outlier: 4.962A pdb=" N THR D 630 " --> pdb=" O GLY D 874 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N GLY D 874 " --> pdb=" O THR D 630 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N PHE D 632 " --> pdb=" O GLY D 872 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N GLY D 872 " --> pdb=" O PHE D 632 " (cutoff:3.500A) removed outlier: 9.789A pdb=" N GLY D 865 " --> pdb=" O VAL D 657 " (cutoff:3.500A) removed outlier: 10.237A pdb=" N VAL D 657 " --> pdb=" O GLY D 865 " (cutoff:3.500A) removed outlier: 9.093A pdb=" N ILE D 655 " --> pdb=" O PRO D 867 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N ALA D 869 " --> pdb=" O LEU D 653 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU D 653 " --> pdb=" O ALA D 869 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N PHE D 649 " --> pdb=" O TYR D 873 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N GLY D 795 " --> pdb=" O ILE D 843 " (cutoff:3.500A) removed outlier: 8.971A pdb=" N ASP D 845 " --> pdb=" O GLY D 795 " (cutoff:3.500A) 611 hydrogen bonds defined for protein. 1788 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: 1.76 Time building geometry restraints manager: 0.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.33: 2716 1.33 - 1.48: 4128 1.48 - 1.64: 4805 1.64 - 1.79: 10 1.79 - 1.94: 99 Bond restraints: 11758 Sorted by residual: bond pdb=" C5 J86 C 903 " pdb=" N3 J86 C 903 " ideal model delta sigma weight residual 1.384 1.490 -0.106 2.00e-02 2.50e+03 2.81e+01 bond pdb=" C4 J86 A 903 " pdb=" N2 J86 A 903 " ideal model delta sigma weight residual 1.383 1.488 -0.105 2.00e-02 2.50e+03 2.77e+01 bond pdb=" C5 J86 A 903 " pdb=" N3 J86 A 903 " ideal model delta sigma weight residual 1.384 1.488 -0.104 2.00e-02 2.50e+03 2.71e+01 bond pdb=" C4 J86 C 903 " pdb=" N2 J86 C 903 " ideal model delta sigma weight residual 1.383 1.486 -0.103 2.00e-02 2.50e+03 2.65e+01 bond pdb=" C10 J86 A 903 " pdb=" N2 J86 A 903 " ideal model delta sigma weight residual 1.346 1.426 -0.080 2.00e-02 2.50e+03 1.60e+01 ... (remaining 11753 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.34: 15988 3.34 - 6.67: 65 6.67 - 10.01: 2 10.01 - 13.35: 0 13.35 - 16.68: 4 Bond angle restraints: 16059 Sorted by residual: angle pdb=" C2 J86 C 903 " pdb=" C3 J86 C 903 " pdb=" C7 J86 C 903 " ideal model delta sigma weight residual 120.09 103.41 16.68 3.00e+00 1.11e-01 3.09e+01 angle pdb=" C2 J86 A 903 " pdb=" C3 J86 A 903 " pdb=" C7 J86 A 903 " ideal model delta sigma weight residual 120.09 103.68 16.41 3.00e+00 1.11e-01 2.99e+01 angle pdb=" C2 J86 C 903 " pdb=" C3 J86 C 903 " pdb=" C4 J86 C 903 " ideal model delta sigma weight residual 121.16 135.83 -14.67 3.00e+00 1.11e-01 2.39e+01 angle pdb=" C2 J86 A 903 " pdb=" C3 J86 A 903 " pdb=" C4 J86 A 903 " ideal model delta sigma weight residual 121.16 135.39 -14.23 3.00e+00 1.11e-01 2.25e+01 angle pdb=" C THR A 683 " pdb=" N VAL A 684 " pdb=" CA VAL A 684 " ideal model delta sigma weight residual 121.97 115.76 6.21 1.80e+00 3.09e-01 1.19e+01 ... (remaining 16054 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.30: 6530 17.30 - 34.61: 366 34.61 - 51.91: 63 51.91 - 69.22: 10 69.22 - 86.52: 4 Dihedral angle restraints: 6973 sinusoidal: 2391 harmonic: 4582 Sorted by residual: dihedral pdb=" CB CYS B 537 " pdb=" SG CYS B 537 " pdb=" SG CYS B 575 " pdb=" CB CYS B 575 " ideal model delta sinusoidal sigma weight residual 93.00 142.77 -49.77 1 1.00e+01 1.00e-02 3.40e+01 dihedral pdb=" CA ALA A 682 " pdb=" C ALA A 682 " pdb=" N THR A 683 " pdb=" CA THR A 683 " ideal model delta harmonic sigma weight residual 180.00 164.53 15.47 0 5.00e+00 4.00e-02 9.57e+00 dihedral pdb=" CA ALA C 682 " pdb=" C ALA C 682 " pdb=" N THR C 683 " pdb=" CA THR C 683 " ideal model delta harmonic sigma weight residual 180.00 164.59 15.41 0 5.00e+00 4.00e-02 9.50e+00 ... (remaining 6970 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1343 0.040 - 0.080: 380 0.080 - 0.120: 131 0.120 - 0.160: 9 0.160 - 0.199: 6 Chirality restraints: 1869 Sorted by residual: chirality pdb=" CA LEU A 752 " pdb=" N LEU A 752 " pdb=" C LEU A 752 " pdb=" CB LEU A 752 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.95e-01 chirality pdb=" C1 NAG D1001 " pdb=" ND2 ASN D 886 " pdb=" C2 NAG D1001 " pdb=" O5 NAG D1001 " both_signs ideal model delta sigma weight residual False -2.40 -2.21 -0.19 2.00e-01 2.50e+01 9.44e-01 chirality pdb=" CA LEU C 752 " pdb=" N LEU C 752 " pdb=" C LEU C 752 " pdb=" CB LEU C 752 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 9.05e-01 ... (remaining 1866 not shown) Planarity restraints: 2058 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL D 822 " -0.028 5.00e-02 4.00e+02 4.20e-02 2.82e+00 pdb=" N PRO D 823 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO D 823 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO D 823 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 822 " 0.027 5.00e-02 4.00e+02 4.04e-02 2.61e+00 pdb=" N PRO B 823 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO B 823 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 823 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP D 835 " 0.020 5.00e-02 4.00e+02 2.96e-02 1.40e+00 pdb=" N PRO D 836 " -0.051 5.00e-02 4.00e+02 pdb=" CA PRO D 836 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO D 836 " 0.015 5.00e-02 4.00e+02 ... (remaining 2055 not shown) Histogram of nonbonded interaction distances: 1.69 - 2.34: 16 2.34 - 2.98: 5911 2.98 - 3.62: 17621 3.62 - 4.26: 24663 4.26 - 4.90: 41425 Nonbonded interactions: 89636 Sorted by model distance: nonbonded pdb=" O ALA B 824 " pdb=" OD1 ASP B 827 " model vdw 1.694 3.040 nonbonded pdb=" O THR C 396 " pdb=" OG1 THR C 473 " model vdw 2.134 3.040 nonbonded pdb=" O PRO A 516 " pdb=" N3 J86 A 903 " model vdw 2.212 3.120 nonbonded pdb=" O VAL A 684 " pdb=" N TYR A 711 " model vdw 2.266 3.120 nonbonded pdb=" O PRO C 516 " pdb=" N3 J86 C 903 " model vdw 2.270 3.120 ... (remaining 89631 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 395 through 441 or (resid 448 and (name N or name CA or na \ me C or name O or name CB )) or resid 449 through 535 or (resid 536 and (name N \ or name CA or name C or name O or name CB )) or resid 537 through 554 or (resid \ 555 through 556 and (name N or name CA or name C or name O or name CB )) or resi \ d 557 through 565 or (resid 566 and (name N or name CA or name C or name O or na \ me CB )) or resid 567 through 634 or (resid 635 and (name N or name CA or name C \ or name O or name CB )) or resid 636 through 694 or (resid 695 and (name N or n \ ame CA or name C or name O or name CB )) or resid 696 through 764 or (resid 765 \ and (name N or name CA or name C or name O or name CB )) or resid 766 through 76 \ 8 or (resid 769 through 770 and (name N or name CA or name C or name O or name C \ B )) or resid 771 through 798 or (resid 808 through 814 and (name N or name CA o \ r name C or name O or name CB )) or resid 815 through 903)) selection = (chain 'C' and (resid 395 through 542 or (resid 543 through 546 and (name N or n \ ame CA or name C or name O or name CB )) or resid 547 through 673 or (resid 674 \ and (name N or name CA or name C or name O or name CB )) or resid 675 through 90 \ 3)) } ncs_group { reference = (chain 'B' and (resid 513 through 550 or (resid 551 through 552 and (name N or n \ ame CA or name C or name O or name CB )) or resid 553 through 563 or (resid 564 \ through 567 and (name N or name CA or name C or name O or name CB )) or resid 56 \ 8 through 661 or (resid 667 through 673 and (name N or name CA or name C or name \ O or name CB )) or resid 674 through 717 or (resid 718 through 719 and (name N \ or name CA or name C or name O or name CB )) or resid 720 through 722 or (resid \ 723 through 726 and (name N or name CA or name C or name O or name CB )) or resi \ d 727 through 750 or (resid 751 and (name N or name CA or name C or name O or na \ me CB )) or resid 752 through 757 or (resid 758 and (name N or name CA or name C \ or name O or name CB )) or resid 759 through 797 or (resid 798 through 799 and \ (name N or name CA or name C or name O or name CB )) or resid 800 through 806 or \ (resid 807 and (name N or name CA or name C or name O or name CB )) or resid 80 \ 8 through 811 or (resid 812 and (name N or name CA or name C or name O or name C \ B )) or resid 813 through 837 or (resid 838 and (name N or name CA or name C or \ name O or name CB )) or resid 839 through 857 or (resid 858 and (name N or name \ CA or name C or name O or name CB )) or resid 859 through 865 or (resid 866 and \ (name N or name CA or name C or name O or name CB )) or resid 867 through 892 or \ (resid 893 and (name N or name CA or name C or name O or name CB )) or resid 89 \ 4 through 1001)) selection = (chain 'D' and (resid 513 through 546 or (resid 547 through 548 and (name N or n \ ame CA or name C or name O or name CB )) or resid 549 through 555 or (resid 556 \ and (name N or name CA or name C or name O or name CB )) or resid 557 through 58 \ 1 or (resid 582 and (name N or name CA or name C or name O or name CB )) or resi \ d 583 through 584 or (resid 585 and (name N or name CA or name C or name O or na \ me CB )) or resid 586 through 603 or (resid 604 and (name N or name CA or name C \ or name O or name CB )) or resid 605 through 671 or (resid 672 through 673 and \ (name N or name CA or name C or name O or name CB )) or resid 674 through 723 or \ (resid 724 through 726 and (name N or name CA or name C or name O or name CB )) \ or resid 727 through 783 or (resid 784 through 785 and (name N or name CA or na \ me C or name O or name CB )) or resid 786 through 829 or (resid 830 and (name N \ or name CA or name C or name O or name CB )) or resid 831 through 832 or (resid \ 833 and (name N or name CA or name C or name O or name CB )) or resid 834 throug \ h 908 or (resid 909 through 911 and (name N or name CA or name C or name O or na \ me CB )) or resid 912 through 913 or (resid 925 through 926 and (name N or name \ CA or name C or name O or name CB )) or resid 927 through 1001)) } ncs_group { reference = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 11.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.580 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.106 11779 Z= 0.222 Angle : 0.640 16.682 16110 Z= 0.312 Chirality : 0.042 0.199 1869 Planarity : 0.003 0.042 2051 Dihedral : 11.376 86.525 3971 Min Nonbonded Distance : 1.694 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 0.30 % Allowed : 9.20 % Favored : 90.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.96 % 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: 0.58 (0.23), residues: 1547 helix: 2.00 (0.19), residues: 753 sheet: -1.77 (0.36), residues: 192 loop : -0.96 (0.27), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 694 TYR 0.013 0.001 TYR B 579 PHE 0.014 0.001 PHE A 458 TRP 0.016 0.001 TRP B 749 HIS 0.002 0.001 HIS A 477 Details of bonding type rmsd/Z covalent geometry : bond 0.00440 / 0.22 (11758) covalent geometry : angle 0.63574 / 0.31 (16059) SS BOND : bond 0.00248 / 0.18 ( 12) SS BOND : angle 0.44069 / 0.26 ( 24) hydrogen bonds : bond 0.13553 / 9.17 ( 611) hydrogen bonds : angle 6.19169 / 4.48 ( 1788) link_BETA1-4 : bond 0.00220 / 0.11 ( 2) link_BETA1-4 : angle 2.47129 / 1.30 ( 6) link_NAG-ASN : bond 0.00366 / 0.30 ( 7) link_NAG-ASN : angle 1.83719 / 1.21 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3094 Ramachandran restraints generated. 1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3094 Ramachandran restraints generated. 1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 286 time to evaluate : 0.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 614 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.8225 (tt) REVERT: A 703 TYR cc_start: 0.8742 (t80) cc_final: 0.8518 (t80) REVERT: C 399 LYS cc_start: 0.7831 (mttm) cc_final: 0.7375 (mtpt) REVERT: C 636 TRP cc_start: 0.8889 (t-100) cc_final: 0.8638 (t-100) REVERT: C 650 ASN cc_start: 0.7979 (t0) cc_final: 0.7695 (m-40) REVERT: C 745 ASP cc_start: 0.8517 (p0) cc_final: 0.8233 (p0) REVERT: C 787 ASP cc_start: 0.8497 (t70) cc_final: 0.8097 (t0) REVERT: B 675 TRP cc_start: 0.6490 (p-90) cc_final: 0.5786 (m100) REVERT: B 799 GLU cc_start: 0.7405 (pt0) cc_final: 0.6746 (tm-30) REVERT: B 837 GLU cc_start: 0.7123 (mp0) cc_final: 0.6662 (pm20) REVERT: B 883 LEU cc_start: 0.7242 (pp) cc_final: 0.7042 (tp) REVERT: D 728 PHE cc_start: 0.7366 (m-80) cc_final: 0.7127 (m-80) REVERT: D 803 GLU cc_start: 0.8266 (tt0) cc_final: 0.7776 (tp30) REVERT: D 808 GLN cc_start: 0.8428 (mm-40) cc_final: 0.8214 (mm-40) REVERT: D 840 ASP cc_start: 0.7324 (t0) cc_final: 0.7067 (t0) outliers start: 3 outliers final: 1 residues processed: 289 average time/residue: 0.0991 time to fit residues: 41.6728 Evaluate side-chains 224 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 222 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain C residue 420 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: [98, 107, 10, 66, 130, 124, 103, 77, 122, 91, 149] chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.0030 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 0.6980 chunk 149 optimal weight: 2.9990 overall best weight: 0.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 404 HIS A 536 GLN C 705 HIS C 710 ASN D 747 ASN D 830 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.153610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.123807 restraints weight = 19954.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.126809 restraints weight = 12408.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.128971 restraints weight = 9107.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.130231 restraints weight = 7333.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.131431 restraints weight = 6354.515| |-----------------------------------------------------------------------------| r_work (final): 0.3720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.1347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11779 Z= 0.139 Angle : 0.592 7.370 16110 Z= 0.307 Chirality : 0.042 0.166 1869 Planarity : 0.004 0.044 2051 Dihedral : 7.361 88.745 1902 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 2.63 % Allowed : 14.76 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.96 % 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: 0.70 (0.23), residues: 1547 helix: 2.02 (0.19), residues: 750 sheet: -1.68 (0.37), residues: 189 loop : -0.76 (0.27), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 755 TYR 0.020 0.002 TYR C 703 PHE 0.021 0.002 PHE C 609 TRP 0.027 0.001 TRP B 749 HIS 0.003 0.001 HIS B 562 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 (11758) covalent geometry : angle 0.58532 / 0.31 (16059) SS BOND : bond 0.00326 / 0.22 ( 12) SS BOND : angle 1.14296 / 0.75 ( 24) hydrogen bonds : bond 0.03515 / 2.40 ( 611) hydrogen bonds : angle 4.93085 / 3.54 ( 1788) link_BETA1-4 : bond 0.00567 / 0.30 ( 2) link_BETA1-4 : angle 2.29566 / 1.17 ( 6) link_NAG-ASN : bond 0.00301 / 0.21 ( 7) link_NAG-ASN : angle 2.02319 / 1.38 ( 21) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3094 Ramachandran restraints generated. 1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3094 Ramachandran restraints generated. 1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 250 time to evaluate : 0.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 399 LYS cc_start: 0.7741 (mttm) cc_final: 0.7351 (mtpt) REVERT: C 475 GLU cc_start: 0.7723 (pm20) cc_final: 0.7119 (pm20) REVERT: C 650 ASN cc_start: 0.8227 (t0) cc_final: 0.7911 (m-40) REVERT: C 745 ASP cc_start: 0.8477 (p0) cc_final: 0.8159 (p0) REVERT: C 787 ASP cc_start: 0.8447 (t70) cc_final: 0.8075 (t0) REVERT: B 626 ASN cc_start: 0.7015 (m-40) cc_final: 0.6770 (t0) REVERT: B 675 TRP cc_start: 0.6480 (p-90) cc_final: 0.5754 (m100) REVERT: B 799 GLU cc_start: 0.7278 (pt0) cc_final: 0.6558 (tm-30) REVERT: B 832 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8632 (tp) REVERT: B 837 GLU cc_start: 0.7091 (mp0) cc_final: 0.6791 (pm20) REVERT: B 846 LYS cc_start: 0.8628 (ttmm) cc_final: 0.8425 (ttmm) REVERT: B 883 LEU cc_start: 0.7371 (pp) cc_final: 0.7031 (tp) REVERT: B 900 MET cc_start: 0.8638 (mmm) cc_final: 0.7846 (mmt) REVERT: D 813 MET cc_start: 0.8577 (tpp) cc_final: 0.8331 (tpp) REVERT: D 830 GLN cc_start: 0.8127 (tp-100) cc_final: 0.7861 (tp40) outliers start: 26 outliers final: 11 residues processed: 263 average time/residue: 0.0934 time to fit residues: 36.5857 Evaluate side-chains 236 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 224 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 526 TYR Chi-restraints excluded: chain C residue 420 CYS Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 642 ILE Chi-restraints excluded: chain C residue 665 THR Chi-restraints excluded: chain B residue 537 CYS Chi-restraints excluded: chain B residue 627 MET Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 767 VAL Chi-restraints excluded: chain B residue 832 LEU Chi-restraints excluded: chain D residue 678 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: [3, 39, 66, 19, 112, 130, 136, 61, 108, 114, 137] chunk 3 optimal weight: 0.0170 chunk 39 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 19 optimal weight: 0.0020 chunk 112 optimal weight: 0.8980 chunk 130 optimal weight: 0.6980 chunk 136 optimal weight: 10.0000 chunk 61 optimal weight: 6.9990 chunk 108 optimal weight: 3.9990 chunk 114 optimal weight: 3.9990 chunk 137 optimal weight: 7.9990 overall best weight: 0.9228 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 814 HIS D 686 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.152854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.122914 restraints weight = 20053.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.126023 restraints weight = 12433.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.128118 restraints weight = 9070.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.129598 restraints weight = 7324.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.130458 restraints weight = 6286.077| |-----------------------------------------------------------------------------| r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.1678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11779 Z= 0.149 Angle : 0.587 6.458 16110 Z= 0.303 Chirality : 0.041 0.169 1869 Planarity : 0.003 0.047 2051 Dihedral : 7.162 89.025 1900 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 3.03 % Allowed : 15.27 % Favored : 81.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.96 % 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 (0.23), residues: 1547 helix: 1.98 (0.19), residues: 759 sheet: -1.72 (0.37), residues: 191 loop : -0.83 (0.27), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 798 TYR 0.017 0.002 TYR A 703 PHE 0.014 0.001 PHE C 609 TRP 0.030 0.002 TRP B 749 HIS 0.004 0.001 HIS D 897 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 (11758) covalent geometry : angle 0.58131 / 0.30 (16059) SS BOND : bond 0.00187 / 0.14 ( 12) SS BOND : angle 0.99255 / 0.66 ( 24) hydrogen bonds : bond 0.03283 / 2.22 ( 611) hydrogen bonds : angle 4.72481 / 3.38 ( 1788) link_BETA1-4 : bond 0.00417 / 0.22 ( 2) link_BETA1-4 : angle 2.11440 / 1.09 ( 6) link_NAG-ASN : bond 0.00302 / 0.23 ( 7) link_NAG-ASN : angle 1.87949 / 1.24 ( 21) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3094 Ramachandran restraints generated. 1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3094 Ramachandran restraints generated. 1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 241 time to evaluate : 0.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 651 LEU cc_start: 0.8729 (mm) cc_final: 0.8500 (mm) REVERT: A 696 GLN cc_start: 0.8218 (mm-40) cc_final: 0.7955 (mp10) REVERT: C 399 LYS cc_start: 0.7696 (mttm) cc_final: 0.7371 (mtpt) REVERT: C 745 ASP cc_start: 0.8472 (p0) cc_final: 0.8147 (p0) REVERT: C 787 ASP cc_start: 0.8476 (t70) cc_final: 0.8128 (t0) REVERT: B 675 TRP cc_start: 0.6485 (p-90) cc_final: 0.5736 (m100) REVERT: B 730 ARG cc_start: 0.7887 (mtm-85) cc_final: 0.7536 (mtm-85) REVERT: B 799 GLU cc_start: 0.7095 (pt0) cc_final: 0.6453 (tm-30) REVERT: B 837 GLU cc_start: 0.6988 (mp0) cc_final: 0.6757 (pm20) REVERT: B 883 LEU cc_start: 0.7342 (pp) cc_final: 0.6804 (tp) REVERT: D 728 PHE cc_start: 0.7099 (m-80) cc_final: 0.6834 (m-80) REVERT: D 730 ARG cc_start: 0.7144 (mmp-170) cc_final: 0.6858 (mmp-170) REVERT: D 830 GLN cc_start: 0.8212 (tp-100) cc_final: 0.7936 (tp40) REVERT: D 831 TYR cc_start: 0.8168 (m-10) cc_final: 0.7944 (m-10) outliers start: 30 outliers final: 16 residues processed: 257 average time/residue: 0.0921 time to fit residues: 35.5326 Evaluate side-chains 239 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 223 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 526 TYR Chi-restraints excluded: chain A residue 576 MET Chi-restraints excluded: chain C residue 420 CYS Chi-restraints excluded: chain C residue 642 ILE Chi-restraints excluded: chain C residue 665 THR Chi-restraints excluded: chain B residue 537 CYS Chi-restraints excluded: chain B residue 621 LEU Chi-restraints excluded: chain B residue 627 MET Chi-restraints excluded: chain B residue 723 CYS Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 767 VAL Chi-restraints excluded: chain D residue 678 TRP Chi-restraints excluded: chain D residue 767 VAL Chi-restraints excluded: chain D residue 797 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: [151, 19, 16, 21, 87, 26, 121, 136, 98, 68, 41] chunk 151 optimal weight: 3.9990 chunk 19 optimal weight: 6.9990 chunk 16 optimal weight: 9.9990 chunk 21 optimal weight: 0.6980 chunk 87 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 chunk 121 optimal weight: 3.9990 chunk 136 optimal weight: 10.0000 chunk 98 optimal weight: 20.0000 chunk 68 optimal weight: 0.2980 chunk 41 optimal weight: 9.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 626 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 = 0.3967 r_free = 0.3967 target = 0.147838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.117241 restraints weight = 20049.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.120225 restraints weight = 12600.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.122344 restraints weight = 9294.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.123782 restraints weight = 7536.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.124768 restraints weight = 6514.123| |-----------------------------------------------------------------------------| r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 11779 Z= 0.275 Angle : 0.693 7.443 16110 Z= 0.355 Chirality : 0.045 0.206 1869 Planarity : 0.004 0.049 2051 Dihedral : 7.317 88.879 1900 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 4.04 % Allowed : 17.49 % Favored : 78.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.22), residues: 1547 helix: 1.80 (0.19), residues: 755 sheet: -1.67 (0.38), residues: 181 loop : -0.98 (0.26), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 798 TYR 0.029 0.002 TYR A 703 PHE 0.025 0.002 PHE A 533 TRP 0.034 0.002 TRP B 749 HIS 0.008 0.001 HIS C 477 Details of bonding type rmsd/Z covalent geometry : bond 0.00648 / 0.28 (11758) covalent geometry : angle 0.68674 / 0.35 (16059) SS BOND : bond 0.00246 / 0.17 ( 12) SS BOND : angle 1.17922 / 0.80 ( 24) hydrogen bonds : bond 0.03580 / 2.39 ( 611) hydrogen bonds : angle 4.94399 / 3.57 ( 1788) link_BETA1-4 : bond 0.00383 / 0.20 ( 2) link_BETA1-4 : angle 1.98165 / 1.02 ( 6) link_NAG-ASN : bond 0.00438 / 0.32 ( 7) link_NAG-ASN : angle 2.35581 / 1.52 ( 21) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3094 Ramachandran restraints generated. 1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3094 Ramachandran restraints generated. 1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 220 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 555 MET cc_start: 0.7259 (OUTLIER) cc_final: 0.6905 (ttt) REVERT: A 651 LEU cc_start: 0.8734 (mm) cc_final: 0.8503 (mm) REVERT: A 696 GLN cc_start: 0.8430 (mm-40) cc_final: 0.7931 (mp10) REVERT: C 399 LYS cc_start: 0.7746 (mttm) cc_final: 0.7368 (mtpt) REVERT: C 787 ASP cc_start: 0.8630 (t70) cc_final: 0.8359 (t0) REVERT: B 675 TRP cc_start: 0.6501 (p-90) cc_final: 0.5729 (m100) REVERT: B 730 ARG cc_start: 0.8067 (mtm-85) cc_final: 0.7574 (mtm-85) REVERT: B 799 GLU cc_start: 0.7305 (pt0) cc_final: 0.6613 (tm-30) REVERT: B 837 GLU cc_start: 0.7100 (mp0) cc_final: 0.6849 (pm20) REVERT: B 883 LEU cc_start: 0.7345 (pp) cc_final: 0.6827 (tt) REVERT: D 730 ARG cc_start: 0.7360 (mmp-170) cc_final: 0.7006 (mmp-170) REVERT: D 808 GLN cc_start: 0.8448 (mm-40) cc_final: 0.8231 (mm-40) REVERT: D 935 PHE cc_start: 0.6865 (OUTLIER) cc_final: 0.6383 (m-80) outliers start: 40 outliers final: 24 residues processed: 246 average time/residue: 0.0855 time to fit residues: 32.0460 Evaluate side-chains 232 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 206 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 529 PHE Chi-restraints excluded: chain A residue 555 MET Chi-restraints excluded: chain A residue 576 MET Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 513 ILE Chi-restraints excluded: chain C residue 642 ILE Chi-restraints excluded: chain C residue 665 THR Chi-restraints excluded: chain B residue 537 CYS Chi-restraints excluded: chain B residue 575 CYS Chi-restraints excluded: chain B residue 621 LEU Chi-restraints excluded: chain B residue 627 MET Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 767 VAL Chi-restraints excluded: chain D residue 642 ILE Chi-restraints excluded: chain D residue 646 SER Chi-restraints excluded: chain D residue 678 TRP Chi-restraints excluded: chain D residue 727 LEU Chi-restraints excluded: chain D residue 767 VAL Chi-restraints excluded: chain D residue 803 GLU Chi-restraints excluded: chain D residue 935 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: [21, 120, 28, 46, 8, 150, 85, 41, 151, 140, 34] chunk 21 optimal weight: 2.9990 chunk 120 optimal weight: 0.0980 chunk 28 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 chunk 150 optimal weight: 0.0000 chunk 85 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 chunk 151 optimal weight: 0.5980 chunk 140 optimal weight: 6.9990 chunk 34 optimal weight: 1.9990 overall best weight: 0.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 626 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 = 0.4037 r_free = 0.4037 target = 0.153513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.123852 restraints weight = 19853.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.127035 restraints weight = 12275.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.129220 restraints weight = 8847.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.130730 restraints weight = 7068.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.131605 restraints weight = 6032.861| |-----------------------------------------------------------------------------| r_work (final): 0.3726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.2006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11779 Z= 0.120 Angle : 0.589 7.110 16110 Z= 0.303 Chirality : 0.041 0.171 1869 Planarity : 0.003 0.043 2051 Dihedral : 6.846 88.962 1899 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.63 % Allowed : 19.72 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.96 % 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 (0.23), residues: 1547 helix: 1.95 (0.19), residues: 755 sheet: -1.82 (0.37), residues: 192 loop : -0.69 (0.27), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 523 TYR 0.035 0.002 TYR C 703 PHE 0.016 0.001 PHE C 609 TRP 0.032 0.001 TRP B 749 HIS 0.003 0.001 HIS C 780 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (11758) covalent geometry : angle 0.58262 / 0.30 (16059) SS BOND : bond 0.00159 / 0.12 ( 12) SS BOND : angle 0.73336 / 0.45 ( 24) hydrogen bonds : bond 0.03034 / 2.06 ( 611) hydrogen bonds : angle 4.60269 / 3.29 ( 1788) link_BETA1-4 : bond 0.00450 / 0.23 ( 2) link_BETA1-4 : angle 2.08406 / 1.09 ( 6) link_NAG-ASN : bond 0.00440 / 0.30 ( 7) link_NAG-ASN : angle 2.10471 / 1.47 ( 21) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3094 Ramachandran restraints generated. 1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3094 Ramachandran restraints generated. 1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 232 time to evaluate : 0.459 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 555 MET cc_start: 0.7066 (OUTLIER) cc_final: 0.6713 (ttt) REVERT: A 696 GLN cc_start: 0.8344 (mm-40) cc_final: 0.7885 (mp10) REVERT: A 698 GLU cc_start: 0.8708 (pm20) cc_final: 0.8436 (pm20) REVERT: C 399 LYS cc_start: 0.7620 (mttm) cc_final: 0.7281 (mtpt) REVERT: C 474 TYR cc_start: 0.8169 (p90) cc_final: 0.7825 (p90) REVERT: C 502 MET cc_start: 0.6760 (mtm) cc_final: 0.6445 (mtm) REVERT: C 540 ILE cc_start: 0.9143 (OUTLIER) cc_final: 0.8939 (mt) REVERT: C 787 ASP cc_start: 0.8612 (t70) cc_final: 0.8321 (t0) REVERT: B 675 TRP cc_start: 0.6449 (p-90) cc_final: 0.5685 (m100) REVERT: B 730 ARG cc_start: 0.8048 (mtm-85) cc_final: 0.7638 (mtm-85) REVERT: B 799 GLU cc_start: 0.6961 (pt0) cc_final: 0.6394 (tm-30) REVERT: B 837 GLU cc_start: 0.6993 (mp0) cc_final: 0.6716 (pm20) REVERT: B 883 LEU cc_start: 0.7243 (pp) cc_final: 0.6736 (tt) REVERT: D 730 ARG cc_start: 0.7407 (mmp-170) cc_final: 0.7035 (mmp-170) REVERT: D 935 PHE cc_start: 0.6821 (OUTLIER) cc_final: 0.6367 (m-80) outliers start: 26 outliers final: 12 residues processed: 246 average time/residue: 0.0869 time to fit residues: 32.8334 Evaluate side-chains 233 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 218 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 526 TYR Chi-restraints excluded: chain A residue 529 PHE Chi-restraints excluded: chain A residue 555 MET Chi-restraints excluded: chain C residue 513 ILE Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 540 ILE Chi-restraints excluded: chain C residue 642 ILE Chi-restraints excluded: chain B residue 537 CYS Chi-restraints excluded: chain B residue 575 CYS Chi-restraints excluded: chain B residue 621 LEU Chi-restraints excluded: chain D residue 528 THR Chi-restraints excluded: chain D residue 646 SER Chi-restraints excluded: chain D residue 678 TRP Chi-restraints excluded: chain D residue 935 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: [137, 110, 95, 8, 35, 100, 50, 118, 53, 93, 9] chunk 137 optimal weight: 6.9990 chunk 110 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 100 optimal weight: 4.9990 chunk 50 optimal weight: 0.1980 chunk 118 optimal weight: 2.9990 chunk 53 optimal weight: 7.9990 chunk 93 optimal weight: 20.0000 chunk 9 optimal weight: 0.7980 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 897 HIS ** D 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.151480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.121458 restraints weight = 19893.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.124513 restraints weight = 12404.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.126673 restraints weight = 9040.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.128095 restraints weight = 7294.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.128754 restraints weight = 6299.433| |-----------------------------------------------------------------------------| r_work (final): 0.3685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.2115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11779 Z= 0.176 Angle : 0.624 8.048 16110 Z= 0.318 Chirality : 0.042 0.212 1869 Planarity : 0.004 0.044 2051 Dihedral : 6.871 88.331 1899 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 3.84 % Allowed : 20.22 % Favored : 75.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.23), residues: 1547 helix: 1.84 (0.19), residues: 762 sheet: -1.85 (0.37), residues: 197 loop : -0.78 (0.27), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 818 TYR 0.028 0.002 TYR A 703 PHE 0.030 0.002 PHE D 728 TRP 0.036 0.002 TRP B 749 HIS 0.004 0.001 HIS B 897 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.18 (11758) covalent geometry : angle 0.61550 / 0.32 (16059) SS BOND : bond 0.00184 / 0.13 ( 12) SS BOND : angle 0.87731 / 0.57 ( 24) hydrogen bonds : bond 0.03115 / 2.09 ( 611) hydrogen bonds : angle 4.60896 / 3.31 ( 1788) link_BETA1-4 : bond 0.00329 / 0.17 ( 2) link_BETA1-4 : angle 2.00053 / 1.04 ( 6) link_NAG-ASN : bond 0.00332 / 0.26 ( 7) link_NAG-ASN : angle 2.65299 / 1.86 ( 21) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3094 Ramachandran restraints generated. 1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3094 Ramachandran restraints generated. 1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 218 time to evaluate : 0.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 423 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.7635 (pm20) REVERT: A 555 MET cc_start: 0.7137 (OUTLIER) cc_final: 0.6802 (ttt) REVERT: A 639 PHE cc_start: 0.8637 (t80) cc_final: 0.8266 (t80) REVERT: A 651 LEU cc_start: 0.8971 (mm) cc_final: 0.8723 (mt) REVERT: A 696 GLN cc_start: 0.8415 (mm-40) cc_final: 0.7836 (mp10) REVERT: C 399 LYS cc_start: 0.7680 (mttm) cc_final: 0.7358 (mtpt) REVERT: C 474 TYR cc_start: 0.8206 (p90) cc_final: 0.7889 (p90) REVERT: C 540 ILE cc_start: 0.9188 (OUTLIER) cc_final: 0.8985 (mm) REVERT: C 787 ASP cc_start: 0.8623 (t70) cc_final: 0.8359 (t0) REVERT: B 675 TRP cc_start: 0.6451 (p-90) cc_final: 0.5677 (m100) REVERT: B 730 ARG cc_start: 0.8107 (mtm-85) cc_final: 0.7723 (mtm-85) REVERT: B 799 GLU cc_start: 0.7221 (pt0) cc_final: 0.6556 (tm-30) REVERT: B 837 GLU cc_start: 0.7078 (mp0) cc_final: 0.6748 (pm20) REVERT: B 883 LEU cc_start: 0.7298 (pp) cc_final: 0.6757 (tp) REVERT: D 730 ARG cc_start: 0.7456 (mmp-170) cc_final: 0.7096 (mmp-170) REVERT: D 808 GLN cc_start: 0.8460 (mm-40) cc_final: 0.8117 (mm-40) REVERT: D 830 GLN cc_start: 0.8208 (tp40) cc_final: 0.7713 (tp40) REVERT: D 935 PHE cc_start: 0.6886 (OUTLIER) cc_final: 0.6403 (m-80) outliers start: 38 outliers final: 26 residues processed: 243 average time/residue: 0.0839 time to fit residues: 31.2737 Evaluate side-chains 247 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 217 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 423 GLU Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 526 TYR Chi-restraints excluded: chain A residue 529 PHE Chi-restraints excluded: chain A residue 555 MET Chi-restraints excluded: chain A residue 576 MET Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 762 MET Chi-restraints excluded: chain C residue 469 THR Chi-restraints excluded: chain C residue 513 ILE Chi-restraints excluded: chain C residue 540 ILE Chi-restraints excluded: chain C residue 642 ILE Chi-restraints excluded: chain C residue 665 THR Chi-restraints excluded: chain B residue 537 CYS Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 575 CYS Chi-restraints excluded: chain B residue 621 LEU Chi-restraints excluded: chain B residue 767 VAL Chi-restraints excluded: chain B residue 880 ASN Chi-restraints excluded: chain B residue 886 ASN Chi-restraints excluded: chain D residue 528 THR Chi-restraints excluded: chain D residue 568 VAL Chi-restraints excluded: chain D residue 646 SER Chi-restraints excluded: chain D residue 678 TRP Chi-restraints excluded: chain D residue 720 LEU Chi-restraints excluded: chain D residue 797 VAL Chi-restraints excluded: chain D residue 803 GLU Chi-restraints excluded: chain D residue 935 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: [131, 1, 46, 123, 32, 90, 98, 119, 79, 150, 125] chunk 131 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 123 optimal weight: 0.7980 chunk 32 optimal weight: 0.0870 chunk 90 optimal weight: 1.9990 chunk 98 optimal weight: 10.0000 chunk 119 optimal weight: 0.4980 chunk 79 optimal weight: 0.9990 chunk 150 optimal weight: 3.9990 chunk 125 optimal weight: 0.6980 overall best weight: 0.6160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 449 HIS ** B 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.154058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.124512 restraints weight = 19855.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.127587 restraints weight = 12281.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.129760 restraints weight = 8934.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.131265 restraints weight = 7170.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.131950 restraints weight = 6143.216| |-----------------------------------------------------------------------------| r_work (final): 0.3728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.2252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11779 Z= 0.128 Angle : 0.593 8.620 16110 Z= 0.304 Chirality : 0.041 0.181 1869 Planarity : 0.003 0.044 2051 Dihedral : 6.724 89.177 1899 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 3.24 % Allowed : 21.03 % Favored : 75.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.96 % 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: 0.68 (0.23), residues: 1547 helix: 1.97 (0.19), residues: 753 sheet: -1.86 (0.38), residues: 181 loop : -0.70 (0.27), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 793 TYR 0.030 0.002 TYR A 703 PHE 0.040 0.001 PHE D 728 TRP 0.033 0.002 TRP B 749 HIS 0.005 0.001 HIS C 477 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (11758) covalent geometry : angle 0.58547 / 0.30 (16059) SS BOND : bond 0.00170 / 0.13 ( 12) SS BOND : angle 0.73274 / 0.45 ( 24) hydrogen bonds : bond 0.02944 / 2.00 ( 611) hydrogen bonds : angle 4.48811 / 3.21 ( 1788) link_BETA1-4 : bond 0.00321 / 0.17 ( 2) link_BETA1-4 : angle 2.02629 / 1.06 ( 6) link_NAG-ASN : bond 0.00315 / 0.24 ( 7) link_NAG-ASN : angle 2.44293 / 1.76 ( 21) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3094 Ramachandran restraints generated. 1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3094 Ramachandran restraints generated. 1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 237 time to evaluate : 0.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 423 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.7616 (pm20) REVERT: A 555 MET cc_start: 0.7201 (OUTLIER) cc_final: 0.6846 (ttt) REVERT: A 651 LEU cc_start: 0.8986 (mm) cc_final: 0.8682 (mt) REVERT: A 696 GLN cc_start: 0.8430 (mm-40) cc_final: 0.7859 (mp10) REVERT: C 399 LYS cc_start: 0.7715 (mttm) cc_final: 0.7363 (mtpt) REVERT: C 474 TYR cc_start: 0.8140 (p90) cc_final: 0.7905 (p90) REVERT: C 787 ASP cc_start: 0.8604 (t70) cc_final: 0.8353 (t0) REVERT: B 675 TRP cc_start: 0.6446 (p-90) cc_final: 0.5674 (m100) REVERT: B 730 ARG cc_start: 0.8046 (mtm-85) cc_final: 0.7728 (mtm-85) REVERT: B 799 GLU cc_start: 0.7187 (pt0) cc_final: 0.6547 (tm-30) REVERT: B 837 GLU cc_start: 0.6932 (mp0) cc_final: 0.6618 (pm20) REVERT: B 883 LEU cc_start: 0.7209 (pp) cc_final: 0.6657 (tp) REVERT: D 678 TRP cc_start: 0.8129 (OUTLIER) cc_final: 0.7284 (m-90) REVERT: D 730 ARG cc_start: 0.7345 (mmp-170) cc_final: 0.6991 (mmp-170) REVERT: D 830 GLN cc_start: 0.8130 (tp40) cc_final: 0.7900 (tp40) REVERT: D 831 TYR cc_start: 0.8094 (m-10) cc_final: 0.7886 (m-10) REVERT: D 935 PHE cc_start: 0.6848 (OUTLIER) cc_final: 0.6367 (m-80) outliers start: 32 outliers final: 20 residues processed: 256 average time/residue: 0.0871 time to fit residues: 34.0423 Evaluate side-chains 254 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 230 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 423 GLU Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 526 TYR Chi-restraints excluded: chain A residue 529 PHE Chi-restraints excluded: chain A residue 555 MET Chi-restraints excluded: chain A residue 762 MET Chi-restraints excluded: chain C residue 420 CYS Chi-restraints excluded: chain C residue 513 ILE Chi-restraints excluded: chain C residue 665 THR Chi-restraints excluded: chain B residue 537 CYS Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 575 CYS Chi-restraints excluded: chain B residue 621 LEU Chi-restraints excluded: chain B residue 627 MET Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 880 ASN Chi-restraints excluded: chain B residue 886 ASN Chi-restraints excluded: chain B residue 897 HIS Chi-restraints excluded: chain D residue 528 THR Chi-restraints excluded: chain D residue 646 SER Chi-restraints excluded: chain D residue 678 TRP Chi-restraints excluded: chain D residue 720 LEU Chi-restraints excluded: chain D residue 935 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: [127, 37, 119, 59, 87, 68, 69, 117, 30, 120, 32] chunk 127 optimal weight: 3.9990 chunk 37 optimal weight: 20.0000 chunk 119 optimal weight: 0.7980 chunk 59 optimal weight: 0.7980 chunk 87 optimal weight: 0.0270 chunk 68 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 chunk 117 optimal weight: 5.9990 chunk 30 optimal weight: 4.9990 chunk 120 optimal weight: 3.9990 chunk 32 optimal weight: 0.3980 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 477 HIS C 650 ASN ** B 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.154532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.125177 restraints weight = 19675.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.128221 restraints weight = 12199.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.130194 restraints weight = 8885.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.131727 restraints weight = 7225.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.132598 restraints weight = 6197.898| |-----------------------------------------------------------------------------| r_work (final): 0.3736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11779 Z= 0.129 Angle : 0.611 9.937 16110 Z= 0.310 Chirality : 0.041 0.212 1869 Planarity : 0.003 0.043 2051 Dihedral : 6.649 88.078 1899 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 3.24 % Allowed : 21.44 % Favored : 75.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.96 % 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: 0.57 (0.23), residues: 1547 helix: 1.90 (0.19), residues: 766 sheet: -1.76 (0.37), residues: 191 loop : -0.89 (0.27), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 818 TYR 0.025 0.002 TYR A 703 PHE 0.030 0.001 PHE D 728 TRP 0.028 0.001 TRP B 749 HIS 0.009 0.001 HIS C 477 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (11758) covalent geometry : angle 0.60435 / 0.31 (16059) SS BOND : bond 0.00174 / 0.13 ( 12) SS BOND : angle 0.73702 / 0.45 ( 24) hydrogen bonds : bond 0.02899 / 1.98 ( 611) hydrogen bonds : angle 4.39489 / 3.14 ( 1788) link_BETA1-4 : bond 0.00364 / 0.19 ( 2) link_BETA1-4 : angle 1.98583 / 1.05 ( 6) link_NAG-ASN : bond 0.00304 / 0.24 ( 7) link_NAG-ASN : angle 2.34880 / 1.69 ( 21) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3094 Ramachandran restraints generated. 1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3094 Ramachandran restraints generated. 1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 238 time to evaluate : 0.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 536 GLN cc_start: 0.8604 (pp30) cc_final: 0.8344 (pp30) REVERT: A 555 MET cc_start: 0.7253 (OUTLIER) cc_final: 0.6920 (ttt) REVERT: A 639 PHE cc_start: 0.8565 (t80) cc_final: 0.8181 (t80) REVERT: A 651 LEU cc_start: 0.8973 (mm) cc_final: 0.8663 (mt) REVERT: A 696 GLN cc_start: 0.8473 (mm-40) cc_final: 0.7895 (mp10) REVERT: C 399 LYS cc_start: 0.7719 (mttm) cc_final: 0.7368 (mtpt) REVERT: C 474 TYR cc_start: 0.8116 (p90) cc_final: 0.7826 (p90) REVERT: C 787 ASP cc_start: 0.8649 (t70) cc_final: 0.8358 (t0) REVERT: B 675 TRP cc_start: 0.6474 (p-90) cc_final: 0.5597 (m100) REVERT: B 730 ARG cc_start: 0.8079 (mtm-85) cc_final: 0.7773 (mtm-85) REVERT: B 799 GLU cc_start: 0.7193 (pt0) cc_final: 0.6546 (tm-30) REVERT: B 837 GLU cc_start: 0.6897 (mp0) cc_final: 0.6616 (pm20) REVERT: B 883 LEU cc_start: 0.7145 (pp) cc_final: 0.6585 (tp) REVERT: D 678 TRP cc_start: 0.8095 (OUTLIER) cc_final: 0.7325 (m-90) REVERT: D 730 ARG cc_start: 0.7335 (mmp-170) cc_final: 0.7015 (mmp-170) REVERT: D 808 GLN cc_start: 0.8476 (mm-40) cc_final: 0.8132 (mm-40) REVERT: D 935 PHE cc_start: 0.6830 (OUTLIER) cc_final: 0.6374 (m-80) outliers start: 32 outliers final: 27 residues processed: 256 average time/residue: 0.0883 time to fit residues: 34.4140 Evaluate side-chains 258 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 228 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain A residue 526 TYR Chi-restraints excluded: chain A residue 529 PHE Chi-restraints excluded: chain A residue 555 MET Chi-restraints excluded: chain A residue 576 MET Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain C residue 420 CYS Chi-restraints excluded: chain C residue 469 THR Chi-restraints excluded: chain C residue 513 ILE Chi-restraints excluded: chain C residue 642 ILE Chi-restraints excluded: chain C residue 650 ASN Chi-restraints excluded: chain C residue 665 THR Chi-restraints excluded: chain B residue 537 CYS Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 575 CYS Chi-restraints excluded: chain B residue 621 LEU Chi-restraints excluded: chain B residue 627 MET Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 880 ASN Chi-restraints excluded: chain B residue 886 ASN Chi-restraints excluded: chain B residue 897 HIS Chi-restraints excluded: chain D residue 528 THR Chi-restraints excluded: chain D residue 646 SER Chi-restraints excluded: chain D residue 678 TRP Chi-restraints excluded: chain D residue 720 LEU Chi-restraints excluded: chain D residue 794 PHE Chi-restraints excluded: chain D residue 839 LEU Chi-restraints excluded: chain D residue 935 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: [100, 119, 76, 66, 141, 52, 18, 93, 15, 102, 74] chunk 100 optimal weight: 4.9990 chunk 119 optimal weight: 0.7980 chunk 76 optimal weight: 0.1980 chunk 66 optimal weight: 2.9990 chunk 141 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 93 optimal weight: 10.0000 chunk 15 optimal weight: 5.9990 chunk 102 optimal weight: 4.9990 chunk 74 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 449 HIS C 650 ASN ** B 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 830 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.154485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.124891 restraints weight = 19708.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.127926 restraints weight = 12292.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.130131 restraints weight = 8957.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.131619 restraints weight = 7207.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.132307 restraints weight = 6174.827| |-----------------------------------------------------------------------------| r_work (final): 0.3729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11779 Z= 0.139 Angle : 0.619 9.387 16110 Z= 0.315 Chirality : 0.041 0.179 1869 Planarity : 0.004 0.042 2051 Dihedral : 6.651 88.170 1899 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 3.34 % Allowed : 21.74 % Favored : 74.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.96 % 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 (0.23), residues: 1547 helix: 1.96 (0.19), residues: 759 sheet: -1.84 (0.39), residues: 175 loop : -0.85 (0.27), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 793 TYR 0.030 0.002 TYR A 703 PHE 0.026 0.001 PHE D 728 TRP 0.035 0.002 TRP C 498 HIS 0.003 0.001 HIS A 477 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 (11758) covalent geometry : angle 0.61192 / 0.31 (16059) SS BOND : bond 0.00163 / 0.12 ( 12) SS BOND : angle 0.74593 / 0.46 ( 24) hydrogen bonds : bond 0.02879 / 1.95 ( 611) hydrogen bonds : angle 4.39361 / 3.14 ( 1788) link_BETA1-4 : bond 0.00373 / 0.19 ( 2) link_BETA1-4 : angle 1.97873 / 1.04 ( 6) link_NAG-ASN : bond 0.00318 / 0.25 ( 7) link_NAG-ASN : angle 2.35164 / 1.69 ( 21) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3094 Ramachandran restraints generated. 1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3094 Ramachandran restraints generated. 1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 232 time to evaluate : 0.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 536 GLN cc_start: 0.8580 (pp30) cc_final: 0.8348 (pp30) REVERT: A 555 MET cc_start: 0.7279 (OUTLIER) cc_final: 0.6938 (ttt) REVERT: A 651 LEU cc_start: 0.8970 (mm) cc_final: 0.8653 (mt) REVERT: A 696 GLN cc_start: 0.8517 (mm-40) cc_final: 0.7871 (mp10) REVERT: C 399 LYS cc_start: 0.7744 (mttm) cc_final: 0.7320 (mtpt) REVERT: C 474 TYR cc_start: 0.8155 (p90) cc_final: 0.7833 (p90) REVERT: C 787 ASP cc_start: 0.8655 (t70) cc_final: 0.8374 (t0) REVERT: B 675 TRP cc_start: 0.6472 (p-90) cc_final: 0.5603 (m100) REVERT: B 730 ARG cc_start: 0.8053 (mtm-85) cc_final: 0.7771 (mtm-85) REVERT: B 799 GLU cc_start: 0.7269 (pt0) cc_final: 0.6562 (tm-30) REVERT: B 837 GLU cc_start: 0.7089 (mp0) cc_final: 0.6676 (pm20) REVERT: B 844 MET cc_start: 0.8757 (tpt) cc_final: 0.8390 (tpt) REVERT: B 883 LEU cc_start: 0.7113 (pp) cc_final: 0.6503 (tp) REVERT: D 678 TRP cc_start: 0.8101 (OUTLIER) cc_final: 0.7399 (m-90) REVERT: D 730 ARG cc_start: 0.7294 (mmp-170) cc_final: 0.7007 (mmp-170) REVERT: D 808 GLN cc_start: 0.8485 (mm-40) cc_final: 0.8136 (mm-40) REVERT: D 935 PHE cc_start: 0.6783 (OUTLIER) cc_final: 0.6344 (m-80) outliers start: 33 outliers final: 25 residues processed: 251 average time/residue: 0.0864 time to fit residues: 33.2618 Evaluate side-chains 252 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 224 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain A residue 526 TYR Chi-restraints excluded: chain A residue 529 PHE Chi-restraints excluded: chain A residue 555 MET Chi-restraints excluded: chain A residue 576 MET Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain C residue 420 CYS Chi-restraints excluded: chain C residue 498 TRP Chi-restraints excluded: chain C residue 513 ILE Chi-restraints excluded: chain C residue 650 ASN Chi-restraints excluded: chain B residue 537 CYS Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 575 CYS Chi-restraints excluded: chain B residue 621 LEU Chi-restraints excluded: chain B residue 627 MET Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 880 ASN Chi-restraints excluded: chain B residue 886 ASN Chi-restraints excluded: chain B residue 897 HIS Chi-restraints excluded: chain D residue 528 THR Chi-restraints excluded: chain D residue 568 VAL Chi-restraints excluded: chain D residue 646 SER Chi-restraints excluded: chain D residue 678 TRP Chi-restraints excluded: chain D residue 720 LEU Chi-restraints excluded: chain D residue 839 LEU Chi-restraints excluded: chain D residue 935 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: [142, 22, 103, 42, 108, 26, 98, 15, 94, 123, 91] chunk 142 optimal weight: 4.9990 chunk 22 optimal weight: 0.8980 chunk 103 optimal weight: 2.9990 chunk 42 optimal weight: 0.0070 chunk 108 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 98 optimal weight: 10.0000 chunk 15 optimal weight: 7.9990 chunk 94 optimal weight: 4.9990 chunk 123 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 overall best weight: 1.3804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 449 HIS ** B 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.152256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.122401 restraints weight = 19759.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.125411 restraints weight = 12382.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.127499 restraints weight = 9087.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.128712 restraints weight = 7363.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.129870 restraints weight = 6435.560| |-----------------------------------------------------------------------------| r_work (final): 0.3695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 11779 Z= 0.193 Angle : 0.656 9.553 16110 Z= 0.334 Chirality : 0.043 0.177 1869 Planarity : 0.004 0.042 2051 Dihedral : 6.780 89.631 1899 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 3.24 % Allowed : 22.35 % Favored : 74.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.96 % 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: 0.58 (0.23), residues: 1547 helix: 1.91 (0.19), residues: 757 sheet: -1.93 (0.37), residues: 192 loop : -0.77 (0.27), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 818 TYR 0.029 0.002 TYR A 703 PHE 0.024 0.002 PHE D 728 TRP 0.035 0.002 TRP A 636 HIS 0.003 0.001 HIS A 477 Details of bonding type rmsd/Z covalent geometry : bond 0.00454 / 0.19 (11758) covalent geometry : angle 0.64936 / 0.33 (16059) SS BOND : bond 0.00175 / 0.12 ( 12) SS BOND : angle 0.82534 / 0.53 ( 24) hydrogen bonds : bond 0.03096 / 2.08 ( 611) hydrogen bonds : angle 4.48843 / 3.20 ( 1788) link_BETA1-4 : bond 0.00357 / 0.19 ( 2) link_BETA1-4 : angle 1.95019 / 1.02 ( 6) link_NAG-ASN : bond 0.00331 / 0.26 ( 7) link_NAG-ASN : angle 2.46530 / 1.75 ( 21) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3094 Ramachandran restraints generated. 1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3094 Ramachandran restraints generated. 1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 225 time to evaluate : 0.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 536 GLN cc_start: 0.8586 (pp30) cc_final: 0.8372 (pp30) REVERT: A 555 MET cc_start: 0.7400 (OUTLIER) cc_final: 0.7066 (ttt) REVERT: A 651 LEU cc_start: 0.8946 (mm) cc_final: 0.8621 (mt) REVERT: A 696 GLN cc_start: 0.8539 (mm-40) cc_final: 0.8184 (mp10) REVERT: C 399 LYS cc_start: 0.7723 (mttm) cc_final: 0.7332 (mtpt) REVERT: C 474 TYR cc_start: 0.8229 (p90) cc_final: 0.7867 (p90) REVERT: C 787 ASP cc_start: 0.8695 (t70) cc_final: 0.8414 (t0) REVERT: B 675 TRP cc_start: 0.6490 (p-90) cc_final: 0.5610 (m100) REVERT: B 682 PHE cc_start: 0.5849 (m-80) cc_final: 0.5586 (m-10) REVERT: B 730 ARG cc_start: 0.8109 (mtm-85) cc_final: 0.7805 (mtm-85) REVERT: B 799 GLU cc_start: 0.7273 (pt0) cc_final: 0.6595 (tm-30) REVERT: B 837 GLU cc_start: 0.7121 (mp0) cc_final: 0.6750 (pm20) REVERT: B 883 LEU cc_start: 0.7156 (pp) cc_final: 0.6523 (tp) REVERT: D 678 TRP cc_start: 0.8122 (OUTLIER) cc_final: 0.7334 (m-90) REVERT: D 730 ARG cc_start: 0.7398 (mmp-170) cc_final: 0.7040 (mmp-170) REVERT: D 935 PHE cc_start: 0.6801 (OUTLIER) cc_final: 0.6339 (m-80) outliers start: 32 outliers final: 26 residues processed: 243 average time/residue: 0.0816 time to fit residues: 30.4647 Evaluate side-chains 249 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 220 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 526 TYR Chi-restraints excluded: chain A residue 529 PHE Chi-restraints excluded: chain A residue 555 MET Chi-restraints excluded: chain A residue 576 MET Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain C residue 420 CYS Chi-restraints excluded: chain C residue 498 TRP Chi-restraints excluded: chain C residue 513 ILE Chi-restraints excluded: chain B residue 537 CYS Chi-restraints excluded: chain B residue 575 CYS Chi-restraints excluded: chain B residue 621 LEU Chi-restraints excluded: chain B residue 627 MET Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 767 VAL Chi-restraints excluded: chain B residue 880 ASN Chi-restraints excluded: chain B residue 886 ASN Chi-restraints excluded: chain D residue 528 THR Chi-restraints excluded: chain D residue 568 VAL Chi-restraints excluded: chain D residue 646 SER Chi-restraints excluded: chain D residue 678 TRP Chi-restraints excluded: chain D residue 720 LEU Chi-restraints excluded: chain D residue 794 PHE Chi-restraints excluded: chain D residue 803 GLU Chi-restraints excluded: chain D residue 935 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: [29, 87, 74, 90, 28, 152, 94, 32, 68, 71, 107] chunk 29 optimal weight: 0.9990 chunk 87 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 90 optimal weight: 0.5980 chunk 28 optimal weight: 0.7980 chunk 152 optimal weight: 0.0970 chunk 94 optimal weight: 4.9990 chunk 32 optimal weight: 0.9990 chunk 68 optimal weight: 3.9990 chunk 71 optimal weight: 0.9990 chunk 107 optimal weight: 1.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 626 ASN ** D 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.154198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.124520 restraints weight = 19770.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.127573 restraints weight = 12310.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.129718 restraints weight = 8984.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.131081 restraints weight = 7248.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.132166 restraints weight = 6280.984| |-----------------------------------------------------------------------------| r_work (final): 0.3732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.2491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11779 Z= 0.135 Angle : 0.619 9.640 16110 Z= 0.315 Chirality : 0.041 0.179 1869 Planarity : 0.004 0.045 2051 Dihedral : 6.674 89.062 1899 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 2.63 % Allowed : 23.15 % Favored : 74.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.96 % 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: 0.64 (0.23), residues: 1547 helix: 1.93 (0.19), residues: 757 sheet: -1.74 (0.39), residues: 177 loop : -0.80 (0.27), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 818 TYR 0.029 0.002 TYR A 703 PHE 0.035 0.001 PHE D 728 TRP 0.044 0.002 TRP B 749 HIS 0.003 0.000 HIS A 477 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.13 (11758) covalent geometry : angle 0.61265 / 0.31 (16059) SS BOND : bond 0.00151 / 0.11 ( 12) SS BOND : angle 0.72677 / 0.44 ( 24) hydrogen bonds : bond 0.02917 / 1.99 ( 611) hydrogen bonds : angle 4.40900 / 3.14 ( 1788) link_BETA1-4 : bond 0.00365 / 0.19 ( 2) link_BETA1-4 : angle 2.01398 / 1.06 ( 6) link_NAG-ASN : bond 0.00309 / 0.24 ( 7) link_NAG-ASN : angle 2.31693 / 1.67 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2217.23 seconds wall clock time: 38 minutes 47.55 seconds (2327.55 seconds total)