Starting phenix.real_space_refine on Thu Mar 13 19:51:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rtm_24683/03_2025/7rtm_24683.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rtm_24683/03_2025/7rtm_24683.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7rtm_24683/03_2025/7rtm_24683.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rtm_24683/03_2025/7rtm_24683.map" model { file = "/net/cci-nas-00/data/ceres_data/7rtm_24683/03_2025/7rtm_24683.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rtm_24683/03_2025/7rtm_24683.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 8 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 76 5.16 5 Na 2 4.78 5 C 6052 2.51 5 N 1452 2.21 5 O 1579 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 9161 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 571, 4520 Classifications: {'peptide': 571} Link IDs: {'PTRANS': 30, 'TRANS': 540} Chain: "B" Number of atoms: 4519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 571, 4519 Classifications: {'peptide': 571} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 30, 'TRANS': 540} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 19 Unusual residues: {' NA': 1, 'CO3': 1, 'NAG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 19 Unusual residues: {' NA': 1, 'CO3': 1, 'NAG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Residues with excluded nonbonded symmetry interactions: 1051 residue: pdb=" N LEU A 451 " occ=0.00 ... (6 atoms not shown) pdb=" CD2 LEU A 451 " occ=0.00 residue: pdb=" N PHE A 452 " occ=0.00 ... (9 atoms not shown) pdb=" CZ PHE A 452 " occ=0.00 residue: pdb=" N GLY A 453 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY A 453 " occ=0.00 residue: pdb=" N GLY A 454 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY A 454 " occ=0.00 residue: pdb=" N LEU A 455 " occ=0.00 ... (6 atoms not shown) pdb=" CD2 LEU A 455 " occ=0.00 residue: pdb=" N VAL A 456 " occ=0.00 ... (5 atoms not shown) pdb=" CG2 VAL A 456 " occ=0.00 residue: pdb=" N LEU A 457 " occ=0.00 ... (6 atoms not shown) pdb=" CD2 LEU A 457 " occ=0.00 residue: pdb=" N ASP A 458 " occ=0.00 ... (6 atoms not shown) pdb=" OD2 ASP A 458 " occ=0.00 residue: pdb=" N VAL A 459 " occ=0.00 ... (5 atoms not shown) pdb=" CG2 VAL A 459 " occ=0.00 residue: pdb=" N LYS A 460 " occ=0.00 ... (7 atoms not shown) pdb=" NZ LYS A 460 " occ=0.00 residue: pdb=" N ARG A 461 " occ=0.00 ... (9 atoms not shown) pdb=" NH2 ARG A 461 " occ=0.00 residue: pdb=" N LYS A 462 " occ=0.00 ... (7 atoms not shown) pdb=" NZ LYS A 462 " occ=0.00 ... (remaining 1039 not shown) Time building chain proxies: 6.10, per 1000 atoms: 0.67 Number of scatterers: 9161 At special positions: 0 Unit cell: (130.54, 85.6, 108.07, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 76 16.00 Na 2 11.00 O 1579 8.00 N 1452 7.00 C 6052 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 636 " - pdb=" SG CYS A 684 " distance=1.98 Simple disulfide: pdb=" SG CYS A 638 " - pdb=" SG CYS A 672 " distance=2.07 Simple disulfide: pdb=" SG CYS B 636 " - pdb=" SG CYS B 684 " distance=1.73 Simple disulfide: pdb=" SG CYS B 638 " - pdb=" SG CYS B 672 " distance=2.00 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=1, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " NAG C 3 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " NAG D 3 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.20 Conformation dependent library (CDL) restraints added in 1.2 seconds 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2160 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 3 sheets defined 68.6% alpha, 1.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.55 Creating SS restraints... Processing helix chain 'A' and resid 455 through 461 removed outlier: 4.185A pdb=" N VAL A 459 " --> pdb=" O LEU A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 472 removed outlier: 3.777A pdb=" N ARG A 471 " --> pdb=" O TRP A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 491 removed outlier: 3.814A pdb=" N CYS A 487 " --> pdb=" O LEU A 483 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER A 491 " --> pdb=" O CYS A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 504 removed outlier: 3.791A pdb=" N ALA A 503 " --> pdb=" O LEU A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 528 removed outlier: 3.570A pdb=" N LEU A 526 " --> pdb=" O ILE A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 552 removed outlier: 4.205A pdb=" N LEU A 542 " --> pdb=" O THR A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 581 removed outlier: 3.734A pdb=" N LEU A 562 " --> pdb=" O SER A 558 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N THR A 580 " --> pdb=" O VAL A 576 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASP A 581 " --> pdb=" O LEU A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 583 through 589 Processing helix chain 'A' and resid 590 through 620 removed outlier: 3.637A pdb=" N LEU A 600 " --> pdb=" O ALA A 596 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 634 removed outlier: 4.355A pdb=" N SER A 632 " --> pdb=" O ASP A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 645 through 655 removed outlier: 3.640A pdb=" N HIS A 655 " --> pdb=" O TYR A 651 " (cutoff:3.500A) Processing helix chain 'A' and resid 659 through 663 removed outlier: 3.693A pdb=" N VAL A 662 " --> pdb=" O THR A 659 " (cutoff:3.500A) Processing helix chain 'A' and resid 668 through 675 removed outlier: 3.570A pdb=" N GLU A 674 " --> pdb=" O SER A 670 " (cutoff:3.500A) Processing helix chain 'A' and resid 693 through 714 removed outlier: 3.910A pdb=" N SER A 710 " --> pdb=" O PHE A 706 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR A 714 " --> pdb=" O SER A 710 " (cutoff:3.500A) Processing helix chain 'A' and resid 715 through 718 Processing helix chain 'A' and resid 722 through 732 removed outlier: 4.137A pdb=" N THR A 728 " --> pdb=" O ARG A 724 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N VAL A 729 " --> pdb=" O VAL A 725 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N SER A 730 " --> pdb=" O ARG A 726 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASP A 731 " --> pdb=" O SER A 727 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N PHE A 732 " --> pdb=" O THR A 728 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 748 Processing helix chain 'A' and resid 779 through 786 removed outlier: 4.280A pdb=" N VAL A 783 " --> pdb=" O PRO A 779 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ILE A 784 " --> pdb=" O TRP A 780 " (cutoff:3.500A) Processing helix chain 'A' and resid 786 through 809 Processing helix chain 'A' and resid 820 through 838 Processing helix chain 'A' and resid 846 through 857 removed outlier: 3.681A pdb=" N SER A 850 " --> pdb=" O ALA A 846 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU A 857 " --> pdb=" O HIS A 853 " (cutoff:3.500A) Processing helix chain 'A' and resid 880 through 892 removed outlier: 3.579A pdb=" N MET A 884 " --> pdb=" O VAL A 880 " (cutoff:3.500A) Processing helix chain 'A' and resid 903 through 919 removed outlier: 3.959A pdb=" N LEU A 907 " --> pdb=" O PRO A 903 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N LEU A 919 " --> pdb=" O GLY A 915 " (cutoff:3.500A) Processing helix chain 'A' and resid 922 through 929 removed outlier: 3.603A pdb=" N ASP A 926 " --> pdb=" O ILE A 922 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 947 removed outlier: 3.579A pdb=" N HIS A 946 " --> pdb=" O ILE A 942 " (cutoff:3.500A) Processing helix chain 'A' and resid 948 through 971 Processing helix chain 'A' and resid 980 through 996 removed outlier: 3.868A pdb=" N ALA A 984 " --> pdb=" O MET A 980 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG A 989 " --> pdb=" O LEU A 985 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N MET A 992 " --> pdb=" O VAL A 988 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ASP A 993 " --> pdb=" O ARG A 989 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N LEU A 994 " --> pdb=" O LYS A 990 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N CYS A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 998 through 1002 Processing helix chain 'A' and resid 1009 through 1019 removed outlier: 3.518A pdb=" N LYS A1013 " --> pdb=" O PRO A1009 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 463 removed outlier: 4.117A pdb=" N VAL B 459 " --> pdb=" O LEU B 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 469 removed outlier: 4.610A pdb=" N TRP B 467 " --> pdb=" O ALA B 463 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N SER B 468 " --> pdb=" O PRO B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 504 removed outlier: 3.603A pdb=" N SER B 491 " --> pdb=" O CYS B 487 " (cutoff:3.500A) Proline residue: B 492 - end of helix removed outlier: 4.072A pdb=" N ALA B 503 " --> pdb=" O LEU B 499 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 528 removed outlier: 3.840A pdb=" N LEU B 526 " --> pdb=" O ILE B 522 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA B 528 " --> pdb=" O TYR B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 552 removed outlier: 3.684A pdb=" N LEU B 542 " --> pdb=" O THR B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 558 through 581 removed outlier: 3.754A pdb=" N LEU B 562 " --> pdb=" O SER B 558 " (cutoff:3.500A) Processing helix chain 'B' and resid 585 through 589 removed outlier: 3.754A pdb=" N ILE B 589 " --> pdb=" O VAL B 586 " (cutoff:3.500A) Processing helix chain 'B' and resid 590 through 620 Processing helix chain 'B' and resid 627 through 634 removed outlier: 4.359A pdb=" N SER B 632 " --> pdb=" O ASP B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 645 through 655 removed outlier: 3.642A pdb=" N HIS B 655 " --> pdb=" O TYR B 651 " (cutoff:3.500A) Processing helix chain 'B' and resid 660 through 664 Processing helix chain 'B' and resid 668 through 673 removed outlier: 3.922A pdb=" N GLN B 673 " --> pdb=" O VAL B 669 " (cutoff:3.500A) Processing helix chain 'B' and resid 693 through 714 removed outlier: 3.661A pdb=" N ILE B 707 " --> pdb=" O PHE B 703 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N SER B 710 " --> pdb=" O PHE B 706 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR B 714 " --> pdb=" O SER B 710 " (cutoff:3.500A) Processing helix chain 'B' and resid 715 through 718 Processing helix chain 'B' and resid 722 through 727 removed outlier: 3.658A pdb=" N ARG B 726 " --> pdb=" O PRO B 722 " (cutoff:3.500A) Processing helix chain 'B' and resid 732 through 748 Processing helix chain 'B' and resid 763 through 767 removed outlier: 4.354A pdb=" N ASP B 766 " --> pdb=" O PRO B 763 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ASP B 767 " --> pdb=" O THR B 764 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 763 through 767' Processing helix chain 'B' and resid 779 through 786 removed outlier: 4.576A pdb=" N VAL B 783 " --> pdb=" O PRO B 779 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ILE B 784 " --> pdb=" O TRP B 780 " (cutoff:3.500A) Processing helix chain 'B' and resid 786 through 809 removed outlier: 3.515A pdb=" N ILE B 795 " --> pdb=" O LEU B 791 " (cutoff:3.500A) Processing helix chain 'B' and resid 820 through 838 removed outlier: 3.797A pdb=" N ASP B 824 " --> pdb=" O GLY B 820 " (cutoff:3.500A) Processing helix chain 'B' and resid 846 through 857 removed outlier: 3.732A pdb=" N SER B 850 " --> pdb=" O ALA B 846 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LEU B 857 " --> pdb=" O HIS B 853 " (cutoff:3.500A) Processing helix chain 'B' and resid 880 through 891 Processing helix chain 'B' and resid 892 through 894 No H-bonds generated for 'chain 'B' and resid 892 through 894' Processing helix chain 'B' and resid 896 through 901 removed outlier: 3.818A pdb=" N PHE B 901 " --> pdb=" O ALA B 897 " (cutoff:3.500A) Processing helix chain 'B' and resid 903 through 919 removed outlier: 4.041A pdb=" N LEU B 907 " --> pdb=" O PRO B 903 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LEU B 919 " --> pdb=" O GLY B 915 " (cutoff:3.500A) Processing helix chain 'B' and resid 922 through 929 removed outlier: 4.187A pdb=" N ASP B 926 " --> pdb=" O ILE B 922 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ARG B 927 " --> pdb=" O GLN B 923 " (cutoff:3.500A) Processing helix chain 'B' and resid 941 through 945 Processing helix chain 'B' and resid 948 through 972 Processing helix chain 'B' and resid 977 through 996 removed outlier: 3.953A pdb=" N VAL B 982 " --> pdb=" O PHE B 978 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N LEU B 983 " --> pdb=" O PRO B 979 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ALA B 984 " --> pdb=" O MET B 980 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG B 989 " --> pdb=" O LEU B 985 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N VAL B 991 " --> pdb=" O PHE B 987 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ASP B 993 " --> pdb=" O ARG B 989 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N LEU B 994 " --> pdb=" O LYS B 990 " (cutoff:3.500A) Processing helix chain 'B' and resid 997 through 1001 Processing helix chain 'B' and resid 1009 through 1019 removed outlier: 3.772A pdb=" N LYS B1013 " --> pdb=" O PRO B1009 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 535 through 536 Processing sheet with id=AA2, first strand: chain 'A' and resid 636 through 639 Processing sheet with id=AA3, first strand: chain 'B' and resid 636 through 639 487 hydrogen bonds defined for protein. 1380 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.62 Time building geometry restraints manager: 2.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.32: 1448 1.32 - 1.47: 3650 1.47 - 1.63: 4191 1.63 - 1.78: 21 1.78 - 1.94: 101 Bond restraints: 9411 Sorted by residual: bond pdb=" CA GLY B 501 " pdb=" C GLY B 501 " ideal model delta sigma weight residual 1.516 1.387 0.129 1.09e-02 8.42e+03 1.41e+02 bond pdb=" NE ARG A 471 " pdb=" CZ ARG A 471 " ideal model delta sigma weight residual 1.326 1.444 -0.118 1.10e-02 8.26e+03 1.15e+02 bond pdb=" C ALA A 897 " pdb=" N VAL A 898 " ideal model delta sigma weight residual 1.335 1.463 -0.129 1.26e-02 6.30e+03 1.04e+02 bond pdb=" N PHE B 702 " pdb=" CA PHE B 702 " ideal model delta sigma weight residual 1.459 1.345 0.114 1.17e-02 7.31e+03 9.44e+01 bond pdb=" ND1 HIS B 625 " pdb=" CE1 HIS B 625 " ideal model delta sigma weight residual 1.321 1.416 -0.095 1.00e-02 1.00e+04 9.11e+01 ... (remaining 9406 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.78: 8745 2.78 - 5.55: 3033 5.55 - 8.33: 827 8.33 - 11.10: 163 11.10 - 13.88: 27 Bond angle restraints: 12795 Sorted by residual: angle pdb=" N VAL A 893 " pdb=" CA VAL A 893 " pdb=" C VAL A 893 " ideal model delta sigma weight residual 113.53 102.71 10.82 9.80e-01 1.04e+00 1.22e+02 angle pdb=" CA ALA B 463 " pdb=" C ALA B 463 " pdb=" N PRO B 464 " ideal model delta sigma weight residual 120.93 132.26 -11.33 1.06e+00 8.90e-01 1.14e+02 angle pdb=" CA ALA B 463 " pdb=" C ALA B 463 " pdb=" O ALA B 463 " ideal model delta sigma weight residual 118.34 108.90 9.44 9.70e-01 1.06e+00 9.47e+01 angle pdb=" N GLN B 920 " pdb=" CA GLN B 920 " pdb=" C GLN B 920 " ideal model delta sigma weight residual 113.23 101.30 11.93 1.24e+00 6.50e-01 9.26e+01 angle pdb=" N GLU B1010 " pdb=" CA GLU B1010 " pdb=" C GLU B1010 " ideal model delta sigma weight residual 111.71 122.71 -11.00 1.15e+00 7.56e-01 9.15e+01 ... (remaining 12790 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.66: 5358 24.66 - 49.31: 213 49.31 - 73.97: 45 73.97 - 98.62: 21 98.62 - 123.28: 10 Dihedral angle restraints: 5647 sinusoidal: 2311 harmonic: 3336 Sorted by residual: dihedral pdb=" C SER A 468 " pdb=" N SER A 468 " pdb=" CA SER A 468 " pdb=" CB SER A 468 " ideal model delta harmonic sigma weight residual -122.60 -140.76 18.16 0 2.50e+00 1.60e-01 5.28e+01 dihedral pdb=" N MET B 981 " pdb=" C MET B 981 " pdb=" CA MET B 981 " pdb=" CB MET B 981 " ideal model delta harmonic sigma weight residual 122.80 139.52 -16.72 0 2.50e+00 1.60e-01 4.47e+01 dihedral pdb=" C GLU B1010 " pdb=" N GLU B1010 " pdb=" CA GLU B1010 " pdb=" CB GLU B1010 " ideal model delta harmonic sigma weight residual -122.60 -138.66 16.06 0 2.50e+00 1.60e-01 4.13e+01 ... (remaining 5644 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.147: 944 0.147 - 0.294: 389 0.294 - 0.442: 130 0.442 - 0.589: 35 0.589 - 0.736: 6 Chirality restraints: 1504 Sorted by residual: chirality pdb=" C1 NAG D 3 " pdb=" O4 NAG D 2 " pdb=" C2 NAG D 3 " pdb=" O5 NAG D 3 " both_signs ideal model delta sigma weight residual False -2.40 -1.88 -0.52 2.00e-02 2.50e+03 6.78e+02 chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-02 2.50e+03 1.61e+02 chirality pdb=" C1 NAG C 2 " pdb=" O4 NAG C 1 " pdb=" C2 NAG C 2 " pdb=" O5 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.53 0.13 2.00e-02 2.50e+03 4.18e+01 ... (remaining 1501 not shown) Planarity restraints: 1548 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 3 " 0.313 2.00e-02 2.50e+03 2.69e-01 9.04e+02 pdb=" C7 NAG D 3 " -0.075 2.00e-02 2.50e+03 pdb=" C8 NAG D 3 " 0.167 2.00e-02 2.50e+03 pdb=" N2 NAG D 3 " -0.475 2.00e-02 2.50e+03 pdb=" O7 NAG D 3 " 0.070 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 2 " 0.305 2.00e-02 2.50e+03 2.63e-01 8.61e+02 pdb=" C7 NAG D 2 " -0.068 2.00e-02 2.50e+03 pdb=" C8 NAG D 2 " -0.002 2.00e-02 2.50e+03 pdb=" N2 NAG D 2 " -0.449 2.00e-02 2.50e+03 pdb=" O7 NAG D 2 " 0.214 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 1 " -0.270 2.00e-02 2.50e+03 2.30e-01 6.64e+02 pdb=" C7 NAG D 1 " 0.067 2.00e-02 2.50e+03 pdb=" C8 NAG D 1 " -0.169 2.00e-02 2.50e+03 pdb=" N2 NAG D 1 " 0.398 2.00e-02 2.50e+03 pdb=" O7 NAG D 1 " -0.026 2.00e-02 2.50e+03 ... (remaining 1545 not shown) Histogram of nonbonded interaction distances: 1.05 - 1.82: 8 1.82 - 2.59: 171 2.59 - 3.36: 11742 3.36 - 4.13: 21331 4.13 - 4.90: 37386 Nonbonded interactions: 70638 Sorted by model distance: nonbonded pdb=" CD2 HIS A 937 " pdb=" CB PRO B 866 " model vdw 1.051 3.660 nonbonded pdb=" O ALA A 845 " pdb="NA NA A1102 " model vdw 1.122 2.470 nonbonded pdb=" O LEU A 476 " pdb=" OD2 ASP A 731 " model vdw 1.520 3.040 nonbonded pdb=" SG CYS A 565 " pdb=" CD1 ILE A 775 " model vdw 1.625 3.820 nonbonded pdb=" CD1 PHE A 484 " pdb=" CG1 VAL A 734 " model vdw 1.667 3.760 ... (remaining 70633 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 451 through 772 or (resid 773 and (name N or name CA or na \ me C or name O or name CB )) or resid 774 through 1021 or resid 1101 through 110 \ 3)) selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.06 Reset to 1. Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 1.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.010 Set scattering table: 0.090 Process input model: 25.750 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.320 Load rotamer database and sin/cos tables:3.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4590 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 : 0.031 0.131 9411 Z= 1.992 Angle : 3.049 13.876 12795 Z= 2.132 Chirality : 0.185 0.736 1504 Planarity : 0.028 0.269 1548 Dihedral : 16.560 123.278 3475 Min Nonbonded Distance : 1.051 Molprobity Statistics. All-atom Clashscore : 36.92 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.77 % Favored : 92.97 % Rotamer: Outliers : 2.80 % Allowed : 9.29 % Favored : 87.91 % Cbeta Deviations : 4.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.23), residues: 1138 helix: 0.06 (0.19), residues: 672 sheet: None (None), residues: 0 loop : -1.93 (0.25), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.275 0.042 TRP B 467 HIS 0.043 0.007 HIS B 822 PHE 0.214 0.030 PHE B 955 TYR 0.184 0.042 TYR A 607 ARG 0.055 0.007 ARG B 637 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 352 time to evaluate : 1.009 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 988 VAL cc_start: 0.2821 (p) cc_final: 0.2144 (t) REVERT: B 700 ILE cc_start: 0.4583 (mt) cc_final: 0.4293 (mt) REVERT: B 881 THR cc_start: 0.4669 (p) cc_final: 0.4140 (p) REVERT: B 988 VAL cc_start: 0.3922 (p) cc_final: 0.3317 (t) outliers start: 28 outliers final: 5 residues processed: 373 average time/residue: 0.2079 time to fit residues: 106.9141 Evaluate side-chains 202 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 197 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 623 HIS Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 943 TYR Chi-restraints excluded: chain B residue 657 ILE Chi-restraints excluded: chain B residue 691 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 0.9990 chunk 86 optimal weight: 0.6980 chunk 47 optimal weight: 0.9990 chunk 29 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 89 optimal weight: 5.9990 chunk 34 optimal weight: 0.9990 chunk 54 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 chunk 103 optimal weight: 0.7980 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 477 GLN ** A 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 630 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 647 HIS A 655 HIS A 663 ASN A 686 HIS A 937 HIS ** B 625 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 627 GLN B 643 ASN B 646 ASN B 676 HIS B 686 HIS B 822 HIS B 855 ASN B 869 GLN B 923 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4435 r_free = 0.4435 target = 0.145613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.130087 restraints weight = 28311.499| |-----------------------------------------------------------------------------| r_work (start): 0.4215 rms_B_bonded: 3.68 r_work: 0.4096 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.4096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6884 moved from start: 0.4514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 9411 Z= 0.292 Angle : 0.903 11.555 12795 Z= 0.456 Chirality : 0.050 0.231 1504 Planarity : 0.007 0.068 1548 Dihedral : 13.051 109.635 1390 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.43 % Favored : 96.49 % Rotamer: Outliers : 3.30 % Allowed : 16.98 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.24), residues: 1138 helix: 0.30 (0.19), residues: 702 sheet: None (None), residues: 0 loop : -1.32 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP B 467 HIS 0.016 0.002 HIS A 630 PHE 0.023 0.003 PHE A 496 TYR 0.033 0.002 TYR B 486 ARG 0.006 0.001 ARG A 927 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 198 time to evaluate : 0.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 486 TYR cc_start: 0.7620 (t80) cc_final: 0.7362 (t80) REVERT: A 663 ASN cc_start: 0.8241 (m110) cc_final: 0.7966 (p0) REVERT: A 831 MET cc_start: 0.7219 (mmm) cc_final: 0.6551 (mmm) REVERT: A 888 LEU cc_start: 0.8776 (tp) cc_final: 0.8087 (tp) REVERT: A 923 GLN cc_start: 0.6861 (tt0) cc_final: 0.6645 (tt0) REVERT: A 990 LYS cc_start: 0.6139 (tmtt) cc_final: 0.5586 (mmmt) REVERT: A 1012 LYS cc_start: 0.8721 (OUTLIER) cc_final: 0.8419 (mmpt) REVERT: B 478 CYS cc_start: 0.8203 (OUTLIER) cc_final: 0.7719 (p) REVERT: B 615 HIS cc_start: 0.8349 (t70) cc_final: 0.7909 (m-70) REVERT: B 643 ASN cc_start: 0.8364 (m-40) cc_final: 0.8098 (m110) REVERT: B 700 ILE cc_start: 0.5857 (mt) cc_final: 0.5477 (mt) REVERT: B 906 VAL cc_start: 0.5756 (p) cc_final: 0.4361 (t) outliers start: 33 outliers final: 14 residues processed: 222 average time/residue: 0.1886 time to fit residues: 60.1289 Evaluate side-chains 175 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 159 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 720 TYR Chi-restraints excluded: chain A residue 737 THR Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 828 VAL Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 881 THR Chi-restraints excluded: chain A residue 930 LEU Chi-restraints excluded: chain A residue 947 VAL Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1012 LYS Chi-restraints excluded: chain B residue 472 ASP Chi-restraints excluded: chain B residue 478 CYS Chi-restraints excluded: chain B residue 629 ASP Chi-restraints excluded: chain B residue 640 LEU Chi-restraints excluded: chain B residue 712 LEU Chi-restraints excluded: chain B residue 844 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 110 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 40 optimal weight: 0.0030 chunk 26 optimal weight: 6.9990 chunk 19 optimal weight: 0.2980 chunk 103 optimal weight: 0.8980 chunk 94 optimal weight: 10.0000 chunk 69 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 chunk 27 optimal weight: 0.2980 chunk 23 optimal weight: 9.9990 overall best weight: 0.4390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 630 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 923 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.143214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.127154 restraints weight = 28673.411| |-----------------------------------------------------------------------------| r_work (start): 0.4171 rms_B_bonded: 3.73 r_work: 0.4055 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.4055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6986 moved from start: 0.5334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9411 Z= 0.213 Angle : 0.780 11.129 12795 Z= 0.386 Chirality : 0.047 0.229 1504 Planarity : 0.005 0.060 1548 Dihedral : 11.845 103.672 1383 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.13 % Favored : 95.78 % Rotamer: Outliers : 3.30 % Allowed : 17.78 % Favored : 78.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.24), residues: 1138 helix: 0.47 (0.19), residues: 704 sheet: None (None), residues: 0 loop : -1.07 (0.29), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 770 HIS 0.014 0.001 HIS B 647 PHE 0.017 0.002 PHE B 679 TYR 0.029 0.002 TYR A 634 ARG 0.003 0.001 ARG A 927 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 181 time to evaluate : 1.071 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 486 TYR cc_start: 0.7517 (t80) cc_final: 0.7131 (t80) REVERT: A 624 MET cc_start: 0.7619 (tpt) cc_final: 0.6612 (ttp) REVERT: A 673 GLN cc_start: 0.7968 (tm-30) cc_final: 0.7728 (tm-30) REVERT: A 851 ILE cc_start: 0.8270 (mm) cc_final: 0.8009 (mm) REVERT: A 857 LEU cc_start: 0.7452 (OUTLIER) cc_final: 0.7159 (pp) REVERT: A 888 LEU cc_start: 0.8596 (tp) cc_final: 0.7842 (tp) REVERT: A 923 GLN cc_start: 0.6752 (tt0) cc_final: 0.6549 (tt0) REVERT: A 990 LYS cc_start: 0.6067 (tmtt) cc_final: 0.5381 (mmtp) REVERT: B 486 TYR cc_start: 0.7955 (t80) cc_final: 0.7527 (t80) REVERT: B 490 MET cc_start: 0.7748 (OUTLIER) cc_final: 0.7316 (ttt) REVERT: B 615 HIS cc_start: 0.8255 (OUTLIER) cc_final: 0.7771 (m-70) REVERT: B 643 ASN cc_start: 0.8269 (m-40) cc_final: 0.7936 (m110) REVERT: B 700 ILE cc_start: 0.6248 (mt) cc_final: 0.5742 (mt) REVERT: B 762 LYS cc_start: 0.7081 (OUTLIER) cc_final: 0.6829 (pptt) REVERT: B 831 MET cc_start: 0.7468 (mmm) cc_final: 0.7161 (mmm) REVERT: B 906 VAL cc_start: 0.6069 (p) cc_final: 0.4739 (t) outliers start: 33 outliers final: 13 residues processed: 207 average time/residue: 0.1955 time to fit residues: 59.3196 Evaluate side-chains 160 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 143 time to evaluate : 1.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 720 TYR Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 857 LEU Chi-restraints excluded: chain A residue 881 THR Chi-restraints excluded: chain A residue 947 VAL Chi-restraints excluded: chain B residue 472 ASP Chi-restraints excluded: chain B residue 490 MET Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 602 CYS Chi-restraints excluded: chain B residue 615 HIS Chi-restraints excluded: chain B residue 668 THR Chi-restraints excluded: chain B residue 712 LEU Chi-restraints excluded: chain B residue 762 LYS Chi-restraints excluded: chain B residue 844 VAL Chi-restraints excluded: chain B residue 977 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 80 optimal weight: 10.0000 chunk 36 optimal weight: 0.0980 chunk 87 optimal weight: 0.5980 chunk 60 optimal weight: 0.9990 chunk 67 optimal weight: 9.9990 chunk 106 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 41 optimal weight: 10.0000 chunk 85 optimal weight: 0.9980 chunk 86 optimal weight: 0.9990 chunk 20 optimal weight: 6.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 630 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 645 ASN ** B 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.138255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.121710 restraints weight = 28304.183| |-----------------------------------------------------------------------------| r_work (start): 0.4091 rms_B_bonded: 3.66 r_work: 0.3973 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.3973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7165 moved from start: 0.5998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9411 Z= 0.207 Angle : 0.745 10.025 12795 Z= 0.361 Chirality : 0.045 0.240 1504 Planarity : 0.005 0.058 1548 Dihedral : 11.156 97.388 1383 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.18 % Favored : 94.73 % Rotamer: Outliers : 4.20 % Allowed : 19.78 % Favored : 76.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.24), residues: 1138 helix: 0.64 (0.19), residues: 701 sheet: None (None), residues: 0 loop : -1.00 (0.29), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 652 HIS 0.007 0.001 HIS A 630 PHE 0.035 0.002 PHE A 987 TYR 0.022 0.001 TYR A 634 ARG 0.002 0.001 ARG A 563 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 149 time to evaluate : 1.021 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 486 TYR cc_start: 0.7789 (t80) cc_final: 0.7506 (t80) REVERT: A 624 MET cc_start: 0.7732 (tpt) cc_final: 0.6678 (ttp) REVERT: A 831 MET cc_start: 0.7569 (mmm) cc_final: 0.6798 (mmm) REVERT: A 851 ILE cc_start: 0.8368 (mm) cc_final: 0.8110 (mm) REVERT: A 888 LEU cc_start: 0.8677 (tp) cc_final: 0.8274 (tp) REVERT: A 923 GLN cc_start: 0.6924 (tt0) cc_final: 0.6690 (tt0) REVERT: A 990 LYS cc_start: 0.6148 (tmtt) cc_final: 0.5412 (mmtp) REVERT: B 490 MET cc_start: 0.7987 (OUTLIER) cc_final: 0.7406 (ttt) REVERT: B 615 HIS cc_start: 0.8273 (OUTLIER) cc_final: 0.7877 (t70) outliers start: 42 outliers final: 25 residues processed: 180 average time/residue: 0.1495 time to fit residues: 41.8438 Evaluate side-chains 158 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 131 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 487 CYS Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 664 TRP Chi-restraints excluded: chain A residue 700 ILE Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 720 TYR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 828 VAL Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 881 THR Chi-restraints excluded: chain A residue 891 CYS Chi-restraints excluded: chain A residue 930 LEU Chi-restraints excluded: chain A residue 947 VAL Chi-restraints excluded: chain A residue 1006 ASP Chi-restraints excluded: chain B residue 472 ASP Chi-restraints excluded: chain B residue 490 MET Chi-restraints excluded: chain B residue 513 SER Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 602 CYS Chi-restraints excluded: chain B residue 615 HIS Chi-restraints excluded: chain B residue 616 LEU Chi-restraints excluded: chain B residue 668 THR Chi-restraints excluded: chain B residue 844 VAL Chi-restraints excluded: chain B residue 962 CYS Chi-restraints excluded: chain B residue 977 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 98 optimal weight: 5.9990 chunk 79 optimal weight: 0.9990 chunk 23 optimal weight: 3.9990 chunk 102 optimal weight: 0.9990 chunk 59 optimal weight: 0.0470 chunk 62 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 chunk 89 optimal weight: 0.3980 chunk 71 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 6 optimal weight: 0.2980 overall best weight: 0.5480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 650 GLN B 801 GLN B 953 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.135940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.118919 restraints weight = 28340.236| |-----------------------------------------------------------------------------| r_work (start): 0.4047 rms_B_bonded: 3.65 r_work: 0.3927 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.3927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7253 moved from start: 0.6435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9411 Z= 0.188 Angle : 0.722 10.254 12795 Z= 0.346 Chirality : 0.045 0.236 1504 Planarity : 0.005 0.059 1548 Dihedral : 10.386 90.242 1383 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.18 % Favored : 94.73 % Rotamer: Outliers : 3.90 % Allowed : 21.38 % Favored : 74.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.25), residues: 1138 helix: 0.78 (0.20), residues: 704 sheet: None (None), residues: 0 loop : -0.94 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 652 HIS 0.006 0.001 HIS A 630 PHE 0.025 0.002 PHE A 496 TYR 0.019 0.001 TYR B 486 ARG 0.004 0.000 ARG B 950 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 150 time to evaluate : 0.946 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 486 TYR cc_start: 0.7937 (t80) cc_final: 0.7561 (t80) REVERT: A 624 MET cc_start: 0.7732 (tpt) cc_final: 0.6725 (ttp) REVERT: A 851 ILE cc_start: 0.8442 (mm) cc_final: 0.8196 (mm) REVERT: A 888 LEU cc_start: 0.8681 (tp) cc_final: 0.8261 (tp) REVERT: A 923 GLN cc_start: 0.7002 (tt0) cc_final: 0.6797 (tt0) REVERT: A 990 LYS cc_start: 0.6265 (tmtt) cc_final: 0.5526 (mmtp) REVERT: B 615 HIS cc_start: 0.8243 (OUTLIER) cc_final: 0.7853 (t70) REVERT: B 931 PHE cc_start: 0.6717 (OUTLIER) cc_final: 0.6397 (m-10) outliers start: 39 outliers final: 24 residues processed: 177 average time/residue: 0.1576 time to fit residues: 42.6183 Evaluate side-chains 158 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 132 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 487 CYS Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 664 TRP Chi-restraints excluded: chain A residue 700 ILE Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 720 TYR Chi-restraints excluded: chain A residue 828 VAL Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 881 THR Chi-restraints excluded: chain A residue 891 CYS Chi-restraints excluded: chain A residue 947 VAL Chi-restraints excluded: chain A residue 1006 ASP Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1017 ASP Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 602 CYS Chi-restraints excluded: chain B residue 615 HIS Chi-restraints excluded: chain B residue 616 LEU Chi-restraints excluded: chain B residue 668 THR Chi-restraints excluded: chain B residue 760 VAL Chi-restraints excluded: chain B residue 844 VAL Chi-restraints excluded: chain B residue 906 VAL Chi-restraints excluded: chain B residue 931 PHE Chi-restraints excluded: chain B residue 977 VAL Chi-restraints excluded: chain B residue 996 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 33 optimal weight: 3.9990 chunk 81 optimal weight: 5.9990 chunk 45 optimal weight: 0.0870 chunk 72 optimal weight: 2.9990 chunk 23 optimal weight: 7.9990 chunk 93 optimal weight: 0.2980 chunk 60 optimal weight: 0.0870 chunk 104 optimal weight: 5.9990 chunk 54 optimal weight: 0.9980 chunk 84 optimal weight: 0.5980 chunk 47 optimal weight: 0.9980 overall best weight: 0.4136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 625 HIS A 920 GLN B 822 HIS B 855 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.134731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.117501 restraints weight = 28173.219| |-----------------------------------------------------------------------------| r_work (start): 0.4023 rms_B_bonded: 3.63 r_work: 0.3905 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.3905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7297 moved from start: 0.6756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9411 Z= 0.178 Angle : 0.728 9.012 12795 Z= 0.351 Chirality : 0.045 0.247 1504 Planarity : 0.005 0.058 1548 Dihedral : 9.738 84.108 1382 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.57 % Favored : 95.34 % Rotamer: Outliers : 3.80 % Allowed : 21.78 % Favored : 74.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.25), residues: 1138 helix: 0.85 (0.20), residues: 698 sheet: None (None), residues: 0 loop : -0.88 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 770 HIS 0.010 0.001 HIS A 687 PHE 0.064 0.002 PHE A 987 TYR 0.044 0.001 TYR B 486 ARG 0.004 0.000 ARG B 765 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 160 time to evaluate : 0.948 Fit side-chains revert: symmetry clash REVERT: A 486 TYR cc_start: 0.7950 (t80) cc_final: 0.7502 (t80) REVERT: A 624 MET cc_start: 0.7723 (tpt) cc_final: 0.6660 (ttp) REVERT: A 851 ILE cc_start: 0.8453 (mm) cc_final: 0.8225 (mm) REVERT: A 888 LEU cc_start: 0.8652 (tp) cc_final: 0.8164 (tp) REVERT: A 923 GLN cc_start: 0.7076 (tt0) cc_final: 0.6869 (tt0) REVERT: A 990 LYS cc_start: 0.6304 (tmtt) cc_final: 0.5503 (mmtm) REVERT: B 615 HIS cc_start: 0.8269 (OUTLIER) cc_final: 0.7908 (t70) REVERT: B 801 GLN cc_start: 0.7285 (mm110) cc_final: 0.6791 (tp40) REVERT: B 931 PHE cc_start: 0.6735 (OUTLIER) cc_final: 0.6376 (m-10) outliers start: 38 outliers final: 26 residues processed: 190 average time/residue: 0.1705 time to fit residues: 48.2167 Evaluate side-chains 163 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 135 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 487 CYS Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 664 TRP Chi-restraints excluded: chain A residue 700 ILE Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 720 TYR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 891 CYS Chi-restraints excluded: chain A residue 898 VAL Chi-restraints excluded: chain A residue 906 VAL Chi-restraints excluded: chain A residue 930 LEU Chi-restraints excluded: chain A residue 947 VAL Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1006 ASP Chi-restraints excluded: chain A residue 1017 ASP Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 602 CYS Chi-restraints excluded: chain B residue 615 HIS Chi-restraints excluded: chain B residue 616 LEU Chi-restraints excluded: chain B residue 668 THR Chi-restraints excluded: chain B residue 813 HIS Chi-restraints excluded: chain B residue 844 VAL Chi-restraints excluded: chain B residue 906 VAL Chi-restraints excluded: chain B residue 930 LEU Chi-restraints excluded: chain B residue 931 PHE Chi-restraints excluded: chain B residue 977 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 51 optimal weight: 2.9990 chunk 22 optimal weight: 0.4980 chunk 67 optimal weight: 0.9990 chunk 97 optimal weight: 0.6980 chunk 87 optimal weight: 0.9980 chunk 109 optimal weight: 0.0970 chunk 20 optimal weight: 5.9990 chunk 29 optimal weight: 0.8980 chunk 105 optimal weight: 7.9990 chunk 16 optimal weight: 2.9990 chunk 99 optimal weight: 4.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 920 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.131758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.114007 restraints weight = 28926.404| |-----------------------------------------------------------------------------| r_work (start): 0.3965 rms_B_bonded: 3.69 r_work: 0.3847 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.3847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 moved from start: 0.7180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9411 Z= 0.191 Angle : 0.759 13.541 12795 Z= 0.359 Chirality : 0.045 0.255 1504 Planarity : 0.005 0.057 1548 Dihedral : 9.220 79.923 1382 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.75 % Favored : 95.17 % Rotamer: Outliers : 4.00 % Allowed : 22.38 % Favored : 73.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.25), residues: 1138 helix: 0.89 (0.20), residues: 697 sheet: -1.87 (1.18), residues: 10 loop : -0.95 (0.29), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 465 HIS 0.004 0.001 HIS A 630 PHE 0.047 0.002 PHE A 987 TYR 0.064 0.001 TYR B 486 ARG 0.003 0.000 ARG B 768 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 147 time to evaluate : 0.947 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 486 TYR cc_start: 0.7823 (t80) cc_final: 0.7490 (t80) REVERT: A 624 MET cc_start: 0.7699 (tpt) cc_final: 0.6575 (ttp) REVERT: A 851 ILE cc_start: 0.8639 (mm) cc_final: 0.8426 (mm) REVERT: A 888 LEU cc_start: 0.8604 (tp) cc_final: 0.8232 (tp) REVERT: A 923 GLN cc_start: 0.7137 (tt0) cc_final: 0.6913 (tt0) REVERT: A 990 LYS cc_start: 0.6305 (tmtt) cc_final: 0.5530 (mmtm) REVERT: A 1008 MET cc_start: 0.7695 (ttp) cc_final: 0.7486 (tmm) REVERT: B 478 CYS cc_start: 0.8180 (OUTLIER) cc_final: 0.7817 (p) REVERT: B 615 HIS cc_start: 0.8224 (OUTLIER) cc_final: 0.7646 (t70) REVERT: B 761 PHE cc_start: 0.5602 (t80) cc_final: 0.5301 (t80) REVERT: B 801 GLN cc_start: 0.7379 (mm110) cc_final: 0.6954 (tp40) REVERT: B 931 PHE cc_start: 0.6859 (OUTLIER) cc_final: 0.6462 (m-10) outliers start: 40 outliers final: 24 residues processed: 174 average time/residue: 0.1499 time to fit residues: 40.3392 Evaluate side-chains 157 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 130 time to evaluate : 1.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 487 CYS Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 664 TRP Chi-restraints excluded: chain A residue 700 ILE Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 720 TYR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 828 VAL Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 891 CYS Chi-restraints excluded: chain A residue 906 VAL Chi-restraints excluded: chain A residue 930 LEU Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1006 ASP Chi-restraints excluded: chain A residue 1017 ASP Chi-restraints excluded: chain B residue 478 CYS Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 615 HIS Chi-restraints excluded: chain B residue 616 LEU Chi-restraints excluded: chain B residue 668 THR Chi-restraints excluded: chain B residue 760 VAL Chi-restraints excluded: chain B residue 813 HIS Chi-restraints excluded: chain B residue 844 VAL Chi-restraints excluded: chain B residue 906 VAL Chi-restraints excluded: chain B residue 930 LEU Chi-restraints excluded: chain B residue 931 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 95 optimal weight: 6.9990 chunk 94 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 101 optimal weight: 5.9990 chunk 3 optimal weight: 0.7980 chunk 57 optimal weight: 9.9990 chunk 52 optimal weight: 0.0010 chunk 23 optimal weight: 8.9990 chunk 5 optimal weight: 0.7980 chunk 21 optimal weight: 0.3980 chunk 75 optimal weight: 0.9980 overall best weight: 0.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 920 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.129131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.111463 restraints weight = 28435.171| |-----------------------------------------------------------------------------| r_work (start): 0.3928 rms_B_bonded: 3.63 r_work: 0.3807 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.3807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.7550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9411 Z= 0.189 Angle : 0.785 19.432 12795 Z= 0.368 Chirality : 0.046 0.265 1504 Planarity : 0.005 0.057 1548 Dihedral : 8.728 77.315 1382 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.31 % Favored : 95.61 % Rotamer: Outliers : 3.10 % Allowed : 24.08 % Favored : 72.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.25), residues: 1138 helix: 0.82 (0.20), residues: 705 sheet: -1.78 (1.26), residues: 10 loop : -1.11 (0.29), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 465 HIS 0.004 0.001 HIS A 630 PHE 0.041 0.002 PHE A 987 TYR 0.009 0.001 TYR B 486 ARG 0.003 0.000 ARG B 876 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 148 time to evaluate : 0.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 486 TYR cc_start: 0.7757 (t80) cc_final: 0.7429 (t80) REVERT: A 624 MET cc_start: 0.7697 (tpt) cc_final: 0.6626 (ttp) REVERT: A 888 LEU cc_start: 0.8600 (tp) cc_final: 0.8198 (tp) REVERT: A 923 GLN cc_start: 0.7146 (tt0) cc_final: 0.6941 (tt0) REVERT: A 990 LYS cc_start: 0.6388 (tmtt) cc_final: 0.5670 (mmtm) REVERT: A 1008 MET cc_start: 0.7662 (ttp) cc_final: 0.7304 (ttp) REVERT: B 478 CYS cc_start: 0.8163 (OUTLIER) cc_final: 0.7849 (p) REVERT: B 519 MET cc_start: 0.8022 (mtm) cc_final: 0.7811 (mtm) REVERT: B 615 HIS cc_start: 0.8284 (OUTLIER) cc_final: 0.7719 (t70) REVERT: B 624 MET cc_start: 0.8014 (mmm) cc_final: 0.7534 (ttm) REVERT: B 739 PHE cc_start: 0.7266 (OUTLIER) cc_final: 0.6202 (m-80) REVERT: B 801 GLN cc_start: 0.7704 (mm110) cc_final: 0.7299 (tp40) REVERT: B 931 PHE cc_start: 0.6870 (OUTLIER) cc_final: 0.6427 (m-10) outliers start: 31 outliers final: 22 residues processed: 173 average time/residue: 0.1507 time to fit residues: 40.3935 Evaluate side-chains 161 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 135 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 487 CYS Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 664 TRP Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 720 TYR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 828 VAL Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 891 CYS Chi-restraints excluded: chain A residue 906 VAL Chi-restraints excluded: chain A residue 930 LEU Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1006 ASP Chi-restraints excluded: chain A residue 1017 ASP Chi-restraints excluded: chain B residue 478 CYS Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 615 HIS Chi-restraints excluded: chain B residue 616 LEU Chi-restraints excluded: chain B residue 668 THR Chi-restraints excluded: chain B residue 739 PHE Chi-restraints excluded: chain B residue 813 HIS Chi-restraints excluded: chain B residue 844 VAL Chi-restraints excluded: chain B residue 857 LEU Chi-restraints excluded: chain B residue 906 VAL Chi-restraints excluded: chain B residue 930 LEU Chi-restraints excluded: chain B residue 931 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 100 optimal weight: 0.9990 chunk 41 optimal weight: 0.6980 chunk 67 optimal weight: 0.0070 chunk 105 optimal weight: 0.9980 chunk 69 optimal weight: 3.9990 chunk 49 optimal weight: 6.9990 chunk 82 optimal weight: 4.9990 chunk 13 optimal weight: 4.9990 chunk 92 optimal weight: 0.9990 chunk 110 optimal weight: 0.9980 chunk 76 optimal weight: 0.4980 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 920 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.127431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.109559 restraints weight = 27857.845| |-----------------------------------------------------------------------------| r_work (start): 0.3894 rms_B_bonded: 3.57 r_work: 0.3773 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.3773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.7889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9411 Z= 0.193 Angle : 0.789 15.114 12795 Z= 0.367 Chirality : 0.046 0.263 1504 Planarity : 0.005 0.056 1548 Dihedral : 8.313 76.157 1382 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.57 % Favored : 95.34 % Rotamer: Outliers : 2.60 % Allowed : 25.07 % Favored : 72.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.25), residues: 1138 helix: 0.80 (0.20), residues: 711 sheet: -1.87 (1.33), residues: 10 loop : -1.20 (0.29), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B1003 HIS 0.004 0.001 HIS A 630 PHE 0.038 0.002 PHE A 987 TYR 0.012 0.001 TYR A 524 ARG 0.003 0.000 ARG A 768 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 148 time to evaluate : 0.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 486 TYR cc_start: 0.7868 (t80) cc_final: 0.7563 (t80) REVERT: A 888 LEU cc_start: 0.8659 (tp) cc_final: 0.8305 (tp) REVERT: A 889 MET cc_start: 0.7572 (ptp) cc_final: 0.7299 (ptp) REVERT: A 895 MET cc_start: 0.5252 (tmm) cc_final: 0.5037 (tmm) REVERT: A 923 GLN cc_start: 0.7210 (tt0) cc_final: 0.7003 (tt0) REVERT: A 990 LYS cc_start: 0.6399 (tmtt) cc_final: 0.5711 (mmtm) REVERT: A 1008 MET cc_start: 0.7686 (ttp) cc_final: 0.7334 (ttp) REVERT: B 478 CYS cc_start: 0.8123 (OUTLIER) cc_final: 0.7853 (p) REVERT: B 615 HIS cc_start: 0.8287 (OUTLIER) cc_final: 0.7738 (t70) REVERT: B 624 MET cc_start: 0.8094 (mmm) cc_final: 0.7532 (ttm) REVERT: B 739 PHE cc_start: 0.7305 (OUTLIER) cc_final: 0.6214 (m-80) REVERT: B 801 GLN cc_start: 0.7779 (mm110) cc_final: 0.7449 (tp40) REVERT: B 931 PHE cc_start: 0.6972 (OUTLIER) cc_final: 0.6487 (m-10) outliers start: 26 outliers final: 20 residues processed: 167 average time/residue: 0.1620 time to fit residues: 41.3402 Evaluate side-chains 161 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 137 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 487 CYS Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 664 TRP Chi-restraints excluded: chain A residue 720 TYR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 906 VAL Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1006 ASP Chi-restraints excluded: chain B residue 478 CYS Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 615 HIS Chi-restraints excluded: chain B residue 616 LEU Chi-restraints excluded: chain B residue 668 THR Chi-restraints excluded: chain B residue 739 PHE Chi-restraints excluded: chain B residue 813 HIS Chi-restraints excluded: chain B residue 844 VAL Chi-restraints excluded: chain B residue 875 ILE Chi-restraints excluded: chain B residue 906 VAL Chi-restraints excluded: chain B residue 930 LEU Chi-restraints excluded: chain B residue 931 PHE Chi-restraints excluded: chain B residue 951 LYS Chi-restraints excluded: chain B residue 977 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 112 optimal weight: 4.9990 chunk 67 optimal weight: 0.0670 chunk 68 optimal weight: 7.9990 chunk 102 optimal weight: 0.7980 chunk 78 optimal weight: 7.9990 chunk 65 optimal weight: 5.9990 chunk 63 optimal weight: 1.9990 chunk 17 optimal weight: 0.0020 chunk 34 optimal weight: 0.9990 chunk 110 optimal weight: 0.7980 chunk 103 optimal weight: 0.0670 overall best weight: 0.3464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 920 GLN ** B 946 HIS ** 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 = 0.4184 r_free = 0.4184 target = 0.127266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.109409 restraints weight = 28507.232| |-----------------------------------------------------------------------------| r_work (start): 0.3893 rms_B_bonded: 3.62 r_work: 0.3772 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.3772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.8072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9411 Z= 0.186 Angle : 0.791 15.156 12795 Z= 0.369 Chirality : 0.045 0.255 1504 Planarity : 0.005 0.057 1548 Dihedral : 7.829 74.980 1382 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.31 % Favored : 95.61 % Rotamer: Outliers : 1.90 % Allowed : 26.87 % Favored : 71.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.24), residues: 1138 helix: 0.78 (0.20), residues: 709 sheet: -1.86 (1.28), residues: 10 loop : -1.17 (0.29), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B1003 HIS 0.004 0.001 HIS B 853 PHE 0.035 0.001 PHE A 987 TYR 0.011 0.001 TYR B 486 ARG 0.004 0.000 ARG B 989 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 139 time to evaluate : 0.963 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 486 TYR cc_start: 0.7801 (t80) cc_final: 0.7584 (t80) REVERT: A 888 LEU cc_start: 0.8655 (tp) cc_final: 0.8316 (tp) REVERT: A 889 MET cc_start: 0.7573 (ptp) cc_final: 0.7295 (ptp) REVERT: A 923 GLN cc_start: 0.7225 (tt0) cc_final: 0.7012 (tt0) REVERT: A 990 LYS cc_start: 0.6484 (tmtt) cc_final: 0.5784 (mmtm) REVERT: A 1008 MET cc_start: 0.7641 (ttp) cc_final: 0.7292 (ttp) REVERT: B 478 CYS cc_start: 0.8051 (OUTLIER) cc_final: 0.7817 (p) REVERT: B 615 HIS cc_start: 0.8280 (OUTLIER) cc_final: 0.7730 (t70) REVERT: B 624 MET cc_start: 0.8073 (mmm) cc_final: 0.7547 (ttm) REVERT: B 739 PHE cc_start: 0.7303 (OUTLIER) cc_final: 0.6210 (m-80) REVERT: B 801 GLN cc_start: 0.7800 (mm110) cc_final: 0.7528 (tp40) REVERT: B 931 PHE cc_start: 0.6985 (OUTLIER) cc_final: 0.6457 (m-10) outliers start: 19 outliers final: 14 residues processed: 153 average time/residue: 0.1811 time to fit residues: 43.6386 Evaluate side-chains 152 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 134 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 664 TRP Chi-restraints excluded: chain A residue 720 TYR Chi-restraints excluded: chain A residue 828 VAL Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 906 VAL Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1006 ASP Chi-restraints excluded: chain B residue 478 CYS Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 615 HIS Chi-restraints excluded: chain B residue 616 LEU Chi-restraints excluded: chain B residue 668 THR Chi-restraints excluded: chain B residue 739 PHE Chi-restraints excluded: chain B residue 844 VAL Chi-restraints excluded: chain B residue 930 LEU Chi-restraints excluded: chain B residue 931 PHE Chi-restraints excluded: chain B residue 977 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 48 optimal weight: 0.0670 chunk 9 optimal weight: 0.9990 chunk 83 optimal weight: 0.8980 chunk 66 optimal weight: 0.7980 chunk 6 optimal weight: 0.8980 chunk 36 optimal weight: 5.9990 chunk 39 optimal weight: 0.9990 chunk 95 optimal weight: 9.9990 chunk 101 optimal weight: 0.9980 chunk 50 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 overall best weight: 0.7318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 813 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 920 GLN ** B 946 HIS ** 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 = 0.4143 r_free = 0.4143 target = 0.124467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.106464 restraints weight = 28092.259| |-----------------------------------------------------------------------------| r_work (start): 0.3844 rms_B_bonded: 3.56 r_work: 0.3721 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.3721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.8389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9411 Z= 0.200 Angle : 0.814 16.028 12795 Z= 0.380 Chirality : 0.046 0.247 1504 Planarity : 0.005 0.056 1548 Dihedral : 7.364 73.482 1382 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.39 % Favored : 95.52 % Rotamer: Outliers : 2.40 % Allowed : 26.37 % Favored : 71.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.25), residues: 1138 helix: 0.80 (0.20), residues: 706 sheet: -1.49 (1.32), residues: 10 loop : -1.13 (0.29), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 465 HIS 0.004 0.001 HIS B 676 PHE 0.033 0.002 PHE B 987 TYR 0.012 0.001 TYR A 524 ARG 0.002 0.000 ARG A 563 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4219.29 seconds wall clock time: 74 minutes 17.91 seconds (4457.91 seconds total)