Starting phenix.real_space_refine on Wed Sep 25 01:07:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rtm_24683/09_2024/7rtm_24683.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rtm_24683/09_2024/7rtm_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rtm_24683/09_2024/7rtm_24683.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rtm_24683/09_2024/7rtm_24683.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rtm_24683/09_2024/7rtm_24683.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rtm_24683/09_2024/7rtm_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 6.05, per 1000 atoms: 0.66 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: 2.57 Conformation dependent library (CDL) restraints added in 1.1 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: 0.88 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: 2.27 Time building geometry restraints manager: 2.92 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: 2.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.010 Extract box with map and model: 0.520 Check model and map are aligned: 0.010 Set scattering table: 0.170 Process input model: 23.680 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.290 Load rotamer database and sin/cos tables:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.790 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 28 poor density : 352 time to evaluate : 0.899 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: 0.2006 time to fit residues: 102.5693 Evaluate side-chains 202 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 197 time to evaluate : 0.903 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5241 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 fitting. rotamer outliers: 33 poor density : 198 time to evaluate : 1.044 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 831 MET cc_start: 0.4215 (mmm) cc_final: 0.3849 (mmm) REVERT: A 923 GLN cc_start: 0.5192 (tt0) cc_final: 0.4931 (tt0) REVERT: B 906 VAL cc_start: 0.4716 (p) cc_final: 0.3582 (t) outliers start: 33 outliers final: 14 residues processed: 222 average time/residue: 0.1827 time to fit residues: 58.2913 Evaluate side-chains 168 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 154 time to evaluate : 0.941 ------------------------------------------------------------------------------- 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 B residue 472 ASP 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 57 optimal weight: 9.9990 chunk 32 optimal weight: 0.0670 chunk 86 optimal weight: 3.9990 chunk 70 optimal weight: 0.9980 chunk 28 optimal weight: 0.8980 chunk 103 optimal weight: 0.8980 chunk 112 optimal weight: 1.9990 chunk 92 optimal weight: 0.6980 chunk 102 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 83 optimal weight: 5.9990 overall best weight: 0.7118 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5423 moved from start: 0.5549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9411 Z= 0.219 Angle : 0.785 11.443 12795 Z= 0.388 Chirality : 0.047 0.229 1504 Planarity : 0.006 0.059 1548 Dihedral : 11.703 102.668 1383 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.57 % Favored : 95.34 % Rotamer: Outliers : 3.40 % Allowed : 17.88 % Favored : 78.72 % 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: -0.15 (0.24), residues: 1138 helix: 0.56 (0.19), residues: 690 sheet: None (None), residues: 0 loop : -1.08 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 465 HIS 0.010 0.001 HIS A 630 PHE 0.017 0.002 PHE A 544 TYR 0.049 0.002 TYR A 486 ARG 0.009 0.001 ARG B 471 *********************** 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 215 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 181 time to evaluate : 1.000 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 923 GLN cc_start: 0.5287 (tt0) cc_final: 0.5019 (tt0) REVERT: B 490 MET cc_start: 0.5342 (OUTLIER) cc_final: 0.4626 (ttt) REVERT: B 906 VAL cc_start: 0.5443 (p) cc_final: 0.4395 (t) outliers start: 34 outliers final: 16 residues processed: 207 average time/residue: 0.1789 time to fit residues: 53.7445 Evaluate side-chains 155 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 138 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 533 THR 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 824 ASP Chi-restraints excluded: chain A residue 881 THR Chi-restraints excluded: chain A residue 947 VAL 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 640 LEU Chi-restraints excluded: chain B residue 668 THR Chi-restraints excluded: chain B residue 712 LEU 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 102 optimal weight: 4.9990 chunk 77 optimal weight: 8.9990 chunk 53 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 69 optimal weight: 6.9990 chunk 104 optimal weight: 0.1980 chunk 110 optimal weight: 0.9980 chunk 54 optimal weight: 6.9990 chunk 98 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 625 HIS ** A 878 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 855 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5845 moved from start: 0.6877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 9411 Z= 0.284 Angle : 0.812 11.862 12795 Z= 0.399 Chirality : 0.048 0.226 1504 Planarity : 0.006 0.072 1548 Dihedral : 10.980 93.921 1383 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.01 % Favored : 94.90 % Rotamer: Outliers : 4.90 % Allowed : 18.88 % Favored : 76.22 % 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: 0.55 (0.20), residues: 707 sheet: None (None), residues: 0 loop : -0.97 (0.30), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 652 HIS 0.014 0.002 HIS B 647 PHE 0.024 0.002 PHE A 987 TYR 0.027 0.002 TYR A 486 ARG 0.008 0.001 ARG B 765 *********************** 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 215 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 166 time to evaluate : 1.014 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 831 MET cc_start: 0.4644 (mmm) cc_final: 0.3989 (mmm) REVERT: A 923 GLN cc_start: 0.5593 (tt0) cc_final: 0.5331 (tt0) REVERT: B 739 PHE cc_start: 0.4974 (OUTLIER) cc_final: 0.4443 (m-80) outliers start: 49 outliers final: 29 residues processed: 199 average time/residue: 0.1486 time to fit residues: 45.0463 Evaluate side-chains 162 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 132 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 482 PHE Chi-restraints excluded: chain A residue 508 ILE 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 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 844 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 1007 LEU Chi-restraints excluded: chain A residue 1017 ASP 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 640 LEU Chi-restraints excluded: chain B residue 668 THR Chi-restraints excluded: chain B residue 739 PHE Chi-restraints excluded: chain B residue 750 VAL Chi-restraints excluded: chain B residue 772 ILE Chi-restraints excluded: chain B residue 813 HIS Chi-restraints excluded: chain B residue 826 LEU 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 91 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 82 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 94 optimal weight: 1.9990 chunk 76 optimal weight: 8.9990 chunk 0 optimal weight: 9.9990 chunk 56 optimal weight: 5.9990 chunk 98 optimal weight: 8.9990 chunk 27 optimal weight: 8.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- 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 855 ASN ** B 813 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 822 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6178 moved from start: 0.8181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 9411 Z= 0.306 Angle : 0.783 10.702 12795 Z= 0.390 Chirality : 0.049 0.272 1504 Planarity : 0.006 0.081 1548 Dihedral : 10.027 84.127 1383 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.27 % Favored : 94.64 % Rotamer: Outliers : 4.70 % Allowed : 21.68 % 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 (0.24), residues: 1138 helix: 0.58 (0.19), residues: 700 sheet: None (None), residues: 0 loop : -1.30 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 569 HIS 0.011 0.002 HIS B 686 PHE 0.030 0.002 PHE A 496 TYR 0.040 0.002 TYR A 486 ARG 0.006 0.001 ARG B 945 *********************** 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 197 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 150 time to evaluate : 1.074 Fit side-chains revert: symmetry clash REVERT: A 923 GLN cc_start: 0.5918 (tt0) cc_final: 0.5684 (tt0) REVERT: B 739 PHE cc_start: 0.5521 (OUTLIER) cc_final: 0.4849 (m-80) outliers start: 47 outliers final: 27 residues processed: 188 average time/residue: 0.1513 time to fit residues: 43.6825 Evaluate side-chains 148 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 120 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 482 PHE Chi-restraints excluded: chain A residue 490 MET Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 594 GLU 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 757 VAL Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 847 THR Chi-restraints excluded: chain A residue 906 VAL Chi-restraints excluded: chain A residue 947 VAL Chi-restraints excluded: chain B residue 513 SER Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 640 LEU Chi-restraints excluded: chain B residue 668 THR Chi-restraints excluded: chain B residue 739 PHE 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 857 LEU Chi-restraints excluded: chain B residue 895 MET Chi-restraints excluded: chain B residue 902 ILE Chi-restraints excluded: chain B residue 930 LEU Chi-restraints excluded: chain B residue 962 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 37 optimal weight: 4.9990 chunk 99 optimal weight: 7.9990 chunk 21 optimal weight: 0.9990 chunk 64 optimal weight: 0.6980 chunk 27 optimal weight: 8.9990 chunk 110 optimal weight: 3.9990 chunk 91 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 57 optimal weight: 10.0000 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 959 GLN ** B 822 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 953 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6206 moved from start: 0.8620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9411 Z= 0.225 Angle : 0.761 12.503 12795 Z= 0.365 Chirality : 0.045 0.261 1504 Planarity : 0.005 0.059 1548 Dihedral : 9.476 80.100 1383 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.57 % Favored : 95.34 % Rotamer: Outliers : 4.50 % Allowed : 23.08 % Favored : 72.43 % 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: -0.03 (0.24), residues: 1138 helix: 0.75 (0.19), residues: 697 sheet: None (None), residues: 0 loop : -1.23 (0.29), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 465 HIS 0.006 0.001 HIS A 630 PHE 0.025 0.002 PHE A 987 TYR 0.016 0.001 TYR B 486 ARG 0.004 0.000 ARG A 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 183 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 138 time to evaluate : 0.991 Fit side-chains revert: symmetry clash REVERT: A 701 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8168 (mt) REVERT: B 739 PHE cc_start: 0.5420 (OUTLIER) cc_final: 0.4864 (m-80) outliers start: 45 outliers final: 25 residues processed: 172 average time/residue: 0.1642 time to fit residues: 42.5061 Evaluate side-chains 146 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 119 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 482 PHE Chi-restraints excluded: chain A residue 490 MET Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 594 GLU 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 844 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 B residue 533 THR Chi-restraints excluded: chain B residue 668 THR Chi-restraints excluded: chain B residue 739 PHE Chi-restraints excluded: chain B residue 750 VAL 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 895 MET Chi-restraints excluded: chain B residue 902 ILE Chi-restraints excluded: chain B residue 906 VAL Chi-restraints excluded: chain B residue 930 LEU 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 106 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 61 optimal weight: 0.0870 chunk 109 optimal weight: 0.5980 chunk 68 optimal weight: 0.7980 chunk 66 optimal weight: 0.9990 chunk 50 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 overall best weight: 0.6962 ------------------------------------------------------------------------------- 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 A 923 GLN B 646 ASN B 822 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6206 moved from start: 0.8869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9411 Z= 0.202 Angle : 0.756 12.782 12795 Z= 0.358 Chirality : 0.045 0.257 1504 Planarity : 0.005 0.066 1548 Dihedral : 8.945 77.853 1382 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.31 % Favored : 95.61 % Rotamer: Outliers : 4.30 % Allowed : 22.68 % Favored : 73.03 % 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: -0.01 (0.24), residues: 1138 helix: 0.75 (0.19), residues: 707 sheet: None (None), residues: 0 loop : -1.24 (0.29), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 652 HIS 0.005 0.001 HIS A 630 PHE 0.019 0.001 PHE A 987 TYR 0.026 0.001 TYR A 486 ARG 0.004 0.000 ARG B 945 *********************** 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 178 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 135 time to evaluate : 0.978 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 701 LEU cc_start: 0.8719 (OUTLIER) cc_final: 0.8217 (mt) REVERT: B 739 PHE cc_start: 0.5370 (OUTLIER) cc_final: 0.4629 (m-80) outliers start: 43 outliers final: 25 residues processed: 167 average time/residue: 0.1726 time to fit residues: 42.6396 Evaluate side-chains 148 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 121 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 594 GLU Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 664 TRP Chi-restraints excluded: chain A residue 686 HIS 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 859 LEU 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 B residue 482 PHE Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 668 THR Chi-restraints excluded: chain B residue 739 PHE Chi-restraints excluded: chain B residue 750 VAL Chi-restraints excluded: chain B residue 766 ASP 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 930 LEU Chi-restraints excluded: chain B residue 955 PHE Chi-restraints excluded: chain B residue 977 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 43 optimal weight: 1.9990 chunk 65 optimal weight: 0.0050 chunk 33 optimal weight: 2.9990 chunk 21 optimal weight: 7.9990 chunk 69 optimal weight: 0.9980 chunk 74 optimal weight: 6.9990 chunk 54 optimal weight: 7.9990 chunk 10 optimal weight: 20.0000 chunk 86 optimal weight: 0.8980 chunk 99 optimal weight: 1.9990 chunk 105 optimal weight: 0.6980 overall best weight: 0.9196 ------------------------------------------------------------------------------- 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 A 923 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6258 moved from start: 0.9158 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= 0.214 Angle : 0.765 12.860 12795 Z= 0.363 Chirality : 0.045 0.266 1504 Planarity : 0.005 0.069 1548 Dihedral : 8.552 76.654 1382 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.75 % Favored : 95.17 % Rotamer: Outliers : 3.50 % Allowed : 24.38 % Favored : 72.13 % 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: -0.18 (0.24), residues: 1138 helix: 0.61 (0.19), residues: 728 sheet: -2.27 (0.90), residues: 20 loop : -1.29 (0.30), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 652 HIS 0.005 0.001 HIS A 630 PHE 0.026 0.002 PHE A 496 TYR 0.024 0.001 TYR A 486 ARG 0.003 0.000 ARG B 945 *********************** 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 160 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 125 time to evaluate : 1.026 Fit side-chains revert: symmetry clash REVERT: A 701 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8240 (mt) REVERT: B 739 PHE cc_start: 0.5390 (OUTLIER) cc_final: 0.4546 (m-80) outliers start: 35 outliers final: 22 residues processed: 149 average time/residue: 0.1473 time to fit residues: 34.1606 Evaluate side-chains 140 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 116 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 594 GLU Chi-restraints excluded: chain A residue 616 LEU 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 844 VAL Chi-restraints excluded: chain A residue 859 LEU 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 977 VAL Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1006 ASP Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 668 THR Chi-restraints excluded: chain B residue 739 PHE Chi-restraints excluded: chain B residue 766 ASP Chi-restraints excluded: chain B residue 813 HIS Chi-restraints excluded: chain B residue 844 VAL Chi-restraints excluded: chain B residue 930 LEU Chi-restraints excluded: chain B residue 955 PHE Chi-restraints excluded: chain B residue 977 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 0.7980 chunk 102 optimal weight: 0.9980 chunk 105 optimal weight: 0.3980 chunk 61 optimal weight: 0.6980 chunk 44 optimal weight: 0.9990 chunk 80 optimal weight: 7.9990 chunk 31 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 67 optimal weight: 9.9990 chunk 108 optimal weight: 0.4980 chunk 66 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 923 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6261 moved from start: 0.9311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9411 Z= 0.201 Angle : 0.764 12.453 12795 Z= 0.362 Chirality : 0.044 0.262 1504 Planarity : 0.005 0.070 1548 Dihedral : 8.206 76.313 1382 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.66 % Favored : 95.25 % Rotamer: Outliers : 2.50 % Allowed : 25.07 % Favored : 72.43 % 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: -0.15 (0.24), residues: 1138 helix: 0.61 (0.19), residues: 732 sheet: -2.31 (0.91), residues: 20 loop : -1.25 (0.30), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 652 HIS 0.010 0.001 HIS A 686 PHE 0.024 0.002 PHE A 496 TYR 0.023 0.001 TYR B 486 ARG 0.003 0.000 ARG B 989 *********************** 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 150 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 125 time to evaluate : 1.123 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 485 LEU cc_start: 0.7351 (mt) cc_final: 0.7137 (mt) REVERT: A 701 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8204 (mt) outliers start: 25 outliers final: 21 residues processed: 144 average time/residue: 0.1556 time to fit residues: 34.6656 Evaluate side-chains 136 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 114 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 594 GLU Chi-restraints excluded: chain A residue 616 LEU 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 844 VAL Chi-restraints excluded: chain A residue 859 LEU 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 B residue 533 THR Chi-restraints excluded: chain B residue 668 THR Chi-restraints excluded: chain B residue 766 ASP Chi-restraints excluded: chain B residue 813 HIS Chi-restraints excluded: chain B residue 844 VAL Chi-restraints excluded: chain B residue 930 LEU Chi-restraints excluded: chain B residue 955 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 51 optimal weight: 7.9990 chunk 75 optimal weight: 1.9990 chunk 113 optimal weight: 0.9980 chunk 104 optimal weight: 6.9990 chunk 90 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 69 optimal weight: 0.8980 chunk 55 optimal weight: 10.0000 chunk 71 optimal weight: 4.9990 chunk 96 optimal weight: 1.9990 chunk 27 optimal weight: 0.0980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6284 moved from start: 0.9513 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= 0.206 Angle : 0.797 19.105 12795 Z= 0.373 Chirality : 0.045 0.252 1504 Planarity : 0.005 0.069 1548 Dihedral : 7.887 75.467 1382 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.75 % Favored : 95.17 % Rotamer: Outliers : 2.40 % Allowed : 25.67 % Favored : 71.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.12 (0.24), residues: 1138 helix: 0.59 (0.19), residues: 726 sheet: None (None), residues: 0 loop : -1.22 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 652 HIS 0.004 0.001 HIS A 813 PHE 0.052 0.002 PHE A 496 TYR 0.027 0.001 TYR B 486 ARG 0.003 0.000 ARG B 876 ********************** 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 146 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 122 time to evaluate : 1.232 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 701 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8249 (mt) REVERT: A 831 MET cc_start: 0.4849 (mmm) cc_final: 0.4016 (mmm) outliers start: 24 outliers final: 20 residues processed: 142 average time/residue: 0.1542 time to fit residues: 33.8523 Evaluate side-chains 140 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 119 time to evaluate : 1.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 594 GLU Chi-restraints excluded: chain A residue 616 LEU 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 844 VAL Chi-restraints excluded: chain A residue 859 LEU 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 B residue 533 THR Chi-restraints excluded: chain B residue 668 THR Chi-restraints excluded: chain B residue 766 ASP Chi-restraints excluded: chain B residue 813 HIS Chi-restraints excluded: chain B residue 844 VAL Chi-restraints excluded: chain B residue 930 LEU 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 83 optimal weight: 6.9990 chunk 13 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 90 optimal weight: 0.6980 chunk 37 optimal weight: 0.8980 chunk 93 optimal weight: 0.2980 chunk 11 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 79 optimal weight: 0.8980 chunk 5 optimal weight: 4.9990 chunk 65 optimal weight: 0.0070 overall best weight: 0.5598 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.115779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.096937 restraints weight = 27988.232| |-----------------------------------------------------------------------------| r_work (start): 0.3679 rms_B_bonded: 3.43 r_work: 0.3548 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.9640 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= 0.202 Angle : 0.787 16.638 12795 Z= 0.373 Chirality : 0.045 0.238 1504 Planarity : 0.005 0.068 1548 Dihedral : 7.557 74.858 1382 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.66 % Favored : 95.25 % Rotamer: Outliers : 2.10 % Allowed : 26.27 % Favored : 71.63 % 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: 0.01 (0.24), residues: 1138 helix: 0.77 (0.19), residues: 706 sheet: None (None), residues: 0 loop : -1.24 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 652 HIS 0.004 0.001 HIS A 630 PHE 0.031 0.002 PHE B 544 TYR 0.024 0.001 TYR B 486 ARG 0.002 0.000 ARG B 945 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2093.23 seconds wall clock time: 38 minutes 16.27 seconds (2296.27 seconds total)