Starting phenix.real_space_refine on Wed Sep 17 14:45:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rtm_24683/09_2025/7rtm_24683.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rtm_24683/09_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_24683/09_2025/7rtm_24683.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rtm_24683/09_2025/7rtm_24683.map" model { file = "/net/cci-nas-00/data/ceres_data/7rtm_24683/09_2025/7rtm_24683.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rtm_24683/09_2025/7rtm_24683.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 2.62, per 1000 atoms: 0.29 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: 0.98 Conformation dependent library (CDL) restraints added in 355.4 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.31 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: 1.39 Time building geometry restraints manager: 1.24 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 1103)) 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: 1.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.000 Set scattering table: 0.030 Process input model: 10.390 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.110 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.630 ------------------------------------------------------------------------------- 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 : 0.032 0.626 9420 Z= 2.080 Angle : 3.084 51.238 12815 Z= 2.143 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 : 36.97 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.055 0.007 ARG B 637 TYR 0.184 0.042 TYR A 607 PHE 0.214 0.030 PHE B 955 TRP 0.275 0.042 TRP B 467 HIS 0.043 0.007 HIS B 822 Details of bonding type rmsd covalent geometry : bond 0.03074 ( 9411) covalent geometry : angle 3.04911 (12795) SS BOND : bond 0.15574 ( 4) SS BOND : angle 18.90423 ( 8) hydrogen bonds : bond 0.22213 ( 487) hydrogen bonds : angle 7.42107 ( 1380) Misc. bond : bond 0.62592 ( 1) link_BETA1-4 : bond 0.01188 ( 4) link_BETA1-4 : angle 2.84756 ( 12) *********************** 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 : 0.289 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: 0.4303 (mt) REVERT: B 881 THR cc_start: 0.4669 (p) cc_final: 0.4136 (p) REVERT: B 988 VAL cc_start: 0.3922 (p) cc_final: 0.3314 (t) outliers start: 28 outliers final: 5 residues processed: 373 average time/residue: 0.0994 time to fit residues: 51.3618 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 : 0.353 ------------------------------------------------------------------------------- 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 108 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 0.8980 chunk 113 optimal weight: 7.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 8.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 5.9990 chunk 100 optimal weight: 5.9990 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 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 630 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 647 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 813 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 822 HIS B 869 GLN B 923 GLN ** B 938 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 946 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.138949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.122331 restraints weight = 28534.839| |-----------------------------------------------------------------------------| r_work (start): 0.4095 rms_B_bonded: 3.67 r_work: 0.3971 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.3971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7154 moved from start: 0.5098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 9420 Z= 0.238 Angle : 0.942 11.498 12815 Z= 0.473 Chirality : 0.052 0.213 1504 Planarity : 0.007 0.070 1548 Dihedral : 12.771 106.376 1390 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.04 % Favored : 95.87 % Rotamer: Outliers : 4.30 % Allowed : 15.68 % Favored : 80.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.62 (0.24), residues: 1138 helix: 0.24 (0.19), residues: 700 sheet: None (None), residues: 0 loop : -1.41 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 765 TYR 0.035 0.003 TYR B 486 PHE 0.025 0.003 PHE A 496 TRP 0.024 0.003 TRP B 664 HIS 0.016 0.002 HIS A 630 Details of bonding type rmsd covalent geometry : bond 0.00526 ( 9411) covalent geometry : angle 0.93448 (12795) SS BOND : bond 0.00591 ( 4) SS BOND : angle 0.97546 ( 8) hydrogen bonds : bond 0.05892 ( 487) hydrogen bonds : angle 4.94166 ( 1380) Misc. bond : bond 0.00260 ( 1) link_BETA1-4 : bond 0.01097 ( 4) link_BETA1-4 : angle 4.01559 ( 12) *********************** 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 242 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 199 time to evaluate : 0.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 486 TYR cc_start: 0.7749 (t80) cc_final: 0.7393 (t80) REVERT: A 831 MET cc_start: 0.7410 (mmm) cc_final: 0.6791 (mmm) REVERT: A 888 LEU cc_start: 0.8775 (tp) cc_final: 0.8145 (tp) REVERT: A 895 MET cc_start: 0.4586 (tmm) cc_final: 0.4232 (tmm) REVERT: A 990 LYS cc_start: 0.6427 (tmtt) cc_final: 0.5867 (mmtt) REVERT: B 478 CYS cc_start: 0.8234 (OUTLIER) cc_final: 0.7775 (p) REVERT: B 640 LEU cc_start: 0.6714 (OUTLIER) cc_final: 0.6249 (mt) REVERT: B 643 ASN cc_start: 0.8385 (m-40) cc_final: 0.8111 (m110) REVERT: B 712 LEU cc_start: 0.8241 (OUTLIER) cc_final: 0.8027 (mm) outliers start: 43 outliers final: 22 residues processed: 229 average time/residue: 0.0874 time to fit residues: 28.8988 Evaluate side-chains 179 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 154 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 484 PHE Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 720 TYR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 737 THR Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 793 CYS 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 906 VAL 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 478 CYS Chi-restraints excluded: chain B residue 490 MET Chi-restraints excluded: chain B residue 570 THR Chi-restraints excluded: chain B residue 604 ILE Chi-restraints excluded: chain B residue 640 LEU Chi-restraints excluded: chain B residue 712 LEU Chi-restraints excluded: chain B residue 762 LYS 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 24 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 76 optimal weight: 4.9990 chunk 40 optimal weight: 0.7980 chunk 23 optimal weight: 9.9990 chunk 105 optimal weight: 4.9990 chunk 4 optimal weight: 0.4980 chunk 6 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 25 optimal weight: 0.8980 chunk 112 optimal weight: 6.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 477 GLN ** B 625 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 645 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.136164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.119335 restraints weight = 28215.007| |-----------------------------------------------------------------------------| r_work (start): 0.4048 rms_B_bonded: 3.63 r_work: 0.3925 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.3925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 moved from start: 0.5923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9420 Z= 0.157 Angle : 0.778 9.709 12815 Z= 0.380 Chirality : 0.046 0.278 1504 Planarity : 0.005 0.058 1548 Dihedral : 11.722 102.482 1383 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.39 % Favored : 95.52 % Rotamer: Outliers : 4.20 % Allowed : 18.48 % Favored : 77.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.14 (0.24), residues: 1138 helix: 0.52 (0.19), residues: 706 sheet: None (None), residues: 0 loop : -1.03 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 471 TYR 0.021 0.002 TYR A 486 PHE 0.017 0.002 PHE B 987 TRP 0.010 0.001 TRP A 465 HIS 0.010 0.001 HIS A 630 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 9411) covalent geometry : angle 0.77172 (12795) SS BOND : bond 0.00322 ( 4) SS BOND : angle 0.64720 ( 8) hydrogen bonds : bond 0.04999 ( 487) hydrogen bonds : angle 4.36959 ( 1380) Misc. bond : bond 0.00012 ( 1) link_BETA1-4 : bond 0.01065 ( 4) link_BETA1-4 : angle 3.36083 ( 12) *********************** 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 211 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 169 time to evaluate : 0.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 486 TYR cc_start: 0.7645 (t80) cc_final: 0.7292 (t80) REVERT: A 831 MET cc_start: 0.7447 (mmm) cc_final: 0.6843 (mmm) REVERT: A 888 LEU cc_start: 0.8720 (tp) cc_final: 0.8124 (tp) REVERT: A 990 LYS cc_start: 0.6196 (tmtt) cc_final: 0.5474 (mmtp) REVERT: B 615 HIS cc_start: 0.8302 (OUTLIER) cc_final: 0.7886 (t70) REVERT: B 643 ASN cc_start: 0.8305 (m-40) cc_final: 0.8104 (m-40) REVERT: B 801 GLN cc_start: 0.7613 (mm-40) cc_final: 0.7253 (tp40) outliers start: 42 outliers final: 19 residues processed: 199 average time/residue: 0.0750 time to fit residues: 22.6072 Evaluate side-chains 162 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 142 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 720 TYR Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 847 THR Chi-restraints excluded: chain A residue 881 THR 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 947 VAL Chi-restraints excluded: chain A residue 1006 ASP Chi-restraints excluded: chain B residue 490 MET Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 604 ILE Chi-restraints excluded: chain B residue 615 HIS Chi-restraints excluded: chain B residue 640 LEU Chi-restraints excluded: chain B residue 645 ASN Chi-restraints excluded: chain B residue 750 VAL Chi-restraints excluded: chain B residue 844 VAL Chi-restraints excluded: chain B residue 906 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 101 optimal weight: 0.9980 chunk 98 optimal weight: 4.9990 chunk 26 optimal weight: 5.9990 chunk 46 optimal weight: 0.9990 chunk 48 optimal weight: 7.9990 chunk 23 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 113 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 79 optimal weight: 4.9990 chunk 93 optimal weight: 6.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 625 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 953 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.130614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.112914 restraints weight = 28538.175| |-----------------------------------------------------------------------------| r_work (start): 0.3947 rms_B_bonded: 3.66 r_work: 0.3822 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.3822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.6694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 9420 Z= 0.157 Angle : 0.746 9.643 12815 Z= 0.363 Chirality : 0.045 0.228 1504 Planarity : 0.005 0.057 1548 Dihedral : 10.942 96.009 1383 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.83 % Favored : 95.08 % Rotamer: Outliers : 4.50 % Allowed : 19.28 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.10 (0.24), residues: 1138 helix: 0.60 (0.19), residues: 708 sheet: None (None), residues: 0 loop : -1.11 (0.29), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 471 TYR 0.017 0.002 TYR B 486 PHE 0.023 0.002 PHE A 987 TRP 0.010 0.001 TRP A 465 HIS 0.008 0.001 HIS A 630 Details of bonding type rmsd covalent geometry : bond 0.00350 ( 9411) covalent geometry : angle 0.73911 (12795) SS BOND : bond 0.00338 ( 4) SS BOND : angle 0.72889 ( 8) hydrogen bonds : bond 0.04595 ( 487) hydrogen bonds : angle 4.23665 ( 1380) Misc. bond : bond 0.00017 ( 1) link_BETA1-4 : bond 0.00936 ( 4) link_BETA1-4 : angle 3.48401 ( 12) *********************** 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 201 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 156 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 486 TYR cc_start: 0.8036 (t80) cc_final: 0.7651 (t80) REVERT: A 831 MET cc_start: 0.7443 (mmm) cc_final: 0.6833 (mmm) REVERT: A 888 LEU cc_start: 0.8770 (tp) cc_final: 0.8383 (tp) REVERT: A 889 MET cc_start: 0.7779 (ptp) cc_final: 0.7529 (ptp) REVERT: A 990 LYS cc_start: 0.6354 (tmtt) cc_final: 0.5598 (mmtp) REVERT: B 486 TYR cc_start: 0.8361 (OUTLIER) cc_final: 0.8094 (t80) REVERT: B 615 HIS cc_start: 0.8414 (OUTLIER) cc_final: 0.8052 (t70) REVERT: B 739 PHE cc_start: 0.7065 (OUTLIER) cc_final: 0.6248 (m-80) REVERT: B 801 GLN cc_start: 0.7874 (mm-40) cc_final: 0.7623 (tp40) REVERT: B 931 PHE cc_start: 0.7005 (OUTLIER) cc_final: 0.6657 (m-10) outliers start: 45 outliers final: 25 residues processed: 187 average time/residue: 0.0753 time to fit residues: 21.3171 Evaluate side-chains 160 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 131 time to evaluate : 0.306 ------------------------------------------------------------------------------- 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 622 ILE 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 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 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 486 TYR 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 640 LEU Chi-restraints excluded: chain B residue 739 PHE Chi-restraints excluded: chain B residue 740 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 931 PHE 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 16 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 84 optimal weight: 0.4980 chunk 66 optimal weight: 4.9990 chunk 54 optimal weight: 0.9980 chunk 102 optimal weight: 0.4980 chunk 69 optimal weight: 2.9990 chunk 103 optimal weight: 0.8980 chunk 55 optimal weight: 7.9990 chunk 106 optimal weight: 7.9990 chunk 78 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 855 ASN A 920 GLN A 923 GLN B 645 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.128321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.110486 restraints weight = 27969.854| |-----------------------------------------------------------------------------| r_work (start): 0.3910 rms_B_bonded: 3.58 r_work: 0.3786 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.3786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.7152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9420 Z= 0.135 Angle : 0.725 9.033 12815 Z= 0.346 Chirality : 0.044 0.227 1504 Planarity : 0.005 0.057 1548 Dihedral : 10.321 90.340 1383 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.01 % Favored : 94.90 % Rotamer: Outliers : 3.90 % Allowed : 20.28 % Favored : 75.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.01 (0.24), residues: 1138 helix: 0.73 (0.19), residues: 710 sheet: None (None), residues: 0 loop : -1.21 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 768 TYR 0.013 0.001 TYR A 486 PHE 0.021 0.002 PHE B 987 TRP 0.013 0.001 TRP B 652 HIS 0.006 0.001 HIS A 630 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 9411) covalent geometry : angle 0.71740 (12795) SS BOND : bond 0.00248 ( 4) SS BOND : angle 0.52627 ( 8) hydrogen bonds : bond 0.04298 ( 487) hydrogen bonds : angle 4.06368 ( 1380) Misc. bond : bond 0.00022 ( 1) link_BETA1-4 : bond 0.00926 ( 4) link_BETA1-4 : angle 3.42844 ( 12) *********************** 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 194 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 155 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 486 TYR cc_start: 0.8072 (t80) cc_final: 0.7590 (t80) REVERT: A 542 LEU cc_start: 0.8617 (pp) cc_final: 0.8313 (tt) REVERT: A 888 LEU cc_start: 0.8663 (tp) cc_final: 0.8217 (tp) REVERT: A 987 PHE cc_start: 0.6722 (m-80) cc_final: 0.6503 (m-80) REVERT: A 990 LYS cc_start: 0.6355 (tmtt) cc_final: 0.5621 (mmtp) REVERT: A 1008 MET cc_start: 0.8071 (ttp) cc_final: 0.7734 (ttp) REVERT: B 486 TYR cc_start: 0.8418 (t80) cc_final: 0.8101 (t80) REVERT: B 615 HIS cc_start: 0.8443 (OUTLIER) cc_final: 0.8066 (t70) REVERT: B 739 PHE cc_start: 0.7228 (OUTLIER) cc_final: 0.6361 (m-80) REVERT: B 801 GLN cc_start: 0.7947 (mm-40) cc_final: 0.7746 (tp40) REVERT: B 931 PHE cc_start: 0.7061 (OUTLIER) cc_final: 0.6645 (m-10) outliers start: 39 outliers final: 24 residues processed: 187 average time/residue: 0.0744 time to fit residues: 21.1899 Evaluate side-chains 154 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 127 time to evaluate : 0.353 ------------------------------------------------------------------------------- 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 508 ILE Chi-restraints excluded: chain A residue 514 LEU 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 720 TYR Chi-restraints excluded: chain A residue 828 VAL Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 878 GLN Chi-restraints excluded: chain A residue 891 CYS 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 A residue 1017 ASP Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 615 HIS Chi-restraints excluded: chain B residue 640 LEU 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 79 optimal weight: 0.8980 chunk 86 optimal weight: 0.2980 chunk 72 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 chunk 93 optimal weight: 6.9990 chunk 46 optimal weight: 0.9980 chunk 89 optimal weight: 0.3980 chunk 109 optimal weight: 0.1980 chunk 31 optimal weight: 0.4980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 920 GLN A 923 GLN B 946 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.127485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.109346 restraints weight = 28174.519| |-----------------------------------------------------------------------------| r_work (start): 0.3890 rms_B_bonded: 3.59 r_work: 0.3769 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.3769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.7424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9420 Z= 0.127 Angle : 0.730 11.180 12815 Z= 0.342 Chirality : 0.043 0.241 1504 Planarity : 0.005 0.057 1548 Dihedral : 9.900 85.925 1382 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.31 % Favored : 95.61 % Rotamer: Outliers : 3.60 % Allowed : 21.28 % Favored : 75.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.12 (0.25), residues: 1138 helix: 0.87 (0.20), residues: 708 sheet: None (None), residues: 0 loop : -1.21 (0.29), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 876 TYR 0.015 0.001 TYR B 486 PHE 0.019 0.001 PHE B 987 TRP 0.008 0.001 TRP B 569 HIS 0.005 0.001 HIS A 630 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 9411) covalent geometry : angle 0.72267 (12795) SS BOND : bond 0.00289 ( 4) SS BOND : angle 0.37587 ( 8) hydrogen bonds : bond 0.04168 ( 487) hydrogen bonds : angle 3.97590 ( 1380) Misc. bond : bond 0.00018 ( 1) link_BETA1-4 : bond 0.00899 ( 4) link_BETA1-4 : angle 3.44724 ( 12) *********************** 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 177 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 141 time to evaluate : 0.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 486 TYR cc_start: 0.8039 (t80) cc_final: 0.7758 (t80) REVERT: A 542 LEU cc_start: 0.8635 (pp) cc_final: 0.8383 (tt) REVERT: A 799 MET cc_start: 0.8163 (ptp) cc_final: 0.7963 (ptp) REVERT: A 831 MET cc_start: 0.7867 (mmm) cc_final: 0.6995 (mmm) REVERT: A 888 LEU cc_start: 0.8687 (tp) cc_final: 0.8463 (tp) REVERT: A 919 LEU cc_start: 0.9157 (OUTLIER) cc_final: 0.8921 (pp) REVERT: A 990 LYS cc_start: 0.6361 (tmtt) cc_final: 0.5596 (mmtp) REVERT: B 615 HIS cc_start: 0.8489 (OUTLIER) cc_final: 0.8156 (t70) REVERT: B 739 PHE cc_start: 0.7226 (OUTLIER) cc_final: 0.6282 (m-80) REVERT: B 931 PHE cc_start: 0.7077 (OUTLIER) cc_final: 0.6572 (m-10) outliers start: 36 outliers final: 22 residues processed: 167 average time/residue: 0.0725 time to fit residues: 18.7827 Evaluate side-chains 155 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 129 time to evaluate : 0.362 ------------------------------------------------------------------------------- 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 586 VAL Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 664 TRP Chi-restraints excluded: chain A residue 720 TYR Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 898 VAL Chi-restraints excluded: chain A residue 906 VAL Chi-restraints excluded: chain A residue 919 LEU 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 533 THR Chi-restraints excluded: chain B residue 615 HIS 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 Chi-restraints excluded: chain B residue 977 VAL Chi-restraints excluded: chain B residue 996 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 84 optimal weight: 0.7980 chunk 79 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 17 optimal weight: 0.4980 chunk 113 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 23 optimal weight: 9.9990 chunk 89 optimal weight: 0.0060 chunk 22 optimal weight: 0.3980 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 920 GLN A 959 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.126503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.108432 restraints weight = 28262.057| |-----------------------------------------------------------------------------| r_work (start): 0.3875 rms_B_bonded: 3.58 r_work: 0.3749 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.3749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.7660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9420 Z= 0.127 Angle : 0.761 18.895 12815 Z= 0.349 Chirality : 0.044 0.252 1504 Planarity : 0.005 0.056 1548 Dihedral : 9.414 81.231 1382 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.83 % Favored : 95.08 % Rotamer: Outliers : 3.30 % Allowed : 22.58 % Favored : 74.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.08 (0.25), residues: 1138 helix: 0.89 (0.20), residues: 706 sheet: None (None), residues: 0 loop : -1.33 (0.28), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 989 TYR 0.045 0.001 TYR B 486 PHE 0.026 0.001 PHE A 496 TRP 0.007 0.001 TRP B 569 HIS 0.004 0.001 HIS A 630 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 9411) covalent geometry : angle 0.75375 (12795) SS BOND : bond 0.00237 ( 4) SS BOND : angle 0.41432 ( 8) hydrogen bonds : bond 0.04111 ( 487) hydrogen bonds : angle 3.98174 ( 1380) Misc. bond : bond 0.00004 ( 1) link_BETA1-4 : bond 0.00883 ( 4) link_BETA1-4 : angle 3.46932 ( 12) *********************** 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 179 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 146 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 486 TYR cc_start: 0.7895 (t80) cc_final: 0.7682 (t80) REVERT: A 542 LEU cc_start: 0.8706 (pp) cc_final: 0.8482 (tt) REVERT: A 831 MET cc_start: 0.7962 (mmm) cc_final: 0.7035 (mmm) REVERT: A 888 LEU cc_start: 0.8571 (tp) cc_final: 0.8316 (tp) REVERT: A 895 MET cc_start: 0.4679 (tmm) cc_final: 0.3963 (tmm) REVERT: A 919 LEU cc_start: 0.9185 (OUTLIER) cc_final: 0.8932 (pp) REVERT: A 987 PHE cc_start: 0.6769 (m-80) cc_final: 0.6512 (m-80) REVERT: A 990 LYS cc_start: 0.6314 (tmtt) cc_final: 0.5549 (mmtp) REVERT: A 1008 MET cc_start: 0.7848 (ttp) cc_final: 0.7644 (tmm) REVERT: B 478 CYS cc_start: 0.8174 (OUTLIER) cc_final: 0.7854 (p) REVERT: B 486 TYR cc_start: 0.8344 (t80) cc_final: 0.8142 (t80) REVERT: B 615 HIS cc_start: 0.8431 (OUTLIER) cc_final: 0.8097 (t70) REVERT: B 739 PHE cc_start: 0.7399 (OUTLIER) cc_final: 0.6422 (m-80) REVERT: B 931 PHE cc_start: 0.7127 (OUTLIER) cc_final: 0.6583 (m-10) outliers start: 33 outliers final: 24 residues processed: 168 average time/residue: 0.0751 time to fit residues: 19.0452 Evaluate side-chains 163 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 134 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 622 ILE Chi-restraints excluded: chain A residue 664 TRP Chi-restraints excluded: chain A residue 720 TYR Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 859 LEU Chi-restraints excluded: chain A residue 906 VAL Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 930 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 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 902 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 977 VAL Chi-restraints excluded: chain B residue 996 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 80 optimal weight: 0.4980 chunk 105 optimal weight: 0.7980 chunk 113 optimal weight: 0.8980 chunk 68 optimal weight: 9.9990 chunk 87 optimal weight: 0.6980 chunk 78 optimal weight: 0.0980 chunk 60 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 102 optimal weight: 0.2980 chunk 53 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 920 GLN ** B 813 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 = 0.4159 r_free = 0.4159 target = 0.125433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.107093 restraints weight = 27901.914| |-----------------------------------------------------------------------------| r_work (start): 0.3857 rms_B_bonded: 3.57 r_work: 0.3733 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.3733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.7962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9420 Z= 0.129 Angle : 0.755 14.560 12815 Z= 0.352 Chirality : 0.044 0.261 1504 Planarity : 0.005 0.056 1548 Dihedral : 8.916 79.300 1382 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.57 % Favored : 95.34 % Rotamer: Outliers : 3.00 % Allowed : 23.08 % Favored : 73.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.18 (0.25), residues: 1138 helix: 0.94 (0.20), residues: 708 sheet: None (None), residues: 0 loop : -1.24 (0.29), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 765 TYR 0.038 0.001 TYR B 486 PHE 0.038 0.001 PHE B 496 TRP 0.006 0.001 TRP B 569 HIS 0.004 0.001 HIS A 630 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 9411) covalent geometry : angle 0.74785 (12795) SS BOND : bond 0.00222 ( 4) SS BOND : angle 0.34369 ( 8) hydrogen bonds : bond 0.04128 ( 487) hydrogen bonds : angle 3.97397 ( 1380) Misc. bond : bond 0.00004 ( 1) link_BETA1-4 : bond 0.00933 ( 4) link_BETA1-4 : angle 3.51105 ( 12) *********************** 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 169 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 139 time to evaluate : 0.370 Fit side-chains revert: symmetry clash REVERT: A 888 LEU cc_start: 0.8530 (tp) cc_final: 0.8314 (tp) REVERT: A 919 LEU cc_start: 0.9165 (OUTLIER) cc_final: 0.8917 (pp) REVERT: A 987 PHE cc_start: 0.6843 (m-80) cc_final: 0.6493 (m-80) REVERT: A 990 LYS cc_start: 0.6431 (tmtt) cc_final: 0.5622 (mmtp) REVERT: B 478 CYS cc_start: 0.8124 (OUTLIER) cc_final: 0.7859 (p) REVERT: B 615 HIS cc_start: 0.8373 (OUTLIER) cc_final: 0.7867 (t70) REVERT: B 624 MET cc_start: 0.8119 (mmm) cc_final: 0.7516 (ttm) REVERT: B 735 PHE cc_start: 0.5875 (t80) cc_final: 0.5659 (t80) REVERT: B 739 PHE cc_start: 0.7322 (OUTLIER) cc_final: 0.6197 (m-80) REVERT: B 931 PHE cc_start: 0.7174 (OUTLIER) cc_final: 0.6614 (m-10) outliers start: 30 outliers final: 22 residues processed: 158 average time/residue: 0.0705 time to fit residues: 17.2932 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 : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 622 ILE 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 848 VAL Chi-restraints excluded: chain A residue 859 LEU Chi-restraints excluded: chain A residue 906 VAL Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 930 LEU Chi-restraints excluded: chain A residue 1004 LEU 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 739 PHE Chi-restraints excluded: chain B residue 844 VAL Chi-restraints excluded: chain B residue 857 LEU 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 931 PHE Chi-restraints excluded: chain B residue 977 VAL Chi-restraints excluded: chain B residue 996 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 64 optimal weight: 0.8980 chunk 86 optimal weight: 2.9990 chunk 48 optimal weight: 0.0020 chunk 38 optimal weight: 0.8980 chunk 67 optimal weight: 0.0970 chunk 6 optimal weight: 0.9990 chunk 110 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 chunk 57 optimal weight: 10.0000 chunk 91 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 overall best weight: 0.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 920 GLN ** B 813 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 = 0.124258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.105963 restraints weight = 27893.502| |-----------------------------------------------------------------------------| r_work (start): 0.3836 rms_B_bonded: 3.55 r_work: 0.3713 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.3713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.8173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9420 Z= 0.131 Angle : 0.764 12.873 12815 Z= 0.358 Chirality : 0.044 0.251 1504 Planarity : 0.005 0.056 1548 Dihedral : 8.688 78.778 1382 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.48 % Favored : 95.43 % Rotamer: Outliers : 2.90 % Allowed : 24.28 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.16 (0.25), residues: 1138 helix: 0.90 (0.20), residues: 712 sheet: None (None), residues: 0 loop : -1.22 (0.29), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 945 TYR 0.071 0.002 TYR B 486 PHE 0.030 0.001 PHE B 496 TRP 0.006 0.001 TRP B 697 HIS 0.004 0.001 HIS A 630 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 9411) covalent geometry : angle 0.75842 (12795) SS BOND : bond 0.00212 ( 4) SS BOND : angle 0.25733 ( 8) hydrogen bonds : bond 0.04176 ( 487) hydrogen bonds : angle 3.99500 ( 1380) Misc. bond : bond 0.00007 ( 1) link_BETA1-4 : bond 0.01026 ( 4) link_BETA1-4 : angle 3.28152 ( 12) *********************** 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 167 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 138 time to evaluate : 0.369 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 486 TYR cc_start: 0.8021 (t80) cc_final: 0.7287 (t80) REVERT: A 831 MET cc_start: 0.7829 (mmm) cc_final: 0.6800 (mmm) REVERT: A 895 MET cc_start: 0.5126 (tmm) cc_final: 0.4805 (tmm) REVERT: A 919 LEU cc_start: 0.9149 (OUTLIER) cc_final: 0.8904 (pp) REVERT: A 987 PHE cc_start: 0.6859 (m-80) cc_final: 0.6541 (m-80) REVERT: A 990 LYS cc_start: 0.6496 (tmtt) cc_final: 0.5742 (mmtp) REVERT: B 478 CYS cc_start: 0.8200 (OUTLIER) cc_final: 0.7901 (p) REVERT: B 486 TYR cc_start: 0.7754 (t80) cc_final: 0.7385 (t80) REVERT: B 615 HIS cc_start: 0.8345 (OUTLIER) cc_final: 0.7812 (t70) REVERT: B 624 MET cc_start: 0.8080 (mmm) cc_final: 0.7488 (ttm) REVERT: B 735 PHE cc_start: 0.5908 (t80) cc_final: 0.5696 (t80) REVERT: B 739 PHE cc_start: 0.7346 (OUTLIER) cc_final: 0.6221 (m-80) REVERT: B 931 PHE cc_start: 0.7216 (OUTLIER) cc_final: 0.6576 (m-10) outliers start: 29 outliers final: 21 residues processed: 159 average time/residue: 0.0690 time to fit residues: 16.8806 Evaluate side-chains 154 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 128 time to evaluate : 0.314 ------------------------------------------------------------------------------- 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 622 ILE 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 848 VAL Chi-restraints excluded: chain A residue 859 LEU Chi-restraints excluded: chain A residue 919 LEU 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 739 PHE Chi-restraints excluded: chain B residue 844 VAL Chi-restraints excluded: chain B residue 857 LEU 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 931 PHE Chi-restraints excluded: chain B residue 996 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 18 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 98 optimal weight: 10.0000 chunk 13 optimal weight: 0.8980 chunk 11 optimal weight: 0.6980 chunk 46 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 39 optimal weight: 0.1980 chunk 74 optimal weight: 4.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 920 GLN ** B 813 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 855 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.122426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.103841 restraints weight = 28021.315| |-----------------------------------------------------------------------------| r_work (start): 0.3799 rms_B_bonded: 3.58 r_work: 0.3674 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.8486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9420 Z= 0.134 Angle : 0.782 16.591 12815 Z= 0.365 Chirality : 0.045 0.246 1504 Planarity : 0.005 0.056 1548 Dihedral : 8.110 77.756 1382 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.75 % Favored : 95.17 % Rotamer: Outliers : 2.90 % Allowed : 24.98 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.17 (0.25), residues: 1138 helix: 0.90 (0.20), residues: 715 sheet: None (None), residues: 0 loop : -1.20 (0.29), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 989 TYR 0.040 0.001 TYR B 486 PHE 0.030 0.002 PHE B 496 TRP 0.008 0.001 TRP B 697 HIS 0.004 0.001 HIS A 630 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 9411) covalent geometry : angle 0.77548 (12795) SS BOND : bond 0.00280 ( 4) SS BOND : angle 0.43748 ( 8) hydrogen bonds : bond 0.04213 ( 487) hydrogen bonds : angle 4.03722 ( 1380) Misc. bond : bond 0.00002 ( 1) link_BETA1-4 : bond 0.00866 ( 4) link_BETA1-4 : angle 3.45012 ( 12) ********************** 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 164 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 135 time to evaluate : 0.364 Fit side-chains revert: symmetry clash REVERT: A 831 MET cc_start: 0.7899 (mmm) cc_final: 0.6827 (mmm) REVERT: A 895 MET cc_start: 0.5094 (tmm) cc_final: 0.4818 (tmm) REVERT: A 919 LEU cc_start: 0.9098 (OUTLIER) cc_final: 0.8849 (pp) REVERT: A 969 ILE cc_start: 0.8961 (mm) cc_final: 0.8668 (mp) REVERT: A 990 LYS cc_start: 0.6534 (tmtt) cc_final: 0.5772 (mmtm) REVERT: B 486 TYR cc_start: 0.8070 (t80) cc_final: 0.7646 (t80) REVERT: B 615 HIS cc_start: 0.8366 (OUTLIER) cc_final: 0.7868 (t70) REVERT: B 624 MET cc_start: 0.8043 (mmm) cc_final: 0.7400 (ttm) REVERT: B 739 PHE cc_start: 0.7258 (OUTLIER) cc_final: 0.6035 (m-80) REVERT: B 931 PHE cc_start: 0.7301 (OUTLIER) cc_final: 0.6760 (m-10) outliers start: 29 outliers final: 20 residues processed: 157 average time/residue: 0.0702 time to fit residues: 17.3526 Evaluate side-chains 152 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 128 time to evaluate : 0.332 ------------------------------------------------------------------------------- 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 594 GLU Chi-restraints excluded: chain A residue 622 ILE 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 848 VAL Chi-restraints excluded: chain A residue 859 LEU Chi-restraints excluded: chain A residue 919 LEU 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 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 739 PHE Chi-restraints excluded: chain B residue 844 VAL 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 931 PHE Chi-restraints excluded: chain B residue 996 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 21 optimal weight: 0.8980 chunk 65 optimal weight: 0.0670 chunk 102 optimal weight: 0.9980 chunk 60 optimal weight: 0.9980 chunk 36 optimal weight: 10.0000 chunk 78 optimal weight: 8.9990 chunk 39 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 70 optimal weight: 0.4980 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 923 GLN ** B 813 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 = 0.4104 r_free = 0.4104 target = 0.121387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.102897 restraints weight = 27679.412| |-----------------------------------------------------------------------------| r_work (start): 0.3786 rms_B_bonded: 3.47 r_work: 0.3663 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.3663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.8725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.121 9420 Z= 0.139 Angle : 0.788 14.447 12815 Z= 0.368 Chirality : 0.045 0.243 1504 Planarity : 0.005 0.056 1548 Dihedral : 7.688 77.121 1382 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.57 % Favored : 95.34 % Rotamer: Outliers : 2.80 % Allowed : 25.47 % Favored : 71.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.13 (0.25), residues: 1138 helix: 0.82 (0.20), residues: 713 sheet: None (None), residues: 0 loop : -1.14 (0.29), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 876 TYR 0.045 0.001 TYR B 486 PHE 0.026 0.001 PHE B 496 TRP 0.007 0.001 TRP B 697 HIS 0.004 0.001 HIS A 630 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 9411) covalent geometry : angle 0.78173 (12795) SS BOND : bond 0.00231 ( 4) SS BOND : angle 0.33246 ( 8) hydrogen bonds : bond 0.04179 ( 487) hydrogen bonds : angle 4.13653 ( 1380) Misc. bond : bond 0.00004 ( 1) link_BETA1-4 : bond 0.00976 ( 4) link_BETA1-4 : angle 3.41108 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2204.75 seconds wall clock time: 38 minutes 41.79 seconds (2321.79 seconds total)