Starting phenix.real_space_refine on Wed Sep 17 15:40:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vba_43118/09_2025/8vba_43118.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vba_43118/09_2025/8vba_43118.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8vba_43118/09_2025/8vba_43118.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vba_43118/09_2025/8vba_43118.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8vba_43118/09_2025/8vba_43118.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vba_43118/09_2025/8vba_43118.map" } resolution = 3.29 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= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 20 5.16 5 C 5660 2.51 5 N 1638 2.21 5 O 2098 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 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: 9416 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 7293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1038, 7293 Classifications: {'peptide': 1038} Link IDs: {'PTRANS': 8, 'TRANS': 1029} Chain: "H" Number of atoms: 887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 887 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 4, 'TRANS': 111} Chain: "L" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 807 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 101} Chain: "A" Number of atoms: 429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 429 Unusual residues: {'BGC': 39} Classifications: {'undetermined': 39} Link IDs: {None: 38} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 117 Unresolved non-hydrogen chiralities: 39 Time building chain proxies: 2.34, per 1000 atoms: 0.25 Number of scatterers: 9416 At special positions: 0 Unit cell: (63.075, 95.7, 187.775, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 20 16.00 O 2098 8.00 N 1638 7.00 C 5660 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 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=39, symmetry=0 Number of additional bonds: simple=39, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.93 Conformation dependent library (CDL) restraints added in 361.7 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2182 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 12 sheets defined 3.7% alpha, 29.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'A' and resid 175 through 181 Processing helix chain 'A' and resid 366 through 370 Processing helix chain 'A' and resid 481 through 485 removed outlier: 3.810A pdb=" N PHE A 484 " --> pdb=" O HIS A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 504 Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.718A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.603A pdb=" N PHE L 83 " --> pdb=" O SER L 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 73 through 76 removed outlier: 6.609A pdb=" N VAL A 99 " --> pdb=" O VAL A 75 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N MET A 98 " --> pdb=" O LEU A 125 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N ARG A 127 " --> pdb=" O MET A 98 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ALA A 100 " --> pdb=" O ARG A 127 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 123 through 128 current: chain 'A' and resid 400 through 411 removed outlier: 6.432A pdb=" N ALA A 401 " --> pdb=" O GLU A 430 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N SER A 432 " --> pdb=" O ALA A 401 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N LEU A 403 " --> pdb=" O SER A 432 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 428 through 433 current: chain 'A' and resid 507 through 511 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 562 through 565 current: chain 'A' and resid 634 through 648 removed outlier: 6.648A pdb=" N ASN A 635 " --> pdb=" O THR A 661 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N ASN A 663 " --> pdb=" O ASN A 635 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N LEU A 637 " --> pdb=" O ASN A 663 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N THR A 665 " --> pdb=" O LEU A 637 " (cutoff:3.500A) removed outlier: 8.528A pdb=" N ALA A 639 " --> pdb=" O THR A 665 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ASN A 667 " --> pdb=" O ALA A 639 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ASN A 641 " --> pdb=" O ASN A 667 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N THR A 669 " --> pdb=" O ASN A 641 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ALA A 643 " --> pdb=" O THR A 669 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N THR A 671 " --> pdb=" O ALA A 643 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N THR A 645 " --> pdb=" O THR A 671 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N SER A 673 " --> pdb=" O THR A 645 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N ASN A 647 " --> pdb=" O SER A 673 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ALA A 660 " --> pdb=" O ASN A 686 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N LEU A 688 " --> pdb=" O ALA A 660 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N LEU A 662 " --> pdb=" O LEU A 688 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N ALA A 690 " --> pdb=" O LEU A 662 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ALA A 664 " --> pdb=" O ALA A 690 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ASN A 692 " --> pdb=" O ALA A 664 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ASN A 666 " --> pdb=" O ASN A 692 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N THR A 694 " --> pdb=" O ASN A 666 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ILE A 668 " --> pdb=" O THR A 694 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N THR A 696 " --> pdb=" O ILE A 668 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N LEU A 670 " --> pdb=" O THR A 696 " (cutoff:3.500A) removed outlier: 8.053A pdb=" N GLU A 698 " --> pdb=" O LEU A 670 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N GLY A 672 " --> pdb=" O GLU A 698 " (cutoff:3.500A) removed outlier: 9.935A pdb=" N THR A 687 " --> pdb=" O ASN A 717 " (cutoff:3.500A) removed outlier: 12.184A pdb=" N THR A 719 " --> pdb=" O THR A 687 " (cutoff:3.500A) removed outlier: 11.751A pdb=" N THR A 689 " --> pdb=" O THR A 719 " (cutoff:3.500A) removed outlier: 10.858A pdb=" N ASN A 721 " --> pdb=" O THR A 689 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N SER A 691 " --> pdb=" O ASN A 721 " (cutoff:3.500A) removed outlier: 8.286A pdb=" N THR A 723 " --> pdb=" O SER A 691 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N ILE A 693 " --> pdb=" O THR A 723 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N GLN A 725 " --> pdb=" O ILE A 693 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N LEU A 695 " --> pdb=" O GLN A 725 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N THR A 714 " --> pdb=" O ASN A 735 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N THR A 737 " --> pdb=" O THR A 714 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N LEU A 716 " --> pdb=" O THR A 737 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 734 through 738 current: chain 'A' and resid 808 through 823 removed outlier: 6.493A pdb=" N VAL A 809 " --> pdb=" O ARG A 838 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N THR A 840 " --> pdb=" O VAL A 809 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N LEU A 811 " --> pdb=" O THR A 840 " (cutoff:3.500A) removed outlier: 8.141A pdb=" N SER A 842 " --> pdb=" O LEU A 811 " (cutoff:3.500A) removed outlier: 9.011A pdb=" N ALA A 813 " --> pdb=" O SER A 842 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N ILE A 844 " --> pdb=" O ALA A 813 " (cutoff:3.500A) removed outlier: 12.813A pdb=" N ASN A 815 " --> pdb=" O ILE A 844 " (cutoff:3.500A) removed outlier: 16.093A pdb=" N LEU A 846 " --> pdb=" O ASN A 815 " (cutoff:3.500A) removed outlier: 13.675A pdb=" N ARG A 817 " --> pdb=" O LEU A 846 " (cutoff:3.500A) removed outlier: 15.046A pdb=" N GLY A 848 " --> pdb=" O ARG A 817 " (cutoff:3.500A) removed outlier: 13.748A pdb=" N LYS A 819 " --> pdb=" O GLY A 848 " (cutoff:3.500A) removed outlier: 15.675A pdb=" N SER A 850 " --> pdb=" O LYS A 819 " (cutoff:3.500A) removed outlier: 14.261A pdb=" N THR A 821 " --> pdb=" O SER A 850 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 861 through 866 current: chain 'A' and resid 1036 through 1052 removed outlier: 6.452A pdb=" N VAL A1037 " --> pdb=" O ARG A1066 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N THR A1068 " --> pdb=" O VAL A1037 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N LEU A1039 " --> pdb=" O THR A1068 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N SER A1070 " --> pdb=" O LEU A1039 " (cutoff:3.500A) removed outlier: 9.230A pdb=" N ALA A1041 " --> pdb=" O SER A1070 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N ILE A1072 " --> pdb=" O ALA A1041 " (cutoff:3.500A) removed outlier: 13.210A pdb=" N ASN A1043 " --> pdb=" O ILE A1072 " (cutoff:3.500A) removed outlier: 16.211A pdb=" N LEU A1074 " --> pdb=" O ASN A1043 " (cutoff:3.500A) removed outlier: 13.957A pdb=" N ARG A1045 " --> pdb=" O LEU A1074 " (cutoff:3.500A) removed outlier: 14.946A pdb=" N GLY A1076 " --> pdb=" O ARG A1045 " (cutoff:3.500A) removed outlier: 13.707A pdb=" N LYS A1047 " --> pdb=" O GLY A1076 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 79 through 85 removed outlier: 6.810A pdb=" N GLN A 88 " --> pdb=" O PRO A 84 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N VAL A 162 " --> pdb=" O THR A 203 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N LEU A 202 " --> pdb=" O ARG A 224 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ILE A 223 " --> pdb=" O SER A 268 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N VAL A 267 " --> pdb=" O GLU A 296 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N VAL A 295 " --> pdb=" O GLN A 324 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 184 through 187 removed outlier: 4.315A pdb=" N TYR A 184 " --> pdb=" O LEU A 240 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N ASP A 243 " --> pdb=" O LEU A 247 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N LEU A 247 " --> pdb=" O ASP A 243 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 387 through 389 removed outlier: 6.528A pdb=" N ILE A 415 " --> pdb=" O SER A 444 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 491 through 494 Processing sheet with id=AA6, first strand: chain 'A' and resid 531 through 533 removed outlier: 6.383A pdb=" N ILE A 531 " --> pdb=" O THR A 556 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 575 through 578 removed outlier: 3.554A pdb=" N ASN A 607 " --> pdb=" O ILE A 578 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ILE A 604 " --> pdb=" O LEU A 630 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N ALA A 632 " --> pdb=" O ILE A 604 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N ILE A 606 " --> pdb=" O ALA A 632 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N SER A 627 " --> pdb=" O ALA A 653 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N ASN A 655 " --> pdb=" O SER A 627 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ILE A 629 " --> pdb=" O ASN A 655 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ASN A 681 " --> pdb=" O ASN A 652 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N ILE A 654 " --> pdb=" O ASN A 681 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 705 through 706 removed outlier: 7.370A pdb=" N ILE A 705 " --> pdb=" O GLN A 730 " (cutoff:3.500A) removed outlier: 8.319A pdb=" N LYS A 732 " --> pdb=" O ILE A 705 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N VAL A 729 " --> pdb=" O GLU A 751 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N SER A 753 " --> pdb=" O VAL A 729 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ILE A 731 " --> pdb=" O SER A 753 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N SER A 750 " --> pdb=" O TYR A 777 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N LYS A 779 " --> pdb=" O SER A 750 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N ILE A 752 " --> pdb=" O LYS A 779 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N THR A 803 " --> pdb=" O LEU A 832 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ILE A 831 " --> pdb=" O ASN A 857 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ILE A 933 " --> pdb=" O GLN A 958 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N LYS A 960 " --> pdb=" O ILE A 933 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N LEU A 935 " --> pdb=" O LYS A 960 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N VAL A 957 " --> pdb=" O GLU A 979 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N SER A 981 " --> pdb=" O VAL A 957 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ILE A 959 " --> pdb=" O SER A 981 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N SER A 978 " --> pdb=" O TYR A1005 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N LYS A1007 " --> pdb=" O SER A 978 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ILE A 980 " --> pdb=" O LYS A1007 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N VAL A1004 " --> pdb=" O HIS A1032 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N ASP A1034 " --> pdb=" O VAL A1004 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N LEU A1006 " --> pdb=" O ASP A1034 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N THR A1031 " --> pdb=" O LEU A1060 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ILE A1059 " --> pdb=" O ASN A1085 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 10 through 12 removed outlier: 5.841A pdb=" N GLU H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N TRP H 47 " --> pdb=" O GLU H 38 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N ARG H 40 " --> pdb=" O LEU H 45 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N LEU H 45 " --> pdb=" O ARG H 40 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 18 through 19 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 18 through 19 current: chain 'H' and resid 77 through 82 No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AB3, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.508A pdb=" N VAL L 13 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) 134 hydrogen bonds defined for protein. 339 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: 1.75 Time building geometry restraints manager: 1.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2661 1.33 - 1.45: 1783 1.45 - 1.58: 4962 1.58 - 1.70: 66 1.70 - 1.82: 35 Bond restraints: 9507 Sorted by residual: bond pdb=" N ILE H 34 " pdb=" CA ILE H 34 " ideal model delta sigma weight residual 1.459 1.504 -0.045 1.19e-02 7.06e+03 1.45e+01 bond pdb=" C2 BGC A1614 " pdb=" C3 BGC A1614 " ideal model delta sigma weight residual 1.522 1.598 -0.076 2.00e-02 2.50e+03 1.45e+01 bond pdb=" C2 BGC A1638 " pdb=" C3 BGC A1638 " ideal model delta sigma weight residual 1.522 1.595 -0.073 2.00e-02 2.50e+03 1.32e+01 bond pdb=" C2 BGC A1605 " pdb=" C3 BGC A1605 " ideal model delta sigma weight residual 1.522 1.593 -0.071 2.00e-02 2.50e+03 1.28e+01 bond pdb=" C2 BGC A1630 " pdb=" C3 BGC A1630 " ideal model delta sigma weight residual 1.522 1.593 -0.071 2.00e-02 2.50e+03 1.26e+01 ... (remaining 9502 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.31: 11971 2.31 - 4.62: 773 4.62 - 6.92: 101 6.92 - 9.23: 81 9.23 - 11.54: 1 Bond angle restraints: 12927 Sorted by residual: angle pdb=" N ASN A 580 " pdb=" CA ASN A 580 " pdb=" C ASN A 580 " ideal model delta sigma weight residual 111.17 122.71 -11.54 1.41e+00 5.03e-01 6.70e+01 angle pdb=" C ALA H 78 " pdb=" N TYR H 79 " pdb=" CA TYR H 79 " ideal model delta sigma weight residual 122.87 114.33 8.54 1.61e+00 3.86e-01 2.81e+01 angle pdb=" N TRP L 92 " pdb=" CA TRP L 92 " pdb=" C TRP L 92 " ideal model delta sigma weight residual 113.38 106.89 6.49 1.23e+00 6.61e-01 2.79e+01 angle pdb=" N THR A 171 " pdb=" CA THR A 171 " pdb=" C THR A 171 " ideal model delta sigma weight residual 113.17 107.14 6.03 1.26e+00 6.30e-01 2.29e+01 angle pdb=" N THR A 558 " pdb=" CA THR A 558 " pdb=" C THR A 558 " ideal model delta sigma weight residual 113.30 106.94 6.36 1.34e+00 5.57e-01 2.26e+01 ... (remaining 12922 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 5672 17.85 - 35.70: 291 35.70 - 53.55: 67 53.55 - 71.40: 39 71.40 - 89.25: 3 Dihedral angle restraints: 6072 sinusoidal: 2612 harmonic: 3460 Sorted by residual: dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 92 " pdb=" CB CYS H 92 " ideal model delta sinusoidal sigma weight residual 93.00 60.43 32.57 1 1.00e+01 1.00e-02 1.51e+01 dihedral pdb=" C CYS H 92 " pdb=" N CYS H 92 " pdb=" CA CYS H 92 " pdb=" CB CYS H 92 " ideal model delta harmonic sigma weight residual -122.60 -114.11 -8.49 0 2.50e+00 1.60e-01 1.15e+01 dihedral pdb=" CA ASP A 255 " pdb=" CB ASP A 255 " pdb=" CG ASP A 255 " pdb=" OD1 ASP A 255 " ideal model delta sinusoidal sigma weight residual -30.00 -85.07 55.07 1 2.00e+01 2.50e-03 1.03e+01 ... (remaining 6069 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.101: 1373 0.101 - 0.202: 165 0.202 - 0.303: 43 0.303 - 0.404: 36 0.404 - 0.505: 37 Chirality restraints: 1654 Sorted by residual: chirality pdb=" C3 BGC A1629 " pdb=" C2 BGC A1629 " pdb=" C4 BGC A1629 " pdb=" O3 BGC A1629 " both_signs ideal model delta sigma weight residual False 2.44 2.95 -0.51 2.00e-01 2.50e+01 6.38e+00 chirality pdb=" C3 BGC A1626 " pdb=" C2 BGC A1626 " pdb=" C4 BGC A1626 " pdb=" O3 BGC A1626 " both_signs ideal model delta sigma weight residual False 2.44 2.95 -0.51 2.00e-01 2.50e+01 6.38e+00 chirality pdb=" C3 BGC A1636 " pdb=" C2 BGC A1636 " pdb=" C4 BGC A1636 " pdb=" O3 BGC A1636 " both_signs ideal model delta sigma weight residual False 2.44 2.95 -0.50 2.00e-01 2.50e+01 6.35e+00 ... (remaining 1651 not shown) Planarity restraints: 1634 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA A 704 " -0.018 2.00e-02 2.50e+03 3.70e-02 1.37e+01 pdb=" C ALA A 704 " 0.064 2.00e-02 2.50e+03 pdb=" O ALA A 704 " -0.025 2.00e-02 2.50e+03 pdb=" N ILE A 705 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 721 " -0.017 2.00e-02 2.50e+03 3.48e-02 1.21e+01 pdb=" CG ASN A 721 " 0.060 2.00e-02 2.50e+03 pdb=" OD1 ASN A 721 " -0.023 2.00e-02 2.50e+03 pdb=" ND2 ASN A 721 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 491 " 0.013 2.00e-02 2.50e+03 2.62e-02 6.87e+00 pdb=" C SER A 491 " -0.045 2.00e-02 2.50e+03 pdb=" O SER A 491 " 0.017 2.00e-02 2.50e+03 pdb=" N ALA A 492 " 0.015 2.00e-02 2.50e+03 ... (remaining 1631 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 945 2.74 - 3.28: 9298 3.28 - 3.82: 16314 3.82 - 4.36: 20403 4.36 - 4.90: 34595 Nonbonded interactions: 81555 Sorted by model distance: nonbonded pdb=" O GLY A 853 " pdb=" OG SER A 876 " model vdw 2.200 3.040 nonbonded pdb=" OD1 ASN A 666 " pdb=" O2 BGC A1611 " model vdw 2.202 3.040 nonbonded pdb=" ND2 ASN A 735 " pdb=" OG1 THR A 756 " model vdw 2.210 3.120 nonbonded pdb=" O ALA A 569 " pdb=" ND2 ASN A 600 " model vdw 2.218 3.120 nonbonded pdb=" ND2 ASN A 717 " pdb=" O2 BGC A1621 " model vdw 2.227 2.496 ... (remaining 81550 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 3.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.350 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 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 : 0.010 0.080 9548 Z= 0.516 Angle : 1.309 11.541 12931 Z= 0.704 Chirality : 0.117 0.505 1654 Planarity : 0.004 0.049 1634 Dihedral : 12.480 89.246 3884 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 14.82 Ramachandran Plot: Outliers : 0.48 % Allowed : 4.63 % Favored : 94.90 % Rotamer: Outliers : 0.51 % Allowed : 10.15 % Favored : 89.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -0.19 (0.24), residues: 1254 helix: -1.64 (0.98), residues: 25 sheet: 0.33 (0.19), residues: 758 loop : -0.66 (0.27), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.002 ARG A 728 TYR 0.019 0.003 TYR L 30 PHE 0.026 0.003 PHE H 29 TRP 0.018 0.002 TRP H 33 HIS 0.009 0.002 HIS A 804 Details of bonding type rmsd covalent geometry : bond 0.00971 ( 9507) covalent geometry : angle 1.30890 (12927) SS BOND : bond 0.00749 ( 2) SS BOND : angle 2.33506 ( 4) hydrogen bonds : bond 0.15233 ( 134) hydrogen bonds : angle 7.93783 ( 339) Misc. bond : bond 0.00202 ( 39) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 160 time to evaluate : 0.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 678 ASN cc_start: 0.7677 (m-40) cc_final: 0.7402 (m-40) REVERT: A 705 ILE cc_start: 0.7964 (mm) cc_final: 0.7598 (mt) REVERT: A 823 ASN cc_start: 0.7917 (m-40) cc_final: 0.7427 (m-40) REVERT: A 953 GLN cc_start: 0.5653 (tt0) cc_final: 0.5169 (tm-30) REVERT: A 989 ASN cc_start: 0.7449 (m-40) cc_final: 0.6954 (t0) REVERT: L 52 THR cc_start: 0.8579 (m) cc_final: 0.8306 (t) outliers start: 5 outliers final: 2 residues processed: 162 average time/residue: 0.0941 time to fit residues: 21.3274 Evaluate side-chains 107 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 105 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 503 ASN Chi-restraints excluded: chain H residue 98 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 108 optimal weight: 0.0770 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 5.9990 chunk 113 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.0770 chunk 33 optimal weight: 0.6980 chunk 123 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.8980 overall best weight: 0.4896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN ** A 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 327 ASN A 331 GLN A 383 GLN A 394 GLN A 434 HIS A 503 ASN A 652 ASN A 725 GLN A 730 GLN A 836 ASN A 891 ASN A 906 ASN H 43 HIS L 28 ASN L 76 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4705 r_free = 0.4705 target = 0.199837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.144161 restraints weight = 8827.790| |-----------------------------------------------------------------------------| r_work (start): 0.4222 rms_B_bonded: 3.06 r_work: 0.4008 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.4008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9548 Z= 0.134 Angle : 0.572 6.040 12931 Z= 0.307 Chirality : 0.044 0.201 1654 Planarity : 0.003 0.034 1634 Dihedral : 7.018 59.140 2055 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.63 % Favored : 97.21 % Rotamer: Outliers : 2.46 % Allowed : 12.00 % Favored : 85.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -0.42 (0.24), residues: 1254 helix: -0.40 (1.08), residues: 25 sheet: 0.17 (0.20), residues: 745 loop : -0.85 (0.26), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 24 TYR 0.011 0.001 TYR L 96 PHE 0.015 0.002 PHE H 29 TRP 0.007 0.001 TRP H 36 HIS 0.004 0.001 HIS A 513 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 9507) covalent geometry : angle 0.57142 (12927) SS BOND : bond 0.00378 ( 2) SS BOND : angle 0.98499 ( 4) hydrogen bonds : bond 0.03988 ( 134) hydrogen bonds : angle 6.38812 ( 339) Misc. bond : bond 0.00169 ( 39) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 117 time to evaluate : 0.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 ASP cc_start: 0.7424 (t0) cc_final: 0.7045 (m-30) REVERT: A 137 MET cc_start: 0.8031 (mmt) cc_final: 0.7771 (mmm) REVERT: A 158 GLU cc_start: 0.7654 (mt-10) cc_final: 0.7417 (mm-30) REVERT: A 243 ASP cc_start: 0.8157 (OUTLIER) cc_final: 0.7918 (m-30) REVERT: A 368 GLN cc_start: 0.8311 (mt0) cc_final: 0.8071 (mm-40) REVERT: A 397 ASN cc_start: 0.8196 (m-40) cc_final: 0.7956 (m-40) REVERT: A 601 ARG cc_start: 0.7415 (mtp180) cc_final: 0.6965 (ttm110) REVERT: A 678 ASN cc_start: 0.7959 (m-40) cc_final: 0.7534 (m-40) REVERT: A 823 ASN cc_start: 0.8033 (m-40) cc_final: 0.7604 (m110) REVERT: A 831 ILE cc_start: 0.8129 (tt) cc_final: 0.7920 (pt) REVERT: A 953 GLN cc_start: 0.6033 (tt0) cc_final: 0.5578 (tm-30) REVERT: A 990 ASN cc_start: 0.6428 (m-40) cc_final: 0.6208 (p0) REVERT: H 62 LYS cc_start: 0.8381 (OUTLIER) cc_final: 0.8046 (ttpt) REVERT: L 90 GLN cc_start: 0.8884 (pp30) cc_final: 0.8597 (pp30) outliers start: 24 outliers final: 15 residues processed: 133 average time/residue: 0.0872 time to fit residues: 16.6862 Evaluate side-chains 115 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 98 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 548 ASN Chi-restraints excluded: chain A residue 553 ASN Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain A residue 901 SER Chi-restraints excluded: chain A residue 906 ASN Chi-restraints excluded: chain A residue 1014 THR Chi-restraints excluded: chain H residue 62 LYS Chi-restraints excluded: chain H residue 98 TYR Chi-restraints excluded: chain H residue 110 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 15 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 6 optimal weight: 7.9990 chunk 105 optimal weight: 1.9990 chunk 98 optimal weight: 10.0000 chunk 40 optimal weight: 10.0000 chunk 61 optimal weight: 1.9990 chunk 109 optimal weight: 7.9990 chunk 62 optimal weight: 0.5980 chunk 17 optimal weight: 2.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 ASN ** A 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 563 ASN A 652 ASN A 837 ASN L 38 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4617 r_free = 0.4617 target = 0.186140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.134083 restraints weight = 8926.152| |-----------------------------------------------------------------------------| r_work (start): 0.4124 rms_B_bonded: 2.77 r_work: 0.3907 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.2395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 9548 Z= 0.251 Angle : 0.602 7.248 12931 Z= 0.324 Chirality : 0.045 0.153 1654 Planarity : 0.003 0.048 1634 Dihedral : 6.370 58.369 2053 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.35 % Favored : 96.49 % Rotamer: Outliers : 4.41 % Allowed : 11.90 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -0.85 (0.24), residues: 1254 helix: -0.93 (0.95), residues: 25 sheet: -0.27 (0.19), residues: 756 loop : -0.83 (0.27), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG L 24 TYR 0.018 0.002 TYR A 184 PHE 0.017 0.002 PHE A 631 TRP 0.008 0.001 TRP H 103 HIS 0.005 0.001 HIS A 318 Details of bonding type rmsd covalent geometry : bond 0.00537 ( 9507) covalent geometry : angle 0.60169 (12927) SS BOND : bond 0.00480 ( 2) SS BOND : angle 0.91297 ( 4) hydrogen bonds : bond 0.03580 ( 134) hydrogen bonds : angle 5.84152 ( 339) Misc. bond : bond 0.00083 ( 39) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 98 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 116 ASP cc_start: 0.7468 (t0) cc_final: 0.7127 (m-30) REVERT: A 137 MET cc_start: 0.8121 (mmt) cc_final: 0.7828 (mmm) REVERT: A 183 ARG cc_start: 0.7308 (mtm-85) cc_final: 0.6995 (mtm-85) REVERT: A 243 ASP cc_start: 0.8139 (OUTLIER) cc_final: 0.7875 (m-30) REVERT: A 397 ASN cc_start: 0.8237 (m-40) cc_final: 0.7999 (m-40) REVERT: A 601 ARG cc_start: 0.7415 (mtp180) cc_final: 0.7031 (ttm110) REVERT: A 678 ASN cc_start: 0.8165 (m-40) cc_final: 0.7876 (m-40) REVERT: A 743 LEU cc_start: 0.8462 (mt) cc_final: 0.8143 (tt) REVERT: A 953 GLN cc_start: 0.6280 (tt0) cc_final: 0.5738 (tm-30) REVERT: H 81 LYS cc_start: 0.7941 (ttmt) cc_final: 0.7645 (tptt) REVERT: L 27 GLU cc_start: 0.7814 (tt0) cc_final: 0.7387 (tt0) outliers start: 43 outliers final: 35 residues processed: 127 average time/residue: 0.0836 time to fit residues: 15.5720 Evaluate side-chains 121 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 85 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 143 ASN Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 548 ASN Chi-restraints excluded: chain A residue 553 ASN Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain A residue 758 THR Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 906 ASN Chi-restraints excluded: chain A residue 1014 THR Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 38 GLU Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 62 LYS Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 98 TYR Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 42 LYS Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 72 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 40 optimal weight: 5.9990 chunk 1 optimal weight: 6.9990 chunk 59 optimal weight: 0.9980 chunk 7 optimal weight: 4.9990 chunk 101 optimal weight: 30.0000 chunk 44 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 6 optimal weight: 0.6980 chunk 32 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 116 optimal weight: 4.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 ASN A 152 ASN A 730 GLN A 906 ASN L 32 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4610 r_free = 0.4610 target = 0.185705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.133665 restraints weight = 9035.345| |-----------------------------------------------------------------------------| r_work (start): 0.4117 rms_B_bonded: 2.78 r_work: 0.3902 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.2748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9548 Z= 0.179 Angle : 0.553 7.338 12931 Z= 0.297 Chirality : 0.044 0.163 1654 Planarity : 0.003 0.052 1634 Dihedral : 5.998 55.578 2053 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.03 % Favored : 96.89 % Rotamer: Outliers : 3.79 % Allowed : 12.82 % Favored : 83.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -1.11 (0.24), residues: 1254 helix: -0.65 (0.95), residues: 25 sheet: -0.47 (0.19), residues: 753 loop : -0.96 (0.27), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 24 TYR 0.011 0.001 TYR A 408 PHE 0.021 0.002 PHE A 147 TRP 0.007 0.001 TRP H 103 HIS 0.004 0.001 HIS A 318 Details of bonding type rmsd covalent geometry : bond 0.00395 ( 9507) covalent geometry : angle 0.55325 (12927) SS BOND : bond 0.00422 ( 2) SS BOND : angle 0.69051 ( 4) hydrogen bonds : bond 0.03065 ( 134) hydrogen bonds : angle 5.48543 ( 339) Misc. bond : bond 0.00146 ( 39) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 92 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 ASP cc_start: 0.7506 (t0) cc_final: 0.7134 (m-30) REVERT: A 183 ARG cc_start: 0.7217 (mtm-85) cc_final: 0.6972 (mtm-85) REVERT: A 283 MET cc_start: 0.7280 (mtm) cc_final: 0.6907 (ptp) REVERT: A 397 ASN cc_start: 0.8279 (m-40) cc_final: 0.8024 (m-40) REVERT: A 601 ARG cc_start: 0.7424 (mtp180) cc_final: 0.7053 (ttm110) REVERT: A 678 ASN cc_start: 0.8167 (m-40) cc_final: 0.7899 (m-40) REVERT: A 705 ILE cc_start: 0.8350 (mm) cc_final: 0.8074 (mt) REVERT: A 743 LEU cc_start: 0.8469 (mt) cc_final: 0.8083 (tt) REVERT: A 875 SER cc_start: 0.7323 (t) cc_final: 0.6684 (p) REVERT: A 953 GLN cc_start: 0.6592 (tt0) cc_final: 0.6267 (tm-30) REVERT: H 62 LYS cc_start: 0.8398 (OUTLIER) cc_final: 0.8122 (ttpt) REVERT: H 81 LYS cc_start: 0.7933 (ttmt) cc_final: 0.7712 (tptt) REVERT: L 27 GLU cc_start: 0.7775 (tt0) cc_final: 0.7336 (tt0) outliers start: 37 outliers final: 32 residues processed: 117 average time/residue: 0.0965 time to fit residues: 16.0640 Evaluate side-chains 116 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 83 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 548 ASN Chi-restraints excluded: chain A residue 553 ASN Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 906 ASN Chi-restraints excluded: chain A residue 945 ASN Chi-restraints excluded: chain A residue 990 ASN Chi-restraints excluded: chain A residue 1012 THR Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 38 GLU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 62 LYS Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 98 TYR Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 42 LYS Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 72 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 95 optimal weight: 5.9990 chunk 69 optimal weight: 0.6980 chunk 92 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 109 optimal weight: 7.9990 chunk 5 optimal weight: 2.9990 chunk 79 optimal weight: 0.9980 chunk 93 optimal weight: 9.9990 chunk 24 optimal weight: 0.9980 chunk 6 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4580 r_free = 0.4580 target = 0.182157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.130269 restraints weight = 9173.121| |-----------------------------------------------------------------------------| r_work (start): 0.4077 rms_B_bonded: 2.81 r_work: 0.3861 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.3127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 9548 Z= 0.206 Angle : 0.556 7.787 12931 Z= 0.299 Chirality : 0.044 0.182 1654 Planarity : 0.003 0.054 1634 Dihedral : 5.737 55.272 2053 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.23 % Favored : 95.69 % Rotamer: Outliers : 4.21 % Allowed : 12.92 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -1.38 (0.24), residues: 1254 helix: -0.57 (0.99), residues: 25 sheet: -0.67 (0.20), residues: 737 loop : -1.10 (0.26), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 728 TYR 0.013 0.002 TYR A 408 PHE 0.022 0.002 PHE A 147 TRP 0.008 0.001 TRP H 103 HIS 0.003 0.001 HIS A 513 Details of bonding type rmsd covalent geometry : bond 0.00460 ( 9507) covalent geometry : angle 0.55569 (12927) SS BOND : bond 0.00468 ( 2) SS BOND : angle 0.88444 ( 4) hydrogen bonds : bond 0.02978 ( 134) hydrogen bonds : angle 5.45161 ( 339) Misc. bond : bond 0.00085 ( 39) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 97 time to evaluate : 0.278 Fit side-chains revert: symmetry clash REVERT: A 116 ASP cc_start: 0.7583 (t0) cc_final: 0.7142 (m-30) REVERT: A 183 ARG cc_start: 0.7214 (mtm-85) cc_final: 0.6983 (mtm-85) REVERT: A 243 ASP cc_start: 0.8152 (OUTLIER) cc_final: 0.7882 (m-30) REVERT: A 283 MET cc_start: 0.7224 (mtm) cc_final: 0.6823 (ptp) REVERT: A 387 ARG cc_start: 0.7415 (ttt-90) cc_final: 0.6502 (mtt180) REVERT: A 397 ASN cc_start: 0.8270 (m-40) cc_final: 0.7995 (m-40) REVERT: A 601 ARG cc_start: 0.7399 (mtp180) cc_final: 0.7088 (ttm110) REVERT: A 640 SER cc_start: 0.8517 (m) cc_final: 0.8253 (t) REVERT: A 678 ASN cc_start: 0.8176 (m-40) cc_final: 0.7903 (m-40) REVERT: A 705 ILE cc_start: 0.8393 (mm) cc_final: 0.8108 (mt) REVERT: A 743 LEU cc_start: 0.8534 (mt) cc_final: 0.8208 (tt) REVERT: A 875 SER cc_start: 0.7448 (t) cc_final: 0.6932 (p) REVERT: A 953 GLN cc_start: 0.7002 (tt0) cc_final: 0.6674 (tm-30) REVERT: L 24 ARG cc_start: 0.7894 (ttt-90) cc_final: 0.7610 (ttt-90) REVERT: L 27 GLU cc_start: 0.7774 (tt0) cc_final: 0.7335 (tt0) outliers start: 41 outliers final: 35 residues processed: 123 average time/residue: 0.0930 time to fit residues: 16.4523 Evaluate side-chains 127 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 91 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 553 ASN Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain A residue 758 THR Chi-restraints excluded: chain A residue 784 THR Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 945 ASN Chi-restraints excluded: chain A residue 990 ASN Chi-restraints excluded: chain A residue 1012 THR Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 38 GLU Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 62 LYS Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 98 TYR Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 42 LYS Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 72 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 30 optimal weight: 0.7980 chunk 120 optimal weight: 0.8980 chunk 31 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 28 optimal weight: 0.8980 chunk 7 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 95 optimal weight: 20.0000 chunk 123 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 635 ASN A 906 ASN L 38 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4596 r_free = 0.4596 target = 0.186511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.132434 restraints weight = 9301.385| |-----------------------------------------------------------------------------| r_work (start): 0.4076 rms_B_bonded: 3.10 r_work: 0.3858 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.3330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9548 Z= 0.141 Angle : 0.523 8.324 12931 Z= 0.272 Chirality : 0.043 0.182 1654 Planarity : 0.003 0.053 1634 Dihedral : 5.283 56.014 2053 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.51 % Favored : 96.41 % Rotamer: Outliers : 3.90 % Allowed : 13.95 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -1.40 (0.24), residues: 1254 helix: -0.31 (1.01), residues: 25 sheet: -0.69 (0.20), residues: 735 loop : -1.13 (0.26), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 387 TYR 0.009 0.001 TYR A 408 PHE 0.014 0.001 PHE A 147 TRP 0.008 0.001 TRP H 103 HIS 0.003 0.001 HIS A 513 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 9507) covalent geometry : angle 0.52342 (12927) SS BOND : bond 0.00378 ( 2) SS BOND : angle 0.73163 ( 4) hydrogen bonds : bond 0.02666 ( 134) hydrogen bonds : angle 5.28896 ( 339) Misc. bond : bond 0.00061 ( 39) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 88 time to evaluate : 0.331 Fit side-chains revert: symmetry clash REVERT: A 116 ASP cc_start: 0.7644 (t0) cc_final: 0.7197 (t0) REVERT: A 183 ARG cc_start: 0.7037 (mtm-85) cc_final: 0.6832 (mtm-85) REVERT: A 243 ASP cc_start: 0.8206 (OUTLIER) cc_final: 0.7956 (m-30) REVERT: A 283 MET cc_start: 0.7116 (mtm) cc_final: 0.6751 (ptp) REVERT: A 387 ARG cc_start: 0.7340 (ttt-90) cc_final: 0.6362 (mtt-85) REVERT: A 397 ASN cc_start: 0.8277 (m-40) cc_final: 0.7969 (m-40) REVERT: A 601 ARG cc_start: 0.7371 (mtp180) cc_final: 0.7089 (ttm110) REVERT: A 640 SER cc_start: 0.8472 (m) cc_final: 0.8196 (t) REVERT: A 678 ASN cc_start: 0.8217 (m-40) cc_final: 0.7889 (m-40) REVERT: A 705 ILE cc_start: 0.8438 (mm) cc_final: 0.8161 (mt) REVERT: A 743 LEU cc_start: 0.8536 (mt) cc_final: 0.8097 (tt) REVERT: A 875 SER cc_start: 0.7352 (t) cc_final: 0.6841 (p) REVERT: A 953 GLN cc_start: 0.7041 (tt0) cc_final: 0.6759 (tm-30) REVERT: L 24 ARG cc_start: 0.7878 (ttt-90) cc_final: 0.7562 (ttt-90) REVERT: L 27 GLU cc_start: 0.7779 (tt0) cc_final: 0.7308 (tt0) REVERT: L 90 GLN cc_start: 0.8784 (pp30) cc_final: 0.8272 (pp30) outliers start: 38 outliers final: 29 residues processed: 113 average time/residue: 0.0944 time to fit residues: 15.2464 Evaluate side-chains 116 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 86 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 548 ASN Chi-restraints excluded: chain A residue 553 ASN Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain A residue 635 ASN Chi-restraints excluded: chain A residue 755 THR Chi-restraints excluded: chain A residue 758 THR Chi-restraints excluded: chain A residue 784 THR Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 919 SER Chi-restraints excluded: chain A residue 990 ASN Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 98 TYR Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 42 LYS Chi-restraints excluded: chain L residue 69 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 113 optimal weight: 0.9990 chunk 42 optimal weight: 0.2980 chunk 91 optimal weight: 9.9990 chunk 90 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 99 optimal weight: 20.0000 chunk 108 optimal weight: 1.9990 chunk 95 optimal weight: 20.0000 chunk 16 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 chunk 32 optimal weight: 0.9980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 906 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4618 r_free = 0.4618 target = 0.189609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.134020 restraints weight = 9501.286| |-----------------------------------------------------------------------------| r_work (start): 0.4047 rms_B_bonded: 3.23 r_work: 0.3829 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.3475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9548 Z= 0.165 Angle : 0.531 8.404 12931 Z= 0.278 Chirality : 0.043 0.163 1654 Planarity : 0.003 0.053 1634 Dihedral : 4.987 52.431 2053 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.31 % Favored : 95.61 % Rotamer: Outliers : 3.69 % Allowed : 13.74 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -1.52 (0.24), residues: 1254 helix: -0.36 (1.00), residues: 25 sheet: -0.78 (0.20), residues: 737 loop : -1.18 (0.26), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 636 TYR 0.011 0.001 TYR A 408 PHE 0.016 0.002 PHE A 147 TRP 0.008 0.001 TRP H 103 HIS 0.003 0.001 HIS A 513 Details of bonding type rmsd covalent geometry : bond 0.00367 ( 9507) covalent geometry : angle 0.53124 (12927) SS BOND : bond 0.00423 ( 2) SS BOND : angle 0.69406 ( 4) hydrogen bonds : bond 0.02687 ( 134) hydrogen bonds : angle 5.23605 ( 339) Misc. bond : bond 0.00065 ( 39) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 100 time to evaluate : 0.359 Fit side-chains revert: symmetry clash REVERT: A 116 ASP cc_start: 0.7693 (t0) cc_final: 0.7241 (t0) REVERT: A 283 MET cc_start: 0.7088 (mtm) cc_final: 0.6684 (ptp) REVERT: A 387 ARG cc_start: 0.7348 (ttt-90) cc_final: 0.6399 (mtt-85) REVERT: A 397 ASN cc_start: 0.8291 (m-40) cc_final: 0.7973 (m-40) REVERT: A 601 ARG cc_start: 0.7405 (mtp180) cc_final: 0.7119 (ttm110) REVERT: A 635 ASN cc_start: 0.7539 (m-40) cc_final: 0.6826 (m-40) REVERT: A 640 SER cc_start: 0.8511 (m) cc_final: 0.8261 (t) REVERT: A 678 ASN cc_start: 0.8237 (m-40) cc_final: 0.7892 (m-40) REVERT: A 705 ILE cc_start: 0.8455 (mm) cc_final: 0.8174 (mt) REVERT: A 743 LEU cc_start: 0.8567 (mt) cc_final: 0.8211 (tt) REVERT: A 875 SER cc_start: 0.7486 (t) cc_final: 0.6957 (p) REVERT: L 24 ARG cc_start: 0.7878 (ttt-90) cc_final: 0.7558 (ttt-90) REVERT: L 27 GLU cc_start: 0.7803 (tt0) cc_final: 0.7366 (tt0) outliers start: 36 outliers final: 32 residues processed: 125 average time/residue: 0.0950 time to fit residues: 17.1116 Evaluate side-chains 127 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 95 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 548 ASN Chi-restraints excluded: chain A residue 553 ASN Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain A residue 755 THR Chi-restraints excluded: chain A residue 758 THR Chi-restraints excluded: chain A residue 784 THR Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 919 SER Chi-restraints excluded: chain A residue 990 ASN Chi-restraints excluded: chain A residue 1012 THR Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 38 GLU Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 98 TYR Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 42 LYS Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 72 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 121 optimal weight: 0.5980 chunk 102 optimal weight: 8.9990 chunk 120 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 113 optimal weight: 0.1980 chunk 109 optimal weight: 7.9990 chunk 24 optimal weight: 0.5980 chunk 65 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 412 HIS A 666 ASN A 906 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4603 r_free = 0.4603 target = 0.187248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.133149 restraints weight = 9325.633| |-----------------------------------------------------------------------------| r_work (start): 0.4088 rms_B_bonded: 3.12 r_work: 0.3872 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.3620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9548 Z= 0.110 Angle : 0.496 7.917 12931 Z= 0.259 Chirality : 0.042 0.153 1654 Planarity : 0.003 0.051 1634 Dihedral : 4.465 52.045 2053 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.79 % Favored : 97.13 % Rotamer: Outliers : 3.28 % Allowed : 14.77 % Favored : 81.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -1.41 (0.24), residues: 1254 helix: -0.29 (1.04), residues: 25 sheet: -0.72 (0.20), residues: 732 loop : -1.09 (0.27), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 183 TYR 0.009 0.001 TYR L 86 PHE 0.010 0.001 PHE A 147 TRP 0.008 0.001 TRP H 103 HIS 0.003 0.001 HIS A 513 Details of bonding type rmsd covalent geometry : bond 0.00240 ( 9507) covalent geometry : angle 0.49641 (12927) SS BOND : bond 0.00357 ( 2) SS BOND : angle 0.64290 ( 4) hydrogen bonds : bond 0.02483 ( 134) hydrogen bonds : angle 5.13810 ( 339) Misc. bond : bond 0.00046 ( 39) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 102 time to evaluate : 0.347 Fit side-chains REVERT: A 116 ASP cc_start: 0.7695 (t0) cc_final: 0.7218 (t0) REVERT: A 387 ARG cc_start: 0.7298 (ttt-90) cc_final: 0.6383 (mtt180) REVERT: A 397 ASN cc_start: 0.8301 (m-40) cc_final: 0.7987 (m-40) REVERT: A 601 ARG cc_start: 0.7364 (mtp180) cc_final: 0.7080 (ttm110) REVERT: A 640 SER cc_start: 0.8512 (m) cc_final: 0.8310 (t) REVERT: A 678 ASN cc_start: 0.8225 (m-40) cc_final: 0.7923 (m-40) REVERT: A 705 ILE cc_start: 0.8449 (mm) cc_final: 0.8158 (mt) REVERT: A 743 LEU cc_start: 0.8559 (mt) cc_final: 0.8093 (tt) REVERT: A 875 SER cc_start: 0.7510 (t) cc_final: 0.6975 (p) REVERT: A 990 ASN cc_start: 0.6973 (OUTLIER) cc_final: 0.6251 (p0) REVERT: H 12 MET cc_start: 0.7002 (mpp) cc_final: 0.6114 (mpp) REVERT: H 30 THR cc_start: 0.8972 (p) cc_final: 0.8488 (t) REVERT: L 27 GLU cc_start: 0.7760 (tt0) cc_final: 0.7274 (tt0) REVERT: L 90 GLN cc_start: 0.8798 (pp30) cc_final: 0.8285 (pp30) outliers start: 32 outliers final: 26 residues processed: 125 average time/residue: 0.0916 time to fit residues: 16.5557 Evaluate side-chains 121 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 94 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 553 ASN Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain A residue 755 THR Chi-restraints excluded: chain A residue 758 THR Chi-restraints excluded: chain A residue 784 THR Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 919 SER Chi-restraints excluded: chain A residue 990 ASN Chi-restraints excluded: chain A residue 1012 THR Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 38 GLU Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 98 TYR Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 42 LYS Chi-restraints excluded: chain L residue 72 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 85 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 78 optimal weight: 7.9990 chunk 52 optimal weight: 0.0270 chunk 86 optimal weight: 6.9990 chunk 72 optimal weight: 4.9990 chunk 99 optimal weight: 20.0000 chunk 55 optimal weight: 0.6980 chunk 65 optimal weight: 2.9990 overall best weight: 1.5242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN A 635 ASN A 720 ASN A 906 ASN A1053 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4542 r_free = 0.4542 target = 0.180772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.127606 restraints weight = 9530.404| |-----------------------------------------------------------------------------| r_work (start): 0.4014 rms_B_bonded: 3.08 r_work: 0.3794 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.3922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 9548 Z= 0.229 Angle : 0.594 8.830 12931 Z= 0.310 Chirality : 0.045 0.177 1654 Planarity : 0.003 0.054 1634 Dihedral : 4.745 52.380 2053 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.34 % Favored : 94.58 % Rotamer: Outliers : 3.59 % Allowed : 14.67 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -1.74 (0.24), residues: 1254 helix: -0.55 (0.99), residues: 25 sheet: -1.00 (0.20), residues: 742 loop : -1.18 (0.27), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 281 TYR 0.016 0.002 TYR A 408 PHE 0.021 0.002 PHE A 147 TRP 0.011 0.002 TRP A 102 HIS 0.004 0.001 HIS A 513 Details of bonding type rmsd covalent geometry : bond 0.00518 ( 9507) covalent geometry : angle 0.59368 (12927) SS BOND : bond 0.00501 ( 2) SS BOND : angle 0.82222 ( 4) hydrogen bonds : bond 0.02979 ( 134) hydrogen bonds : angle 5.27108 ( 339) Misc. bond : bond 0.00059 ( 39) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 92 time to evaluate : 0.322 Fit side-chains revert: symmetry clash REVERT: A 116 ASP cc_start: 0.7789 (t0) cc_final: 0.7333 (t0) REVERT: A 283 MET cc_start: 0.6974 (mtm) cc_final: 0.6604 (ptp) REVERT: A 387 ARG cc_start: 0.7389 (ttt-90) cc_final: 0.6465 (mtt180) REVERT: A 397 ASN cc_start: 0.8272 (m-40) cc_final: 0.7943 (m-40) REVERT: A 601 ARG cc_start: 0.7401 (mtp180) cc_final: 0.7155 (ttm110) REVERT: A 678 ASN cc_start: 0.8170 (m-40) cc_final: 0.7860 (m-40) REVERT: A 705 ILE cc_start: 0.8489 (mm) cc_final: 0.8199 (mt) REVERT: A 743 LEU cc_start: 0.8715 (mt) cc_final: 0.8348 (tt) REVERT: A 875 SER cc_start: 0.7659 (t) cc_final: 0.7049 (p) REVERT: A 896 ILE cc_start: 0.8217 (mt) cc_final: 0.7895 (mt) REVERT: H 30 THR cc_start: 0.9004 (p) cc_final: 0.8575 (t) REVERT: L 27 GLU cc_start: 0.7826 (tt0) cc_final: 0.7360 (tt0) outliers start: 35 outliers final: 32 residues processed: 115 average time/residue: 0.0948 time to fit residues: 15.7910 Evaluate side-chains 116 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 84 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 553 ASN Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain A residue 713 THR Chi-restraints excluded: chain A residue 755 THR Chi-restraints excluded: chain A residue 758 THR Chi-restraints excluded: chain A residue 784 THR Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 945 ASN Chi-restraints excluded: chain A residue 990 ASN Chi-restraints excluded: chain A residue 1012 THR Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 38 GLU Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 98 TYR Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 42 LYS Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 72 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 chunk 93 optimal weight: 10.0000 chunk 102 optimal weight: 9.9990 chunk 52 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 101 optimal weight: 6.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 198 ASN A 481 HIS A 635 ASN A 906 ASN A1065 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4497 r_free = 0.4497 target = 0.175579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.123536 restraints weight = 9942.419| |-----------------------------------------------------------------------------| r_work (start): 0.3959 rms_B_bonded: 3.09 r_work: 0.3734 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.4321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 9548 Z= 0.316 Angle : 0.689 10.149 12931 Z= 0.360 Chirality : 0.048 0.213 1654 Planarity : 0.004 0.061 1634 Dihedral : 5.242 53.718 2053 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.46 % Favored : 93.46 % Rotamer: Outliers : 3.79 % Allowed : 14.77 % Favored : 81.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -2.24 (0.24), residues: 1254 helix: -1.19 (0.85), residues: 26 sheet: -1.39 (0.20), residues: 718 loop : -1.39 (0.26), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 281 TYR 0.021 0.002 TYR A 408 PHE 0.030 0.003 PHE A 631 TRP 0.014 0.002 TRP A 455 HIS 0.005 0.001 HIS A 513 Details of bonding type rmsd covalent geometry : bond 0.00718 ( 9507) covalent geometry : angle 0.68887 (12927) SS BOND : bond 0.00585 ( 2) SS BOND : angle 0.89016 ( 4) hydrogen bonds : bond 0.03403 ( 134) hydrogen bonds : angle 5.46157 ( 339) Misc. bond : bond 0.00081 ( 39) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 101 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 116 ASP cc_start: 0.7864 (t0) cc_final: 0.7491 (t0) REVERT: A 283 MET cc_start: 0.7003 (mtm) cc_final: 0.6585 (ptp) REVERT: A 387 ARG cc_start: 0.7473 (ttt-90) cc_final: 0.7044 (mtm110) REVERT: A 601 ARG cc_start: 0.7392 (mtp180) cc_final: 0.7167 (ttm110) REVERT: A 743 LEU cc_start: 0.8803 (mt) cc_final: 0.8435 (tt) REVERT: A 875 SER cc_start: 0.7830 (t) cc_final: 0.7473 (m) REVERT: A 896 ILE cc_start: 0.8207 (mt) cc_final: 0.7895 (mt) REVERT: A 913 ASN cc_start: 0.7001 (m-40) cc_final: 0.5553 (t0) outliers start: 37 outliers final: 33 residues processed: 126 average time/residue: 0.0946 time to fit residues: 17.1466 Evaluate side-chains 127 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 94 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 553 ASN Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain A residue 635 ASN Chi-restraints excluded: chain A residue 713 THR Chi-restraints excluded: chain A residue 755 THR Chi-restraints excluded: chain A residue 758 THR Chi-restraints excluded: chain A residue 784 THR Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 945 ASN Chi-restraints excluded: chain A residue 990 ASN Chi-restraints excluded: chain A residue 1012 THR Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 38 GLU Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 98 TYR Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 72 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 68 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 111 optimal weight: 4.9990 chunk 87 optimal weight: 4.9990 chunk 102 optimal weight: 5.9990 chunk 122 optimal weight: 0.9990 chunk 71 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 chunk 78 optimal weight: 4.9990 chunk 93 optimal weight: 9.9990 chunk 29 optimal weight: 0.8980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 198 ASN A 331 GLN A 635 ASN A 906 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4500 r_free = 0.4500 target = 0.176067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.124104 restraints weight = 9710.693| |-----------------------------------------------------------------------------| r_work (start): 0.3967 rms_B_bonded: 3.05 r_work: 0.3745 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.4358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.130 9548 Z= 0.287 Angle : 0.981 59.199 12931 Z= 0.562 Chirality : 0.047 0.244 1654 Planarity : 0.004 0.060 1634 Dihedral : 5.268 53.683 2053 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.46 % Favored : 93.46 % Rotamer: Outliers : 3.49 % Allowed : 15.08 % Favored : 81.44 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 6.25 % 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: -2.28 (0.24), residues: 1254 helix: -1.17 (0.85), residues: 26 sheet: -1.43 (0.20), residues: 718 loop : -1.40 (0.26), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 281 TYR 0.019 0.002 TYR A 408 PHE 0.027 0.002 PHE A 631 TRP 0.011 0.002 TRP H 103 HIS 0.004 0.001 HIS A 707 Details of bonding type rmsd covalent geometry : bond 0.00637 ( 9507) covalent geometry : angle 0.98123 (12927) SS BOND : bond 0.00547 ( 2) SS BOND : angle 0.88101 ( 4) hydrogen bonds : bond 0.03339 ( 134) hydrogen bonds : angle 5.46334 ( 339) Misc. bond : bond 0.00132 ( 39) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2272.10 seconds wall clock time: 40 minutes 6.58 seconds (2406.58 seconds total)