Starting phenix.real_space_refine on Wed May 14 16:24:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8kgo_37228/05_2025/8kgo_37228.cif Found real_map, /net/cci-nas-00/data/ceres_data/8kgo_37228/05_2025/8kgo_37228.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8kgo_37228/05_2025/8kgo_37228.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8kgo_37228/05_2025/8kgo_37228.map" model { file = "/net/cci-nas-00/data/ceres_data/8kgo_37228/05_2025/8kgo_37228.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8kgo_37228/05_2025/8kgo_37228.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 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 50 5.16 5 C 7813 2.51 5 N 2086 2.21 5 O 2192 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 12141 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 747, 6072 Classifications: {'peptide': 747} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 716} Chain breaks: 2 Chain: "B" Number of atoms: 6069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 747, 6069 Classifications: {'peptide': 747} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 716} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 7.40, per 1000 atoms: 0.61 Number of scatterers: 12141 At special positions: 0 Unit cell: (113.75, 120.25, 111.8, 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 50 16.00 O 2192 8.00 N 2086 7.00 C 7813 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.90 Conformation dependent library (CDL) restraints added in 1.5 seconds 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2808 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 18 sheets defined 44.8% alpha, 9.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.41 Creating SS restraints... Processing helix chain 'A' and resid 440 through 451 removed outlier: 3.684A pdb=" N SER A 444 " --> pdb=" O ASP A 440 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR A 451 " --> pdb=" O ARG A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 513 Processing helix chain 'A' and resid 547 through 560 removed outlier: 3.558A pdb=" N PHE A 559 " --> pdb=" O TYR A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 603 removed outlier: 3.806A pdb=" N PHE A 596 " --> pdb=" O TYR A 592 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LYS A 601 " --> pdb=" O ASP A 597 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LYS A 602 " --> pdb=" O ALA A 598 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N GLN A 603 " --> pdb=" O TRP A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 620 removed outlier: 4.166A pdb=" N HIS A 620 " --> pdb=" O LEU A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 629 Processing helix chain 'A' and resid 631 through 634 Processing helix chain 'A' and resid 644 through 653 removed outlier: 3.785A pdb=" N LEU A 648 " --> pdb=" O SER A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 657 through 664 Processing helix chain 'A' and resid 672 through 683 Processing helix chain 'A' and resid 687 through 704 removed outlier: 4.288A pdb=" N THR A 695 " --> pdb=" O LEU A 691 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N LYS A 696 " --> pdb=" O GLN A 692 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ILE A 703 " --> pdb=" O LYS A 699 " (cutoff:3.500A) Processing helix chain 'A' and resid 715 through 729 removed outlier: 3.621A pdb=" N LYS A 727 " --> pdb=" O ALA A 723 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N PHE A 729 " --> pdb=" O GLY A 725 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 749 Processing helix chain 'A' and resid 755 through 765 Processing helix chain 'A' and resid 787 through 791 removed outlier: 3.773A pdb=" N LEU A 790 " --> pdb=" O SER A 787 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLY A 791 " --> pdb=" O ARG A 788 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 787 through 791' Processing helix chain 'A' and resid 809 through 814 Processing helix chain 'A' and resid 864 through 866 No H-bonds generated for 'chain 'A' and resid 864 through 866' Processing helix chain 'A' and resid 867 through 877 removed outlier: 3.979A pdb=" N LEU A 871 " --> pdb=" O ASP A 867 " (cutoff:3.500A) Processing helix chain 'A' and resid 884 through 889 removed outlier: 3.885A pdb=" N ALA A 889 " --> pdb=" O LEU A 885 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 952 Processing helix chain 'A' and resid 953 through 958 removed outlier: 3.897A pdb=" N THR A 958 " --> pdb=" O SER A 954 " (cutoff:3.500A) Processing helix chain 'A' and resid 999 through 1004 Processing helix chain 'A' and resid 1027 through 1034 removed outlier: 4.084A pdb=" N ILE A1031 " --> pdb=" O THR A1027 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LEU A1032 " --> pdb=" O TYR A1028 " (cutoff:3.500A) Processing helix chain 'A' and resid 1035 through 1038 Processing helix chain 'A' and resid 1039 through 1075 removed outlier: 3.564A pdb=" N ASN A1069 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N ALA A1072 " --> pdb=" O ILE A1068 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N GLU A1073 " --> pdb=" O ASN A1069 " (cutoff:3.500A) Processing helix chain 'A' and resid 1076 through 1079 Processing helix chain 'A' and resid 1081 through 1092 removed outlier: 3.687A pdb=" N ALA A1085 " --> pdb=" O ASP A1081 " (cutoff:3.500A) Processing helix chain 'A' and resid 1098 through 1103 removed outlier: 3.645A pdb=" N ILE A1102 " --> pdb=" O ASN A1098 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ILE A1103 " --> pdb=" O HIS A1099 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1098 through 1103' Processing helix chain 'A' and resid 1109 through 1116 Processing helix chain 'A' and resid 1134 through 1159 Processing helix chain 'A' and resid 1166 through 1186 removed outlier: 3.578A pdb=" N LEU A1171 " --> pdb=" O ALA A1167 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N GLU A1172 " --> pdb=" O SER A1168 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLU A1173 " --> pdb=" O VAL A1169 " (cutoff:3.500A) Processing helix chain 'B' and resid 440 through 451 removed outlier: 3.683A pdb=" N SER B 444 " --> pdb=" O ASP B 440 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N THR B 451 " --> pdb=" O ARG B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 503 through 513 Processing helix chain 'B' and resid 547 through 560 removed outlier: 3.558A pdb=" N PHE B 559 " --> pdb=" O TYR B 555 " (cutoff:3.500A) Processing helix chain 'B' and resid 592 through 603 removed outlier: 3.806A pdb=" N PHE B 596 " --> pdb=" O TYR B 592 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LYS B 601 " --> pdb=" O ASP B 597 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LYS B 602 " --> pdb=" O ALA B 598 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N GLN B 603 " --> pdb=" O TRP B 599 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 620 removed outlier: 4.161A pdb=" N HIS B 620 " --> pdb=" O LEU B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 621 through 629 Processing helix chain 'B' and resid 631 through 634 Processing helix chain 'B' and resid 644 through 653 removed outlier: 3.783A pdb=" N LEU B 648 " --> pdb=" O SER B 644 " (cutoff:3.500A) Processing helix chain 'B' and resid 657 through 664 Processing helix chain 'B' and resid 672 through 683 Processing helix chain 'B' and resid 687 through 707 removed outlier: 4.266A pdb=" N THR B 695 " --> pdb=" O LEU B 691 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N LYS B 696 " --> pdb=" O GLN B 692 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ILE B 703 " --> pdb=" O LYS B 699 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG B 705 " --> pdb=" O ASP B 701 " (cutoff:3.500A) Processing helix chain 'B' and resid 715 through 729 removed outlier: 3.657A pdb=" N LYS B 727 " --> pdb=" O ALA B 723 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N PHE B 729 " --> pdb=" O GLY B 725 " (cutoff:3.500A) Processing helix chain 'B' and resid 738 through 749 Processing helix chain 'B' and resid 755 through 767 Processing helix chain 'B' and resid 787 through 791 removed outlier: 3.772A pdb=" N LEU B 790 " --> pdb=" O SER B 787 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLY B 791 " --> pdb=" O ARG B 788 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 787 through 791' Processing helix chain 'B' and resid 809 through 814 Processing helix chain 'B' and resid 864 through 867 removed outlier: 3.857A pdb=" N ASP B 867 " --> pdb=" O GLN B 864 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 864 through 867' Processing helix chain 'B' and resid 868 through 877 Processing helix chain 'B' and resid 882 through 886 removed outlier: 3.652A pdb=" N LEU B 885 " --> pdb=" O LYS B 882 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 952 Processing helix chain 'B' and resid 953 through 958 removed outlier: 3.897A pdb=" N THR B 958 " --> pdb=" O SER B 954 " (cutoff:3.500A) Processing helix chain 'B' and resid 999 through 1004 Processing helix chain 'B' and resid 1027 through 1034 removed outlier: 4.083A pdb=" N ILE B1031 " --> pdb=" O THR B1027 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LEU B1032 " --> pdb=" O TYR B1028 " (cutoff:3.500A) Processing helix chain 'B' and resid 1035 through 1038 Processing helix chain 'B' and resid 1039 through 1075 removed outlier: 3.564A pdb=" N ASN B1069 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N ALA B1072 " --> pdb=" O ILE B1068 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N GLU B1073 " --> pdb=" O ASN B1069 " (cutoff:3.500A) Processing helix chain 'B' and resid 1076 through 1079 Processing helix chain 'B' and resid 1081 through 1092 removed outlier: 3.688A pdb=" N ALA B1085 " --> pdb=" O ASP B1081 " (cutoff:3.500A) Processing helix chain 'B' and resid 1098 through 1103 removed outlier: 3.645A pdb=" N ILE B1102 " --> pdb=" O ASN B1098 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE B1103 " --> pdb=" O HIS B1099 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1098 through 1103' Processing helix chain 'B' and resid 1109 through 1116 Processing helix chain 'B' and resid 1134 through 1159 Processing helix chain 'B' and resid 1166 through 1186 removed outlier: 3.578A pdb=" N LEU B1171 " --> pdb=" O ALA B1167 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N GLU B1172 " --> pdb=" O SER B1168 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N GLU B1173 " --> pdb=" O VAL B1169 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 465 through 469 Processing sheet with id=AA2, first strand: chain 'A' and resid 570 through 572 Processing sheet with id=AA3, first strand: chain 'A' and resid 577 through 581 Processing sheet with id=AA4, first strand: chain 'A' and resid 736 through 737 Processing sheet with id=AA5, first strand: chain 'A' and resid 824 through 827 removed outlier: 4.082A pdb=" N GLU A 833 " --> pdb=" O VAL A 825 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N GLU A 827 " --> pdb=" O ARG A 831 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N ARG A 831 " --> pdb=" O GLU A 827 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 849 through 850 Processing sheet with id=AA7, first strand: chain 'A' and resid 909 through 913 removed outlier: 3.589A pdb=" N HIS A 909 " --> pdb=" O TYR A 920 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TYR A 916 " --> pdb=" O PHE A 913 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N TYR A 917 " --> pdb=" O LEU A1009 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 922 through 925 removed outlier: 6.339A pdb=" N THR A 922 " --> pdb=" O THR A 935 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE A 932 " --> pdb=" O VAL A 976 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N LEU A 975 " --> pdb=" O ILE A 963 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N ILE A 963 " --> pdb=" O LEU A 975 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N LYS A 977 " --> pdb=" O GLU A 961 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1014 through 1016 removed outlier: 3.529A pdb=" N ILE A1023 " --> pdb=" O PHE A1015 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 465 through 469 Processing sheet with id=AB2, first strand: chain 'B' and resid 570 through 572 Processing sheet with id=AB3, first strand: chain 'B' and resid 577 through 581 Processing sheet with id=AB4, first strand: chain 'B' and resid 736 through 737 Processing sheet with id=AB5, first strand: chain 'B' and resid 824 through 826 removed outlier: 4.171A pdb=" N GLU B 833 " --> pdb=" O VAL B 825 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 849 through 850 Processing sheet with id=AB7, first strand: chain 'B' and resid 910 through 913 removed outlier: 3.600A pdb=" N TYR B 916 " --> pdb=" O PHE B 913 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N TYR B 917 " --> pdb=" O LEU B1009 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 922 through 925 removed outlier: 6.344A pdb=" N THR B 922 " --> pdb=" O THR B 935 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ILE B 932 " --> pdb=" O VAL B 976 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N LEU B 975 " --> pdb=" O ILE B 963 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N ILE B 963 " --> pdb=" O LEU B 975 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N LYS B 977 " --> pdb=" O GLU B 961 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 1014 through 1016 removed outlier: 3.609A pdb=" N ILE B1023 " --> pdb=" O PHE B1015 " (cutoff:3.500A) 449 hydrogen bonds defined for protein. 1302 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: 3.40 Time building geometry restraints manager: 3.41 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: 3375 1.33 - 1.45: 2213 1.45 - 1.57: 6765 1.57 - 1.69: 0 1.69 - 1.81: 78 Bond restraints: 12431 Sorted by residual: bond pdb=" C LEU A 897 " pdb=" N PRO A 898 " ideal model delta sigma weight residual 1.332 1.391 -0.060 1.34e-02 5.57e+03 1.97e+01 bond pdb=" CA SER B 968 " pdb=" C SER B 968 " ideal model delta sigma weight residual 1.526 1.474 0.052 1.37e-02 5.33e+03 1.45e+01 bond pdb=" N ILE B 703 " pdb=" CA ILE B 703 " ideal model delta sigma weight residual 1.461 1.496 -0.035 1.19e-02 7.06e+03 8.77e+00 bond pdb=" CA LEU A 897 " pdb=" C LEU A 897 " ideal model delta sigma weight residual 1.524 1.560 -0.037 1.26e-02 6.30e+03 8.40e+00 bond pdb=" CA SER B 968 " pdb=" CB SER B 968 " ideal model delta sigma weight residual 1.530 1.491 0.040 1.52e-02 4.33e+03 6.86e+00 ... (remaining 12426 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.20: 16439 3.20 - 6.41: 308 6.41 - 9.61: 31 9.61 - 12.82: 10 12.82 - 16.02: 4 Bond angle restraints: 16792 Sorted by residual: angle pdb=" N GLU A 808 " pdb=" CA GLU A 808 " pdb=" C GLU A 808 " ideal model delta sigma weight residual 114.62 107.70 6.92 1.14e+00 7.69e-01 3.69e+01 angle pdb=" C ALA B 889 " pdb=" N ILE B 890 " pdb=" CA ILE B 890 " ideal model delta sigma weight residual 122.66 117.58 5.08 9.70e-01 1.06e+00 2.74e+01 angle pdb=" N LYS A 893 " pdb=" CA LYS A 893 " pdb=" C LYS A 893 " ideal model delta sigma weight residual 111.39 118.51 -7.12 1.38e+00 5.25e-01 2.66e+01 angle pdb=" C LYS B1055 " pdb=" N LEU B1056 " pdb=" CA LEU B1056 " ideal model delta sigma weight residual 121.58 112.51 9.07 1.95e+00 2.63e-01 2.16e+01 angle pdb=" C LYS A1055 " pdb=" N LEU A1056 " pdb=" CA LEU A1056 " ideal model delta sigma weight residual 121.58 112.52 9.06 1.95e+00 2.63e-01 2.16e+01 ... (remaining 16787 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.12: 6887 15.12 - 30.23: 428 30.23 - 45.35: 122 45.35 - 60.47: 12 60.47 - 75.59: 9 Dihedral angle restraints: 7458 sinusoidal: 3078 harmonic: 4380 Sorted by residual: dihedral pdb=" CA ASP B 867 " pdb=" C ASP B 867 " pdb=" N ILE B 868 " pdb=" CA ILE B 868 " ideal model delta harmonic sigma weight residual 180.00 156.84 23.16 0 5.00e+00 4.00e-02 2.15e+01 dihedral pdb=" CA ASP A 867 " pdb=" C ASP A 867 " pdb=" N ILE A 868 " pdb=" CA ILE A 868 " ideal model delta harmonic sigma weight residual 180.00 156.93 23.07 0 5.00e+00 4.00e-02 2.13e+01 dihedral pdb=" CA PHE B 629 " pdb=" C PHE B 629 " pdb=" N LYS B 630 " pdb=" CA LYS B 630 " ideal model delta harmonic sigma weight residual 180.00 158.68 21.32 0 5.00e+00 4.00e-02 1.82e+01 ... (remaining 7455 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 1330 0.069 - 0.137: 417 0.137 - 0.206: 58 0.206 - 0.274: 9 0.274 - 0.343: 5 Chirality restraints: 1819 Sorted by residual: chirality pdb=" CA LYS A 893 " pdb=" N LYS A 893 " pdb=" C LYS A 893 " pdb=" CB LYS A 893 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.94e+00 chirality pdb=" CB VAL B 825 " pdb=" CA VAL B 825 " pdb=" CG1 VAL B 825 " pdb=" CG2 VAL B 825 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.37e+00 chirality pdb=" CB VAL A 803 " pdb=" CA VAL A 803 " pdb=" CG1 VAL A 803 " pdb=" CG2 VAL A 803 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.31e+00 ... (remaining 1816 not shown) Planarity restraints: 2136 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A1170 " -0.028 2.00e-02 2.50e+03 2.29e-02 1.31e+01 pdb=" CG TRP A1170 " 0.062 2.00e-02 2.50e+03 pdb=" CD1 TRP A1170 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP A1170 " 0.006 2.00e-02 2.50e+03 pdb=" NE1 TRP A1170 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP A1170 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A1170 " -0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP A1170 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP A1170 " -0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP A1170 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B1170 " 0.028 2.00e-02 2.50e+03 2.28e-02 1.30e+01 pdb=" CG TRP B1170 " -0.061 2.00e-02 2.50e+03 pdb=" CD1 TRP B1170 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP B1170 " -0.005 2.00e-02 2.50e+03 pdb=" NE1 TRP B1170 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP B1170 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B1170 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP B1170 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP B1170 " 0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP B1170 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 824 " 0.021 2.00e-02 2.50e+03 2.08e-02 8.61e+00 pdb=" CG TYR A 824 " -0.051 2.00e-02 2.50e+03 pdb=" CD1 TYR A 824 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 TYR A 824 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR A 824 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR A 824 " 0.010 2.00e-02 2.50e+03 pdb=" CZ TYR A 824 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR A 824 " -0.001 2.00e-02 2.50e+03 ... (remaining 2133 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1953 2.76 - 3.29: 10337 3.29 - 3.83: 18939 3.83 - 4.36: 22826 4.36 - 4.90: 40538 Nonbonded interactions: 94593 Sorted by model distance: nonbonded pdb=" NZ LYS B 893 " pdb=" OE1 GLU B1030 " model vdw 2.219 3.120 nonbonded pdb=" OE2 GLU A1161 " pdb=" OG SER A1168 " model vdw 2.283 3.040 nonbonded pdb=" OE2 GLU B1161 " pdb=" OG SER B1168 " model vdw 2.283 3.040 nonbonded pdb=" O SER A 819 " pdb=" OH TYR A 824 " model vdw 2.290 3.040 nonbonded pdb=" O PHE B1094 " pdb=" OH TYR B1122 " model vdw 2.303 3.040 ... (remaining 94588 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 415 through 893 or (resid 894 and (name N or name CA or na \ me C or name O or name CB )) or resid 895 through 1192)) selection = chain 'B' } 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: 1.700 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: 0.010 Extract box with map and model: 0.530 Check model and map are aligned: 0.080 Set scattering table: 0.120 Process input model: 28.810 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 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 : 0.011 0.096 12431 Z= 0.438 Angle : 1.138 16.021 16792 Z= 0.597 Chirality : 0.067 0.343 1819 Planarity : 0.008 0.058 2136 Dihedral : 11.212 75.586 4650 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.15 % Favored : 92.85 % Rotamer: Outliers : 0.92 % Allowed : 4.74 % Favored : 94.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.07 (0.18), residues: 1482 helix: -2.90 (0.15), residues: 644 sheet: -1.95 (0.35), residues: 212 loop : -2.58 (0.21), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.005 TRP A1170 HIS 0.012 0.003 HIS B1099 PHE 0.039 0.005 PHE B 990 TYR 0.051 0.004 TYR A 824 ARG 0.008 0.001 ARG B 956 Details of bonding type rmsd hydrogen bonds : bond 0.19041 ( 449) hydrogen bonds : angle 7.35854 ( 1302) covalent geometry : bond 0.01075 (12431) covalent geometry : angle 1.13760 (16792) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 190 time to evaluate : 1.273 Fit side-chains REVERT: A 735 GLU cc_start: 0.7603 (mt-10) cc_final: 0.7330 (mt-10) REVERT: A 964 ILE cc_start: 0.7743 (OUTLIER) cc_final: 0.7541 (tp) REVERT: A 1149 GLN cc_start: 0.8477 (tp40) cc_final: 0.7865 (mt0) REVERT: B 735 GLU cc_start: 0.7569 (mt-10) cc_final: 0.7333 (mt-10) REVERT: B 887 HIS cc_start: 0.5693 (OUTLIER) cc_final: 0.5356 (p90) REVERT: B 964 ILE cc_start: 0.7688 (OUTLIER) cc_final: 0.7487 (tp) REVERT: B 1149 GLN cc_start: 0.8461 (tp40) cc_final: 0.7847 (mt0) outliers start: 12 outliers final: 2 residues processed: 198 average time/residue: 0.2514 time to fit residues: 70.9276 Evaluate side-chains 129 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 124 time to evaluate : 1.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 964 ILE Chi-restraints excluded: chain A residue 969 SER Chi-restraints excluded: chain B residue 825 VAL Chi-restraints excluded: chain B residue 887 HIS Chi-restraints excluded: chain B residue 964 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 124 optimal weight: 0.9980 chunk 112 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 75 optimal weight: 9.9990 chunk 59 optimal weight: 0.8980 chunk 116 optimal weight: 0.7980 chunk 44 optimal weight: 10.0000 chunk 70 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 134 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 557 HIS A 609 HIS A 883 HIS A1010 HIS A1069 ASN A1115 GLN B 557 HIS B 609 HIS B 883 HIS B1010 HIS B1069 ASN B1115 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.153144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.124968 restraints weight = 14863.359| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 1.59 r_work: 0.3197 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 12431 Z= 0.115 Angle : 0.573 7.930 16792 Z= 0.288 Chirality : 0.042 0.149 1819 Planarity : 0.005 0.047 2136 Dihedral : 5.102 37.586 1666 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.61 % Allowed : 7.88 % Favored : 90.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.44 (0.20), residues: 1482 helix: -1.18 (0.20), residues: 634 sheet: -1.63 (0.36), residues: 208 loop : -1.95 (0.22), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A1170 HIS 0.007 0.001 HIS B 609 PHE 0.012 0.001 PHE A 990 TYR 0.015 0.001 TYR A1067 ARG 0.003 0.000 ARG A 660 Details of bonding type rmsd hydrogen bonds : bond 0.05125 ( 449) hydrogen bonds : angle 4.88101 ( 1302) covalent geometry : bond 0.00248 (12431) covalent geometry : angle 0.57311 (16792) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 160 time to evaluate : 1.451 Fit side-chains REVERT: A 523 GLN cc_start: 0.7742 (tp40) cc_final: 0.7428 (tp40) REVERT: A 701 ASP cc_start: 0.8886 (t70) cc_final: 0.8383 (t0) REVERT: A 749 MET cc_start: 0.8656 (mmt) cc_final: 0.8104 (mmt) REVERT: A 964 ILE cc_start: 0.7669 (OUTLIER) cc_final: 0.7397 (tp) REVERT: A 1088 ILE cc_start: 0.7301 (mt) cc_final: 0.7054 (mt) REVERT: A 1149 GLN cc_start: 0.8459 (tp40) cc_final: 0.7872 (mt0) REVERT: B 523 GLN cc_start: 0.7730 (tp40) cc_final: 0.7467 (tp40) REVERT: B 566 HIS cc_start: 0.7478 (m-70) cc_final: 0.7241 (m-70) REVERT: B 735 GLU cc_start: 0.8039 (mt-10) cc_final: 0.7822 (mt-10) REVERT: B 756 MET cc_start: 0.7519 (tmm) cc_final: 0.7311 (ttp) REVERT: B 964 ILE cc_start: 0.7585 (OUTLIER) cc_final: 0.7374 (tp) REVERT: B 1088 ILE cc_start: 0.7268 (mt) cc_final: 0.7060 (mt) REVERT: B 1149 GLN cc_start: 0.8449 (tp40) cc_final: 0.7875 (mt0) outliers start: 21 outliers final: 8 residues processed: 174 average time/residue: 0.2675 time to fit residues: 65.7382 Evaluate side-chains 142 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 132 time to evaluate : 1.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 964 ILE Chi-restraints excluded: chain A residue 1076 LEU Chi-restraints excluded: chain A residue 1102 ILE Chi-restraints excluded: chain A residue 1118 LEU Chi-restraints excluded: chain B residue 825 VAL Chi-restraints excluded: chain B residue 964 ILE Chi-restraints excluded: chain B residue 1076 LEU Chi-restraints excluded: chain B residue 1102 ILE Chi-restraints excluded: chain B residue 1118 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 25 optimal weight: 4.9990 chunk 8 optimal weight: 10.0000 chunk 145 optimal weight: 0.2980 chunk 33 optimal weight: 0.9990 chunk 80 optimal weight: 10.0000 chunk 118 optimal weight: 0.5980 chunk 146 optimal weight: 2.9990 chunk 71 optimal weight: 0.3980 chunk 14 optimal weight: 6.9990 chunk 29 optimal weight: 5.9990 chunk 13 optimal weight: 6.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 634 ASN A1115 GLN B 634 ASN B1115 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.155454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.126555 restraints weight = 14986.071| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 1.61 r_work: 0.3258 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3136 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 12431 Z= 0.104 Angle : 0.521 7.742 16792 Z= 0.258 Chirality : 0.041 0.142 1819 Planarity : 0.004 0.043 2136 Dihedral : 4.478 33.653 1663 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.07 % Allowed : 7.88 % Favored : 90.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.22), residues: 1482 helix: -0.36 (0.21), residues: 638 sheet: -1.42 (0.36), residues: 218 loop : -1.51 (0.24), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B1170 HIS 0.005 0.001 HIS B1051 PHE 0.011 0.001 PHE B 959 TYR 0.012 0.001 TYR A1067 ARG 0.002 0.000 ARG B1057 Details of bonding type rmsd hydrogen bonds : bond 0.04486 ( 449) hydrogen bonds : angle 4.33054 ( 1302) covalent geometry : bond 0.00241 (12431) covalent geometry : angle 0.52067 (16792) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 145 time to evaluate : 1.506 Fit side-chains REVERT: A 749 MET cc_start: 0.8681 (mmt) cc_final: 0.8138 (mmt) REVERT: A 1088 ILE cc_start: 0.7310 (mt) cc_final: 0.6967 (mt) REVERT: A 1149 GLN cc_start: 0.8517 (tp40) cc_final: 0.7890 (mt0) REVERT: B 749 MET cc_start: 0.8495 (mmp) cc_final: 0.8104 (mmp) REVERT: B 964 ILE cc_start: 0.7561 (OUTLIER) cc_final: 0.7323 (tp) REVERT: B 1088 ILE cc_start: 0.7336 (mt) cc_final: 0.6996 (mt) REVERT: B 1149 GLN cc_start: 0.8497 (tp40) cc_final: 0.7883 (mt0) outliers start: 27 outliers final: 17 residues processed: 165 average time/residue: 0.2697 time to fit residues: 62.7711 Evaluate side-chains 154 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 136 time to evaluate : 1.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 610 THR Chi-restraints excluded: chain A residue 688 SER Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 714 MET Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 967 SER Chi-restraints excluded: chain A residue 1076 LEU Chi-restraints excluded: chain A residue 1102 ILE Chi-restraints excluded: chain A residue 1118 LEU Chi-restraints excluded: chain B residue 610 THR Chi-restraints excluded: chain B residue 688 SER Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 714 MET Chi-restraints excluded: chain B residue 825 VAL Chi-restraints excluded: chain B residue 964 ILE Chi-restraints excluded: chain B residue 1076 LEU Chi-restraints excluded: chain B residue 1102 ILE Chi-restraints excluded: chain B residue 1118 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 86 optimal weight: 4.9990 chunk 40 optimal weight: 0.9980 chunk 71 optimal weight: 0.0030 chunk 58 optimal weight: 3.9990 chunk 121 optimal weight: 10.0000 chunk 33 optimal weight: 0.7980 chunk 12 optimal weight: 4.9990 chunk 125 optimal weight: 8.9990 chunk 133 optimal weight: 4.9990 chunk 101 optimal weight: 5.9990 chunk 31 optimal weight: 8.9990 overall best weight: 2.1594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 690 HIS A1115 GLN B 690 HIS B1115 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.142178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.111321 restraints weight = 15250.327| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 1.76 r_work: 0.3158 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12431 Z= 0.155 Angle : 0.550 8.650 16792 Z= 0.276 Chirality : 0.043 0.142 1819 Planarity : 0.004 0.045 2136 Dihedral : 4.521 35.943 1661 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 2.30 % Allowed : 9.72 % Favored : 87.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.22), residues: 1482 helix: -0.06 (0.22), residues: 638 sheet: -1.27 (0.36), residues: 230 loop : -1.35 (0.24), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B1170 HIS 0.006 0.001 HIS B1051 PHE 0.015 0.002 PHE A 739 TYR 0.014 0.002 TYR A 824 ARG 0.003 0.000 ARG B 530 Details of bonding type rmsd hydrogen bonds : bond 0.05070 ( 449) hydrogen bonds : angle 4.18531 ( 1302) covalent geometry : bond 0.00380 (12431) covalent geometry : angle 0.54964 (16792) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 135 time to evaluate : 1.464 Fit side-chains REVERT: A 1060 MET cc_start: 0.8433 (ttt) cc_final: 0.8203 (ttm) REVERT: A 1088 ILE cc_start: 0.7324 (mt) cc_final: 0.7043 (mt) REVERT: A 1149 GLN cc_start: 0.8553 (tp40) cc_final: 0.7902 (mt0) REVERT: B 1060 MET cc_start: 0.8429 (ttt) cc_final: 0.8201 (ttm) REVERT: B 1088 ILE cc_start: 0.7304 (mt) cc_final: 0.7013 (mt) REVERT: B 1149 GLN cc_start: 0.8549 (tp40) cc_final: 0.7894 (mt0) outliers start: 30 outliers final: 20 residues processed: 157 average time/residue: 0.2715 time to fit residues: 60.6216 Evaluate side-chains 147 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 127 time to evaluate : 1.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 610 THR Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 688 SER Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 714 MET Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 967 SER Chi-restraints excluded: chain A residue 969 SER Chi-restraints excluded: chain A residue 1076 LEU Chi-restraints excluded: chain A residue 1102 ILE Chi-restraints excluded: chain A residue 1118 LEU Chi-restraints excluded: chain B residue 610 THR Chi-restraints excluded: chain B residue 674 THR Chi-restraints excluded: chain B residue 688 SER Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 714 MET Chi-restraints excluded: chain B residue 825 VAL Chi-restraints excluded: chain B residue 1076 LEU Chi-restraints excluded: chain B residue 1102 ILE Chi-restraints excluded: chain B residue 1118 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 18 optimal weight: 4.9990 chunk 29 optimal weight: 0.9980 chunk 72 optimal weight: 6.9990 chunk 134 optimal weight: 2.9990 chunk 141 optimal weight: 8.9990 chunk 41 optimal weight: 10.0000 chunk 89 optimal weight: 0.8980 chunk 25 optimal weight: 3.9990 chunk 2 optimal weight: 9.9990 chunk 34 optimal weight: 5.9990 chunk 147 optimal weight: 0.7980 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 680 HIS A1115 GLN B1115 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.142360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.111324 restraints weight = 15300.378| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 1.77 r_work: 0.3116 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12431 Z= 0.140 Angle : 0.532 8.431 16792 Z= 0.265 Chirality : 0.042 0.138 1819 Planarity : 0.004 0.044 2136 Dihedral : 4.299 30.874 1659 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.68 % Allowed : 10.79 % Favored : 86.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.22), residues: 1482 helix: 0.12 (0.22), residues: 642 sheet: -1.13 (0.37), residues: 218 loop : -1.28 (0.24), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B1170 HIS 0.006 0.001 HIS B1051 PHE 0.013 0.001 PHE B 990 TYR 0.012 0.001 TYR A 824 ARG 0.002 0.000 ARG A 734 Details of bonding type rmsd hydrogen bonds : bond 0.04820 ( 449) hydrogen bonds : angle 4.07126 ( 1302) covalent geometry : bond 0.00342 (12431) covalent geometry : angle 0.53208 (16792) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 124 time to evaluate : 1.510 Fit side-chains REVERT: A 1050 GLU cc_start: 0.8667 (OUTLIER) cc_final: 0.8214 (pp20) REVERT: A 1054 LEU cc_start: 0.7573 (OUTLIER) cc_final: 0.7034 (mp) REVERT: A 1149 GLN cc_start: 0.8560 (tp40) cc_final: 0.7899 (mt0) REVERT: B 1050 GLU cc_start: 0.8674 (OUTLIER) cc_final: 0.8224 (pp20) REVERT: B 1054 LEU cc_start: 0.7583 (OUTLIER) cc_final: 0.7061 (mp) REVERT: B 1149 GLN cc_start: 0.8544 (tp40) cc_final: 0.7894 (mt0) outliers start: 35 outliers final: 23 residues processed: 149 average time/residue: 0.2720 time to fit residues: 56.9776 Evaluate side-chains 153 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 126 time to evaluate : 1.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 610 THR Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 688 SER Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 714 MET Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 964 ILE Chi-restraints excluded: chain A residue 967 SER Chi-restraints excluded: chain A residue 969 SER Chi-restraints excluded: chain A residue 1050 GLU Chi-restraints excluded: chain A residue 1054 LEU Chi-restraints excluded: chain A residue 1076 LEU Chi-restraints excluded: chain A residue 1102 ILE Chi-restraints excluded: chain A residue 1118 LEU Chi-restraints excluded: chain B residue 610 THR Chi-restraints excluded: chain B residue 674 THR Chi-restraints excluded: chain B residue 688 SER Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 714 MET Chi-restraints excluded: chain B residue 825 VAL Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1050 GLU Chi-restraints excluded: chain B residue 1054 LEU Chi-restraints excluded: chain B residue 1076 LEU Chi-restraints excluded: chain B residue 1102 ILE Chi-restraints excluded: chain B residue 1118 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 51 optimal weight: 8.9990 chunk 53 optimal weight: 1.9990 chunk 136 optimal weight: 0.9980 chunk 145 optimal weight: 0.0370 chunk 143 optimal weight: 2.9990 chunk 34 optimal weight: 0.2980 chunk 99 optimal weight: 0.8980 chunk 18 optimal weight: 0.8980 chunk 141 optimal weight: 8.9990 chunk 78 optimal weight: 6.9990 chunk 21 optimal weight: 2.9990 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1115 GLN B 680 HIS B1115 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.148002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.116273 restraints weight = 15293.479| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 1.79 r_work: 0.3148 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.2665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 12431 Z= 0.081 Angle : 0.460 7.015 16792 Z= 0.228 Chirality : 0.040 0.142 1819 Planarity : 0.003 0.042 2136 Dihedral : 3.806 23.893 1659 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.45 % Allowed : 12.09 % Favored : 85.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.23), residues: 1482 helix: 0.51 (0.22), residues: 634 sheet: -1.02 (0.38), residues: 218 loop : -1.20 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1170 HIS 0.004 0.001 HIS B1051 PHE 0.009 0.001 PHE A1164 TYR 0.008 0.001 TYR B1067 ARG 0.002 0.000 ARG B 530 Details of bonding type rmsd hydrogen bonds : bond 0.03638 ( 449) hydrogen bonds : angle 3.84123 ( 1302) covalent geometry : bond 0.00179 (12431) covalent geometry : angle 0.46003 (16792) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 135 time to evaluate : 1.431 Fit side-chains REVERT: A 991 LYS cc_start: 0.8226 (mmtm) cc_final: 0.7829 (mmmt) REVERT: A 1149 GLN cc_start: 0.8471 (tp40) cc_final: 0.7779 (mt0) REVERT: B 991 LYS cc_start: 0.8145 (mmtm) cc_final: 0.7731 (mmmt) REVERT: B 1149 GLN cc_start: 0.8460 (tp40) cc_final: 0.7767 (mt0) outliers start: 32 outliers final: 15 residues processed: 156 average time/residue: 0.2703 time to fit residues: 59.3068 Evaluate side-chains 144 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 129 time to evaluate : 1.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 610 THR Chi-restraints excluded: chain A residue 628 MET Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 964 ILE Chi-restraints excluded: chain A residue 967 SER Chi-restraints excluded: chain A residue 1076 LEU Chi-restraints excluded: chain A residue 1118 LEU Chi-restraints excluded: chain B residue 610 THR Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 825 VAL Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1076 LEU Chi-restraints excluded: chain B residue 1118 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 125 optimal weight: 5.9990 chunk 4 optimal weight: 8.9990 chunk 27 optimal weight: 4.9990 chunk 70 optimal weight: 7.9990 chunk 54 optimal weight: 7.9990 chunk 89 optimal weight: 0.9980 chunk 59 optimal weight: 5.9990 chunk 143 optimal weight: 10.0000 chunk 67 optimal weight: 9.9990 chunk 81 optimal weight: 9.9990 chunk 79 optimal weight: 10.0000 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 930 ASN A1115 GLN B 930 ASN B1115 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.136010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.105657 restraints weight = 15631.063| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 1.81 r_work: 0.2958 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2826 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.2323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.064 12431 Z= 0.323 Angle : 0.709 10.152 16792 Z= 0.358 Chirality : 0.050 0.171 1819 Planarity : 0.006 0.048 2136 Dihedral : 4.902 41.638 1659 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 3.06 % Allowed : 11.78 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.22), residues: 1482 helix: -0.05 (0.21), residues: 652 sheet: -1.35 (0.36), residues: 232 loop : -1.33 (0.25), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A1170 HIS 0.009 0.002 HIS B1099 PHE 0.020 0.003 PHE A 739 TYR 0.020 0.003 TYR A 824 ARG 0.005 0.001 ARG A 719 Details of bonding type rmsd hydrogen bonds : bond 0.06739 ( 449) hydrogen bonds : angle 4.38016 ( 1302) covalent geometry : bond 0.00814 (12431) covalent geometry : angle 0.70852 (16792) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 127 time to evaluate : 1.421 Fit side-chains REVERT: A 833 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.7793 (pm20) REVERT: A 1149 GLN cc_start: 0.8605 (tp40) cc_final: 0.8313 (tp40) REVERT: B 1149 GLN cc_start: 0.8596 (tp40) cc_final: 0.8307 (tp40) outliers start: 40 outliers final: 23 residues processed: 158 average time/residue: 0.2776 time to fit residues: 62.9801 Evaluate side-chains 152 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 128 time to evaluate : 1.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 610 THR Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 688 SER Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 714 MET Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 833 GLU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 967 SER Chi-restraints excluded: chain A residue 1050 GLU Chi-restraints excluded: chain A residue 1076 LEU Chi-restraints excluded: chain A residue 1118 LEU Chi-restraints excluded: chain B residue 608 ASN Chi-restraints excluded: chain B residue 610 THR Chi-restraints excluded: chain B residue 674 THR Chi-restraints excluded: chain B residue 688 SER Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 714 MET Chi-restraints excluded: chain B residue 825 VAL Chi-restraints excluded: chain B residue 833 GLU Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1050 GLU Chi-restraints excluded: chain B residue 1076 LEU Chi-restraints excluded: chain B residue 1118 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 106 optimal weight: 0.9980 chunk 122 optimal weight: 3.9990 chunk 51 optimal weight: 7.9990 chunk 102 optimal weight: 0.6980 chunk 72 optimal weight: 2.9990 chunk 144 optimal weight: 6.9990 chunk 32 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 chunk 137 optimal weight: 3.9990 chunk 68 optimal weight: 10.0000 chunk 33 optimal weight: 1.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 887 HIS A1115 GLN B1115 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.142900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.112334 restraints weight = 15491.762| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 1.73 r_work: 0.3089 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.2582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 12431 Z= 0.103 Angle : 0.506 7.693 16792 Z= 0.253 Chirality : 0.042 0.174 1819 Planarity : 0.004 0.046 2136 Dihedral : 4.194 30.947 1659 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.84 % Allowed : 13.54 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.22), residues: 1482 helix: 0.36 (0.22), residues: 650 sheet: -1.00 (0.37), residues: 216 loop : -1.20 (0.24), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1170 HIS 0.005 0.001 HIS B1051 PHE 0.011 0.001 PHE B1164 TYR 0.010 0.001 TYR B1067 ARG 0.002 0.000 ARG A 530 Details of bonding type rmsd hydrogen bonds : bond 0.04440 ( 449) hydrogen bonds : angle 4.00612 ( 1302) covalent geometry : bond 0.00240 (12431) covalent geometry : angle 0.50610 (16792) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 134 time to evaluate : 1.509 Fit side-chains REVERT: A 1149 GLN cc_start: 0.8493 (tp40) cc_final: 0.7645 (mt0) REVERT: B 1149 GLN cc_start: 0.8483 (tp40) cc_final: 0.7645 (mt0) outliers start: 24 outliers final: 19 residues processed: 151 average time/residue: 0.2826 time to fit residues: 59.2881 Evaluate side-chains 146 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 127 time to evaluate : 1.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 610 THR Chi-restraints excluded: chain A residue 688 SER Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 964 ILE Chi-restraints excluded: chain A residue 967 SER Chi-restraints excluded: chain A residue 969 SER Chi-restraints excluded: chain A residue 1050 GLU Chi-restraints excluded: chain A residue 1076 LEU Chi-restraints excluded: chain A residue 1118 LEU Chi-restraints excluded: chain B residue 610 THR Chi-restraints excluded: chain B residue 688 SER Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 825 VAL Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1050 GLU Chi-restraints excluded: chain B residue 1076 LEU Chi-restraints excluded: chain B residue 1118 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 128 optimal weight: 10.0000 chunk 48 optimal weight: 10.0000 chunk 14 optimal weight: 5.9990 chunk 89 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 chunk 125 optimal weight: 4.9990 chunk 96 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 chunk 117 optimal weight: 0.0020 chunk 85 optimal weight: 3.9990 chunk 124 optimal weight: 0.9990 overall best weight: 2.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1115 GLN B1115 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.147031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.117506 restraints weight = 15146.012| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 1.57 r_work: 0.3155 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.2549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12431 Z= 0.153 Angle : 0.539 8.540 16792 Z= 0.270 Chirality : 0.043 0.172 1819 Planarity : 0.004 0.038 2136 Dihedral : 4.295 33.334 1659 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 1.68 % Allowed : 13.62 % Favored : 84.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.22), residues: 1482 helix: 0.39 (0.22), residues: 648 sheet: -1.01 (0.37), residues: 216 loop : -1.16 (0.24), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1170 HIS 0.005 0.001 HIS A1051 PHE 0.014 0.001 PHE B 739 TYR 0.011 0.001 TYR A 824 ARG 0.002 0.000 ARG B 530 Details of bonding type rmsd hydrogen bonds : bond 0.04924 ( 449) hydrogen bonds : angle 3.99389 ( 1302) covalent geometry : bond 0.00377 (12431) covalent geometry : angle 0.53940 (16792) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 127 time to evaluate : 1.458 Fit side-chains REVERT: A 1149 GLN cc_start: 0.8571 (tp40) cc_final: 0.7918 (mt0) REVERT: B 1149 GLN cc_start: 0.8551 (tp40) cc_final: 0.7910 (mt0) outliers start: 22 outliers final: 20 residues processed: 143 average time/residue: 0.2613 time to fit residues: 53.5598 Evaluate side-chains 142 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 122 time to evaluate : 1.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 610 THR Chi-restraints excluded: chain A residue 688 SER Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 964 ILE Chi-restraints excluded: chain A residue 967 SER Chi-restraints excluded: chain A residue 969 SER Chi-restraints excluded: chain A residue 1050 GLU Chi-restraints excluded: chain A residue 1076 LEU Chi-restraints excluded: chain A residue 1118 LEU Chi-restraints excluded: chain B residue 610 THR Chi-restraints excluded: chain B residue 688 SER Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 825 VAL Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 964 ILE Chi-restraints excluded: chain B residue 1050 GLU Chi-restraints excluded: chain B residue 1076 LEU Chi-restraints excluded: chain B residue 1118 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 100 optimal weight: 0.0980 chunk 47 optimal weight: 6.9990 chunk 46 optimal weight: 0.7980 chunk 124 optimal weight: 0.9990 chunk 31 optimal weight: 7.9990 chunk 13 optimal weight: 0.9980 chunk 89 optimal weight: 0.8980 chunk 4 optimal weight: 0.9990 chunk 129 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 54 optimal weight: 9.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1115 GLN B1115 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.145857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.114533 restraints weight = 15215.499| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 1.73 r_work: 0.3131 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.2846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 12431 Z= 0.087 Angle : 0.476 7.188 16792 Z= 0.235 Chirality : 0.041 0.165 1819 Planarity : 0.003 0.039 2136 Dihedral : 3.852 26.888 1659 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.84 % Allowed : 13.70 % Favored : 84.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.23), residues: 1482 helix: 0.70 (0.22), residues: 632 sheet: -0.91 (0.38), residues: 216 loop : -1.04 (0.24), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1170 HIS 0.005 0.001 HIS B1051 PHE 0.011 0.001 PHE B1164 TYR 0.010 0.001 TYR B 769 ARG 0.002 0.000 ARG A 530 Details of bonding type rmsd hydrogen bonds : bond 0.03729 ( 449) hydrogen bonds : angle 3.81279 ( 1302) covalent geometry : bond 0.00198 (12431) covalent geometry : angle 0.47572 (16792) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 130 time to evaluate : 1.456 Fit side-chains REVERT: A 749 MET cc_start: 0.8876 (mmt) cc_final: 0.8116 (mmt) REVERT: A 1149 GLN cc_start: 0.8478 (tp40) cc_final: 0.7783 (mt0) REVERT: B 1149 GLN cc_start: 0.8468 (tp40) cc_final: 0.7782 (mt0) outliers start: 24 outliers final: 19 residues processed: 147 average time/residue: 0.2805 time to fit residues: 57.3614 Evaluate side-chains 145 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 126 time to evaluate : 1.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 610 THR Chi-restraints excluded: chain A residue 628 MET Chi-restraints excluded: chain A residue 688 SER Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 964 ILE Chi-restraints excluded: chain A residue 967 SER Chi-restraints excluded: chain A residue 969 SER Chi-restraints excluded: chain A residue 1076 LEU Chi-restraints excluded: chain A residue 1118 LEU Chi-restraints excluded: chain B residue 610 THR Chi-restraints excluded: chain B residue 688 SER Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 825 VAL Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 964 ILE Chi-restraints excluded: chain B residue 1076 LEU Chi-restraints excluded: chain B residue 1118 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 131 optimal weight: 0.7980 chunk 30 optimal weight: 4.9990 chunk 1 optimal weight: 10.0000 chunk 12 optimal weight: 9.9990 chunk 135 optimal weight: 0.9990 chunk 69 optimal weight: 10.0000 chunk 106 optimal weight: 0.7980 chunk 137 optimal weight: 0.9990 chunk 114 optimal weight: 0.0870 chunk 20 optimal weight: 2.9990 chunk 49 optimal weight: 0.0980 overall best weight: 0.5560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1115 GLN B1115 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.147192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.117101 restraints weight = 15339.635| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 1.74 r_work: 0.3161 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.3018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 12431 Z= 0.081 Angle : 0.454 6.775 16792 Z= 0.228 Chirality : 0.040 0.162 1819 Planarity : 0.003 0.035 2136 Dihedral : 3.656 23.474 1659 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.53 % Allowed : 13.85 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.23), residues: 1482 helix: 0.87 (0.22), residues: 624 sheet: -0.87 (0.38), residues: 216 loop : -0.94 (0.24), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B1170 HIS 0.005 0.001 HIS B1051 PHE 0.011 0.001 PHE A1164 TYR 0.007 0.001 TYR B1067 ARG 0.002 0.000 ARG A1185 Details of bonding type rmsd hydrogen bonds : bond 0.03464 ( 449) hydrogen bonds : angle 3.67697 ( 1302) covalent geometry : bond 0.00180 (12431) covalent geometry : angle 0.45420 (16792) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6285.91 seconds wall clock time: 109 minutes 24.75 seconds (6564.75 seconds total)