Starting phenix.real_space_refine on Sat Aug 23 12:15:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8kgo_37228/08_2025/8kgo_37228.cif Found real_map, /net/cci-nas-00/data/ceres_data/8kgo_37228/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8kgo_37228/08_2025/8kgo_37228.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8kgo_37228/08_2025/8kgo_37228.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8kgo_37228/08_2025/8kgo_37228.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8kgo_37228/08_2025/8kgo_37228.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 2.39, per 1000 atoms: 0.20 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: 0.76 Conformation dependent library (CDL) restraints added in 420.0 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.40 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: 1.66 Time building geometry restraints manager: 1.01 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: 1.580 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: 0.020 Extract box with map and model: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 9.700 Find NCS groups from input model: 0.130 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:0.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.640 ------------------------------------------------------------------------------- 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 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: -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 ARG 0.008 0.001 ARG B 956 TYR 0.051 0.004 TYR A 824 PHE 0.039 0.005 PHE B 990 TRP 0.062 0.005 TRP A1170 HIS 0.012 0.003 HIS B1099 Details of bonding type rmsd covalent geometry : bond 0.01075 (12431) covalent geometry : angle 1.13760 (16792) hydrogen bonds : bond 0.19041 ( 449) hydrogen bonds : angle 7.35854 ( 1302) *********************** 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 : 0.485 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: 0.1023 time to fit residues: 28.8850 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 : 0.467 ------------------------------------------------------------------------------- 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 98 optimal weight: 0.9990 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 B1115 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.153386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.125173 restraints weight = 14892.115| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 1.60 r_work: 0.3211 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.1804 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= 0.110 Angle : 0.566 7.835 16792 Z= 0.285 Chirality : 0.042 0.151 1819 Planarity : 0.005 0.046 2136 Dihedral : 5.098 37.263 1666 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.76 % Allowed : 7.50 % Favored : 90.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -2.45 (0.20), residues: 1482 helix: -1.19 (0.20), residues: 634 sheet: -1.65 (0.36), residues: 208 loop : -1.95 (0.22), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 660 TYR 0.015 0.001 TYR B1067 PHE 0.012 0.001 PHE A 990 TRP 0.028 0.002 TRP A1170 HIS 0.004 0.001 HIS B1051 Details of bonding type rmsd covalent geometry : bond 0.00242 (12431) covalent geometry : angle 0.56643 (16792) hydrogen bonds : bond 0.05136 ( 449) hydrogen bonds : angle 4.89201 ( 1302) *********************** 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 185 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 162 time to evaluate : 0.396 Fit side-chains REVERT: A 523 GLN cc_start: 0.7729 (tp40) cc_final: 0.7449 (tp40) REVERT: A 566 HIS cc_start: 0.7472 (m-70) cc_final: 0.7224 (m-70) REVERT: A 701 ASP cc_start: 0.8892 (t70) cc_final: 0.8384 (t0) REVERT: A 749 MET cc_start: 0.8651 (mmt) cc_final: 0.8088 (mmt) REVERT: A 964 ILE cc_start: 0.7671 (OUTLIER) cc_final: 0.7405 (tp) REVERT: A 1088 ILE cc_start: 0.7306 (mt) cc_final: 0.7060 (mt) REVERT: A 1149 GLN cc_start: 0.8444 (tp40) cc_final: 0.7871 (mt0) REVERT: B 523 GLN cc_start: 0.7725 (tp40) cc_final: 0.7454 (tp40) REVERT: B 566 HIS cc_start: 0.7470 (m-70) cc_final: 0.7231 (m-70) REVERT: B 735 GLU cc_start: 0.8065 (mt-10) cc_final: 0.7834 (mt-10) REVERT: B 756 MET cc_start: 0.7512 (tmm) cc_final: 0.7293 (ttp) REVERT: B 964 ILE cc_start: 0.7569 (OUTLIER) cc_final: 0.7362 (tp) REVERT: B 1088 ILE cc_start: 0.7282 (mt) cc_final: 0.7070 (mt) REVERT: B 1149 GLN cc_start: 0.8439 (tp40) cc_final: 0.7876 (mt0) outliers start: 23 outliers final: 10 residues processed: 179 average time/residue: 0.1063 time to fit residues: 26.8317 Evaluate side-chains 143 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 131 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 688 SER 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 688 SER 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 82 optimal weight: 10.0000 chunk 29 optimal weight: 4.9990 chunk 26 optimal weight: 0.9980 chunk 106 optimal weight: 0.5980 chunk 122 optimal weight: 0.9990 chunk 97 optimal weight: 4.9990 chunk 147 optimal weight: 3.9990 chunk 89 optimal weight: 0.7980 chunk 70 optimal weight: 9.9990 chunk 146 optimal weight: 5.9990 chunk 145 optimal weight: 0.0060 overall best weight: 0.6798 ------------------------------------------------------------------------------- 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 = 0.3762 r_free = 0.3762 target = 0.157722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.129932 restraints weight = 14964.930| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 1.56 r_work: 0.3288 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.2264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 12431 Z= 0.091 Angle : 0.503 7.188 16792 Z= 0.249 Chirality : 0.041 0.141 1819 Planarity : 0.004 0.043 2136 Dihedral : 4.329 33.077 1663 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.68 % Allowed : 8.19 % Favored : 90.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -1.44 (0.22), residues: 1482 helix: -0.20 (0.22), residues: 628 sheet: -1.41 (0.36), residues: 218 loop : -1.46 (0.24), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 660 TYR 0.012 0.001 TYR B1067 PHE 0.013 0.001 PHE A 959 TRP 0.018 0.001 TRP A1170 HIS 0.004 0.001 HIS B1051 Details of bonding type rmsd covalent geometry : bond 0.00203 (12431) covalent geometry : angle 0.50264 (16792) hydrogen bonds : bond 0.04119 ( 449) hydrogen bonds : angle 4.25411 ( 1302) *********************** 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 177 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 155 time to evaluate : 0.431 Fit side-chains REVERT: A 749 MET cc_start: 0.8647 (mmt) cc_final: 0.8142 (mmt) REVERT: A 1088 ILE cc_start: 0.7344 (mt) cc_final: 0.6993 (mt) REVERT: A 1149 GLN cc_start: 0.8506 (tp40) cc_final: 0.8242 (tp40) REVERT: B 1088 ILE cc_start: 0.7358 (mt) cc_final: 0.7009 (mt) REVERT: B 1149 GLN cc_start: 0.8492 (tp40) cc_final: 0.8225 (tp40) outliers start: 22 outliers final: 14 residues processed: 170 average time/residue: 0.1089 time to fit residues: 25.7629 Evaluate side-chains 151 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 137 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 610 THR 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 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 49 optimal weight: 0.6980 chunk 42 optimal weight: 4.9990 chunk 84 optimal weight: 7.9990 chunk 65 optimal weight: 20.0000 chunk 120 optimal weight: 3.9990 chunk 115 optimal weight: 5.9990 chunk 62 optimal weight: 5.9990 chunk 121 optimal weight: 6.9990 chunk 60 optimal weight: 0.8980 chunk 51 optimal weight: 10.0000 chunk 104 optimal weight: 6.9990 overall best weight: 3.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 690 HIS B 690 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.139970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.109713 restraints weight = 15546.087| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 1.80 r_work: 0.3019 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2889 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 12431 Z= 0.216 Angle : 0.618 9.287 16792 Z= 0.311 Chirality : 0.046 0.145 1819 Planarity : 0.005 0.045 2136 Dihedral : 4.676 35.007 1659 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 2.52 % Allowed : 9.79 % Favored : 87.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -1.32 (0.22), residues: 1482 helix: -0.13 (0.21), residues: 638 sheet: -1.21 (0.36), residues: 226 loop : -1.43 (0.24), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 530 TYR 0.018 0.002 TYR A 824 PHE 0.018 0.002 PHE B 990 TRP 0.020 0.002 TRP B1170 HIS 0.006 0.001 HIS A1051 Details of bonding type rmsd covalent geometry : bond 0.00540 (12431) covalent geometry : angle 0.61816 (16792) hydrogen bonds : bond 0.05795 ( 449) hydrogen bonds : angle 4.32371 ( 1302) *********************** 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: 33 poor density : 132 time to evaluate : 0.309 Fit side-chains REVERT: A 735 GLU cc_start: 0.8323 (mt-10) cc_final: 0.8100 (mt-10) REVERT: A 1060 MET cc_start: 0.8463 (ttt) cc_final: 0.8215 (ttm) REVERT: A 1088 ILE cc_start: 0.7306 (mt) cc_final: 0.7032 (mt) REVERT: A 1149 GLN cc_start: 0.8541 (tp40) cc_final: 0.8264 (tp40) REVERT: B 1060 MET cc_start: 0.8454 (ttt) cc_final: 0.8208 (ttm) REVERT: B 1088 ILE cc_start: 0.7226 (mt) cc_final: 0.6954 (mt) REVERT: B 1149 GLN cc_start: 0.8541 (tp40) cc_final: 0.8254 (tp40) outliers start: 33 outliers final: 24 residues processed: 155 average time/residue: 0.0967 time to fit residues: 21.5090 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 : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 509 VAL 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 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 509 VAL 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 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 108 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 123 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 84 optimal weight: 7.9990 chunk 22 optimal weight: 4.9990 chunk 3 optimal weight: 7.9990 chunk 104 optimal weight: 3.9990 chunk 73 optimal weight: 4.9990 chunk 25 optimal weight: 0.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.148845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.118424 restraints weight = 15208.563| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 1.74 r_work: 0.3160 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.2268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12431 Z= 0.163 Angle : 0.564 8.857 16792 Z= 0.281 Chirality : 0.044 0.142 1819 Planarity : 0.004 0.045 2136 Dihedral : 4.467 32.330 1659 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 3.21 % Allowed : 10.94 % Favored : 85.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.12 (0.22), residues: 1482 helix: 0.08 (0.22), residues: 638 sheet: -1.06 (0.38), residues: 214 loop : -1.39 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 530 TYR 0.014 0.002 TYR A 824 PHE 0.014 0.002 PHE A 990 TRP 0.014 0.002 TRP B1170 HIS 0.006 0.001 HIS A1051 Details of bonding type rmsd covalent geometry : bond 0.00402 (12431) covalent geometry : angle 0.56446 (16792) hydrogen bonds : bond 0.05212 ( 449) hydrogen bonds : angle 4.17350 ( 1302) *********************** 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 165 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 123 time to evaluate : 0.545 Fit side-chains REVERT: A 735 GLU cc_start: 0.8289 (mt-10) cc_final: 0.8087 (mt-10) REVERT: A 1149 GLN cc_start: 0.8547 (tp40) cc_final: 0.7883 (mt0) REVERT: B 1149 GLN cc_start: 0.8527 (tp40) cc_final: 0.7872 (mt0) outliers start: 42 outliers final: 24 residues processed: 156 average time/residue: 0.1076 time to fit residues: 24.0790 Evaluate side-chains 149 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 125 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 509 VAL 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 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 509 VAL 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 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 134 optimal weight: 0.9980 chunk 132 optimal weight: 2.9990 chunk 131 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 77 optimal weight: 9.9990 chunk 32 optimal weight: 2.9990 chunk 14 optimal weight: 5.9990 chunk 44 optimal weight: 10.0000 chunk 59 optimal weight: 0.8980 chunk 129 optimal weight: 6.9990 chunk 93 optimal weight: 5.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 680 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.148445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.118671 restraints weight = 15189.728| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 1.61 r_work: 0.3153 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.2392 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 : 0.550 8.675 16792 Z= 0.274 Chirality : 0.043 0.159 1819 Planarity : 0.004 0.040 2136 Dihedral : 4.385 31.856 1659 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 2.83 % Allowed : 12.39 % Favored : 84.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -1.02 (0.22), residues: 1482 helix: 0.15 (0.22), residues: 648 sheet: -0.97 (0.38), residues: 214 loop : -1.38 (0.24), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 530 TYR 0.012 0.001 TYR A 824 PHE 0.013 0.001 PHE B 739 TRP 0.011 0.001 TRP A1170 HIS 0.006 0.001 HIS A1051 Details of bonding type rmsd covalent geometry : bond 0.00377 (12431) covalent geometry : angle 0.54980 (16792) hydrogen bonds : bond 0.05023 ( 449) hydrogen bonds : angle 4.08671 ( 1302) *********************** 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 163 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 126 time to evaluate : 0.507 Fit side-chains REVERT: A 833 GLU cc_start: 0.8408 (OUTLIER) cc_final: 0.7706 (pm20) REVERT: A 1060 MET cc_start: 0.8447 (ttt) cc_final: 0.8192 (ttm) REVERT: A 1149 GLN cc_start: 0.8565 (tp40) cc_final: 0.7918 (mt0) REVERT: B 1060 MET cc_start: 0.8440 (ttt) cc_final: 0.8187 (ttm) REVERT: B 1149 GLN cc_start: 0.8551 (tp40) cc_final: 0.7936 (mt0) outliers start: 37 outliers final: 27 residues processed: 153 average time/residue: 0.1239 time to fit residues: 26.6491 Evaluate side-chains 150 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 122 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 610 THR Chi-restraints excluded: chain A residue 628 MET 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 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 1102 ILE Chi-restraints excluded: chain A residue 1118 LEU Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 610 THR Chi-restraints excluded: chain B residue 628 MET 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 1076 LEU Chi-restraints excluded: chain B residue 1102 ILE 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 0 optimal weight: 10.0000 chunk 128 optimal weight: 9.9990 chunk 27 optimal weight: 0.6980 chunk 44 optimal weight: 5.9990 chunk 94 optimal weight: 4.9990 chunk 131 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 41 optimal weight: 8.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- 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 = 0.3530 r_free = 0.3530 target = 0.138238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.107243 restraints weight = 15426.750| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 1.76 r_work: 0.2994 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2865 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.2394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 12431 Z= 0.215 Angle : 0.609 9.554 16792 Z= 0.306 Chirality : 0.046 0.151 1819 Planarity : 0.005 0.042 2136 Dihedral : 4.632 35.766 1659 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 2.75 % Allowed : 12.70 % Favored : 84.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -1.05 (0.22), residues: 1482 helix: 0.16 (0.21), residues: 640 sheet: -1.08 (0.36), residues: 226 loop : -1.36 (0.25), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A1040 TYR 0.015 0.002 TYR A 824 PHE 0.017 0.002 PHE B 739 TRP 0.015 0.002 TRP B1170 HIS 0.006 0.001 HIS A1051 Details of bonding type rmsd covalent geometry : bond 0.00537 (12431) covalent geometry : angle 0.60922 (16792) hydrogen bonds : bond 0.05782 ( 449) hydrogen bonds : angle 4.20293 ( 1302) *********************** 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 157 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 121 time to evaluate : 0.296 Fit side-chains REVERT: A 833 GLU cc_start: 0.8464 (OUTLIER) cc_final: 0.7730 (pm20) REVERT: A 1060 MET cc_start: 0.8448 (ttt) cc_final: 0.8200 (ttm) REVERT: A 1149 GLN cc_start: 0.8562 (tp40) cc_final: 0.7865 (mt0) REVERT: B 1060 MET cc_start: 0.8442 (ttt) cc_final: 0.8203 (ttm) REVERT: B 1149 GLN cc_start: 0.8559 (tp40) cc_final: 0.7876 (mt0) outliers start: 36 outliers final: 27 residues processed: 148 average time/residue: 0.1100 time to fit residues: 23.3508 Evaluate side-chains 147 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 119 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 509 VAL 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 964 ILE Chi-restraints excluded: chain A residue 967 SER Chi-restraints excluded: chain A residue 969 SER Chi-restraints excluded: chain A residue 1065 VAL 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 509 VAL 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 1065 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 53 optimal weight: 10.0000 chunk 2 optimal weight: 9.9990 chunk 46 optimal weight: 5.9990 chunk 111 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 113 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 39 optimal weight: 0.0970 chunk 86 optimal weight: 9.9990 chunk 82 optimal weight: 0.0570 chunk 14 optimal weight: 0.0570 overall best weight: 0.8418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 680 HIS A 887 HIS A1115 GLN B1115 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.144460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.114677 restraints weight = 15296.005| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 1.76 r_work: 0.3160 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.2706 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= 0.093 Angle : 0.493 7.680 16792 Z= 0.244 Chirality : 0.041 0.184 1819 Planarity : 0.004 0.039 2136 Dihedral : 4.033 27.041 1659 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.84 % Allowed : 13.93 % Favored : 84.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -0.70 (0.22), residues: 1482 helix: 0.43 (0.22), residues: 644 sheet: -0.90 (0.38), residues: 216 loop : -1.17 (0.24), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 530 TYR 0.009 0.001 TYR B 769 PHE 0.010 0.001 PHE B1164 TRP 0.014 0.001 TRP B1170 HIS 0.005 0.001 HIS A1051 Details of bonding type rmsd covalent geometry : bond 0.00213 (12431) covalent geometry : angle 0.49340 (16792) hydrogen bonds : bond 0.04036 ( 449) hydrogen bonds : angle 3.94106 ( 1302) *********************** 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 156 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 132 time to evaluate : 0.342 Fit side-chains REVERT: A 1149 GLN cc_start: 0.8494 (tp40) cc_final: 0.7847 (mt0) REVERT: B 1149 GLN cc_start: 0.8493 (tp40) cc_final: 0.7855 (mt0) outliers start: 24 outliers final: 19 residues processed: 147 average time/residue: 0.1120 time to fit residues: 23.0092 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 : 0.504 ------------------------------------------------------------------------------- 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 714 MET Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 958 THR 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 628 MET 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 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 147 optimal weight: 7.9990 chunk 49 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 chunk 132 optimal weight: 0.7980 chunk 110 optimal weight: 3.9990 chunk 81 optimal weight: 0.4980 chunk 108 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 104 optimal weight: 0.8980 chunk 20 optimal weight: 9.9990 chunk 12 optimal weight: 10.0000 overall best weight: 1.6384 ------------------------------------------------------------------------------- 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 = 0.3666 r_free = 0.3666 target = 0.148909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.119057 restraints weight = 15057.954| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 1.71 r_work: 0.3084 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.2680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12431 Z= 0.125 Angle : 0.512 8.177 16792 Z= 0.256 Chirality : 0.042 0.158 1819 Planarity : 0.004 0.036 2136 Dihedral : 4.120 30.867 1659 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.99 % Allowed : 13.85 % Favored : 84.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.65 (0.22), residues: 1482 helix: 0.46 (0.22), residues: 650 sheet: -0.90 (0.38), residues: 216 loop : -1.12 (0.24), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 530 TYR 0.010 0.001 TYR A1067 PHE 0.012 0.001 PHE B 739 TRP 0.014 0.001 TRP A1170 HIS 0.005 0.001 HIS A1051 Details of bonding type rmsd covalent geometry : bond 0.00304 (12431) covalent geometry : angle 0.51214 (16792) hydrogen bonds : bond 0.04489 ( 449) hydrogen bonds : angle 3.90314 ( 1302) *********************** 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 151 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 125 time to evaluate : 0.503 Fit side-chains REVERT: A 1054 LEU cc_start: 0.7503 (OUTLIER) cc_final: 0.7024 (mp) REVERT: A 1149 GLN cc_start: 0.8493 (tp40) cc_final: 0.7807 (mt0) REVERT: B 1054 LEU cc_start: 0.7488 (OUTLIER) cc_final: 0.7011 (mp) REVERT: B 1149 GLN cc_start: 0.8488 (tp40) cc_final: 0.7824 (mt0) outliers start: 26 outliers final: 21 residues processed: 141 average time/residue: 0.1169 time to fit residues: 23.4426 Evaluate side-chains 147 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 124 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 610 THR 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 983 LEU 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 711 LEU Chi-restraints excluded: chain B residue 714 MET Chi-restraints excluded: chain B residue 801 ILE Chi-restraints excluded: chain B residue 825 VAL Chi-restraints excluded: chain B residue 931 ILE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 125 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 67 optimal weight: 7.9990 chunk 18 optimal weight: 3.9990 chunk 64 optimal weight: 6.9990 chunk 2 optimal weight: 10.0000 chunk 34 optimal weight: 0.9980 chunk 85 optimal weight: 2.9990 chunk 100 optimal weight: 0.4980 chunk 143 optimal weight: 10.0000 chunk 46 optimal weight: 3.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- 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 = 0.3648 r_free = 0.3648 target = 0.147360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.117183 restraints weight = 15179.796| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 1.73 r_work: 0.3062 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.2641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12431 Z= 0.148 Angle : 0.538 8.675 16792 Z= 0.270 Chirality : 0.043 0.154 1819 Planarity : 0.004 0.038 2136 Dihedral : 4.259 33.855 1659 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 1.68 % Allowed : 14.00 % Favored : 84.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -0.64 (0.22), residues: 1482 helix: 0.46 (0.22), residues: 646 sheet: -0.90 (0.37), residues: 216 loop : -1.10 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 526 TYR 0.011 0.001 TYR A 824 PHE 0.013 0.001 PHE A 739 TRP 0.015 0.001 TRP A1170 HIS 0.006 0.001 HIS A1051 Details of bonding type rmsd covalent geometry : bond 0.00365 (12431) covalent geometry : angle 0.53844 (16792) hydrogen bonds : bond 0.04891 ( 449) hydrogen bonds : angle 3.98040 ( 1302) ********************** 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 142 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 120 time to evaluate : 0.490 Fit side-chains REVERT: A 597 ASP cc_start: 0.7907 (t0) cc_final: 0.7387 (t0) REVERT: A 1054 LEU cc_start: 0.7559 (OUTLIER) cc_final: 0.7037 (mp) REVERT: A 1149 GLN cc_start: 0.8489 (tp40) cc_final: 0.7782 (mt0) REVERT: B 597 ASP cc_start: 0.7933 (t0) cc_final: 0.7409 (t0) REVERT: B 1054 LEU cc_start: 0.7560 (OUTLIER) cc_final: 0.7035 (mp) REVERT: B 1149 GLN cc_start: 0.8490 (tp40) cc_final: 0.7804 (mt0) outliers start: 22 outliers final: 18 residues processed: 136 average time/residue: 0.0989 time to fit residues: 19.4593 Evaluate side-chains 138 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 118 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 610 THR 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 1054 LEU 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 714 MET Chi-restraints excluded: chain B residue 801 ILE Chi-restraints excluded: chain B residue 825 VAL Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1054 LEU 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 120 optimal weight: 4.9990 chunk 10 optimal weight: 7.9990 chunk 70 optimal weight: 5.9990 chunk 12 optimal weight: 8.9990 chunk 140 optimal weight: 3.9990 chunk 48 optimal weight: 9.9990 chunk 103 optimal weight: 2.9990 chunk 46 optimal weight: 0.6980 chunk 134 optimal weight: 1.9990 chunk 147 optimal weight: 5.9990 chunk 1 optimal weight: 9.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- 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 = 0.3541 r_free = 0.3541 target = 0.139131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.107565 restraints weight = 15532.255| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 1.75 r_work: 0.3122 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.2590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 12431 Z= 0.192 Angle : 0.585 9.180 16792 Z= 0.293 Chirality : 0.045 0.153 1819 Planarity : 0.004 0.038 2136 Dihedral : 4.473 37.087 1659 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 1.84 % Allowed : 14.15 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -0.74 (0.22), residues: 1482 helix: 0.38 (0.21), residues: 644 sheet: -1.02 (0.37), residues: 218 loop : -1.13 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 526 TYR 0.013 0.002 TYR A 824 PHE 0.015 0.002 PHE B 739 TRP 0.016 0.002 TRP A1170 HIS 0.006 0.001 HIS A1051 Details of bonding type rmsd covalent geometry : bond 0.00480 (12431) covalent geometry : angle 0.58473 (16792) hydrogen bonds : bond 0.05467 ( 449) hydrogen bonds : angle 4.10700 ( 1302) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2637.55 seconds wall clock time: 45 minutes 53.16 seconds (2753.16 seconds total)