Starting phenix.real_space_refine on Sat Aug 23 12:42:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8kgp_37229/08_2025/8kgp_37229.cif Found real_map, /net/cci-nas-00/data/ceres_data/8kgp_37229/08_2025/8kgp_37229.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8kgp_37229/08_2025/8kgp_37229.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8kgp_37229/08_2025/8kgp_37229.map" model { file = "/net/cci-nas-00/data/ceres_data/8kgp_37229/08_2025/8kgp_37229.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8kgp_37229/08_2025/8kgp_37229.cif" } resolution = 3.3 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= 0.002 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 7822 2.51 5 N 2092 2.21 5 O 2204 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 50 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: 12168 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 6084 Number of conformers: 1 Conformer: "" Number of residues, atoms: 749, 6084 Classifications: {'peptide': 749} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 718} Chain breaks: 2 Chain: "A" Number of atoms: 6084 Number of conformers: 1 Conformer: "" Number of residues, atoms: 749, 6084 Classifications: {'peptide': 749} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 718} Chain breaks: 2 Time building chain proxies: 3.20, per 1000 atoms: 0.26 Number of scatterers: 12168 At special positions: 0 Unit cell: (113.75, 117.65, 113.75, 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 2204 8.00 N 2092 7.00 C 7822 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: 0.95 Conformation dependent library (CDL) restraints added in 602.9 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2812 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 14 sheets defined 46.4% alpha, 9.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'B' and resid 441 through 451 removed outlier: 3.780A pdb=" N THR B 451 " --> pdb=" O ARG B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 513 removed outlier: 3.768A pdb=" N GLN B 510 " --> pdb=" O GLN B 506 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL B 511 " --> pdb=" O GLY B 507 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 560 removed outlier: 4.506A pdb=" N LEU B 549 " --> pdb=" O CYS B 545 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLY B 550 " --> pdb=" O GLY B 546 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 565 removed outlier: 4.184A pdb=" N ILE B 564 " --> pdb=" O TRP B 560 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ILE B 565 " --> pdb=" O PRO B 561 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 560 through 565' Processing helix chain 'B' and resid 593 through 601 removed outlier: 3.749A pdb=" N TRP B 599 " --> pdb=" O GLU B 595 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 620 removed outlier: 3.901A pdb=" N HIS B 620 " --> pdb=" O LEU B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 621 through 629 removed outlier: 3.695A pdb=" N PHE B 629 " --> pdb=" O VAL B 625 " (cutoff:3.500A) Processing helix chain 'B' and resid 632 through 634 No H-bonds generated for 'chain 'B' and resid 632 through 634' Processing helix chain 'B' and resid 644 through 653 removed outlier: 3.576A pdb=" N PHE B 653 " --> pdb=" O PHE B 649 " (cutoff:3.500A) Processing helix chain 'B' and resid 656 through 664 Processing helix chain 'B' and resid 672 through 683 removed outlier: 3.970A pdb=" N VAL B 682 " --> pdb=" O SER B 678 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 695 Processing helix chain 'B' and resid 695 through 703 removed outlier: 3.747A pdb=" N ILE B 703 " --> pdb=" O LYS B 699 " (cutoff:3.500A) Processing helix chain 'B' and resid 715 through 729 Processing helix chain 'B' and resid 738 through 749 Processing helix chain 'B' and resid 755 through 766 removed outlier: 3.780A pdb=" N ALA B 766 " --> pdb=" O ILE B 762 " (cutoff:3.500A) Processing helix chain 'B' and resid 787 through 791 removed outlier: 3.857A pdb=" N LEU B 790 " --> pdb=" O SER B 787 " (cutoff:3.500A) removed outlier: 3.846A 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 removed outlier: 3.812A pdb=" N PHE B 814 " --> pdb=" O ILE B 810 " (cutoff:3.500A) Processing helix chain 'B' and resid 815 through 819 removed outlier: 3.601A pdb=" N SER B 819 " --> pdb=" O ALA B 816 " (cutoff:3.500A) Processing helix chain 'B' and resid 864 through 877 removed outlier: 3.812A pdb=" N ALA B 870 " --> pdb=" O GLU B 866 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LEU B 871 " --> pdb=" O ASP B 867 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASP B 877 " --> pdb=" O ARG B 873 " (cutoff:3.500A) Processing helix chain 'B' and resid 882 through 888 removed outlier: 3.652A pdb=" N LEU B 885 " --> pdb=" O LYS B 882 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LEU B 886 " --> pdb=" O HIS B 883 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 953 removed outlier: 3.821A pdb=" N SER B 953 " --> pdb=" O SER B 949 " (cutoff:3.500A) Processing helix chain 'B' and resid 953 through 958 Processing helix chain 'B' and resid 982 through 990 removed outlier: 3.845A pdb=" N VAL B 987 " --> pdb=" O LEU B 983 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N GLU B 988 " --> pdb=" O ASN B 984 " (cutoff:3.500A) Processing helix chain 'B' and resid 998 through 1003 removed outlier: 3.513A pdb=" N PHE B1002 " --> pdb=" O SER B 998 " (cutoff:3.500A) Processing helix chain 'B' and resid 1028 through 1070 removed outlier: 3.662A pdb=" N LEU B1032 " --> pdb=" O TYR B1028 " (cutoff:3.500A) Proline residue: B1037 - end of helix removed outlier: 3.694A pdb=" N ARG B1040 " --> pdb=" O LEU B1036 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU B1041 " --> pdb=" O PRO B1037 " (cutoff:3.500A) Processing helix chain 'B' and resid 1081 through 1092 removed outlier: 3.577A pdb=" N GLU B1091 " --> pdb=" O ARG B1087 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N HIS B1092 " --> pdb=" O ILE B1088 " (cutoff:3.500A) Processing helix chain 'B' and resid 1098 through 1104 Processing helix chain 'B' and resid 1109 through 1117 Processing helix chain 'B' and resid 1134 through 1159 removed outlier: 3.742A pdb=" N LYS B1138 " --> pdb=" O LEU B1134 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N THR B1139 " --> pdb=" O ILE B1135 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N ARG B1140 " --> pdb=" O ALA B1136 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG B1141 " --> pdb=" O ALA B1137 " (cutoff:3.500A) Processing helix chain 'B' and resid 1166 through 1186 removed outlier: 4.152A pdb=" N GLU B1172 " --> pdb=" O SER B1168 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASN B1186 " --> pdb=" O ILE B1182 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 451 removed outlier: 3.705A pdb=" N SER A 444 " --> pdb=" O ASP A 440 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N THR A 451 " --> pdb=" O ARG A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 513 removed outlier: 3.772A pdb=" N GLN A 510 " --> pdb=" O GLN A 506 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL A 511 " --> pdb=" O GLY A 507 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 560 removed outlier: 4.508A pdb=" N LEU A 549 " --> pdb=" O CYS A 545 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLY A 550 " --> pdb=" O GLY A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 565 removed outlier: 4.183A pdb=" N ILE A 564 " --> pdb=" O TRP A 560 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ILE A 565 " --> pdb=" O PRO A 561 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 560 through 565' Processing helix chain 'A' and resid 593 through 601 removed outlier: 3.751A pdb=" N TRP A 599 " --> pdb=" O GLU A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 620 removed outlier: 3.905A pdb=" N HIS A 620 " --> pdb=" O LEU A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 629 removed outlier: 3.711A pdb=" N PHE A 629 " --> pdb=" O VAL A 625 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 634 No H-bonds generated for 'chain 'A' and resid 632 through 634' Processing helix chain 'A' and resid 644 through 653 removed outlier: 3.575A pdb=" N PHE A 653 " --> pdb=" O PHE A 649 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 664 Processing helix chain 'A' and resid 672 through 683 removed outlier: 3.970A pdb=" N VAL A 682 " --> pdb=" O SER A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 695 Processing helix chain 'A' and resid 695 through 703 removed outlier: 3.747A pdb=" N ILE A 703 " --> pdb=" O LYS A 699 " (cutoff:3.500A) Processing helix chain 'A' and resid 715 through 729 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: 3.909A pdb=" N LEU A 790 " --> pdb=" O SER A 787 " (cutoff:3.500A) removed outlier: 3.837A 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 removed outlier: 3.812A pdb=" N PHE A 814 " --> pdb=" O ILE A 810 " (cutoff:3.500A) Processing helix chain 'A' and resid 815 through 819 removed outlier: 3.600A pdb=" N SER A 819 " --> pdb=" O ALA A 816 " (cutoff:3.500A) Processing helix chain 'A' and resid 864 through 877 removed outlier: 3.814A pdb=" N ALA A 870 " --> pdb=" O GLU A 866 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LEU A 871 " --> pdb=" O ASP A 867 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASP A 877 " --> pdb=" O ARG A 873 " (cutoff:3.500A) Processing helix chain 'A' and resid 882 through 888 removed outlier: 3.652A pdb=" N LEU A 885 " --> pdb=" O LYS A 882 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LEU A 886 " --> pdb=" O HIS A 883 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 953 removed outlier: 3.823A pdb=" N SER A 953 " --> pdb=" O SER A 949 " (cutoff:3.500A) Processing helix chain 'A' and resid 953 through 958 removed outlier: 3.502A pdb=" N THR A 958 " --> pdb=" O SER A 954 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 990 removed outlier: 3.850A pdb=" N VAL A 987 " --> pdb=" O LEU A 983 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N GLU A 988 " --> pdb=" O ASN A 984 " (cutoff:3.500A) Processing helix chain 'A' and resid 998 through 1003 Processing helix chain 'A' and resid 1028 through 1070 removed outlier: 3.660A pdb=" N LEU A1032 " --> pdb=" O TYR A1028 " (cutoff:3.500A) Proline residue: A1037 - end of helix removed outlier: 3.698A pdb=" N ARG A1040 " --> pdb=" O LEU A1036 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLU A1041 " --> pdb=" O PRO A1037 " (cutoff:3.500A) Processing helix chain 'A' and resid 1075 through 1079 removed outlier: 3.837A pdb=" N HIS A1078 " --> pdb=" O ASN A1075 " (cutoff:3.500A) Processing helix chain 'A' and resid 1081 through 1092 removed outlier: 3.565A pdb=" N GLU A1091 " --> pdb=" O ARG A1087 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N HIS A1092 " --> pdb=" O ILE A1088 " (cutoff:3.500A) Processing helix chain 'A' and resid 1098 through 1104 Processing helix chain 'A' and resid 1109 through 1117 Processing helix chain 'A' and resid 1134 through 1159 removed outlier: 3.745A pdb=" N LYS A1138 " --> pdb=" O LEU A1134 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N THR A1139 " --> pdb=" O ILE A1135 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N ARG A1140 " --> pdb=" O ALA A1136 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ARG A1141 " --> pdb=" O ALA A1137 " (cutoff:3.500A) Processing helix chain 'A' and resid 1166 through 1186 removed outlier: 4.153A pdb=" N GLU A1172 " --> pdb=" O SER A1168 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASN A1186 " --> pdb=" O ILE A1182 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 465 through 469 removed outlier: 5.764A pdb=" N VAL B 569 " --> pdb=" O PHE B 639 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N ILE B 685 " --> pdb=" O VAL B 636 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N THR B 638 " --> pdb=" O ILE B 685 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 588 through 590 Processing sheet with id=AA3, first strand: chain 'B' and resid 736 through 737 Processing sheet with id=AA4, first strand: chain 'B' and resid 824 through 827 removed outlier: 5.059A pdb=" N GLU B 833 " --> pdb=" O VAL B 825 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N GLU B 827 " --> pdb=" O ARG B 831 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N ARG B 831 " --> pdb=" O GLU B 827 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 909 through 913 removed outlier: 3.680A pdb=" N HIS B 909 " --> pdb=" O TYR B 920 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N TYR B 916 " --> pdb=" O PHE B 913 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 922 through 925 removed outlier: 6.155A pdb=" N THR B 922 " --> pdb=" O THR B 935 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 1013 through 1015 removed outlier: 4.513A pdb=" N LEU B1013 " --> pdb=" O PHE B1025 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 465 through 469 removed outlier: 5.765A pdb=" N VAL A 569 " --> pdb=" O PHE A 639 " (cutoff:3.500A) removed outlier: 8.269A pdb=" N ILE A 685 " --> pdb=" O VAL A 636 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N THR A 638 " --> pdb=" O ILE A 685 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 588 through 590 Processing sheet with id=AB1, first strand: chain 'A' and resid 736 through 737 Processing sheet with id=AB2, first strand: chain 'A' and resid 824 through 827 removed outlier: 5.048A pdb=" N GLU A 833 " --> pdb=" O VAL A 825 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N GLU A 827 " --> pdb=" O ARG A 831 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N ARG A 831 " --> pdb=" O GLU A 827 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 909 through 913 removed outlier: 3.680A pdb=" N HIS A 909 " --> pdb=" O TYR A 920 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N TYR A 916 " --> pdb=" O PHE A 913 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 922 through 925 removed outlier: 6.156A pdb=" N THR A 922 " --> pdb=" O THR A 935 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1013 through 1015 removed outlier: 4.513A pdb=" N LEU A1013 " --> pdb=" O PHE A1025 " (cutoff:3.500A) 465 hydrogen bonds defined for protein. 1338 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.21 Time building geometry restraints manager: 1.34 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: 3304 1.33 - 1.45: 2369 1.45 - 1.57: 6707 1.57 - 1.69: 0 1.69 - 1.81: 78 Bond restraints: 12458 Sorted by residual: bond pdb=" N LEU B1036 " pdb=" CA LEU B1036 " ideal model delta sigma weight residual 1.459 1.491 -0.032 1.04e-02 9.25e+03 9.23e+00 bond pdb=" N ILE B 763 " pdb=" CA ILE B 763 " ideal model delta sigma weight residual 1.460 1.495 -0.036 1.21e-02 6.83e+03 8.79e+00 bond pdb=" N LEU A1036 " pdb=" CA LEU A1036 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.04e-02 9.25e+03 8.68e+00 bond pdb=" N ILE A1031 " pdb=" CA ILE A1031 " ideal model delta sigma weight residual 1.461 1.493 -0.033 1.19e-02 7.06e+03 7.50e+00 bond pdb=" N TYR A 848 " pdb=" CA TYR A 848 " ideal model delta sigma weight residual 1.456 1.490 -0.033 1.23e-02 6.61e+03 7.23e+00 ... (remaining 12453 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.32: 16081 2.32 - 4.64: 660 4.64 - 6.96: 64 6.96 - 9.28: 18 9.28 - 11.60: 3 Bond angle restraints: 16826 Sorted by residual: angle pdb=" C ARG A 929 " pdb=" N ASN A 930 " pdb=" CA ASN A 930 " ideal model delta sigma weight residual 122.82 129.74 -6.92 1.42e+00 4.96e-01 2.37e+01 angle pdb=" C ARG B 929 " pdb=" N ASN B 930 " pdb=" CA ASN B 930 " ideal model delta sigma weight residual 122.82 129.73 -6.91 1.42e+00 4.96e-01 2.37e+01 angle pdb=" C SER A 902 " pdb=" N ASN A 903 " pdb=" CA ASN A 903 " ideal model delta sigma weight residual 121.54 129.65 -8.11 1.91e+00 2.74e-01 1.80e+01 angle pdb=" C SER B 902 " pdb=" N ASN B 903 " pdb=" CA ASN B 903 " ideal model delta sigma weight residual 121.54 129.65 -8.11 1.91e+00 2.74e-01 1.80e+01 angle pdb=" C ILE A 565 " pdb=" N HIS A 566 " pdb=" CA HIS A 566 " ideal model delta sigma weight residual 121.54 129.36 -7.82 1.91e+00 2.74e-01 1.68e+01 ... (remaining 16821 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.26: 6868 14.26 - 28.51: 447 28.51 - 42.77: 129 42.77 - 57.02: 20 57.02 - 71.28: 10 Dihedral angle restraints: 7474 sinusoidal: 3086 harmonic: 4388 Sorted by residual: dihedral pdb=" CA PRO A 901 " pdb=" C PRO A 901 " pdb=" N SER A 902 " pdb=" CA SER A 902 " ideal model delta harmonic sigma weight residual -180.00 -154.80 -25.20 0 5.00e+00 4.00e-02 2.54e+01 dihedral pdb=" CA PRO B 901 " pdb=" C PRO B 901 " pdb=" N SER B 902 " pdb=" CA SER B 902 " ideal model delta harmonic sigma weight residual -180.00 -154.82 -25.18 0 5.00e+00 4.00e-02 2.54e+01 dihedral pdb=" CA THR A 695 " pdb=" C THR A 695 " pdb=" N LYS A 696 " pdb=" CA LYS A 696 " ideal model delta harmonic sigma weight residual 180.00 159.45 20.55 0 5.00e+00 4.00e-02 1.69e+01 ... (remaining 7471 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 1420 0.074 - 0.149: 359 0.149 - 0.223: 23 0.223 - 0.298: 14 0.298 - 0.372: 2 Chirality restraints: 1818 Sorted by residual: chirality pdb=" CB ILE A 963 " pdb=" CA ILE A 963 " pdb=" CG1 ILE A 963 " pdb=" CG2 ILE A 963 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.37 2.00e-01 2.50e+01 3.46e+00 chirality pdb=" CB ILE B 685 " pdb=" CA ILE B 685 " pdb=" CG1 ILE B 685 " pdb=" CG2 ILE B 685 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.30 2.00e-01 2.50e+01 2.27e+00 chirality pdb=" CB ILE A 685 " pdb=" CA ILE A 685 " pdb=" CG1 ILE A 685 " pdb=" CG2 ILE A 685 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.30 2.00e-01 2.50e+01 2.19e+00 ... (remaining 1815 not shown) Planarity restraints: 2144 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B1170 " -0.023 2.00e-02 2.50e+03 2.50e-02 1.56e+01 pdb=" CG TRP B1170 " 0.065 2.00e-02 2.50e+03 pdb=" CD1 TRP B1170 " -0.036 2.00e-02 2.50e+03 pdb=" CD2 TRP B1170 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP B1170 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B1170 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B1170 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP B1170 " 0.006 2.00e-02 2.50e+03 pdb=" CZ3 TRP B1170 " -0.012 2.00e-02 2.50e+03 pdb=" CH2 TRP B1170 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A1170 " 0.023 2.00e-02 2.50e+03 2.50e-02 1.56e+01 pdb=" CG TRP A1170 " -0.065 2.00e-02 2.50e+03 pdb=" CD1 TRP A1170 " 0.036 2.00e-02 2.50e+03 pdb=" CD2 TRP A1170 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A1170 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A1170 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A1170 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A1170 " -0.006 2.00e-02 2.50e+03 pdb=" CZ3 TRP A1170 " 0.011 2.00e-02 2.50e+03 pdb=" CH2 TRP A1170 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 824 " -0.027 2.00e-02 2.50e+03 2.38e-02 1.13e+01 pdb=" CG TYR A 824 " 0.057 2.00e-02 2.50e+03 pdb=" CD1 TYR A 824 " -0.019 2.00e-02 2.50e+03 pdb=" CD2 TYR A 824 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR A 824 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR A 824 " -0.007 2.00e-02 2.50e+03 pdb=" CZ TYR A 824 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR A 824 " -0.004 2.00e-02 2.50e+03 ... (remaining 2141 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 3771 2.83 - 3.35: 10055 3.35 - 3.87: 18690 3.87 - 4.38: 21819 4.38 - 4.90: 38780 Nonbonded interactions: 93115 Sorted by model distance: nonbonded pdb=" OH TYR A 946 " pdb=" O LEU A1003 " model vdw 2.314 3.040 nonbonded pdb=" OH TYR B 946 " pdb=" O LEU B1003 " model vdw 2.318 3.040 nonbonded pdb=" O VAL B 840 " pdb=" CH2 TRP B1035 " model vdw 2.330 3.340 nonbonded pdb=" OG1 THR A 922 " pdb=" OG1 THR A 935 " model vdw 2.340 3.040 nonbonded pdb=" OG1 THR B 922 " pdb=" OG1 THR B 935 " model vdw 2.341 3.040 ... (remaining 93110 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' 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: 3.220 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: 0.300 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.980 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 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 0.075 12458 Z= 0.457 Angle : 1.053 11.602 16826 Z= 0.590 Chirality : 0.066 0.372 1818 Planarity : 0.007 0.065 2144 Dihedral : 11.202 71.281 4662 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 0.76 % Allowed : 4.96 % Favored : 94.27 % 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: -3.96 (0.18), residues: 1486 helix: -2.64 (0.16), residues: 598 sheet: -1.81 (0.35), residues: 218 loop : -2.81 (0.20), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.002 ARG A 578 TYR 0.057 0.004 TYR A 824 PHE 0.046 0.004 PHE B 785 TRP 0.065 0.004 TRP A1170 HIS 0.015 0.002 HIS B1192 Details of bonding type rmsd covalent geometry : bond 0.01083 (12458) covalent geometry : angle 1.05316 (16826) hydrogen bonds : bond 0.18670 ( 465) hydrogen bonds : angle 6.85743 ( 1338) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 276 time to evaluate : 0.504 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 747 ASP cc_start: 0.8578 (t70) cc_final: 0.8336 (t0) REVERT: B 977 LYS cc_start: 0.8188 (ttmt) cc_final: 0.7577 (tttm) REVERT: A 573 LEU cc_start: 0.8108 (OUTLIER) cc_final: 0.7715 (mp) REVERT: A 747 ASP cc_start: 0.8591 (t70) cc_final: 0.8371 (t0) REVERT: A 964 ILE cc_start: 0.8994 (mt) cc_final: 0.8729 (mm) REVERT: A 977 LYS cc_start: 0.8112 (ttmt) cc_final: 0.7330 (tttm) outliers start: 10 outliers final: 1 residues processed: 282 average time/residue: 0.1394 time to fit residues: 53.2273 Evaluate side-chains 147 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 145 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 574 THR Chi-restraints excluded: chain A residue 573 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 620 HIS B 634 ASN B1119 GLN B1157 GLN A 620 HIS A 634 ASN A1051 HIS A1119 GLN A1157 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.134896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.100384 restraints weight = 16191.169| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 2.11 r_work: 0.2895 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2759 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12458 Z= 0.123 Angle : 0.583 9.621 16826 Z= 0.302 Chirality : 0.043 0.182 1818 Planarity : 0.005 0.041 2144 Dihedral : 4.978 36.726 1665 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 1.37 % Allowed : 10.76 % Favored : 87.86 % 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: -2.39 (0.20), residues: 1486 helix: -0.92 (0.19), residues: 614 sheet: -1.28 (0.36), residues: 202 loop : -2.29 (0.21), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 530 TYR 0.015 0.001 TYR B 888 PHE 0.013 0.001 PHE B 559 TRP 0.027 0.001 TRP A1170 HIS 0.005 0.001 HIS A 650 Details of bonding type rmsd covalent geometry : bond 0.00283 (12458) covalent geometry : angle 0.58290 (16826) hydrogen bonds : bond 0.04723 ( 465) hydrogen bonds : angle 4.59382 ( 1338) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 184 time to evaluate : 0.466 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 551 LEU cc_start: 0.9004 (mp) cc_final: 0.8651 (tt) REVERT: B 747 ASP cc_start: 0.9025 (t70) cc_final: 0.8734 (t0) REVERT: B 977 LYS cc_start: 0.8189 (ttmt) cc_final: 0.7541 (tttm) REVERT: B 995 GLU cc_start: 0.8145 (mt-10) cc_final: 0.7894 (mp0) REVERT: B 1134 LEU cc_start: 0.6420 (OUTLIER) cc_final: 0.6076 (pp) REVERT: A 417 LYS cc_start: 0.8894 (mtmt) cc_final: 0.8649 (mtpp) REVERT: A 551 LEU cc_start: 0.8988 (mp) cc_final: 0.8631 (tt) REVERT: A 747 ASP cc_start: 0.9019 (t70) cc_final: 0.8780 (t0) REVERT: A 957 MET cc_start: 0.9078 (mmm) cc_final: 0.8741 (tpt) REVERT: A 964 ILE cc_start: 0.9003 (mt) cc_final: 0.8693 (mm) REVERT: A 977 LYS cc_start: 0.7928 (ttmt) cc_final: 0.7444 (tttp) REVERT: A 995 GLU cc_start: 0.8140 (mt-10) cc_final: 0.7883 (mp0) REVERT: A 1064 ILE cc_start: 0.8167 (mt) cc_final: 0.7924 (mt) REVERT: A 1134 LEU cc_start: 0.6384 (OUTLIER) cc_final: 0.6036 (pp) outliers start: 18 outliers final: 8 residues processed: 200 average time/residue: 0.1093 time to fit residues: 31.3049 Evaluate side-chains 158 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 148 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 540 GLN Chi-restraints excluded: chain B residue 644 SER Chi-restraints excluded: chain B residue 833 GLU Chi-restraints excluded: chain B residue 1111 GLU Chi-restraints excluded: chain B residue 1134 LEU Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 644 SER Chi-restraints excluded: chain A residue 998 SER Chi-restraints excluded: chain A residue 1111 GLU Chi-restraints excluded: chain A residue 1134 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 1 optimal weight: 10.0000 chunk 129 optimal weight: 2.9990 chunk 7 optimal weight: 8.9990 chunk 19 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 chunk 92 optimal weight: 0.6980 chunk 117 optimal weight: 3.9990 chunk 126 optimal weight: 6.9990 chunk 141 optimal weight: 9.9990 chunk 24 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- 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 = 0.3496 r_free = 0.3496 target = 0.132215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.097458 restraints weight = 16403.886| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 2.09 r_work: 0.2809 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2673 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 12458 Z= 0.161 Angle : 0.578 10.637 16826 Z= 0.292 Chirality : 0.044 0.142 1818 Planarity : 0.004 0.035 2144 Dihedral : 4.547 17.074 1662 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.29 % Allowed : 13.05 % Favored : 84.66 % 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: -1.52 (0.21), residues: 1486 helix: 0.01 (0.21), residues: 618 sheet: -1.03 (0.36), residues: 202 loop : -1.97 (0.22), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 684 TYR 0.020 0.002 TYR A 824 PHE 0.014 0.001 PHE B 785 TRP 0.020 0.001 TRP A1170 HIS 0.005 0.001 HIS B1192 Details of bonding type rmsd covalent geometry : bond 0.00402 (12458) covalent geometry : angle 0.57792 (16826) hydrogen bonds : bond 0.04534 ( 465) hydrogen bonds : angle 4.32196 ( 1338) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 158 time to evaluate : 0.330 Fit side-chains REVERT: B 417 LYS cc_start: 0.8909 (mtmt) cc_final: 0.8618 (mtpp) REVERT: B 515 ASP cc_start: 0.8235 (t70) cc_final: 0.7509 (p0) REVERT: B 582 LYS cc_start: 0.8204 (mttm) cc_final: 0.7851 (mtmm) REVERT: B 747 ASP cc_start: 0.9049 (t70) cc_final: 0.8817 (t0) REVERT: B 817 GLU cc_start: 0.8999 (OUTLIER) cc_final: 0.8559 (pm20) REVERT: B 833 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.7675 (pp20) REVERT: B 977 LYS cc_start: 0.8153 (ttmt) cc_final: 0.7493 (tttm) REVERT: B 995 GLU cc_start: 0.8109 (OUTLIER) cc_final: 0.7860 (mp0) REVERT: B 1064 ILE cc_start: 0.8066 (mt) cc_final: 0.7806 (mt) REVERT: B 1134 LEU cc_start: 0.6373 (OUTLIER) cc_final: 0.6047 (pp) REVERT: A 417 LYS cc_start: 0.8920 (mtmt) cc_final: 0.8640 (mtpp) REVERT: A 515 ASP cc_start: 0.8245 (t70) cc_final: 0.7507 (p0) REVERT: A 582 LYS cc_start: 0.8203 (mttm) cc_final: 0.7872 (mtmm) REVERT: A 747 ASP cc_start: 0.9057 (t70) cc_final: 0.8827 (t0) REVERT: A 817 GLU cc_start: 0.8963 (pt0) cc_final: 0.8526 (pm20) REVERT: A 977 LYS cc_start: 0.8057 (ttmt) cc_final: 0.7398 (tttm) REVERT: A 995 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.7856 (mp0) REVERT: A 1064 ILE cc_start: 0.8076 (mt) cc_final: 0.7822 (mt) REVERT: A 1134 LEU cc_start: 0.6373 (OUTLIER) cc_final: 0.6034 (pp) outliers start: 30 outliers final: 16 residues processed: 175 average time/residue: 0.0918 time to fit residues: 24.2530 Evaluate side-chains 169 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 147 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 608 ASN Chi-restraints excluded: chain B residue 644 SER Chi-restraints excluded: chain B residue 731 SER Chi-restraints excluded: chain B residue 817 GLU Chi-restraints excluded: chain B residue 833 GLU Chi-restraints excluded: chain B residue 890 ILE Chi-restraints excluded: chain B residue 949 SER Chi-restraints excluded: chain B residue 995 GLU Chi-restraints excluded: chain B residue 1058 ILE Chi-restraints excluded: chain B residue 1065 VAL Chi-restraints excluded: chain B residue 1111 GLU Chi-restraints excluded: chain B residue 1134 LEU Chi-restraints excluded: chain A residue 608 ASN Chi-restraints excluded: chain A residue 644 SER Chi-restraints excluded: chain A residue 731 SER Chi-restraints excluded: chain A residue 890 ILE Chi-restraints excluded: chain A residue 949 SER Chi-restraints excluded: chain A residue 961 GLU Chi-restraints excluded: chain A residue 995 GLU Chi-restraints excluded: chain A residue 1065 VAL Chi-restraints excluded: chain A residue 1111 GLU Chi-restraints excluded: chain A residue 1134 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 57 optimal weight: 2.9990 chunk 75 optimal weight: 9.9990 chunk 131 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 5 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 chunk 30 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 80 optimal weight: 4.9990 chunk 90 optimal weight: 7.9990 chunk 28 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 634 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.128437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.092604 restraints weight = 16492.660| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 2.18 r_work: 0.2757 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2619 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8816 moved from start: 0.2620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 12458 Z= 0.276 Angle : 0.673 16.082 16826 Z= 0.335 Chirality : 0.048 0.155 1818 Planarity : 0.005 0.046 2144 Dihedral : 4.769 19.018 1662 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 3.36 % Allowed : 13.51 % Favored : 83.13 % 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: -1.40 (0.21), residues: 1486 helix: 0.21 (0.22), residues: 622 sheet: -1.31 (0.34), residues: 206 loop : -1.90 (0.22), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 571 TYR 0.024 0.002 TYR A 824 PHE 0.016 0.002 PHE B 785 TRP 0.019 0.002 TRP A1170 HIS 0.008 0.002 HIS B1192 Details of bonding type rmsd covalent geometry : bond 0.00693 (12458) covalent geometry : angle 0.67270 (16826) hydrogen bonds : bond 0.05377 ( 465) hydrogen bonds : angle 4.52566 ( 1338) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 150 time to evaluate : 0.325 Fit side-chains revert: symmetry clash REVERT: B 417 LYS cc_start: 0.8952 (mtmt) cc_final: 0.8575 (mtpp) REVERT: B 515 ASP cc_start: 0.8326 (t70) cc_final: 0.7497 (p0) REVERT: B 582 LYS cc_start: 0.8210 (mttm) cc_final: 0.7850 (mtmm) REVERT: B 747 ASP cc_start: 0.9093 (t70) cc_final: 0.8856 (t0) REVERT: B 833 GLU cc_start: 0.8622 (OUTLIER) cc_final: 0.7889 (pp20) REVERT: B 964 ILE cc_start: 0.8966 (mt) cc_final: 0.8754 (mm) REVERT: B 977 LYS cc_start: 0.8241 (ttmt) cc_final: 0.7627 (tttm) REVERT: B 995 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.7775 (mp0) REVERT: B 1134 LEU cc_start: 0.6310 (OUTLIER) cc_final: 0.6014 (pp) REVERT: A 417 LYS cc_start: 0.8949 (mtmt) cc_final: 0.8621 (mtpp) REVERT: A 582 LYS cc_start: 0.8195 (mttm) cc_final: 0.7868 (mtmm) REVERT: A 691 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8490 (mp) REVERT: A 756 MET cc_start: 0.8379 (mtp) cc_final: 0.7993 (mmp) REVERT: A 817 GLU cc_start: 0.9023 (OUTLIER) cc_final: 0.8679 (pm20) REVERT: A 977 LYS cc_start: 0.8160 (ttmt) cc_final: 0.7510 (tttm) REVERT: A 995 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7800 (mp0) REVERT: A 1134 LEU cc_start: 0.6374 (OUTLIER) cc_final: 0.6064 (pp) outliers start: 44 outliers final: 28 residues processed: 183 average time/residue: 0.0927 time to fit residues: 25.0218 Evaluate side-chains 181 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 146 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 508 ILE Chi-restraints excluded: chain B residue 540 GLN Chi-restraints excluded: chain B residue 608 ASN Chi-restraints excluded: chain B residue 644 SER Chi-restraints excluded: chain B residue 731 SER Chi-restraints excluded: chain B residue 790 LEU Chi-restraints excluded: chain B residue 833 GLU Chi-restraints excluded: chain B residue 890 ILE Chi-restraints excluded: chain B residue 949 SER Chi-restraints excluded: chain B residue 995 GLU Chi-restraints excluded: chain B residue 1058 ILE Chi-restraints excluded: chain B residue 1065 VAL Chi-restraints excluded: chain B residue 1111 GLU Chi-restraints excluded: chain B residue 1123 THR Chi-restraints excluded: chain B residue 1134 LEU Chi-restraints excluded: chain B residue 1142 VAL Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 540 GLN Chi-restraints excluded: chain A residue 608 ASN Chi-restraints excluded: chain A residue 624 GLU Chi-restraints excluded: chain A residue 644 SER Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 731 SER Chi-restraints excluded: chain A residue 790 LEU Chi-restraints excluded: chain A residue 817 GLU Chi-restraints excluded: chain A residue 890 ILE Chi-restraints excluded: chain A residue 949 SER Chi-restraints excluded: chain A residue 961 GLU Chi-restraints excluded: chain A residue 995 GLU Chi-restraints excluded: chain A residue 1058 ILE Chi-restraints excluded: chain A residue 1065 VAL Chi-restraints excluded: chain A residue 1111 GLU Chi-restraints excluded: chain A residue 1123 THR Chi-restraints excluded: chain A residue 1134 LEU Chi-restraints excluded: chain A residue 1142 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 61 optimal weight: 0.9980 chunk 48 optimal weight: 4.9990 chunk 88 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 113 optimal weight: 0.9990 chunk 60 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 19 optimal weight: 0.4980 chunk 1 optimal weight: 9.9990 chunk 71 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1119 GLN A1119 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.133107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.098410 restraints weight = 16281.510| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 2.05 r_work: 0.2850 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2717 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.2935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 12458 Z= 0.104 Angle : 0.510 10.393 16826 Z= 0.255 Chirality : 0.041 0.133 1818 Planarity : 0.003 0.034 2144 Dihedral : 4.115 13.885 1662 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.21 % Allowed : 15.34 % Favored : 82.44 % 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: -0.77 (0.22), residues: 1486 helix: 0.77 (0.22), residues: 618 sheet: -0.62 (0.36), residues: 196 loop : -1.72 (0.22), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 530 TYR 0.010 0.001 TYR A 888 PHE 0.011 0.001 PHE A 710 TRP 0.008 0.001 TRP B 820 HIS 0.007 0.001 HIS A 650 Details of bonding type rmsd covalent geometry : bond 0.00245 (12458) covalent geometry : angle 0.50984 (16826) hydrogen bonds : bond 0.03543 ( 465) hydrogen bonds : angle 4.17790 ( 1338) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 168 time to evaluate : 0.496 Fit side-chains revert: symmetry clash REVERT: B 417 LYS cc_start: 0.8886 (mtmt) cc_final: 0.8532 (mtpp) REVERT: B 551 LEU cc_start: 0.9038 (mp) cc_final: 0.8703 (tt) REVERT: B 747 ASP cc_start: 0.9033 (t70) cc_final: 0.8784 (t0) REVERT: B 977 LYS cc_start: 0.8130 (ttmt) cc_final: 0.7493 (tttm) REVERT: B 995 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7780 (mp0) REVERT: B 1134 LEU cc_start: 0.6332 (OUTLIER) cc_final: 0.5995 (pp) REVERT: A 582 LYS cc_start: 0.8179 (mttm) cc_final: 0.7861 (mtmm) REVERT: A 817 GLU cc_start: 0.8970 (pt0) cc_final: 0.8582 (pm20) REVERT: A 890 ILE cc_start: 0.7994 (OUTLIER) cc_final: 0.7523 (tt) REVERT: A 977 LYS cc_start: 0.8038 (ttmt) cc_final: 0.7375 (tttp) REVERT: A 995 GLU cc_start: 0.8013 (mt-10) cc_final: 0.7768 (mp0) REVERT: A 1134 LEU cc_start: 0.6309 (OUTLIER) cc_final: 0.5956 (pp) outliers start: 29 outliers final: 16 residues processed: 190 average time/residue: 0.0961 time to fit residues: 27.6749 Evaluate side-chains 166 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 146 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 608 ASN Chi-restraints excluded: chain B residue 644 SER Chi-restraints excluded: chain B residue 687 CYS Chi-restraints excluded: chain B residue 731 SER Chi-restraints excluded: chain B residue 790 LEU Chi-restraints excluded: chain B residue 890 ILE Chi-restraints excluded: chain B residue 995 GLU Chi-restraints excluded: chain B residue 1111 GLU Chi-restraints excluded: chain B residue 1123 THR Chi-restraints excluded: chain B residue 1134 LEU Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 608 ASN Chi-restraints excluded: chain A residue 687 CYS Chi-restraints excluded: chain A residue 731 SER Chi-restraints excluded: chain A residue 890 ILE Chi-restraints excluded: chain A residue 961 GLU Chi-restraints excluded: chain A residue 1111 GLU Chi-restraints excluded: chain A residue 1123 THR Chi-restraints excluded: chain A residue 1134 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 144 optimal weight: 2.9990 chunk 132 optimal weight: 3.9990 chunk 137 optimal weight: 20.0000 chunk 91 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 116 optimal weight: 0.6980 chunk 82 optimal weight: 7.9990 chunk 37 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 127 optimal weight: 2.9990 chunk 78 optimal weight: 7.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 634 ASN B1119 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.129440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.093553 restraints weight = 16494.125| |-----------------------------------------------------------------------------| r_work (start): 0.2885 rms_B_bonded: 2.14 r_work: 0.2701 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2566 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8756 moved from start: 0.2967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 12458 Z= 0.210 Angle : 0.603 14.615 16826 Z= 0.300 Chirality : 0.045 0.144 1818 Planarity : 0.004 0.040 2144 Dihedral : 4.331 17.406 1662 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 2.60 % Allowed : 16.56 % Favored : 80.84 % 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: -0.78 (0.22), residues: 1486 helix: 0.87 (0.22), residues: 620 sheet: -0.73 (0.36), residues: 196 loop : -1.81 (0.22), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 578 TYR 0.015 0.002 TYR A 848 PHE 0.011 0.001 PHE A 739 TRP 0.010 0.002 TRP B1170 HIS 0.006 0.001 HIS A 650 Details of bonding type rmsd covalent geometry : bond 0.00528 (12458) covalent geometry : angle 0.60259 (16826) hydrogen bonds : bond 0.04606 ( 465) hydrogen bonds : angle 4.27182 ( 1338) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 146 time to evaluate : 0.540 Fit side-chains REVERT: B 582 LYS cc_start: 0.8162 (mttm) cc_final: 0.7785 (mtmm) REVERT: B 747 ASP cc_start: 0.9076 (t70) cc_final: 0.8826 (t0) REVERT: B 833 GLU cc_start: 0.8576 (OUTLIER) cc_final: 0.7910 (pp20) REVERT: B 977 LYS cc_start: 0.8128 (ttmt) cc_final: 0.7503 (tttm) REVERT: B 995 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7757 (mp0) REVERT: B 1134 LEU cc_start: 0.6304 (OUTLIER) cc_final: 0.5978 (pp) REVERT: A 582 LYS cc_start: 0.8134 (mttm) cc_final: 0.7829 (mtmm) REVERT: A 817 GLU cc_start: 0.9001 (pt0) cc_final: 0.8620 (pm20) REVERT: A 977 LYS cc_start: 0.8032 (ttmt) cc_final: 0.7346 (tttp) REVERT: A 995 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.7770 (mp0) REVERT: A 1134 LEU cc_start: 0.6333 (OUTLIER) cc_final: 0.6010 (pp) outliers start: 34 outliers final: 24 residues processed: 170 average time/residue: 0.1009 time to fit residues: 25.9955 Evaluate side-chains 168 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 139 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 608 ASN Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 644 SER Chi-restraints excluded: chain B residue 687 CYS Chi-restraints excluded: chain B residue 703 ILE Chi-restraints excluded: chain B residue 731 SER Chi-restraints excluded: chain B residue 790 LEU Chi-restraints excluded: chain B residue 833 GLU Chi-restraints excluded: chain B residue 890 ILE Chi-restraints excluded: chain B residue 995 GLU Chi-restraints excluded: chain B residue 1111 GLU Chi-restraints excluded: chain B residue 1119 GLN Chi-restraints excluded: chain B residue 1123 THR Chi-restraints excluded: chain B residue 1134 LEU Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 608 ASN Chi-restraints excluded: chain A residue 644 SER Chi-restraints excluded: chain A residue 687 CYS Chi-restraints excluded: chain A residue 703 ILE Chi-restraints excluded: chain A residue 731 SER Chi-restraints excluded: chain A residue 790 LEU Chi-restraints excluded: chain A residue 803 VAL Chi-restraints excluded: chain A residue 890 ILE Chi-restraints excluded: chain A residue 961 GLU Chi-restraints excluded: chain A residue 995 GLU Chi-restraints excluded: chain A residue 1111 GLU Chi-restraints excluded: chain A residue 1123 THR Chi-restraints excluded: chain A residue 1134 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 67 optimal weight: 10.0000 chunk 60 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 120 optimal weight: 0.9980 chunk 38 optimal weight: 0.6980 chunk 141 optimal weight: 8.9990 chunk 61 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 117 optimal weight: 1.9990 chunk 22 optimal weight: 4.9990 chunk 109 optimal weight: 2.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 634 ASN A1119 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.130372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.094502 restraints weight = 16326.969| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 2.16 r_work: 0.2779 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2645 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8761 moved from start: 0.3050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 12458 Z= 0.167 Angle : 0.569 13.479 16826 Z= 0.281 Chirality : 0.044 0.184 1818 Planarity : 0.004 0.036 2144 Dihedral : 4.210 16.215 1662 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 3.13 % Allowed : 16.26 % Favored : 80.61 % 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: 1486 helix: 1.03 (0.22), residues: 616 sheet: -0.85 (0.35), residues: 200 loop : -1.80 (0.22), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 578 TYR 0.012 0.001 TYR A 848 PHE 0.012 0.001 PHE A 559 TRP 0.010 0.001 TRP B 820 HIS 0.006 0.001 HIS A 650 Details of bonding type rmsd covalent geometry : bond 0.00417 (12458) covalent geometry : angle 0.56851 (16826) hydrogen bonds : bond 0.04255 ( 465) hydrogen bonds : angle 4.22804 ( 1338) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 142 time to evaluate : 0.444 Fit side-chains REVERT: B 551 LEU cc_start: 0.9020 (mp) cc_final: 0.8665 (tt) REVERT: B 582 LYS cc_start: 0.8140 (mttm) cc_final: 0.7798 (mtmm) REVERT: B 747 ASP cc_start: 0.9066 (t70) cc_final: 0.8817 (t0) REVERT: B 833 GLU cc_start: 0.8488 (OUTLIER) cc_final: 0.7821 (pp20) REVERT: B 977 LYS cc_start: 0.8179 (ttmt) cc_final: 0.7562 (tttm) REVERT: B 995 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7784 (mp0) REVERT: B 1134 LEU cc_start: 0.6376 (OUTLIER) cc_final: 0.6027 (pp) REVERT: A 582 LYS cc_start: 0.8138 (mttm) cc_final: 0.7848 (mtmm) REVERT: A 817 GLU cc_start: 0.9003 (OUTLIER) cc_final: 0.8637 (pm20) REVERT: A 977 LYS cc_start: 0.8110 (ttmt) cc_final: 0.7437 (tttp) REVERT: A 995 GLU cc_start: 0.8100 (OUTLIER) cc_final: 0.7825 (mp0) REVERT: A 1134 LEU cc_start: 0.6353 (OUTLIER) cc_final: 0.6015 (pp) outliers start: 41 outliers final: 29 residues processed: 174 average time/residue: 0.0874 time to fit residues: 23.0030 Evaluate side-chains 176 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 141 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 540 GLN Chi-restraints excluded: chain B residue 608 ASN Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 642 ASP Chi-restraints excluded: chain B residue 644 SER Chi-restraints excluded: chain B residue 687 CYS Chi-restraints excluded: chain B residue 731 SER Chi-restraints excluded: chain B residue 790 LEU Chi-restraints excluded: chain B residue 803 VAL Chi-restraints excluded: chain B residue 833 GLU Chi-restraints excluded: chain B residue 890 ILE Chi-restraints excluded: chain B residue 995 GLU Chi-restraints excluded: chain B residue 1065 VAL Chi-restraints excluded: chain B residue 1123 THR Chi-restraints excluded: chain B residue 1134 LEU Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 608 ASN Chi-restraints excluded: chain A residue 642 ASP Chi-restraints excluded: chain A residue 644 SER Chi-restraints excluded: chain A residue 687 CYS Chi-restraints excluded: chain A residue 731 SER Chi-restraints excluded: chain A residue 790 LEU Chi-restraints excluded: chain A residue 803 VAL Chi-restraints excluded: chain A residue 817 GLU Chi-restraints excluded: chain A residue 890 ILE Chi-restraints excluded: chain A residue 949 SER Chi-restraints excluded: chain A residue 961 GLU Chi-restraints excluded: chain A residue 995 GLU Chi-restraints excluded: chain A residue 1065 VAL Chi-restraints excluded: chain A residue 1111 GLU Chi-restraints excluded: chain A residue 1119 GLN Chi-restraints excluded: chain A residue 1123 THR Chi-restraints excluded: chain A residue 1134 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 23 optimal weight: 0.3980 chunk 22 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 63 optimal weight: 6.9990 chunk 9 optimal weight: 2.9990 chunk 118 optimal weight: 6.9990 chunk 49 optimal weight: 2.9990 chunk 119 optimal weight: 0.0670 chunk 99 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 88 optimal weight: 0.0980 overall best weight: 0.4320 ------------------------------------------------------------------------------- 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 = 0.3492 r_free = 0.3492 target = 0.132150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.095922 restraints weight = 16259.568| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 2.19 r_work: 0.2862 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2726 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 moved from start: 0.3221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 12458 Z= 0.089 Angle : 0.501 10.291 16826 Z= 0.250 Chirality : 0.041 0.163 1818 Planarity : 0.003 0.030 2144 Dihedral : 3.899 12.948 1662 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.06 % Allowed : 17.33 % Favored : 80.61 % 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: -0.48 (0.22), residues: 1486 helix: 1.13 (0.22), residues: 628 sheet: -0.65 (0.36), residues: 198 loop : -1.67 (0.22), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 530 TYR 0.011 0.001 TYR B 966 PHE 0.014 0.001 PHE A 559 TRP 0.008 0.001 TRP A 820 HIS 0.006 0.001 HIS B 650 Details of bonding type rmsd covalent geometry : bond 0.00197 (12458) covalent geometry : angle 0.50104 (16826) hydrogen bonds : bond 0.03353 ( 465) hydrogen bonds : angle 4.07188 ( 1338) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 154 time to evaluate : 0.514 Fit side-chains REVERT: B 551 LEU cc_start: 0.9016 (mp) cc_final: 0.8715 (tt) REVERT: B 582 LYS cc_start: 0.8100 (mttm) cc_final: 0.7800 (mtmm) REVERT: B 833 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.7617 (pp20) REVERT: B 977 LYS cc_start: 0.8185 (ttmt) cc_final: 0.7597 (tttm) REVERT: B 995 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.7726 (mp0) REVERT: B 1134 LEU cc_start: 0.6408 (OUTLIER) cc_final: 0.6041 (pp) REVERT: A 551 LEU cc_start: 0.8998 (mp) cc_final: 0.8688 (tt) REVERT: A 582 LYS cc_start: 0.8123 (mttm) cc_final: 0.7822 (mtmm) REVERT: A 817 GLU cc_start: 0.9020 (OUTLIER) cc_final: 0.8641 (pm20) REVERT: A 977 LYS cc_start: 0.8101 (ttmt) cc_final: 0.7431 (tttp) REVERT: A 995 GLU cc_start: 0.8100 (OUTLIER) cc_final: 0.7781 (mp0) REVERT: A 1134 LEU cc_start: 0.6373 (OUTLIER) cc_final: 0.6014 (pp) outliers start: 27 outliers final: 19 residues processed: 170 average time/residue: 0.1032 time to fit residues: 26.9877 Evaluate side-chains 168 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 143 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 608 ASN Chi-restraints excluded: chain B residue 644 SER Chi-restraints excluded: chain B residue 731 SER Chi-restraints excluded: chain B residue 790 LEU Chi-restraints excluded: chain B residue 803 VAL Chi-restraints excluded: chain B residue 833 GLU Chi-restraints excluded: chain B residue 890 ILE Chi-restraints excluded: chain B residue 949 SER Chi-restraints excluded: chain B residue 995 GLU Chi-restraints excluded: chain B residue 1123 THR Chi-restraints excluded: chain B residue 1134 LEU Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 608 ASN Chi-restraints excluded: chain A residue 644 SER Chi-restraints excluded: chain A residue 687 CYS Chi-restraints excluded: chain A residue 731 SER Chi-restraints excluded: chain A residue 817 GLU Chi-restraints excluded: chain A residue 890 ILE Chi-restraints excluded: chain A residue 961 GLU Chi-restraints excluded: chain A residue 995 GLU Chi-restraints excluded: chain A residue 1111 GLU Chi-restraints excluded: chain A residue 1123 THR Chi-restraints excluded: chain A residue 1134 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 113 optimal weight: 0.9990 chunk 35 optimal weight: 0.0770 chunk 22 optimal weight: 0.0670 chunk 52 optimal weight: 7.9990 chunk 134 optimal weight: 5.9990 chunk 132 optimal weight: 4.9990 chunk 97 optimal weight: 5.9990 chunk 69 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 144 optimal weight: 8.9990 overall best weight: 1.4282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1119 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.131643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.095891 restraints weight = 16258.701| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 2.15 r_work: 0.2821 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2686 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 moved from start: 0.3222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12458 Z= 0.132 Angle : 0.520 11.833 16826 Z= 0.258 Chirality : 0.042 0.134 1818 Planarity : 0.003 0.030 2144 Dihedral : 3.924 14.172 1662 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 2.52 % Allowed : 17.02 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.41 (0.22), residues: 1486 helix: 1.20 (0.22), residues: 632 sheet: -0.65 (0.36), residues: 198 loop : -1.65 (0.22), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 578 TYR 0.013 0.001 TYR A 966 PHE 0.011 0.001 PHE A 739 TRP 0.008 0.001 TRP A 820 HIS 0.005 0.001 HIS B 650 Details of bonding type rmsd covalent geometry : bond 0.00328 (12458) covalent geometry : angle 0.51954 (16826) hydrogen bonds : bond 0.03728 ( 465) hydrogen bonds : angle 4.06323 ( 1338) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 150 time to evaluate : 0.521 Fit side-chains REVERT: B 551 LEU cc_start: 0.9011 (mp) cc_final: 0.8691 (tt) REVERT: B 582 LYS cc_start: 0.8116 (mttm) cc_final: 0.7797 (mtmm) REVERT: B 833 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.7748 (pp20) REVERT: B 977 LYS cc_start: 0.8198 (ttmt) cc_final: 0.7562 (tttm) REVERT: B 995 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7791 (mp0) REVERT: B 1134 LEU cc_start: 0.6456 (OUTLIER) cc_final: 0.6111 (pp) REVERT: A 551 LEU cc_start: 0.9001 (mp) cc_final: 0.8673 (tt) REVERT: A 582 LYS cc_start: 0.8124 (mttm) cc_final: 0.7815 (mtmm) REVERT: A 817 GLU cc_start: 0.9011 (OUTLIER) cc_final: 0.8614 (pm20) REVERT: A 977 LYS cc_start: 0.8078 (ttmt) cc_final: 0.7396 (tttp) REVERT: A 994 GLU cc_start: 0.8372 (pt0) cc_final: 0.7909 (pt0) REVERT: A 995 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.7809 (mp0) REVERT: A 1134 LEU cc_start: 0.6447 (OUTLIER) cc_final: 0.6099 (pp) outliers start: 33 outliers final: 26 residues processed: 172 average time/residue: 0.1065 time to fit residues: 27.7983 Evaluate side-chains 177 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 145 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 540 GLN Chi-restraints excluded: chain B residue 608 ASN Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 644 SER Chi-restraints excluded: chain B residue 731 SER Chi-restraints excluded: chain B residue 790 LEU Chi-restraints excluded: chain B residue 803 VAL Chi-restraints excluded: chain B residue 833 GLU Chi-restraints excluded: chain B residue 890 ILE Chi-restraints excluded: chain B residue 949 SER Chi-restraints excluded: chain B residue 963 ILE Chi-restraints excluded: chain B residue 995 GLU Chi-restraints excluded: chain B residue 1111 GLU Chi-restraints excluded: chain B residue 1119 GLN Chi-restraints excluded: chain B residue 1123 THR Chi-restraints excluded: chain B residue 1134 LEU Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 608 ASN Chi-restraints excluded: chain A residue 644 SER Chi-restraints excluded: chain A residue 687 CYS Chi-restraints excluded: chain A residue 731 SER Chi-restraints excluded: chain A residue 790 LEU Chi-restraints excluded: chain A residue 817 GLU Chi-restraints excluded: chain A residue 890 ILE Chi-restraints excluded: chain A residue 949 SER Chi-restraints excluded: chain A residue 961 GLU Chi-restraints excluded: chain A residue 995 GLU Chi-restraints excluded: chain A residue 1111 GLU Chi-restraints excluded: chain A residue 1123 THR Chi-restraints excluded: chain A residue 1134 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 104 optimal weight: 3.9990 chunk 62 optimal weight: 10.0000 chunk 111 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 110 optimal weight: 2.9990 chunk 59 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 chunk 133 optimal weight: 0.9980 chunk 138 optimal weight: 6.9990 chunk 47 optimal weight: 2.9990 chunk 108 optimal weight: 0.0980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 634 ASN B1119 GLN A1119 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.131914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.096069 restraints weight = 16398.879| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 2.16 r_work: 0.2743 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2608 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.3244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12458 Z= 0.126 Angle : 0.521 11.907 16826 Z= 0.259 Chirality : 0.042 0.134 1818 Planarity : 0.003 0.029 2144 Dihedral : 3.900 14.013 1662 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.60 % Allowed : 16.72 % Favored : 80.69 % 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: -0.37 (0.22), residues: 1486 helix: 1.25 (0.22), residues: 632 sheet: -0.66 (0.36), residues: 198 loop : -1.64 (0.22), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 578 TYR 0.011 0.001 TYR B 848 PHE 0.012 0.001 PHE B 559 TRP 0.008 0.001 TRP A 820 HIS 0.008 0.001 HIS B 650 Details of bonding type rmsd covalent geometry : bond 0.00312 (12458) covalent geometry : angle 0.52097 (16826) hydrogen bonds : bond 0.03687 ( 465) hydrogen bonds : angle 4.05857 ( 1338) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 147 time to evaluate : 0.519 Fit side-chains REVERT: B 551 LEU cc_start: 0.8995 (mp) cc_final: 0.8669 (tt) REVERT: B 582 LYS cc_start: 0.8092 (mttm) cc_final: 0.7761 (mtmm) REVERT: B 833 GLU cc_start: 0.8372 (OUTLIER) cc_final: 0.7730 (pp20) REVERT: B 977 LYS cc_start: 0.8130 (ttmt) cc_final: 0.7481 (tttm) REVERT: B 995 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7753 (mp0) REVERT: B 1134 LEU cc_start: 0.6476 (OUTLIER) cc_final: 0.6130 (pp) REVERT: A 551 LEU cc_start: 0.8985 (mp) cc_final: 0.8654 (tt) REVERT: A 582 LYS cc_start: 0.8100 (mttm) cc_final: 0.7776 (mtmm) REVERT: A 817 GLU cc_start: 0.9026 (OUTLIER) cc_final: 0.8619 (pm20) REVERT: A 977 LYS cc_start: 0.7985 (ttmt) cc_final: 0.7290 (tttp) REVERT: A 995 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.7770 (mp0) REVERT: A 1134 LEU cc_start: 0.6465 (OUTLIER) cc_final: 0.6116 (pp) outliers start: 34 outliers final: 27 residues processed: 168 average time/residue: 0.0953 time to fit residues: 24.5216 Evaluate side-chains 179 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 146 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 540 GLN Chi-restraints excluded: chain B residue 608 ASN Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 644 SER Chi-restraints excluded: chain B residue 687 CYS Chi-restraints excluded: chain B residue 731 SER Chi-restraints excluded: chain B residue 790 LEU Chi-restraints excluded: chain B residue 803 VAL Chi-restraints excluded: chain B residue 833 GLU Chi-restraints excluded: chain B residue 890 ILE Chi-restraints excluded: chain B residue 949 SER Chi-restraints excluded: chain B residue 963 ILE Chi-restraints excluded: chain B residue 995 GLU Chi-restraints excluded: chain B residue 1111 GLU Chi-restraints excluded: chain B residue 1119 GLN Chi-restraints excluded: chain B residue 1123 THR Chi-restraints excluded: chain B residue 1134 LEU Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 608 ASN Chi-restraints excluded: chain A residue 644 SER Chi-restraints excluded: chain A residue 687 CYS Chi-restraints excluded: chain A residue 731 SER Chi-restraints excluded: chain A residue 790 LEU Chi-restraints excluded: chain A residue 817 GLU Chi-restraints excluded: chain A residue 890 ILE Chi-restraints excluded: chain A residue 961 GLU Chi-restraints excluded: chain A residue 995 GLU Chi-restraints excluded: chain A residue 1111 GLU Chi-restraints excluded: chain A residue 1119 GLN Chi-restraints excluded: chain A residue 1123 THR Chi-restraints excluded: chain A residue 1134 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 53 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 chunk 119 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 32 optimal weight: 0.6980 chunk 128 optimal weight: 6.9990 chunk 55 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 83 optimal weight: 9.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 634 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.133199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.097480 restraints weight = 16381.877| |-----------------------------------------------------------------------------| r_work (start): 0.2942 rms_B_bonded: 2.16 r_work: 0.2762 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2627 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.3306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12458 Z= 0.105 Angle : 0.505 11.254 16826 Z= 0.252 Chirality : 0.041 0.132 1818 Planarity : 0.003 0.029 2144 Dihedral : 3.829 13.047 1662 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.52 % Allowed : 16.64 % Favored : 80.84 % 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: -0.30 (0.22), residues: 1486 helix: 1.31 (0.22), residues: 632 sheet: -0.65 (0.36), residues: 198 loop : -1.60 (0.23), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 578 TYR 0.013 0.001 TYR A 966 PHE 0.011 0.001 PHE A 710 TRP 0.008 0.001 TRP A 820 HIS 0.008 0.001 HIS A 650 Details of bonding type rmsd covalent geometry : bond 0.00252 (12458) covalent geometry : angle 0.50510 (16826) hydrogen bonds : bond 0.03479 ( 465) hydrogen bonds : angle 4.02737 ( 1338) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3266.36 seconds wall clock time: 56 minutes 37.38 seconds (3397.38 seconds total)