Starting phenix.real_space_refine on Wed Jul 30 07:16:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8kgp_37229/07_2025/8kgp_37229.cif Found real_map, /net/cci-nas-00/data/ceres_data/8kgp_37229/07_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_37229/07_2025/8kgp_37229.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8kgp_37229/07_2025/8kgp_37229.map" model { file = "/net/cci-nas-00/data/ceres_data/8kgp_37229/07_2025/8kgp_37229.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8kgp_37229/07_2025/8kgp_37229.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 7.80, per 1000 atoms: 0.64 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: 2.67 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 1.33 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: 3.54 Time building geometry restraints manager: 3.19 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: 0.06 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: 2.600 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: 0.620 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 29.450 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.050 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: 0.010 Load rotamer database and sin/cos tables:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.070 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.065 0.004 TRP A1170 HIS 0.015 0.002 HIS B1192 PHE 0.046 0.004 PHE B 785 TYR 0.057 0.004 TYR A 824 ARG 0.015 0.002 ARG A 578 Details of bonding type rmsd hydrogen bonds : bond 0.18670 ( 465) hydrogen bonds : angle 6.85743 ( 1338) covalent geometry : bond 0.01083 (12458) covalent geometry : angle 1.05316 (16826) *********************** 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 : 1.259 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: 0.8370 (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: 0.2977 time to fit residues: 113.6845 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 : 1.301 ------------------------------------------------------------------------------- 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 124 optimal weight: 1.9990 chunk 112 optimal weight: 0.9980 chunk 62 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 75 optimal weight: 10.0000 chunk 59 optimal weight: 0.7980 chunk 116 optimal weight: 0.6980 chunk 44 optimal weight: 0.0570 chunk 70 optimal weight: 1.9990 chunk 86 optimal weight: 0.6980 chunk 134 optimal weight: 0.9980 overall best weight: 0.6498 ------------------------------------------------------------------------------- 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 = 0.3541 r_free = 0.3541 target = 0.135725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.101369 restraints weight = 16122.010| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 2.10 r_work: 0.2866 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2731 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.2187 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= 0.116 Angle : 0.574 9.231 16826 Z= 0.297 Chirality : 0.042 0.180 1818 Planarity : 0.005 0.041 2144 Dihedral : 4.926 37.128 1665 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.45 % Allowed : 10.53 % Favored : 88.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.36 (0.20), residues: 1486 helix: -0.88 (0.19), residues: 612 sheet: -1.29 (0.36), residues: 202 loop : -2.27 (0.21), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A1170 HIS 0.005 0.001 HIS A 650 PHE 0.013 0.001 PHE B 559 TYR 0.014 0.001 TYR B 888 ARG 0.005 0.001 ARG B 530 Details of bonding type rmsd hydrogen bonds : bond 0.04577 ( 465) hydrogen bonds : angle 4.58717 ( 1338) covalent geometry : bond 0.00263 (12458) covalent geometry : angle 0.57419 (16826) *********************** 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 204 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 185 time to evaluate : 1.298 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 551 LEU cc_start: 0.8994 (mp) cc_final: 0.8637 (tt) REVERT: B 747 ASP cc_start: 0.9016 (t70) cc_final: 0.8728 (t0) REVERT: B 977 LYS cc_start: 0.8122 (ttmt) cc_final: 0.7442 (tttm) REVERT: B 1064 ILE cc_start: 0.8108 (mt) cc_final: 0.7858 (mt) REVERT: B 1134 LEU cc_start: 0.6389 (OUTLIER) cc_final: 0.6045 (pp) REVERT: A 417 LYS cc_start: 0.8882 (mtmt) cc_final: 0.8622 (mtpp) REVERT: A 551 LEU cc_start: 0.8973 (mp) cc_final: 0.8605 (tt) REVERT: A 612 LYS cc_start: 0.8701 (ttmt) cc_final: 0.8468 (mtpp) REVERT: A 673 GLU cc_start: 0.7901 (tp30) cc_final: 0.7672 (tp30) REVERT: A 747 ASP cc_start: 0.9011 (t70) cc_final: 0.8775 (t0) REVERT: A 957 MET cc_start: 0.9056 (mmm) cc_final: 0.8718 (tpt) REVERT: A 964 ILE cc_start: 0.8995 (mt) cc_final: 0.8665 (mm) REVERT: A 977 LYS cc_start: 0.7828 (ttmt) cc_final: 0.7344 (tttp) REVERT: A 1064 ILE cc_start: 0.8096 (mt) cc_final: 0.7853 (mt) REVERT: A 1134 LEU cc_start: 0.6409 (OUTLIER) cc_final: 0.6059 (pp) outliers start: 19 outliers final: 8 residues processed: 201 average time/residue: 0.2534 time to fit residues: 72.9169 Evaluate side-chains 157 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 147 time to evaluate : 1.376 ------------------------------------------------------------------------------- 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 6 optimal weight: 2.9990 chunk 5 optimal weight: 7.9990 chunk 41 optimal weight: 6.9990 chunk 107 optimal weight: 4.9990 chunk 147 optimal weight: 1.9990 chunk 67 optimal weight: 9.9990 chunk 92 optimal weight: 6.9990 chunk 122 optimal weight: 0.0070 chunk 108 optimal weight: 4.9990 chunk 31 optimal weight: 9.9990 chunk 123 optimal weight: 1.9990 overall best weight: 2.4006 ------------------------------------------------------------------------------- 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 = 0.3479 r_free = 0.3479 target = 0.130843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.095923 restraints weight = 16502.760| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 2.09 r_work: 0.2774 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2638 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.2370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 12458 Z= 0.207 Angle : 0.615 11.200 16826 Z= 0.311 Chirality : 0.046 0.176 1818 Planarity : 0.005 0.041 2144 Dihedral : 4.689 18.039 1662 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 2.44 % Allowed : 12.67 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.21), residues: 1486 helix: -0.07 (0.21), residues: 618 sheet: -1.09 (0.36), residues: 202 loop : -2.03 (0.22), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B1170 HIS 0.007 0.001 HIS B1192 PHE 0.016 0.002 PHE B 785 TYR 0.023 0.002 TYR A 824 ARG 0.005 0.001 ARG B 684 Details of bonding type rmsd hydrogen bonds : bond 0.04937 ( 465) hydrogen bonds : angle 4.39878 ( 1338) covalent geometry : bond 0.00519 (12458) covalent geometry : angle 0.61499 (16826) *********************** 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 190 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 158 time to evaluate : 1.303 Fit side-chains REVERT: B 417 LYS cc_start: 0.8915 (mtmt) cc_final: 0.8623 (mtpp) REVERT: B 515 ASP cc_start: 0.8227 (t70) cc_final: 0.7485 (p0) REVERT: B 582 LYS cc_start: 0.8220 (mttm) cc_final: 0.7849 (mtmm) REVERT: B 747 ASP cc_start: 0.9063 (t70) cc_final: 0.8833 (t0) REVERT: B 817 GLU cc_start: 0.9009 (OUTLIER) cc_final: 0.8600 (pm20) REVERT: B 833 GLU cc_start: 0.8489 (OUTLIER) cc_final: 0.7712 (pp20) REVERT: B 977 LYS cc_start: 0.8149 (ttmt) cc_final: 0.7497 (tttm) REVERT: B 1134 LEU cc_start: 0.6428 (OUTLIER) cc_final: 0.6097 (pp) REVERT: A 417 LYS cc_start: 0.8921 (mtmt) cc_final: 0.8646 (mtpp) REVERT: A 515 ASP cc_start: 0.8226 (t70) cc_final: 0.7470 (p0) REVERT: A 582 LYS cc_start: 0.8230 (mttm) cc_final: 0.7876 (mtmm) REVERT: A 747 ASP cc_start: 0.9059 (t70) cc_final: 0.8838 (t0) REVERT: A 817 GLU cc_start: 0.8974 (OUTLIER) cc_final: 0.8600 (pm20) REVERT: A 977 LYS cc_start: 0.8061 (ttmt) cc_final: 0.7389 (tttm) REVERT: A 1064 ILE cc_start: 0.8055 (mt) cc_final: 0.7803 (mt) REVERT: A 1134 LEU cc_start: 0.6399 (OUTLIER) cc_final: 0.6072 (pp) outliers start: 32 outliers final: 19 residues processed: 179 average time/residue: 0.2219 time to fit residues: 58.8402 Evaluate side-chains 166 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 142 time to evaluate : 1.290 ------------------------------------------------------------------------------- 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 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 1065 VAL Chi-restraints excluded: chain B residue 1111 GLU Chi-restraints excluded: chain B residue 1134 LEU Chi-restraints excluded: chain B residue 1142 VAL Chi-restraints excluded: chain A residue 569 VAL 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 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 1065 VAL Chi-restraints excluded: chain A residue 1111 GLU Chi-restraints excluded: chain A residue 1134 LEU Chi-restraints excluded: chain A residue 1142 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 61 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 73 optimal weight: 0.7980 chunk 69 optimal weight: 0.0030 chunk 13 optimal weight: 0.9980 chunk 127 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 115 optimal weight: 2.9990 chunk 80 optimal weight: 4.9990 chunk 118 optimal weight: 7.9990 chunk 88 optimal weight: 0.9980 overall best weight: 0.9592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1051 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.134342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.099138 restraints weight = 16204.278| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 2.13 r_work: 0.2826 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2687 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 moved from start: 0.2761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12458 Z= 0.109 Angle : 0.513 9.925 16826 Z= 0.258 Chirality : 0.041 0.137 1818 Planarity : 0.003 0.032 2144 Dihedral : 4.201 15.212 1662 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.67 % Allowed : 13.05 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.22), residues: 1486 helix: 0.51 (0.22), residues: 614 sheet: -0.70 (0.36), residues: 196 loop : -1.83 (0.22), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B1170 HIS 0.005 0.001 HIS B1051 PHE 0.011 0.001 PHE A 710 TYR 0.011 0.001 TYR B 888 ARG 0.003 0.000 ARG A 530 Details of bonding type rmsd hydrogen bonds : bond 0.03728 ( 465) hydrogen bonds : angle 4.20454 ( 1338) covalent geometry : bond 0.00259 (12458) covalent geometry : angle 0.51313 (16826) *********************** 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 204 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 169 time to evaluate : 1.684 Fit side-chains revert: symmetry clash REVERT: B 417 LYS cc_start: 0.8915 (mtmt) cc_final: 0.8650 (mtpp) REVERT: B 515 ASP cc_start: 0.8241 (t70) cc_final: 0.7411 (p0) REVERT: B 747 ASP cc_start: 0.9036 (t70) cc_final: 0.8781 (t0) REVERT: B 817 GLU cc_start: 0.9050 (OUTLIER) cc_final: 0.8630 (pm20) REVERT: B 977 LYS cc_start: 0.8180 (ttmt) cc_final: 0.7553 (tttm) REVERT: B 1134 LEU cc_start: 0.6380 (OUTLIER) cc_final: 0.6051 (pp) REVERT: A 417 LYS cc_start: 0.8933 (mtmt) cc_final: 0.8647 (mtpp) REVERT: A 515 ASP cc_start: 0.8263 (t70) cc_final: 0.7418 (p0) REVERT: A 582 LYS cc_start: 0.8177 (mttm) cc_final: 0.7866 (mtmm) REVERT: A 747 ASP cc_start: 0.9038 (t70) cc_final: 0.8787 (t0) REVERT: A 817 GLU cc_start: 0.9013 (pt0) cc_final: 0.8618 (pm20) REVERT: A 977 LYS cc_start: 0.8086 (ttmt) cc_final: 0.7443 (tttp) REVERT: A 1064 ILE cc_start: 0.8101 (mt) cc_final: 0.7848 (mt) REVERT: A 1134 LEU cc_start: 0.6336 (OUTLIER) cc_final: 0.5986 (pp) outliers start: 35 outliers final: 19 residues processed: 196 average time/residue: 0.3180 time to fit residues: 94.6399 Evaluate side-chains 167 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 145 time to evaluate : 1.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 540 GLN Chi-restraints excluded: chain B residue 551 LEU 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 817 GLU Chi-restraints excluded: chain B residue 890 ILE 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 25 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 chunk 93 optimal weight: 0.5980 chunk 47 optimal weight: 8.9990 chunk 44 optimal weight: 8.9990 chunk 110 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 143 optimal weight: 0.2980 chunk 84 optimal weight: 3.9990 chunk 137 optimal weight: 9.9990 chunk 118 optimal weight: 7.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- 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 = 0.3462 r_free = 0.3462 target = 0.129624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.094027 restraints weight = 16255.150| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 2.12 r_work: 0.2786 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2650 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8761 moved from start: 0.2811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 12458 Z= 0.199 Angle : 0.586 13.954 16826 Z= 0.293 Chirality : 0.044 0.145 1818 Planarity : 0.004 0.040 2144 Dihedral : 4.348 17.746 1662 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 2.98 % Allowed : 14.20 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.22), residues: 1486 helix: 0.74 (0.22), residues: 620 sheet: -0.70 (0.36), residues: 200 loop : -1.78 (0.22), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A1170 HIS 0.006 0.001 HIS A1192 PHE 0.012 0.001 PHE A 785 TYR 0.017 0.002 TYR A 824 ARG 0.003 0.000 ARG A 578 Details of bonding type rmsd hydrogen bonds : bond 0.04609 ( 465) hydrogen bonds : angle 4.25041 ( 1338) covalent geometry : bond 0.00498 (12458) covalent geometry : angle 0.58587 (16826) *********************** 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 191 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 152 time to evaluate : 2.338 Fit side-chains REVERT: B 417 LYS cc_start: 0.8927 (mtmt) cc_final: 0.8535 (mtpp) REVERT: B 582 LYS cc_start: 0.8193 (mttm) cc_final: 0.7819 (mtmm) REVERT: B 747 ASP cc_start: 0.9065 (t70) cc_final: 0.8827 (t0) REVERT: B 756 MET cc_start: 0.8335 (OUTLIER) cc_final: 0.7819 (tpt) REVERT: B 817 GLU cc_start: 0.9033 (OUTLIER) cc_final: 0.8608 (pm20) REVERT: B 833 GLU cc_start: 0.8568 (OUTLIER) cc_final: 0.7855 (pp20) REVERT: B 977 LYS cc_start: 0.8177 (ttmt) cc_final: 0.7553 (tttm) REVERT: B 1134 LEU cc_start: 0.6394 (OUTLIER) cc_final: 0.6062 (pp) REVERT: A 417 LYS cc_start: 0.8920 (mtmt) cc_final: 0.8575 (mtpp) REVERT: A 582 LYS cc_start: 0.8198 (mttm) cc_final: 0.7868 (mtmm) REVERT: A 756 MET cc_start: 0.8293 (OUTLIER) cc_final: 0.7728 (tpt) REVERT: A 817 GLU cc_start: 0.9037 (OUTLIER) cc_final: 0.8628 (pm20) REVERT: A 977 LYS cc_start: 0.8067 (ttmt) cc_final: 0.7405 (tttp) REVERT: A 1134 LEU cc_start: 0.6350 (OUTLIER) cc_final: 0.5999 (pp) outliers start: 39 outliers final: 28 residues processed: 182 average time/residue: 0.2814 time to fit residues: 78.6745 Evaluate side-chains 178 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 143 time to evaluate : 1.465 ------------------------------------------------------------------------------- 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 687 CYS Chi-restraints excluded: chain B residue 731 SER Chi-restraints excluded: chain B residue 756 MET Chi-restraints excluded: chain B residue 790 LEU 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 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 A residue 508 ILE Chi-restraints excluded: chain A residue 540 GLN Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 572 LEU 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 756 MET 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 37 optimal weight: 0.9980 chunk 20 optimal weight: 0.0270 chunk 74 optimal weight: 0.0170 chunk 21 optimal weight: 0.9990 chunk 79 optimal weight: 7.9990 chunk 10 optimal weight: 0.9990 chunk 33 optimal weight: 0.5980 chunk 50 optimal weight: 0.9990 chunk 76 optimal weight: 0.7980 chunk 147 optimal weight: 0.9990 chunk 64 optimal weight: 8.9990 overall best weight: 0.4876 ------------------------------------------------------------------------------- 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 = 0.3526 r_free = 0.3526 target = 0.134675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.099407 restraints weight = 16457.686| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 2.15 r_work: 0.2853 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2717 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.3163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 12458 Z= 0.088 Angle : 0.488 9.425 16826 Z= 0.246 Chirality : 0.041 0.132 1818 Planarity : 0.003 0.029 2144 Dihedral : 3.862 13.146 1662 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.60 % Allowed : 15.95 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.22), residues: 1486 helix: 1.12 (0.22), residues: 616 sheet: -0.29 (0.37), residues: 196 loop : -1.63 (0.22), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 820 HIS 0.007 0.001 HIS A 650 PHE 0.011 0.001 PHE A 710 TYR 0.010 0.001 TYR A 966 ARG 0.003 0.000 ARG A 912 Details of bonding type rmsd hydrogen bonds : bond 0.03171 ( 465) hydrogen bonds : angle 4.02565 ( 1338) covalent geometry : bond 0.00197 (12458) covalent geometry : angle 0.48783 (16826) *********************** 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 183 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 162 time to evaluate : 1.401 Fit side-chains revert: symmetry clash REVERT: B 417 LYS cc_start: 0.8899 (mtmt) cc_final: 0.8553 (mtpp) REVERT: B 817 GLU cc_start: 0.9069 (pt0) cc_final: 0.8599 (pm20) REVERT: B 833 GLU cc_start: 0.8191 (OUTLIER) cc_final: 0.7547 (pp20) REVERT: B 977 LYS cc_start: 0.8156 (ttmt) cc_final: 0.7550 (tttm) REVERT: B 1134 LEU cc_start: 0.6299 (OUTLIER) cc_final: 0.5813 (mt) REVERT: A 417 LYS cc_start: 0.8901 (mtmt) cc_final: 0.8629 (mtpp) REVERT: A 582 LYS cc_start: 0.8164 (mttm) cc_final: 0.7851 (mtmt) REVERT: A 817 GLU cc_start: 0.9070 (pt0) cc_final: 0.8631 (pm20) REVERT: A 890 ILE cc_start: 0.7978 (OUTLIER) cc_final: 0.7458 (tt) REVERT: A 977 LYS cc_start: 0.8061 (ttmt) cc_final: 0.7406 (tttp) REVERT: A 1134 LEU cc_start: 0.6342 (OUTLIER) cc_final: 0.5894 (mt) outliers start: 21 outliers final: 13 residues processed: 177 average time/residue: 0.2319 time to fit residues: 60.2090 Evaluate side-chains 160 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 143 time to evaluate : 1.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 608 ASN Chi-restraints excluded: chain B residue 687 CYS Chi-restraints excluded: chain B residue 731 SER Chi-restraints excluded: chain B residue 833 GLU Chi-restraints excluded: chain B residue 890 ILE 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 70 optimal weight: 1.9990 chunk 83 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 38 optimal weight: 6.9990 chunk 51 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 31 optimal weight: 10.0000 chunk 144 optimal weight: 0.8980 chunk 115 optimal weight: 2.9990 chunk 126 optimal weight: 0.8980 chunk 71 optimal weight: 4.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- 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 = 0.3496 r_free = 0.3496 target = 0.132251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.096493 restraints weight = 16386.935| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 2.16 r_work: 0.2756 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2622 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.3138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 12458 Z= 0.138 Angle : 0.519 11.178 16826 Z= 0.260 Chirality : 0.042 0.137 1818 Planarity : 0.003 0.030 2144 Dihedral : 3.903 14.608 1662 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 1.98 % Allowed : 16.18 % Favored : 81.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.22), residues: 1486 helix: 1.23 (0.22), residues: 620 sheet: -0.26 (0.37), residues: 196 loop : -1.64 (0.22), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 820 HIS 0.005 0.001 HIS A 650 PHE 0.010 0.001 PHE A 739 TYR 0.011 0.001 TYR A 888 ARG 0.005 0.000 ARG B 578 Details of bonding type rmsd hydrogen bonds : bond 0.03729 ( 465) hydrogen bonds : angle 4.02557 ( 1338) covalent geometry : bond 0.00344 (12458) covalent geometry : angle 0.51865 (16826) *********************** 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 175 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 149 time to evaluate : 1.855 Fit side-chains revert: symmetry clash REVERT: B 747 ASP cc_start: 0.9047 (t70) cc_final: 0.8784 (t0) REVERT: B 756 MET cc_start: 0.8290 (OUTLIER) cc_final: 0.7766 (tpt) REVERT: B 817 GLU cc_start: 0.9049 (pt0) cc_final: 0.8581 (pm20) REVERT: B 833 GLU cc_start: 0.8427 (OUTLIER) cc_final: 0.7789 (pp20) REVERT: B 977 LYS cc_start: 0.8106 (ttmt) cc_final: 0.7439 (tttm) REVERT: B 1134 LEU cc_start: 0.6364 (OUTLIER) cc_final: 0.5872 (mt) REVERT: A 582 LYS cc_start: 0.8148 (mttm) cc_final: 0.7824 (mtmm) REVERT: A 747 ASP cc_start: 0.9050 (t70) cc_final: 0.8799 (t0) REVERT: A 756 MET cc_start: 0.8216 (OUTLIER) cc_final: 0.7710 (tpt) REVERT: A 817 GLU cc_start: 0.9032 (pt0) cc_final: 0.8610 (pm20) REVERT: A 977 LYS cc_start: 0.8009 (ttmt) cc_final: 0.7320 (tttp) REVERT: A 1134 LEU cc_start: 0.6470 (OUTLIER) cc_final: 0.5993 (mt) outliers start: 26 outliers final: 20 residues processed: 166 average time/residue: 0.2811 time to fit residues: 70.7761 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 : 1.506 ------------------------------------------------------------------------------- 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 756 MET Chi-restraints excluded: chain B residue 833 GLU Chi-restraints excluded: chain B residue 890 ILE Chi-restraints excluded: chain B residue 963 ILE Chi-restraints excluded: chain B residue 1123 THR Chi-restraints excluded: chain B residue 1134 LEU Chi-restraints excluded: chain A residue 540 GLN Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 572 LEU 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 756 MET Chi-restraints excluded: chain A residue 790 LEU Chi-restraints excluded: chain A residue 890 ILE Chi-restraints excluded: chain A residue 926 SER 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 109 optimal weight: 2.9990 chunk 65 optimal weight: 0.2980 chunk 16 optimal weight: 6.9990 chunk 37 optimal weight: 0.8980 chunk 136 optimal weight: 10.0000 chunk 17 optimal weight: 2.9990 chunk 85 optimal weight: 0.9980 chunk 8 optimal weight: 6.9990 chunk 119 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 chunk 107 optimal weight: 4.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 = 0.3518 r_free = 0.3518 target = 0.134079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.098439 restraints weight = 16328.259| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 2.18 r_work: 0.2775 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2642 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.3269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12458 Z= 0.107 Angle : 0.491 9.878 16826 Z= 0.247 Chirality : 0.041 0.133 1818 Planarity : 0.003 0.028 2144 Dihedral : 3.782 13.235 1662 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.91 % Allowed : 16.87 % Favored : 81.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.22), residues: 1486 helix: 1.34 (0.22), residues: 624 sheet: -0.21 (0.38), residues: 196 loop : -1.62 (0.22), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 820 HIS 0.007 0.001 HIS B 650 PHE 0.010 0.001 PHE A 710 TYR 0.010 0.001 TYR A 888 ARG 0.004 0.000 ARG B 578 Details of bonding type rmsd hydrogen bonds : bond 0.03394 ( 465) hydrogen bonds : angle 3.96914 ( 1338) covalent geometry : bond 0.00259 (12458) covalent geometry : angle 0.49115 (16826) *********************** 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 171 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 146 time to evaluate : 1.451 Fit side-chains revert: symmetry clash REVERT: B 817 GLU cc_start: 0.9068 (pt0) cc_final: 0.8606 (pm20) REVERT: B 833 GLU cc_start: 0.8270 (OUTLIER) cc_final: 0.7565 (pp20) REVERT: B 977 LYS cc_start: 0.8068 (ttmt) cc_final: 0.7411 (tttm) REVERT: B 1134 LEU cc_start: 0.6388 (OUTLIER) cc_final: 0.5879 (mt) REVERT: A 582 LYS cc_start: 0.8105 (mttm) cc_final: 0.7790 (mtmm) REVERT: A 817 GLU cc_start: 0.9044 (pt0) cc_final: 0.8591 (pm20) REVERT: A 977 LYS cc_start: 0.7966 (ttmt) cc_final: 0.7297 (tttp) REVERT: A 1134 LEU cc_start: 0.6427 (OUTLIER) cc_final: 0.5929 (mt) outliers start: 25 outliers final: 18 residues processed: 164 average time/residue: 0.2396 time to fit residues: 60.1125 Evaluate side-chains 163 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 142 time to evaluate : 1.724 ------------------------------------------------------------------------------- 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 833 GLU Chi-restraints excluded: chain B residue 890 ILE Chi-restraints excluded: chain B residue 1123 THR Chi-restraints excluded: chain B residue 1134 LEU Chi-restraints excluded: chain A residue 540 GLN Chi-restraints excluded: chain A residue 542 LEU 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 803 VAL 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 79 optimal weight: 3.9990 chunk 114 optimal weight: 0.9980 chunk 137 optimal weight: 0.0070 chunk 2 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 146 optimal weight: 0.9990 chunk 132 optimal weight: 2.9990 chunk 85 optimal weight: 0.8980 overall best weight: 1.1802 ------------------------------------------------------------------------------- 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 = 0.3493 r_free = 0.3493 target = 0.132139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.096733 restraints weight = 16267.242| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 2.12 r_work: 0.2792 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2658 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 0.3285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 12458 Z= 0.117 Angle : 0.497 10.517 16826 Z= 0.250 Chirality : 0.041 0.134 1818 Planarity : 0.003 0.030 2144 Dihedral : 3.767 13.576 1662 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 1.91 % Allowed : 16.72 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.22), residues: 1486 helix: 1.28 (0.22), residues: 636 sheet: -0.27 (0.38), residues: 198 loop : -1.58 (0.22), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 820 HIS 0.007 0.001 HIS B 650 PHE 0.010 0.001 PHE B 710 TYR 0.010 0.001 TYR A 888 ARG 0.003 0.000 ARG B 578 Details of bonding type rmsd hydrogen bonds : bond 0.03487 ( 465) hydrogen bonds : angle 3.95937 ( 1338) covalent geometry : bond 0.00290 (12458) covalent geometry : angle 0.49713 (16826) *********************** 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 170 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 145 time to evaluate : 1.387 Fit side-chains REVERT: B 551 LEU cc_start: 0.8999 (mp) cc_final: 0.8673 (tt) REVERT: B 582 LYS cc_start: 0.8069 (mttm) cc_final: 0.7795 (mtmt) REVERT: B 756 MET cc_start: 0.8275 (OUTLIER) cc_final: 0.7765 (tpt) REVERT: B 817 GLU cc_start: 0.9068 (pt0) cc_final: 0.8610 (pm20) REVERT: B 833 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.7657 (pp20) REVERT: B 977 LYS cc_start: 0.8087 (ttmt) cc_final: 0.7428 (tttm) REVERT: B 1134 LEU cc_start: 0.6439 (OUTLIER) cc_final: 0.5897 (mt) REVERT: A 582 LYS cc_start: 0.8092 (mttm) cc_final: 0.7808 (mtmt) REVERT: A 747 ASP cc_start: 0.9032 (t70) cc_final: 0.8792 (t0) REVERT: A 756 MET cc_start: 0.8195 (OUTLIER) cc_final: 0.7703 (tpt) REVERT: A 817 GLU cc_start: 0.9038 (pt0) cc_final: 0.8585 (pm20) REVERT: A 977 LYS cc_start: 0.7982 (ttmt) cc_final: 0.7295 (tttm) REVERT: A 1134 LEU cc_start: 0.6420 (OUTLIER) cc_final: 0.5868 (mt) outliers start: 25 outliers final: 19 residues processed: 162 average time/residue: 0.2241 time to fit residues: 54.5095 Evaluate side-chains 170 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 146 time to evaluate : 1.425 ------------------------------------------------------------------------------- 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 644 SER Chi-restraints excluded: chain B residue 687 CYS Chi-restraints excluded: chain B residue 756 MET 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 1123 THR Chi-restraints excluded: chain B residue 1134 LEU Chi-restraints excluded: chain A residue 540 GLN Chi-restraints excluded: chain A residue 542 LEU 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 756 MET 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 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 3 optimal weight: 3.9990 chunk 139 optimal weight: 0.9980 chunk 2 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 65 optimal weight: 0.0670 chunk 93 optimal weight: 3.9990 chunk 124 optimal weight: 0.4980 chunk 99 optimal weight: 1.9990 chunk 112 optimal weight: 0.8980 chunk 113 optimal weight: 0.0270 chunk 114 optimal weight: 0.9990 overall best weight: 0.4976 ------------------------------------------------------------------------------- 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 = 0.3535 r_free = 0.3535 target = 0.135569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.100839 restraints weight = 16134.152| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 2.07 r_work: 0.2846 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2712 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.3510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 12458 Z= 0.086 Angle : 0.471 9.189 16826 Z= 0.240 Chirality : 0.040 0.130 1818 Planarity : 0.003 0.026 2144 Dihedral : 3.548 12.789 1662 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.53 % Allowed : 17.25 % Favored : 81.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.23), residues: 1486 helix: 1.47 (0.22), residues: 630 sheet: -0.21 (0.38), residues: 198 loop : -1.46 (0.23), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 820 HIS 0.008 0.001 HIS A 650 PHE 0.009 0.001 PHE A 710 TYR 0.012 0.001 TYR A 966 ARG 0.002 0.000 ARG B 912 Details of bonding type rmsd hydrogen bonds : bond 0.02890 ( 465) hydrogen bonds : angle 3.88999 ( 1338) covalent geometry : bond 0.00196 (12458) covalent geometry : angle 0.47125 (16826) ********************** 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 173 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 153 time to evaluate : 1.362 Fit side-chains REVERT: B 551 LEU cc_start: 0.9000 (mp) cc_final: 0.8690 (tt) REVERT: B 582 LYS cc_start: 0.8049 (mttm) cc_final: 0.7752 (mtmm) REVERT: B 817 GLU cc_start: 0.9068 (pt0) cc_final: 0.8607 (pm20) REVERT: B 977 LYS cc_start: 0.8040 (ttmt) cc_final: 0.7384 (tttm) REVERT: B 1134 LEU cc_start: 0.6454 (OUTLIER) cc_final: 0.5893 (mt) REVERT: A 582 LYS cc_start: 0.8089 (mttm) cc_final: 0.7854 (mttt) REVERT: A 817 GLU cc_start: 0.9026 (pt0) cc_final: 0.8578 (pm20) REVERT: A 977 LYS cc_start: 0.7869 (ttmt) cc_final: 0.7202 (tttm) REVERT: A 1134 LEU cc_start: 0.6461 (OUTLIER) cc_final: 0.5910 (mt) outliers start: 20 outliers final: 17 residues processed: 167 average time/residue: 0.2218 time to fit residues: 55.3029 Evaluate side-chains 167 residues out of total 1310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 148 time to evaluate : 1.346 ------------------------------------------------------------------------------- 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 644 SER Chi-restraints excluded: chain B residue 687 CYS Chi-restraints excluded: chain B residue 731 SER Chi-restraints excluded: chain B residue 833 GLU Chi-restraints excluded: chain B residue 890 ILE Chi-restraints excluded: chain B residue 1134 LEU Chi-restraints excluded: chain A residue 540 GLN Chi-restraints excluded: chain A residue 542 LEU 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 57 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 64 optimal weight: 10.0000 chunk 108 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 chunk 121 optimal weight: 8.9990 chunk 101 optimal weight: 2.9990 chunk 48 optimal weight: 0.0170 chunk 131 optimal weight: 2.9990 chunk 1 optimal weight: 10.0000 chunk 140 optimal weight: 2.9990 overall best weight: 0.7420 ------------------------------------------------------------------------------- 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 = 0.3528 r_free = 0.3528 target = 0.134887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.099843 restraints weight = 16217.892| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 2.11 r_work: 0.2885 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2752 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.3524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 12458 Z= 0.093 Angle : 0.471 9.202 16826 Z= 0.239 Chirality : 0.040 0.132 1818 Planarity : 0.003 0.027 2144 Dihedral : 3.527 12.738 1662 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.83 % Allowed : 16.64 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.23), residues: 1486 helix: 1.48 (0.22), residues: 638 sheet: -0.15 (0.39), residues: 198 loop : -1.48 (0.23), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1189 HIS 0.006 0.001 HIS B 650 PHE 0.010 0.001 PHE B 710 TYR 0.014 0.001 TYR B 966 ARG 0.002 0.000 ARG B 578 Details of bonding type rmsd hydrogen bonds : bond 0.03021 ( 465) hydrogen bonds : angle 3.86924 ( 1338) covalent geometry : bond 0.00223 (12458) covalent geometry : angle 0.47086 (16826) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7073.46 seconds wall clock time: 126 minutes 22.67 seconds (7582.67 seconds total)