Starting phenix.real_space_refine on Fri May 16 03:33:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8kgr_37231/05_2025/8kgr_37231.cif Found real_map, /net/cci-nas-00/data/ceres_data/8kgr_37231/05_2025/8kgr_37231.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8kgr_37231/05_2025/8kgr_37231.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8kgr_37231/05_2025/8kgr_37231.map" model { file = "/net/cci-nas-00/data/ceres_data/8kgr_37231/05_2025/8kgr_37231.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8kgr_37231/05_2025/8kgr_37231.cif" } resolution = 3.2 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= 0.001 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: 6 Type Number sf(0) Gaussians P 65 5.49 5 Mg 2 5.21 5 S 56 5.16 5 C 8745 2.51 5 N 2405 2.21 5 O 2687 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 13960 Number of models: 1 Model: "" Number of chains: 6 Chain: "C" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 658 Classifications: {'DNA': 32} Link IDs: {'rna3p': 31} Chain: "D" Number of atoms: 675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 675 Classifications: {'DNA': 33} Link IDs: {'rna3p': 32} Chain: "A" Number of atoms: 6320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 780, 6320 Classifications: {'peptide': 780} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 749} Chain: "B" Number of atoms: 6305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 778, 6305 Classifications: {'peptide': 778} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 747} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 9.04, per 1000 atoms: 0.65 Number of scatterers: 13960 At special positions: 0 Unit cell: (108.55, 122.2, 128.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 56 16.00 P 65 15.00 Mg 2 11.99 O 2687 8.00 N 2405 7.00 C 8745 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: 3.00 Conformation dependent library (CDL) restraints added in 1.6 seconds 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2928 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 18 sheets defined 51.3% alpha, 10.1% beta 22 base pairs and 48 stacking pairs defined. Time for finding SS restraints: 4.28 Creating SS restraints... Processing helix chain 'A' and resid 440 through 450 Processing helix chain 'A' and resid 496 through 501 Processing helix chain 'A' and resid 502 through 512 Processing helix chain 'A' and resid 541 through 546 Processing helix chain 'A' and resid 546 through 560 Processing helix chain 'A' and resid 560 through 567 removed outlier: 4.057A pdb=" N ILE A 564 " --> pdb=" O TRP A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 602 removed outlier: 3.721A pdb=" N LYS A 602 " --> pdb=" O ALA A 598 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 620 removed outlier: 3.759A pdb=" N ALA A 619 " --> pdb=" O GLY A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 630 removed outlier: 4.414A pdb=" N SER A 627 " --> pdb=" O HIS A 623 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 636 removed outlier: 3.948A pdb=" N VAL A 636 " --> pdb=" O ASP A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 642 through 644 No H-bonds generated for 'chain 'A' and resid 642 through 644' Processing helix chain 'A' and resid 645 through 654 Processing helix chain 'A' and resid 657 through 665 Processing helix chain 'A' and resid 672 through 683 Processing helix chain 'A' and resid 687 through 692 Processing helix chain 'A' and resid 693 through 707 Processing helix chain 'A' and resid 715 through 729 Processing helix chain 'A' and resid 738 through 749 removed outlier: 3.501A pdb=" N MET A 749 " --> pdb=" O VAL A 745 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 765 Processing helix chain 'A' and resid 787 through 791 removed outlier: 3.912A pdb=" N LEU A 790 " --> pdb=" O SER A 787 " (cutoff:3.500A) Processing helix chain 'A' and resid 806 through 814 Processing helix chain 'A' and resid 815 through 819 Processing helix chain 'A' and resid 842 through 846 removed outlier: 3.566A pdb=" N MET A 846 " --> pdb=" O LEU A 843 " (cutoff:3.500A) Processing helix chain 'A' and resid 864 through 877 removed outlier: 3.653A pdb=" N ILE A 868 " --> pdb=" O GLN A 864 " (cutoff:3.500A) Processing helix chain 'A' and resid 883 through 893 Processing helix chain 'A' and resid 942 through 953 removed outlier: 3.787A pdb=" N SER A 953 " --> pdb=" O SER A 949 " (cutoff:3.500A) Processing helix chain 'A' and resid 953 through 958 removed outlier: 3.817A pdb=" N THR A 958 " --> pdb=" O SER A 954 " (cutoff:3.500A) Processing helix chain 'A' and resid 983 through 990 removed outlier: 4.360A pdb=" N VAL A 987 " --> pdb=" O LEU A 983 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N GLU A 988 " --> pdb=" O ASN A 984 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU A 989 " --> pdb=" O ARG A 985 " (cutoff:3.500A) Processing helix chain 'A' and resid 997 through 1003 Processing helix chain 'A' and resid 1027 through 1075 removed outlier: 3.731A pdb=" N ILE A1031 " --> pdb=" O THR A1027 " (cutoff:3.500A) Proline residue: A1037 - end of helix removed outlier: 4.062A pdb=" N ALA A1063 " --> pdb=" O ILE A1059 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE A1064 " --> pdb=" O MET A1060 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N ARG A1066 " --> pdb=" O THR A1062 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N ALA A1072 " --> pdb=" O ILE A1068 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N GLU A1073 " --> pdb=" O ASN A1069 " (cutoff:3.500A) Processing helix chain 'A' and resid 1076 through 1079 removed outlier: 3.507A pdb=" N TYR A1079 " --> pdb=" O LEU A1076 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1076 through 1079' Processing helix chain 'A' and resid 1081 through 1091 Processing helix chain 'A' and resid 1098 through 1104 Processing helix chain 'A' and resid 1109 through 1116 Processing helix chain 'A' and resid 1122 through 1127 Processing helix chain 'A' and resid 1129 through 1133 removed outlier: 3.692A pdb=" N LEU A1133 " --> pdb=" O ALA A1130 " (cutoff:3.500A) Processing helix chain 'A' and resid 1134 through 1159 Processing helix chain 'A' and resid 1168 through 1187 Processing helix chain 'B' and resid 428 through 431 Processing helix chain 'B' and resid 440 through 450 Processing helix chain 'B' and resid 496 through 501 Processing helix chain 'B' and resid 502 through 513 Processing helix chain 'B' and resid 541 through 560 removed outlier: 4.251A pdb=" N ILE B 548 " --> pdb=" O GLY B 544 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N LEU B 549 " --> pdb=" O CYS B 545 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 566 removed outlier: 3.987A pdb=" N ILE B 564 " --> pdb=" O TRP B 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 592 through 603 removed outlier: 3.600A pdb=" N LYS B 602 " --> pdb=" O ALA B 598 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLN B 603 " --> pdb=" O TRP B 599 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 620 removed outlier: 3.615A pdb=" N HIS B 620 " --> pdb=" O LEU B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 621 through 630 Processing helix chain 'B' and resid 632 through 636 removed outlier: 3.944A pdb=" N VAL B 636 " --> pdb=" O ASP B 633 " (cutoff:3.500A) Processing helix chain 'B' and resid 644 through 654 removed outlier: 3.899A pdb=" N LEU B 648 " --> pdb=" O SER B 644 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N PHE B 653 " --> pdb=" O PHE B 649 " (cutoff:3.500A) Processing helix chain 'B' and resid 657 through 664 Processing helix chain 'B' and resid 672 through 683 Processing helix chain 'B' and resid 687 through 692 Processing helix chain 'B' and resid 693 through 707 Processing helix chain 'B' and resid 715 through 729 Processing helix chain 'B' and resid 738 through 749 removed outlier: 3.633A pdb=" N MET B 749 " --> pdb=" O VAL B 745 " (cutoff:3.500A) Processing helix chain 'B' and resid 754 through 767 removed outlier: 3.998A pdb=" N LEU B 758 " --> pdb=" O GLY B 754 " (cutoff:3.500A) Processing helix chain 'B' and resid 806 through 814 Processing helix chain 'B' and resid 815 through 819 Processing helix chain 'B' and resid 842 through 846 Processing helix chain 'B' and resid 864 through 877 removed outlier: 3.616A pdb=" N ILE B 868 " --> pdb=" O GLN B 864 " (cutoff:3.500A) Processing helix chain 'B' and resid 882 through 893 removed outlier: 3.659A pdb=" N LEU B 886 " --> pdb=" O LYS B 882 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 951 Processing helix chain 'B' and resid 953 through 958 removed outlier: 3.514A pdb=" N THR B 958 " --> pdb=" O SER B 954 " (cutoff:3.500A) Processing helix chain 'B' and resid 982 through 990 Processing helix chain 'B' and resid 997 through 1003 Processing helix chain 'B' and resid 1027 through 1075 removed outlier: 3.716A pdb=" N ILE B1031 " --> pdb=" O THR B1027 " (cutoff:3.500A) Proline residue: B1037 - end of helix removed outlier: 4.021A pdb=" N ALA B1063 " --> pdb=" O ILE B1059 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE B1064 " --> pdb=" O MET B1060 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N ARG B1066 " --> pdb=" O THR B1062 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N ALA B1072 " --> pdb=" O ILE B1068 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N GLU B1073 " --> pdb=" O ASN B1069 " (cutoff:3.500A) Processing helix chain 'B' and resid 1076 through 1079 Processing helix chain 'B' and resid 1081 through 1091 Processing helix chain 'B' and resid 1098 through 1103 Processing helix chain 'B' and resid 1109 through 1117 removed outlier: 3.966A pdb=" N LYS B1116 " --> pdb=" O GLU B1112 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ALA B1117 " --> pdb=" O LEU B1113 " (cutoff:3.500A) Processing helix chain 'B' and resid 1122 through 1127 Processing helix chain 'B' and resid 1129 through 1133 removed outlier: 3.500A pdb=" N LEU B1133 " --> pdb=" O ALA B1130 " (cutoff:3.500A) Processing helix chain 'B' and resid 1134 through 1159 Processing helix chain 'B' and resid 1166 through 1187 removed outlier: 3.973A pdb=" N TRP B1170 " --> pdb=" O GLY B1166 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU B1171 " --> pdb=" O ALA B1167 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N THR B1187 " --> pdb=" O LYS B1183 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 465 through 469 removed outlier: 3.789A pdb=" N ILE A 468 " --> pdb=" O LEU A 435 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N LEU A 434 " --> pdb=" O VAL A 535 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N CYS A 537 " --> pdb=" O LEU A 434 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ALA A 436 " --> pdb=" O CYS A 537 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N VAL A 569 " --> pdb=" O PHE A 639 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 481 through 484 Processing sheet with id=AA3, first strand: chain 'A' and resid 588 through 590 Processing sheet with id=AA4, first strand: chain 'A' and resid 736 through 737 Processing sheet with id=AA5, first strand: chain 'A' and resid 824 through 827 removed outlier: 3.667A pdb=" N GLU A 833 " --> pdb=" O VAL A 825 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N GLU A 827 " --> pdb=" O ARG A 831 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N ARG A 831 " --> pdb=" O GLU A 827 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 849 through 852 removed outlier: 3.545A pdb=" N GLY A 849 " --> pdb=" O THR A 860 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 909 through 912 removed outlier: 3.722A pdb=" N HIS A 909 " --> pdb=" O TYR A 920 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N TYR A 917 " --> pdb=" O LEU A1009 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 933 through 934 removed outlier: 3.727A pdb=" N GLU A 962 " --> pdb=" O LYS A 977 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1014 through 1016 Processing sheet with id=AB1, first strand: chain 'B' and resid 465 through 469 removed outlier: 3.710A pdb=" N ILE B 468 " --> pdb=" O LEU B 435 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N LEU B 434 " --> pdb=" O VAL B 535 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N CYS B 537 " --> pdb=" O LEU B 434 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N ALA B 436 " --> pdb=" O CYS B 537 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N VAL B 569 " --> pdb=" O PHE B 639 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 481 through 485 Processing sheet with id=AB3, first strand: chain 'B' and resid 588 through 590 Processing sheet with id=AB4, first strand: chain 'B' and resid 736 through 737 removed outlier: 3.693A pdb=" N ARG B 736 " --> pdb=" O VAL B 803 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 824 through 827 removed outlier: 3.770A pdb=" N GLU B 833 " --> pdb=" O VAL B 825 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N GLU B 827 " --> pdb=" O ARG B 831 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N ARG B 831 " --> pdb=" O GLU B 827 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 849 through 852 removed outlier: 3.652A pdb=" N GLY B 849 " --> pdb=" O THR B 860 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 909 through 913 removed outlier: 3.514A pdb=" N TYR B 916 " --> pdb=" O PHE B 913 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 925 through 926 removed outlier: 4.201A pdb=" N ILE B 932 " --> pdb=" O VAL B 976 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLU B 962 " --> pdb=" O LYS B 977 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 1014 through 1016 557 hydrogen bonds defined for protein. 1575 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 50 hydrogen bonds 100 hydrogen bond angles 0 basepair planarities 22 basepair parallelities 48 stacking parallelities Total time for adding SS restraints: 5.08 Time building geometry restraints manager: 3.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2687 1.33 - 1.45: 3807 1.45 - 1.57: 7703 1.57 - 1.69: 128 1.69 - 1.81: 88 Bond restraints: 14413 Sorted by residual: bond pdb=" N ARG A 734 " pdb=" CA ARG A 734 " ideal model delta sigma weight residual 1.455 1.488 -0.033 1.33e-02 5.65e+03 5.99e+00 bond pdb=" N LYS A 857 " pdb=" CA LYS A 857 " ideal model delta sigma weight residual 1.455 1.483 -0.028 1.25e-02 6.40e+03 5.13e+00 bond pdb=" CA LEU B1036 " pdb=" C LEU B1036 " ideal model delta sigma weight residual 1.522 1.549 -0.027 1.29e-02 6.01e+03 4.36e+00 bond pdb=" CA LEU A1036 " pdb=" C LEU A1036 " ideal model delta sigma weight residual 1.522 1.548 -0.026 1.29e-02 6.01e+03 4.18e+00 bond pdb=" C3' DT C 44 " pdb=" O3' DT C 44 " ideal model delta sigma weight residual 1.422 1.473 -0.051 3.00e-02 1.11e+03 2.86e+00 ... (remaining 14408 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.24: 19531 3.24 - 6.47: 204 6.47 - 9.71: 20 9.71 - 12.95: 2 12.95 - 16.18: 1 Bond angle restraints: 19758 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 121.54 130.55 -9.01 1.91e+00 2.74e-01 2.22e+01 angle pdb=" N LYS A 615 " pdb=" CA LYS A 615 " pdb=" C LYS A 615 " ideal model delta sigma weight residual 108.96 102.34 6.62 1.59e+00 3.96e-01 1.73e+01 angle pdb=" N LEU A1036 " pdb=" CA LEU A1036 " pdb=" C LEU A1036 " ideal model delta sigma weight residual 113.45 119.07 -5.62 1.39e+00 5.18e-01 1.63e+01 angle pdb=" CA TYR A 531 " pdb=" CB TYR A 531 " pdb=" CG TYR A 531 " ideal model delta sigma weight residual 113.90 121.07 -7.17 1.80e+00 3.09e-01 1.59e+01 angle pdb=" N LEU B1036 " pdb=" CA LEU B1036 " pdb=" C LEU B1036 " ideal model delta sigma weight residual 113.45 118.85 -5.40 1.39e+00 5.18e-01 1.51e+01 ... (remaining 19753 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.56: 8079 28.56 - 57.13: 403 57.13 - 85.69: 37 85.69 - 114.25: 0 114.25 - 142.82: 2 Dihedral angle restraints: 8521 sinusoidal: 3953 harmonic: 4568 Sorted by residual: dihedral pdb=" CA THR A1062 " pdb=" C THR A1062 " pdb=" N ALA A1063 " pdb=" CA ALA A1063 " ideal model delta harmonic sigma weight residual 180.00 153.38 26.62 0 5.00e+00 4.00e-02 2.84e+01 dihedral pdb=" CA GLU B 663 " pdb=" C GLU B 663 " pdb=" N LEU B 664 " pdb=" CA LEU B 664 " ideal model delta harmonic sigma weight residual -180.00 -154.84 -25.16 0 5.00e+00 4.00e-02 2.53e+01 dihedral pdb=" CA TYR A 531 " pdb=" C TYR A 531 " pdb=" N GLY A 532 " pdb=" CA GLY A 532 " ideal model delta harmonic sigma weight residual -180.00 -154.84 -25.16 0 5.00e+00 4.00e-02 2.53e+01 ... (remaining 8518 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 1751 0.075 - 0.151: 377 0.151 - 0.226: 30 0.226 - 0.301: 3 0.301 - 0.376: 2 Chirality restraints: 2163 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 0.38 2.00e-01 2.50e+01 3.54e+00 chirality pdb=" CB ILE B 963 " pdb=" CA ILE B 963 " pdb=" CG1 ILE B 963 " pdb=" CG2 ILE B 963 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.32 2.00e-01 2.50e+01 2.49e+00 chirality pdb=" CB ILE B 534 " pdb=" CA ILE B 534 " pdb=" CG1 ILE B 534 " pdb=" CG2 ILE B 534 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 2.00e+00 ... (remaining 2160 not shown) Planarity restraints: 2290 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B1170 " -0.026 2.00e-02 2.50e+03 2.67e-02 1.78e+01 pdb=" CG TRP B1170 " 0.071 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 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP B1170 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP B1170 " -0.008 2.00e-02 2.50e+03 pdb=" CZ2 TRP B1170 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B1170 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP B1170 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A1170 " 0.025 2.00e-02 2.50e+03 2.62e-02 1.72e+01 pdb=" CG TRP A1170 " -0.069 2.00e-02 2.50e+03 pdb=" CD1 TRP A1170 " 0.037 2.00e-02 2.50e+03 pdb=" CD2 TRP A1170 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP A1170 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A1170 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A1170 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP A1170 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A1170 " 0.010 2.00e-02 2.50e+03 pdb=" CH2 TRP A1170 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 531 " 0.037 2.00e-02 2.50e+03 2.57e-02 1.32e+01 pdb=" CG TYR A 531 " -0.061 2.00e-02 2.50e+03 pdb=" CD1 TYR A 531 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR A 531 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR A 531 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR A 531 " 0.008 2.00e-02 2.50e+03 pdb=" CZ TYR A 531 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR A 531 " 0.007 2.00e-02 2.50e+03 ... (remaining 2287 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.57: 68 2.57 - 3.15: 10090 3.15 - 3.73: 20881 3.73 - 4.32: 30185 4.32 - 4.90: 49790 Nonbonded interactions: 111014 Sorted by model distance: nonbonded pdb=" OD2 ASP A 539 " pdb="MG MG A1301 " model vdw 1.983 2.170 nonbonded pdb=" OD2 ASP B 539 " pdb="MG MG B1301 " model vdw 2.091 2.170 nonbonded pdb=" OP1 DA C 31 " pdb=" OH TYR A 800 " model vdw 2.197 3.040 nonbonded pdb=" OG SER A 919 " pdb=" OD1 ASN A1007 " model vdw 2.248 3.040 nonbonded pdb=" OH TYR A1043 " pdb=" OE1 GLU A1173 " model vdw 2.251 3.040 ... (remaining 111009 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 415 through 1192 or resid 1301)) 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: 12.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.530 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 34.690 Find NCS groups from input model: 0.480 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: 0.000 Load rotamer database and sin/cos tables:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 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 : 0.008 0.071 14413 Z= 0.342 Angle : 0.954 16.181 19758 Z= 0.522 Chirality : 0.060 0.376 2163 Planarity : 0.007 0.077 2290 Dihedral : 15.372 142.818 5593 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 0.07 % Allowed : 3.59 % Favored : 96.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.81 (0.17), residues: 1554 helix: -2.44 (0.15), residues: 684 sheet: -2.50 (0.34), residues: 201 loop : -2.47 (0.20), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.071 0.005 TRP B1170 HIS 0.014 0.003 HIS B 892 PHE 0.026 0.003 PHE B 739 TYR 0.061 0.003 TYR A 531 ARG 0.017 0.002 ARG B1039 Details of bonding type rmsd hydrogen bonds : bond 0.17193 ( 607) hydrogen bonds : angle 7.18625 ( 1675) covalent geometry : bond 0.00809 (14413) covalent geometry : angle 0.95379 (19758) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 233 time to evaluate : 1.494 Fit side-chains revert: symmetry clash REVERT: A 455 SER cc_start: 0.8007 (t) cc_final: 0.7794 (t) REVERT: A 461 SER cc_start: 0.8536 (p) cc_final: 0.8323 (t) REVERT: A 474 ILE cc_start: 0.8775 (mm) cc_final: 0.8562 (mt) REVERT: A 749 MET cc_start: 0.8213 (mmp) cc_final: 0.7565 (mmt) REVERT: A 905 ASN cc_start: 0.8518 (t0) cc_final: 0.8241 (t0) REVERT: B 543 ASP cc_start: 0.8270 (t70) cc_final: 0.7921 (m-30) REVERT: B 854 GLU cc_start: 0.8298 (mm-30) cc_final: 0.8080 (mm-30) outliers start: 1 outliers final: 0 residues processed: 234 average time/residue: 0.3219 time to fit residues: 103.4221 Evaluate side-chains 111 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 1.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 135 optimal weight: 5.9990 chunk 122 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 41 optimal weight: 0.5980 chunk 82 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 126 optimal weight: 0.8980 chunk 48 optimal weight: 5.9990 chunk 76 optimal weight: 0.7980 chunk 93 optimal weight: 0.9990 chunk 146 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 566 HIS A 880 ASN A1051 HIS A1078 HIS ** B 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 502 ASN B 566 HIS B 692 GLN B 892 HIS B 905 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.139666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.114739 restraints weight = 20629.034| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 1.72 r_work: 0.3266 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 14413 Z= 0.131 Angle : 0.567 15.359 19758 Z= 0.308 Chirality : 0.041 0.150 2163 Planarity : 0.005 0.055 2290 Dihedral : 17.641 145.751 2480 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.98 % Allowed : 7.61 % Favored : 90.41 % 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: -2.00 (0.20), residues: 1554 helix: -0.48 (0.19), residues: 675 sheet: -2.15 (0.34), residues: 215 loop : -1.84 (0.22), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B1170 HIS 0.010 0.001 HIS A1078 PHE 0.014 0.001 PHE B 959 TYR 0.025 0.001 TYR A 531 ARG 0.003 0.000 ARG B1046 Details of bonding type rmsd hydrogen bonds : bond 0.05073 ( 607) hydrogen bonds : angle 4.93469 ( 1675) covalent geometry : bond 0.00284 (14413) covalent geometry : angle 0.56746 (19758) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 145 time to evaluate : 1.605 Fit side-chains revert: symmetry clash REVERT: A 474 ILE cc_start: 0.8776 (mm) cc_final: 0.8547 (mt) REVERT: A 531 TYR cc_start: 0.7743 (OUTLIER) cc_final: 0.7324 (p90) REVERT: A 778 VAL cc_start: 0.8731 (t) cc_final: 0.8468 (m) REVERT: B 636 VAL cc_start: 0.8344 (OUTLIER) cc_final: 0.8107 (t) REVERT: B 676 THR cc_start: 0.8704 (m) cc_final: 0.8431 (p) REVERT: B 716 ARG cc_start: 0.8194 (tpp80) cc_final: 0.7957 (mtt180) REVERT: B 736 ARG cc_start: 0.8414 (mpt180) cc_final: 0.8102 (mpt180) REVERT: B 854 GLU cc_start: 0.8740 (mm-30) cc_final: 0.8521 (mm-30) REVERT: B 882 LYS cc_start: 0.7829 (mttt) cc_final: 0.7444 (mtpp) REVERT: B 886 LEU cc_start: 0.8211 (OUTLIER) cc_final: 0.7947 (tm) outliers start: 27 outliers final: 9 residues processed: 165 average time/residue: 0.3480 time to fit residues: 83.8816 Evaluate side-chains 123 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 111 time to evaluate : 1.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 483 ASN Chi-restraints excluded: chain A residue 531 TYR Chi-restraints excluded: chain A residue 539 ASP Chi-restraints excluded: chain A residue 543 ASP Chi-restraints excluded: chain A residue 640 THR Chi-restraints excluded: chain B residue 633 ASP Chi-restraints excluded: chain B residue 636 VAL Chi-restraints excluded: chain B residue 803 VAL Chi-restraints excluded: chain B residue 886 LEU Chi-restraints excluded: chain B residue 895 THR Chi-restraints excluded: chain B residue 949 SER Chi-restraints excluded: chain B residue 1143 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 90 optimal weight: 0.4980 chunk 3 optimal weight: 6.9990 chunk 31 optimal weight: 3.9990 chunk 125 optimal weight: 3.9990 chunk 93 optimal weight: 0.8980 chunk 151 optimal weight: 7.9990 chunk 141 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 159 optimal weight: 0.0040 chunk 47 optimal weight: 0.6980 chunk 138 optimal weight: 0.8980 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 557 HIS A 892 HIS A1149 GLN ** B 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 864 GLN B 892 HIS B 905 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.140365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.115500 restraints weight = 20640.744| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 1.68 r_work: 0.3289 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 14413 Z= 0.113 Angle : 0.507 14.885 19758 Z= 0.275 Chirality : 0.039 0.140 2163 Planarity : 0.004 0.047 2290 Dihedral : 17.379 144.958 2480 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.90 % Allowed : 10.61 % Favored : 87.48 % 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 (0.21), residues: 1554 helix: 0.44 (0.20), residues: 689 sheet: -2.04 (0.34), residues: 223 loop : -1.32 (0.23), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B1170 HIS 0.006 0.001 HIS A 892 PHE 0.010 0.001 PHE B 739 TYR 0.018 0.001 TYR A 531 ARG 0.003 0.000 ARG A 831 Details of bonding type rmsd hydrogen bonds : bond 0.04333 ( 607) hydrogen bonds : angle 4.41558 ( 1675) covalent geometry : bond 0.00239 (14413) covalent geometry : angle 0.50728 (19758) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 131 time to evaluate : 1.546 Fit side-chains revert: symmetry clash REVERT: A 474 ILE cc_start: 0.8710 (mm) cc_final: 0.8455 (mt) REVERT: A 531 TYR cc_start: 0.7709 (OUTLIER) cc_final: 0.7150 (p90) REVERT: A 778 VAL cc_start: 0.8739 (t) cc_final: 0.8465 (m) REVERT: A 957 MET cc_start: 0.8175 (mmp) cc_final: 0.7920 (mmt) REVERT: B 676 THR cc_start: 0.8775 (m) cc_final: 0.8504 (p) REVERT: B 749 MET cc_start: 0.8752 (mmp) cc_final: 0.8475 (mmp) REVERT: B 882 LYS cc_start: 0.7764 (mttt) cc_final: 0.7349 (mtpp) REVERT: B 886 LEU cc_start: 0.8204 (OUTLIER) cc_final: 0.7999 (tm) REVERT: B 957 MET cc_start: 0.7645 (mmm) cc_final: 0.7395 (mmm) outliers start: 26 outliers final: 11 residues processed: 151 average time/residue: 0.2834 time to fit residues: 62.3443 Evaluate side-chains 128 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 115 time to evaluate : 1.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 483 ASN Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 531 TYR Chi-restraints excluded: chain A residue 539 ASP Chi-restraints excluded: chain A residue 543 ASP Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 640 THR Chi-restraints excluded: chain A residue 644 SER Chi-restraints excluded: chain A residue 801 ILE Chi-restraints excluded: chain B residue 610 THR Chi-restraints excluded: chain B residue 636 VAL Chi-restraints excluded: chain B residue 886 LEU Chi-restraints excluded: chain B residue 1143 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 50 optimal weight: 2.9990 chunk 105 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 60 optimal weight: 4.9990 chunk 25 optimal weight: 6.9990 chunk 101 optimal weight: 4.9990 chunk 142 optimal weight: 0.5980 chunk 158 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 chunk 11 optimal weight: 0.5980 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 892 HIS ** B 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1099 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.136218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.111194 restraints weight = 20644.842| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 1.67 r_work: 0.3219 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.2223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 14413 Z= 0.166 Angle : 0.557 14.527 19758 Z= 0.302 Chirality : 0.041 0.141 2163 Planarity : 0.004 0.043 2290 Dihedral : 17.487 145.671 2480 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.78 % Allowed : 10.40 % Favored : 86.82 % 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: -0.68 (0.21), residues: 1554 helix: 0.81 (0.21), residues: 682 sheet: -1.81 (0.36), residues: 210 loop : -1.26 (0.23), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B1170 HIS 0.007 0.001 HIS B 789 PHE 0.017 0.002 PHE B 739 TYR 0.027 0.002 TYR A 531 ARG 0.005 0.001 ARG A 985 Details of bonding type rmsd hydrogen bonds : bond 0.04953 ( 607) hydrogen bonds : angle 4.44245 ( 1675) covalent geometry : bond 0.00386 (14413) covalent geometry : angle 0.55716 (19758) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 118 time to evaluate : 1.473 Fit side-chains REVERT: A 474 ILE cc_start: 0.8752 (mm) cc_final: 0.8516 (mt) REVERT: A 531 TYR cc_start: 0.7847 (OUTLIER) cc_final: 0.7002 (p90) REVERT: A 778 VAL cc_start: 0.8853 (t) cc_final: 0.8609 (m) REVERT: A 833 GLU cc_start: 0.8729 (OUTLIER) cc_final: 0.7969 (pm20) REVERT: A 892 HIS cc_start: 0.5642 (m170) cc_final: 0.5312 (m170) REVERT: A 1080 GLU cc_start: 0.7737 (OUTLIER) cc_final: 0.6995 (tm-30) REVERT: B 676 THR cc_start: 0.8854 (m) cc_final: 0.8551 (p) REVERT: B 882 LYS cc_start: 0.7848 (mttt) cc_final: 0.7418 (mtpp) REVERT: B 957 MET cc_start: 0.7855 (mmm) cc_final: 0.7606 (mmm) REVERT: B 1143 GLU cc_start: 0.8329 (OUTLIER) cc_final: 0.7839 (mp0) outliers start: 38 outliers final: 23 residues processed: 150 average time/residue: 0.2777 time to fit residues: 61.1414 Evaluate side-chains 134 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 107 time to evaluate : 1.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 483 ASN Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 531 TYR Chi-restraints excluded: chain A residue 539 ASP Chi-restraints excluded: chain A residue 543 ASP Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 640 THR Chi-restraints excluded: chain A residue 644 SER Chi-restraints excluded: chain A residue 801 ILE Chi-restraints excluded: chain A residue 833 GLU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 1024 GLU Chi-restraints excluded: chain A residue 1074 LEU Chi-restraints excluded: chain A residue 1080 GLU Chi-restraints excluded: chain A residue 1125 ILE Chi-restraints excluded: chain B residue 433 MET Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 610 THR Chi-restraints excluded: chain B residue 630 LYS Chi-restraints excluded: chain B residue 636 VAL Chi-restraints excluded: chain B residue 778 VAL Chi-restraints excluded: chain B residue 803 VAL Chi-restraints excluded: chain B residue 895 THR Chi-restraints excluded: chain B residue 949 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1062 THR Chi-restraints excluded: chain B residue 1143 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 27 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 122 optimal weight: 0.9980 chunk 100 optimal weight: 4.9990 chunk 102 optimal weight: 0.8980 chunk 30 optimal weight: 0.4980 chunk 123 optimal weight: 0.7980 chunk 25 optimal weight: 0.0010 chunk 15 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 overall best weight: 0.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 892 HIS ** B 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.139168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.114705 restraints weight = 20790.821| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 1.67 r_work: 0.3270 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3157 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 14413 Z= 0.111 Angle : 0.497 14.128 19758 Z= 0.270 Chirality : 0.039 0.138 2163 Planarity : 0.004 0.039 2290 Dihedral : 17.302 145.327 2480 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.05 % Allowed : 11.05 % Favored : 86.90 % 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: 1554 helix: 1.14 (0.21), residues: 677 sheet: -1.73 (0.35), residues: 223 loop : -1.06 (0.23), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A1170 HIS 0.004 0.001 HIS B 789 PHE 0.019 0.001 PHE B 959 TYR 0.016 0.001 TYR A 888 ARG 0.003 0.000 ARG A 571 Details of bonding type rmsd hydrogen bonds : bond 0.04193 ( 607) hydrogen bonds : angle 4.24063 ( 1675) covalent geometry : bond 0.00239 (14413) covalent geometry : angle 0.49654 (19758) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 120 time to evaluate : 1.420 Fit side-chains REVERT: A 474 ILE cc_start: 0.8713 (mm) cc_final: 0.8476 (mt) REVERT: A 531 TYR cc_start: 0.7751 (OUTLIER) cc_final: 0.6962 (p90) REVERT: A 634 ASN cc_start: 0.8640 (t0) cc_final: 0.8423 (m-40) REVERT: A 778 VAL cc_start: 0.8816 (t) cc_final: 0.8556 (m) REVERT: A 1080 GLU cc_start: 0.7686 (OUTLIER) cc_final: 0.6977 (tm-30) REVERT: B 636 VAL cc_start: 0.8477 (OUTLIER) cc_final: 0.8221 (t) REVERT: B 676 THR cc_start: 0.8824 (m) cc_final: 0.8574 (p) REVERT: B 749 MET cc_start: 0.8763 (mmp) cc_final: 0.8298 (mmt) REVERT: B 882 LYS cc_start: 0.7696 (mttt) cc_final: 0.7273 (mtpp) REVERT: B 957 MET cc_start: 0.7797 (mmm) cc_final: 0.7490 (mmm) REVERT: B 1074 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8594 (tt) REVERT: B 1079 TYR cc_start: 0.8108 (m-80) cc_final: 0.7404 (m-80) REVERT: B 1143 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.7828 (mp0) outliers start: 28 outliers final: 15 residues processed: 142 average time/residue: 0.2489 time to fit residues: 52.9777 Evaluate side-chains 126 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 106 time to evaluate : 1.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 483 ASN Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 531 TYR Chi-restraints excluded: chain A residue 539 ASP Chi-restraints excluded: chain A residue 543 ASP Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 801 ILE Chi-restraints excluded: chain A residue 1080 GLU Chi-restraints excluded: chain B residue 433 MET Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 610 THR Chi-restraints excluded: chain B residue 636 VAL Chi-restraints excluded: chain B residue 803 VAL Chi-restraints excluded: chain B residue 895 THR Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 983 LEU Chi-restraints excluded: chain B residue 1062 THR Chi-restraints excluded: chain B residue 1074 LEU Chi-restraints excluded: chain B residue 1143 GLU Chi-restraints excluded: chain B residue 1158 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 84 optimal weight: 2.9990 chunk 153 optimal weight: 0.0770 chunk 146 optimal weight: 0.8980 chunk 76 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 160 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 99 optimal weight: 6.9990 chunk 159 optimal weight: 0.9990 chunk 7 optimal weight: 0.0030 chunk 71 optimal weight: 2.9990 overall best weight: 0.5952 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 928 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.139723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.115290 restraints weight = 20984.775| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 1.68 r_work: 0.3286 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3173 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.2692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 14413 Z= 0.108 Angle : 0.493 14.147 19758 Z= 0.265 Chirality : 0.039 0.140 2163 Planarity : 0.003 0.039 2290 Dihedral : 17.139 144.443 2480 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.05 % Allowed : 11.35 % Favored : 86.60 % 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: -0.05 (0.22), residues: 1554 helix: 1.38 (0.21), residues: 677 sheet: -1.59 (0.35), residues: 223 loop : -0.92 (0.23), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A1170 HIS 0.003 0.001 HIS B 789 PHE 0.020 0.001 PHE B 959 TYR 0.015 0.001 TYR A 531 ARG 0.003 0.000 ARG B 662 Details of bonding type rmsd hydrogen bonds : bond 0.03959 ( 607) hydrogen bonds : angle 4.10690 ( 1675) covalent geometry : bond 0.00233 (14413) covalent geometry : angle 0.49287 (19758) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 133 time to evaluate : 1.554 Fit side-chains REVERT: A 474 ILE cc_start: 0.8732 (mm) cc_final: 0.8493 (mt) REVERT: A 531 TYR cc_start: 0.7787 (OUTLIER) cc_final: 0.6894 (p90) REVERT: A 778 VAL cc_start: 0.8823 (t) cc_final: 0.8553 (m) REVERT: A 1080 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.7015 (tm-30) REVERT: B 454 LYS cc_start: 0.7582 (mmtm) cc_final: 0.6666 (ttpp) REVERT: B 636 VAL cc_start: 0.8480 (OUTLIER) cc_final: 0.8228 (t) REVERT: B 676 THR cc_start: 0.8786 (m) cc_final: 0.8562 (p) REVERT: B 882 LYS cc_start: 0.7689 (mttt) cc_final: 0.7264 (mtpp) REVERT: B 957 MET cc_start: 0.7795 (mmm) cc_final: 0.7422 (mmm) REVERT: B 1074 LEU cc_start: 0.8823 (OUTLIER) cc_final: 0.8574 (tt) REVERT: B 1079 TYR cc_start: 0.8114 (m-80) cc_final: 0.7424 (m-80) REVERT: B 1143 GLU cc_start: 0.8318 (OUTLIER) cc_final: 0.7842 (mp0) outliers start: 28 outliers final: 17 residues processed: 153 average time/residue: 0.2736 time to fit residues: 61.5218 Evaluate side-chains 135 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 113 time to evaluate : 1.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 483 ASN Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 531 TYR Chi-restraints excluded: chain A residue 539 ASP Chi-restraints excluded: chain A residue 543 ASP Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 640 THR Chi-restraints excluded: chain A residue 801 ILE Chi-restraints excluded: chain A residue 1080 GLU Chi-restraints excluded: chain A residue 1125 ILE Chi-restraints excluded: chain B residue 433 MET Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 610 THR Chi-restraints excluded: chain B residue 633 ASP Chi-restraints excluded: chain B residue 636 VAL Chi-restraints excluded: chain B residue 803 VAL Chi-restraints excluded: chain B residue 895 THR Chi-restraints excluded: chain B residue 949 SER Chi-restraints excluded: chain B residue 1062 THR Chi-restraints excluded: chain B residue 1074 LEU Chi-restraints excluded: chain B residue 1143 GLU Chi-restraints excluded: chain B residue 1158 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 41 optimal weight: 0.3980 chunk 130 optimal weight: 0.8980 chunk 123 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 93 optimal weight: 3.9990 chunk 116 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 106 optimal weight: 0.9990 chunk 62 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 892 HIS B 483 ASN B 692 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.139110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.114287 restraints weight = 20931.706| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 1.70 r_work: 0.3268 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3156 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.2726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 14413 Z= 0.119 Angle : 0.501 13.777 19758 Z= 0.271 Chirality : 0.039 0.145 2163 Planarity : 0.004 0.038 2290 Dihedral : 17.162 144.783 2480 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.49 % Allowed : 11.57 % Favored : 85.94 % 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: 0.05 (0.22), residues: 1554 helix: 1.44 (0.21), residues: 683 sheet: -1.50 (0.35), residues: 237 loop : -0.84 (0.24), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1170 HIS 0.004 0.001 HIS B 789 PHE 0.018 0.001 PHE B 959 TYR 0.027 0.001 TYR B 966 ARG 0.008 0.000 ARG A 530 Details of bonding type rmsd hydrogen bonds : bond 0.04100 ( 607) hydrogen bonds : angle 4.11134 ( 1675) covalent geometry : bond 0.00265 (14413) covalent geometry : angle 0.50116 (19758) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 125 time to evaluate : 1.455 Fit side-chains REVERT: A 474 ILE cc_start: 0.8755 (mm) cc_final: 0.8518 (mt) REVERT: A 531 TYR cc_start: 0.7781 (OUTLIER) cc_final: 0.6784 (p90) REVERT: A 778 VAL cc_start: 0.8841 (t) cc_final: 0.8570 (m) REVERT: A 833 GLU cc_start: 0.8714 (OUTLIER) cc_final: 0.7961 (pm20) REVERT: A 1080 GLU cc_start: 0.7773 (OUTLIER) cc_final: 0.7006 (tm-30) REVERT: B 454 LYS cc_start: 0.7583 (mmtm) cc_final: 0.6668 (ttpp) REVERT: B 636 VAL cc_start: 0.8510 (OUTLIER) cc_final: 0.8230 (t) REVERT: B 882 LYS cc_start: 0.7766 (mttt) cc_final: 0.7346 (mtpp) REVERT: B 957 MET cc_start: 0.7862 (mmm) cc_final: 0.7485 (mmm) REVERT: B 1074 LEU cc_start: 0.8835 (OUTLIER) cc_final: 0.8592 (tt) REVERT: B 1079 TYR cc_start: 0.8123 (m-80) cc_final: 0.7424 (m-80) REVERT: B 1143 GLU cc_start: 0.8284 (OUTLIER) cc_final: 0.7822 (mp0) outliers start: 34 outliers final: 22 residues processed: 151 average time/residue: 0.2589 time to fit residues: 58.2227 Evaluate side-chains 145 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 117 time to evaluate : 1.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 483 ASN Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 531 TYR Chi-restraints excluded: chain A residue 539 ASP Chi-restraints excluded: chain A residue 543 ASP Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 640 THR Chi-restraints excluded: chain A residue 644 SER Chi-restraints excluded: chain A residue 801 ILE Chi-restraints excluded: chain A residue 833 GLU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 1024 GLU Chi-restraints excluded: chain A residue 1080 GLU Chi-restraints excluded: chain A residue 1125 ILE Chi-restraints excluded: chain B residue 433 MET Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 610 THR Chi-restraints excluded: chain B residue 630 LYS Chi-restraints excluded: chain B residue 633 ASP Chi-restraints excluded: chain B residue 636 VAL Chi-restraints excluded: chain B residue 803 VAL Chi-restraints excluded: chain B residue 895 THR Chi-restraints excluded: chain B residue 949 SER Chi-restraints excluded: chain B residue 983 LEU Chi-restraints excluded: chain B residue 1062 THR Chi-restraints excluded: chain B residue 1074 LEU Chi-restraints excluded: chain B residue 1143 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 128 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 37 optimal weight: 0.7980 chunk 153 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 100 optimal weight: 6.9990 chunk 141 optimal weight: 6.9990 chunk 48 optimal weight: 0.3980 chunk 77 optimal weight: 4.9990 chunk 27 optimal weight: 0.3980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 892 HIS A1078 HIS B 892 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.138328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.113598 restraints weight = 20771.675| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 1.67 r_work: 0.3257 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.2762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 14413 Z= 0.125 Angle : 0.511 12.401 19758 Z= 0.276 Chirality : 0.040 0.179 2163 Planarity : 0.004 0.038 2290 Dihedral : 17.182 144.951 2480 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.49 % Allowed : 11.79 % Favored : 85.72 % 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: 0.11 (0.22), residues: 1554 helix: 1.44 (0.21), residues: 684 sheet: -1.42 (0.35), residues: 237 loop : -0.77 (0.24), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 820 HIS 0.005 0.001 HIS B 789 PHE 0.022 0.001 PHE B 959 TYR 0.018 0.001 TYR A 531 ARG 0.007 0.000 ARG A 530 Details of bonding type rmsd hydrogen bonds : bond 0.04191 ( 607) hydrogen bonds : angle 4.17010 ( 1675) covalent geometry : bond 0.00282 (14413) covalent geometry : angle 0.51144 (19758) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 120 time to evaluate : 1.513 Fit side-chains REVERT: A 474 ILE cc_start: 0.8758 (mm) cc_final: 0.8529 (mt) REVERT: A 531 TYR cc_start: 0.7798 (OUTLIER) cc_final: 0.6839 (p90) REVERT: A 778 VAL cc_start: 0.8858 (t) cc_final: 0.8585 (m) REVERT: A 833 GLU cc_start: 0.8745 (OUTLIER) cc_final: 0.7993 (pm20) REVERT: A 892 HIS cc_start: 0.5858 (m90) cc_final: 0.5382 (m170) REVERT: A 1080 GLU cc_start: 0.7790 (OUTLIER) cc_final: 0.7030 (tm-30) REVERT: B 454 LYS cc_start: 0.7567 (mmtm) cc_final: 0.6629 (ttpp) REVERT: B 636 VAL cc_start: 0.8523 (OUTLIER) cc_final: 0.8248 (t) REVERT: B 882 LYS cc_start: 0.7770 (mttt) cc_final: 0.7344 (mtpp) REVERT: B 957 MET cc_start: 0.7837 (mmm) cc_final: 0.7468 (mmm) REVERT: B 1074 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8586 (tt) REVERT: B 1079 TYR cc_start: 0.8149 (m-80) cc_final: 0.7419 (m-80) REVERT: B 1143 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.7842 (mp0) outliers start: 34 outliers final: 25 residues processed: 145 average time/residue: 0.2655 time to fit residues: 56.9733 Evaluate side-chains 146 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 115 time to evaluate : 1.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 483 ASN Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 531 TYR Chi-restraints excluded: chain A residue 539 ASP Chi-restraints excluded: chain A residue 543 ASP Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 640 THR Chi-restraints excluded: chain A residue 644 SER Chi-restraints excluded: chain A residue 801 ILE Chi-restraints excluded: chain A residue 833 GLU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 1024 GLU Chi-restraints excluded: chain A residue 1080 GLU Chi-restraints excluded: chain A residue 1125 ILE Chi-restraints excluded: chain B residue 433 MET Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 610 THR Chi-restraints excluded: chain B residue 630 LYS Chi-restraints excluded: chain B residue 636 VAL Chi-restraints excluded: chain B residue 803 VAL Chi-restraints excluded: chain B residue 895 THR Chi-restraints excluded: chain B residue 949 SER Chi-restraints excluded: chain B residue 983 LEU Chi-restraints excluded: chain B residue 1048 MET Chi-restraints excluded: chain B residue 1062 THR Chi-restraints excluded: chain B residue 1074 LEU Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1143 GLU Chi-restraints excluded: chain B residue 1179 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 149 optimal weight: 0.7980 chunk 88 optimal weight: 4.9990 chunk 113 optimal weight: 2.9990 chunk 117 optimal weight: 0.0980 chunk 115 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 132 optimal weight: 1.9990 chunk 131 optimal weight: 4.9990 chunk 83 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 122 optimal weight: 0.5980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 892 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.137465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.112759 restraints weight = 20722.124| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 1.64 r_work: 0.3248 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3135 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.2728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 14413 Z= 0.138 Angle : 0.526 12.495 19758 Z= 0.284 Chirality : 0.040 0.177 2163 Planarity : 0.004 0.038 2290 Dihedral : 17.242 145.062 2480 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.49 % Allowed : 11.64 % Favored : 85.87 % 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: 0.08 (0.22), residues: 1554 helix: 1.37 (0.21), residues: 690 sheet: -1.37 (0.35), residues: 237 loop : -0.79 (0.24), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 820 HIS 0.005 0.001 HIS B 789 PHE 0.021 0.001 PHE B 959 TYR 0.024 0.001 TYR B 966 ARG 0.006 0.000 ARG A 530 Details of bonding type rmsd hydrogen bonds : bond 0.04415 ( 607) hydrogen bonds : angle 4.21957 ( 1675) covalent geometry : bond 0.00315 (14413) covalent geometry : angle 0.52586 (19758) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 114 time to evaluate : 1.438 Fit side-chains REVERT: A 474 ILE cc_start: 0.8762 (mm) cc_final: 0.8534 (mt) REVERT: A 531 TYR cc_start: 0.7866 (OUTLIER) cc_final: 0.6853 (p90) REVERT: A 778 VAL cc_start: 0.8864 (t) cc_final: 0.8605 (m) REVERT: A 833 GLU cc_start: 0.8765 (OUTLIER) cc_final: 0.8005 (pm20) REVERT: A 1080 GLU cc_start: 0.7824 (OUTLIER) cc_final: 0.7056 (tm-30) REVERT: B 454 LYS cc_start: 0.7619 (mmtm) cc_final: 0.6646 (ttpp) REVERT: B 636 VAL cc_start: 0.8526 (OUTLIER) cc_final: 0.8246 (t) REVERT: B 882 LYS cc_start: 0.7816 (mttt) cc_final: 0.7386 (mtpp) REVERT: B 1143 GLU cc_start: 0.8303 (OUTLIER) cc_final: 0.7812 (mp0) outliers start: 34 outliers final: 26 residues processed: 139 average time/residue: 0.2633 time to fit residues: 54.2242 Evaluate side-chains 143 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 112 time to evaluate : 1.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 483 ASN Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 531 TYR Chi-restraints excluded: chain A residue 539 ASP Chi-restraints excluded: chain A residue 543 ASP Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 640 THR Chi-restraints excluded: chain A residue 644 SER Chi-restraints excluded: chain A residue 801 ILE Chi-restraints excluded: chain A residue 830 GLN Chi-restraints excluded: chain A residue 833 GLU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 960 ILE Chi-restraints excluded: chain A residue 1024 GLU Chi-restraints excluded: chain A residue 1080 GLU Chi-restraints excluded: chain A residue 1125 ILE Chi-restraints excluded: chain B residue 433 MET Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 610 THR Chi-restraints excluded: chain B residue 630 LYS Chi-restraints excluded: chain B residue 636 VAL Chi-restraints excluded: chain B residue 803 VAL Chi-restraints excluded: chain B residue 895 THR Chi-restraints excluded: chain B residue 949 SER Chi-restraints excluded: chain B residue 983 LEU Chi-restraints excluded: chain B residue 1062 THR Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1143 GLU Chi-restraints excluded: chain B residue 1179 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 78 optimal weight: 0.7980 chunk 74 optimal weight: 0.7980 chunk 31 optimal weight: 0.0370 chunk 144 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 63 optimal weight: 0.0570 chunk 36 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 145 optimal weight: 0.9990 chunk 152 optimal weight: 4.9990 overall best weight: 0.4776 ------------------------------------------------------------------------------- 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 = 0.3776 r_free = 0.3776 target = 0.140751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.116317 restraints weight = 20792.271| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 1.67 r_work: 0.3301 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3189 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.2936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 14413 Z= 0.105 Angle : 0.493 12.337 19758 Z= 0.265 Chirality : 0.039 0.182 2163 Planarity : 0.003 0.039 2290 Dihedral : 17.085 144.582 2480 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.90 % Allowed : 12.30 % Favored : 85.80 % 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: 1554 helix: 1.47 (0.21), residues: 692 sheet: -1.30 (0.36), residues: 237 loop : -0.69 (0.24), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1170 HIS 0.004 0.001 HIS B 909 PHE 0.019 0.001 PHE B 959 TYR 0.015 0.001 TYR A1079 ARG 0.009 0.000 ARG A 985 Details of bonding type rmsd hydrogen bonds : bond 0.03836 ( 607) hydrogen bonds : angle 4.10139 ( 1675) covalent geometry : bond 0.00223 (14413) covalent geometry : angle 0.49273 (19758) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 135 time to evaluate : 1.458 Fit side-chains REVERT: A 474 ILE cc_start: 0.8725 (mm) cc_final: 0.8492 (mt) REVERT: A 531 TYR cc_start: 0.7748 (OUTLIER) cc_final: 0.6715 (p90) REVERT: A 778 VAL cc_start: 0.8857 (t) cc_final: 0.8563 (m) REVERT: A 1080 GLU cc_start: 0.7807 (OUTLIER) cc_final: 0.7062 (tm-30) REVERT: B 454 LYS cc_start: 0.7541 (mmtm) cc_final: 0.6626 (ttpp) REVERT: B 636 VAL cc_start: 0.8481 (OUTLIER) cc_final: 0.8233 (t) REVERT: B 882 LYS cc_start: 0.7687 (mttt) cc_final: 0.7261 (mtpp) REVERT: B 975 LEU cc_start: 0.9130 (tt) cc_final: 0.8912 (mp) REVERT: B 1079 TYR cc_start: 0.8061 (m-80) cc_final: 0.7573 (m-80) REVERT: B 1143 GLU cc_start: 0.8300 (OUTLIER) cc_final: 0.7824 (mp0) outliers start: 26 outliers final: 17 residues processed: 152 average time/residue: 0.2648 time to fit residues: 58.5876 Evaluate side-chains 145 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 124 time to evaluate : 1.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 483 ASN Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 531 TYR Chi-restraints excluded: chain A residue 539 ASP Chi-restraints excluded: chain A residue 543 ASP Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 640 THR Chi-restraints excluded: chain A residue 830 GLN Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 960 ILE Chi-restraints excluded: chain A residue 1024 GLU Chi-restraints excluded: chain A residue 1080 GLU Chi-restraints excluded: chain A residue 1125 ILE Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 610 THR Chi-restraints excluded: chain B residue 636 VAL Chi-restraints excluded: chain B residue 895 THR Chi-restraints excluded: chain B residue 983 LEU Chi-restraints excluded: chain B residue 1062 THR Chi-restraints excluded: chain B residue 1143 GLU Chi-restraints excluded: chain B residue 1147 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 113 optimal weight: 0.9990 chunk 85 optimal weight: 0.9990 chunk 31 optimal weight: 0.5980 chunk 79 optimal weight: 1.9990 chunk 156 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 68 optimal weight: 0.1980 chunk 38 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 892 HIS B 634 ASN B 883 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.138595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.113848 restraints weight = 20856.879| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 1.66 r_work: 0.3265 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.2878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14413 Z= 0.130 Angle : 0.528 12.358 19758 Z= 0.283 Chirality : 0.040 0.171 2163 Planarity : 0.004 0.039 2290 Dihedral : 17.121 144.615 2480 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.90 % Allowed : 12.66 % Favored : 85.43 % 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: 0.19 (0.22), residues: 1554 helix: 1.42 (0.21), residues: 698 sheet: -1.27 (0.36), residues: 237 loop : -0.72 (0.24), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 820 HIS 0.005 0.001 HIS B 789 PHE 0.028 0.001 PHE A 596 TYR 0.022 0.001 TYR B 966 ARG 0.007 0.000 ARG A 985 Details of bonding type rmsd hydrogen bonds : bond 0.04217 ( 607) hydrogen bonds : angle 4.16517 ( 1675) covalent geometry : bond 0.00294 (14413) covalent geometry : angle 0.52844 (19758) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7368.05 seconds wall clock time: 129 minutes 0.40 seconds (7740.40 seconds total)