Starting phenix.real_space_refine on Sat Aug 23 18:36:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8kgr_37231/08_2025/8kgr_37231.cif Found real_map, /net/cci-nas-00/data/ceres_data/8kgr_37231/08_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_37231/08_2025/8kgr_37231.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8kgr_37231/08_2025/8kgr_37231.map" model { file = "/net/cci-nas-00/data/ceres_data/8kgr_37231/08_2025/8kgr_37231.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8kgr_37231/08_2025/8kgr_37231.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 3.14, per 1000 atoms: 0.22 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: 0.74 Conformation dependent library (CDL) restraints added in 445.5 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 1.38 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: 2.70 Time building geometry restraints manager: 1.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 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 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: 9.660 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: 0.240 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 12.730 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.880 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.81 (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 ARG 0.017 0.002 ARG B1039 TYR 0.061 0.003 TYR A 531 PHE 0.026 0.003 PHE B 739 TRP 0.071 0.005 TRP B1170 HIS 0.014 0.003 HIS B 892 Details of bonding type rmsd covalent geometry : bond 0.00809 (14413) covalent geometry : angle 0.95379 (19758) hydrogen bonds : bond 0.17193 ( 607) hydrogen bonds : angle 7.18625 ( 1675) *********************** 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 : 0.552 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: 0.1505 time to fit residues: 48.0768 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 : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.4980 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 0.2980 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 0.9980 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 = 0.3766 r_free = 0.3766 target = 0.139896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.114964 restraints weight = 20765.414| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 1.72 r_work: 0.3268 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.1768 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= 0.129 Angle : 0.565 15.345 19758 Z= 0.307 Chirality : 0.041 0.155 2163 Planarity : 0.005 0.055 2290 Dihedral : 17.637 145.796 2480 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.05 % Allowed : 7.69 % Favored : 90.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.98 (0.20), residues: 1554 helix: -0.46 (0.19), residues: 675 sheet: -2.14 (0.34), residues: 215 loop : -1.84 (0.22), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B1046 TYR 0.025 0.001 TYR A 531 PHE 0.013 0.001 PHE B 959 TRP 0.028 0.002 TRP B1170 HIS 0.010 0.001 HIS A1078 Details of bonding type rmsd covalent geometry : bond 0.00275 (14413) covalent geometry : angle 0.56464 (19758) hydrogen bonds : bond 0.05007 ( 607) hydrogen bonds : angle 4.92149 ( 1675) *********************** 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 173 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 145 time to evaluate : 0.533 Fit side-chains revert: symmetry clash REVERT: A 474 ILE cc_start: 0.8782 (mm) cc_final: 0.8550 (mt) REVERT: A 531 TYR cc_start: 0.7735 (OUTLIER) cc_final: 0.7326 (p90) REVERT: A 778 VAL cc_start: 0.8742 (t) cc_final: 0.8461 (m) REVERT: B 636 VAL cc_start: 0.8352 (OUTLIER) cc_final: 0.8114 (t) REVERT: B 676 THR cc_start: 0.8704 (m) cc_final: 0.8432 (p) REVERT: B 716 ARG cc_start: 0.8189 (tpp80) cc_final: 0.7954 (mtt180) REVERT: B 736 ARG cc_start: 0.8408 (mpt180) cc_final: 0.8101 (mpt180) REVERT: B 854 GLU cc_start: 0.8743 (mm-30) cc_final: 0.8522 (mm-30) REVERT: B 1106 GLU cc_start: 0.7724 (OUTLIER) cc_final: 0.7464 (mt-10) outliers start: 28 outliers final: 9 residues processed: 166 average time/residue: 0.1297 time to fit residues: 31.2004 Evaluate side-chains 120 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 108 time to evaluate : 0.505 ------------------------------------------------------------------------------- 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 895 THR Chi-restraints excluded: chain B residue 949 SER Chi-restraints excluded: chain B residue 1106 GLU 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 133 optimal weight: 3.9990 chunk 100 optimal weight: 6.9990 chunk 20 optimal weight: 0.5980 chunk 43 optimal weight: 6.9990 chunk 63 optimal weight: 6.9990 chunk 58 optimal weight: 0.4980 chunk 39 optimal weight: 2.9990 chunk 80 optimal weight: 7.9990 chunk 97 optimal weight: 1.9990 chunk 59 optimal weight: 0.6980 chunk 103 optimal weight: 0.8980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 557 HIS A 566 HIS A1149 GLN ** B 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 634 ASN B 864 GLN B 892 HIS B 905 ASN B 928 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.138451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.113425 restraints weight = 20814.756| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 1.69 r_work: 0.3252 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.2033 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= 0.132 Angle : 0.538 15.058 19758 Z= 0.290 Chirality : 0.040 0.141 2163 Planarity : 0.004 0.048 2290 Dihedral : 17.495 145.394 2480 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.20 % Allowed : 10.47 % Favored : 87.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.15 (0.21), residues: 1554 helix: 0.38 (0.20), residues: 680 sheet: -2.06 (0.34), residues: 225 loop : -1.43 (0.23), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 571 TYR 0.023 0.001 TYR A 531 PHE 0.014 0.001 PHE B 739 TRP 0.018 0.001 TRP B1170 HIS 0.005 0.001 HIS B 789 Details of bonding type rmsd covalent geometry : bond 0.00294 (14413) covalent geometry : angle 0.53779 (19758) hydrogen bonds : bond 0.04720 ( 607) hydrogen bonds : angle 4.54421 ( 1675) *********************** 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 145 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 115 time to evaluate : 0.571 Fit side-chains REVERT: A 474 ILE cc_start: 0.8738 (mm) cc_final: 0.8488 (mt) REVERT: A 531 TYR cc_start: 0.7745 (OUTLIER) cc_final: 0.7171 (p90) REVERT: A 778 VAL cc_start: 0.8759 (t) cc_final: 0.8500 (m) REVERT: A 957 MET cc_start: 0.8210 (mmp) cc_final: 0.7932 (mmt) REVERT: B 676 THR cc_start: 0.8782 (m) cc_final: 0.8505 (p) REVERT: B 716 ARG cc_start: 0.8156 (tpp80) cc_final: 0.7938 (mtt180) REVERT: B 736 ARG cc_start: 0.8399 (mpt180) cc_final: 0.8047 (mpt180) REVERT: B 882 LYS cc_start: 0.7783 (mttt) cc_final: 0.7312 (mtpp) REVERT: B 1143 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.7906 (mp0) outliers start: 30 outliers final: 13 residues processed: 141 average time/residue: 0.1372 time to fit residues: 27.8605 Evaluate side-chains 121 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 106 time to evaluate : 0.521 ------------------------------------------------------------------------------- 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 803 VAL 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 28 optimal weight: 0.9980 chunk 159 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 7 optimal weight: 0.0670 chunk 157 optimal weight: 2.9990 chunk 132 optimal weight: 3.9990 chunk 158 optimal weight: 0.9980 chunk 95 optimal weight: 0.7980 chunk 18 optimal weight: 7.9990 chunk 139 optimal weight: 3.9990 chunk 103 optimal weight: 7.9990 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 892 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.139400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.114704 restraints weight = 20809.055| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 1.66 r_work: 0.3280 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.2353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 14413 Z= 0.114 Angle : 0.501 14.569 19758 Z= 0.272 Chirality : 0.039 0.142 2163 Planarity : 0.004 0.044 2290 Dihedral : 17.317 145.149 2480 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.90 % Allowed : 10.91 % Favored : 87.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.59 (0.22), residues: 1554 helix: 0.93 (0.21), residues: 675 sheet: -1.87 (0.35), residues: 222 loop : -1.19 (0.23), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 571 TYR 0.017 0.001 TYR A 531 PHE 0.016 0.001 PHE B 959 TRP 0.012 0.001 TRP B1170 HIS 0.004 0.001 HIS B 789 Details of bonding type rmsd covalent geometry : bond 0.00247 (14413) covalent geometry : angle 0.50067 (19758) hydrogen bonds : bond 0.04223 ( 607) hydrogen bonds : angle 4.29626 ( 1675) *********************** 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 151 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 125 time to evaluate : 0.452 Fit side-chains revert: symmetry clash REVERT: A 474 ILE cc_start: 0.8726 (mm) cc_final: 0.8494 (mt) REVERT: A 531 TYR cc_start: 0.7745 (OUTLIER) cc_final: 0.7055 (p90) REVERT: A 634 ASN cc_start: 0.8640 (t0) cc_final: 0.8407 (m-40) REVERT: A 778 VAL cc_start: 0.8776 (t) cc_final: 0.8503 (m) REVERT: B 454 LYS cc_start: 0.7656 (mmtm) cc_final: 0.6767 (ttpp) REVERT: B 636 VAL cc_start: 0.8434 (OUTLIER) cc_final: 0.8182 (t) REVERT: B 676 THR cc_start: 0.8795 (m) cc_final: 0.8520 (p) REVERT: B 957 MET cc_start: 0.7671 (mmm) cc_final: 0.7378 (mmm) outliers start: 26 outliers final: 14 residues processed: 144 average time/residue: 0.1413 time to fit residues: 29.1708 Evaluate side-chains 120 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 104 time to evaluate : 0.532 ------------------------------------------------------------------------------- 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 1074 LEU Chi-restraints excluded: chain B residue 433 MET Chi-restraints excluded: chain B residue 610 THR Chi-restraints excluded: chain B residue 636 VAL Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1062 THR Chi-restraints excluded: chain B residue 1143 GLU Chi-restraints excluded: chain B residue 1158 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 58 optimal weight: 1.9990 chunk 158 optimal weight: 5.9990 chunk 72 optimal weight: 7.9990 chunk 33 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 141 optimal weight: 5.9990 chunk 118 optimal weight: 0.8980 chunk 69 optimal weight: 0.7980 chunk 78 optimal weight: 0.1980 chunk 36 optimal weight: 0.8980 chunk 100 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3761 r_free = 0.3761 target = 0.139470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.114788 restraints weight = 20893.413| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 1.70 r_work: 0.3274 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 14413 Z= 0.116 Angle : 0.495 14.414 19758 Z= 0.270 Chirality : 0.039 0.139 2163 Planarity : 0.004 0.037 2290 Dihedral : 17.245 144.919 2480 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.34 % Allowed : 11.05 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.31 (0.22), residues: 1554 helix: 1.16 (0.21), residues: 683 sheet: -1.76 (0.35), residues: 223 loop : -1.05 (0.23), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 662 TYR 0.018 0.001 TYR A 531 PHE 0.016 0.001 PHE B 959 TRP 0.010 0.001 TRP B1170 HIS 0.004 0.001 HIS B 789 Details of bonding type rmsd covalent geometry : bond 0.00254 (14413) covalent geometry : angle 0.49541 (19758) hydrogen bonds : bond 0.04164 ( 607) hydrogen bonds : angle 4.18725 ( 1675) *********************** 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 153 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 121 time to evaluate : 0.601 Fit side-chains REVERT: A 474 ILE cc_start: 0.8744 (mm) cc_final: 0.8513 (mt) REVERT: A 531 TYR cc_start: 0.7747 (OUTLIER) cc_final: 0.6971 (p90) REVERT: A 634 ASN cc_start: 0.8644 (t0) cc_final: 0.8426 (m-40) REVERT: A 778 VAL cc_start: 0.8800 (t) cc_final: 0.8537 (m) REVERT: A 833 GLU cc_start: 0.8677 (OUTLIER) cc_final: 0.7947 (pm20) REVERT: A 892 HIS cc_start: 0.5729 (m170) cc_final: 0.5292 (m170) REVERT: A 1080 GLU cc_start: 0.7721 (OUTLIER) cc_final: 0.7047 (tm-30) REVERT: A 1148 MET cc_start: 0.8605 (ttm) cc_final: 0.8357 (ttp) REVERT: B 454 LYS cc_start: 0.7659 (mmtm) cc_final: 0.6730 (ttpp) REVERT: B 636 VAL cc_start: 0.8471 (OUTLIER) cc_final: 0.8201 (t) REVERT: B 676 THR cc_start: 0.8802 (m) cc_final: 0.8560 (p) REVERT: B 957 MET cc_start: 0.7796 (mmm) cc_final: 0.7510 (mmm) REVERT: B 1074 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8594 (tt) REVERT: B 1079 TYR cc_start: 0.8103 (m-80) cc_final: 0.7397 (m-80) REVERT: B 1143 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.7813 (mp0) outliers start: 32 outliers final: 20 residues processed: 145 average time/residue: 0.1296 time to fit residues: 27.6495 Evaluate side-chains 136 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 110 time to evaluate : 0.530 ------------------------------------------------------------------------------- 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 833 GLU 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 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 976 VAL 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 Chi-restraints excluded: chain B residue 1179 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 92 optimal weight: 0.9980 chunk 158 optimal weight: 3.9990 chunk 137 optimal weight: 0.9980 chunk 52 optimal weight: 0.8980 chunk 5 optimal weight: 4.9990 chunk 122 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 47 optimal weight: 0.5980 chunk 74 optimal weight: 1.9990 chunk 62 optimal weight: 7.9990 chunk 120 optimal weight: 1.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 = 0.3734 r_free = 0.3734 target = 0.137350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.112344 restraints weight = 20697.292| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 1.65 r_work: 0.3242 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.2491 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= 0.137 Angle : 0.516 14.288 19758 Z= 0.281 Chirality : 0.040 0.139 2163 Planarity : 0.004 0.038 2290 Dihedral : 17.298 145.230 2480 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.42 % Allowed : 10.61 % Favored : 86.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.19 (0.22), residues: 1554 helix: 1.25 (0.21), residues: 683 sheet: -1.64 (0.35), residues: 223 loop : -1.01 (0.24), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 662 TYR 0.022 0.001 TYR A 531 PHE 0.019 0.001 PHE B 959 TRP 0.010 0.001 TRP B1170 HIS 0.005 0.001 HIS B 789 Details of bonding type rmsd covalent geometry : bond 0.00312 (14413) covalent geometry : angle 0.51587 (19758) hydrogen bonds : bond 0.04471 ( 607) hydrogen bonds : angle 4.23214 ( 1675) *********************** 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 147 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 114 time to evaluate : 0.615 Fit side-chains REVERT: A 474 ILE cc_start: 0.8760 (mm) cc_final: 0.8529 (mt) REVERT: A 531 TYR cc_start: 0.7811 (OUTLIER) cc_final: 0.6930 (p90) REVERT: A 634 ASN cc_start: 0.8671 (t0) cc_final: 0.8439 (m-40) REVERT: A 778 VAL cc_start: 0.8865 (t) cc_final: 0.8606 (m) REVERT: A 833 GLU cc_start: 0.8750 (OUTLIER) cc_final: 0.7983 (pm20) REVERT: A 1080 GLU cc_start: 0.7727 (OUTLIER) cc_final: 0.7018 (tm-30) REVERT: A 1148 MET cc_start: 0.8674 (ttm) cc_final: 0.8423 (ttp) REVERT: B 454 LYS cc_start: 0.7646 (mmtm) cc_final: 0.6690 (ttpp) REVERT: B 636 VAL cc_start: 0.8486 (OUTLIER) cc_final: 0.8213 (t) REVERT: B 676 THR cc_start: 0.8841 (m) cc_final: 0.8594 (p) REVERT: B 957 MET cc_start: 0.7854 (mmm) cc_final: 0.7551 (mmm) REVERT: B 1074 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8652 (tt) REVERT: B 1143 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.7864 (mp0) outliers start: 33 outliers final: 21 residues processed: 142 average time/residue: 0.1260 time to fit residues: 26.8005 Evaluate side-chains 137 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 110 time to evaluate : 0.636 ------------------------------------------------------------------------------- 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 573 LEU 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 1143 GLU Chi-restraints excluded: chain B residue 1179 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 9 optimal weight: 3.9990 chunk 132 optimal weight: 10.0000 chunk 44 optimal weight: 4.9990 chunk 15 optimal weight: 0.8980 chunk 84 optimal weight: 2.9990 chunk 73 optimal weight: 5.9990 chunk 117 optimal weight: 0.8980 chunk 119 optimal weight: 2.9990 chunk 142 optimal weight: 1.9990 chunk 93 optimal weight: 0.9990 chunk 50 optimal weight: 4.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 892 HIS B 692 GLN B 892 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.135369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.110362 restraints weight = 20693.351| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 1.69 r_work: 0.3206 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.2462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 14413 Z= 0.170 Angle : 0.548 13.865 19758 Z= 0.298 Chirality : 0.041 0.143 2163 Planarity : 0.004 0.039 2290 Dihedral : 17.427 145.604 2480 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.42 % Allowed : 11.20 % Favored : 86.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.20 (0.22), residues: 1554 helix: 1.23 (0.21), residues: 682 sheet: -1.57 (0.35), residues: 223 loop : -1.03 (0.24), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 662 TYR 0.027 0.002 TYR A 531 PHE 0.023 0.002 PHE B 959 TRP 0.011 0.001 TRP A 820 HIS 0.007 0.001 HIS B 752 Details of bonding type rmsd covalent geometry : bond 0.00398 (14413) covalent geometry : angle 0.54783 (19758) hydrogen bonds : bond 0.04913 ( 607) hydrogen bonds : angle 4.34839 ( 1675) *********************** 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 149 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 116 time to evaluate : 0.530 Fit side-chains REVERT: A 455 SER cc_start: 0.7989 (t) cc_final: 0.7780 (t) REVERT: A 474 ILE cc_start: 0.8805 (mm) cc_final: 0.8582 (mt) REVERT: A 531 TYR cc_start: 0.7861 (OUTLIER) cc_final: 0.6893 (p90) REVERT: A 778 VAL cc_start: 0.8895 (t) cc_final: 0.8651 (m) REVERT: A 833 GLU cc_start: 0.8788 (OUTLIER) cc_final: 0.7995 (pm20) REVERT: A 892 HIS cc_start: 0.5890 (m90) cc_final: 0.5490 (m170) REVERT: A 1080 GLU cc_start: 0.7773 (OUTLIER) cc_final: 0.7055 (tm-30) REVERT: A 1148 MET cc_start: 0.8720 (ttm) cc_final: 0.8460 (ttp) REVERT: B 676 THR cc_start: 0.8893 (m) cc_final: 0.8643 (p) REVERT: B 957 MET cc_start: 0.7953 (mmm) cc_final: 0.7633 (mmm) REVERT: B 1074 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8662 (tt) REVERT: B 1143 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.7885 (mp0) outliers start: 33 outliers final: 26 residues processed: 142 average time/residue: 0.1383 time to fit residues: 28.6245 Evaluate side-chains 142 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 111 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 483 ASN Chi-restraints excluded: chain A residue 494 VAL 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 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 976 VAL 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 1143 GLU Chi-restraints excluded: chain B residue 1158 LEU Chi-restraints excluded: chain B residue 1179 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 158 optimal weight: 3.9990 chunk 36 optimal weight: 0.6980 chunk 121 optimal weight: 3.9990 chunk 143 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 87 optimal weight: 8.9990 chunk 113 optimal weight: 0.8980 chunk 160 optimal weight: 2.9990 chunk 88 optimal weight: 0.8980 chunk 67 optimal weight: 0.7980 chunk 89 optimal weight: 2.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 = 0.3733 r_free = 0.3733 target = 0.137460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.112695 restraints weight = 20717.656| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 1.65 r_work: 0.3247 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.2610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 14413 Z= 0.135 Angle : 0.514 13.513 19758 Z= 0.280 Chirality : 0.040 0.140 2163 Planarity : 0.004 0.037 2290 Dihedral : 17.325 145.242 2480 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.49 % Allowed : 11.27 % Favored : 86.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.08 (0.22), residues: 1554 helix: 1.33 (0.21), residues: 683 sheet: -1.48 (0.35), residues: 223 loop : -0.97 (0.24), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 662 TYR 0.021 0.001 TYR A 531 PHE 0.021 0.001 PHE B 959 TRP 0.017 0.001 TRP A1170 HIS 0.005 0.001 HIS B 789 Details of bonding type rmsd covalent geometry : bond 0.00305 (14413) covalent geometry : angle 0.51434 (19758) hydrogen bonds : bond 0.04490 ( 607) hydrogen bonds : angle 4.25176 ( 1675) *********************** 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 : 0.523 Fit side-chains REVERT: A 455 SER cc_start: 0.7915 (t) cc_final: 0.7702 (t) REVERT: A 474 ILE cc_start: 0.8790 (mm) cc_final: 0.8562 (mt) REVERT: A 531 TYR cc_start: 0.7849 (OUTLIER) cc_final: 0.6891 (p90) REVERT: A 778 VAL cc_start: 0.8876 (t) cc_final: 0.8619 (m) REVERT: A 833 GLU cc_start: 0.8761 (OUTLIER) cc_final: 0.8011 (pm20) REVERT: A 882 LYS cc_start: 0.7911 (mmmm) cc_final: 0.7705 (mmmm) REVERT: A 1080 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.7065 (tm-30) REVERT: A 1148 MET cc_start: 0.8671 (ttm) cc_final: 0.8402 (ttp) REVERT: B 636 VAL cc_start: 0.8529 (OUTLIER) cc_final: 0.8252 (t) REVERT: B 676 THR cc_start: 0.8880 (m) cc_final: 0.8635 (p) REVERT: B 1074 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8668 (tt) REVERT: B 1143 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.7845 (mp0) outliers start: 34 outliers final: 25 residues processed: 148 average time/residue: 0.1260 time to fit residues: 27.6115 Evaluate side-chains 142 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 111 time to evaluate : 0.588 ------------------------------------------------------------------------------- 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 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 633 ASP 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 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 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 42 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 chunk 147 optimal weight: 0.5980 chunk 144 optimal weight: 0.9980 chunk 4 optimal weight: 3.9990 chunk 98 optimal weight: 0.9980 chunk 58 optimal weight: 0.4980 chunk 88 optimal weight: 3.9990 chunk 36 optimal weight: 0.6980 chunk 83 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 892 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.138460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.113892 restraints weight = 20811.793| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 1.67 r_work: 0.3264 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.2733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14413 Z= 0.115 Angle : 0.500 13.723 19758 Z= 0.272 Chirality : 0.039 0.140 2163 Planarity : 0.003 0.036 2290 Dihedral : 17.191 144.737 2480 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.27 % Allowed : 11.49 % Favored : 86.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.10 (0.22), residues: 1554 helix: 1.46 (0.21), residues: 683 sheet: -1.39 (0.36), residues: 225 loop : -0.85 (0.24), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 662 TYR 0.016 0.001 TYR A 531 PHE 0.020 0.001 PHE B 959 TRP 0.012 0.001 TRP A1170 HIS 0.004 0.001 HIS B 789 Details of bonding type rmsd covalent geometry : bond 0.00253 (14413) covalent geometry : angle 0.50039 (19758) hydrogen bonds : bond 0.04115 ( 607) hydrogen bonds : angle 4.15356 ( 1675) *********************** 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 162 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 131 time to evaluate : 0.550 Fit side-chains REVERT: A 455 SER cc_start: 0.7906 (t) cc_final: 0.7702 (t) REVERT: A 474 ILE cc_start: 0.8791 (mm) cc_final: 0.8563 (mt) REVERT: A 531 TYR cc_start: 0.7773 (OUTLIER) cc_final: 0.6850 (p90) REVERT: A 778 VAL cc_start: 0.8874 (t) cc_final: 0.8594 (m) REVERT: A 833 GLU cc_start: 0.8742 (OUTLIER) cc_final: 0.8015 (pm20) REVERT: A 882 LYS cc_start: 0.7848 (mmmm) cc_final: 0.7636 (mmmm) REVERT: A 1080 GLU cc_start: 0.7803 (OUTLIER) cc_final: 0.7075 (tm-30) REVERT: A 1148 MET cc_start: 0.8692 (ttm) cc_final: 0.8422 (ttp) REVERT: B 435 LEU cc_start: 0.8976 (mp) cc_final: 0.8729 (mt) REVERT: B 454 LYS cc_start: 0.7601 (mmtm) cc_final: 0.6654 (ttpp) REVERT: B 636 VAL cc_start: 0.8509 (OUTLIER) cc_final: 0.8259 (t) REVERT: B 676 THR cc_start: 0.8850 (m) cc_final: 0.8619 (p) REVERT: B 1074 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8590 (tt) REVERT: B 1079 TYR cc_start: 0.8191 (m-80) cc_final: 0.7562 (m-80) REVERT: B 1143 GLU cc_start: 0.8355 (OUTLIER) cc_final: 0.7874 (mp0) outliers start: 31 outliers final: 24 residues processed: 155 average time/residue: 0.1298 time to fit residues: 29.7495 Evaluate side-chains 149 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 119 time to evaluate : 0.592 ------------------------------------------------------------------------------- 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 1024 GLU Chi-restraints excluded: chain A residue 1080 GLU Chi-restraints excluded: chain A residue 1125 ILE Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 573 LEU 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 976 VAL 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 1143 GLU Chi-restraints excluded: chain B residue 1158 LEU 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 9 optimal weight: 0.2980 chunk 95 optimal weight: 0.9980 chunk 88 optimal weight: 0.7980 chunk 133 optimal weight: 3.9990 chunk 110 optimal weight: 5.9990 chunk 97 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 159 optimal weight: 4.9990 chunk 20 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1078 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.138600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.114137 restraints weight = 20881.680| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 1.64 r_work: 0.3267 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3154 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.2797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14413 Z= 0.120 Angle : 0.513 13.582 19758 Z= 0.277 Chirality : 0.039 0.146 2163 Planarity : 0.004 0.035 2290 Dihedral : 17.160 144.649 2480 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.42 % Allowed : 11.79 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.17 (0.22), residues: 1554 helix: 1.51 (0.21), residues: 682 sheet: -1.33 (0.36), residues: 225 loop : -0.81 (0.24), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 985 TYR 0.017 0.001 TYR A 531 PHE 0.020 0.001 PHE B 959 TRP 0.012 0.001 TRP A1170 HIS 0.004 0.001 HIS B 789 Details of bonding type rmsd covalent geometry : bond 0.00268 (14413) covalent geometry : angle 0.51276 (19758) hydrogen bonds : bond 0.04147 ( 607) hydrogen bonds : angle 4.14038 ( 1675) ********************** 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 153 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 120 time to evaluate : 0.686 Fit side-chains REVERT: A 455 SER cc_start: 0.7876 (t) cc_final: 0.7670 (t) REVERT: A 474 ILE cc_start: 0.8792 (mm) cc_final: 0.8561 (mt) REVERT: A 531 TYR cc_start: 0.7755 (OUTLIER) cc_final: 0.6807 (p90) REVERT: A 778 VAL cc_start: 0.8876 (t) cc_final: 0.8594 (m) REVERT: A 833 GLU cc_start: 0.8736 (OUTLIER) cc_final: 0.7969 (pm20) REVERT: A 882 LYS cc_start: 0.7857 (mmmm) cc_final: 0.7642 (mmmm) REVERT: A 1080 GLU cc_start: 0.7811 (OUTLIER) cc_final: 0.7069 (tm-30) REVERT: A 1148 MET cc_start: 0.8685 (ttm) cc_final: 0.8419 (ttp) REVERT: B 454 LYS cc_start: 0.7564 (mmtm) cc_final: 0.6630 (ttpp) REVERT: B 636 VAL cc_start: 0.8497 (OUTLIER) cc_final: 0.8243 (t) REVERT: B 676 THR cc_start: 0.8829 (m) cc_final: 0.8612 (p) REVERT: B 1074 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8619 (tt) REVERT: B 1079 TYR cc_start: 0.8158 (m-80) cc_final: 0.7536 (m-80) REVERT: B 1143 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.7851 (mp0) outliers start: 33 outliers final: 24 residues processed: 145 average time/residue: 0.1329 time to fit residues: 28.3073 Evaluate side-chains 145 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 115 time to evaluate : 0.547 ------------------------------------------------------------------------------- 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 481 VAL Chi-restraints excluded: chain B residue 573 LEU 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 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 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 158 optimal weight: 4.9990 chunk 104 optimal weight: 3.9990 chunk 119 optimal weight: 2.9990 chunk 126 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 6 optimal weight: 0.5980 chunk 127 optimal weight: 0.6980 chunk 90 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 95 optimal weight: 0.0060 overall best weight: 0.7998 ------------------------------------------------------------------------------- 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 = 0.3751 r_free = 0.3751 target = 0.138728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.114486 restraints weight = 20770.229| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 1.62 r_work: 0.3277 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.2825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14413 Z= 0.120 Angle : 0.519 11.848 19758 Z= 0.279 Chirality : 0.040 0.193 2163 Planarity : 0.003 0.035 2290 Dihedral : 17.138 144.729 2480 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.17 (0.22), residues: 1554 helix: 1.47 (0.21), residues: 689 sheet: -1.29 (0.36), residues: 225 loop : -0.79 (0.24), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 662 TYR 0.026 0.001 TYR B 966 PHE 0.020 0.001 PHE B 959 TRP 0.011 0.001 TRP A1170 HIS 0.004 0.001 HIS B 789 Details of bonding type rmsd covalent geometry : bond 0.00269 (14413) covalent geometry : angle 0.51874 (19758) hydrogen bonds : bond 0.04126 ( 607) hydrogen bonds : angle 4.15463 ( 1675) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4091.40 seconds wall clock time: 70 minutes 58.95 seconds (4258.95 seconds total)