Starting phenix.real_space_refine on Thu Aug 6 06:23:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8kgr_37231/08_2026/8kgr_37231.cif Found real_map, /net/cci-nas-00/data/ceres_data/8kgr_37231/08_2026/8kgr_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 { model { file = "/net/cci-nas-00/data/ceres_data/8kgr_37231/08_2026/8kgr_37231.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8kgr_37231/08_2026/8kgr_37231.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8kgr_37231/08_2026/8kgr_37231.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8kgr_37231/08_2026/8kgr_37231.map" } 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-2.2rc3-6140/lib/python3.11/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: 3.20, per 1000 atoms: 0.23 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: 1.13 Conformation dependent library (CDL) restraints added in 631.0 milliseconds 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: 1.80 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: 2.87 Time building geometry restraints manager: 1.54 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=" C1' DT D 22 " pdb=" N1 DT D 22 " ideal model delta sigma weight residual 1.468 1.538 -0.070 1.40e-02 5.10e+03 2.49e+01 bond pdb=" C3' DT C 40 " pdb=" O3' DT C 40 " ideal model delta sigma weight residual 1.435 1.384 0.051 1.30e-02 5.92e+03 1.56e+01 bond pdb=" C3' DA D 27 " pdb=" O3' DA D 27 " ideal model delta sigma weight residual 1.435 1.385 0.050 1.30e-02 5.92e+03 1.48e+01 bond pdb=" C5 DT C 24 " pdb=" C6 DT C 24 " ideal model delta sigma weight residual 1.339 1.312 0.027 7.00e-03 2.04e+04 1.47e+01 bond pdb=" C3' DG C 27 " pdb=" O3' DG C 27 " ideal model delta sigma weight residual 1.435 1.386 0.049 1.30e-02 5.92e+03 1.43e+01 ... (remaining 14408 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.24: 19517 3.24 - 6.47: 218 6.47 - 9.71: 20 9.71 - 12.95: 2 12.95 - 16.18: 1 Bond angle restraints: 19758 Sorted by residual: angle pdb=" O4' DA C 31 " pdb=" C4' DA C 31 " pdb=" C3' DA C 31 " ideal model delta sigma weight residual 106.00 102.45 3.55 6.00e-01 2.78e+00 3.50e+01 angle pdb=" O4' DT D 18 " pdb=" C4' DT D 18 " pdb=" C3' DT D 18 " ideal model delta sigma weight residual 106.00 102.53 3.47 6.00e-01 2.78e+00 3.34e+01 angle pdb=" O4' DT D 24 " pdb=" C4' DT D 24 " pdb=" C3' DT D 24 " ideal model delta sigma weight residual 106.00 102.91 3.09 6.00e-01 2.78e+00 2.65e+01 angle pdb=" O4' DT C 30 " pdb=" C4' DT C 30 " pdb=" C3' DT C 30 " ideal model delta sigma weight residual 106.00 103.05 2.95 6.00e-01 2.78e+00 2.41e+01 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 ... (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: 1731 0.075 - 0.151: 388 0.151 - 0.226: 38 0.226 - 0.301: 4 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: 11.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 16.130 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.030 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:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 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= 0.470 Angle : 0.984 16.181 19758 Z= 0.619 Chirality : 0.061 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 are 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/Z covalent geometry : bond 0.00827 / 0.47 (14413) covalent geometry : angle 0.98362 / 0.62 (19758) hydrogen bonds : bond 0.17193 / 18.81 ( 607) hydrogen bonds : angle 7.18625 / 8.92 ( 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 : 0.623 Fit side-chains revert: symmetry clash REVERT: A 455 SER cc_start: 0.8007 (t) cc_final: 0.7798 (t) REVERT: A 461 SER cc_start: 0.8535 (p) cc_final: 0.8324 (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: 0.8240 (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: 0.1522 time to fit residues: 49.3740 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 : 0.598 ------------------------------------------------------------------------------- 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: 0.9980 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 566 HIS A 880 ASN A 883 HIS A1051 HIS A1078 HIS ** B 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 502 ASN B 566 HIS B 634 ASN B 692 GLN B 892 HIS B 905 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.138599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.113459 restraints weight = 20711.275| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 1.71 r_work: 0.3248 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 moved from start: 0.1468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14413 Z= 0.144 Angle : 0.623 15.993 19758 Z= 0.344 Chirality : 0.045 0.202 2163 Planarity : 0.005 0.049 2290 Dihedral : 18.097 147.923 2480 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.61 % Allowed : 7.76 % Favored : 90.63 % 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 are not related in a simple way. whole: -2.14 (0.20), residues: 1554 helix: -0.63 (0.19), residues: 679 sheet: -2.19 (0.35), residues: 203 loop : -1.90 (0.22), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B1046 TYR 0.031 0.002 TYR A 531 PHE 0.014 0.001 PHE B 739 TRP 0.030 0.002 TRP B1170 HIS 0.009 0.001 HIS A 789 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.14 (14413) covalent geometry : angle 0.62313 / 0.34 (19758) hydrogen bonds : bond 0.05819 / 6.60 ( 607) hydrogen bonds : angle 5.24422 / 6.72 ( 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 153 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 131 time to evaluate : 0.521 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 461 SER cc_start: 0.8615 (p) cc_final: 0.8408 (t) REVERT: A 474 ILE cc_start: 0.8794 (mm) cc_final: 0.8562 (mt) REVERT: A 531 TYR cc_start: 0.7729 (OUTLIER) cc_final: 0.7389 (p90) REVERT: B 543 ASP cc_start: 0.8449 (t70) cc_final: 0.8045 (m-30) REVERT: B 716 ARG cc_start: 0.8186 (tpp80) cc_final: 0.7913 (mtt180) REVERT: B 736 ARG cc_start: 0.8436 (mpt180) cc_final: 0.8075 (mpt180) REVERT: B 886 LEU cc_start: 0.8173 (OUTLIER) cc_final: 0.7896 (tm) REVERT: B 905 ASN cc_start: 0.8710 (t160) cc_final: 0.8507 (t0) outliers start: 22 outliers final: 11 residues processed: 150 average time/residue: 0.1326 time to fit residues: 29.0063 Evaluate side-chains 122 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 109 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 483 ASN Chi-restraints excluded: chain A residue 492 ILE 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 640 THR Chi-restraints excluded: chain A residue 644 SER Chi-restraints excluded: chain B residue 630 LYS 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 1143 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 133 optimal weight: 5.9990 chunk 100 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 63 optimal weight: 6.9990 chunk 58 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 80 optimal weight: 6.9990 chunk 97 optimal weight: 0.9990 chunk 59 optimal weight: 0.5980 chunk 103 optimal weight: 0.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 566 HIS A 883 HIS ** B 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 864 GLN B 892 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.136094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.111000 restraints weight = 20829.211| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 1.70 r_work: 0.3215 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8762 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 14413 Z= 0.175 Angle : 0.603 15.775 19758 Z= 0.332 Chirality : 0.045 0.243 2163 Planarity : 0.005 0.047 2290 Dihedral : 17.972 147.510 2480 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.05 % Allowed : 9.74 % Favored : 88.21 % 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 are not related in a simple way. whole: -1.37 (0.21), residues: 1554 helix: 0.18 (0.20), residues: 679 sheet: -1.96 (0.35), residues: 215 loop : -1.64 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A1046 TYR 0.033 0.002 TYR A 531 PHE 0.017 0.002 PHE B 739 TRP 0.018 0.002 TRP B1170 HIS 0.008 0.001 HIS B 752 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.17 (14413) covalent geometry : angle 0.60270 / 0.33 (19758) hydrogen bonds : bond 0.05701 / 6.47 ( 607) hydrogen bonds : angle 4.86645 / 6.26 ( 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 139 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 111 time to evaluate : 0.519 Fit side-chains revert: symmetry clash REVERT: A 474 ILE cc_start: 0.8815 (mm) cc_final: 0.8573 (mt) REVERT: A 531 TYR cc_start: 0.7825 (OUTLIER) cc_final: 0.7354 (p90) REVERT: B 676 THR cc_start: 0.8742 (m) cc_final: 0.8424 (p) REVERT: B 716 ARG cc_start: 0.8272 (tpp80) cc_final: 0.7993 (mtt180) REVERT: B 886 LEU cc_start: 0.8236 (OUTLIER) cc_final: 0.7970 (tm) REVERT: B 905 ASN cc_start: 0.8780 (OUTLIER) cc_final: 0.8570 (t0) REVERT: B 1079 TYR cc_start: 0.8172 (m-80) cc_final: 0.7972 (m-80) outliers start: 28 outliers final: 12 residues processed: 135 average time/residue: 0.1294 time to fit residues: 25.4901 Evaluate side-chains 116 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 101 time to evaluate : 0.498 ------------------------------------------------------------------------------- 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 640 THR Chi-restraints excluded: chain A residue 801 ILE 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 905 ASN Chi-restraints excluded: chain B residue 952 LYS Chi-restraints excluded: chain B residue 1062 THR 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: 0.8980 chunk 159 optimal weight: 0.7980 chunk 30 optimal weight: 3.9990 chunk 7 optimal weight: 0.0470 chunk 157 optimal weight: 5.9990 chunk 132 optimal weight: 0.8980 chunk 158 optimal weight: 0.9980 chunk 95 optimal weight: 0.5980 chunk 18 optimal weight: 3.9990 chunk 139 optimal weight: 1.9990 chunk 103 optimal weight: 6.9990 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 892 HIS ** B 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 892 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.138675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.113960 restraints weight = 20816.502| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 1.64 r_work: 0.3265 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8718 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 14413 Z= 0.120 Angle : 0.525 14.642 19758 Z= 0.295 Chirality : 0.041 0.190 2163 Planarity : 0.004 0.045 2290 Dihedral : 17.844 147.378 2480 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.68 % Allowed : 10.61 % Favored : 87.70 % 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 are not related in a simple way. whole: -0.90 (0.21), residues: 1554 helix: 0.63 (0.20), residues: 679 sheet: -1.91 (0.34), residues: 225 loop : -1.36 (0.23), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1131 TYR 0.022 0.001 TYR A 531 PHE 0.010 0.001 PHE B 739 TRP 0.010 0.001 TRP B1170 HIS 0.004 0.001 HIS B 789 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.12 (14413) covalent geometry : angle 0.52507 / 0.29 (19758) hydrogen bonds : bond 0.04815 / 5.53 ( 607) hydrogen bonds : angle 4.58796 / 5.94 ( 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 132 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 109 time to evaluate : 0.635 Fit side-chains revert: symmetry clash REVERT: A 474 ILE cc_start: 0.8744 (mm) cc_final: 0.8532 (mt) REVERT: A 531 TYR cc_start: 0.7722 (OUTLIER) cc_final: 0.7213 (p90) REVERT: A 833 GLU cc_start: 0.8638 (OUTLIER) cc_final: 0.7874 (pm20) REVERT: A 892 HIS cc_start: 0.5838 (m90) cc_final: 0.5569 (m170) REVERT: B 676 THR cc_start: 0.8753 (m) cc_final: 0.8476 (p) REVERT: B 716 ARG cc_start: 0.8135 (tpp80) cc_final: 0.7918 (mtt180) REVERT: B 886 LEU cc_start: 0.8211 (OUTLIER) cc_final: 0.7962 (tm) REVERT: B 905 ASN cc_start: 0.8780 (OUTLIER) cc_final: 0.8575 (t0) REVERT: B 1079 TYR cc_start: 0.8121 (m-80) cc_final: 0.7919 (m-80) outliers start: 23 outliers final: 10 residues processed: 125 average time/residue: 0.1272 time to fit residues: 23.5550 Evaluate side-chains 117 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 103 time to evaluate : 0.549 ------------------------------------------------------------------------------- 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 640 THR Chi-restraints excluded: chain A residue 801 ILE Chi-restraints excluded: chain A residue 833 GLU Chi-restraints excluded: chain A residue 1125 ILE Chi-restraints excluded: chain B residue 633 ASP Chi-restraints excluded: chain B residue 886 LEU Chi-restraints excluded: chain B residue 905 ASN Chi-restraints excluded: chain B residue 976 VAL 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 58 optimal weight: 3.9990 chunk 158 optimal weight: 4.9990 chunk 72 optimal weight: 8.9990 chunk 33 optimal weight: 0.0030 chunk 48 optimal weight: 0.9990 chunk 141 optimal weight: 7.9990 chunk 118 optimal weight: 0.6980 chunk 69 optimal weight: 4.9990 chunk 78 optimal weight: 0.8980 chunk 36 optimal weight: 0.9980 chunk 100 optimal weight: 4.9990 overall best weight: 0.7192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.138588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.113695 restraints weight = 20844.563| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 1.66 r_work: 0.3260 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 0.2159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 14413 Z= 0.120 Angle : 0.514 14.656 19758 Z= 0.289 Chirality : 0.041 0.200 2163 Planarity : 0.004 0.044 2290 Dihedral : 17.753 147.007 2480 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.20 % Allowed : 10.03 % Favored : 87.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.22), residues: 1554 helix: 0.86 (0.21), residues: 682 sheet: -1.82 (0.33), residues: 237 loop : -1.17 (0.24), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 831 TYR 0.022 0.001 TYR A 531 PHE 0.016 0.001 PHE B 959 TRP 0.009 0.001 TRP B1170 HIS 0.005 0.001 HIS B 789 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.12 (14413) covalent geometry : angle 0.51356 / 0.29 (19758) hydrogen bonds : bond 0.04633 / 5.30 ( 607) hydrogen bonds : angle 4.43897 / 5.76 ( 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 147 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 117 time to evaluate : 0.510 Fit side-chains revert: symmetry clash REVERT: A 474 ILE cc_start: 0.8757 (mm) cc_final: 0.8542 (mt) REVERT: A 531 TYR cc_start: 0.7735 (OUTLIER) cc_final: 0.7145 (p90) REVERT: A 833 GLU cc_start: 0.8665 (OUTLIER) cc_final: 0.7905 (pm20) REVERT: A 1080 GLU cc_start: 0.7679 (OUTLIER) cc_final: 0.6934 (tt0) REVERT: B 636 VAL cc_start: 0.8471 (OUTLIER) cc_final: 0.8217 (t) REVERT: B 676 THR cc_start: 0.8768 (m) cc_final: 0.8498 (p) REVERT: B 716 ARG cc_start: 0.8147 (tpp80) cc_final: 0.7943 (mtt180) REVERT: B 882 LYS cc_start: 0.7769 (mttt) cc_final: 0.7296 (mtpp) REVERT: B 886 LEU cc_start: 0.8234 (OUTLIER) cc_final: 0.7994 (tm) outliers start: 30 outliers final: 19 residues processed: 139 average time/residue: 0.1260 time to fit residues: 26.1777 Evaluate side-chains 129 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 105 time to evaluate : 0.533 ------------------------------------------------------------------------------- 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 1024 GLU Chi-restraints excluded: chain A residue 1080 GLU Chi-restraints excluded: chain A residue 1125 ILE 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 886 LEU Chi-restraints excluded: chain B residue 895 THR Chi-restraints excluded: chain B residue 976 VAL 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 1158 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 92 optimal weight: 2.9990 chunk 158 optimal weight: 4.9990 chunk 137 optimal weight: 0.4980 chunk 52 optimal weight: 5.9990 chunk 5 optimal weight: 10.0000 chunk 122 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 chunk 62 optimal weight: 5.9990 chunk 120 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 892 HIS B 905 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.136786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.111959 restraints weight = 20683.733| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 1.67 r_work: 0.3233 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8744 moved from start: 0.2213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14413 Z= 0.149 Angle : 0.540 14.965 19758 Z= 0.302 Chirality : 0.043 0.222 2163 Planarity : 0.004 0.044 2290 Dihedral : 17.757 146.813 2480 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.12 % Allowed : 11.13 % Favored : 86.75 % 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 are not related in a simple way. whole: -0.52 (0.22), residues: 1554 helix: 0.95 (0.21), residues: 688 sheet: -1.74 (0.35), residues: 223 loop : -1.18 (0.23), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 788 TYR 0.025 0.001 TYR A 531 PHE 0.014 0.001 PHE B 739 TRP 0.009 0.001 TRP A 820 HIS 0.006 0.001 HIS B 789 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.15 (14413) covalent geometry : angle 0.54050 / 0.30 (19758) hydrogen bonds : bond 0.04838 / 5.51 ( 607) hydrogen bonds : angle 4.41410 / 5.72 ( 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 142 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 113 time to evaluate : 0.542 Fit side-chains REVERT: A 531 TYR cc_start: 0.7814 (OUTLIER) cc_final: 0.7091 (p90) REVERT: A 833 GLU cc_start: 0.8734 (OUTLIER) cc_final: 0.7927 (pm20) REVERT: A 1080 GLU cc_start: 0.7673 (OUTLIER) cc_final: 0.6843 (tm-30) REVERT: A 1116 LYS cc_start: 0.7782 (ptpt) cc_final: 0.7274 (ptpp) REVERT: B 676 THR cc_start: 0.8823 (m) cc_final: 0.8536 (p) REVERT: B 716 ARG cc_start: 0.8209 (tpp80) cc_final: 0.7978 (mtt180) REVERT: B 882 LYS cc_start: 0.7849 (mttt) cc_final: 0.7380 (mtpp) REVERT: B 886 LEU cc_start: 0.8281 (OUTLIER) cc_final: 0.8052 (tm) REVERT: B 1074 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8633 (tt) REVERT: B 1143 GLU cc_start: 0.8304 (OUTLIER) cc_final: 0.7838 (mp0) outliers start: 29 outliers final: 18 residues processed: 135 average time/residue: 0.1339 time to fit residues: 26.5918 Evaluate side-chains 130 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 106 time to evaluate : 0.476 ------------------------------------------------------------------------------- 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 1024 GLU Chi-restraints excluded: chain A residue 1080 GLU Chi-restraints excluded: chain A residue 1125 ILE 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 886 LEU Chi-restraints excluded: chain B residue 895 THR 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 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: 5.9990 chunk 44 optimal weight: 0.9980 chunk 15 optimal weight: 0.5980 chunk 84 optimal weight: 5.9990 chunk 73 optimal weight: 4.9990 chunk 117 optimal weight: 0.4980 chunk 119 optimal weight: 2.9990 chunk 142 optimal weight: 0.0370 chunk 93 optimal weight: 0.8980 chunk 50 optimal weight: 3.9990 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1149 GLN ** 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 = 0.3752 r_free = 0.3752 target = 0.138834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.114284 restraints weight = 20686.104| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 1.64 r_work: 0.3271 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.2379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 14413 Z= 0.112 Angle : 0.499 14.398 19758 Z= 0.282 Chirality : 0.041 0.191 2163 Planarity : 0.003 0.042 2290 Dihedral : 17.711 146.693 2480 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.34 % Allowed : 11.20 % Favored : 86.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.22), residues: 1554 helix: 1.09 (0.21), residues: 690 sheet: -1.63 (0.35), residues: 223 loop : -1.04 (0.23), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 985 TYR 0.018 0.001 TYR A 531 PHE 0.018 0.001 PHE A 959 TRP 0.007 0.001 TRP A1189 HIS 0.003 0.001 HIS A 789 Details of bonding type rmsd/Z covalent geometry : bond 0.00214 / 0.11 (14413) covalent geometry : angle 0.49914 / 0.28 (19758) hydrogen bonds : bond 0.04403 / 5.05 ( 607) hydrogen bonds : angle 4.30764 / 5.62 ( 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 156 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 124 time to evaluate : 0.543 Fit side-chains REVERT: A 531 TYR cc_start: 0.7744 (OUTLIER) cc_final: 0.7025 (p90) REVERT: A 833 GLU cc_start: 0.8673 (OUTLIER) cc_final: 0.7917 (pm20) REVERT: A 1080 GLU cc_start: 0.7703 (OUTLIER) cc_final: 0.6899 (tm-30) REVERT: B 636 VAL cc_start: 0.8482 (OUTLIER) cc_final: 0.8245 (t) REVERT: B 676 THR cc_start: 0.8799 (m) cc_final: 0.8570 (p) REVERT: B 882 LYS cc_start: 0.7788 (mttt) cc_final: 0.7304 (mtpp) REVERT: B 886 LEU cc_start: 0.8257 (OUTLIER) cc_final: 0.8036 (tm) REVERT: B 1074 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8612 (tt) REVERT: B 1143 GLU cc_start: 0.8258 (OUTLIER) cc_final: 0.7811 (mp0) outliers start: 32 outliers final: 17 residues processed: 150 average time/residue: 0.1135 time to fit residues: 25.7515 Evaluate side-chains 130 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 106 time to evaluate : 0.344 ------------------------------------------------------------------------------- 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 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 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 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 1158 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 158 optimal weight: 4.9990 chunk 36 optimal weight: 0.9980 chunk 121 optimal weight: 4.9990 chunk 143 optimal weight: 7.9990 chunk 83 optimal weight: 1.9990 chunk 87 optimal weight: 5.9990 chunk 113 optimal weight: 0.7980 chunk 160 optimal weight: 1.9990 chunk 88 optimal weight: 0.9980 chunk 67 optimal weight: 0.9990 chunk 89 optimal weight: 4.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1149 GLN ** 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 = 0.3731 r_free = 0.3731 target = 0.137196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.112524 restraints weight = 20752.505| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 1.64 r_work: 0.3245 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8736 moved from start: 0.2410 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= 0.141 Angle : 0.533 14.916 19758 Z= 0.296 Chirality : 0.042 0.219 2163 Planarity : 0.004 0.041 2290 Dihedral : 17.712 146.670 2480 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.05 % Allowed : 12.01 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.22), residues: 1554 helix: 1.12 (0.21), residues: 690 sheet: -1.53 (0.36), residues: 223 loop : -1.04 (0.24), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 662 TYR 0.022 0.001 TYR A 531 PHE 0.024 0.001 PHE A 959 TRP 0.009 0.001 TRP A 820 HIS 0.006 0.001 HIS B 789 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.14 (14413) covalent geometry : angle 0.53296 / 0.30 (19758) hydrogen bonds : bond 0.04642 / 5.29 ( 607) hydrogen bonds : angle 4.30854 / 5.61 ( 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 137 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 109 time to evaluate : 0.524 Fit side-chains REVERT: A 531 TYR cc_start: 0.7781 (OUTLIER) cc_final: 0.6976 (p90) REVERT: A 833 GLU cc_start: 0.8740 (OUTLIER) cc_final: 0.7930 (pm20) REVERT: A 1080 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.6916 (tm-30) REVERT: A 1116 LYS cc_start: 0.7743 (ptpt) cc_final: 0.7225 (ptpp) REVERT: B 636 VAL cc_start: 0.8519 (OUTLIER) cc_final: 0.8248 (t) REVERT: B 676 THR cc_start: 0.8825 (m) cc_final: 0.8588 (p) REVERT: B 882 LYS cc_start: 0.7872 (mttt) cc_final: 0.7391 (mtpp) REVERT: B 886 LEU cc_start: 0.8256 (OUTLIER) cc_final: 0.8048 (tm) REVERT: B 1074 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8644 (tt) REVERT: B 1143 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.7845 (mp0) outliers start: 28 outliers final: 21 residues processed: 130 average time/residue: 0.1173 time to fit residues: 23.0807 Evaluate side-chains 136 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 108 time to evaluate : 0.469 ------------------------------------------------------------------------------- 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 950 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 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 983 LEU 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 1158 LEU 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: 0.7980 chunk 144 optimal weight: 0.2980 chunk 4 optimal weight: 10.0000 chunk 98 optimal weight: 0.0870 chunk 58 optimal weight: 0.9990 chunk 88 optimal weight: 3.9990 chunk 36 optimal weight: 0.5980 chunk 83 optimal weight: 0.5980 chunk 8 optimal weight: 3.9990 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1149 GLN ** B 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 483 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.139130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.114589 restraints weight = 20840.200| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 1.64 r_work: 0.3275 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3162 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.2531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 14413 Z= 0.109 Angle : 0.502 14.236 19758 Z= 0.281 Chirality : 0.041 0.186 2163 Planarity : 0.004 0.048 2290 Dihedral : 17.680 146.483 2480 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.83 % Allowed : 12.08 % Favored : 86.09 % 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 are not related in a simple way. whole: -0.08 (0.22), residues: 1554 helix: 1.24 (0.21), residues: 690 sheet: -1.46 (0.36), residues: 223 loop : -0.89 (0.24), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 985 TYR 0.018 0.001 TYR A 531 PHE 0.017 0.001 PHE A 959 TRP 0.007 0.001 TRP A 820 HIS 0.003 0.001 HIS B 909 Details of bonding type rmsd/Z covalent geometry : bond 0.00208 / 0.11 (14413) covalent geometry : angle 0.50162 / 0.28 (19758) hydrogen bonds : bond 0.04264 / 4.91 ( 607) hydrogen bonds : angle 4.23634 / 5.54 ( 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 138 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 113 time to evaluate : 0.526 Fit side-chains REVERT: A 531 TYR cc_start: 0.7728 (OUTLIER) cc_final: 0.6953 (p90) REVERT: A 833 GLU cc_start: 0.8692 (OUTLIER) cc_final: 0.7938 (pm20) REVERT: A 1080 GLU cc_start: 0.7699 (OUTLIER) cc_final: 0.6913 (tm-30) REVERT: B 454 LYS cc_start: 0.7581 (mmtm) cc_final: 0.6699 (ttpp) REVERT: B 636 VAL cc_start: 0.8498 (OUTLIER) cc_final: 0.8272 (t) REVERT: B 676 THR cc_start: 0.8807 (m) cc_final: 0.8584 (p) REVERT: B 882 LYS cc_start: 0.7764 (mttt) cc_final: 0.7290 (mtpp) REVERT: B 1074 LEU cc_start: 0.8845 (OUTLIER) cc_final: 0.8556 (tt) REVERT: B 1079 TYR cc_start: 0.8178 (m-80) cc_final: 0.7505 (m-80) REVERT: B 1143 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.7809 (mp0) outliers start: 25 outliers final: 16 residues processed: 133 average time/residue: 0.1252 time to fit residues: 25.0255 Evaluate side-chains 129 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 107 time to evaluate : 0.533 ------------------------------------------------------------------------------- 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 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 636 VAL Chi-restraints excluded: chain B residue 803 VAL 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 1158 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 9 optimal weight: 1.9990 chunk 95 optimal weight: 0.7980 chunk 88 optimal weight: 0.8980 chunk 133 optimal weight: 3.9990 chunk 110 optimal weight: 4.9990 chunk 97 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 chunk 66 optimal weight: 0.6980 chunk 159 optimal weight: 3.9990 chunk 20 optimal weight: 0.6980 chunk 12 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1078 HIS A1149 GLN ** B 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.138367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.113759 restraints weight = 20836.316| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 1.65 r_work: 0.3265 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 moved from start: 0.2541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 14413 Z= 0.121 Angle : 0.516 14.544 19758 Z= 0.286 Chirality : 0.041 0.203 2163 Planarity : 0.004 0.071 2290 Dihedral : 17.657 146.453 2480 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.83 % Allowed : 12.23 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.22), residues: 1554 helix: 1.31 (0.21), residues: 684 sheet: -1.44 (0.35), residues: 235 loop : -0.86 (0.24), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 985 TYR 0.018 0.001 TYR A 531 PHE 0.022 0.001 PHE A 959 TRP 0.008 0.001 TRP A 820 HIS 0.004 0.001 HIS B 789 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.12 (14413) covalent geometry : angle 0.51581 / 0.29 (19758) hydrogen bonds : bond 0.04333 / 4.95 ( 607) hydrogen bonds : angle 4.21909 / 5.51 ( 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 135 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 110 time to evaluate : 0.529 Fit side-chains REVERT: A 531 TYR cc_start: 0.7748 (OUTLIER) cc_final: 0.6943 (p90) REVERT: A 833 GLU cc_start: 0.8713 (OUTLIER) cc_final: 0.7932 (pm20) REVERT: A 957 MET cc_start: 0.8193 (mmt) cc_final: 0.7932 (mmt) REVERT: A 1080 GLU cc_start: 0.7751 (OUTLIER) cc_final: 0.6953 (tm-30) REVERT: A 1116 LYS cc_start: 0.7756 (ptpt) cc_final: 0.7232 (ptpp) REVERT: B 454 LYS cc_start: 0.7549 (mmtm) cc_final: 0.6655 (ttpp) REVERT: B 636 VAL cc_start: 0.8497 (OUTLIER) cc_final: 0.8240 (t) REVERT: B 676 THR cc_start: 0.8812 (m) cc_final: 0.8593 (p) REVERT: B 882 LYS cc_start: 0.7823 (mttt) cc_final: 0.7344 (mtpp) REVERT: B 1074 LEU cc_start: 0.8845 (OUTLIER) cc_final: 0.8577 (tt) REVERT: B 1079 TYR cc_start: 0.8204 (m-80) cc_final: 0.7526 (m-80) REVERT: B 1143 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.7803 (mp0) outliers start: 25 outliers final: 15 residues processed: 131 average time/residue: 0.1228 time to fit residues: 24.0746 Evaluate side-chains 128 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 107 time to evaluate : 0.558 ------------------------------------------------------------------------------- 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 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 636 VAL Chi-restraints excluded: chain B residue 803 VAL 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 1158 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 158 optimal weight: 0.9980 chunk 104 optimal weight: 3.9990 chunk 119 optimal weight: 2.9990 chunk 126 optimal weight: 0.9980 chunk 83 optimal weight: 0.3980 chunk 20 optimal weight: 0.3980 chunk 6 optimal weight: 4.9990 chunk 127 optimal weight: 0.6980 chunk 90 optimal weight: 0.9980 chunk 48 optimal weight: 0.0370 chunk 95 optimal weight: 4.9990 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 557 HIS A1149 GLN ** B 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.139113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.114557 restraints weight = 20721.589| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 1.65 r_work: 0.3277 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3164 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.2597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 14413 Z= 0.110 Angle : 0.511 14.361 19758 Z= 0.284 Chirality : 0.041 0.272 2163 Planarity : 0.004 0.050 2290 Dihedral : 17.638 146.238 2480 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.68 % Allowed : 12.45 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.22), residues: 1554 helix: 1.35 (0.21), residues: 684 sheet: -1.41 (0.35), residues: 235 loop : -0.81 (0.24), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 985 TYR 0.020 0.001 TYR A1079 PHE 0.022 0.001 PHE A 959 TRP 0.007 0.001 TRP A1189 HIS 0.003 0.001 HIS B 789 Details of bonding type rmsd/Z covalent geometry : bond 0.00207 / 0.11 (14413) covalent geometry : angle 0.51078 / 0.28 (19758) hydrogen bonds : bond 0.04198 / 4.82 ( 607) hydrogen bonds : angle 4.21072 / 5.51 ( 1675) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3779.01 seconds wall clock time: 65 minutes 32.06 seconds (3932.06 seconds total)