Starting phenix.real_space_refine on Fri Jul 3 11:38:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8kgr_37231/07_2026/8kgr_37231.cif Found real_map, /net/cci-nas-00/data/ceres_data/8kgr_37231/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8kgr_37231/07_2026/8kgr_37231.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8kgr_37231/07_2026/8kgr_37231.map" model { file = "/net/cci-nas-00/data/ceres_data/8kgr_37231/07_2026/8kgr_37231.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8kgr_37231/07_2026/8kgr_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-dev-6108/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: 3.41, per 1000 atoms: 0.24 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: 1.22 Conformation dependent library (CDL) restraints added in 634.8 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: 1.68 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: 1.65 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: 13.670 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: 0.440 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 15.840 Find NCS groups from input model: 0.230 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: 0.000 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.680 ------------------------------------------------------------------------------- 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= 0.469 Angle : 0.983 16.181 19758 Z= 0.618 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 0.98269 / 0.62 (19758) hydrogen bonds : bond 0.17193 / 18.73 ( 607) hydrogen bonds : angle 7.18625 / 8.91 ( 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 : 0.533 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: 0.8535 (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: 0.1537 time to fit residues: 49.8219 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 : 0.481 ------------------------------------------------------------------------------- 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... 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 864 GLN B 892 HIS B 905 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.138613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.113452 restraints weight = 20703.062| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 1.72 r_work: 0.3245 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8729 moved from start: 0.1466 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= 0.144 Angle : 0.621 16.012 19758 Z= 0.344 Chirality : 0.044 0.193 2163 Planarity : 0.005 0.049 2290 Dihedral : 18.113 148.514 2480 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.61 % Allowed : 7.83 % Favored : 90.56 % 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 (0.21), 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 0.62088 / 0.34 (19758) hydrogen bonds : bond 0.05859 / 6.60 ( 607) hydrogen bonds : angle 5.24994 / 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 152 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 130 time to evaluate : 0.529 Fit side-chains revert: symmetry clash REVERT: A 461 SER cc_start: 0.8604 (p) cc_final: 0.8402 (t) REVERT: A 474 ILE cc_start: 0.8792 (mm) cc_final: 0.8561 (mt) REVERT: A 531 TYR cc_start: 0.7716 (OUTLIER) cc_final: 0.7389 (p90) REVERT: B 543 ASP cc_start: 0.8452 (t70) cc_final: 0.8043 (m-30) REVERT: B 716 ARG cc_start: 0.8187 (tpp80) cc_final: 0.7913 (mtt180) REVERT: B 736 ARG cc_start: 0.8437 (mpt180) cc_final: 0.8076 (mpt180) REVERT: B 886 LEU cc_start: 0.8180 (OUTLIER) cc_final: 0.7906 (tm) REVERT: B 905 ASN cc_start: 0.8709 (t160) cc_final: 0.8506 (t0) outliers start: 22 outliers final: 11 residues processed: 149 average time/residue: 0.1283 time to fit residues: 27.9935 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 : 0.528 ------------------------------------------------------------------------------- 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: 5.9990 chunk 58 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 80 optimal weight: 5.9990 chunk 97 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 chunk 103 optimal weight: 0.9980 overall best weight: 1.9586 ------------------------------------------------------------------------------- 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 634 ASN B 892 HIS B 905 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.135048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.109845 restraints weight = 20855.440| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 1.70 r_work: 0.3197 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8781 moved from start: 0.1695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 14413 Z= 0.203 Angle : 0.636 16.003 19758 Z= 0.348 Chirality : 0.046 0.244 2163 Planarity : 0.005 0.048 2290 Dihedral : 18.047 148.374 2480 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.27 % Allowed : 9.88 % Favored : 87.85 % 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: -1.48 (0.21), residues: 1554 helix: 0.07 (0.20), residues: 683 sheet: -1.97 (0.35), residues: 215 loop : -1.70 (0.23), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1046 TYR 0.038 0.002 TYR A 531 PHE 0.019 0.002 PHE B 739 TRP 0.018 0.002 TRP B1170 HIS 0.009 0.002 HIS B 752 Details of bonding type rmsd/Z covalent geometry : bond 0.00463 / 0.20 (14413) covalent geometry : angle 0.63603 / 0.35 (19758) hydrogen bonds : bond 0.06011 / 6.76 ( 607) hydrogen bonds : angle 4.94054 / 6.34 ( 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 142 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 111 time to evaluate : 0.340 Fit side-chains REVERT: A 474 ILE cc_start: 0.8811 (mm) cc_final: 0.8566 (mt) REVERT: A 531 TYR cc_start: 0.7854 (OUTLIER) cc_final: 0.7314 (p90) REVERT: A 985 ARG cc_start: 0.8059 (mpt-90) cc_final: 0.7825 (mtm-85) REVERT: B 676 THR cc_start: 0.8764 (m) cc_final: 0.8432 (p) REVERT: B 716 ARG cc_start: 0.8323 (tpp80) cc_final: 0.8020 (mtt180) REVERT: B 886 LEU cc_start: 0.8240 (OUTLIER) cc_final: 0.7961 (tm) REVERT: B 963 ILE cc_start: 0.7506 (OUTLIER) cc_final: 0.7235 (tp) REVERT: B 1079 TYR cc_start: 0.8199 (m-80) cc_final: 0.7997 (m-80) REVERT: B 1143 GLU cc_start: 0.8329 (OUTLIER) cc_final: 0.7851 (mp0) outliers start: 31 outliers final: 16 residues processed: 138 average time/residue: 0.1366 time to fit residues: 27.1272 Evaluate side-chains 120 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 100 time to evaluate : 0.573 ------------------------------------------------------------------------------- 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 610 THR Chi-restraints excluded: chain A residue 640 THR Chi-restraints excluded: chain A residue 644 SER Chi-restraints excluded: chain B residue 633 ASP Chi-restraints excluded: chain B residue 634 ASN 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 952 LYS Chi-restraints excluded: chain B residue 963 ILE Chi-restraints excluded: chain B residue 1062 THR Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1115 GLN 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: 0.5980 chunk 159 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 7 optimal weight: 0.0570 chunk 157 optimal weight: 4.9990 chunk 132 optimal weight: 0.0670 chunk 158 optimal weight: 0.7980 chunk 95 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 139 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 overall best weight: 0.4836 ------------------------------------------------------------------------------- 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 = 0.3748 r_free = 0.3748 target = 0.138507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.113509 restraints weight = 20822.642| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 1.67 r_work: 0.3256 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8723 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 14413 Z= 0.121 Angle : 0.531 14.545 19758 Z= 0.299 Chirality : 0.041 0.183 2163 Planarity : 0.004 0.044 2290 Dihedral : 17.910 148.110 2480 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.76 % Allowed : 10.47 % 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: -0.98 (0.21), residues: 1554 helix: 0.53 (0.20), residues: 687 sheet: -1.94 (0.34), residues: 225 loop : -1.38 (0.23), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 985 TYR 0.022 0.001 TYR A 531 PHE 0.010 0.001 PHE B 739 TRP 0.010 0.001 TRP B1170 HIS 0.005 0.001 HIS A 789 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.12 (14413) covalent geometry : angle 0.53119 / 0.30 (19758) hydrogen bonds : bond 0.04895 / 5.59 ( 607) hydrogen bonds : angle 4.62853 / 5.99 ( 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 136 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 112 time to evaluate : 0.645 Fit side-chains revert: symmetry clash REVERT: A 474 ILE cc_start: 0.8767 (mm) cc_final: 0.8550 (mt) REVERT: A 531 TYR cc_start: 0.7728 (OUTLIER) cc_final: 0.7213 (p90) REVERT: A 833 GLU cc_start: 0.8651 (OUTLIER) cc_final: 0.7862 (pm20) REVERT: A 892 HIS cc_start: 0.5758 (m90) cc_final: 0.5484 (m170) REVERT: A 985 ARG cc_start: 0.8112 (mpt-90) cc_final: 0.7880 (mtm-85) REVERT: B 676 THR cc_start: 0.8746 (m) cc_final: 0.8463 (p) REVERT: B 716 ARG cc_start: 0.8168 (tpp80) cc_final: 0.7947 (mtt180) REVERT: B 886 LEU cc_start: 0.8211 (OUTLIER) cc_final: 0.7961 (tm) outliers start: 24 outliers final: 10 residues processed: 131 average time/residue: 0.1192 time to fit residues: 23.0430 Evaluate side-chains 115 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 102 time to evaluate : 0.512 ------------------------------------------------------------------------------- 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 636 VAL Chi-restraints excluded: chain B residue 803 VAL Chi-restraints excluded: chain B residue 886 LEU 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: 10.0000 chunk 33 optimal weight: 5.9990 chunk 48 optimal weight: 0.9990 chunk 141 optimal weight: 7.9990 chunk 118 optimal weight: 0.9980 chunk 69 optimal weight: 4.9990 chunk 78 optimal weight: 6.9990 chunk 36 optimal weight: 0.6980 chunk 100 optimal weight: 4.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- 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 = 0.3690 r_free = 0.3690 target = 0.134023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.108914 restraints weight = 20905.224| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 1.70 r_work: 0.3186 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8792 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 14413 Z= 0.227 Angle : 0.624 15.281 19758 Z= 0.343 Chirality : 0.046 0.250 2163 Planarity : 0.005 0.047 2290 Dihedral : 17.950 148.330 2480 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 2.27 % Allowed : 10.40 % 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 are not related in a simple way. whole: -0.96 (0.21), residues: 1554 helix: 0.57 (0.20), residues: 687 sheet: -1.85 (0.34), residues: 227 loop : -1.44 (0.23), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 788 TYR 0.037 0.002 TYR A 531 PHE 0.019 0.002 PHE B 739 TRP 0.011 0.002 TRP A 820 HIS 0.009 0.002 HIS B 752 Details of bonding type rmsd/Z covalent geometry : bond 0.00528 / 0.23 (14413) covalent geometry : angle 0.62421 / 0.34 (19758) hydrogen bonds : bond 0.05756 / 6.47 ( 607) hydrogen bonds : angle 4.69825 / 6.03 ( 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 141 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 110 time to evaluate : 0.563 Fit side-chains REVERT: A 531 TYR cc_start: 0.7905 (OUTLIER) cc_final: 0.7197 (p90) REVERT: A 833 GLU cc_start: 0.8776 (OUTLIER) cc_final: 0.7916 (pm20) REVERT: A 1080 GLU cc_start: 0.7690 (OUTLIER) cc_final: 0.6839 (tm-30) REVERT: A 1116 LYS cc_start: 0.7781 (ptpt) cc_final: 0.7169 (ptpp) REVERT: B 676 THR cc_start: 0.8864 (m) cc_final: 0.8545 (p) REVERT: B 716 ARG cc_start: 0.8315 (tpp80) cc_final: 0.8029 (mtt180) REVERT: B 882 LYS cc_start: 0.7931 (mttt) cc_final: 0.7479 (mtpp) REVERT: B 886 LEU cc_start: 0.8305 (OUTLIER) cc_final: 0.8061 (tm) REVERT: B 1143 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.7844 (mp0) outliers start: 31 outliers final: 21 residues processed: 131 average time/residue: 0.1380 time to fit residues: 26.3544 Evaluate side-chains 128 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 102 time to evaluate : 0.645 ------------------------------------------------------------------------------- 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 778 VAL 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 778 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 1100 THR Chi-restraints excluded: chain B residue 1143 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 92 optimal weight: 3.9990 chunk 158 optimal weight: 4.9990 chunk 137 optimal weight: 0.8980 chunk 52 optimal weight: 4.9990 chunk 5 optimal weight: 9.9990 chunk 122 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 47 optimal weight: 0.2980 chunk 74 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 120 optimal weight: 0.5980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3720 r_free = 0.3720 target = 0.136400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.111686 restraints weight = 20685.311| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 1.66 r_work: 0.3230 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3116 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 moved from start: 0.2158 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= 0.135 Angle : 0.538 14.789 19758 Z= 0.301 Chirality : 0.042 0.194 2163 Planarity : 0.004 0.043 2290 Dihedral : 17.883 147.870 2480 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.27 % Allowed : 10.98 % 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: -0.68 (0.22), residues: 1554 helix: 0.79 (0.20), residues: 689 sheet: -1.79 (0.34), residues: 225 loop : -1.24 (0.24), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 985 TYR 0.025 0.001 TYR A 531 PHE 0.012 0.001 PHE B 739 TRP 0.008 0.001 TRP A1189 HIS 0.004 0.001 HIS B 789 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.14 (14413) covalent geometry : angle 0.53812 / 0.30 (19758) hydrogen bonds : bond 0.04962 / 5.63 ( 607) hydrogen bonds : angle 4.51892 / 5.83 ( 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: 31 poor density : 111 time to evaluate : 0.510 Fit side-chains REVERT: A 531 TYR cc_start: 0.7819 (OUTLIER) cc_final: 0.7128 (p90) REVERT: A 833 GLU cc_start: 0.8734 (OUTLIER) cc_final: 0.7962 (pm20) REVERT: A 1080 GLU cc_start: 0.7660 (OUTLIER) cc_final: 0.6827 (tm-30) REVERT: A 1116 LYS cc_start: 0.7790 (ptpt) cc_final: 0.7298 (ptpp) REVERT: B 636 VAL cc_start: 0.8458 (OUTLIER) cc_final: 0.8222 (t) REVERT: B 676 THR cc_start: 0.8861 (m) cc_final: 0.8575 (p) REVERT: B 716 ARG cc_start: 0.8217 (tpp80) cc_final: 0.7989 (mtt180) REVERT: B 882 LYS cc_start: 0.7856 (mttt) cc_final: 0.7386 (mtpp) REVERT: B 886 LEU cc_start: 0.8280 (OUTLIER) cc_final: 0.8041 (tm) REVERT: B 1074 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8634 (tt) REVERT: B 1143 GLU cc_start: 0.8333 (OUTLIER) cc_final: 0.7849 (mp0) outliers start: 31 outliers final: 17 residues processed: 137 average time/residue: 0.1278 time to fit residues: 25.5591 Evaluate side-chains 128 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 104 time to evaluate : 0.436 ------------------------------------------------------------------------------- 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 976 VAL 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 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 949 SER Chi-restraints excluded: chain B residue 1062 THR Chi-restraints excluded: chain B residue 1074 LEU Chi-restraints excluded: chain B residue 1143 GLU Chi-restraints excluded: chain B residue 1158 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 9 optimal weight: 3.9990 chunk 132 optimal weight: 4.9990 chunk 44 optimal weight: 0.5980 chunk 15 optimal weight: 0.8980 chunk 84 optimal weight: 6.9990 chunk 73 optimal weight: 4.9990 chunk 117 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 chunk 142 optimal weight: 0.6980 chunk 93 optimal weight: 0.7980 chunk 50 optimal weight: 3.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 = 0.3718 r_free = 0.3718 target = 0.136302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.111542 restraints weight = 20684.520| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 1.66 r_work: 0.3231 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3116 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8746 moved from start: 0.2262 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= 0.134 Angle : 0.533 14.670 19758 Z= 0.298 Chirality : 0.042 0.198 2163 Planarity : 0.004 0.041 2290 Dihedral : 17.841 147.734 2480 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.12 % Allowed : 11.86 % Favored : 86.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.54 (0.22), residues: 1554 helix: 0.94 (0.20), residues: 689 sheet: -1.81 (0.33), residues: 239 loop : -1.16 (0.24), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 985 TYR 0.024 0.001 TYR A 531 PHE 0.012 0.001 PHE B 739 TRP 0.008 0.001 TRP A1189 HIS 0.005 0.001 HIS B 789 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.13 (14413) covalent geometry : angle 0.53306 / 0.30 (19758) hydrogen bonds : bond 0.04848 / 5.50 ( 607) hydrogen bonds : angle 4.44661 / 5.74 ( 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 140 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 111 time to evaluate : 0.543 Fit side-chains REVERT: A 531 TYR cc_start: 0.7803 (OUTLIER) cc_final: 0.7083 (p90) REVERT: A 833 GLU cc_start: 0.8749 (OUTLIER) cc_final: 0.7972 (pm20) REVERT: A 1080 GLU cc_start: 0.7649 (OUTLIER) cc_final: 0.6811 (tm-30) REVERT: A 1116 LYS cc_start: 0.7777 (ptpt) cc_final: 0.7287 (ptpp) REVERT: B 636 VAL cc_start: 0.8467 (OUTLIER) cc_final: 0.8212 (t) REVERT: B 676 THR cc_start: 0.8851 (m) cc_final: 0.8574 (p) REVERT: B 716 ARG cc_start: 0.8201 (tpp80) cc_final: 0.7992 (mtt180) REVERT: B 882 LYS cc_start: 0.7882 (mttt) cc_final: 0.7421 (mtpp) REVERT: B 886 LEU cc_start: 0.8299 (OUTLIER) cc_final: 0.8059 (tm) REVERT: B 1074 LEU cc_start: 0.8883 (OUTLIER) cc_final: 0.8650 (tt) REVERT: B 1143 GLU cc_start: 0.8333 (OUTLIER) cc_final: 0.7855 (mp0) outliers start: 29 outliers final: 18 residues processed: 134 average time/residue: 0.1268 time to fit residues: 25.2319 Evaluate side-chains 129 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 104 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 415 VAL 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 830 GLN Chi-restraints excluded: chain A residue 833 GLU Chi-restraints excluded: chain A residue 950 ILE Chi-restraints excluded: chain A residue 976 VAL 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 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 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: 3.9990 chunk 143 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 87 optimal weight: 10.0000 chunk 113 optimal weight: 0.9990 chunk 160 optimal weight: 0.7980 chunk 88 optimal weight: 0.0970 chunk 67 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3738 r_free = 0.3738 target = 0.137800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.113293 restraints weight = 20766.047| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 1.63 r_work: 0.3256 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8723 moved from start: 0.2399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 14413 Z= 0.121 Angle : 0.512 14.467 19758 Z= 0.289 Chirality : 0.041 0.185 2163 Planarity : 0.004 0.040 2290 Dihedral : 17.768 147.327 2480 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.98 % Allowed : 11.93 % 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: -0.29 (0.22), residues: 1554 helix: 1.13 (0.21), residues: 690 sheet: -1.73 (0.34), residues: 237 loop : -0.98 (0.24), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 985 TYR 0.019 0.001 TYR A 531 PHE 0.017 0.001 PHE A 959 TRP 0.008 0.001 TRP A1189 HIS 0.004 0.001 HIS B 789 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.12 (14413) covalent geometry : angle 0.51250 / 0.29 (19758) hydrogen bonds : bond 0.04512 / 5.14 ( 607) hydrogen bonds : angle 4.32625 / 5.60 ( 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 146 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 119 time to evaluate : 0.541 Fit side-chains REVERT: A 531 TYR cc_start: 0.7801 (OUTLIER) cc_final: 0.7008 (p90) REVERT: A 833 GLU cc_start: 0.8711 (OUTLIER) cc_final: 0.7936 (pm20) REVERT: A 1080 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.6910 (tm-30) REVERT: A 1116 LYS cc_start: 0.7764 (ptpt) cc_final: 0.7262 (ptpp) REVERT: B 636 VAL cc_start: 0.8480 (OUTLIER) cc_final: 0.8237 (t) REVERT: B 676 THR cc_start: 0.8847 (m) cc_final: 0.8594 (p) REVERT: B 882 LYS cc_start: 0.7857 (mttt) cc_final: 0.7387 (mtpp) REVERT: B 886 LEU cc_start: 0.8255 (OUTLIER) cc_final: 0.8034 (tm) REVERT: B 1074 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8644 (tt) REVERT: B 1143 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.7838 (mp0) outliers start: 27 outliers final: 15 residues processed: 141 average time/residue: 0.1201 time to fit residues: 25.0262 Evaluate side-chains 133 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 111 time to evaluate : 0.527 ------------------------------------------------------------------------------- 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 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 633 ASP Chi-restraints excluded: chain B residue 636 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 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: 0.7980 chunk 119 optimal weight: 2.9990 chunk 147 optimal weight: 0.7980 chunk 144 optimal weight: 0.0470 chunk 4 optimal weight: 9.9990 chunk 98 optimal weight: 0.9980 chunk 58 optimal weight: 0.2980 chunk 88 optimal weight: 4.9990 chunk 36 optimal weight: 0.6980 chunk 83 optimal weight: 0.7980 chunk 8 optimal weight: 4.9990 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 483 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.138629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.114197 restraints weight = 20850.230| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 1.66 r_work: 0.3267 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3154 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.2527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 14413 Z= 0.113 Angle : 0.508 14.517 19758 Z= 0.284 Chirality : 0.041 0.177 2163 Planarity : 0.003 0.040 2290 Dihedral : 17.695 147.034 2480 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.76 % Allowed : 12.52 % 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 are not related in a simple way. whole: -0.15 (0.22), residues: 1554 helix: 1.23 (0.21), residues: 690 sheet: -1.62 (0.34), residues: 237 loop : -0.91 (0.24), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 985 TYR 0.017 0.001 TYR A 531 PHE 0.009 0.001 PHE A 739 TRP 0.007 0.001 TRP A1189 HIS 0.003 0.001 HIS B 909 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.11 (14413) covalent geometry : angle 0.50820 / 0.28 (19758) hydrogen bonds : bond 0.04294 / 4.90 ( 607) hydrogen bonds : angle 4.25020 / 5.51 ( 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 144 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 120 time to evaluate : 0.516 Fit side-chains REVERT: A 455 SER cc_start: 0.8016 (t) cc_final: 0.7781 (t) REVERT: A 531 TYR cc_start: 0.7754 (OUTLIER) cc_final: 0.6967 (p90) REVERT: A 833 GLU cc_start: 0.8697 (OUTLIER) cc_final: 0.7924 (pm20) REVERT: A 1080 GLU cc_start: 0.7747 (OUTLIER) cc_final: 0.6940 (tm-30) REVERT: A 1116 LYS cc_start: 0.7766 (ptpt) cc_final: 0.7257 (ptpp) REVERT: B 454 LYS cc_start: 0.7606 (mmtm) cc_final: 0.6703 (ttpp) REVERT: B 636 VAL cc_start: 0.8475 (OUTLIER) cc_final: 0.8242 (t) REVERT: B 676 THR cc_start: 0.8819 (m) cc_final: 0.8587 (p) REVERT: B 882 LYS cc_start: 0.7791 (mttt) cc_final: 0.7305 (mtpp) REVERT: B 886 LEU cc_start: 0.8236 (OUTLIER) cc_final: 0.8032 (tm) REVERT: B 1074 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8645 (tt) REVERT: B 1143 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.7848 (mp0) outliers start: 24 outliers final: 17 residues processed: 139 average time/residue: 0.1007 time to fit residues: 21.0767 Evaluate side-chains 134 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 110 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 415 VAL 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 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 633 ASP Chi-restraints excluded: chain B residue 636 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 9 optimal weight: 3.9990 chunk 95 optimal weight: 5.9990 chunk 88 optimal weight: 1.9990 chunk 133 optimal weight: 4.9990 chunk 110 optimal weight: 6.9990 chunk 97 optimal weight: 0.5980 chunk 83 optimal weight: 3.9990 chunk 66 optimal weight: 0.0370 chunk 159 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 overall best weight: 1.3264 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 692 GLN B 892 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.136391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.111789 restraints weight = 20874.160| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 1.64 r_work: 0.3235 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.2483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14413 Z= 0.153 Angle : 0.552 14.879 19758 Z= 0.305 Chirality : 0.043 0.212 2163 Planarity : 0.004 0.040 2290 Dihedral : 17.743 147.018 2480 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.90 % Allowed : 12.52 % Favored : 85.58 % 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: -0.16 (0.22), residues: 1554 helix: 1.22 (0.21), residues: 690 sheet: -1.53 (0.35), residues: 237 loop : -0.95 (0.24), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 985 TYR 0.023 0.001 TYR A 531 PHE 0.014 0.001 PHE B 739 TRP 0.010 0.001 TRP A 820 HIS 0.006 0.001 HIS B 789 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 (14413) covalent geometry : angle 0.55193 / 0.30 (19758) hydrogen bonds : bond 0.04717 / 5.33 ( 607) hydrogen bonds : angle 4.29511 / 5.54 ( 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 140 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 114 time to evaluate : 0.551 Fit side-chains REVERT: A 455 SER cc_start: 0.8053 (t) cc_final: 0.7816 (t) REVERT: A 531 TYR cc_start: 0.7803 (OUTLIER) cc_final: 0.6943 (p90) REVERT: A 833 GLU cc_start: 0.8768 (OUTLIER) cc_final: 0.7921 (pm20) REVERT: A 957 MET cc_start: 0.8242 (mmp) cc_final: 0.7840 (mmt) REVERT: A 960 ILE cc_start: 0.8415 (pp) cc_final: 0.7740 (mt) REVERT: A 1080 GLU cc_start: 0.7769 (OUTLIER) cc_final: 0.6950 (tm-30) REVERT: A 1116 LYS cc_start: 0.7766 (ptpt) cc_final: 0.7261 (ptpp) REVERT: B 636 VAL cc_start: 0.8536 (OUTLIER) cc_final: 0.8247 (t) REVERT: B 676 THR cc_start: 0.8860 (m) cc_final: 0.8620 (p) REVERT: B 882 LYS cc_start: 0.7865 (mttt) cc_final: 0.7390 (mtpp) REVERT: B 1074 LEU cc_start: 0.8876 (OUTLIER) cc_final: 0.8611 (tt) REVERT: B 1079 TYR cc_start: 0.8249 (m-80) cc_final: 0.7595 (m-80) REVERT: B 1143 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.7820 (mp0) outliers start: 26 outliers final: 17 residues processed: 135 average time/residue: 0.1044 time to fit residues: 21.1520 Evaluate side-chains 134 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 111 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 415 VAL 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 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 633 ASP Chi-restraints excluded: chain B residue 636 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 158 optimal weight: 0.0070 chunk 104 optimal weight: 3.9990 chunk 119 optimal weight: 2.9990 chunk 126 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 chunk 127 optimal weight: 0.8980 chunk 90 optimal weight: 7.9990 chunk 48 optimal weight: 0.3980 chunk 95 optimal weight: 5.9990 overall best weight: 0.6600 ------------------------------------------------------------------------------- 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 = 0.3740 r_free = 0.3740 target = 0.137862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.113203 restraints weight = 20751.901| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 1.67 r_work: 0.3253 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 moved from start: 0.2571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 14413 Z= 0.118 Angle : 0.522 14.223 19758 Z= 0.289 Chirality : 0.041 0.184 2163 Planarity : 0.004 0.040 2290 Dihedral : 17.712 147.009 2480 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.90 % Allowed : 12.66 % Favored : 85.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.02 (0.22), residues: 1554 helix: 1.34 (0.21), residues: 685 sheet: -1.39 (0.36), residues: 223 loop : -0.93 (0.23), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 985 TYR 0.019 0.001 TYR A 531 PHE 0.010 0.001 PHE B 739 TRP 0.007 0.001 TRP A1189 HIS 0.004 0.001 HIS B 789 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.12 (14413) covalent geometry : angle 0.52210 / 0.29 (19758) hydrogen bonds : bond 0.04378 / 4.98 ( 607) hydrogen bonds : angle 4.24249 / 5.49 ( 1675) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3544.16 seconds wall clock time: 61 minutes 29.14 seconds (3689.14 seconds total)