Starting phenix.real_space_refine on Sun Jul 21 09:31:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kgr_37231/07_2024/8kgr_37231_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kgr_37231/07_2024/8kgr_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kgr_37231/07_2024/8kgr_37231.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kgr_37231/07_2024/8kgr_37231.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kgr_37231/07_2024/8kgr_37231_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kgr_37231/07_2024/8kgr_37231_neut.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 65 5.49 5 Mg 2 5.21 5 S 56 5.16 5 C 8745 2.51 5 N 2405 2.21 5 O 2687 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 769": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 769": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 923": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1039": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 13960 Number of models: 1 Model: "" Number of chains: 6 Chain: "C" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 658 Classifications: {'DNA': 32} Link IDs: {'rna3p': 31} Chain: "D" Number of atoms: 675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 675 Classifications: {'DNA': 33} Link IDs: {'rna3p': 32} Chain: "A" Number of atoms: 6320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 780, 6320 Classifications: {'peptide': 780} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 749} Chain: "B" Number of atoms: 6305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 778, 6305 Classifications: {'peptide': 778} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 747} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 9.59, per 1000 atoms: 0.69 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 - 3.50 Amino acid : False - 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: 5.41 Conformation dependent library (CDL) restraints added in 2.4 seconds 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2928 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 18 sheets defined 51.3% alpha, 10.1% beta 22 base pairs and 48 stacking pairs defined. Time for finding SS restraints: 4.75 Creating SS restraints... Processing helix chain 'A' and resid 440 through 450 Processing helix chain 'A' and resid 496 through 501 Processing helix chain 'A' and resid 502 through 512 Processing helix chain 'A' and resid 541 through 546 Processing helix chain 'A' and resid 546 through 560 Processing helix chain 'A' and resid 560 through 567 removed outlier: 4.057A pdb=" N ILE A 564 " --> pdb=" O TRP A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 602 removed outlier: 3.721A pdb=" N LYS A 602 " --> pdb=" O ALA A 598 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 620 removed outlier: 3.759A pdb=" N ALA A 619 " --> pdb=" O GLY A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 630 removed outlier: 4.414A pdb=" N SER A 627 " --> pdb=" O HIS A 623 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 636 removed outlier: 3.948A pdb=" N VAL A 636 " --> pdb=" O ASP A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 642 through 644 No H-bonds generated for 'chain 'A' and resid 642 through 644' Processing helix chain 'A' and resid 645 through 654 Processing helix chain 'A' and resid 657 through 665 Processing helix chain 'A' and resid 672 through 683 Processing helix chain 'A' and resid 687 through 692 Processing helix chain 'A' and resid 693 through 707 Processing helix chain 'A' and resid 715 through 729 Processing helix chain 'A' and resid 738 through 749 removed outlier: 3.501A pdb=" N MET A 749 " --> pdb=" O VAL A 745 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 765 Processing helix chain 'A' and resid 787 through 791 removed outlier: 3.912A pdb=" N LEU A 790 " --> pdb=" O SER A 787 " (cutoff:3.500A) Processing helix chain 'A' and resid 806 through 814 Processing helix chain 'A' and resid 815 through 819 Processing helix chain 'A' and resid 842 through 846 removed outlier: 3.566A pdb=" N MET A 846 " --> pdb=" O LEU A 843 " (cutoff:3.500A) Processing helix chain 'A' and resid 864 through 877 removed outlier: 3.653A pdb=" N ILE A 868 " --> pdb=" O GLN A 864 " (cutoff:3.500A) Processing helix chain 'A' and resid 883 through 893 Processing helix chain 'A' and resid 942 through 953 removed outlier: 3.787A pdb=" N SER A 953 " --> pdb=" O SER A 949 " (cutoff:3.500A) Processing helix chain 'A' and resid 953 through 958 removed outlier: 3.817A pdb=" N THR A 958 " --> pdb=" O SER A 954 " (cutoff:3.500A) Processing helix chain 'A' and resid 983 through 990 removed outlier: 4.360A pdb=" N VAL A 987 " --> pdb=" O LEU A 983 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N GLU A 988 " --> pdb=" O ASN A 984 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU A 989 " --> pdb=" O ARG A 985 " (cutoff:3.500A) Processing helix chain 'A' and resid 997 through 1003 Processing helix chain 'A' and resid 1027 through 1075 removed outlier: 3.731A pdb=" N ILE A1031 " --> pdb=" O THR A1027 " (cutoff:3.500A) Proline residue: A1037 - end of helix removed outlier: 4.062A pdb=" N ALA A1063 " --> pdb=" O ILE A1059 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE A1064 " --> pdb=" O MET A1060 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N ARG A1066 " --> pdb=" O THR A1062 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N ALA A1072 " --> pdb=" O ILE A1068 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N GLU A1073 " --> pdb=" O ASN A1069 " (cutoff:3.500A) Processing helix chain 'A' and resid 1076 through 1079 removed outlier: 3.507A pdb=" N TYR A1079 " --> pdb=" O LEU A1076 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1076 through 1079' Processing helix chain 'A' and resid 1081 through 1091 Processing helix chain 'A' and resid 1098 through 1104 Processing helix chain 'A' and resid 1109 through 1116 Processing helix chain 'A' and resid 1122 through 1127 Processing helix chain 'A' and resid 1129 through 1133 removed outlier: 3.692A pdb=" N LEU A1133 " --> pdb=" O ALA A1130 " (cutoff:3.500A) Processing helix chain 'A' and resid 1134 through 1159 Processing helix chain 'A' and resid 1168 through 1187 Processing helix chain 'B' and resid 428 through 431 Processing helix chain 'B' and resid 440 through 450 Processing helix chain 'B' and resid 496 through 501 Processing helix chain 'B' and resid 502 through 513 Processing helix chain 'B' and resid 541 through 560 removed outlier: 4.251A pdb=" N ILE B 548 " --> pdb=" O GLY B 544 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N LEU B 549 " --> pdb=" O CYS B 545 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 566 removed outlier: 3.987A pdb=" N ILE B 564 " --> pdb=" O TRP B 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 592 through 603 removed outlier: 3.600A pdb=" N LYS B 602 " --> pdb=" O ALA B 598 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLN B 603 " --> pdb=" O TRP B 599 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 620 removed outlier: 3.615A pdb=" N HIS B 620 " --> pdb=" O LEU B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 621 through 630 Processing helix chain 'B' and resid 632 through 636 removed outlier: 3.944A pdb=" N VAL B 636 " --> pdb=" O ASP B 633 " (cutoff:3.500A) Processing helix chain 'B' and resid 644 through 654 removed outlier: 3.899A pdb=" N LEU B 648 " --> pdb=" O SER B 644 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N PHE B 653 " --> pdb=" O PHE B 649 " (cutoff:3.500A) Processing helix chain 'B' and resid 657 through 664 Processing helix chain 'B' and resid 672 through 683 Processing helix chain 'B' and resid 687 through 692 Processing helix chain 'B' and resid 693 through 707 Processing helix chain 'B' and resid 715 through 729 Processing helix chain 'B' and resid 738 through 749 removed outlier: 3.633A pdb=" N MET B 749 " --> pdb=" O VAL B 745 " (cutoff:3.500A) Processing helix chain 'B' and resid 754 through 767 removed outlier: 3.998A pdb=" N LEU B 758 " --> pdb=" O GLY B 754 " (cutoff:3.500A) Processing helix chain 'B' and resid 806 through 814 Processing helix chain 'B' and resid 815 through 819 Processing helix chain 'B' and resid 842 through 846 Processing helix chain 'B' and resid 864 through 877 removed outlier: 3.616A pdb=" N ILE B 868 " --> pdb=" O GLN B 864 " (cutoff:3.500A) Processing helix chain 'B' and resid 882 through 893 removed outlier: 3.659A pdb=" N LEU B 886 " --> pdb=" O LYS B 882 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 951 Processing helix chain 'B' and resid 953 through 958 removed outlier: 3.514A pdb=" N THR B 958 " --> pdb=" O SER B 954 " (cutoff:3.500A) Processing helix chain 'B' and resid 982 through 990 Processing helix chain 'B' and resid 997 through 1003 Processing helix chain 'B' and resid 1027 through 1075 removed outlier: 3.716A pdb=" N ILE B1031 " --> pdb=" O THR B1027 " (cutoff:3.500A) Proline residue: B1037 - end of helix removed outlier: 4.021A pdb=" N ALA B1063 " --> pdb=" O ILE B1059 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE B1064 " --> pdb=" O MET B1060 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N ARG B1066 " --> pdb=" O THR B1062 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N ALA B1072 " --> pdb=" O ILE B1068 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N GLU B1073 " --> pdb=" O ASN B1069 " (cutoff:3.500A) Processing helix chain 'B' and resid 1076 through 1079 Processing helix chain 'B' and resid 1081 through 1091 Processing helix chain 'B' and resid 1098 through 1103 Processing helix chain 'B' and resid 1109 through 1117 removed outlier: 3.966A pdb=" N LYS B1116 " --> pdb=" O GLU B1112 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ALA B1117 " --> pdb=" O LEU B1113 " (cutoff:3.500A) Processing helix chain 'B' and resid 1122 through 1127 Processing helix chain 'B' and resid 1129 through 1133 removed outlier: 3.500A pdb=" N LEU B1133 " --> pdb=" O ALA B1130 " (cutoff:3.500A) Processing helix chain 'B' and resid 1134 through 1159 Processing helix chain 'B' and resid 1166 through 1187 removed outlier: 3.973A pdb=" N TRP B1170 " --> pdb=" O GLY B1166 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU B1171 " --> pdb=" O ALA B1167 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N THR B1187 " --> pdb=" O LYS B1183 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 465 through 469 removed outlier: 3.789A pdb=" N ILE A 468 " --> pdb=" O LEU A 435 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N LEU A 434 " --> pdb=" O VAL A 535 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N CYS A 537 " --> pdb=" O LEU A 434 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ALA A 436 " --> pdb=" O CYS A 537 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N VAL A 569 " --> pdb=" O PHE A 639 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 481 through 484 Processing sheet with id=AA3, first strand: chain 'A' and resid 588 through 590 Processing sheet with id=AA4, first strand: chain 'A' and resid 736 through 737 Processing sheet with id=AA5, first strand: chain 'A' and resid 824 through 827 removed outlier: 3.667A pdb=" N GLU A 833 " --> pdb=" O VAL A 825 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N GLU A 827 " --> pdb=" O ARG A 831 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N ARG A 831 " --> pdb=" O GLU A 827 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 849 through 852 removed outlier: 3.545A pdb=" N GLY A 849 " --> pdb=" O THR A 860 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 909 through 912 removed outlier: 3.722A pdb=" N HIS A 909 " --> pdb=" O TYR A 920 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N TYR A 917 " --> pdb=" O LEU A1009 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 933 through 934 removed outlier: 3.727A pdb=" N GLU A 962 " --> pdb=" O LYS A 977 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1014 through 1016 Processing sheet with id=AB1, first strand: chain 'B' and resid 465 through 469 removed outlier: 3.710A pdb=" N ILE B 468 " --> pdb=" O LEU B 435 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N LEU B 434 " --> pdb=" O VAL B 535 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N CYS B 537 " --> pdb=" O LEU B 434 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N ALA B 436 " --> pdb=" O CYS B 537 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N VAL B 569 " --> pdb=" O PHE B 639 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 481 through 485 Processing sheet with id=AB3, first strand: chain 'B' and resid 588 through 590 Processing sheet with id=AB4, first strand: chain 'B' and resid 736 through 737 removed outlier: 3.693A pdb=" N ARG B 736 " --> pdb=" O VAL B 803 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 824 through 827 removed outlier: 3.770A pdb=" N GLU B 833 " --> pdb=" O VAL B 825 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N GLU B 827 " --> pdb=" O ARG B 831 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N ARG B 831 " --> pdb=" O GLU B 827 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 849 through 852 removed outlier: 3.652A pdb=" N GLY B 849 " --> pdb=" O THR B 860 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 909 through 913 removed outlier: 3.514A pdb=" N TYR B 916 " --> pdb=" O PHE B 913 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 925 through 926 removed outlier: 4.201A pdb=" N ILE B 932 " --> pdb=" O VAL B 976 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLU B 962 " --> pdb=" O LYS B 977 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 1014 through 1016 557 hydrogen bonds defined for protein. 1575 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 50 hydrogen bonds 100 hydrogen bond angles 0 basepair planarities 22 basepair parallelities 48 stacking parallelities Total time for adding SS restraints: 5.56 Time building geometry restraints manager: 5.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2687 1.33 - 1.45: 3807 1.45 - 1.57: 7703 1.57 - 1.69: 128 1.69 - 1.81: 88 Bond restraints: 14413 Sorted by residual: bond pdb=" N ARG A 734 " pdb=" CA ARG A 734 " ideal model delta sigma weight residual 1.455 1.488 -0.033 1.33e-02 5.65e+03 5.99e+00 bond pdb=" N LYS A 857 " pdb=" CA LYS A 857 " ideal model delta sigma weight residual 1.455 1.483 -0.028 1.25e-02 6.40e+03 5.13e+00 bond pdb=" CA LEU B1036 " pdb=" C LEU B1036 " ideal model delta sigma weight residual 1.522 1.549 -0.027 1.29e-02 6.01e+03 4.36e+00 bond pdb=" CA LEU A1036 " pdb=" C LEU A1036 " ideal model delta sigma weight residual 1.522 1.548 -0.026 1.29e-02 6.01e+03 4.18e+00 bond pdb=" C3' DT C 44 " pdb=" O3' DT C 44 " ideal model delta sigma weight residual 1.422 1.473 -0.051 3.00e-02 1.11e+03 2.86e+00 ... (remaining 14408 not shown) Histogram of bond angle deviations from ideal: 98.37 - 105.99: 623 105.99 - 113.61: 7908 113.61 - 121.24: 7472 121.24 - 128.86: 3617 128.86 - 136.48: 138 Bond angle restraints: 19758 Sorted by residual: angle pdb=" C ARG A 929 " pdb=" N ASN A 930 " pdb=" CA ASN A 930 " ideal model delta sigma weight residual 121.54 130.55 -9.01 1.91e+00 2.74e-01 2.22e+01 angle pdb=" N LYS A 615 " pdb=" CA LYS A 615 " pdb=" C LYS A 615 " ideal model delta sigma weight residual 108.96 102.34 6.62 1.59e+00 3.96e-01 1.73e+01 angle pdb=" N LEU A1036 " pdb=" CA LEU A1036 " pdb=" C LEU A1036 " ideal model delta sigma weight residual 113.45 119.07 -5.62 1.39e+00 5.18e-01 1.63e+01 angle pdb=" CA TYR A 531 " pdb=" CB TYR A 531 " pdb=" CG TYR A 531 " ideal model delta sigma weight residual 113.90 121.07 -7.17 1.80e+00 3.09e-01 1.59e+01 angle pdb=" N LEU B1036 " pdb=" CA LEU B1036 " pdb=" C LEU B1036 " ideal model delta sigma weight residual 113.45 118.85 -5.40 1.39e+00 5.18e-01 1.51e+01 ... (remaining 19753 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.56: 8079 28.56 - 57.13: 403 57.13 - 85.69: 37 85.69 - 114.25: 0 114.25 - 142.82: 2 Dihedral angle restraints: 8521 sinusoidal: 3953 harmonic: 4568 Sorted by residual: dihedral pdb=" CA THR A1062 " pdb=" C THR A1062 " pdb=" N ALA A1063 " pdb=" CA ALA A1063 " ideal model delta harmonic sigma weight residual 180.00 153.38 26.62 0 5.00e+00 4.00e-02 2.84e+01 dihedral pdb=" CA GLU B 663 " pdb=" C GLU B 663 " pdb=" N LEU B 664 " pdb=" CA LEU B 664 " ideal model delta harmonic sigma weight residual -180.00 -154.84 -25.16 0 5.00e+00 4.00e-02 2.53e+01 dihedral pdb=" CA TYR A 531 " pdb=" C TYR A 531 " pdb=" N GLY A 532 " pdb=" CA GLY A 532 " ideal model delta harmonic sigma weight residual -180.00 -154.84 -25.16 0 5.00e+00 4.00e-02 2.53e+01 ... (remaining 8518 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 1751 0.075 - 0.151: 377 0.151 - 0.226: 30 0.226 - 0.301: 3 0.301 - 0.376: 2 Chirality restraints: 2163 Sorted by residual: chirality pdb=" CB ILE A 963 " pdb=" CA ILE A 963 " pdb=" CG1 ILE A 963 " pdb=" CG2 ILE A 963 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.38 2.00e-01 2.50e+01 3.54e+00 chirality pdb=" CB ILE B 963 " pdb=" CA ILE B 963 " pdb=" CG1 ILE B 963 " pdb=" CG2 ILE B 963 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.32 2.00e-01 2.50e+01 2.49e+00 chirality pdb=" CB ILE B 534 " pdb=" CA ILE B 534 " pdb=" CG1 ILE B 534 " pdb=" CG2 ILE B 534 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 2.00e+00 ... (remaining 2160 not shown) Planarity restraints: 2290 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B1170 " -0.026 2.00e-02 2.50e+03 2.67e-02 1.78e+01 pdb=" CG TRP B1170 " 0.071 2.00e-02 2.50e+03 pdb=" CD1 TRP B1170 " -0.036 2.00e-02 2.50e+03 pdb=" CD2 TRP B1170 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP B1170 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP B1170 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP B1170 " -0.008 2.00e-02 2.50e+03 pdb=" CZ2 TRP B1170 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B1170 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP B1170 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A1170 " 0.025 2.00e-02 2.50e+03 2.62e-02 1.72e+01 pdb=" CG TRP A1170 " -0.069 2.00e-02 2.50e+03 pdb=" CD1 TRP A1170 " 0.037 2.00e-02 2.50e+03 pdb=" CD2 TRP A1170 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP A1170 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A1170 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A1170 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP A1170 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A1170 " 0.010 2.00e-02 2.50e+03 pdb=" CH2 TRP A1170 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 531 " 0.037 2.00e-02 2.50e+03 2.57e-02 1.32e+01 pdb=" CG TYR A 531 " -0.061 2.00e-02 2.50e+03 pdb=" CD1 TYR A 531 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR A 531 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR A 531 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR A 531 " 0.008 2.00e-02 2.50e+03 pdb=" CZ TYR A 531 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR A 531 " 0.007 2.00e-02 2.50e+03 ... (remaining 2287 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.57: 68 2.57 - 3.15: 10090 3.15 - 3.73: 20881 3.73 - 4.32: 30185 4.32 - 4.90: 49790 Nonbonded interactions: 111014 Sorted by model distance: nonbonded pdb=" OD2 ASP A 539 " pdb="MG MG A1301 " model vdw 1.983 2.170 nonbonded pdb=" OD2 ASP B 539 " pdb="MG MG B1301 " model vdw 2.091 2.170 nonbonded pdb=" OP1 DA C 31 " pdb=" OH TYR A 800 " model vdw 2.197 2.440 nonbonded pdb=" OG SER A 919 " pdb=" OD1 ASN A1007 " model vdw 2.248 2.440 nonbonded pdb=" OH TYR A1043 " pdb=" OE1 GLU A1173 " model vdw 2.251 2.440 ... (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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 415 through 1192 or resid 1301)) selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.630 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 44.210 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.071 14413 Z= 0.513 Angle : 0.954 16.181 19758 Z= 0.522 Chirality : 0.060 0.376 2163 Planarity : 0.007 0.077 2290 Dihedral : 15.372 142.818 5593 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 0.07 % Allowed : 3.59 % Favored : 96.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.81 (0.17), residues: 1554 helix: -2.44 (0.15), residues: 684 sheet: -2.50 (0.34), residues: 201 loop : -2.47 (0.20), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.071 0.005 TRP B1170 HIS 0.014 0.003 HIS B 892 PHE 0.026 0.003 PHE B 739 TYR 0.061 0.003 TYR A 531 ARG 0.017 0.002 ARG B1039 *********************** 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 fitting. rotamer outliers: 1 poor density : 233 time to evaluate : 1.410 Fit side-chains revert: symmetry clash REVERT: A 455 SER cc_start: 0.8007 (t) cc_final: 0.7794 (t) REVERT: A 461 SER cc_start: 0.8536 (p) cc_final: 0.8323 (t) REVERT: A 474 ILE cc_start: 0.8775 (mm) cc_final: 0.8562 (mt) REVERT: A 749 MET cc_start: 0.8213 (mmp) cc_final: 0.7565 (mmt) REVERT: A 905 ASN cc_start: 0.8518 (t0) cc_final: 0.8241 (t0) REVERT: B 543 ASP cc_start: 0.8270 (t70) cc_final: 0.7921 (m-30) REVERT: B 854 GLU cc_start: 0.8298 (mm-30) cc_final: 0.8080 (mm-30) outliers start: 1 outliers final: 0 residues processed: 234 average time/residue: 0.3187 time to fit residues: 102.4183 Evaluate side-chains 111 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 111 time to evaluate : 1.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 135 optimal weight: 4.9990 chunk 122 optimal weight: 0.9990 chunk 67 optimal weight: 0.9980 chunk 41 optimal weight: 0.9980 chunk 82 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 126 optimal weight: 0.6980 chunk 48 optimal weight: 5.9990 chunk 76 optimal weight: 0.7980 chunk 93 optimal weight: 0.9990 chunk 146 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 566 HIS ** A 880 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1051 HIS A1078 HIS ** B 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 ASN B 502 ASN B 566 HIS B 692 GLN B 892 HIS B 905 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.1706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 14413 Z= 0.181 Angle : 0.561 15.253 19758 Z= 0.304 Chirality : 0.041 0.154 2163 Planarity : 0.005 0.055 2290 Dihedral : 17.587 145.843 2480 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.27 % Allowed : 7.61 % Favored : 90.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.20), residues: 1554 helix: -0.44 (0.19), residues: 675 sheet: -2.12 (0.34), residues: 215 loop : -1.85 (0.22), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B1170 HIS 0.010 0.001 HIS A1078 PHE 0.013 0.001 PHE B 959 TYR 0.026 0.001 TYR A 531 ARG 0.004 0.001 ARG B1046 *********************** 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 179 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 148 time to evaluate : 1.533 Fit side-chains revert: symmetry clash REVERT: A 778 VAL cc_start: 0.8670 (t) cc_final: 0.8418 (m) REVERT: B 676 THR cc_start: 0.8627 (m) cc_final: 0.8387 (p) REVERT: B 854 GLU cc_start: 0.8204 (mm-30) cc_final: 0.7978 (mm-30) REVERT: B 882 LYS cc_start: 0.7787 (mttt) cc_final: 0.7457 (mtpp) REVERT: B 886 LEU cc_start: 0.8068 (OUTLIER) cc_final: 0.7829 (tm) outliers start: 31 outliers final: 13 residues processed: 169 average time/residue: 0.2851 time to fit residues: 69.2807 Evaluate side-chains 127 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 113 time to evaluate : 1.404 ------------------------------------------------------------------------------- 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 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 610 THR Chi-restraints excluded: chain B residue 633 ASP 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 1100 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 81 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 121 optimal weight: 0.0980 chunk 99 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 146 optimal weight: 3.9990 chunk 158 optimal weight: 1.9990 chunk 130 optimal weight: 0.9990 chunk 145 optimal weight: 0.9990 chunk 49 optimal weight: 0.7980 chunk 117 optimal weight: 0.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 557 HIS A 566 HIS ** A 880 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1149 GLN ** B 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 892 HIS B 905 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.2087 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= 0.162 Angle : 0.512 14.824 19758 Z= 0.277 Chirality : 0.039 0.140 2163 Planarity : 0.004 0.047 2290 Dihedral : 17.401 145.135 2480 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.68 % Allowed : 10.69 % Favored : 87.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.21), residues: 1554 helix: 0.49 (0.20), residues: 681 sheet: -2.09 (0.34), residues: 223 loop : -1.41 (0.23), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B1170 HIS 0.006 0.001 HIS A 892 PHE 0.012 0.001 PHE B 739 TYR 0.017 0.001 TYR A 531 ARG 0.003 0.000 ARG A 571 *********************** 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 143 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 120 time to evaluate : 1.616 Fit side-chains revert: symmetry clash REVERT: A 531 TYR cc_start: 0.7400 (p90) cc_final: 0.7073 (p90) REVERT: A 778 VAL cc_start: 0.8660 (t) cc_final: 0.8403 (m) REVERT: A 957 MET cc_start: 0.7906 (mmp) cc_final: 0.7705 (mmt) REVERT: B 676 THR cc_start: 0.8684 (m) cc_final: 0.8477 (p) REVERT: B 736 ARG cc_start: 0.8114 (mpt180) cc_final: 0.7854 (mpt180) REVERT: B 882 LYS cc_start: 0.7714 (mttt) cc_final: 0.7341 (mtpp) REVERT: B 886 LEU cc_start: 0.8130 (OUTLIER) cc_final: 0.7925 (tm) outliers start: 23 outliers final: 10 residues processed: 140 average time/residue: 0.2886 time to fit residues: 59.1350 Evaluate side-chains 122 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 111 time to evaluate : 1.515 ------------------------------------------------------------------------------- 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 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 B residue 633 ASP 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 1143 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 144 optimal weight: 0.5980 chunk 110 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 chunk 16 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 98 optimal weight: 0.5980 chunk 146 optimal weight: 2.9990 chunk 155 optimal weight: 3.9990 chunk 139 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 129 optimal weight: 2.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 501 ASN ** A 880 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 892 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 864 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 892 HIS B 909 HIS B 928 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.2150 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= 0.259 Angle : 0.553 14.385 19758 Z= 0.300 Chirality : 0.042 0.144 2163 Planarity : 0.004 0.043 2290 Dihedral : 17.523 145.763 2480 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 2.86 % Allowed : 10.40 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.22), residues: 1554 helix: 0.79 (0.21), residues: 678 sheet: -1.96 (0.34), residues: 223 loop : -1.36 (0.23), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B1170 HIS 0.007 0.001 HIS B 752 PHE 0.017 0.002 PHE B 739 TYR 0.027 0.002 TYR A 531 ARG 0.004 0.001 ARG A 571 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 117 time to evaluate : 1.509 Fit side-chains REVERT: A 531 TYR cc_start: 0.7596 (p90) cc_final: 0.7086 (p90) REVERT: A 778 VAL cc_start: 0.8733 (t) cc_final: 0.8502 (m) REVERT: A 833 GLU cc_start: 0.8669 (OUTLIER) cc_final: 0.7858 (pm20) REVERT: A 960 ILE cc_start: 0.8175 (pp) cc_final: 0.7499 (mt) REVERT: B 676 THR cc_start: 0.8772 (m) cc_final: 0.8508 (p) REVERT: B 882 LYS cc_start: 0.7816 (mttt) cc_final: 0.7436 (mtpp) REVERT: B 957 MET cc_start: 0.7048 (mmm) cc_final: 0.6821 (mmm) REVERT: B 1074 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8637 (tt) REVERT: B 1143 GLU cc_start: 0.7924 (OUTLIER) cc_final: 0.7534 (mp0) outliers start: 39 outliers final: 25 residues processed: 146 average time/residue: 0.2923 time to fit residues: 61.6720 Evaluate side-chains 138 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 110 time to evaluate : 1.544 ------------------------------------------------------------------------------- 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 539 ASP Chi-restraints excluded: chain A residue 543 ASP Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 640 THR Chi-restraints excluded: chain A residue 644 SER Chi-restraints excluded: chain A residue 801 ILE Chi-restraints excluded: chain A residue 833 GLU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 1024 GLU Chi-restraints excluded: chain A residue 1074 LEU Chi-restraints excluded: chain A residue 1125 ILE Chi-restraints excluded: chain B residue 433 MET Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 610 THR Chi-restraints excluded: chain B residue 630 LYS Chi-restraints excluded: chain B residue 778 VAL Chi-restraints excluded: chain B residue 803 VAL Chi-restraints excluded: chain B residue 895 THR Chi-restraints excluded: chain B residue 949 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 983 LEU Chi-restraints excluded: chain B residue 1062 THR Chi-restraints excluded: chain B residue 1074 LEU Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1143 GLU Chi-restraints excluded: chain B residue 1158 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 88 optimal weight: 7.9990 chunk 2 optimal weight: 3.9990 chunk 115 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 chunk 132 optimal weight: 8.9990 chunk 107 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 79 optimal weight: 2.9990 chunk 139 optimal weight: 6.9990 chunk 39 optimal weight: 0.9980 chunk 52 optimal weight: 5.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 880 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 892 HIS ** B 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 864 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 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 : 0.004 0.032 14413 Z= 0.247 Angle : 0.547 14.301 19758 Z= 0.296 Chirality : 0.041 0.152 2163 Planarity : 0.004 0.040 2290 Dihedral : 17.499 145.686 2480 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 2.64 % Allowed : 11.20 % Favored : 86.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.22), residues: 1554 helix: 0.91 (0.21), residues: 681 sheet: -1.94 (0.33), residues: 225 loop : -1.31 (0.23), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 820 HIS 0.006 0.001 HIS B 752 PHE 0.016 0.002 PHE B 959 TYR 0.027 0.002 TYR A 531 ARG 0.004 0.000 ARG A 571 *********************** 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 156 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 120 time to evaluate : 1.562 Fit side-chains REVERT: A 531 TYR cc_start: 0.7626 (p90) cc_final: 0.7047 (p90) REVERT: A 778 VAL cc_start: 0.8740 (t) cc_final: 0.8527 (m) REVERT: A 833 GLU cc_start: 0.8685 (OUTLIER) cc_final: 0.7901 (pm20) REVERT: A 892 HIS cc_start: 0.5933 (m170) cc_final: 0.5587 (m170) REVERT: A 960 ILE cc_start: 0.8356 (pp) cc_final: 0.7694 (mt) REVERT: A 1080 GLU cc_start: 0.7462 (OUTLIER) cc_final: 0.6664 (tm-30) REVERT: A 1116 LYS cc_start: 0.7591 (ptpt) cc_final: 0.7168 (ptpp) REVERT: B 676 THR cc_start: 0.8804 (m) cc_final: 0.8563 (p) REVERT: B 854 GLU cc_start: 0.8221 (mm-30) cc_final: 0.8009 (mm-30) REVERT: B 882 LYS cc_start: 0.7818 (mttt) cc_final: 0.7438 (mtpp) REVERT: B 957 MET cc_start: 0.7146 (mmm) cc_final: 0.6943 (mmm) REVERT: B 1074 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8667 (tt) REVERT: B 1143 GLU cc_start: 0.7928 (OUTLIER) cc_final: 0.7523 (mp0) outliers start: 36 outliers final: 24 residues processed: 146 average time/residue: 0.2696 time to fit residues: 58.3675 Evaluate side-chains 138 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 110 time to evaluate : 1.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 483 ASN Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 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 755 ASP Chi-restraints excluded: chain A residue 801 ILE Chi-restraints excluded: chain A residue 833 GLU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 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 433 MET Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 610 THR Chi-restraints excluded: chain B residue 778 VAL Chi-restraints excluded: chain B residue 803 VAL Chi-restraints excluded: chain B residue 895 THR Chi-restraints excluded: chain B residue 949 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1062 THR Chi-restraints excluded: chain B residue 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 140 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 91 optimal weight: 5.9990 chunk 38 optimal weight: 0.9980 chunk 155 optimal weight: 3.9990 chunk 129 optimal weight: 1.9990 chunk 72 optimal weight: 10.0000 chunk 12 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 81 optimal weight: 0.0470 chunk 150 optimal weight: 8.9990 overall best weight: 1.1882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 880 ASN A 892 HIS ** B 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 864 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 892 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 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 0.027 14413 Z= 0.203 Angle : 0.514 14.154 19758 Z= 0.280 Chirality : 0.040 0.141 2163 Planarity : 0.004 0.041 2290 Dihedral : 17.386 145.169 2480 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.71 % Allowed : 11.57 % Favored : 85.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.22), residues: 1554 helix: 1.12 (0.21), residues: 681 sheet: -1.79 (0.34), residues: 225 loop : -1.22 (0.23), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 820 HIS 0.005 0.001 HIS B 752 PHE 0.020 0.001 PHE B 959 TYR 0.023 0.001 TYR A 531 ARG 0.003 0.000 ARG A 571 *********************** 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 155 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 118 time to evaluate : 1.549 Fit side-chains REVERT: A 531 TYR cc_start: 0.7600 (OUTLIER) cc_final: 0.6975 (p90) REVERT: A 778 VAL cc_start: 0.8747 (t) cc_final: 0.8525 (m) REVERT: A 833 GLU cc_start: 0.8666 (OUTLIER) cc_final: 0.7889 (pm20) REVERT: A 957 MET cc_start: 0.8180 (mmm) cc_final: 0.7891 (mmt) REVERT: A 1080 GLU cc_start: 0.7500 (OUTLIER) cc_final: 0.6685 (tm-30) REVERT: B 676 THR cc_start: 0.8796 (m) cc_final: 0.8593 (p) REVERT: B 854 GLU cc_start: 0.8218 (mm-30) cc_final: 0.8009 (mm-30) REVERT: B 882 LYS cc_start: 0.7798 (mttt) cc_final: 0.7419 (mtpp) REVERT: B 957 MET cc_start: 0.7220 (mmm) cc_final: 0.6976 (mmm) REVERT: B 1074 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8651 (tt) REVERT: B 1143 GLU cc_start: 0.7904 (OUTLIER) cc_final: 0.7528 (mp0) outliers start: 37 outliers final: 25 residues processed: 146 average time/residue: 0.2680 time to fit residues: 57.9148 Evaluate side-chains 136 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 106 time to evaluate : 1.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 455 SER 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 755 ASP Chi-restraints excluded: chain A residue 801 ILE Chi-restraints excluded: chain A residue 833 GLU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 950 ILE Chi-restraints excluded: chain A residue 1080 GLU Chi-restraints excluded: chain A residue 1125 ILE Chi-restraints excluded: chain B residue 433 MET Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 633 ASP Chi-restraints excluded: chain B residue 778 VAL Chi-restraints excluded: chain B residue 803 VAL Chi-restraints excluded: chain B residue 895 THR Chi-restraints excluded: chain B residue 949 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 983 LEU Chi-restraints excluded: chain B residue 1062 THR Chi-restraints excluded: chain B residue 1074 LEU Chi-restraints excluded: chain B residue 1100 THR 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 17 optimal weight: 3.9990 chunk 88 optimal weight: 0.3980 chunk 113 optimal weight: 2.9990 chunk 131 optimal weight: 0.4980 chunk 86 optimal weight: 2.9990 chunk 155 optimal weight: 6.9990 chunk 97 optimal weight: 3.9990 chunk 94 optimal weight: 0.5980 chunk 71 optimal weight: 3.9990 chunk 96 optimal weight: 4.9990 chunk 61 optimal weight: 5.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 880 ASN A 892 HIS ** B 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 692 GLN ** B 864 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.2451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 14413 Z= 0.243 Angle : 0.539 14.043 19758 Z= 0.293 Chirality : 0.041 0.142 2163 Planarity : 0.004 0.041 2290 Dihedral : 17.435 145.304 2480 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.64 % Allowed : 11.79 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.22), residues: 1554 helix: 1.16 (0.21), residues: 681 sheet: -1.72 (0.34), residues: 225 loop : -1.19 (0.24), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 820 HIS 0.006 0.001 HIS B 752 PHE 0.018 0.002 PHE B 959 TYR 0.027 0.001 TYR A 531 ARG 0.003 0.000 ARG A 571 *********************** 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 147 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 111 time to evaluate : 1.460 Fit side-chains REVERT: A 531 TYR cc_start: 0.7645 (OUTLIER) cc_final: 0.7029 (p90) REVERT: A 778 VAL cc_start: 0.8743 (t) cc_final: 0.8539 (m) REVERT: A 833 GLU cc_start: 0.8704 (OUTLIER) cc_final: 0.7908 (pm20) REVERT: A 892 HIS cc_start: 0.6025 (m170) cc_final: 0.5777 (m170) REVERT: A 1080 GLU cc_start: 0.7528 (OUTLIER) cc_final: 0.6695 (tm-30) REVERT: A 1116 LYS cc_start: 0.7559 (ptpt) cc_final: 0.7141 (ptpp) REVERT: B 548 ILE cc_start: 0.7924 (OUTLIER) cc_final: 0.7445 (mt) REVERT: B 882 LYS cc_start: 0.7838 (mttt) cc_final: 0.7441 (mtpp) REVERT: B 957 MET cc_start: 0.7275 (mmm) cc_final: 0.7011 (mmm) REVERT: B 1074 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8666 (tt) REVERT: B 1143 GLU cc_start: 0.7913 (OUTLIER) cc_final: 0.7516 (mp0) outliers start: 36 outliers final: 27 residues processed: 137 average time/residue: 0.2993 time to fit residues: 61.6534 Evaluate side-chains 140 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 107 time to evaluate : 1.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 455 SER 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 755 ASP Chi-restraints excluded: chain A residue 801 ILE Chi-restraints excluded: chain A residue 830 GLN Chi-restraints excluded: chain A residue 833 GLU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 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 433 MET Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 610 THR Chi-restraints excluded: chain B residue 778 VAL Chi-restraints excluded: chain B residue 803 VAL Chi-restraints excluded: chain B residue 895 THR Chi-restraints excluded: chain B residue 949 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 983 LEU Chi-restraints excluded: chain B residue 1062 THR Chi-restraints excluded: chain B residue 1074 LEU Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1143 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 92 optimal weight: 0.4980 chunk 46 optimal weight: 0.9980 chunk 30 optimal weight: 0.6980 chunk 98 optimal weight: 0.7980 chunk 105 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 121 optimal weight: 2.9990 chunk 141 optimal weight: 0.8980 chunk 148 optimal weight: 1.9990 chunk 135 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 864 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 880 ASN ** B 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 864 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 892 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.2629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 14413 Z= 0.150 Angle : 0.496 13.980 19758 Z= 0.269 Chirality : 0.039 0.155 2163 Planarity : 0.004 0.041 2290 Dihedral : 17.262 144.910 2480 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.12 % Allowed : 12.37 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.22), residues: 1554 helix: 1.34 (0.21), residues: 683 sheet: -1.59 (0.35), residues: 223 loop : -1.05 (0.24), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1189 HIS 0.004 0.001 HIS B 789 PHE 0.016 0.001 PHE B 959 TYR 0.018 0.001 TYR A 531 ARG 0.002 0.000 ARG A 831 *********************** 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 144 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 115 time to evaluate : 1.476 Fit side-chains REVERT: A 531 TYR cc_start: 0.7523 (p90) cc_final: 0.6881 (p90) REVERT: A 778 VAL cc_start: 0.8717 (t) cc_final: 0.8487 (m) REVERT: A 957 MET cc_start: 0.7956 (mmm) cc_final: 0.7711 (mmt) REVERT: A 1080 GLU cc_start: 0.7524 (OUTLIER) cc_final: 0.6705 (tm-30) REVERT: B 454 LYS cc_start: 0.7457 (mmtm) cc_final: 0.6584 (ttpp) REVERT: B 882 LYS cc_start: 0.7715 (mttt) cc_final: 0.7303 (mtpp) REVERT: B 957 MET cc_start: 0.7275 (mmm) cc_final: 0.6979 (mmm) REVERT: B 1074 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8579 (tt) REVERT: B 1079 TYR cc_start: 0.8049 (m-80) cc_final: 0.7367 (m-80) REVERT: B 1143 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.7476 (mp0) outliers start: 29 outliers final: 23 residues processed: 137 average time/residue: 0.2885 time to fit residues: 58.1611 Evaluate side-chains 136 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 110 time to evaluate : 1.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 455 SER Chi-restraints excluded: chain A residue 483 ASN Chi-restraints excluded: chain A residue 508 ILE 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 931 ILE Chi-restraints excluded: chain A residue 1024 GLU Chi-restraints excluded: chain A residue 1080 GLU Chi-restraints excluded: chain A residue 1125 ILE Chi-restraints excluded: chain B residue 433 MET Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 610 THR Chi-restraints excluded: chain B residue 778 VAL Chi-restraints excluded: chain B residue 803 VAL Chi-restraints excluded: chain B residue 895 THR Chi-restraints excluded: chain B residue 949 SER Chi-restraints excluded: chain B residue 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 144 optimal weight: 4.9990 chunk 148 optimal weight: 0.9990 chunk 87 optimal weight: 4.9990 chunk 62 optimal weight: 3.9990 chunk 113 optimal weight: 0.7980 chunk 44 optimal weight: 0.7980 chunk 130 optimal weight: 2.9990 chunk 136 optimal weight: 2.9990 chunk 94 optimal weight: 0.9990 chunk 152 optimal weight: 1.9990 chunk 93 optimal weight: 0.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 864 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 880 ASN ** B 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 864 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.2661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 14413 Z= 0.173 Angle : 0.505 13.970 19758 Z= 0.273 Chirality : 0.039 0.140 2163 Planarity : 0.003 0.040 2290 Dihedral : 17.236 144.796 2480 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.12 % Allowed : 12.37 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.22), residues: 1554 helix: 1.45 (0.21), residues: 677 sheet: -1.61 (0.34), residues: 229 loop : -0.97 (0.24), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 820 HIS 0.004 0.001 HIS B 752 PHE 0.018 0.001 PHE A 959 TYR 0.020 0.001 TYR A 531 ARG 0.005 0.000 ARG B 662 *********************** 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 142 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 113 time to evaluate : 1.486 Fit side-chains REVERT: A 531 TYR cc_start: 0.7560 (OUTLIER) cc_final: 0.6897 (p90) REVERT: A 778 VAL cc_start: 0.8710 (t) cc_final: 0.8470 (m) REVERT: A 957 MET cc_start: 0.7939 (mmm) cc_final: 0.7676 (mmt) REVERT: A 1080 GLU cc_start: 0.7552 (OUTLIER) cc_final: 0.6727 (tm-30) REVERT: B 454 LYS cc_start: 0.7425 (mmtm) cc_final: 0.6555 (ttpp) REVERT: B 882 LYS cc_start: 0.7747 (mttt) cc_final: 0.7341 (mtpp) REVERT: B 957 MET cc_start: 0.7330 (mmm) cc_final: 0.7008 (mmm) REVERT: B 1074 LEU cc_start: 0.8876 (OUTLIER) cc_final: 0.8643 (tt) REVERT: B 1143 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.7483 (mp0) outliers start: 29 outliers final: 25 residues processed: 133 average time/residue: 0.2634 time to fit residues: 51.9487 Evaluate side-chains 139 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 110 time to evaluate : 1.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 455 SER 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 755 ASP Chi-restraints excluded: chain A residue 801 ILE Chi-restraints excluded: chain A residue 830 GLN Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 1024 GLU Chi-restraints excluded: chain A residue 1080 GLU Chi-restraints excluded: chain A residue 1125 ILE Chi-restraints excluded: chain B residue 433 MET Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 610 THR Chi-restraints excluded: chain B residue 778 VAL Chi-restraints excluded: chain B residue 803 VAL Chi-restraints excluded: chain B residue 895 THR Chi-restraints excluded: chain B residue 949 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 983 LEU Chi-restraints excluded: chain B residue 1062 THR Chi-restraints excluded: chain B residue 1074 LEU Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1143 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 72 optimal weight: 8.9990 chunk 106 optimal weight: 0.5980 chunk 160 optimal weight: 1.9990 chunk 147 optimal weight: 0.6980 chunk 127 optimal weight: 4.9990 chunk 13 optimal weight: 8.9990 chunk 98 optimal weight: 0.7980 chunk 78 optimal weight: 0.4980 chunk 101 optimal weight: 2.9990 chunk 136 optimal weight: 0.0670 chunk 39 optimal weight: 3.9990 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 864 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 880 ASN ** B 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 864 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.2740 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= 0.138 Angle : 0.489 13.673 19758 Z= 0.266 Chirality : 0.039 0.138 2163 Planarity : 0.003 0.041 2290 Dihedral : 17.195 144.714 2480 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.76 % Allowed : 12.88 % Favored : 85.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.22), residues: 1554 helix: 1.51 (0.21), residues: 678 sheet: -1.54 (0.35), residues: 229 loop : -0.88 (0.24), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1189 HIS 0.003 0.001 HIS A 909 PHE 0.018 0.001 PHE B 959 TYR 0.016 0.001 TYR A 531 ARG 0.005 0.000 ARG B 662 ********************** 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 fitting. rotamer outliers: 24 poor density : 116 time to evaluate : 1.175 Fit side-chains REVERT: A 531 TYR cc_start: 0.7539 (OUTLIER) cc_final: 0.6849 (p90) REVERT: A 778 VAL cc_start: 0.8703 (t) cc_final: 0.8454 (m) REVERT: A 957 MET cc_start: 0.7907 (mmm) cc_final: 0.7654 (mmt) REVERT: A 1080 GLU cc_start: 0.7546 (OUTLIER) cc_final: 0.6723 (tm-30) REVERT: B 454 LYS cc_start: 0.7421 (mmtm) cc_final: 0.6546 (ttpp) REVERT: B 882 LYS cc_start: 0.7672 (mttt) cc_final: 0.7260 (mtpp) REVERT: B 957 MET cc_start: 0.7314 (mmm) cc_final: 0.6999 (mmm) REVERT: B 1074 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8637 (tt) REVERT: B 1143 GLU cc_start: 0.7915 (OUTLIER) cc_final: 0.7499 (mp0) outliers start: 24 outliers final: 19 residues processed: 132 average time/residue: 0.2534 time to fit residues: 49.6136 Evaluate side-chains 135 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 112 time to evaluate : 1.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 455 SER 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 755 ASP Chi-restraints excluded: chain A residue 801 ILE Chi-restraints excluded: chain A residue 1024 GLU Chi-restraints excluded: chain A residue 1080 GLU Chi-restraints excluded: chain A residue 1125 ILE Chi-restraints excluded: chain B residue 433 MET Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 610 THR Chi-restraints excluded: chain B residue 803 VAL Chi-restraints excluded: chain B residue 983 LEU Chi-restraints excluded: chain B residue 1062 THR Chi-restraints excluded: chain B residue 1074 LEU Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1143 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 117 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 35 optimal weight: 0.2980 chunk 127 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 131 optimal weight: 8.9990 chunk 16 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 112 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 chunk 92 optimal weight: 5.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 864 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 880 ASN ** B 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 864 GLN ** 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 = 0.3714 r_free = 0.3714 target = 0.135748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.111624 restraints weight = 20496.117| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 1.59 r_work: 0.3229 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3116 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.2659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 14413 Z= 0.231 Angle : 0.534 13.939 19758 Z= 0.289 Chirality : 0.041 0.144 2163 Planarity : 0.004 0.040 2290 Dihedral : 17.304 145.147 2480 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 1.98 % Allowed : 12.52 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.22), residues: 1554 helix: 1.45 (0.21), residues: 676 sheet: -1.55 (0.35), residues: 231 loop : -0.95 (0.24), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 820 HIS 0.006 0.001 HIS B 752 PHE 0.018 0.002 PHE B 959 TYR 0.025 0.001 TYR A 531 ARG 0.005 0.000 ARG B 662 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3343.17 seconds wall clock time: 60 minutes 44.42 seconds (3644.42 seconds total)