Starting phenix.real_space_refine on Thu Mar 5 02:09:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6xs6_22301/03_2026/6xs6_22301.cif Found real_map, /net/cci-nas-00/data/ceres_data/6xs6_22301/03_2026/6xs6_22301.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6xs6_22301/03_2026/6xs6_22301.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6xs6_22301/03_2026/6xs6_22301.map" model { file = "/net/cci-nas-00/data/ceres_data/6xs6_22301/03_2026/6xs6_22301.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6xs6_22301/03_2026/6xs6_22301.cif" } resolution = 3.7 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= 0.002 sd= 0.017 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: 4 Type Number sf(0) Gaussians S 81 5.16 5 C 11672 2.51 5 N 3048 2.21 5 O 3493 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18294 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 6093 Number of conformers: 1 Conformer: "" Number of residues, atoms: 785, 6093 Classifications: {'peptide': 785} Link IDs: {'PTRANS': 35, 'TRANS': 749} Chain breaks: 8 Chain: "B" Number of atoms: 6093 Number of conformers: 1 Conformer: "" Number of residues, atoms: 785, 6093 Classifications: {'peptide': 785} Link IDs: {'PTRANS': 35, 'TRANS': 749} Chain breaks: 8 Chain: "C" Number of atoms: 6108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 787, 6108 Classifications: {'peptide': 787} Link IDs: {'PTRANS': 35, 'TRANS': 751} Chain breaks: 8 Time building chain proxies: 4.42, per 1000 atoms: 0.24 Number of scatterers: 18294 At special positions: 0 Unit cell: (136.24, 145.08, 140.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 81 16.00 O 3493 8.00 N 3048 7.00 C 11672 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=27, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.04 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 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: 1.40 Conformation dependent library (CDL) restraints added in 664.5 milliseconds 4606 Ramachandran restraints generated. 2303 Oldfield, 0 Emsley, 2303 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4420 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 44 sheets defined 27.5% alpha, 23.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 747 through 756 Processing helix chain 'A' and resid 758 through 783 Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.513A pdb=" N LYS A 825 " --> pdb=" O LEU A 821 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 941 removed outlier: 6.994A pdb=" N LYS A 921 " --> pdb=" O TYR A 917 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N LEU A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 966 Processing helix chain 'A' and resid 976 through 982 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.047A pdb=" N GLU A 990 " --> pdb=" O PRO A 986 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 removed outlier: 4.118A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.740A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.847A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 913 through 919 Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 967 removed outlier: 3.842A pdb=" N SER B 967 " --> pdb=" O VAL B 963 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.713A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.425A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 737 through 743 removed outlier: 3.632A pdb=" N TYR C 741 " --> pdb=" O ASP C 737 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 756 removed outlier: 3.865A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.765A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.627A pdb=" N LYS C 825 " --> pdb=" O LEU C 821 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.852A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 941 removed outlier: 7.062A pdb=" N LYS C 921 " --> pdb=" O TYR C 917 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N LEU C 922 " --> pdb=" O GLU C 918 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 968 removed outlier: 3.551A pdb=" N VAL C 963 " --> pdb=" O LEU C 959 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.884A pdb=" N ARG C 983 " --> pdb=" O ASP C 979 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.570A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.586A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL A 90 " --> pdb=" O PHE A 194 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ARG A 190 " --> pdb=" O SER A 94 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE A 197 " --> pdb=" O TYR A 200 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 Processing sheet with id=AA3, first strand: chain 'A' and resid 50 through 52 removed outlier: 3.909A pdb=" N PHE A 275 " --> pdb=" O THR A 51 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.750A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N PHE A 238 " --> pdb=" O LEU A 84 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU A 118 " --> pdb=" O LYS A 129 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 278 through 279 removed outlier: 6.942A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 3.502A pdb=" N VAL A 597 " --> pdb=" O TYR A 313 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLN A 613 " --> pdb=" O GLY A 594 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE A 651 " --> pdb=" O VAL A 610 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 327 removed outlier: 6.148A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 565 through 566 removed outlier: 6.837A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 575 through 576 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.378A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.791A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 713 removed outlier: 3.673A pdb=" N VAL A1104 " --> pdb=" O GLN A1113 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 718 through 728 removed outlier: 6.770A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 718 through 728 Processing sheet with id=AB6, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB7, first strand: chain 'A' and resid 787 through 790 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB9, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.514A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA B 93 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL B 90 " --> pdb=" O PHE B 194 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ARG B 190 " --> pdb=" O SER B 94 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE B 197 " --> pdb=" O TYR B 200 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.514A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA B 93 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL B 90 " --> pdb=" O PHE B 194 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ARG B 190 " --> pdb=" O SER B 94 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 48 through 52 removed outlier: 3.535A pdb=" N HIS B 49 " --> pdb=" O LEU B 277 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N THR B 51 " --> pdb=" O PHE B 275 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N PHE B 275 " --> pdb=" O THR B 51 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.788A pdb=" N LEU B 84 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N PHE B 238 " --> pdb=" O LEU B 84 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 319 removed outlier: 3.555A pdb=" N GLY B 311 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N THR B 599 " --> pdb=" O GLY B 311 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLN B 613 " --> pdb=" O GLY B 594 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU B 611 " --> pdb=" O SER B 596 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 325 through 327 removed outlier: 5.882A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 554 through 555 removed outlier: 4.015A pdb=" N ILE B 584 " --> pdb=" O SER B 555 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 664 through 667 removed outlier: 6.026A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE B 670 " --> pdb=" O GLY B 667 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N TYR B 695 " --> pdb=" O CYS B 671 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ILE B 693 " --> pdb=" O SER B 673 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 702 through 704 Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 712 removed outlier: 3.811A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 717 through 728 removed outlier: 3.601A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 717 through 728 Processing sheet with id=AD3, first strand: chain 'B' and resid 734 through 736 removed outlier: 3.521A pdb=" N SER B 735 " --> pdb=" O THR B 859 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N THR B 859 " --> pdb=" O SER B 735 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD5, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.586A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG C 190 " --> pdb=" O SER C 94 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS C 195 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE C 197 " --> pdb=" O TYR C 200 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 50 through 52 removed outlier: 3.715A pdb=" N THR C 51 " --> pdb=" O PHE C 275 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N PHE C 275 " --> pdb=" O THR C 51 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.759A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N PHE C 238 " --> pdb=" O LEU C 84 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU C 118 " --> pdb=" O LYS C 129 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 278 through 279 removed outlier: 7.012A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.647A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLN C 613 " --> pdb=" O GLY C 594 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 325 through 327 removed outlier: 6.306A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLY C 550 " --> pdb=" O VAL C 539 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR C 588 " --> pdb=" O VAL C 551 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 664 through 667 removed outlier: 6.032A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE C 670 " --> pdb=" O GLY C 667 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N TYR C 695 " --> pdb=" O CYS C 671 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ILE C 693 " --> pdb=" O SER C 673 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 711 through 712 Processing sheet with id=AE4, first strand: chain 'C' and resid 717 through 728 removed outlier: 6.823A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 717 through 728 removed outlier: 6.823A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AE7, first strand: chain 'C' and resid 1081 through 1082 Processing sheet with id=AE8, first strand: chain 'C' and resid 1094 through 1097 777 hydrogen bonds defined for protein. 2220 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.53 Time building geometry restraints manager: 1.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 5928 1.35 - 1.47: 4420 1.47 - 1.59: 8213 1.59 - 1.71: 0 1.71 - 1.83: 105 Bond restraints: 18666 Sorted by residual: bond pdb=" N ASP B 745 " pdb=" CA ASP B 745 " ideal model delta sigma weight residual 1.457 1.481 -0.024 1.29e-02 6.01e+03 3.38e+00 bond pdb=" CB THR C1077 " pdb=" CG2 THR C1077 " ideal model delta sigma weight residual 1.521 1.461 0.060 3.30e-02 9.18e+02 3.30e+00 bond pdb=" CB VAL A1129 " pdb=" CG1 VAL A1129 " ideal model delta sigma weight residual 1.521 1.465 0.056 3.30e-02 9.18e+02 2.84e+00 bond pdb=" CG1 ILE A 993 " pdb=" CD1 ILE A 993 " ideal model delta sigma weight residual 1.513 1.452 0.061 3.90e-02 6.57e+02 2.44e+00 bond pdb=" CB THR B1077 " pdb=" CG2 THR B1077 " ideal model delta sigma weight residual 1.521 1.471 0.050 3.30e-02 9.18e+02 2.33e+00 ... (remaining 18661 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.22: 24739 2.22 - 4.44: 536 4.44 - 6.66: 78 6.66 - 8.88: 18 8.88 - 11.10: 11 Bond angle restraints: 25382 Sorted by residual: angle pdb=" C ASP B 215 " pdb=" N LEU B 216 " pdb=" CA LEU B 216 " ideal model delta sigma weight residual 120.94 131.22 -10.28 1.90e+00 2.77e-01 2.93e+01 angle pdb=" N PRO C 986 " pdb=" CA PRO C 986 " pdb=" C PRO C 986 " ideal model delta sigma weight residual 110.70 115.23 -4.53 1.22e+00 6.72e-01 1.38e+01 angle pdb=" C GLY B 744 " pdb=" N ASP B 745 " pdb=" CA ASP B 745 " ideal model delta sigma weight residual 121.54 128.53 -6.99 1.91e+00 2.74e-01 1.34e+01 angle pdb=" N PRO A 561 " pdb=" CA PRO A 561 " pdb=" C PRO A 561 " ideal model delta sigma weight residual 112.47 119.76 -7.29 2.06e+00 2.36e-01 1.25e+01 angle pdb=" N PRO B 986 " pdb=" CA PRO B 986 " pdb=" C PRO B 986 " ideal model delta sigma weight residual 110.70 115.01 -4.31 1.22e+00 6.72e-01 1.25e+01 ... (remaining 25377 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 10006 18.00 - 35.99: 953 35.99 - 53.99: 143 53.99 - 71.99: 32 71.99 - 89.98: 15 Dihedral angle restraints: 11149 sinusoidal: 4321 harmonic: 6828 Sorted by residual: dihedral pdb=" CB CYS B 662 " pdb=" SG CYS B 662 " pdb=" SG CYS B 671 " pdb=" CB CYS B 671 " ideal model delta sinusoidal sigma weight residual 93.00 -178.31 -88.69 1 1.00e+01 1.00e-02 9.38e+01 dihedral pdb=" CB CYS C 662 " pdb=" SG CYS C 662 " pdb=" SG CYS C 671 " pdb=" CB CYS C 671 " ideal model delta sinusoidal sigma weight residual 93.00 177.66 -84.66 1 1.00e+01 1.00e-02 8.71e+01 dihedral pdb=" CB CYS A 538 " pdb=" SG CYS A 538 " pdb=" SG CYS A 590 " pdb=" CB CYS A 590 " ideal model delta sinusoidal sigma weight residual -86.00 -156.95 70.95 1 1.00e+01 1.00e-02 6.47e+01 ... (remaining 11146 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 2444 0.071 - 0.142: 480 0.142 - 0.213: 40 0.213 - 0.284: 2 0.284 - 0.356: 3 Chirality restraints: 2969 Sorted by residual: chirality pdb=" CG LEU C 894 " pdb=" CB LEU C 894 " pdb=" CD1 LEU C 894 " pdb=" CD2 LEU C 894 " both_signs ideal model delta sigma weight residual False -2.59 -2.23 -0.36 2.00e-01 2.50e+01 3.16e+00 chirality pdb=" CG LEU B 894 " pdb=" CB LEU B 894 " pdb=" CD1 LEU B 894 " pdb=" CD2 LEU B 894 " both_signs ideal model delta sigma weight residual False -2.59 -2.23 -0.35 2.00e-01 2.50e+01 3.15e+00 chirality pdb=" CG LEU A 916 " pdb=" CB LEU A 916 " pdb=" CD1 LEU A 916 " pdb=" CD2 LEU A 916 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.12e+00 ... (remaining 2966 not shown) Planarity restraints: 3273 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE C 906 " -0.031 2.00e-02 2.50e+03 2.71e-02 1.28e+01 pdb=" CG PHE C 906 " 0.062 2.00e-02 2.50e+03 pdb=" CD1 PHE C 906 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 PHE C 906 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE C 906 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE C 906 " -0.011 2.00e-02 2.50e+03 pdb=" CZ PHE C 906 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 906 " 0.027 2.00e-02 2.50e+03 2.50e-02 1.10e+01 pdb=" CG PHE A 906 " -0.058 2.00e-02 2.50e+03 pdb=" CD1 PHE A 906 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 PHE A 906 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE A 906 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 906 " 0.009 2.00e-02 2.50e+03 pdb=" CZ PHE A 906 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU C 560 " 0.053 5.00e-02 4.00e+02 8.06e-02 1.04e+01 pdb=" N PRO C 561 " -0.139 5.00e-02 4.00e+02 pdb=" CA PRO C 561 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO C 561 " 0.044 5.00e-02 4.00e+02 ... (remaining 3270 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 3075 2.77 - 3.30: 16062 3.30 - 3.84: 29049 3.84 - 4.37: 32104 4.37 - 4.90: 58469 Nonbonded interactions: 138759 Sorted by model distance: nonbonded pdb=" O GLY A 880 " pdb=" OG SER A 884 " model vdw 2.240 3.040 nonbonded pdb=" O GLY C 880 " pdb=" OG SER C 884 " model vdw 2.253 3.040 nonbonded pdb=" O GLY B 880 " pdb=" OG SER B 884 " model vdw 2.254 3.040 nonbonded pdb=" O ASP C 80 " pdb=" OH TYR C 265 " model vdw 2.256 3.040 nonbonded pdb=" OE1 GLU A 819 " pdb=" OG SER A1055 " model vdw 2.260 3.040 ... (remaining 138754 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' selection = chain 'B' selection = (chain 'C' and (resid 27 through 689 or resid 692 through 1137)) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 12.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.880 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 17.600 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.040 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:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5807 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 : 0.004 0.061 18693 Z= 0.201 Angle : 0.828 11.102 25436 Z= 0.443 Chirality : 0.054 0.356 2969 Planarity : 0.006 0.081 3273 Dihedral : 14.263 89.982 6648 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.99 (0.16), residues: 2303 helix: 0.69 (0.20), residues: 582 sheet: -1.23 (0.25), residues: 419 loop : -2.42 (0.15), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 567 TYR 0.025 0.003 TYR B1067 PHE 0.062 0.003 PHE C 906 TRP 0.011 0.002 TRP C 886 HIS 0.025 0.002 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00446 (18666) covalent geometry : angle 0.82575 (25382) SS BOND : bond 0.00223 ( 27) SS BOND : angle 1.67488 ( 54) hydrogen bonds : bond 0.19322 ( 726) hydrogen bonds : angle 7.75937 ( 2220) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4606 Ramachandran restraints generated. 2303 Oldfield, 0 Emsley, 2303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4606 Ramachandran restraints generated. 2303 Oldfield, 0 Emsley, 2303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 282 time to evaluate : 0.683 Fit side-chains revert: symmetry clash REVERT: A 918 GLU cc_start: 0.6584 (mt-10) cc_final: 0.6227 (mt-10) outliers start: 0 outliers final: 0 residues processed: 282 average time/residue: 0.1211 time to fit residues: 54.1632 Evaluate side-chains 233 residues out of total 2057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 233 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 216 optimal weight: 0.8980 chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 0.9990 chunk 227 optimal weight: 0.6980 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 0.0020 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 4.9990 chunk 200 optimal weight: 0.7980 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 207 HIS A 935 GLN ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS B1054 GLN C 207 HIS ** C1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.141147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.117405 restraints weight = 26214.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.116971 restraints weight = 37367.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.117782 restraints weight = 35442.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.117839 restraints weight = 25655.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.118077 restraints weight = 23477.324| |-----------------------------------------------------------------------------| r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5747 moved from start: 0.0957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18693 Z= 0.125 Angle : 0.595 8.494 25436 Z= 0.317 Chirality : 0.045 0.181 2969 Planarity : 0.005 0.061 3273 Dihedral : 5.116 24.928 2477 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 0.63 % Allowed : 7.49 % Favored : 91.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.49 (0.17), residues: 2303 helix: 1.52 (0.20), residues: 573 sheet: -1.11 (0.24), residues: 452 loop : -2.25 (0.16), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 905 TYR 0.028 0.002 TYR B1067 PHE 0.026 0.002 PHE B1121 TRP 0.005 0.001 TRP C 886 HIS 0.008 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00271 (18666) covalent geometry : angle 0.59227 (25382) SS BOND : bond 0.00474 ( 27) SS BOND : angle 1.43715 ( 54) hydrogen bonds : bond 0.05158 ( 726) hydrogen bonds : angle 5.84105 ( 2220) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4606 Ramachandran restraints generated. 2303 Oldfield, 0 Emsley, 2303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4606 Ramachandran restraints generated. 2303 Oldfield, 0 Emsley, 2303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 265 time to evaluate : 0.561 Fit side-chains REVERT: A 918 GLU cc_start: 0.6539 (mt-10) cc_final: 0.6180 (mt-10) REVERT: B 959 LEU cc_start: 0.6806 (mt) cc_final: 0.6603 (mt) REVERT: B 1023 ASN cc_start: 0.5873 (m110) cc_final: 0.5648 (m110) REVERT: C 309 GLU cc_start: 0.6413 (tp30) cc_final: 0.6153 (mm-30) outliers start: 13 outliers final: 8 residues processed: 271 average time/residue: 0.1176 time to fit residues: 50.5527 Evaluate side-chains 235 residues out of total 2057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 227 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain B residue 911 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 79 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 186 optimal weight: 0.6980 chunk 123 optimal weight: 0.0060 chunk 60 optimal weight: 2.9990 chunk 116 optimal weight: 0.0770 chunk 132 optimal weight: 1.9990 chunk 159 optimal weight: 4.9990 chunk 51 optimal weight: 0.9980 chunk 211 optimal weight: 1.9990 chunk 93 optimal weight: 7.9990 overall best weight: 0.5554 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1135 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 = 0.3868 r_free = 0.3868 target = 0.141679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.117847 restraints weight = 26359.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.117043 restraints weight = 35136.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.118592 restraints weight = 31475.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.117770 restraints weight = 23697.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.118250 restraints weight = 21827.901| |-----------------------------------------------------------------------------| r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5750 moved from start: 0.1229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 18693 Z= 0.115 Angle : 0.563 8.291 25436 Z= 0.298 Chirality : 0.044 0.170 2969 Planarity : 0.004 0.059 3273 Dihedral : 4.866 25.783 2477 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 1.17 % Allowed : 9.53 % Favored : 89.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.25 (0.17), residues: 2303 helix: 1.80 (0.21), residues: 580 sheet: -0.81 (0.24), residues: 459 loop : -2.23 (0.16), residues: 1264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 905 TYR 0.026 0.001 TYR B1067 PHE 0.022 0.001 PHE B 823 TRP 0.005 0.001 TRP B 64 HIS 0.006 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00256 (18666) covalent geometry : angle 0.55904 (25382) SS BOND : bond 0.00260 ( 27) SS BOND : angle 1.50955 ( 54) hydrogen bonds : bond 0.04800 ( 726) hydrogen bonds : angle 5.50704 ( 2220) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4606 Ramachandran restraints generated. 2303 Oldfield, 0 Emsley, 2303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4606 Ramachandran restraints generated. 2303 Oldfield, 0 Emsley, 2303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 258 time to evaluate : 0.709 Fit side-chains revert: symmetry clash REVERT: A 773 GLU cc_start: 0.6198 (pt0) cc_final: 0.5801 (pt0) REVERT: A 918 GLU cc_start: 0.6554 (mt-10) cc_final: 0.6172 (mt-10) REVERT: C 742 ILE cc_start: 0.7286 (OUTLIER) cc_final: 0.7049 (mt) outliers start: 24 outliers final: 15 residues processed: 273 average time/residue: 0.1258 time to fit residues: 54.0367 Evaluate side-chains 253 residues out of total 2057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 237 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 742 ILE Chi-restraints excluded: chain C residue 1038 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 232 optimal weight: 6.9990 chunk 114 optimal weight: 0.0770 chunk 201 optimal weight: 3.9990 chunk 231 optimal weight: 0.6980 chunk 125 optimal weight: 2.9990 chunk 123 optimal weight: 0.0270 chunk 52 optimal weight: 2.9990 chunk 194 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 187 optimal weight: 5.9990 chunk 112 optimal weight: 0.6980 overall best weight: 0.4998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 777 ASN B 965 GLN C 787 GLN C 978 ASN ** C1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.142300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.118465 restraints weight = 26341.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.117528 restraints weight = 32419.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.118188 restraints weight = 29917.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.117654 restraints weight = 23412.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.117981 restraints weight = 22912.147| |-----------------------------------------------------------------------------| r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5746 moved from start: 0.1491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 18693 Z= 0.106 Angle : 0.543 11.147 25436 Z= 0.285 Chirality : 0.044 0.183 2969 Planarity : 0.004 0.051 3273 Dihedral : 4.696 33.304 2477 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 1.80 % Allowed : 10.26 % Favored : 87.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.04 (0.17), residues: 2303 helix: 2.07 (0.21), residues: 573 sheet: -0.60 (0.24), residues: 465 loop : -2.17 (0.16), residues: 1265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B1000 TYR 0.024 0.001 TYR B1067 PHE 0.036 0.001 PHE C 823 TRP 0.005 0.001 TRP C 64 HIS 0.005 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00232 (18666) covalent geometry : angle 0.54007 (25382) SS BOND : bond 0.00252 ( 27) SS BOND : angle 1.23866 ( 54) hydrogen bonds : bond 0.04425 ( 726) hydrogen bonds : angle 5.24357 ( 2220) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4606 Ramachandran restraints generated. 2303 Oldfield, 0 Emsley, 2303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4606 Ramachandran restraints generated. 2303 Oldfield, 0 Emsley, 2303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 2057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 257 time to evaluate : 0.722 Fit side-chains revert: symmetry clash REVERT: A 918 GLU cc_start: 0.6581 (mt-10) cc_final: 0.6173 (mt-10) REVERT: B 907 ASN cc_start: 0.7666 (OUTLIER) cc_final: 0.7368 (t0) REVERT: C 1107 ARG cc_start: 0.6587 (mtp180) cc_final: 0.6322 (ttm170) outliers start: 37 outliers final: 19 residues processed: 278 average time/residue: 0.1282 time to fit residues: 55.6376 Evaluate side-chains 253 residues out of total 2057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 233 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 907 ASN Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 1129 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 88 optimal weight: 7.9990 chunk 59 optimal weight: 7.9990 chunk 54 optimal weight: 2.9990 chunk 215 optimal weight: 6.9990 chunk 212 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 12 optimal weight: 6.9990 chunk 183 optimal weight: 6.9990 chunk 187 optimal weight: 5.9990 chunk 135 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 787 GLN B1135 ASN C 978 ASN ** C1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.137857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.112244 restraints weight = 26559.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.111824 restraints weight = 31598.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.112795 restraints weight = 30855.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.113016 restraints weight = 21041.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.113268 restraints weight = 20097.466| |-----------------------------------------------------------------------------| r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5855 moved from start: 0.1606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 18693 Z= 0.251 Angle : 0.759 11.887 25436 Z= 0.393 Chirality : 0.054 0.240 2969 Planarity : 0.006 0.061 3273 Dihedral : 5.425 32.548 2477 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.56 % Favored : 92.44 % Rotamer: Outliers : 2.33 % Allowed : 13.51 % Favored : 84.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.55 (0.17), residues: 2303 helix: 1.44 (0.20), residues: 576 sheet: -1.05 (0.24), residues: 455 loop : -2.32 (0.16), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 905 TYR 0.049 0.003 TYR B1067 PHE 0.044 0.003 PHE B1121 TRP 0.011 0.002 TRP C1102 HIS 0.004 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00625 (18666) covalent geometry : angle 0.75437 (25382) SS BOND : bond 0.00425 ( 27) SS BOND : angle 1.90601 ( 54) hydrogen bonds : bond 0.06231 ( 726) hydrogen bonds : angle 5.75769 ( 2220) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4606 Ramachandran restraints generated. 2303 Oldfield, 0 Emsley, 2303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4606 Ramachandran restraints generated. 2303 Oldfield, 0 Emsley, 2303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 2057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 241 time to evaluate : 0.682 Fit side-chains revert: symmetry clash REVERT: A 275 PHE cc_start: 0.6838 (m-80) cc_final: 0.6505 (m-80) REVERT: A 585 LEU cc_start: 0.5265 (OUTLIER) cc_final: 0.4938 (pp) REVERT: A 756 TYR cc_start: 0.6830 (m-80) cc_final: 0.6396 (m-80) REVERT: A 777 ASN cc_start: 0.5087 (m-40) cc_final: 0.4795 (m-40) REVERT: B 777 ASN cc_start: 0.4804 (m-40) cc_final: 0.4601 (m-40) REVERT: C 791 THR cc_start: 0.7386 (p) cc_final: 0.7121 (m) outliers start: 48 outliers final: 37 residues processed: 276 average time/residue: 0.1135 time to fit residues: 49.9637 Evaluate side-chains 265 residues out of total 2057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 227 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 909 ILE Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 696 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 775 ASP Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 1129 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 22 optimal weight: 0.8980 chunk 179 optimal weight: 0.0980 chunk 127 optimal weight: 0.8980 chunk 134 optimal weight: 0.6980 chunk 117 optimal weight: 0.4980 chunk 94 optimal weight: 0.9980 chunk 200 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 2 optimal weight: 7.9990 chunk 224 optimal weight: 0.9990 chunk 216 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1135 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 = 0.3852 r_free = 0.3852 target = 0.140495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.116751 restraints weight = 26291.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.116041 restraints weight = 39247.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.117005 restraints weight = 35196.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.116994 restraints weight = 25174.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.117136 restraints weight = 23849.215| |-----------------------------------------------------------------------------| r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5773 moved from start: 0.1646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 18693 Z= 0.117 Angle : 0.570 10.276 25436 Z= 0.301 Chirality : 0.045 0.297 2969 Planarity : 0.004 0.063 3273 Dihedral : 4.887 29.692 2477 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 1.85 % Allowed : 14.29 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.16 (0.17), residues: 2303 helix: 1.96 (0.21), residues: 571 sheet: -0.80 (0.24), residues: 459 loop : -2.17 (0.16), residues: 1273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 34 TYR 0.024 0.002 TYR A1067 PHE 0.022 0.001 PHE B 823 TRP 0.006 0.001 TRP B 64 HIS 0.005 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00260 (18666) covalent geometry : angle 0.56713 (25382) SS BOND : bond 0.00294 ( 27) SS BOND : angle 1.35552 ( 54) hydrogen bonds : bond 0.04804 ( 726) hydrogen bonds : angle 5.36133 ( 2220) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4606 Ramachandran restraints generated. 2303 Oldfield, 0 Emsley, 2303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4606 Ramachandran restraints generated. 2303 Oldfield, 0 Emsley, 2303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 2057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 245 time to evaluate : 0.636 Fit side-chains revert: symmetry clash REVERT: A 275 PHE cc_start: 0.6786 (m-80) cc_final: 0.6536 (m-80) REVERT: A 756 TYR cc_start: 0.6694 (m-80) cc_final: 0.6445 (m-80) REVERT: A 777 ASN cc_start: 0.4530 (m-40) cc_final: 0.4207 (m-40) REVERT: B 777 ASN cc_start: 0.4271 (m-40) cc_final: 0.3981 (m-40) REVERT: C 791 THR cc_start: 0.7300 (p) cc_final: 0.7070 (m) outliers start: 38 outliers final: 23 residues processed: 274 average time/residue: 0.1090 time to fit residues: 47.6991 Evaluate side-chains 257 residues out of total 2057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 234 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 909 ILE Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 1038 LYS Chi-restraints excluded: chain C residue 1129 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 179 optimal weight: 20.0000 chunk 51 optimal weight: 6.9990 chunk 76 optimal weight: 0.8980 chunk 192 optimal weight: 5.9990 chunk 108 optimal weight: 3.9990 chunk 127 optimal weight: 2.9990 chunk 120 optimal weight: 7.9990 chunk 13 optimal weight: 10.0000 chunk 166 optimal weight: 0.8980 chunk 193 optimal weight: 0.9990 chunk 141 optimal weight: 4.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 965 GLN B1135 ASN C 321 GLN C 978 ASN ** C1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.138126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.112084 restraints weight = 26650.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.111639 restraints weight = 34530.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.113005 restraints weight = 29770.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.113122 restraints weight = 21102.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.113753 restraints weight = 20243.216| |-----------------------------------------------------------------------------| r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5839 moved from start: 0.1734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 18693 Z= 0.205 Angle : 0.689 12.312 25436 Z= 0.358 Chirality : 0.051 0.283 2969 Planarity : 0.005 0.065 3273 Dihedral : 5.202 29.911 2477 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 2.28 % Allowed : 14.97 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.42 (0.17), residues: 2303 helix: 1.66 (0.21), residues: 571 sheet: -1.07 (0.24), residues: 473 loop : -2.24 (0.16), residues: 1259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 905 TYR 0.044 0.003 TYR B1067 PHE 0.040 0.003 PHE B1121 TRP 0.008 0.002 TRP C1102 HIS 0.004 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00504 (18666) covalent geometry : angle 0.68529 (25382) SS BOND : bond 0.00355 ( 27) SS BOND : angle 1.62249 ( 54) hydrogen bonds : bond 0.05744 ( 726) hydrogen bonds : angle 5.60677 ( 2220) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4606 Ramachandran restraints generated. 2303 Oldfield, 0 Emsley, 2303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4606 Ramachandran restraints generated. 2303 Oldfield, 0 Emsley, 2303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 2057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 238 time to evaluate : 0.687 Fit side-chains revert: symmetry clash REVERT: A 275 PHE cc_start: 0.6871 (m-80) cc_final: 0.6519 (m-80) REVERT: A 756 TYR cc_start: 0.6730 (m-80) cc_final: 0.6401 (m-80) REVERT: A 777 ASN cc_start: 0.4983 (m-40) cc_final: 0.4760 (m-40) REVERT: B 196 ASN cc_start: 0.6079 (m-40) cc_final: 0.5441 (t0) REVERT: C 742 ILE cc_start: 0.7318 (OUTLIER) cc_final: 0.7023 (mp) REVERT: C 791 THR cc_start: 0.7382 (p) cc_final: 0.7111 (m) outliers start: 47 outliers final: 33 residues processed: 273 average time/residue: 0.1186 time to fit residues: 51.7738 Evaluate side-chains 266 residues out of total 2057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 232 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 909 ILE Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 696 THR Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 742 ILE Chi-restraints excluded: chain C residue 775 ASP Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1129 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 192 optimal weight: 0.0770 chunk 41 optimal weight: 0.8980 chunk 81 optimal weight: 4.9990 chunk 3 optimal weight: 0.9980 chunk 107 optimal weight: 6.9990 chunk 225 optimal weight: 1.9990 chunk 83 optimal weight: 9.9990 chunk 69 optimal weight: 0.6980 chunk 148 optimal weight: 0.6980 chunk 87 optimal weight: 6.9990 chunk 155 optimal weight: 0.2980 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 954 GLN B1135 ASN C 564 GLN ** C1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.140713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.116140 restraints weight = 26239.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.115039 restraints weight = 42393.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.115973 restraints weight = 35575.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.116417 restraints weight = 28355.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.117010 restraints weight = 25681.003| |-----------------------------------------------------------------------------| r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5780 moved from start: 0.1793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18693 Z= 0.114 Angle : 0.567 9.557 25436 Z= 0.299 Chirality : 0.045 0.355 2969 Planarity : 0.004 0.063 3273 Dihedral : 4.799 27.668 2477 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 1.94 % Allowed : 15.65 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.13 (0.17), residues: 2303 helix: 1.96 (0.21), residues: 570 sheet: -0.86 (0.24), residues: 479 loop : -2.11 (0.16), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1019 TYR 0.025 0.002 TYR B1007 PHE 0.036 0.001 PHE C 823 TRP 0.006 0.001 TRP B 64 HIS 0.005 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00253 (18666) covalent geometry : angle 0.56486 (25382) SS BOND : bond 0.00298 ( 27) SS BOND : angle 1.22085 ( 54) hydrogen bonds : bond 0.04726 ( 726) hydrogen bonds : angle 5.35109 ( 2220) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4606 Ramachandran restraints generated. 2303 Oldfield, 0 Emsley, 2303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4606 Ramachandran restraints generated. 2303 Oldfield, 0 Emsley, 2303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 246 time to evaluate : 0.679 Fit side-chains revert: symmetry clash REVERT: A 275 PHE cc_start: 0.6838 (m-80) cc_final: 0.6630 (m-80) REVERT: A 756 TYR cc_start: 0.6644 (m-80) cc_final: 0.6409 (m-80) REVERT: A 777 ASN cc_start: 0.4521 (m-40) cc_final: 0.4300 (m-40) REVERT: B 196 ASN cc_start: 0.5953 (m-40) cc_final: 0.5390 (t0) REVERT: C 791 THR cc_start: 0.7271 (p) cc_final: 0.7039 (m) outliers start: 40 outliers final: 25 residues processed: 273 average time/residue: 0.1211 time to fit residues: 52.2040 Evaluate side-chains 257 residues out of total 2057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 232 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 909 ILE Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1129 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 67 optimal weight: 0.9980 chunk 226 optimal weight: 0.1980 chunk 107 optimal weight: 6.9990 chunk 27 optimal weight: 1.9990 chunk 101 optimal weight: 5.9990 chunk 136 optimal weight: 0.9990 chunk 169 optimal weight: 7.9990 chunk 73 optimal weight: 0.4980 chunk 79 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 232 optimal weight: 0.4980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1135 ASN C 321 GLN C 978 ASN ** C1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.140763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.116344 restraints weight = 26138.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.115740 restraints weight = 41344.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.116331 restraints weight = 33639.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.116458 restraints weight = 29734.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.117170 restraints weight = 24781.466| |-----------------------------------------------------------------------------| r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5770 moved from start: 0.1873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 18693 Z= 0.117 Angle : 0.570 8.623 25436 Z= 0.299 Chirality : 0.045 0.233 2969 Planarity : 0.004 0.064 3273 Dihedral : 4.700 27.639 2477 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 1.51 % Allowed : 16.29 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.03 (0.17), residues: 2303 helix: 2.02 (0.21), residues: 566 sheet: -0.68 (0.24), residues: 479 loop : -2.07 (0.16), residues: 1258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B1091 TYR 0.033 0.002 TYR B1007 PHE 0.034 0.002 PHE C 823 TRP 0.006 0.001 TRP B 64 HIS 0.004 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00267 (18666) covalent geometry : angle 0.56759 (25382) SS BOND : bond 0.00257 ( 27) SS BOND : angle 1.18703 ( 54) hydrogen bonds : bond 0.04688 ( 726) hydrogen bonds : angle 5.30634 ( 2220) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4606 Ramachandran restraints generated. 2303 Oldfield, 0 Emsley, 2303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4606 Ramachandran restraints generated. 2303 Oldfield, 0 Emsley, 2303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 2057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 246 time to evaluate : 0.530 Fit side-chains revert: symmetry clash REVERT: A 585 LEU cc_start: 0.5012 (OUTLIER) cc_final: 0.4494 (pt) REVERT: A 756 TYR cc_start: 0.6625 (m-80) cc_final: 0.6392 (m-80) REVERT: B 196 ASN cc_start: 0.5942 (m-40) cc_final: 0.5357 (t0) REVERT: C 791 THR cc_start: 0.7257 (p) cc_final: 0.7047 (m) outliers start: 31 outliers final: 25 residues processed: 267 average time/residue: 0.1183 time to fit residues: 50.1919 Evaluate side-chains 261 residues out of total 2057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 235 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 909 ILE Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 1038 LYS Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1129 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 127 optimal weight: 4.9990 chunk 149 optimal weight: 2.9990 chunk 9 optimal weight: 0.0570 chunk 112 optimal weight: 4.9990 chunk 35 optimal weight: 0.0050 chunk 92 optimal weight: 0.9980 chunk 132 optimal weight: 0.8980 chunk 98 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 212 optimal weight: 0.8980 chunk 15 optimal weight: 3.9990 overall best weight: 0.5512 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 777 ASN B1135 ASN C 321 GLN C 978 ASN ** C1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.141726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.114279 restraints weight = 26072.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.114448 restraints weight = 28286.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.115670 restraints weight = 26702.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.115749 restraints weight = 18222.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.116084 restraints weight = 17594.778| |-----------------------------------------------------------------------------| r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5766 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 18693 Z= 0.112 Angle : 0.555 7.749 25436 Z= 0.292 Chirality : 0.044 0.187 2969 Planarity : 0.004 0.063 3273 Dihedral : 4.543 25.186 2477 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 1.41 % Allowed : 16.77 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.17), residues: 2303 helix: 1.99 (0.21), residues: 571 sheet: -0.64 (0.23), residues: 514 loop : -2.07 (0.17), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 273 TYR 0.027 0.002 TYR B1007 PHE 0.034 0.001 PHE C 823 TRP 0.007 0.001 TRP B 64 HIS 0.005 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00253 (18666) covalent geometry : angle 0.55292 (25382) SS BOND : bond 0.00247 ( 27) SS BOND : angle 1.12048 ( 54) hydrogen bonds : bond 0.04534 ( 726) hydrogen bonds : angle 5.22935 ( 2220) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4606 Ramachandran restraints generated. 2303 Oldfield, 0 Emsley, 2303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4606 Ramachandran restraints generated. 2303 Oldfield, 0 Emsley, 2303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 2057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 241 time to evaluate : 0.764 Fit side-chains REVERT: A 275 PHE cc_start: 0.6116 (m-80) cc_final: 0.5839 (m-80) REVERT: A 756 TYR cc_start: 0.6548 (m-80) cc_final: 0.6297 (m-80) REVERT: B 196 ASN cc_start: 0.6161 (m-40) cc_final: 0.5306 (t0) outliers start: 29 outliers final: 25 residues processed: 260 average time/residue: 0.1193 time to fit residues: 49.7849 Evaluate side-chains 262 residues out of total 2057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 237 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 909 ILE Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1129 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 59 optimal weight: 2.9990 chunk 172 optimal weight: 9.9990 chunk 46 optimal weight: 0.0770 chunk 57 optimal weight: 0.5980 chunk 123 optimal weight: 0.8980 chunk 228 optimal weight: 0.9990 chunk 134 optimal weight: 0.5980 chunk 108 optimal weight: 4.9990 chunk 26 optimal weight: 0.9990 chunk 176 optimal weight: 7.9990 chunk 170 optimal weight: 0.2980 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1135 ASN C 978 ASN ** C1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.142066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.114755 restraints weight = 26153.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.114497 restraints weight = 29330.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.116144 restraints weight = 26396.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.116200 restraints weight = 17823.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.116513 restraints weight = 16971.593| |-----------------------------------------------------------------------------| r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5760 moved from start: 0.2096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 18693 Z= 0.110 Angle : 0.550 8.044 25436 Z= 0.288 Chirality : 0.044 0.183 2969 Planarity : 0.004 0.063 3273 Dihedral : 4.457 23.639 2477 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 1.41 % Allowed : 16.72 % Favored : 81.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.86 (0.17), residues: 2303 helix: 2.06 (0.21), residues: 569 sheet: -0.56 (0.24), residues: 481 loop : -1.93 (0.17), residues: 1253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 319 TYR 0.028 0.002 TYR B1007 PHE 0.034 0.001 PHE C 823 TRP 0.007 0.001 TRP B 64 HIS 0.004 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00247 (18666) covalent geometry : angle 0.54814 (25382) SS BOND : bond 0.00244 ( 27) SS BOND : angle 1.06905 ( 54) hydrogen bonds : bond 0.04423 ( 726) hydrogen bonds : angle 5.16328 ( 2220) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3483.05 seconds wall clock time: 61 minutes 28.83 seconds (3688.83 seconds total)