Starting phenix.real_space_refine on Thu Mar 5 10:43:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7fb4_31514/03_2026/7fb4_31514.cif Found real_map, /net/cci-nas-00/data/ceres_data/7fb4_31514/03_2026/7fb4_31514.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7fb4_31514/03_2026/7fb4_31514.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7fb4_31514/03_2026/7fb4_31514.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7fb4_31514/03_2026/7fb4_31514.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7fb4_31514/03_2026/7fb4_31514.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.076 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 97 5.16 5 C 13669 2.51 5 N 3560 2.21 5 O 4085 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 98 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: 21411 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 6635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 851, 6635 Classifications: {'peptide': 851} Link IDs: {'PTRANS': 41, 'TRANS': 809} Chain breaks: 7 Chain: "B" Number of atoms: 6632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 852, 6632 Classifications: {'peptide': 852} Link IDs: {'PTRANS': 42, 'TRANS': 809} Chain breaks: 7 Chain: "C" Number of atoms: 8144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1043, 8144 Classifications: {'peptide': 1043} Link IDs: {'PTRANS': 53, 'TRANS': 989} Chain breaks: 6 Time building chain proxies: 4.61, per 1000 atoms: 0.22 Number of scatterers: 21411 At special positions: 0 Unit cell: (142.8, 133.28, 176.8, 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 97 16.00 O 4085 8.00 N 3560 7.00 C 13669 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=30, 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=2.02 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=2.03 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=2.04 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 336 " - pdb=" SG CYS C 361 " distance=2.02 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.05 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " 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=2.04 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: 1.68 Conformation dependent library (CDL) restraints added in 868.5 milliseconds 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5156 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 47 sheets defined 25.3% alpha, 20.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.86 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 737 through 743 removed outlier: 3.608A pdb=" N TYR A 741 " --> pdb=" O ASP A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 747 through 754 Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.676A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 805 removed outlier: 4.493A pdb=" N GLN A 804 " --> pdb=" O ASN A 801 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 850 through 855 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 889 Processing helix chain 'A' and resid 897 through 907 Processing helix chain 'A' and resid 908 through 910 No H-bonds generated for 'chain 'A' and resid 908 through 910' Processing helix chain 'A' and resid 912 through 916 removed outlier: 3.534A pdb=" N VAL A 915 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 939 Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.979A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.653A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 5.651A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 4.309A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 616 through 620 Processing helix chain 'B' and resid 737 through 742 Processing helix chain 'B' and resid 747 through 753 Processing helix chain 'B' and resid 754 through 758 removed outlier: 3.855A pdb=" N GLY B 757 " --> pdb=" O LEU B 754 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N SER B 758 " --> pdb=" O GLN B 755 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 754 through 758' Processing helix chain 'B' and resid 759 through 782 removed outlier: 3.663A pdb=" N ARG B 765 " --> pdb=" O THR B 761 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.622A pdb=" N LYS B 825 " --> pdb=" O LEU B 821 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 850 through 855 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.647A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 916 Processing helix chain 'B' and resid 919 through 939 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 965 removed outlier: 3.778A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1032 removed outlier: 5.391A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 4.434A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASP B1146 " --> pdb=" O GLN B1142 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 365 through 369 Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.055A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 737 through 743 removed outlier: 3.569A pdb=" N CYS C 743 " --> pdb=" O THR C 739 " (cutoff:3.500A) Processing helix chain 'C' and resid 747 through 754 Processing helix chain 'C' and resid 757 through 783 removed outlier: 4.419A pdb=" N THR C 761 " --> pdb=" O GLY C 757 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 824 removed outlier: 3.602A pdb=" N ASN C 824 " --> pdb=" O ASP C 820 " (cutoff:3.500A) Processing helix chain 'C' and resid 852 through 856 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 912 through 917 removed outlier: 4.175A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 939 Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.540A pdb=" N GLN C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 5.451A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 4.086A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 7.974A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N PHE A 65 " --> pdb=" O TYR A 265 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.845A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.098A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LYS A 129 " --> pdb=" O LEU A 118 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 195 through 197 Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 314 Processing sheet with id=AA6, first strand: chain 'A' and resid 538 through 543 removed outlier: 3.578A pdb=" N GLY A 548 " --> pdb=" O PHE A 541 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 553 through 554 Processing sheet with id=AA8, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.413A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 702 through 703 Processing sheet with id=AB1, first strand: chain 'A' and resid 711 through 715 Processing sheet with id=AB2, first strand: chain 'A' and resid 718 through 728 removed outlier: 7.146A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 734 through 735 removed outlier: 3.924A pdb=" N SER A 735 " --> pdb=" O THR A 859 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1086 through 1090 removed outlier: 4.967A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1094 through 1096 Processing sheet with id=AB6, first strand: chain 'B' and resid 27 through 30 removed outlier: 3.692A pdb=" N TRP B 64 " --> pdb=" O ALA B 27 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N PHE B 65 " --> pdb=" O TYR B 265 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N TYR B 265 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU B 212 " --> pdb=" O PHE B 186 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N ASN B 188 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N ILE B 210 " --> pdb=" O ASN B 188 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 27 through 30 removed outlier: 3.692A pdb=" N TRP B 64 " --> pdb=" O ALA B 27 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N PHE B 65 " --> pdb=" O TYR B 265 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N TYR B 265 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLU B 191 " --> pdb=" O LYS B 206 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS B 206 " --> pdb=" O GLU B 191 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 48 through 49 removed outlier: 3.723A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 53 through 55 Processing sheet with id=AC1, first strand: chain 'B' and resid 84 through 85 removed outlier: 7.608A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ASN B 121 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 310 through 319 removed outlier: 6.623A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ARG B 319 " --> pdb=" O SER B 591 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N SER B 591 " --> pdb=" O ARG B 319 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N GLY B 648 " --> pdb=" O THR B 645 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 538 through 543 Processing sheet with id=AC4, first strand: chain 'B' and resid 575 through 577 Processing sheet with id=AC5, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.641A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 711 through 727 removed outlier: 6.456A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 733 through 735 removed outlier: 4.475A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 1080 through 1082 Processing sheet with id=AC9, first strand: chain 'B' and resid 1089 through 1090 Processing sheet with id=AD1, first strand: chain 'B' and resid 1094 through 1096 Processing sheet with id=AD2, first strand: chain 'C' and resid 29 through 30 removed outlier: 3.728A pdb=" N THR C 29 " --> pdb=" O VAL C 62 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 36 through 37 removed outlier: 6.893A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL C 193 " --> pdb=" O TYR C 204 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS C 206 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLU C 191 " --> pdb=" O LYS C 206 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 53 through 55 Processing sheet with id=AD5, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.142A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL C 130 " --> pdb=" O PHE C 168 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.617A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 141 through 142 removed outlier: 3.537A pdb=" N GLY C 142 " --> pdb=" O GLU C 156 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 275 through 278 removed outlier: 3.731A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 311 through 319 removed outlier: 4.271A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N ARG C 319 " --> pdb=" O SER C 591 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N SER C 591 " --> pdb=" O ARG C 319 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 354 through 355 removed outlier: 3.832A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASP C 398 " --> pdb=" O VAL C 512 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 393 through 395 removed outlier: 3.926A pdb=" N GLU C 516 " --> pdb=" O THR C 393 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 538 through 543 removed outlier: 3.510A pdb=" N GLY C 548 " --> pdb=" O PHE C 541 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 553 through 554 removed outlier: 6.609A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 664 through 665 Processing sheet with id=AE6, first strand: chain 'C' and resid 712 through 715 Processing sheet with id=AE7, first strand: chain 'C' and resid 718 through 722 Processing sheet with id=AE8, first strand: chain 'C' and resid 718 through 722 removed outlier: 7.140A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AF1, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 5.632A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 1094 through 1097 796 hydrogen bonds defined for protein. 2136 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: 4.40 Time building geometry restraints manager: 2.29 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: 6948 1.35 - 1.48: 5538 1.48 - 1.61: 9267 1.61 - 1.74: 0 1.74 - 1.87: 126 Bond restraints: 21879 Sorted by residual: bond pdb=" C GLN A 173 " pdb=" N PRO A 174 " ideal model delta sigma weight residual 1.330 1.360 -0.030 1.19e-02 7.06e+03 6.48e+00 bond pdb=" C VAL A 860 " pdb=" N LEU A 861 " ideal model delta sigma weight residual 1.331 1.265 0.066 2.83e-02 1.25e+03 5.44e+00 bond pdb=" C GLU A1111 " pdb=" N PRO A1112 " ideal model delta sigma weight residual 1.335 1.315 0.020 8.70e-03 1.32e+04 5.08e+00 bond pdb=" CB CYS C 379 " pdb=" SG CYS C 379 " ideal model delta sigma weight residual 1.808 1.874 -0.066 3.30e-02 9.18e+02 4.03e+00 bond pdb=" C HIS B1088 " pdb=" N PHE B1089 " ideal model delta sigma weight residual 1.333 1.280 0.053 2.74e-02 1.33e+03 3.69e+00 ... (remaining 21874 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.80: 29508 2.80 - 5.60: 239 5.60 - 8.40: 15 8.40 - 11.19: 1 11.19 - 13.99: 2 Bond angle restraints: 29765 Sorted by residual: angle pdb=" CA CYS C 432 " pdb=" CB CYS C 432 " pdb=" SG CYS C 432 " ideal model delta sigma weight residual 114.40 128.39 -13.99 2.30e+00 1.89e-01 3.70e+01 angle pdb=" N ASN A 603 " pdb=" CA ASN A 603 " pdb=" C ASN A 603 " ideal model delta sigma weight residual 114.39 106.16 8.23 1.45e+00 4.76e-01 3.22e+01 angle pdb=" C ARG B 328 " pdb=" N PHE B 329 " pdb=" CA PHE B 329 " ideal model delta sigma weight residual 121.80 134.77 -12.97 2.44e+00 1.68e-01 2.82e+01 angle pdb=" N CYS C 432 " pdb=" CA CYS C 432 " pdb=" C CYS C 432 " ideal model delta sigma weight residual 108.79 116.73 -7.94 1.53e+00 4.27e-01 2.69e+01 angle pdb=" C LYS A 790 " pdb=" N THR A 791 " pdb=" CA THR A 791 " ideal model delta sigma weight residual 120.68 113.29 7.39 1.52e+00 4.33e-01 2.36e+01 ... (remaining 29760 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 11811 17.87 - 35.74: 1036 35.74 - 53.61: 169 53.61 - 71.48: 34 71.48 - 89.35: 31 Dihedral angle restraints: 13081 sinusoidal: 5098 harmonic: 7983 Sorted by residual: dihedral pdb=" CB CYS C 738 " pdb=" SG CYS C 738 " pdb=" SG CYS C 760 " pdb=" CB CYS C 760 " ideal model delta sinusoidal sigma weight residual -86.00 3.35 -89.35 1 1.00e+01 1.00e-02 9.49e+01 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 -86.00 -5.35 -80.65 1 1.00e+01 1.00e-02 8.04e+01 dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual -86.00 -11.97 -74.03 1 1.00e+01 1.00e-02 6.96e+01 ... (remaining 13078 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 2639 0.052 - 0.104: 675 0.104 - 0.156: 100 0.156 - 0.208: 6 0.208 - 0.260: 3 Chirality restraints: 3423 Sorted by residual: chirality pdb=" CB VAL A 83 " pdb=" CA VAL A 83 " pdb=" CG1 VAL A 83 " pdb=" CG2 VAL A 83 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.69e+00 chirality pdb=" CA CYS C 432 " pdb=" N CYS C 432 " pdb=" C CYS C 432 " pdb=" CB CYS C 432 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" CA CYS A 617 " pdb=" N CYS A 617 " pdb=" C CYS A 617 " pdb=" CB CYS A 617 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.10e+00 ... (remaining 3420 not shown) Planarity restraints: 3859 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 329 " 0.043 5.00e-02 4.00e+02 6.44e-02 6.63e+00 pdb=" N PRO B 330 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO B 330 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 330 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 588 " 0.040 5.00e-02 4.00e+02 6.16e-02 6.06e+00 pdb=" N PRO B 589 " -0.106 5.00e-02 4.00e+02 pdb=" CA PRO B 589 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 589 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B1078 " 0.033 5.00e-02 4.00e+02 5.01e-02 4.02e+00 pdb=" N PRO B1079 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO B1079 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO B1079 " 0.028 5.00e-02 4.00e+02 ... (remaining 3856 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 1110 2.71 - 3.26: 22563 3.26 - 3.81: 34061 3.81 - 4.35: 41208 4.35 - 4.90: 70211 Nonbonded interactions: 169153 Sorted by model distance: nonbonded pdb=" OD1 ASN C 540 " pdb=" OG1 THR C 549 " model vdw 2.164 3.040 nonbonded pdb=" OH TYR C 91 " pdb=" OE2 GLU C 191 " model vdw 2.168 3.040 nonbonded pdb=" OG1 THR A 618 " pdb=" OE2 GLU A 619 " model vdw 2.189 3.040 nonbonded pdb=" O ASP B 80 " pdb=" OH TYR B 265 " model vdw 2.195 3.040 nonbonded pdb=" OG1 THR A1076 " pdb=" OG SER A1097 " model vdw 2.209 3.040 ... (remaining 169148 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 24 through 143 or resid 154 through 245 or resid 259 throu \ gh 1146)) selection = (chain 'B' and (resid 24 through 245 or resid 259 through 528 or resid 530 throu \ gh 620 or resid 641 through 828 or resid 850 through 1146)) } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 19.890 Find NCS groups from input model: 0.280 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:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 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 : 0.005 0.066 21909 Z= 0.238 Angle : 0.718 13.992 29825 Z= 0.414 Chirality : 0.046 0.260 3423 Planarity : 0.004 0.064 3859 Dihedral : 14.046 88.643 7835 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.33 % Favored : 90.67 % Rotamer: Outliers : 0.08 % Allowed : 5.83 % Favored : 94.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -4.07 (0.14), residues: 2700 helix: -0.18 (0.20), residues: 587 sheet: -3.26 (0.17), residues: 581 loop : -3.68 (0.13), residues: 1532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 190 TYR 0.016 0.001 TYR B1067 PHE 0.022 0.002 PHE A 906 TRP 0.007 0.001 TRP A 64 HIS 0.004 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00511 (21879) covalent geometry : angle 0.71305 (29765) SS BOND : bond 0.00619 ( 30) SS BOND : angle 2.03583 ( 60) hydrogen bonds : bond 0.15213 ( 775) hydrogen bonds : angle 7.17181 ( 2136) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 204 time to evaluate : 0.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 329 PHE cc_start: 0.6818 (m-10) cc_final: 0.6569 (m-10) REVERT: A 740 MET cc_start: 0.8863 (tpt) cc_final: 0.8620 (tpt) REVERT: A 988 GLU cc_start: 0.8837 (tp30) cc_final: 0.8537 (tp30) REVERT: A 990 GLU cc_start: 0.8868 (mm-30) cc_final: 0.8259 (mm-30) REVERT: A 1138 TYR cc_start: 0.8015 (t80) cc_final: 0.7613 (t80) REVERT: B 54 LEU cc_start: 0.8882 (mm) cc_final: 0.8554 (mm) REVERT: B 88 ASP cc_start: 0.7835 (p0) cc_final: 0.6985 (p0) REVERT: B 177 MET cc_start: 0.0044 (mtp) cc_final: -0.0474 (mtm) REVERT: B 731 MET cc_start: 0.9336 (ptt) cc_final: 0.9078 (ptm) REVERT: B 787 GLN cc_start: 0.8415 (mm110) cc_final: 0.8207 (mp10) REVERT: C 200 TYR cc_start: 0.9091 (m-80) cc_final: 0.8780 (m-10) REVERT: C 392 PHE cc_start: 0.7942 (m-80) cc_final: 0.7504 (m-10) REVERT: C 421 TYR cc_start: 0.8730 (m-80) cc_final: 0.8133 (m-10) REVERT: C 762 GLN cc_start: 0.8358 (mt0) cc_final: 0.8144 (mt0) REVERT: C 787 GLN cc_start: 0.8422 (mp10) cc_final: 0.7841 (mt0) REVERT: C 995 ARG cc_start: 0.8844 (mmm160) cc_final: 0.8539 (ttm-80) REVERT: C 1002 GLN cc_start: 0.8874 (mm-40) cc_final: 0.8671 (mm-40) outliers start: 2 outliers final: 0 residues processed: 206 average time/residue: 0.1602 time to fit residues: 50.9685 Evaluate side-chains 127 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 20.0000 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 8.9990 chunk 111 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 GLN A 30 ASN A 99 ASN A 188 ASN A 282 ASN A 321 GLN A 544 ASN A 580 GLN A 675 GLN A 690 GLN A 751 ASN A 755 GLN A 787 GLN A 872 GLN A 901 GLN A 954 GLN A 955 ASN A1054 GLN A1058 HIS A1088 HIS A1106 GLN B 115 GLN B 211 ASN B 218 GLN B 317 ASN B 762 GLN B 907 ASN B 925 ASN B 954 GLN B 965 GLN B 992 GLN B1023 ASN B1048 HIS B1064 HIS B1071 GLN B1074 ASN B1106 GLN C 69 HIS C 99 ASN C 165 ASN C 207 HIS C 218 GLN C 343 ASN C 448 ASN C 751 ASN C 901 GLN C 920 GLN C 925 ASN C 954 GLN C 969 ASN C1023 ASN C1058 HIS C1064 HIS C1074 ASN ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1134 ASN Total number of N/Q/H flips: 55 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.113635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.070970 restraints weight = 51423.963| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 4.47 r_work: 0.2897 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.1166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 21909 Z= 0.216 Angle : 0.654 12.382 29825 Z= 0.339 Chirality : 0.046 0.224 3423 Planarity : 0.005 0.060 3859 Dihedral : 5.217 40.520 2912 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.85 % Favored : 91.15 % Rotamer: Outliers : 1.29 % Allowed : 10.79 % Favored : 87.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.01 (0.15), residues: 2700 helix: 1.25 (0.22), residues: 593 sheet: -2.70 (0.19), residues: 562 loop : -3.22 (0.14), residues: 1545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1107 TYR 0.016 0.001 TYR B 756 PHE 0.029 0.002 PHE C 855 TRP 0.010 0.001 TRP A 104 HIS 0.005 0.001 HIS A1088 Details of bonding type rmsd covalent geometry : bond 0.00500 (21879) covalent geometry : angle 0.64873 (29765) SS BOND : bond 0.00586 ( 30) SS BOND : angle 2.01774 ( 60) hydrogen bonds : bond 0.05047 ( 775) hydrogen bonds : angle 5.62020 ( 2136) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 143 time to evaluate : 0.787 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.0754 (mtt) cc_final: 0.0464 (mtp) REVERT: A 194 PHE cc_start: 0.8373 (m-10) cc_final: 0.8009 (m-10) REVERT: A 200 TYR cc_start: 0.8941 (m-10) cc_final: 0.8543 (m-10) REVERT: A 223 LEU cc_start: 0.8187 (mt) cc_final: 0.7938 (mt) REVERT: A 317 ASN cc_start: 0.9058 (p0) cc_final: 0.8663 (p0) REVERT: A 329 PHE cc_start: 0.7037 (m-10) cc_final: 0.6719 (m-10) REVERT: A 661 GLU cc_start: 0.8000 (tm-30) cc_final: 0.7697 (tm-30) REVERT: A 740 MET cc_start: 0.9088 (tpt) cc_final: 0.8859 (tpt) REVERT: A 988 GLU cc_start: 0.9158 (tp30) cc_final: 0.8823 (tp30) REVERT: A 990 GLU cc_start: 0.9030 (mm-30) cc_final: 0.8506 (mm-30) REVERT: A 1017 GLU cc_start: 0.8787 (tm-30) cc_final: 0.8580 (tm-30) REVERT: A 1138 TYR cc_start: 0.8577 (t80) cc_final: 0.8159 (t80) REVERT: B 54 LEU cc_start: 0.9048 (mm) cc_final: 0.8787 (mm) REVERT: B 88 ASP cc_start: 0.7586 (p0) cc_final: 0.6914 (p0) REVERT: B 102 ARG cc_start: 0.8781 (tpp80) cc_final: 0.8303 (tpp80) REVERT: B 177 MET cc_start: 0.0282 (mtp) cc_final: -0.0251 (mtm) REVERT: B 198 ASP cc_start: 0.9349 (m-30) cc_final: 0.9114 (m-30) REVERT: B 237 ARG cc_start: 0.8363 (mtm110) cc_final: 0.7792 (ttp-170) REVERT: B 731 MET cc_start: 0.9478 (ptt) cc_final: 0.9124 (ptm) REVERT: B 756 TYR cc_start: 0.8179 (OUTLIER) cc_final: 0.7457 (m-80) REVERT: B 759 PHE cc_start: 0.8766 (m-80) cc_final: 0.8512 (m-80) REVERT: B 776 LYS cc_start: 0.8868 (tppt) cc_final: 0.8548 (tppt) REVERT: B 780 GLU cc_start: 0.8614 (mm-30) cc_final: 0.8330 (mm-30) REVERT: B 787 GLN cc_start: 0.8665 (mm110) cc_final: 0.8195 (mp10) REVERT: C 200 TYR cc_start: 0.9124 (m-80) cc_final: 0.8875 (m-10) REVERT: C 365 TYR cc_start: 0.7801 (p90) cc_final: 0.7547 (p90) REVERT: C 421 TYR cc_start: 0.8997 (m-80) cc_final: 0.8323 (m-10) REVERT: C 762 GLN cc_start: 0.9029 (mt0) cc_final: 0.8704 (mt0) REVERT: C 787 GLN cc_start: 0.8636 (mp10) cc_final: 0.7891 (mt0) REVERT: C 995 ARG cc_start: 0.8881 (mmm160) cc_final: 0.8421 (ttm-80) REVERT: C 1002 GLN cc_start: 0.9211 (mm-40) cc_final: 0.8842 (mm-40) outliers start: 31 outliers final: 17 residues processed: 166 average time/residue: 0.1359 time to fit residues: 37.4933 Evaluate side-chains 144 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 126 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 775 ASP Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 90 optimal weight: 20.0000 chunk 141 optimal weight: 6.9990 chunk 20 optimal weight: 8.9990 chunk 17 optimal weight: 0.0370 chunk 9 optimal weight: 8.9990 chunk 239 optimal weight: 0.9980 chunk 174 optimal weight: 20.0000 chunk 254 optimal weight: 3.9990 chunk 266 optimal weight: 3.9990 chunk 148 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 overall best weight: 2.6064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 920 GLN ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1106 GLN B 66 HIS ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 544 ASN ** C1083 HIS ** 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 = 0.3814 r_free = 0.3814 target = 0.118932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.078528 restraints weight = 53367.431| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 4.16 r_work: 0.2900 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.1458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 21909 Z= 0.228 Angle : 0.652 12.233 29825 Z= 0.334 Chirality : 0.045 0.229 3423 Planarity : 0.005 0.063 3859 Dihedral : 5.128 39.892 2912 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.22 % Favored : 91.78 % Rotamer: Outliers : 2.04 % Allowed : 13.54 % Favored : 84.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.57 (0.16), residues: 2700 helix: 1.70 (0.22), residues: 593 sheet: -2.48 (0.20), residues: 568 loop : -2.95 (0.14), residues: 1539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 237 TYR 0.035 0.001 TYR C 365 PHE 0.020 0.002 PHE B 329 TRP 0.009 0.001 TRP B 104 HIS 0.004 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00530 (21879) covalent geometry : angle 0.64546 (29765) SS BOND : bond 0.00609 ( 30) SS BOND : angle 2.20089 ( 60) hydrogen bonds : bond 0.04820 ( 775) hydrogen bonds : angle 5.41461 ( 2136) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 138 time to evaluate : 0.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.0912 (mtt) cc_final: 0.0564 (mtp) REVERT: A 200 TYR cc_start: 0.8950 (m-10) cc_final: 0.8604 (m-10) REVERT: A 317 ASN cc_start: 0.9064 (p0) cc_final: 0.8649 (p0) REVERT: A 329 PHE cc_start: 0.7173 (m-10) cc_final: 0.6822 (m-10) REVERT: A 661 GLU cc_start: 0.8008 (tm-30) cc_final: 0.7689 (tm-30) REVERT: A 988 GLU cc_start: 0.9208 (tp30) cc_final: 0.8933 (tp30) REVERT: A 990 GLU cc_start: 0.9084 (mm-30) cc_final: 0.8521 (mm-30) REVERT: A 1017 GLU cc_start: 0.8925 (tm-30) cc_final: 0.8647 (tm-30) REVERT: A 1138 TYR cc_start: 0.8594 (t80) cc_final: 0.8165 (t80) REVERT: A 1141 LEU cc_start: 0.8473 (tp) cc_final: 0.8189 (tt) REVERT: B 54 LEU cc_start: 0.9105 (mm) cc_final: 0.8850 (mm) REVERT: B 88 ASP cc_start: 0.7671 (p0) cc_final: 0.7106 (p0) REVERT: B 102 ARG cc_start: 0.8761 (tpp80) cc_final: 0.8286 (tpp80) REVERT: B 177 MET cc_start: 0.0246 (mtp) cc_final: -0.0285 (mtm) REVERT: B 237 ARG cc_start: 0.8466 (mtm110) cc_final: 0.7963 (ttp-170) REVERT: B 731 MET cc_start: 0.9503 (ptt) cc_final: 0.9145 (ptm) REVERT: B 756 TYR cc_start: 0.8262 (OUTLIER) cc_final: 0.7638 (m-80) REVERT: B 776 LYS cc_start: 0.9006 (tppt) cc_final: 0.8635 (tppt) REVERT: B 780 GLU cc_start: 0.8584 (mm-30) cc_final: 0.8185 (mm-30) REVERT: C 200 TYR cc_start: 0.9129 (m-80) cc_final: 0.8888 (m-10) REVERT: C 421 TYR cc_start: 0.9026 (m-80) cc_final: 0.8360 (m-10) REVERT: C 762 GLN cc_start: 0.9075 (mt0) cc_final: 0.8813 (mt0) REVERT: C 787 GLN cc_start: 0.8709 (mp10) cc_final: 0.8012 (mt0) REVERT: C 995 ARG cc_start: 0.8895 (mmm160) cc_final: 0.8454 (ttm-80) REVERT: C 1002 GLN cc_start: 0.9211 (mm-40) cc_final: 0.8819 (mm-40) outliers start: 49 outliers final: 36 residues processed: 179 average time/residue: 0.1348 time to fit residues: 39.8520 Evaluate side-chains 159 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 122 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 775 ASP Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 920 GLN Chi-restraints excluded: chain A residue 962 LEU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 851 CYS Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 265 optimal weight: 1.9990 chunk 272 optimal weight: 0.0070 chunk 124 optimal weight: 0.7980 chunk 35 optimal weight: 3.9990 chunk 68 optimal weight: 10.0000 chunk 125 optimal weight: 0.9980 chunk 121 optimal weight: 4.9990 chunk 144 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 chunk 79 optimal weight: 1.9990 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1064 HIS C 211 ASN ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN ** C1083 HIS ** 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 = 0.3824 r_free = 0.3824 target = 0.115214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.072643 restraints weight = 50931.157| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 4.45 r_work: 0.2963 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.1846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.077 21909 Z= 0.111 Angle : 0.571 14.695 29825 Z= 0.293 Chirality : 0.044 0.207 3423 Planarity : 0.004 0.062 3859 Dihedral : 4.755 39.100 2912 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 1.75 % Allowed : 14.70 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.15 (0.16), residues: 2700 helix: 2.01 (0.22), residues: 600 sheet: -2.14 (0.20), residues: 592 loop : -2.72 (0.15), residues: 1508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 319 TYR 0.020 0.001 TYR C 365 PHE 0.024 0.001 PHE C 392 TRP 0.010 0.001 TRP A 104 HIS 0.005 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00245 (21879) covalent geometry : angle 0.56595 (29765) SS BOND : bond 0.00588 ( 30) SS BOND : angle 1.72862 ( 60) hydrogen bonds : bond 0.04017 ( 775) hydrogen bonds : angle 4.94522 ( 2136) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 149 time to evaluate : 0.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.0794 (mtt) cc_final: 0.0472 (mtp) REVERT: A 200 TYR cc_start: 0.8941 (m-10) cc_final: 0.8718 (m-10) REVERT: A 229 LEU cc_start: 0.9031 (mt) cc_final: 0.8804 (mp) REVERT: A 317 ASN cc_start: 0.8999 (p0) cc_final: 0.8630 (p0) REVERT: A 329 PHE cc_start: 0.7109 (m-10) cc_final: 0.6732 (m-10) REVERT: A 661 GLU cc_start: 0.7980 (tm-30) cc_final: 0.7605 (tm-30) REVERT: A 988 GLU cc_start: 0.9203 (tp30) cc_final: 0.8907 (tp30) REVERT: A 990 GLU cc_start: 0.9006 (mm-30) cc_final: 0.8466 (mm-30) REVERT: A 1017 GLU cc_start: 0.8903 (tm-30) cc_final: 0.8635 (tm-30) REVERT: A 1138 TYR cc_start: 0.8528 (t80) cc_final: 0.8072 (t80) REVERT: A 1141 LEU cc_start: 0.8434 (tp) cc_final: 0.8189 (tt) REVERT: B 54 LEU cc_start: 0.9068 (mm) cc_final: 0.8792 (mm) REVERT: B 88 ASP cc_start: 0.7474 (p0) cc_final: 0.6787 (p0) REVERT: B 102 ARG cc_start: 0.8690 (tpp80) cc_final: 0.8289 (tpp80) REVERT: B 177 MET cc_start: 0.0017 (mtp) cc_final: -0.0491 (mtm) REVERT: B 237 ARG cc_start: 0.8728 (mtm110) cc_final: 0.8219 (ttp-110) REVERT: B 299 THR cc_start: 0.8926 (m) cc_final: 0.8618 (p) REVERT: B 699 LEU cc_start: 0.9060 (mt) cc_final: 0.8785 (mt) REVERT: B 731 MET cc_start: 0.9507 (ptt) cc_final: 0.9169 (ptm) REVERT: B 756 TYR cc_start: 0.7915 (OUTLIER) cc_final: 0.7131 (m-80) REVERT: B 776 LYS cc_start: 0.8938 (tppt) cc_final: 0.8631 (tppt) REVERT: B 780 GLU cc_start: 0.8558 (mm-30) cc_final: 0.8142 (mm-30) REVERT: B 902 MET cc_start: 0.9008 (tpt) cc_final: 0.8471 (tpt) REVERT: C 421 TYR cc_start: 0.9032 (m-80) cc_final: 0.8392 (m-10) REVERT: C 787 GLN cc_start: 0.8727 (mp10) cc_final: 0.8046 (mt0) REVERT: C 995 ARG cc_start: 0.8750 (mmm160) cc_final: 0.8431 (ttm-80) REVERT: C 1002 GLN cc_start: 0.9117 (mm-40) cc_final: 0.8736 (mm-40) outliers start: 42 outliers final: 24 residues processed: 184 average time/residue: 0.1313 time to fit residues: 39.7949 Evaluate side-chains 150 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 125 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 962 LEU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 851 CYS Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 974 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 11 optimal weight: 20.0000 chunk 144 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 145 optimal weight: 4.9990 chunk 81 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 239 optimal weight: 2.9990 chunk 135 optimal weight: 3.9990 chunk 165 optimal weight: 0.0370 chunk 119 optimal weight: 0.7980 chunk 9 optimal weight: 5.9990 overall best weight: 1.5662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 690 GLN C 211 ASN ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN ** C1083 HIS ** 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 = 0.3837 r_free = 0.3837 target = 0.115017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.072645 restraints weight = 51054.383| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 4.46 r_work: 0.2939 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 21909 Z= 0.151 Angle : 0.577 14.179 29825 Z= 0.296 Chirality : 0.044 0.236 3423 Planarity : 0.004 0.062 3859 Dihedral : 4.704 38.330 2912 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 2.08 % Allowed : 15.83 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.95 (0.16), residues: 2700 helix: 2.14 (0.22), residues: 600 sheet: -2.02 (0.21), residues: 578 loop : -2.57 (0.15), residues: 1522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 815 TYR 0.012 0.001 TYR A 91 PHE 0.046 0.001 PHE C 855 TRP 0.008 0.001 TRP B 104 HIS 0.003 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00351 (21879) covalent geometry : angle 0.57168 (29765) SS BOND : bond 0.00597 ( 30) SS BOND : angle 1.87567 ( 60) hydrogen bonds : bond 0.04114 ( 775) hydrogen bonds : angle 4.92347 ( 2136) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 131 time to evaluate : 0.828 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.0904 (mtt) cc_final: 0.0597 (mtp) REVERT: A 200 TYR cc_start: 0.8969 (m-10) cc_final: 0.8724 (m-10) REVERT: A 317 ASN cc_start: 0.9029 (p0) cc_final: 0.8691 (p0) REVERT: A 329 PHE cc_start: 0.7145 (m-10) cc_final: 0.6705 (m-10) REVERT: A 661 GLU cc_start: 0.8015 (tm-30) cc_final: 0.7601 (tm-30) REVERT: A 988 GLU cc_start: 0.9223 (tp30) cc_final: 0.8944 (tp30) REVERT: A 990 GLU cc_start: 0.9021 (mm-30) cc_final: 0.8481 (mm-30) REVERT: A 1017 GLU cc_start: 0.8991 (tm-30) cc_final: 0.8695 (tm-30) REVERT: A 1138 TYR cc_start: 0.8558 (t80) cc_final: 0.8106 (t80) REVERT: A 1141 LEU cc_start: 0.8429 (tp) cc_final: 0.8189 (tt) REVERT: B 54 LEU cc_start: 0.9095 (mm) cc_final: 0.8818 (mm) REVERT: B 88 ASP cc_start: 0.7427 (p0) cc_final: 0.6689 (p0) REVERT: B 102 ARG cc_start: 0.8674 (tpp80) cc_final: 0.8246 (tpp80) REVERT: B 177 MET cc_start: 0.0984 (mtp) cc_final: 0.0523 (mtm) REVERT: B 237 ARG cc_start: 0.8715 (mtm110) cc_final: 0.8198 (ttp-110) REVERT: B 299 THR cc_start: 0.8939 (m) cc_final: 0.8624 (p) REVERT: B 699 LEU cc_start: 0.9112 (mt) cc_final: 0.8877 (mt) REVERT: B 731 MET cc_start: 0.9532 (ptt) cc_final: 0.9188 (ptm) REVERT: B 756 TYR cc_start: 0.7981 (OUTLIER) cc_final: 0.7213 (m-80) REVERT: B 776 LYS cc_start: 0.8999 (tppt) cc_final: 0.8494 (tppt) REVERT: B 780 GLU cc_start: 0.8610 (mm-30) cc_final: 0.8052 (mm-30) REVERT: C 200 TYR cc_start: 0.8850 (m-80) cc_final: 0.8567 (m-80) REVERT: C 421 TYR cc_start: 0.9050 (m-80) cc_final: 0.8464 (m-10) REVERT: C 787 GLN cc_start: 0.8795 (mp10) cc_final: 0.8150 (mt0) REVERT: C 995 ARG cc_start: 0.8814 (mmm160) cc_final: 0.8503 (ttm-80) REVERT: C 1002 GLN cc_start: 0.9130 (mm-40) cc_final: 0.8747 (mm-40) outliers start: 50 outliers final: 34 residues processed: 172 average time/residue: 0.1412 time to fit residues: 39.9503 Evaluate side-chains 156 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 121 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 775 ASP Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 962 LEU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 851 CYS Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 974 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 59 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 chunk 43 optimal weight: 5.9990 chunk 203 optimal weight: 3.9990 chunk 119 optimal weight: 4.9990 chunk 201 optimal weight: 0.9990 chunk 56 optimal weight: 0.1980 chunk 77 optimal weight: 0.9990 chunk 114 optimal weight: 8.9990 chunk 12 optimal weight: 30.0000 chunk 125 optimal weight: 0.4980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 211 ASN ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN ** C1083 HIS ** 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 = 0.3806 r_free = 0.3806 target = 0.114367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.071035 restraints weight = 50645.667| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 4.64 r_work: 0.2904 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 21909 Z= 0.137 Angle : 0.563 13.756 29825 Z= 0.288 Chirality : 0.044 0.324 3423 Planarity : 0.004 0.060 3859 Dihedral : 4.607 37.620 2912 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 2.00 % Allowed : 16.45 % Favored : 81.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.80 (0.16), residues: 2700 helix: 2.17 (0.22), residues: 600 sheet: -1.84 (0.21), residues: 570 loop : -2.46 (0.15), residues: 1530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 190 TYR 0.015 0.001 TYR C 365 PHE 0.023 0.001 PHE B 92 TRP 0.009 0.001 TRP B 104 HIS 0.003 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00316 (21879) covalent geometry : angle 0.55732 (29765) SS BOND : bond 0.00566 ( 30) SS BOND : angle 1.82469 ( 60) hydrogen bonds : bond 0.04017 ( 775) hydrogen bonds : angle 4.80650 ( 2136) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 130 time to evaluate : 0.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.1087 (mtt) cc_final: 0.0848 (mtp) REVERT: A 200 TYR cc_start: 0.8966 (m-10) cc_final: 0.8703 (m-10) REVERT: A 317 ASN cc_start: 0.9022 (p0) cc_final: 0.8670 (p0) REVERT: A 329 PHE cc_start: 0.7148 (m-10) cc_final: 0.6689 (m-10) REVERT: A 661 GLU cc_start: 0.8051 (tm-30) cc_final: 0.7628 (tm-30) REVERT: A 773 GLU cc_start: 0.8611 (tp30) cc_final: 0.8288 (tt0) REVERT: A 988 GLU cc_start: 0.9219 (tp30) cc_final: 0.8834 (tp30) REVERT: A 1017 GLU cc_start: 0.9039 (tm-30) cc_final: 0.8700 (tm-30) REVERT: A 1138 TYR cc_start: 0.8574 (t80) cc_final: 0.8089 (t80) REVERT: A 1141 LEU cc_start: 0.8554 (tp) cc_final: 0.8326 (tt) REVERT: B 54 LEU cc_start: 0.9058 (mm) cc_final: 0.8786 (mm) REVERT: B 88 ASP cc_start: 0.7385 (p0) cc_final: 0.6666 (p0) REVERT: B 102 ARG cc_start: 0.8881 (tpp80) cc_final: 0.8413 (tpp80) REVERT: B 177 MET cc_start: 0.0913 (mtp) cc_final: 0.0409 (mtm) REVERT: B 237 ARG cc_start: 0.8680 (mtm110) cc_final: 0.8177 (ttp-110) REVERT: B 299 THR cc_start: 0.8934 (m) cc_final: 0.8623 (p) REVERT: B 699 LEU cc_start: 0.9093 (mt) cc_final: 0.8871 (mt) REVERT: B 731 MET cc_start: 0.9554 (ptt) cc_final: 0.9206 (ptm) REVERT: B 756 TYR cc_start: 0.7943 (OUTLIER) cc_final: 0.7167 (m-80) REVERT: B 776 LYS cc_start: 0.9041 (tppt) cc_final: 0.8700 (tppt) REVERT: B 780 GLU cc_start: 0.8622 (mm-30) cc_final: 0.8329 (mt-10) REVERT: B 900 MET cc_start: 0.8904 (mtp) cc_final: 0.8471 (mtt) REVERT: C 200 TYR cc_start: 0.8869 (m-80) cc_final: 0.8590 (m-80) REVERT: C 421 TYR cc_start: 0.9056 (m-80) cc_final: 0.8482 (m-10) REVERT: C 787 GLN cc_start: 0.8921 (mp10) cc_final: 0.8421 (mt0) REVERT: C 995 ARG cc_start: 0.8763 (mmm160) cc_final: 0.8498 (ttm-80) REVERT: C 1002 GLN cc_start: 0.9119 (mm-40) cc_final: 0.8739 (mm-40) outliers start: 48 outliers final: 36 residues processed: 169 average time/residue: 0.1333 time to fit residues: 37.6012 Evaluate side-chains 159 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 122 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 775 ASP Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 962 LEU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 851 CYS Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 23 optimal weight: 0.9980 chunk 22 optimal weight: 7.9990 chunk 12 optimal weight: 10.0000 chunk 178 optimal weight: 20.0000 chunk 172 optimal weight: 8.9990 chunk 171 optimal weight: 5.9990 chunk 216 optimal weight: 8.9990 chunk 113 optimal weight: 6.9990 chunk 189 optimal weight: 0.7980 chunk 133 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1088 HIS ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.112472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.069502 restraints weight = 51260.911| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 4.60 r_work: 0.2847 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.2119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 21909 Z= 0.264 Angle : 0.650 13.823 29825 Z= 0.335 Chirality : 0.046 0.326 3423 Planarity : 0.004 0.065 3859 Dihedral : 4.879 37.068 2912 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.56 % Favored : 91.44 % Rotamer: Outliers : 2.17 % Allowed : 16.70 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.85 (0.16), residues: 2700 helix: 2.07 (0.22), residues: 599 sheet: -1.82 (0.21), residues: 591 loop : -2.48 (0.15), residues: 1510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 190 TYR 0.015 0.001 TYR A 91 PHE 0.019 0.002 PHE B 329 TRP 0.008 0.001 TRP B 104 HIS 0.004 0.001 HIS C1083 Details of bonding type rmsd covalent geometry : bond 0.00613 (21879) covalent geometry : angle 0.64359 (29765) SS BOND : bond 0.00709 ( 30) SS BOND : angle 2.15133 ( 60) hydrogen bonds : bond 0.04620 ( 775) hydrogen bonds : angle 5.07026 ( 2136) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 118 time to evaluate : 0.787 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.1443 (mtt) cc_final: 0.1191 (mtp) REVERT: A 200 TYR cc_start: 0.9043 (m-10) cc_final: 0.8740 (m-10) REVERT: A 317 ASN cc_start: 0.9088 (p0) cc_final: 0.8723 (p0) REVERT: A 988 GLU cc_start: 0.9253 (tp30) cc_final: 0.9034 (tp30) REVERT: A 1017 GLU cc_start: 0.9089 (tm-30) cc_final: 0.8755 (tm-30) REVERT: A 1138 TYR cc_start: 0.8648 (t80) cc_final: 0.8201 (t80) REVERT: A 1141 LEU cc_start: 0.8460 (tp) cc_final: 0.8224 (tt) REVERT: B 54 LEU cc_start: 0.9107 (mm) cc_final: 0.8849 (mm) REVERT: B 88 ASP cc_start: 0.7730 (p0) cc_final: 0.7149 (p0) REVERT: B 102 ARG cc_start: 0.8925 (tpp80) cc_final: 0.8607 (tpp80) REVERT: B 177 MET cc_start: 0.1122 (mtp) cc_final: 0.0604 (mtm) REVERT: B 237 ARG cc_start: 0.8678 (mtm110) cc_final: 0.8143 (ttp-110) REVERT: B 299 THR cc_start: 0.8986 (m) cc_final: 0.8630 (p) REVERT: B 731 MET cc_start: 0.9522 (ptt) cc_final: 0.9186 (ptm) REVERT: B 756 TYR cc_start: 0.8328 (OUTLIER) cc_final: 0.7744 (m-80) REVERT: B 776 LYS cc_start: 0.9052 (tppt) cc_final: 0.8738 (tppt) REVERT: B 780 GLU cc_start: 0.8653 (mm-30) cc_final: 0.8264 (mm-30) REVERT: C 200 TYR cc_start: 0.8903 (m-80) cc_final: 0.8654 (m-80) REVERT: C 319 ARG cc_start: 0.8909 (mmm-85) cc_final: 0.8337 (mmp80) REVERT: C 421 TYR cc_start: 0.9076 (m-80) cc_final: 0.8449 (m-10) REVERT: C 787 GLN cc_start: 0.8832 (mp10) cc_final: 0.8185 (mt0) REVERT: C 995 ARG cc_start: 0.8845 (mmm160) cc_final: 0.8491 (ttm-80) REVERT: C 1002 GLN cc_start: 0.9171 (mm-40) cc_final: 0.8783 (mm-40) outliers start: 52 outliers final: 41 residues processed: 161 average time/residue: 0.1283 time to fit residues: 34.5359 Evaluate side-chains 158 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 116 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 775 ASP Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 851 CYS Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 99 optimal weight: 10.0000 chunk 199 optimal weight: 10.0000 chunk 61 optimal weight: 0.9980 chunk 5 optimal weight: 0.0980 chunk 19 optimal weight: 5.9990 chunk 188 optimal weight: 7.9990 chunk 122 optimal weight: 0.0470 chunk 268 optimal weight: 7.9990 chunk 243 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 148 optimal weight: 0.9980 overall best weight: 0.8280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 439 ASN C 762 GLN ** C1083 HIS ** 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 = 0.3806 r_free = 0.3806 target = 0.113810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.071172 restraints weight = 50623.676| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 4.56 r_work: 0.2914 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 21909 Z= 0.116 Angle : 0.564 13.534 29825 Z= 0.289 Chirality : 0.044 0.316 3423 Planarity : 0.004 0.065 3859 Dihedral : 4.662 36.819 2912 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 1.75 % Allowed : 17.70 % Favored : 80.55 % 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: -1.62 (0.16), residues: 2700 helix: 2.28 (0.22), residues: 594 sheet: -1.65 (0.21), residues: 581 loop : -2.35 (0.15), residues: 1525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 815 TYR 0.013 0.001 TYR C 365 PHE 0.024 0.001 PHE B 92 TRP 0.010 0.001 TRP B 104 HIS 0.005 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00261 (21879) covalent geometry : angle 0.55925 (29765) SS BOND : bond 0.00901 ( 30) SS BOND : angle 1.78530 ( 60) hydrogen bonds : bond 0.03968 ( 775) hydrogen bonds : angle 4.71185 ( 2136) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 134 time to evaluate : 0.834 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.1129 (mtt) cc_final: 0.0912 (mtp) REVERT: A 200 TYR cc_start: 0.8935 (m-10) cc_final: 0.8714 (m-10) REVERT: A 223 LEU cc_start: 0.7241 (mt) cc_final: 0.6590 (mt) REVERT: A 317 ASN cc_start: 0.9015 (p0) cc_final: 0.8666 (p0) REVERT: A 329 PHE cc_start: 0.6875 (m-10) cc_final: 0.6570 (m-10) REVERT: A 661 GLU cc_start: 0.8007 (tm-30) cc_final: 0.7731 (tm-30) REVERT: A 773 GLU cc_start: 0.8610 (tp30) cc_final: 0.8269 (tt0) REVERT: A 988 GLU cc_start: 0.9226 (tp30) cc_final: 0.8876 (tp30) REVERT: A 990 GLU cc_start: 0.9017 (mm-30) cc_final: 0.8591 (mm-30) REVERT: A 1017 GLU cc_start: 0.9100 (tm-30) cc_final: 0.8694 (tm-30) REVERT: A 1138 TYR cc_start: 0.8579 (t80) cc_final: 0.8090 (t80) REVERT: A 1141 LEU cc_start: 0.8559 (tp) cc_final: 0.8343 (tt) REVERT: B 54 LEU cc_start: 0.9063 (mm) cc_final: 0.8767 (mm) REVERT: B 88 ASP cc_start: 0.7369 (p0) cc_final: 0.6601 (p0) REVERT: B 177 MET cc_start: 0.0925 (mtp) cc_final: 0.0414 (mtm) REVERT: B 237 ARG cc_start: 0.8739 (mtm110) cc_final: 0.8244 (ttp-110) REVERT: B 299 THR cc_start: 0.8901 (m) cc_final: 0.8586 (p) REVERT: B 699 LEU cc_start: 0.9067 (mt) cc_final: 0.8862 (mt) REVERT: B 731 MET cc_start: 0.9559 (ptt) cc_final: 0.9228 (ptm) REVERT: B 740 MET cc_start: 0.9032 (tpp) cc_final: 0.8765 (tpt) REVERT: B 756 TYR cc_start: 0.8072 (OUTLIER) cc_final: 0.7278 (m-80) REVERT: B 776 LYS cc_start: 0.9010 (tppt) cc_final: 0.8531 (tppt) REVERT: B 780 GLU cc_start: 0.8633 (mm-30) cc_final: 0.8097 (mm-30) REVERT: C 200 TYR cc_start: 0.8872 (m-80) cc_final: 0.8610 (m-80) REVERT: C 421 TYR cc_start: 0.9070 (m-80) cc_final: 0.8497 (m-10) REVERT: C 762 GLN cc_start: 0.9101 (pt0) cc_final: 0.8846 (pt0) REVERT: C 787 GLN cc_start: 0.8678 (mp10) cc_final: 0.8059 (mt0) REVERT: C 995 ARG cc_start: 0.8747 (mmm160) cc_final: 0.8410 (ttm-80) REVERT: C 1002 GLN cc_start: 0.9119 (mm-40) cc_final: 0.8736 (mm-40) outliers start: 42 outliers final: 33 residues processed: 169 average time/residue: 0.1367 time to fit residues: 38.5004 Evaluate side-chains 157 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 123 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 851 CYS Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 163 optimal weight: 0.6980 chunk 91 optimal weight: 9.9990 chunk 65 optimal weight: 4.9990 chunk 125 optimal weight: 1.9990 chunk 95 optimal weight: 7.9990 chunk 137 optimal weight: 0.8980 chunk 151 optimal weight: 3.9990 chunk 55 optimal weight: 6.9990 chunk 122 optimal weight: 1.9990 chunk 269 optimal weight: 0.3980 chunk 182 optimal weight: 40.0000 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.114261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.071120 restraints weight = 50411.820| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 4.60 r_work: 0.2905 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.2468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 21909 Z= 0.130 Angle : 0.567 13.355 29825 Z= 0.290 Chirality : 0.044 0.265 3423 Planarity : 0.004 0.065 3859 Dihedral : 4.578 36.060 2912 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 1.67 % Allowed : 18.08 % Favored : 80.26 % 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: -1.57 (0.16), residues: 2700 helix: 2.25 (0.22), residues: 601 sheet: -1.58 (0.21), residues: 584 loop : -2.32 (0.15), residues: 1515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 509 TYR 0.012 0.001 TYR C 365 PHE 0.022 0.001 PHE B 329 TRP 0.008 0.001 TRP B 104 HIS 0.004 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00303 (21879) covalent geometry : angle 0.56115 (29765) SS BOND : bond 0.00556 ( 30) SS BOND : angle 1.86023 ( 60) hydrogen bonds : bond 0.03981 ( 775) hydrogen bonds : angle 4.66990 ( 2136) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 130 time to evaluate : 0.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.0995 (mtt) cc_final: 0.0765 (mtp) REVERT: A 200 TYR cc_start: 0.8926 (m-10) cc_final: 0.8699 (m-10) REVERT: A 223 LEU cc_start: 0.7225 (mt) cc_final: 0.6591 (mt) REVERT: A 317 ASN cc_start: 0.9034 (p0) cc_final: 0.8691 (p0) REVERT: A 329 PHE cc_start: 0.6906 (m-10) cc_final: 0.6579 (m-10) REVERT: A 661 GLU cc_start: 0.8036 (tm-30) cc_final: 0.7764 (tm-30) REVERT: A 773 GLU cc_start: 0.8604 (tp30) cc_final: 0.8291 (tt0) REVERT: A 988 GLU cc_start: 0.9232 (tp30) cc_final: 0.8893 (tp30) REVERT: A 1017 GLU cc_start: 0.9093 (tm-30) cc_final: 0.8705 (tm-30) REVERT: A 1138 TYR cc_start: 0.8579 (t80) cc_final: 0.8091 (t80) REVERT: A 1141 LEU cc_start: 0.8544 (tp) cc_final: 0.8336 (tt) REVERT: B 54 LEU cc_start: 0.9097 (mm) cc_final: 0.8807 (mm) REVERT: B 88 ASP cc_start: 0.7471 (p0) cc_final: 0.6839 (p0) REVERT: B 177 MET cc_start: 0.0880 (mtp) cc_final: 0.0375 (mtm) REVERT: B 237 ARG cc_start: 0.8739 (mtm110) cc_final: 0.8426 (ttp-170) REVERT: B 299 THR cc_start: 0.8893 (m) cc_final: 0.8580 (p) REVERT: B 699 LEU cc_start: 0.9086 (mt) cc_final: 0.8880 (mt) REVERT: B 731 MET cc_start: 0.9556 (ptt) cc_final: 0.9240 (ptm) REVERT: B 740 MET cc_start: 0.9021 (tpp) cc_final: 0.8632 (tpt) REVERT: B 756 TYR cc_start: 0.8048 (OUTLIER) cc_final: 0.7226 (m-80) REVERT: B 776 LYS cc_start: 0.9033 (tppt) cc_final: 0.8541 (tppt) REVERT: B 780 GLU cc_start: 0.8646 (mm-30) cc_final: 0.8112 (mm-30) REVERT: B 900 MET cc_start: 0.8906 (mtp) cc_final: 0.8458 (mtt) REVERT: C 200 TYR cc_start: 0.8888 (m-80) cc_final: 0.8632 (m-80) REVERT: C 421 TYR cc_start: 0.9061 (m-80) cc_final: 0.8449 (m-10) REVERT: C 762 GLN cc_start: 0.9040 (pt0) cc_final: 0.8762 (pt0) REVERT: C 787 GLN cc_start: 0.8692 (mp10) cc_final: 0.8129 (mt0) REVERT: C 995 ARG cc_start: 0.8746 (mmm160) cc_final: 0.8505 (ttm-80) REVERT: C 1002 GLN cc_start: 0.9074 (mm-40) cc_final: 0.8699 (mm-40) outliers start: 40 outliers final: 34 residues processed: 163 average time/residue: 0.1379 time to fit residues: 37.5265 Evaluate side-chains 154 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 119 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 962 LEU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 851 CYS Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 89 optimal weight: 20.0000 chunk 28 optimal weight: 4.9990 chunk 222 optimal weight: 6.9990 chunk 44 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 194 optimal weight: 0.7980 chunk 94 optimal weight: 8.9990 chunk 33 optimal weight: 5.9990 chunk 12 optimal weight: 8.9990 chunk 246 optimal weight: 0.8980 chunk 228 optimal weight: 7.9990 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 271 GLN C 901 GLN ** C1083 HIS ** 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 = 0.3788 r_free = 0.3788 target = 0.117031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.076265 restraints weight = 53064.125| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 4.34 r_work: 0.2848 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 21909 Z= 0.261 Angle : 0.657 13.636 29825 Z= 0.338 Chirality : 0.046 0.294 3423 Planarity : 0.005 0.064 3859 Dihedral : 4.904 35.359 2912 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.56 % Favored : 91.44 % Rotamer: Outliers : 1.62 % Allowed : 18.28 % Favored : 80.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.72 (0.16), residues: 2700 helix: 1.96 (0.22), residues: 613 sheet: -1.66 (0.21), residues: 582 loop : -2.37 (0.15), residues: 1505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 509 TYR 0.015 0.001 TYR A 279 PHE 0.038 0.002 PHE A 201 TRP 0.014 0.001 TRP A 104 HIS 0.003 0.001 HIS A1088 Details of bonding type rmsd covalent geometry : bond 0.00609 (21879) covalent geometry : angle 0.65014 (29765) SS BOND : bond 0.00633 ( 30) SS BOND : angle 2.13562 ( 60) hydrogen bonds : bond 0.04714 ( 775) hydrogen bonds : angle 5.02313 ( 2136) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 118 time to evaluate : 0.822 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.1142 (mtt) cc_final: 0.0845 (mtp) REVERT: A 194 PHE cc_start: 0.8288 (m-10) cc_final: 0.7904 (m-10) REVERT: A 317 ASN cc_start: 0.9096 (p0) cc_final: 0.8735 (p0) REVERT: A 329 PHE cc_start: 0.6964 (m-10) cc_final: 0.6624 (m-10) REVERT: A 661 GLU cc_start: 0.8185 (tm-30) cc_final: 0.7908 (tm-30) REVERT: A 1017 GLU cc_start: 0.9098 (tm-30) cc_final: 0.8732 (tm-30) REVERT: A 1138 TYR cc_start: 0.8661 (t80) cc_final: 0.8209 (t80) REVERT: A 1141 LEU cc_start: 0.8612 (tp) cc_final: 0.8391 (tt) REVERT: B 54 LEU cc_start: 0.9143 (mm) cc_final: 0.8900 (mm) REVERT: B 88 ASP cc_start: 0.7781 (p0) cc_final: 0.7254 (p0) REVERT: B 102 ARG cc_start: 0.8898 (tpp80) cc_final: 0.8445 (tpp80) REVERT: B 177 MET cc_start: 0.1077 (mtp) cc_final: 0.0542 (mtm) REVERT: B 237 ARG cc_start: 0.8815 (mtm110) cc_final: 0.8507 (ttp-170) REVERT: B 731 MET cc_start: 0.9516 (ptt) cc_final: 0.9189 (ptm) REVERT: B 740 MET cc_start: 0.9098 (tpp) cc_final: 0.8767 (tpt) REVERT: B 756 TYR cc_start: 0.8380 (OUTLIER) cc_final: 0.7741 (m-80) REVERT: B 776 LYS cc_start: 0.9078 (tppt) cc_final: 0.8762 (tppt) REVERT: B 780 GLU cc_start: 0.8654 (mm-30) cc_final: 0.8255 (mm-30) REVERT: C 421 TYR cc_start: 0.9086 (m-80) cc_final: 0.8401 (m-10) REVERT: C 762 GLN cc_start: 0.9107 (pt0) cc_final: 0.8819 (pt0) REVERT: C 787 GLN cc_start: 0.8841 (mp10) cc_final: 0.8183 (mt0) REVERT: C 995 ARG cc_start: 0.8831 (mmm160) cc_final: 0.8462 (ttm-80) REVERT: C 1002 GLN cc_start: 0.9170 (mm-40) cc_final: 0.8814 (mm-40) outliers start: 39 outliers final: 35 residues processed: 150 average time/residue: 0.1388 time to fit residues: 34.4178 Evaluate side-chains 149 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 113 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 775 ASP Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 47 optimal weight: 0.8980 chunk 41 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 chunk 86 optimal weight: 9.9990 chunk 57 optimal weight: 0.6980 chunk 255 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 chunk 93 optimal weight: 8.9990 chunk 54 optimal weight: 0.9990 chunk 138 optimal weight: 1.9990 chunk 13 optimal weight: 10.0000 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN C 901 GLN ** C1083 HIS ** 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 = 0.3801 r_free = 0.3801 target = 0.114719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.071293 restraints weight = 50316.358| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 4.65 r_work: 0.2894 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 21909 Z= 0.130 Angle : 0.575 13.353 29825 Z= 0.295 Chirality : 0.044 0.234 3423 Planarity : 0.004 0.063 3859 Dihedral : 4.666 35.079 2912 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 1.67 % Allowed : 18.37 % Favored : 79.97 % 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: -1.57 (0.17), residues: 2700 helix: 2.14 (0.22), residues: 613 sheet: -1.56 (0.21), residues: 591 loop : -2.31 (0.15), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 509 TYR 0.011 0.001 TYR C 365 PHE 0.023 0.001 PHE C 86 TRP 0.012 0.001 TRP A 104 HIS 0.005 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00301 (21879) covalent geometry : angle 0.56984 (29765) SS BOND : bond 0.00542 ( 30) SS BOND : angle 1.79254 ( 60) hydrogen bonds : bond 0.04138 ( 775) hydrogen bonds : angle 4.71087 ( 2136) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5498.09 seconds wall clock time: 95 minutes 0.98 seconds (5700.98 seconds total)