Starting phenix.real_space_refine on Tue May 27 11:13:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t22_40978/05_2025/8t22_40978.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t22_40978/05_2025/8t22_40978.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8t22_40978/05_2025/8t22_40978.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t22_40978/05_2025/8t22_40978.map" model { file = "/net/cci-nas-00/data/ceres_data/8t22_40978/05_2025/8t22_40978.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t22_40978/05_2025/8t22_40978.cif" } resolution = 3.83 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.043 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 6357 atoms to isotropic. 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 114 5.16 5 C 15309 2.51 5 N 3980 2.21 5 O 4558 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 23961 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 748, 5813 Classifications: {'peptide': 748} Link IDs: {'PTRANS': 40, 'TRANS': 707} Chain breaks: 8 Chain: "B" Number of atoms: 5813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 748, 5813 Classifications: {'peptide': 748} Link IDs: {'PTRANS': 40, 'TRANS': 707} Chain breaks: 8 Chain: "C" Number of atoms: 7431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 954, 7431 Classifications: {'peptide': 954} Link IDs: {'PTRANS': 51, 'TRANS': 902} Chain breaks: 9 Chain: "D" Number of atoms: 4904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4904 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 30, 'TRANS': 565} Time building chain proxies: 12.44, per 1000 atoms: 0.52 Number of scatterers: 23961 At special positions: 0 Unit cell: (135.42, 153.18, 231.99, 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 114 16.00 O 4558 8.00 N 3980 7.00 C 15309 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=29, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.05 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.04 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 Simple disulfide: pdb=" SG CYS D 133 " - pdb=" SG CYS D 141 " distance=2.04 Simple disulfide: pdb=" SG CYS D 344 " - pdb=" SG CYS D 361 " distance=2.04 Simple disulfide: pdb=" SG CYS D 530 " - pdb=" SG CYS D 542 " distance=2.08 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: 6.10 Conformation dependent library (CDL) restraints added in 3.1 seconds 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5724 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 30 sheets defined 34.9% alpha, 11.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.51 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 616 through 620 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 758 through 782 removed outlier: 3.715A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.770A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 918 removed outlier: 3.743A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 966 removed outlier: 3.560A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LEU A 966 " --> pdb=" O LEU A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1034 removed outlier: 3.791A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1146 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 744 Processing helix chain 'B' and resid 746 through 754 removed outlier: 4.003A pdb=" N LEU B 754 " --> pdb=" O SER B 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.634A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 801 through 805 removed outlier: 4.303A pdb=" N GLN B 804 " --> pdb=" O ASN B 801 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 890 removed outlier: 3.610A pdb=" N ALA B 890 " --> pdb=" O THR B 887 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 910 Processing helix chain 'B' and resid 913 through 941 removed outlier: 3.697A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N LYS B 921 " --> pdb=" O TYR B 917 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N LEU B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 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 979 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 5.933A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1147 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 4.077A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 408 removed outlier: 3.980A 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 438 through 443 Processing helix chain 'C' and resid 674 through 676 No H-bonds generated for 'chain 'C' and resid 674 through 676' Processing helix chain 'C' and resid 690 through 691 No H-bonds generated for 'chain 'C' and resid 690 through 691' Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 removed outlier: 4.284A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.695A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 910 Processing helix chain 'C' and resid 912 through 941 removed outlier: 4.335A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N LYS C 921 " --> pdb=" O TYR C 917 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N LEU C 922 " --> pdb=" O GLU C 918 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 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 983 removed outlier: 4.238A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU C 981 " --> pdb=" O LEU C 977 " (cutoff:3.500A) Processing helix chain 'C' and resid 990 through 1033 Processing helix chain 'C' and resid 1116 through 1118 No H-bonds generated for 'chain 'C' and resid 1116 through 1118' Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 4.084A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 53 removed outlier: 4.214A pdb=" N TYR D 34 " --> pdb=" O GLU D 30 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 61 removed outlier: 3.609A pdb=" N GLN D 60 " --> pdb=" O ASP D 56 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 80 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 109 through 130 removed outlier: 4.975A pdb=" N SER D 128 " --> pdb=" O SER D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 154 removed outlier: 4.254A pdb=" N LEU D 148 " --> pdb=" O LEU D 144 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 177 removed outlier: 5.549A pdb=" N GLY D 173 " --> pdb=" O ARG D 169 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N LYS D 174 " --> pdb=" O SER D 170 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N GLN D 175 " --> pdb=" O GLU D 171 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 192 Processing helix chain 'D' and resid 220 through 252 removed outlier: 4.267A pdb=" N GLN D 232 " --> pdb=" O HIS D 228 " (cutoff:3.500A) Proline residue: D 235 - end of helix Processing helix chain 'D' and resid 278 through 282 removed outlier: 3.648A pdb=" N LEU D 281 " --> pdb=" O LEU D 278 " (cutoff:3.500A) Processing helix chain 'D' and resid 292 through 300 Processing helix chain 'D' and resid 304 through 317 Processing helix chain 'D' and resid 324 through 331 Processing helix chain 'D' and resid 365 through 387 Processing helix chain 'D' and resid 402 through 413 removed outlier: 3.585A pdb=" N MET D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 421 Processing helix chain 'D' and resid 431 through 448 Processing helix chain 'D' and resid 450 through 463 Processing helix chain 'D' and resid 472 through 486 Processing helix chain 'D' and resid 503 through 508 Processing helix chain 'D' and resid 512 through 531 removed outlier: 4.345A pdb=" N GLN D 531 " --> pdb=" O GLU D 527 " (cutoff:3.500A) Processing helix chain 'D' and resid 547 through 557 Processing helix chain 'D' and resid 570 through 575 Processing helix chain 'D' and resid 581 through 598 Proline residue: D 590 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 311 through 314 removed outlier: 3.552A pdb=" N GLY A 311 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N THR A 599 " --> pdb=" O GLY A 311 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE A 598 " --> pdb=" O ALA A 609 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 643 through 644 Processing sheet with id=AA3, first strand: chain 'A' and resid 664 through 667 removed outlier: 3.791A pdb=" N ILE A 666 " --> pdb=" O ILE A 670 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N CYS A 671 " --> pdb=" O TYR A 695 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 712 through 715 removed outlier: 3.808A pdb=" N ILE A 712 " --> pdb=" O PHE A1075 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 718 through 728 removed outlier: 3.507A pdb=" N SER A 721 " --> pdb=" O THR A1066 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AA7, first strand: chain 'A' and resid 1081 through 1082 removed outlier: 3.792A pdb=" N ILE A1081 " --> pdb=" O HIS A1088 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N SER A1123 " --> pdb=" O ALA A1087 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 51 through 55 removed outlier: 3.530A pdb=" N THR B 51 " --> pdb=" O PHE B 275 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLN B 271 " --> pdb=" O PHE B 55 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 195 through 196 Processing sheet with id=AB1, first strand: chain 'B' and resid 278 through 279 removed outlier: 6.596A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 311 through 319 removed outlier: 3.534A pdb=" N GLY B 311 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N THR B 599 " --> pdb=" O GLY B 311 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR B 313 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N GLN B 613 " --> pdb=" O GLY B 594 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N VAL B 610 " --> pdb=" O ILE B 651 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ILE B 651 " --> pdb=" O VAL B 610 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N TYR B 612 " --> pdb=" O CYS B 649 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 664 through 665 removed outlier: 3.815A pdb=" N ILE B 664 " --> pdb=" O ALA B 672 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ALA B 672 " --> pdb=" O ILE B 664 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'B' and resid 702 through 703 Processing sheet with id=AB5, first strand: chain 'B' and resid 712 through 713 removed outlier: 4.441A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 718 through 728 removed outlier: 3.573A pdb=" N THR B 723 " --> pdb=" O HIS B1064 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N HIS B1064 " --> pdb=" O THR B 723 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N GLU B 725 " --> pdb=" O PHE B1062 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE B1062 " --> pdb=" O GLU B 725 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AB8, first strand: chain 'B' and resid 1120 through 1122 removed outlier: 3.619A pdb=" N ILE B1081 " --> pdb=" O HIS B1088 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.831A pdb=" N HIS C 49 " --> pdb=" O LEU C 277 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 63 through 64 removed outlier: 4.182A pdb=" N GLY C 268 " --> pdb=" O TYR C 91 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N TYR C 91 " --> pdb=" O GLY C 268 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 82 through 83 removed outlier: 3.623A pdb=" N LEU C 82 " --> pdb=" O PHE C 238 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 195 through 197 removed outlier: 4.559A pdb=" N LYS C 195 " --> pdb=" O LYS C 202 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 311 through 319 removed outlier: 3.637A pdb=" N THR C 599 " --> pdb=" O GLY C 311 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N VAL C 610 " --> pdb=" O ILE C 651 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ILE C 651 " --> pdb=" O VAL C 610 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 377 through 379 removed outlier: 4.719A pdb=" N TRP C 436 " --> pdb=" O ARG C 509 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AC7, first strand: chain 'C' and resid 664 through 667 removed outlier: 4.421A pdb=" N ILE C 664 " --> pdb=" O ALA C 672 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA C 672 " --> pdb=" O ILE C 664 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE C 666 " --> pdb=" O ILE C 670 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'C' and resid 711 through 728 removed outlier: 3.745A pdb=" N ILE C 712 " --> pdb=" O PHE C1075 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE C 714 " --> pdb=" O LYS C1073 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA C1056 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 711 through 728 removed outlier: 3.745A pdb=" N ILE C 712 " --> pdb=" O PHE C1075 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE C 714 " --> pdb=" O LYS C1073 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL C1094 " --> pdb=" O THR C1105 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N THR C1105 " --> pdb=" O VAL C1094 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AD2, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 3.649A pdb=" N SER C1123 " --> pdb=" O ALA C1087 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 348 through 350 885 hydrogen bonds defined for protein. 2550 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: 8.44 Time building geometry restraints manager: 7.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.36: 7777 1.36 - 1.52: 11804 1.52 - 1.69: 4780 1.69 - 1.85: 157 1.85 - 2.02: 3 Bond restraints: 24521 Sorted by residual: bond pdb=" N ASN D 63 " pdb=" CA ASN D 63 " ideal model delta sigma weight residual 1.459 1.679 -0.221 1.16e-02 7.43e+03 3.62e+02 bond pdb=" C MET D 62 " pdb=" N ASN D 63 " ideal model delta sigma weight residual 1.334 1.556 -0.222 1.20e-02 6.94e+03 3.42e+02 bond pdb=" CA GLN D 60 " pdb=" C GLN D 60 " ideal model delta sigma weight residual 1.522 1.744 -0.222 1.40e-02 5.10e+03 2.52e+02 bond pdb=" CA CYS D 542 " pdb=" C CYS D 542 " ideal model delta sigma weight residual 1.521 1.666 -0.146 1.27e-02 6.20e+03 1.32e+02 bond pdb=" CA CYS D 530 " pdb=" C CYS D 530 " ideal model delta sigma weight residual 1.523 1.672 -0.149 1.48e-02 4.57e+03 1.02e+02 ... (remaining 24516 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.63: 33175 7.63 - 15.26: 166 15.26 - 22.89: 17 22.89 - 30.51: 2 30.51 - 38.14: 2 Bond angle restraints: 33362 Sorted by residual: angle pdb=" C CYS D 542 " pdb=" N ASP D 543 " pdb=" CA ASP D 543 " ideal model delta sigma weight residual 121.54 150.80 -29.26 1.91e+00 2.74e-01 2.35e+02 angle pdb=" N GLY D 200 " pdb=" CA GLY D 200 " pdb=" C GLY D 200 " ideal model delta sigma weight residual 113.18 148.73 -35.55 2.37e+00 1.78e-01 2.25e+02 angle pdb=" CA PRO C 412 " pdb=" N PRO C 412 " pdb=" CD PRO C 412 " ideal model delta sigma weight residual 112.00 92.45 19.55 1.40e+00 5.10e-01 1.95e+02 angle pdb=" CA PRO C 83 " pdb=" N PRO C 83 " pdb=" CD PRO C 83 " ideal model delta sigma weight residual 112.00 93.27 18.73 1.40e+00 5.10e-01 1.79e+02 angle pdb=" CA MET D 62 " pdb=" C MET D 62 " pdb=" O MET D 62 " ideal model delta sigma weight residual 120.42 106.47 13.95 1.06e+00 8.90e-01 1.73e+02 ... (remaining 33357 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.24: 12316 18.24 - 36.49: 1808 36.49 - 54.73: 386 54.73 - 72.97: 76 72.97 - 91.22: 39 Dihedral angle restraints: 14625 sinusoidal: 5758 harmonic: 8867 Sorted by residual: dihedral pdb=" CA GLN A 239 " pdb=" C GLN A 239 " pdb=" N THR A 240 " pdb=" CA THR A 240 " ideal model delta harmonic sigma weight residual 180.00 88.78 91.22 0 5.00e+00 4.00e-02 3.33e+02 dihedral pdb=" CA LYS D 61 " pdb=" C LYS D 61 " pdb=" N MET D 62 " pdb=" CA MET D 62 " ideal model delta harmonic sigma weight residual 180.00 95.06 84.94 0 5.00e+00 4.00e-02 2.89e+02 dihedral pdb=" CA ILE D 532 " pdb=" C ILE D 532 " pdb=" N ALA D 533 " pdb=" CA ALA D 533 " ideal model delta harmonic sigma weight residual 180.00 112.92 67.08 0 5.00e+00 4.00e-02 1.80e+02 ... (remaining 14622 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.120: 3551 0.120 - 0.240: 185 0.240 - 0.360: 22 0.360 - 0.480: 5 0.480 - 0.599: 2 Chirality restraints: 3765 Sorted by residual: chirality pdb=" CA MET D 62 " pdb=" N MET D 62 " pdb=" C MET D 62 " pdb=" CB MET D 62 " both_signs ideal model delta sigma weight residual False 2.51 1.91 0.60 2.00e-01 2.50e+01 8.98e+00 chirality pdb=" CB ILE A 210 " pdb=" CA ILE A 210 " pdb=" CG1 ILE A 210 " pdb=" CG2 ILE A 210 " both_signs ideal model delta sigma weight residual False 2.64 2.13 0.51 2.00e-01 2.50e+01 6.62e+00 chirality pdb=" CA PRO B 80 " pdb=" N PRO B 80 " pdb=" C PRO B 80 " pdb=" CB PRO B 80 " both_signs ideal model delta sigma weight residual False 2.72 2.24 0.48 2.00e-01 2.50e+01 5.72e+00 ... (remaining 3762 not shown) Planarity restraints: 4320 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS D 542 " 0.049 2.00e-02 2.50e+03 9.64e-02 9.29e+01 pdb=" C CYS D 542 " -0.167 2.00e-02 2.50e+03 pdb=" O CYS D 542 " 0.060 2.00e-02 2.50e+03 pdb=" N ASP D 543 " 0.057 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN D 60 " -0.046 2.00e-02 2.50e+03 9.27e-02 8.58e+01 pdb=" C GLN D 60 " 0.160 2.00e-02 2.50e+03 pdb=" O GLN D 60 " -0.059 2.00e-02 2.50e+03 pdb=" N LYS D 61 " -0.055 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN D 58 " -0.041 2.00e-02 2.50e+03 8.02e-02 6.43e+01 pdb=" C ASN D 58 " 0.139 2.00e-02 2.50e+03 pdb=" O ASN D 58 " -0.050 2.00e-02 2.50e+03 pdb=" N ILE D 59 " -0.048 2.00e-02 2.50e+03 ... (remaining 4317 not shown) Histogram of nonbonded interaction distances: 1.65 - 2.30: 131 2.30 - 2.95: 12402 2.95 - 3.60: 37423 3.60 - 4.25: 54344 4.25 - 4.90: 84445 Nonbonded interactions: 188745 Sorted by model distance: nonbonded pdb=" O ILE D 59 " pdb=" O MET D 62 " model vdw 1.654 3.040 nonbonded pdb=" N GLN D 531 " pdb=" N ASP D 543 " model vdw 1.875 3.200 nonbonded pdb=" N GLY A 87 " pdb=" O ARG A 237 " model vdw 1.885 3.120 nonbonded pdb=" O PHE A 84 " pdb=" N PHE A 238 " model vdw 1.913 3.120 nonbonded pdb=" O GLN D 60 " pdb=" N GLY D 66 " model vdw 1.948 3.120 ... (remaining 188740 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.170 Construct map_model_manager: 0.020 Extract box with map and model: 0.940 Check model and map are aligned: 0.170 Set scattering table: 0.210 Process input model: 53.100 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.100 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:3.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7205 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.261 24550 Z= 0.429 Angle : 1.383 38.142 33420 Z= 0.758 Chirality : 0.064 0.599 3765 Planarity : 0.010 0.172 4320 Dihedral : 17.909 91.219 8814 Min Nonbonded Distance : 1.654 Molprobity Statistics. All-atom Clashscore : 35.98 Ramachandran Plot: Outliers : 0.37 % Allowed : 13.15 % Favored : 86.48 % Rotamer: Outliers : 0.22 % Allowed : 29.71 % Favored : 70.06 % Cbeta Deviations : 0.38 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.73 % Twisted General : 1.58 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.97 (0.14), residues: 2988 helix: -0.61 (0.18), residues: 914 sheet: -1.17 (0.29), residues: 298 loop : -3.05 (0.13), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.079 0.004 TRP D 594 HIS 0.016 0.002 HIS B 207 PHE 0.041 0.002 PHE D 464 TYR 0.040 0.002 TYR A 91 ARG 0.024 0.001 ARG B 983 Details of bonding type rmsd hydrogen bonds : bond 0.17019 ( 882) hydrogen bonds : angle 8.61135 ( 2550) SS BOND : bond 0.01027 ( 29) SS BOND : angle 2.86900 ( 58) covalent geometry : bond 0.00766 (24521) covalent geometry : angle 1.37950 (33362) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 2669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 317 time to evaluate : 2.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 LEU cc_start: 0.7798 (tp) cc_final: 0.7494 (tt) REVERT: A 765 ARG cc_start: 0.8458 (ttp-170) cc_final: 0.8223 (tmm-80) REVERT: B 104 TRP cc_start: 0.4374 (m-90) cc_final: 0.3999 (m100) REVERT: B 918 GLU cc_start: 0.8216 (mt-10) cc_final: 0.7717 (mt-10) REVERT: B 994 ASP cc_start: 0.8309 (p0) cc_final: 0.7572 (p0) REVERT: B 1005 GLN cc_start: 0.7213 (tp-100) cc_final: 0.6715 (mm110) REVERT: C 28 TYR cc_start: 0.6366 (m-80) cc_final: 0.5417 (m-80) REVERT: C 303 LEU cc_start: 0.9154 (mp) cc_final: 0.8925 (tp) REVERT: C 387 LEU cc_start: 0.6903 (tt) cc_final: 0.6588 (pp) REVERT: C 505 TYR cc_start: 0.7667 (m-80) cc_final: 0.7118 (m-80) REVERT: C 725 GLU cc_start: 0.8627 (mm-30) cc_final: 0.8257 (mm-30) REVERT: D 43 ASN cc_start: 0.5030 (t0) cc_final: 0.4528 (t0) REVERT: D 62 MET cc_start: 0.1419 (tmm) cc_final: 0.1031 (tpt) REVERT: D 74 GLU cc_start: 0.7034 (mm-30) cc_final: 0.6676 (pt0) REVERT: D 100 LEU cc_start: 0.5281 (tp) cc_final: 0.4918 (tp) REVERT: D 152 MET cc_start: 0.2460 (tpt) cc_final: 0.1862 (ttp) REVERT: D 237 TYR cc_start: 0.2793 (t80) cc_final: 0.2232 (m-10) REVERT: D 249 MET cc_start: 0.1207 (mmm) cc_final: 0.0755 (mtm) REVERT: D 270 MET cc_start: 0.1442 (mpp) cc_final: 0.1139 (ttp) REVERT: D 361 CYS cc_start: 0.4987 (OUTLIER) cc_final: 0.4679 (m) REVERT: D 408 MET cc_start: 0.6278 (mpp) cc_final: 0.5803 (tpp) REVERT: D 453 THR cc_start: 0.1521 (m) cc_final: 0.1230 (m) REVERT: D 455 MET cc_start: 0.2736 (ppp) cc_final: 0.2163 (tpp) REVERT: D 523 PHE cc_start: 0.3627 (t80) cc_final: 0.3299 (t80) outliers start: 6 outliers final: 2 residues processed: 319 average time/residue: 0.3680 time to fit residues: 182.7387 Evaluate side-chains 193 residues out of total 2669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 190 time to evaluate : 2.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain B residue 1000 ARG Chi-restraints excluded: chain D residue 361 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 255 optimal weight: 2.9990 chunk 228 optimal weight: 0.6980 chunk 127 optimal weight: 0.7980 chunk 78 optimal weight: 8.9990 chunk 154 optimal weight: 0.8980 chunk 122 optimal weight: 0.8980 chunk 236 optimal weight: 3.9990 chunk 91 optimal weight: 0.7980 chunk 143 optimal weight: 0.2980 chunk 176 optimal weight: 3.9990 chunk 274 optimal weight: 7.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 777 ASN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN A1005 GLN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 787 GLN D 101 GLN ** D 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 535 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.126207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.098151 restraints weight = 111491.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.099783 restraints weight = 69574.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.099404 restraints weight = 53015.407| |-----------------------------------------------------------------------------| r_work (final): 0.3820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7144 moved from start: 0.1756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.194 24550 Z= 0.312 Angle : 1.108 22.865 33420 Z= 0.594 Chirality : 0.057 0.472 3765 Planarity : 0.008 0.097 4320 Dihedral : 8.645 83.341 3250 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 24.19 Ramachandran Plot: Outliers : 0.33 % Allowed : 12.52 % Favored : 87.15 % Rotamer: Outliers : 4.53 % Allowed : 25.81 % Favored : 69.65 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.11 % Twisted General : 1.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.69 (0.15), residues: 2988 helix: -0.26 (0.18), residues: 912 sheet: -0.99 (0.30), residues: 298 loop : -2.94 (0.13), residues: 1778 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP D 594 HIS 0.010 0.001 HIS D 493 PHE 0.036 0.002 PHE C 559 TYR 0.034 0.002 TYR D 158 ARG 0.007 0.001 ARG B 34 Details of bonding type rmsd hydrogen bonds : bond 0.09212 ( 882) hydrogen bonds : angle 7.75558 ( 2550) SS BOND : bond 0.00456 ( 29) SS BOND : angle 1.81935 ( 58) covalent geometry : bond 0.00551 (24521) covalent geometry : angle 1.10661 (33362) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 2669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 208 time to evaluate : 2.719 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 LEU cc_start: 0.7741 (tp) cc_final: 0.7382 (tt) REVERT: A 202 LYS cc_start: 0.7135 (tppt) cc_final: 0.6397 (ttpp) REVERT: A 900 MET cc_start: 0.8899 (pmm) cc_final: 0.7917 (mtm) REVERT: A 981 LEU cc_start: 0.9042 (OUTLIER) cc_final: 0.8824 (pp) REVERT: B 187 LYS cc_start: 0.5268 (OUTLIER) cc_final: 0.3807 (tttt) REVERT: B 271 GLN cc_start: 0.8078 (tp-100) cc_final: 0.7876 (tm-30) REVERT: B 869 MET cc_start: 0.8373 (pmm) cc_final: 0.8084 (pmm) REVERT: B 918 GLU cc_start: 0.7591 (mt-10) cc_final: 0.7322 (mt-10) REVERT: C 28 TYR cc_start: 0.6220 (m-80) cc_final: 0.5201 (m-80) REVERT: C 241 LEU cc_start: 0.4336 (OUTLIER) cc_final: 0.4092 (pp) REVERT: C 303 LEU cc_start: 0.9007 (mp) cc_final: 0.8711 (tp) REVERT: C 336 CYS cc_start: 0.2786 (OUTLIER) cc_final: 0.1971 (m) REVERT: C 364 ASP cc_start: 0.8646 (t0) cc_final: 0.8045 (p0) REVERT: C 387 LEU cc_start: 0.6740 (tt) cc_final: 0.6465 (pp) REVERT: C 505 TYR cc_start: 0.7344 (m-80) cc_final: 0.6504 (m-80) REVERT: C 515 PHE cc_start: 0.5549 (OUTLIER) cc_final: 0.4732 (p90) REVERT: C 1033 VAL cc_start: 0.8131 (OUTLIER) cc_final: 0.7895 (p) REVERT: D 32 PHE cc_start: 0.7840 (t80) cc_final: 0.7636 (t80) REVERT: D 43 ASN cc_start: 0.7030 (t0) cc_final: 0.6796 (t0) REVERT: D 249 MET cc_start: 0.5633 (mmm) cc_final: 0.4937 (mtm) REVERT: D 323 MET cc_start: 0.4230 (mmp) cc_final: 0.3345 (mmp) REVERT: D 424 LEU cc_start: -0.2686 (OUTLIER) cc_final: -0.3958 (tp) REVERT: D 455 MET cc_start: 0.4009 (ppp) cc_final: 0.2895 (tpp) REVERT: D 480 MET cc_start: -0.0013 (tmm) cc_final: -0.1715 (tpp) REVERT: D 481 LYS cc_start: 0.3717 (tptm) cc_final: 0.3325 (tptp) REVERT: D 523 PHE cc_start: 0.3979 (t80) cc_final: 0.3486 (t80) outliers start: 121 outliers final: 54 residues processed: 312 average time/residue: 0.3286 time to fit residues: 165.8306 Evaluate side-chains 239 residues out of total 2669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 178 time to evaluate : 3.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 170 TYR Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 187 LYS Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 655 HIS Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 1024 LEU Chi-restraints excluded: chain B residue 1137 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 192 PHE Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 1033 VAL Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 119 ILE Chi-restraints excluded: chain D residue 217 TYR Chi-restraints excluded: chain D residue 255 ARG Chi-restraints excluded: chain D residue 269 ASP Chi-restraints excluded: chain D residue 314 PHE Chi-restraints excluded: chain D residue 424 LEU Chi-restraints excluded: chain D residue 442 GLN Chi-restraints excluded: chain D residue 518 ARG Chi-restraints excluded: chain D residue 530 CYS Chi-restraints excluded: chain D residue 542 CYS Chi-restraints excluded: chain D residue 595 LEU Chi-restraints excluded: chain D residue 613 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 162 optimal weight: 0.7980 chunk 69 optimal weight: 2.9990 chunk 188 optimal weight: 0.0980 chunk 287 optimal weight: 8.9990 chunk 87 optimal weight: 10.0000 chunk 27 optimal weight: 0.9990 chunk 29 optimal weight: 3.9990 chunk 75 optimal weight: 7.9990 chunk 105 optimal weight: 10.0000 chunk 25 optimal weight: 0.8980 chunk 120 optimal weight: 0.8980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 ASN A 234 ASN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1101 HIS ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 420 ASN ** D 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 472 GLN ** D 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 531 GLN ** D 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.120191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.093394 restraints weight = 117868.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.094522 restraints weight = 77960.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.095159 restraints weight = 51242.754| |-----------------------------------------------------------------------------| r_work (final): 0.3818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7141 moved from start: 0.2505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.150 24550 Z= 0.274 Angle : 1.018 17.778 33420 Z= 0.547 Chirality : 0.054 0.438 3765 Planarity : 0.007 0.089 4320 Dihedral : 8.254 79.702 3245 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 21.93 Ramachandran Plot: Outliers : 0.27 % Allowed : 12.32 % Favored : 87.42 % Rotamer: Outliers : 4.91 % Allowed : 25.70 % Favored : 69.39 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.11 % Twisted General : 1.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.56 (0.15), residues: 2988 helix: -0.10 (0.18), residues: 906 sheet: -0.78 (0.30), residues: 292 loop : -2.91 (0.13), residues: 1790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 328 HIS 0.007 0.001 HIS D 535 PHE 0.026 0.001 PHE C 559 TYR 0.032 0.002 TYR A 91 ARG 0.012 0.001 ARG A 765 Details of bonding type rmsd hydrogen bonds : bond 0.09080 ( 882) hydrogen bonds : angle 7.45731 ( 2550) SS BOND : bond 0.00939 ( 29) SS BOND : angle 2.42185 ( 58) covalent geometry : bond 0.00483 (24521) covalent geometry : angle 1.01386 (33362) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 196 time to evaluate : 2.873 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 LEU cc_start: 0.7876 (tp) cc_final: 0.7493 (tt) REVERT: A 129 LYS cc_start: 0.7871 (ptpt) cc_final: 0.7515 (tttp) REVERT: A 201 PHE cc_start: 0.7134 (OUTLIER) cc_final: 0.6865 (m-80) REVERT: A 202 LYS cc_start: 0.7443 (tppt) cc_final: 0.6675 (ttpp) REVERT: A 203 ILE cc_start: 0.8570 (OUTLIER) cc_final: 0.8338 (tt) REVERT: A 900 MET cc_start: 0.8690 (OUTLIER) cc_final: 0.7914 (mtm) REVERT: B 187 LYS cc_start: 0.4422 (OUTLIER) cc_final: 0.3163 (tttt) REVERT: B 192 PHE cc_start: 0.8568 (m-10) cc_final: 0.8308 (m-10) REVERT: B 918 GLU cc_start: 0.7552 (mt-10) cc_final: 0.7326 (mt-10) REVERT: C 28 TYR cc_start: 0.6271 (m-80) cc_final: 0.5228 (m-80) REVERT: C 91 TYR cc_start: 0.7251 (OUTLIER) cc_final: 0.6403 (t80) REVERT: C 241 LEU cc_start: 0.4295 (OUTLIER) cc_final: 0.4063 (pp) REVERT: C 286 THR cc_start: 0.9178 (OUTLIER) cc_final: 0.8972 (m) REVERT: C 303 LEU cc_start: 0.9082 (mp) cc_final: 0.8729 (tp) REVERT: C 336 CYS cc_start: 0.2902 (OUTLIER) cc_final: 0.2518 (m) REVERT: C 379 CYS cc_start: 0.4207 (OUTLIER) cc_final: 0.3631 (m) REVERT: C 505 TYR cc_start: 0.7171 (m-80) cc_final: 0.6284 (m-80) REVERT: C 515 PHE cc_start: 0.5515 (OUTLIER) cc_final: 0.4836 (p90) REVERT: C 1033 VAL cc_start: 0.7880 (p) cc_final: 0.7606 (p) REVERT: D 32 PHE cc_start: 0.7639 (t80) cc_final: 0.7432 (t80) REVERT: D 43 ASN cc_start: 0.7236 (t0) cc_final: 0.7019 (t0) REVERT: D 123 MET cc_start: -0.1232 (ttt) cc_final: -0.1474 (ttt) REVERT: D 180 TYR cc_start: 0.4633 (OUTLIER) cc_final: 0.4080 (t80) REVERT: D 183 TYR cc_start: 0.6682 (t80) cc_final: 0.6345 (t80) REVERT: D 249 MET cc_start: 0.6038 (mmm) cc_final: 0.5179 (mtm) REVERT: D 366 MET cc_start: 0.3116 (pmm) cc_final: 0.2198 (pmm) REVERT: D 424 LEU cc_start: -0.2824 (OUTLIER) cc_final: -0.4143 (tp) REVERT: D 455 MET cc_start: 0.4690 (ppp) cc_final: 0.3784 (tpp) REVERT: D 462 MET cc_start: 0.4501 (ppp) cc_final: 0.4251 (ppp) REVERT: D 472 GLN cc_start: 0.1129 (OUTLIER) cc_final: 0.0514 (tp-100) REVERT: D 474 MET cc_start: 0.3117 (ttp) cc_final: 0.2839 (ttp) REVERT: D 480 MET cc_start: 0.0368 (tmm) cc_final: -0.1054 (tpp) REVERT: D 481 LYS cc_start: 0.4333 (OUTLIER) cc_final: 0.3972 (tmtt) REVERT: D 523 PHE cc_start: 0.3770 (t80) cc_final: 0.3315 (t80) REVERT: D 542 CYS cc_start: 0.0207 (OUTLIER) cc_final: -0.0160 (m) REVERT: D 562 ARG cc_start: 0.1177 (OUTLIER) cc_final: 0.0736 (mtt180) outliers start: 131 outliers final: 64 residues processed: 310 average time/residue: 0.3312 time to fit residues: 165.6294 Evaluate side-chains 256 residues out of total 2669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 176 time to evaluate : 3.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 106 PHE Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 170 TYR Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 201 PHE Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 187 LYS Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 655 HIS Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 1024 LEU Chi-restraints excluded: chain B residue 1137 VAL Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 91 TYR Chi-restraints excluded: chain C residue 104 TRP Chi-restraints excluded: chain C residue 192 PHE Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 1084 ASP Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 180 TYR Chi-restraints excluded: chain D residue 211 TRP Chi-restraints excluded: chain D residue 217 TYR Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 255 ARG Chi-restraints excluded: chain D residue 424 LEU Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 472 GLN Chi-restraints excluded: chain D residue 481 LYS Chi-restraints excluded: chain D residue 518 ARG Chi-restraints excluded: chain D residue 530 CYS Chi-restraints excluded: chain D residue 531 GLN Chi-restraints excluded: chain D residue 542 CYS Chi-restraints excluded: chain D residue 562 ARG Chi-restraints excluded: chain D residue 595 LEU Chi-restraints excluded: chain D residue 613 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 263 optimal weight: 7.9990 chunk 48 optimal weight: 1.9990 chunk 189 optimal weight: 6.9990 chunk 3 optimal weight: 10.0000 chunk 197 optimal weight: 0.0470 chunk 183 optimal weight: 4.9990 chunk 157 optimal weight: 2.9990 chunk 94 optimal weight: 10.0000 chunk 67 optimal weight: 2.9990 chunk 74 optimal weight: 9.9990 chunk 117 optimal weight: 2.9990 overall best weight: 2.2086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 ASN A 613 GLN ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN B 49 HIS ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 777 ASN C 992 GLN ** D 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 345 HIS ** D 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 531 GLN ** D 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.116200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.089214 restraints weight = 120363.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.090755 restraints weight = 74888.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.090416 restraints weight = 51240.632| |-----------------------------------------------------------------------------| r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.3494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.127 24550 Z= 0.296 Angle : 1.023 17.880 33420 Z= 0.548 Chirality : 0.055 0.435 3765 Planarity : 0.007 0.083 4320 Dihedral : 8.197 76.742 3245 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 24.26 Ramachandran Plot: Outliers : 0.33 % Allowed : 12.99 % Favored : 86.68 % Rotamer: Outliers : 6.67 % Allowed : 24.17 % Favored : 69.16 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.48 % Twisted General : 0.95 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.74 (0.14), residues: 2988 helix: -0.26 (0.17), residues: 922 sheet: -1.00 (0.30), residues: 295 loop : -3.01 (0.13), residues: 1771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 328 HIS 0.008 0.002 HIS A 207 PHE 0.022 0.002 PHE C 559 TYR 0.029 0.002 TYR D 516 ARG 0.010 0.001 ARG D 572 Details of bonding type rmsd hydrogen bonds : bond 0.09857 ( 882) hydrogen bonds : angle 7.41102 ( 2550) SS BOND : bond 0.00655 ( 29) SS BOND : angle 2.23272 ( 58) covalent geometry : bond 0.00562 (24521) covalent geometry : angle 1.01963 (33362) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 2669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 178 poor density : 183 time to evaluate : 2.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 LEU cc_start: 0.8010 (tp) cc_final: 0.7520 (tt) REVERT: A 129 LYS cc_start: 0.8344 (OUTLIER) cc_final: 0.7791 (tmtt) REVERT: A 189 LEU cc_start: 0.7369 (OUTLIER) cc_final: 0.7132 (pp) REVERT: A 900 MET cc_start: 0.8796 (OUTLIER) cc_final: 0.8148 (mtm) REVERT: A 1106 GLN cc_start: 0.8623 (OUTLIER) cc_final: 0.8280 (pt0) REVERT: B 187 LYS cc_start: 0.4387 (OUTLIER) cc_final: 0.3211 (tttt) REVERT: B 697 MET cc_start: 0.8956 (pmm) cc_final: 0.8754 (pmm) REVERT: B 918 GLU cc_start: 0.7728 (mt-10) cc_final: 0.7437 (mt-10) REVERT: C 28 TYR cc_start: 0.6700 (m-80) cc_final: 0.5558 (m-80) REVERT: C 91 TYR cc_start: 0.7412 (OUTLIER) cc_final: 0.5643 (t80) REVERT: C 117 LEU cc_start: 0.6064 (OUTLIER) cc_final: 0.5854 (tt) REVERT: C 241 LEU cc_start: 0.4571 (OUTLIER) cc_final: 0.4148 (pp) REVERT: C 275 PHE cc_start: 0.7731 (OUTLIER) cc_final: 0.6222 (t80) REVERT: C 387 LEU cc_start: 0.8479 (pp) cc_final: 0.8134 (mp) REVERT: C 505 TYR cc_start: 0.7115 (m-80) cc_final: 0.6209 (m-80) REVERT: C 515 PHE cc_start: 0.5661 (OUTLIER) cc_final: 0.5040 (p90) REVERT: C 1029 MET cc_start: 0.8958 (tmm) cc_final: 0.8720 (tmm) REVERT: D 43 ASN cc_start: 0.7092 (t0) cc_final: 0.6888 (t0) REVERT: D 180 TYR cc_start: 0.4650 (OUTLIER) cc_final: 0.4181 (t80) REVERT: D 183 TYR cc_start: 0.6684 (t80) cc_final: 0.6316 (t80) REVERT: D 190 MET cc_start: 0.1952 (ptm) cc_final: 0.1691 (ppp) REVERT: D 249 MET cc_start: 0.5834 (mmm) cc_final: 0.5308 (mtt) REVERT: D 424 LEU cc_start: -0.2719 (OUTLIER) cc_final: -0.4035 (tp) REVERT: D 455 MET cc_start: 0.4837 (ppp) cc_final: 0.3985 (tpp) REVERT: D 472 GLN cc_start: 0.3155 (OUTLIER) cc_final: 0.2165 (mp10) REVERT: D 479 GLU cc_start: 0.4696 (OUTLIER) cc_final: 0.4255 (pp20) REVERT: D 480 MET cc_start: 0.0563 (tmm) cc_final: -0.0909 (tpp) REVERT: D 481 LYS cc_start: 0.4305 (OUTLIER) cc_final: 0.4003 (tmtt) REVERT: D 523 PHE cc_start: 0.3945 (t80) cc_final: 0.3477 (t80) REVERT: D 542 CYS cc_start: 0.0113 (OUTLIER) cc_final: -0.0101 (m) REVERT: D 562 ARG cc_start: 0.1223 (OUTLIER) cc_final: 0.0820 (mtt180) REVERT: D 594 TRP cc_start: 0.3765 (t60) cc_final: 0.2361 (m-10) outliers start: 178 outliers final: 94 residues processed: 336 average time/residue: 0.3377 time to fit residues: 180.5020 Evaluate side-chains 272 residues out of total 2669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 161 time to evaluate : 2.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain A residue 214 ARG Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 273 ARG Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 888 PHE Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 187 LYS Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 655 HIS Chi-restraints excluded: chain B residue 666 ILE Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 777 ASN Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain B residue 1024 LEU Chi-restraints excluded: chain B residue 1137 VAL Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 91 TYR Chi-restraints excluded: chain C residue 104 TRP Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 192 PHE Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 666 ILE Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain C residue 1066 THR Chi-restraints excluded: chain C residue 1084 ASP Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 56 ASP Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 119 ILE Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 180 TYR Chi-restraints excluded: chain D residue 211 TRP Chi-restraints excluded: chain D residue 217 TYR Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 255 ARG Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 424 LEU Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 472 GLN Chi-restraints excluded: chain D residue 479 GLU Chi-restraints excluded: chain D residue 481 LYS Chi-restraints excluded: chain D residue 530 CYS Chi-restraints excluded: chain D residue 542 CYS Chi-restraints excluded: chain D residue 562 ARG Chi-restraints excluded: chain D residue 595 LEU Chi-restraints excluded: chain D residue 613 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 51 optimal weight: 0.5980 chunk 31 optimal weight: 8.9990 chunk 165 optimal weight: 3.9990 chunk 269 optimal weight: 4.9990 chunk 161 optimal weight: 6.9990 chunk 100 optimal weight: 8.9990 chunk 82 optimal weight: 0.0870 chunk 123 optimal weight: 3.9990 chunk 148 optimal weight: 10.0000 chunk 145 optimal weight: 2.9990 chunk 92 optimal weight: 0.3980 overall best weight: 1.6162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 ASN A 777 ASN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 439 ASN C 506 GLN ** D 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 221 GLN D 232 GLN D 345 HIS ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.125883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.096576 restraints weight = 106576.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.097461 restraints weight = 73994.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.098328 restraints weight = 50038.103| |-----------------------------------------------------------------------------| r_work (final): 0.3747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7271 moved from start: 0.4042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.111 24550 Z= 0.264 Angle : 0.977 15.952 33420 Z= 0.523 Chirality : 0.053 0.346 3765 Planarity : 0.007 0.083 4320 Dihedral : 7.981 74.012 3245 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 22.02 Ramachandran Plot: Outliers : 0.20 % Allowed : 12.18 % Favored : 87.62 % Rotamer: Outliers : 5.73 % Allowed : 25.74 % Favored : 68.53 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.86 % Twisted General : 0.84 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.61 (0.15), residues: 2988 helix: -0.13 (0.17), residues: 920 sheet: -1.10 (0.30), residues: 291 loop : -2.90 (0.13), residues: 1777 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 104 HIS 0.006 0.001 HIS D 535 PHE 0.028 0.002 PHE D 32 TYR 0.033 0.002 TYR D 196 ARG 0.005 0.001 ARG C 408 Details of bonding type rmsd hydrogen bonds : bond 0.09248 ( 882) hydrogen bonds : angle 7.24143 ( 2550) SS BOND : bond 0.00627 ( 29) SS BOND : angle 2.59073 ( 58) covalent geometry : bond 0.00487 (24521) covalent geometry : angle 0.97137 (33362) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 177 time to evaluate : 2.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 LEU cc_start: 0.7918 (tp) cc_final: 0.7480 (tt) REVERT: A 118 LEU cc_start: 0.4179 (OUTLIER) cc_final: 0.3518 (pp) REVERT: A 129 LYS cc_start: 0.8294 (OUTLIER) cc_final: 0.7654 (tmtt) REVERT: A 201 PHE cc_start: 0.7410 (OUTLIER) cc_final: 0.6406 (m-80) REVERT: A 869 MET cc_start: 0.8522 (pmm) cc_final: 0.8290 (pmm) REVERT: A 900 MET cc_start: 0.8985 (OUTLIER) cc_final: 0.8577 (mtm) REVERT: B 40 ASP cc_start: 0.6937 (p0) cc_final: 0.6724 (t0) REVERT: B 187 LYS cc_start: 0.4160 (OUTLIER) cc_final: 0.2946 (tttt) REVERT: B 918 GLU cc_start: 0.7641 (mt-10) cc_final: 0.7389 (mt-10) REVERT: B 1116 THR cc_start: 0.8195 (OUTLIER) cc_final: 0.7885 (m) REVERT: C 28 TYR cc_start: 0.6316 (m-80) cc_final: 0.5315 (m-80) REVERT: C 117 LEU cc_start: 0.6100 (pt) cc_final: 0.5876 (tt) REVERT: C 275 PHE cc_start: 0.7752 (OUTLIER) cc_final: 0.6166 (t80) REVERT: C 387 LEU cc_start: 0.8473 (pp) cc_final: 0.8123 (mp) REVERT: C 505 TYR cc_start: 0.7185 (m-80) cc_final: 0.6345 (m-80) REVERT: C 515 PHE cc_start: 0.5589 (OUTLIER) cc_final: 0.5072 (p90) REVERT: C 877 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8755 (tt) REVERT: C 1029 MET cc_start: 0.8972 (tmm) cc_final: 0.8699 (tmm) REVERT: D 123 MET cc_start: -0.0182 (ttt) cc_final: -0.0516 (ttt) REVERT: D 180 TYR cc_start: 0.4242 (OUTLIER) cc_final: 0.3750 (t80) REVERT: D 183 TYR cc_start: 0.6695 (t80) cc_final: 0.6314 (t80) REVERT: D 232 GLN cc_start: 0.0914 (OUTLIER) cc_final: -0.0696 (mt0) REVERT: D 249 MET cc_start: 0.5355 (mmm) cc_final: 0.5044 (mtt) REVERT: D 455 MET cc_start: 0.4911 (ppp) cc_final: 0.4188 (tpp) REVERT: D 479 GLU cc_start: 0.4462 (OUTLIER) cc_final: 0.4056 (pp20) REVERT: D 480 MET cc_start: 0.0791 (tmm) cc_final: -0.0701 (tpp) REVERT: D 481 LYS cc_start: 0.4125 (OUTLIER) cc_final: 0.3836 (tmtt) REVERT: D 523 PHE cc_start: 0.4261 (t80) cc_final: 0.3835 (t80) REVERT: D 594 TRP cc_start: 0.4018 (t60) cc_final: 0.2681 (m-10) outliers start: 153 outliers final: 87 residues processed: 307 average time/residue: 0.3361 time to fit residues: 168.4249 Evaluate side-chains 261 residues out of total 2669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 161 time to evaluate : 2.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 201 PHE Chi-restraints excluded: chain A residue 214 ARG Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 758 SER Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 64 TRP Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 187 LYS Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 666 ILE Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 777 ASN Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 947 LYS Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 1024 LEU Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain B residue 1068 VAL Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1137 VAL Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 91 TYR Chi-restraints excluded: chain C residue 104 TRP Chi-restraints excluded: chain C residue 192 PHE Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 806 LEU Chi-restraints excluded: chain C residue 877 LEU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain C residue 1084 ASP Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 56 ASP Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain D residue 119 ILE Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 180 TYR Chi-restraints excluded: chain D residue 203 TRP Chi-restraints excluded: chain D residue 211 TRP Chi-restraints excluded: chain D residue 217 TYR Chi-restraints excluded: chain D residue 232 GLN Chi-restraints excluded: chain D residue 255 ARG Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 479 GLU Chi-restraints excluded: chain D residue 481 LYS Chi-restraints excluded: chain D residue 530 CYS Chi-restraints excluded: chain D residue 595 LEU Chi-restraints excluded: chain D residue 613 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 126 optimal weight: 2.9990 chunk 84 optimal weight: 8.9990 chunk 32 optimal weight: 0.7980 chunk 253 optimal weight: 2.9990 chunk 222 optimal weight: 0.0010 chunk 62 optimal weight: 0.9990 chunk 263 optimal weight: 1.9990 chunk 197 optimal weight: 0.9990 chunk 30 optimal weight: 6.9990 chunk 112 optimal weight: 0.6980 chunk 168 optimal weight: 5.9990 overall best weight: 0.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 GLN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 439 ASN D 43 ASN ** D 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 374 HIS D 472 GLN ** D 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.120107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.091371 restraints weight = 115023.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.092021 restraints weight = 73909.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.092295 restraints weight = 52582.983| |-----------------------------------------------------------------------------| r_work (final): 0.3733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 moved from start: 0.4385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.110 24550 Z= 0.245 Angle : 0.956 19.235 33420 Z= 0.506 Chirality : 0.052 0.467 3765 Planarity : 0.006 0.082 4320 Dihedral : 7.726 74.240 3245 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 19.67 Ramachandran Plot: Outliers : 0.23 % Allowed : 11.98 % Favored : 87.78 % Rotamer: Outliers : 5.47 % Allowed : 25.25 % Favored : 69.28 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.86 % Twisted General : 0.84 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.49 (0.15), residues: 2988 helix: -0.02 (0.17), residues: 929 sheet: -0.92 (0.30), residues: 288 loop : -2.87 (0.13), residues: 1771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 478 HIS 0.007 0.001 HIS D 535 PHE 0.032 0.001 PHE D 32 TYR 0.027 0.001 TYR A 38 ARG 0.005 0.000 ARG A1000 Details of bonding type rmsd hydrogen bonds : bond 0.08546 ( 882) hydrogen bonds : angle 7.02868 ( 2550) SS BOND : bond 0.00319 ( 29) SS BOND : angle 2.23472 ( 58) covalent geometry : bond 0.00429 (24521) covalent geometry : angle 0.95225 (33362) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 2669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 183 time to evaluate : 3.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 LEU cc_start: 0.7898 (tp) cc_final: 0.7419 (tt) REVERT: A 118 LEU cc_start: 0.4017 (OUTLIER) cc_final: 0.3412 (pp) REVERT: A 129 LYS cc_start: 0.8347 (OUTLIER) cc_final: 0.7690 (tptt) REVERT: A 194 PHE cc_start: 0.7833 (t80) cc_final: 0.7620 (t80) REVERT: A 201 PHE cc_start: 0.7429 (OUTLIER) cc_final: 0.6948 (m-80) REVERT: A 740 MET cc_start: 0.8112 (ppp) cc_final: 0.7868 (tmm) REVERT: A 869 MET cc_start: 0.8313 (pmm) cc_final: 0.8093 (pmm) REVERT: A 900 MET cc_start: 0.8830 (OUTLIER) cc_final: 0.8189 (mtm) REVERT: A 1106 GLN cc_start: 0.8461 (OUTLIER) cc_final: 0.8226 (pt0) REVERT: B 40 ASP cc_start: 0.6911 (p0) cc_final: 0.6677 (t0) REVERT: B 187 LYS cc_start: 0.3552 (OUTLIER) cc_final: 0.2456 (tttt) REVERT: B 918 GLU cc_start: 0.7734 (mt-10) cc_final: 0.7448 (mt-10) REVERT: B 938 LEU cc_start: 0.8063 (mt) cc_final: 0.7856 (mm) REVERT: B 1116 THR cc_start: 0.8391 (OUTLIER) cc_final: 0.8129 (m) REVERT: C 28 TYR cc_start: 0.6295 (m-80) cc_final: 0.5273 (m-80) REVERT: C 117 LEU cc_start: 0.6038 (OUTLIER) cc_final: 0.5817 (tt) REVERT: C 275 PHE cc_start: 0.7629 (OUTLIER) cc_final: 0.6114 (t80) REVERT: C 387 LEU cc_start: 0.8338 (pp) cc_final: 0.8032 (mp) REVERT: C 505 TYR cc_start: 0.7060 (m-80) cc_final: 0.6125 (m-80) REVERT: C 515 PHE cc_start: 0.5577 (OUTLIER) cc_final: 0.5198 (p90) REVERT: C 1029 MET cc_start: 0.8810 (tmm) cc_final: 0.8538 (tmm) REVERT: D 123 MET cc_start: -0.0624 (ttt) cc_final: -0.0867 (ttt) REVERT: D 152 MET cc_start: 0.0623 (tpp) cc_final: -0.0692 (ttp) REVERT: D 176 LEU cc_start: 0.3413 (OUTLIER) cc_final: 0.3098 (mt) REVERT: D 180 TYR cc_start: 0.4058 (OUTLIER) cc_final: 0.3469 (t80) REVERT: D 183 TYR cc_start: 0.6637 (t80) cc_final: 0.6319 (t80) REVERT: D 217 TYR cc_start: 0.2203 (OUTLIER) cc_final: 0.1997 (m-80) REVERT: D 270 MET cc_start: -0.0246 (tmm) cc_final: -0.0554 (tmm) REVERT: D 323 MET cc_start: 0.3213 (mmp) cc_final: 0.2925 (mmp) REVERT: D 366 MET cc_start: 0.2927 (pmm) cc_final: 0.2358 (pmm) REVERT: D 455 MET cc_start: 0.4841 (ppp) cc_final: 0.4134 (tpp) REVERT: D 472 GLN cc_start: 0.1759 (OUTLIER) cc_final: 0.1178 (tp-100) REVERT: D 474 MET cc_start: 0.3569 (ttp) cc_final: 0.3359 (ttp) REVERT: D 479 GLU cc_start: 0.4415 (OUTLIER) cc_final: 0.4196 (pp20) REVERT: D 480 MET cc_start: 0.0877 (tmm) cc_final: -0.0468 (tpp) REVERT: D 481 LYS cc_start: 0.3882 (OUTLIER) cc_final: 0.3576 (tmtt) REVERT: D 522 GLN cc_start: 0.4937 (OUTLIER) cc_final: 0.4721 (tm-30) REVERT: D 523 PHE cc_start: 0.4606 (t80) cc_final: 0.4399 (t80) REVERT: D 542 CYS cc_start: 0.0046 (OUTLIER) cc_final: -0.0212 (m) outliers start: 146 outliers final: 85 residues processed: 309 average time/residue: 0.3351 time to fit residues: 166.2298 Evaluate side-chains 268 residues out of total 2669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 165 time to evaluate : 2.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 201 PHE Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 758 SER Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 64 TRP Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 187 LYS Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 777 ASN Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 947 LYS Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 1024 LEU Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1137 VAL Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 91 TYR Chi-restraints excluded: chain C residue 104 TRP Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 192 PHE Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 509 ARG Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1084 ASP Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 56 ASP Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 180 TYR Chi-restraints excluded: chain D residue 203 TRP Chi-restraints excluded: chain D residue 211 TRP Chi-restraints excluded: chain D residue 217 TYR Chi-restraints excluded: chain D residue 255 ARG Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 472 GLN Chi-restraints excluded: chain D residue 479 GLU Chi-restraints excluded: chain D residue 481 LYS Chi-restraints excluded: chain D residue 522 GLN Chi-restraints excluded: chain D residue 530 CYS Chi-restraints excluded: chain D residue 542 CYS Chi-restraints excluded: chain D residue 595 LEU Chi-restraints excluded: chain D residue 613 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 1 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 173 optimal weight: 0.6980 chunk 120 optimal weight: 0.9990 chunk 188 optimal weight: 5.9990 chunk 264 optimal weight: 0.9990 chunk 57 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 92 optimal weight: 0.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 43 ASN ** D 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 416 ASN ** D 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.120682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.092540 restraints weight = 114944.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.093511 restraints weight = 70129.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.093978 restraints weight = 46747.039| |-----------------------------------------------------------------------------| r_work (final): 0.3811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7330 moved from start: 0.4710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.108 24550 Z= 0.244 Angle : 0.943 14.440 33420 Z= 0.501 Chirality : 0.052 0.513 3765 Planarity : 0.006 0.085 4320 Dihedral : 7.593 73.733 3243 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 19.50 Ramachandran Plot: Outliers : 0.23 % Allowed : 12.28 % Favored : 87.48 % Rotamer: Outliers : 5.10 % Allowed : 25.67 % Favored : 69.24 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.86 % Twisted General : 0.88 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.40 (0.15), residues: 2988 helix: 0.10 (0.17), residues: 923 sheet: -0.81 (0.31), residues: 275 loop : -2.84 (0.13), residues: 1790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP D 594 HIS 0.006 0.001 HIS D 535 PHE 0.033 0.001 PHE D 32 TYR 0.028 0.001 TYR A 38 ARG 0.005 0.000 ARG C 509 Details of bonding type rmsd hydrogen bonds : bond 0.08340 ( 882) hydrogen bonds : angle 6.97566 ( 2550) SS BOND : bond 0.00528 ( 29) SS BOND : angle 2.07369 ( 58) covalent geometry : bond 0.00434 (24521) covalent geometry : angle 0.94026 (33362) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 2669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 176 time to evaluate : 2.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.8446 (OUTLIER) cc_final: 0.7810 (tptt) REVERT: A 194 PHE cc_start: 0.7723 (t80) cc_final: 0.7516 (t80) REVERT: A 201 PHE cc_start: 0.7724 (OUTLIER) cc_final: 0.7017 (m-80) REVERT: A 900 MET cc_start: 0.8622 (OUTLIER) cc_final: 0.7853 (mtm) REVERT: A 1106 GLN cc_start: 0.8226 (OUTLIER) cc_final: 0.7995 (pt0) REVERT: B 187 LYS cc_start: 0.3019 (OUTLIER) cc_final: 0.2118 (tttt) REVERT: B 938 LEU cc_start: 0.7993 (mt) cc_final: 0.7781 (mm) REVERT: B 1116 THR cc_start: 0.8380 (OUTLIER) cc_final: 0.8099 (m) REVERT: C 28 TYR cc_start: 0.6216 (m-80) cc_final: 0.5245 (m-80) REVERT: C 117 LEU cc_start: 0.6109 (OUTLIER) cc_final: 0.5908 (tt) REVERT: C 275 PHE cc_start: 0.7435 (OUTLIER) cc_final: 0.5940 (t80) REVERT: C 387 LEU cc_start: 0.8270 (pp) cc_final: 0.7969 (mp) REVERT: C 505 TYR cc_start: 0.7109 (m-80) cc_final: 0.6188 (m-80) REVERT: C 515 PHE cc_start: 0.6051 (OUTLIER) cc_final: 0.5537 (p90) REVERT: D 123 MET cc_start: -0.0345 (ttt) cc_final: -0.0702 (ttt) REVERT: D 152 MET cc_start: 0.0664 (tpp) cc_final: -0.0698 (ttp) REVERT: D 176 LEU cc_start: 0.3343 (OUTLIER) cc_final: 0.3025 (mt) REVERT: D 180 TYR cc_start: 0.4086 (OUTLIER) cc_final: 0.3497 (t80) REVERT: D 183 TYR cc_start: 0.6311 (t80) cc_final: 0.5994 (t80) REVERT: D 270 MET cc_start: -0.0321 (tmm) cc_final: -0.0611 (tmm) REVERT: D 323 MET cc_start: 0.3123 (mmp) cc_final: 0.2867 (mmp) REVERT: D 366 MET cc_start: 0.2503 (pmm) cc_final: 0.1943 (pmm) REVERT: D 455 MET cc_start: 0.4853 (OUTLIER) cc_final: 0.4137 (tpp) REVERT: D 472 GLN cc_start: 0.2923 (OUTLIER) cc_final: 0.1867 (mp10) REVERT: D 479 GLU cc_start: 0.4382 (OUTLIER) cc_final: 0.4168 (pp20) REVERT: D 480 MET cc_start: 0.0998 (tmm) cc_final: -0.0371 (tpp) REVERT: D 481 LYS cc_start: 0.4058 (OUTLIER) cc_final: 0.3749 (tmtt) REVERT: D 522 GLN cc_start: 0.4929 (OUTLIER) cc_final: 0.4726 (tm-30) REVERT: D 523 PHE cc_start: 0.4765 (t80) cc_final: 0.4562 (t80) REVERT: D 542 CYS cc_start: -0.0172 (OUTLIER) cc_final: -0.0444 (m) outliers start: 136 outliers final: 90 residues processed: 290 average time/residue: 0.3196 time to fit residues: 150.5393 Evaluate side-chains 275 residues out of total 2669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 168 time to evaluate : 2.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 201 PHE Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 273 ARG Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 782 PHE Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 64 TRP Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 187 LYS Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 666 ILE Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 777 ASN Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 947 LYS Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 1024 LEU Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1137 VAL Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 91 TYR Chi-restraints excluded: chain C residue 104 TRP Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 192 PHE Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 245 HIS Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1084 ASP Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain D residue 158 TYR Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 180 TYR Chi-restraints excluded: chain D residue 203 TRP Chi-restraints excluded: chain D residue 211 TRP Chi-restraints excluded: chain D residue 255 ARG Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain D residue 416 ASN Chi-restraints excluded: chain D residue 455 MET Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 472 GLN Chi-restraints excluded: chain D residue 479 GLU Chi-restraints excluded: chain D residue 481 LYS Chi-restraints excluded: chain D residue 522 GLN Chi-restraints excluded: chain D residue 530 CYS Chi-restraints excluded: chain D residue 542 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 124 optimal weight: 1.9990 chunk 272 optimal weight: 8.9990 chunk 4 optimal weight: 0.2980 chunk 265 optimal weight: 0.9980 chunk 44 optimal weight: 0.6980 chunk 268 optimal weight: 0.8980 chunk 89 optimal weight: 8.9990 chunk 155 optimal weight: 0.5980 chunk 109 optimal weight: 0.9990 chunk 2 optimal weight: 5.9990 chunk 176 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 43 ASN ** D 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 416 ASN ** D 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 522 GLN ** D 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.121066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.092884 restraints weight = 115133.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.093787 restraints weight = 69828.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.094268 restraints weight = 44945.740| |-----------------------------------------------------------------------------| r_work (final): 0.3818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 moved from start: 0.5020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.111 24550 Z= 0.240 Angle : 0.938 15.005 33420 Z= 0.497 Chirality : 0.051 0.460 3765 Planarity : 0.006 0.085 4320 Dihedral : 7.430 74.443 3243 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 19.40 Ramachandran Plot: Outliers : 0.20 % Allowed : 11.71 % Favored : 88.09 % Rotamer: Outliers : 4.38 % Allowed : 26.26 % Favored : 69.35 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.48 % Twisted General : 0.88 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.29 (0.15), residues: 2988 helix: 0.14 (0.17), residues: 934 sheet: -0.89 (0.29), residues: 301 loop : -2.75 (0.13), residues: 1753 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP D 594 HIS 0.006 0.001 HIS D 535 PHE 0.023 0.001 PHE B 84 TYR 0.030 0.001 TYR D 516 ARG 0.005 0.000 ARG B 44 Details of bonding type rmsd hydrogen bonds : bond 0.08066 ( 882) hydrogen bonds : angle 6.85971 ( 2550) SS BOND : bond 0.00623 ( 29) SS BOND : angle 2.06994 ( 58) covalent geometry : bond 0.00420 (24521) covalent geometry : angle 0.93470 (33362) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 176 time to evaluate : 2.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.8120 (ptpt) cc_final: 0.7561 (tptt) REVERT: A 194 PHE cc_start: 0.7847 (t80) cc_final: 0.7640 (t80) REVERT: A 201 PHE cc_start: 0.7610 (OUTLIER) cc_final: 0.6881 (m-80) REVERT: A 900 MET cc_start: 0.8637 (OUTLIER) cc_final: 0.7847 (mtm) REVERT: A 1106 GLN cc_start: 0.8290 (OUTLIER) cc_final: 0.8083 (pt0) REVERT: A 1146 ASP cc_start: 0.6510 (t0) cc_final: 0.5932 (p0) REVERT: B 187 LYS cc_start: 0.2635 (OUTLIER) cc_final: 0.1911 (tttm) REVERT: B 938 LEU cc_start: 0.7906 (mt) cc_final: 0.7693 (mm) REVERT: B 1116 THR cc_start: 0.8393 (OUTLIER) cc_final: 0.8117 (m) REVERT: C 28 TYR cc_start: 0.6085 (m-80) cc_final: 0.5167 (m-80) REVERT: C 117 LEU cc_start: 0.6384 (pt) cc_final: 0.6182 (tt) REVERT: C 275 PHE cc_start: 0.7397 (OUTLIER) cc_final: 0.5845 (t80) REVERT: C 387 LEU cc_start: 0.8375 (pp) cc_final: 0.8043 (mp) REVERT: C 505 TYR cc_start: 0.7271 (m-80) cc_final: 0.6199 (m-80) REVERT: C 515 PHE cc_start: 0.6165 (OUTLIER) cc_final: 0.5659 (p90) REVERT: D 32 PHE cc_start: 0.7375 (t80) cc_final: 0.7110 (t80) REVERT: D 123 MET cc_start: -0.0350 (ttt) cc_final: -0.0800 (ttt) REVERT: D 152 MET cc_start: 0.0470 (tpp) cc_final: -0.0805 (ttp) REVERT: D 180 TYR cc_start: 0.4056 (OUTLIER) cc_final: 0.3545 (t80) REVERT: D 183 TYR cc_start: 0.6547 (t80) cc_final: 0.6257 (t80) REVERT: D 220 ASN cc_start: 0.3882 (p0) cc_final: 0.3652 (t0) REVERT: D 455 MET cc_start: 0.4801 (OUTLIER) cc_final: 0.4130 (tpp) REVERT: D 479 GLU cc_start: 0.4318 (OUTLIER) cc_final: 0.4111 (pp20) REVERT: D 480 MET cc_start: 0.0852 (tmm) cc_final: -0.0422 (tpp) REVERT: D 481 LYS cc_start: 0.3909 (OUTLIER) cc_final: 0.3589 (tmtt) REVERT: D 523 PHE cc_start: 0.4942 (t80) cc_final: 0.4492 (t80) REVERT: D 542 CYS cc_start: -0.0188 (OUTLIER) cc_final: -0.0398 (m) outliers start: 117 outliers final: 85 residues processed: 274 average time/residue: 0.3214 time to fit residues: 145.2280 Evaluate side-chains 265 residues out of total 2669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 168 time to evaluate : 3.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 201 PHE Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 273 ARG Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 758 SER Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 64 TRP Chi-restraints excluded: chain B residue 65 PHE Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 187 LYS Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 666 ILE Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 947 LYS Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 1024 LEU Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1137 VAL Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 104 TRP Chi-restraints excluded: chain C residue 192 PHE Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 245 HIS Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1066 THR Chi-restraints excluded: chain C residue 1084 ASP Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 158 TYR Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 180 TYR Chi-restraints excluded: chain D residue 203 TRP Chi-restraints excluded: chain D residue 211 TRP Chi-restraints excluded: chain D residue 255 ARG Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain D residue 455 MET Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 479 GLU Chi-restraints excluded: chain D residue 481 LYS Chi-restraints excluded: chain D residue 530 CYS Chi-restraints excluded: chain D residue 542 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 87 optimal weight: 2.9990 chunk 188 optimal weight: 0.9990 chunk 82 optimal weight: 7.9990 chunk 157 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 238 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 152 optimal weight: 0.2980 chunk 253 optimal weight: 2.9990 chunk 237 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 658 ASN A 690 GLN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 43 ASN ** D 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 472 GLN ** D 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 524 GLN ** D 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.120431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.092393 restraints weight = 115288.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.092998 restraints weight = 69717.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.093682 restraints weight = 49937.504| |-----------------------------------------------------------------------------| r_work (final): 0.3809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7315 moved from start: 0.5390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.111 24550 Z= 0.240 Angle : 0.934 15.535 33420 Z= 0.495 Chirality : 0.051 0.385 3765 Planarity : 0.006 0.085 4320 Dihedral : 7.343 76.742 3243 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 18.85 Ramachandran Plot: Outliers : 0.17 % Allowed : 12.18 % Favored : 87.65 % Rotamer: Outliers : 4.53 % Allowed : 26.04 % Favored : 69.43 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.86 % Twisted General : 0.88 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.26 (0.15), residues: 2988 helix: 0.27 (0.18), residues: 915 sheet: -1.19 (0.28), residues: 333 loop : -2.71 (0.14), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP D 594 HIS 0.005 0.001 HIS C 66 PHE 0.021 0.001 PHE B 84 TYR 0.040 0.002 TYR A 38 ARG 0.006 0.001 ARG B 44 Details of bonding type rmsd hydrogen bonds : bond 0.08284 ( 882) hydrogen bonds : angle 6.78724 ( 2550) SS BOND : bond 0.00604 ( 29) SS BOND : angle 2.18264 ( 58) covalent geometry : bond 0.00430 (24521) covalent geometry : angle 0.93005 (33362) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 2669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 182 time to evaluate : 2.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.8313 (ptpt) cc_final: 0.7691 (tptt) REVERT: A 194 PHE cc_start: 0.7930 (t80) cc_final: 0.7707 (t80) REVERT: A 201 PHE cc_start: 0.7352 (OUTLIER) cc_final: 0.6406 (m-80) REVERT: A 894 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8656 (mt) REVERT: A 900 MET cc_start: 0.8659 (OUTLIER) cc_final: 0.7915 (mtm) REVERT: A 1106 GLN cc_start: 0.8251 (OUTLIER) cc_final: 0.8007 (pt0) REVERT: B 187 LYS cc_start: 0.1882 (OUTLIER) cc_final: 0.1302 (tttm) REVERT: B 1116 THR cc_start: 0.8476 (OUTLIER) cc_final: 0.8200 (m) REVERT: C 28 TYR cc_start: 0.6072 (m-80) cc_final: 0.5217 (m-80) REVERT: C 275 PHE cc_start: 0.7412 (OUTLIER) cc_final: 0.5878 (t80) REVERT: C 276 LEU cc_start: 0.8345 (OUTLIER) cc_final: 0.7704 (tp) REVERT: C 387 LEU cc_start: 0.8252 (pp) cc_final: 0.7939 (mp) REVERT: C 505 TYR cc_start: 0.6953 (m-80) cc_final: 0.5842 (m-80) REVERT: C 1005 GLN cc_start: 0.8272 (mm-40) cc_final: 0.8022 (mm-40) REVERT: C 1142 GLN cc_start: 0.6958 (tp-100) cc_final: 0.6751 (tp-100) REVERT: D 180 TYR cc_start: 0.3575 (OUTLIER) cc_final: 0.3205 (t80) REVERT: D 249 MET cc_start: 0.5266 (mtt) cc_final: 0.4983 (ppp) REVERT: D 454 TYR cc_start: 0.1558 (OUTLIER) cc_final: 0.1295 (t80) REVERT: D 455 MET cc_start: 0.4840 (OUTLIER) cc_final: 0.4228 (tpp) REVERT: D 480 MET cc_start: 0.0983 (tmm) cc_final: -0.0350 (tpp) REVERT: D 523 PHE cc_start: 0.5012 (t80) cc_final: 0.4620 (t80) REVERT: D 542 CYS cc_start: -0.0147 (OUTLIER) cc_final: -0.0522 (m) outliers start: 121 outliers final: 90 residues processed: 279 average time/residue: 0.3184 time to fit residues: 143.8988 Evaluate side-chains 266 residues out of total 2669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 164 time to evaluate : 2.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 201 PHE Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 273 ARG Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 758 SER Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 782 PHE Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 64 TRP Chi-restraints excluded: chain B residue 65 PHE Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 187 LYS Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 666 ILE Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 825 LYS Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 947 LYS Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 1024 LEU Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1137 VAL Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 91 TYR Chi-restraints excluded: chain C residue 192 PHE Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1066 THR Chi-restraints excluded: chain C residue 1084 ASP Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 180 TYR Chi-restraints excluded: chain D residue 203 TRP Chi-restraints excluded: chain D residue 211 TRP Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain D residue 454 TYR Chi-restraints excluded: chain D residue 455 MET Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 524 GLN Chi-restraints excluded: chain D residue 530 CYS Chi-restraints excluded: chain D residue 542 CYS Chi-restraints excluded: chain D residue 613 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 265 optimal weight: 9.9990 chunk 220 optimal weight: 0.6980 chunk 282 optimal weight: 8.9990 chunk 88 optimal weight: 6.9990 chunk 203 optimal weight: 3.9990 chunk 211 optimal weight: 0.6980 chunk 213 optimal weight: 1.9990 chunk 232 optimal weight: 3.9990 chunk 187 optimal weight: 8.9990 chunk 218 optimal weight: 0.9980 chunk 167 optimal weight: 0.4980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.120523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.092177 restraints weight = 115169.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.093381 restraints weight = 69854.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.093821 restraints weight = 44575.795| |-----------------------------------------------------------------------------| r_work (final): 0.3809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.5621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.111 24550 Z= 0.239 Angle : 0.955 16.033 33420 Z= 0.503 Chirality : 0.051 0.366 3765 Planarity : 0.006 0.086 4320 Dihedral : 7.283 75.481 3243 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 19.04 Ramachandran Plot: Outliers : 0.13 % Allowed : 12.01 % Favored : 87.85 % Rotamer: Outliers : 3.86 % Allowed : 26.98 % Favored : 69.16 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.86 % Twisted General : 0.74 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.25 (0.15), residues: 2988 helix: 0.24 (0.17), residues: 922 sheet: -1.15 (0.28), residues: 333 loop : -2.70 (0.14), residues: 1733 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP C 64 HIS 0.005 0.001 HIS D 239 PHE 0.021 0.001 PHE B 84 TYR 0.027 0.001 TYR D 183 ARG 0.011 0.000 ARG D 115 Details of bonding type rmsd hydrogen bonds : bond 0.08235 ( 882) hydrogen bonds : angle 6.77260 ( 2550) SS BOND : bond 0.00594 ( 29) SS BOND : angle 2.23420 ( 58) covalent geometry : bond 0.00426 (24521) covalent geometry : angle 0.95100 (33362) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 2669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 176 time to evaluate : 2.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.8327 (ptpt) cc_final: 0.7664 (tptt) REVERT: A 201 PHE cc_start: 0.7376 (OUTLIER) cc_final: 0.6426 (m-80) REVERT: A 894 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8674 (mt) REVERT: A 900 MET cc_start: 0.8647 (OUTLIER) cc_final: 0.7889 (mtm) REVERT: A 1106 GLN cc_start: 0.8253 (OUTLIER) cc_final: 0.8022 (pt0) REVERT: A 1146 ASP cc_start: 0.6340 (t0) cc_final: 0.6104 (p0) REVERT: B 187 LYS cc_start: 0.2212 (OUTLIER) cc_final: 0.1610 (ttpt) REVERT: B 1116 THR cc_start: 0.8485 (OUTLIER) cc_final: 0.8211 (m) REVERT: C 28 TYR cc_start: 0.5991 (m-80) cc_final: 0.5140 (m-80) REVERT: C 117 LEU cc_start: 0.5999 (tt) cc_final: 0.5740 (tt) REVERT: C 275 PHE cc_start: 0.7428 (OUTLIER) cc_final: 0.5913 (t80) REVERT: C 276 LEU cc_start: 0.8334 (OUTLIER) cc_final: 0.7715 (tp) REVERT: C 387 LEU cc_start: 0.8280 (pp) cc_final: 0.7977 (mp) REVERT: C 505 TYR cc_start: 0.7090 (m-80) cc_final: 0.5997 (m-80) REVERT: C 1005 GLN cc_start: 0.8354 (mm-40) cc_final: 0.8108 (mm-40) REVERT: D 123 MET cc_start: -0.0792 (ttt) cc_final: -0.1208 (mtp) REVERT: D 152 MET cc_start: 0.0500 (tpp) cc_final: -0.0836 (ttp) REVERT: D 249 MET cc_start: 0.5235 (mtt) cc_final: 0.5035 (ppp) REVERT: D 255 ARG cc_start: 0.7452 (ttm170) cc_final: 0.7161 (ttp-170) REVERT: D 455 MET cc_start: 0.4889 (OUTLIER) cc_final: 0.4219 (tpp) REVERT: D 480 MET cc_start: 0.0196 (tmm) cc_final: -0.1088 (tpp) REVERT: D 481 LYS cc_start: 0.5828 (tmmt) cc_final: 0.5384 (pptt) REVERT: D 523 PHE cc_start: 0.5192 (t80) cc_final: 0.4772 (t80) outliers start: 103 outliers final: 88 residues processed: 261 average time/residue: 0.3237 time to fit residues: 136.5715 Evaluate side-chains 263 residues out of total 2669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 166 time to evaluate : 2.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 201 PHE Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 273 ARG Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 758 SER Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 782 PHE Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 888 PHE Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 64 TRP Chi-restraints excluded: chain B residue 65 PHE Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 187 LYS Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 666 ILE Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 825 LYS Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 947 LYS Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 1024 LEU Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1137 VAL Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 192 PHE Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 245 HIS Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1066 THR Chi-restraints excluded: chain C residue 1084 ASP Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain D residue 203 TRP Chi-restraints excluded: chain D residue 211 TRP Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain D residue 455 MET Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 613 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 246 optimal weight: 5.9990 chunk 190 optimal weight: 6.9990 chunk 17 optimal weight: 1.9990 chunk 157 optimal weight: 3.9990 chunk 109 optimal weight: 0.0470 chunk 214 optimal weight: 2.9990 chunk 210 optimal weight: 0.0670 chunk 103 optimal weight: 7.9990 chunk 125 optimal weight: 0.6980 chunk 84 optimal weight: 10.0000 chunk 64 optimal weight: 4.9990 overall best weight: 1.1620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 524 GLN D 546 ASN ** D 552 GLN ** 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 = 0.4322 r_free = 0.4322 target = 0.119915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.091548 restraints weight = 114670.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.092680 restraints weight = 71687.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.093157 restraints weight = 42779.851| |-----------------------------------------------------------------------------| r_work (final): 0.3793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 moved from start: 0.5927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.109 24550 Z= 0.239 Angle : 0.945 16.517 33420 Z= 0.498 Chirality : 0.051 0.369 3765 Planarity : 0.006 0.086 4320 Dihedral : 7.278 75.784 3243 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 18.85 Ramachandran Plot: Outliers : 0.13 % Allowed : 12.32 % Favored : 87.55 % Rotamer: Outliers : 4.23 % Allowed : 26.26 % Favored : 69.50 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.86 % Twisted General : 0.74 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.23 (0.15), residues: 2988 helix: 0.22 (0.17), residues: 933 sheet: -1.03 (0.28), residues: 323 loop : -2.70 (0.14), residues: 1732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.002 TRP C 64 HIS 0.006 0.001 HIS C 66 PHE 0.032 0.001 PHE D 314 TYR 0.030 0.002 TYR D 180 ARG 0.007 0.001 ARG B 190 Details of bonding type rmsd hydrogen bonds : bond 0.08290 ( 882) hydrogen bonds : angle 6.71682 ( 2550) SS BOND : bond 0.00791 ( 29) SS BOND : angle 1.47441 ( 58) covalent geometry : bond 0.00432 (24521) covalent geometry : angle 0.94404 (33362) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8491.95 seconds wall clock time: 149 minutes 43.06 seconds (8983.06 seconds total)