Starting phenix.real_space_refine on Mon Aug 25 16:51:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t22_40978/08_2025/8t22_40978.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t22_40978/08_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_40978/08_2025/8t22_40978.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t22_40978/08_2025/8t22_40978.map" model { file = "/net/cci-nas-00/data/ceres_data/8t22_40978/08_2025/8t22_40978.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t22_40978/08_2025/8t22_40978.cif" } resolution = 3.83 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.043 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 4.56, per 1000 atoms: 0.19 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: 1.48 Conformation dependent library (CDL) restraints added in 889.5 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.55 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: 2.77 Time building geometry restraints manager: 1.95 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: 12.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 16.630 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.650 ------------------------------------------------------------------------------- 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 : 35.96 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.024 0.001 ARG B 983 TYR 0.040 0.002 TYR A 91 PHE 0.041 0.002 PHE D 464 TRP 0.079 0.004 TRP D 594 HIS 0.016 0.002 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00766 (24521) covalent geometry : angle 1.37950 (33362) SS BOND : bond 0.01027 ( 29) SS BOND : angle 2.86900 ( 58) hydrogen bonds : bond 0.17019 ( 882) hydrogen bonds : angle 8.61135 ( 2550) *********************** 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 : 0.943 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: 0.7495 (tt) REVERT: A 765 ARG cc_start: 0.8458 (ttp-170) cc_final: 0.8224 (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: 0.7716 (mt-10) REVERT: B 994 ASP cc_start: 0.8309 (p0) cc_final: 0.7571 (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: 0.8269 (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: 0.4919 (tp) REVERT: D 152 MET cc_start: 0.2460 (tpt) cc_final: 0.1861 (ttp) REVERT: D 237 TYR cc_start: 0.2793 (t80) cc_final: 0.2233 (m-10) REVERT: D 249 MET cc_start: 0.1207 (mmm) cc_final: 0.0754 (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: 0.5711 (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: 0.1719 time to fit residues: 84.8137 Evaluate side-chains 191 residues out of total 2669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 188 time to evaluate : 0.950 ------------------------------------------------------------------------------- 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 197 optimal weight: 0.4980 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 0.0010 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 9.9990 chunk 298 optimal weight: 4.9990 overall best weight: 0.8790 ------------------------------------------------------------------------------- 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 613 GLN A 777 ASN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN A1005 GLN B 122 ASN ** 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 ** D 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.119995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.093496 restraints weight = 119481.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.094945 restraints weight = 77890.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.095057 restraints weight = 51116.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.095934 restraints weight = 44436.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.095871 restraints weight = 35520.115| |-----------------------------------------------------------------------------| r_work (final): 0.3837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7110 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.186 24550 Z= 0.308 Angle : 1.106 22.288 33420 Z= 0.593 Chirality : 0.057 0.449 3765 Planarity : 0.008 0.095 4320 Dihedral : 8.640 82.844 3250 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 24.38 Ramachandran Plot: Outliers : 0.33 % Allowed : 12.65 % Favored : 87.01 % Rotamer: Outliers : 4.80 % Allowed : 25.70 % Favored : 69.50 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.11 % Twisted General : 1.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.69 (0.15), residues: 2988 helix: -0.24 (0.18), residues: 908 sheet: -1.09 (0.30), residues: 303 loop : -2.93 (0.13), residues: 1777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 177 TYR 0.034 0.002 TYR D 158 PHE 0.038 0.002 PHE C 559 TRP 0.038 0.003 TRP D 594 HIS 0.010 0.001 HIS D 493 Details of bonding type rmsd covalent geometry : bond 0.00547 (24521) covalent geometry : angle 1.10442 (33362) SS BOND : bond 0.00426 ( 29) SS BOND : angle 1.85995 ( 58) hydrogen bonds : bond 0.09204 ( 882) hydrogen bonds : angle 7.72288 ( 2550) *********************** 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 335 residues out of total 2669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 207 time to evaluate : 0.987 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: 0.7711 (tp) cc_final: 0.7341 (tt) REVERT: A 202 LYS cc_start: 0.7363 (tppt) cc_final: 0.6552 (ttpp) REVERT: A 765 ARG cc_start: 0.8381 (ttp-170) cc_final: 0.8173 (tmm-80) REVERT: A 900 MET cc_start: 0.8894 (pmm) cc_final: 0.7938 (mtm) REVERT: B 187 LYS cc_start: 0.5301 (OUTLIER) cc_final: 0.3841 (tttt) REVERT: B 271 GLN cc_start: 0.8006 (tp-100) cc_final: 0.7781 (tm-30) REVERT: B 650 LEU cc_start: 0.7929 (tp) cc_final: 0.7729 (tp) REVERT: B 869 MET cc_start: 0.8344 (pmm) cc_final: 0.8064 (pmm) REVERT: B 918 GLU cc_start: 0.7523 (mt-10) cc_final: 0.7263 (mt-10) REVERT: C 28 TYR cc_start: 0.6303 (m-80) cc_final: 0.5260 (m-80) REVERT: C 91 TYR cc_start: 0.7176 (OUTLIER) cc_final: 0.6529 (t80) REVERT: C 241 LEU cc_start: 0.4444 (OUTLIER) cc_final: 0.4208 (pp) REVERT: C 286 THR cc_start: 0.9167 (OUTLIER) cc_final: 0.8892 (p) REVERT: C 303 LEU cc_start: 0.9047 (mp) cc_final: 0.8753 (tp) REVERT: C 336 CYS cc_start: 0.2585 (OUTLIER) cc_final: 0.1748 (m) REVERT: C 364 ASP cc_start: 0.8511 (t0) cc_final: 0.8020 (p0) REVERT: C 505 TYR cc_start: 0.7155 (m-80) cc_final: 0.6318 (m-80) REVERT: C 515 PHE cc_start: 0.5420 (OUTLIER) cc_final: 0.4652 (p90) REVERT: D 43 ASN cc_start: 0.7223 (t0) cc_final: 0.6992 (t0) REVERT: D 249 MET cc_start: 0.5713 (mmm) cc_final: 0.5038 (mtm) REVERT: D 323 MET cc_start: 0.4241 (mmp) cc_final: 0.3345 (mmp) REVERT: D 424 LEU cc_start: -0.2767 (OUTLIER) cc_final: -0.4034 (tp) REVERT: D 455 MET cc_start: 0.4206 (ppp) cc_final: 0.3042 (tpp) REVERT: D 480 MET cc_start: 0.0051 (tmm) cc_final: -0.1526 (tpp) REVERT: D 481 LYS cc_start: 0.3612 (tptm) cc_final: 0.3281 (tptp) REVERT: D 523 PHE cc_start: 0.3794 (t80) cc_final: 0.3309 (t80) REVERT: D 542 CYS cc_start: -0.0368 (OUTLIER) cc_final: -0.1226 (m) outliers start: 128 outliers final: 56 residues processed: 320 average time/residue: 0.1524 time to fit residues: 78.7078 Evaluate side-chains 245 residues out of total 2669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 181 time to evaluate : 0.928 ------------------------------------------------------------------------------- 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 991 VAL Chi-restraints excluded: chain A residue 1008 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 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 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 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 761 THR Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 1084 ASP Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 61 LYS Chi-restraints excluded: chain D residue 119 ILE Chi-restraints excluded: chain D residue 180 TYR 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 109 optimal weight: 2.9990 chunk 92 optimal weight: 9.9990 chunk 290 optimal weight: 6.9990 chunk 171 optimal weight: 9.9990 chunk 119 optimal weight: 0.0170 chunk 287 optimal weight: 8.9990 chunk 60 optimal weight: 0.7980 chunk 70 optimal weight: 4.9990 chunk 174 optimal weight: 2.9990 chunk 110 optimal weight: 0.8980 chunk 235 optimal weight: 0.9980 overall best weight: 1.1420 ------------------------------------------------------------------------------- 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** A1005 GLN 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 345 HIS D 378 HIS ** D 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 420 ASN ** D 442 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.121147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.092439 restraints weight = 116428.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.092963 restraints weight = 75019.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.093410 restraints weight = 59499.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.093852 restraints weight = 38923.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.093922 restraints weight = 32513.331| |-----------------------------------------------------------------------------| r_work (final): 0.3779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7256 moved from start: 0.2733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.140 24550 Z= 0.276 Angle : 1.017 17.526 33420 Z= 0.547 Chirality : 0.055 0.447 3765 Planarity : 0.007 0.089 4320 Dihedral : 8.258 78.324 3245 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 21.87 Ramachandran Plot: Outliers : 0.20 % Allowed : 12.38 % Favored : 87.42 % Rotamer: Outliers : 5.21 % Allowed : 25.63 % Favored : 69.16 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.48 % Twisted General : 0.98 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.59 (0.15), residues: 2988 helix: -0.10 (0.18), residues: 913 sheet: -0.79 (0.31), residues: 283 loop : -2.94 (0.13), residues: 1792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 393 TYR 0.031 0.002 TYR A 91 PHE 0.027 0.001 PHE C 559 TRP 0.023 0.002 TRP D 594 HIS 0.014 0.001 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00493 (24521) covalent geometry : angle 1.01345 (33362) SS BOND : bond 0.00675 ( 29) SS BOND : angle 2.39962 ( 58) hydrogen bonds : bond 0.09243 ( 882) hydrogen bonds : angle 7.44230 ( 2550) *********************** 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 340 residues out of total 2669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 201 time to evaluate : 0.909 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: 0.7813 (tp) cc_final: 0.7446 (tt) REVERT: A 201 PHE cc_start: 0.7327 (OUTLIER) cc_final: 0.7120 (m-80) REVERT: A 202 LYS cc_start: 0.7742 (tppt) cc_final: 0.6976 (ttpp) REVERT: A 692 ILE cc_start: 0.8021 (mp) cc_final: 0.7733 (mm) REVERT: A 900 MET cc_start: 0.8779 (OUTLIER) cc_final: 0.8094 (mtm) REVERT: B 187 LYS cc_start: 0.4548 (OUTLIER) cc_final: 0.3281 (tttt) REVERT: B 192 PHE cc_start: 0.8612 (m-10) cc_final: 0.8409 (m-10) REVERT: B 918 GLU cc_start: 0.7692 (mt-10) cc_final: 0.7398 (mt-10) REVERT: C 28 TYR cc_start: 0.6389 (m-80) cc_final: 0.5361 (m-80) REVERT: C 91 TYR cc_start: 0.7381 (OUTLIER) cc_final: 0.6433 (t80) REVERT: C 241 LEU cc_start: 0.4304 (OUTLIER) cc_final: 0.4068 (pp) REVERT: C 286 THR cc_start: 0.9171 (OUTLIER) cc_final: 0.8969 (m) REVERT: C 303 LEU cc_start: 0.9088 (mp) cc_final: 0.8648 (tp) REVERT: C 336 CYS cc_start: 0.4015 (OUTLIER) cc_final: 0.3645 (m) REVERT: C 379 CYS cc_start: 0.4505 (OUTLIER) cc_final: 0.4092 (m) REVERT: C 387 LEU cc_start: 0.8352 (pp) cc_final: 0.8072 (mp) REVERT: C 505 TYR cc_start: 0.7351 (m-80) cc_final: 0.6504 (m-80) REVERT: C 515 PHE cc_start: 0.5285 (OUTLIER) cc_final: 0.4704 (p90) REVERT: D 43 ASN cc_start: 0.7011 (t0) cc_final: 0.6811 (t0) REVERT: D 249 MET cc_start: 0.5899 (mmm) cc_final: 0.5315 (mtm) REVERT: D 270 MET cc_start: 0.0259 (ptt) cc_final: 0.0033 (tmm) REVERT: D 323 MET cc_start: 0.3895 (mmp) cc_final: 0.3651 (mmp) REVERT: D 424 LEU cc_start: -0.2461 (OUTLIER) cc_final: -0.3773 (tp) REVERT: D 455 MET cc_start: 0.4802 (ppp) cc_final: 0.3918 (tpp) REVERT: D 462 MET cc_start: 0.3824 (ppp) cc_final: 0.3616 (ppp) REVERT: D 480 MET cc_start: 0.0516 (tmm) cc_final: -0.0705 (tpp) REVERT: D 481 LYS cc_start: 0.4502 (OUTLIER) cc_final: 0.4103 (tmtt) REVERT: D 523 PHE cc_start: 0.4108 (t80) cc_final: 0.3587 (t80) REVERT: D 542 CYS cc_start: -0.0031 (OUTLIER) cc_final: -0.0260 (m) REVERT: D 562 ARG cc_start: 0.1248 (OUTLIER) cc_final: 0.0785 (mtt180) outliers start: 139 outliers final: 71 residues processed: 325 average time/residue: 0.1641 time to fit residues: 85.2883 Evaluate side-chains 264 residues out of total 2669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 180 time to evaluate : 0.920 ------------------------------------------------------------------------------- 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 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 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 759 PHE Chi-restraints excluded: chain A residue 761 THR 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 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 128 ILE Chi-restraints excluded: chain B residue 167 THR 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 308 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 982 SER 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 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 390 LEU 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 666 ILE Chi-restraints excluded: chain C residue 697 MET 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 997 ILE Chi-restraints excluded: chain C residue 1084 ASP Chi-restraints excluded: chain D residue 119 ILE 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 424 LEU Chi-restraints excluded: chain D residue 456 LEU 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 110 optimal weight: 0.9980 chunk 70 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 29 optimal weight: 0.0870 chunk 253 optimal weight: 6.9990 chunk 67 optimal weight: 1.9990 chunk 227 optimal weight: 7.9990 chunk 292 optimal weight: 3.9990 chunk 9 optimal weight: 6.9990 chunk 0 optimal weight: 0.9980 chunk 107 optimal weight: 3.9990 overall best weight: 1.2162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 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 C 992 GLN ** D 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 472 GLN ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.118336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.091011 restraints weight = 119231.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.092787 restraints weight = 76229.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.092935 restraints weight = 48062.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.093580 restraints weight = 38666.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.093427 restraints weight = 33692.701| |-----------------------------------------------------------------------------| r_work (final): 0.3776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7218 moved from start: 0.3326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.120 24550 Z= 0.265 Angle : 0.976 17.253 33420 Z= 0.524 Chirality : 0.053 0.353 3765 Planarity : 0.007 0.088 4320 Dihedral : 8.025 76.714 3245 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 21.62 Ramachandran Plot: Outliers : 0.27 % Allowed : 12.18 % Favored : 87.55 % Rotamer: Outliers : 5.62 % Allowed : 25.25 % Favored : 69.13 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.48 % Twisted General : 0.84 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.57 (0.15), residues: 2988 helix: -0.08 (0.18), residues: 917 sheet: -0.90 (0.31), residues: 287 loop : -2.92 (0.13), residues: 1784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 255 TYR 0.029 0.002 TYR C 91 PHE 0.023 0.001 PHE C 559 TRP 0.021 0.002 TRP D 328 HIS 0.013 0.001 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00474 (24521) covalent geometry : angle 0.97325 (33362) SS BOND : bond 0.00658 ( 29) SS BOND : angle 2.11961 ( 58) hydrogen bonds : bond 0.09013 ( 882) hydrogen bonds : angle 7.28744 ( 2550) *********************** 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 338 residues out of total 2669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 188 time to evaluate : 0.811 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: 0.7729 (tp) cc_final: 0.7276 (tt) REVERT: A 201 PHE cc_start: 0.7340 (OUTLIER) cc_final: 0.6952 (m-80) REVERT: A 900 MET cc_start: 0.8746 (OUTLIER) cc_final: 0.7956 (mtm) REVERT: B 187 LYS cc_start: 0.3999 (OUTLIER) cc_final: 0.2844 (tttt) REVERT: B 918 GLU cc_start: 0.7585 (mt-10) cc_final: 0.7327 (mt-10) REVERT: C 28 TYR cc_start: 0.6512 (m-80) cc_final: 0.5427 (m-80) REVERT: C 91 TYR cc_start: 0.7228 (OUTLIER) cc_final: 0.5659 (t80) REVERT: C 241 LEU cc_start: 0.4452 (OUTLIER) cc_final: 0.4077 (pp) REVERT: C 275 PHE cc_start: 0.7437 (OUTLIER) cc_final: 0.5895 (t80) REVERT: C 379 CYS cc_start: 0.4388 (OUTLIER) cc_final: 0.4019 (m) REVERT: C 387 LEU cc_start: 0.8374 (pp) cc_final: 0.8039 (mp) REVERT: C 505 TYR cc_start: 0.7055 (m-80) cc_final: 0.6056 (m-80) REVERT: C 515 PHE cc_start: 0.5557 (OUTLIER) cc_final: 0.4884 (p90) REVERT: D 190 MET cc_start: 0.2373 (ptt) cc_final: 0.2060 (ptt) REVERT: D 249 MET cc_start: 0.5832 (mmm) cc_final: 0.5271 (mtt) REVERT: D 323 MET cc_start: 0.4437 (mmp) cc_final: 0.4206 (mmp) REVERT: D 424 LEU cc_start: -0.2776 (OUTLIER) cc_final: -0.4096 (tp) REVERT: D 455 MET cc_start: 0.4798 (ppp) cc_final: 0.3976 (tpp) REVERT: D 472 GLN cc_start: 0.1652 (OUTLIER) cc_final: 0.1042 (tp-100) REVERT: D 479 GLU cc_start: 0.4688 (OUTLIER) cc_final: 0.4237 (pp20) REVERT: D 480 MET cc_start: 0.0676 (tmm) cc_final: -0.0707 (tpp) REVERT: D 481 LYS cc_start: 0.4524 (OUTLIER) cc_final: 0.4225 (tmtt) REVERT: D 523 PHE cc_start: 0.4272 (t80) cc_final: 0.3757 (t80) REVERT: D 562 ARG cc_start: 0.1102 (OUTLIER) cc_final: 0.0823 (mtt180) REVERT: D 594 TRP cc_start: 0.3594 (t60) cc_final: 0.2285 (m-10) outliers start: 150 outliers final: 82 residues processed: 320 average time/residue: 0.1621 time to fit residues: 83.1055 Evaluate side-chains 268 residues out of total 2669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 173 time to evaluate : 0.984 ------------------------------------------------------------------------------- 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 126 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 166 CYS 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 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 273 ARG 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 806 LEU 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 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 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 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 959 LEU 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 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 355 ARG Chi-restraints excluded: chain C residue 379 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 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 697 MET 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 916 LEU 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 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 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 518 ARG Chi-restraints excluded: chain D residue 530 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 58 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 294 optimal weight: 20.0000 chunk 190 optimal weight: 0.9990 chunk 144 optimal weight: 4.9990 chunk 287 optimal weight: 3.9990 chunk 234 optimal weight: 0.8980 chunk 203 optimal weight: 2.9990 chunk 83 optimal weight: 4.9990 chunk 74 optimal weight: 9.9990 chunk 53 optimal weight: 0.9980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 439 ASN C 777 ASN ** D 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 221 GLN ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.116974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.089907 restraints weight = 117890.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.091350 restraints weight = 72603.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.090859 restraints weight = 54451.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.091492 restraints weight = 47884.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.092133 restraints weight = 36835.422| |-----------------------------------------------------------------------------| r_work (final): 0.3753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7248 moved from start: 0.3960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.110 24550 Z= 0.260 Angle : 0.971 15.838 33420 Z= 0.517 Chirality : 0.053 0.426 3765 Planarity : 0.007 0.085 4320 Dihedral : 7.909 73.719 3245 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 20.98 Ramachandran Plot: Outliers : 0.20 % Allowed : 12.35 % Favored : 87.45 % Rotamer: Outliers : 6.11 % Allowed : 25.03 % Favored : 68.86 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.86 % Twisted General : 0.84 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.50 (0.15), residues: 2988 helix: -0.03 (0.18), residues: 912 sheet: -0.97 (0.31), residues: 292 loop : -2.85 (0.13), residues: 1784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 995 TYR 0.037 0.002 TYR D 196 PHE 0.022 0.002 PHE C 559 TRP 0.020 0.002 TRP B 104 HIS 0.008 0.001 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00478 (24521) covalent geometry : angle 0.96583 (33362) SS BOND : bond 0.00575 ( 29) SS BOND : angle 2.51572 ( 58) hydrogen bonds : bond 0.09060 ( 882) hydrogen bonds : angle 7.18216 ( 2550) *********************** 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 345 residues out of total 2669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 163 poor density : 182 time to evaluate : 0.954 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: A 117 LEU cc_start: 0.7835 (tp) cc_final: 0.7367 (tt) REVERT: A 201 PHE cc_start: 0.7415 (OUTLIER) cc_final: 0.6813 (m-80) REVERT: A 740 MET cc_start: 0.8122 (ppp) cc_final: 0.7921 (tmm) REVERT: A 900 MET cc_start: 0.8736 (OUTLIER) cc_final: 0.8072 (mtm) REVERT: B 187 LYS cc_start: 0.3957 (OUTLIER) cc_final: 0.2712 (tttt) REVERT: B 697 MET cc_start: 0.8902 (pmm) cc_final: 0.8626 (pmm) REVERT: B 918 GLU cc_start: 0.7653 (mt-10) cc_final: 0.7395 (mt-10) REVERT: B 1116 THR cc_start: 0.8402 (OUTLIER) cc_final: 0.8138 (m) REVERT: C 28 TYR cc_start: 0.6492 (m-80) cc_final: 0.5365 (m-80) REVERT: C 275 PHE cc_start: 0.7724 (OUTLIER) cc_final: 0.6103 (t80) REVERT: C 336 CYS cc_start: 0.3033 (OUTLIER) cc_final: 0.2215 (m) REVERT: C 379 CYS cc_start: 0.4358 (OUTLIER) cc_final: 0.4149 (m) REVERT: C 387 LEU cc_start: 0.8387 (pp) cc_final: 0.8051 (mp) REVERT: C 505 TYR cc_start: 0.6966 (m-80) cc_final: 0.5999 (m-80) REVERT: C 515 PHE cc_start: 0.5757 (OUTLIER) cc_final: 0.5154 (p90) REVERT: D 32 PHE cc_start: 0.8062 (t80) cc_final: 0.7840 (t80) REVERT: D 190 MET cc_start: 0.1979 (ptt) cc_final: 0.1724 (ptm) REVERT: D 249 MET cc_start: 0.5327 (mmm) cc_final: 0.4997 (mtt) REVERT: D 308 PHE cc_start: 0.6647 (OUTLIER) cc_final: 0.6427 (t80) REVERT: D 366 MET cc_start: 0.2763 (pmm) cc_final: 0.2118 (pmm) REVERT: D 455 MET cc_start: 0.4869 (ppp) cc_final: 0.4147 (tpp) REVERT: D 472 GLN cc_start: 0.3811 (OUTLIER) cc_final: 0.2674 (mp10) REVERT: D 479 GLU cc_start: 0.4495 (OUTLIER) cc_final: 0.4090 (pp20) REVERT: D 480 MET cc_start: 0.0712 (tmm) cc_final: -0.0756 (tpp) REVERT: D 481 LYS cc_start: 0.4101 (OUTLIER) cc_final: 0.3858 (tmtt) REVERT: D 522 GLN cc_start: 0.5056 (OUTLIER) cc_final: 0.4798 (tm-30) REVERT: D 542 CYS cc_start: 0.0079 (OUTLIER) cc_final: -0.0218 (m) REVERT: D 562 ARG cc_start: 0.1019 (OUTLIER) cc_final: 0.0728 (mtt180) REVERT: D 594 TRP cc_start: 0.3671 (t60) cc_final: 0.2427 (m-10) outliers start: 163 outliers final: 100 residues processed: 325 average time/residue: 0.1552 time to fit residues: 82.0513 Evaluate side-chains 279 residues out of total 2669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 164 time to evaluate : 0.943 ------------------------------------------------------------------------------- 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 126 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 201 PHE Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 208 THR 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 274 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 818 ILE 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 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 206 LYS Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 610 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 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 948 LEU 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 1024 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 63 THR Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 91 TYR Chi-restraints excluded: chain C residue 141 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 355 ARG Chi-restraints excluded: chain C residue 379 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 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 726 ILE Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 806 LEU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 931 ILE 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 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 244 VAL Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 308 PHE Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 463 VAL 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 562 ARG 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 210 optimal weight: 2.9990 chunk 294 optimal weight: 6.9990 chunk 202 optimal weight: 4.9990 chunk 237 optimal weight: 0.6980 chunk 56 optimal weight: 4.9990 chunk 135 optimal weight: 1.9990 chunk 185 optimal weight: 6.9990 chunk 278 optimal weight: 9.9990 chunk 49 optimal weight: 0.6980 chunk 106 optimal weight: 0.7980 chunk 271 optimal weight: 0.9990 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 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** D 58 ASN ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.119881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.091259 restraints weight = 115787.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.091743 restraints weight = 74714.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.091856 restraints weight = 59772.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.092427 restraints weight = 42655.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.092860 restraints weight = 33377.627| |-----------------------------------------------------------------------------| r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.4396 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= 0.246 Angle : 0.950 14.715 33420 Z= 0.504 Chirality : 0.051 0.350 3765 Planarity : 0.006 0.085 4320 Dihedral : 7.664 72.946 3245 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 19.57 Ramachandran Plot: Outliers : 0.23 % Allowed : 11.85 % Favored : 87.92 % Rotamer: Outliers : 5.88 % Allowed : 24.73 % Favored : 69.39 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.86 % Twisted General : 0.88 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.40 (0.15), residues: 2988 helix: 0.07 (0.18), residues: 924 sheet: -0.91 (0.30), residues: 283 loop : -2.81 (0.13), residues: 1781 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1000 TYR 0.027 0.002 TYR A 38 PHE 0.023 0.001 PHE C 559 TRP 0.014 0.001 TRP D 478 HIS 0.007 0.001 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00435 (24521) covalent geometry : angle 0.94619 (33362) SS BOND : bond 0.00607 ( 29) SS BOND : angle 2.32718 ( 58) hydrogen bonds : bond 0.08490 ( 882) hydrogen bonds : angle 7.01978 ( 2550) *********************** 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 337 residues out of total 2669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 180 time to evaluate : 1.032 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: 0.7783 (tp) cc_final: 0.7334 (tt) REVERT: A 194 PHE cc_start: 0.7804 (t80) cc_final: 0.7555 (t80) REVERT: A 201 PHE cc_start: 0.7729 (OUTLIER) cc_final: 0.7227 (m-80) REVERT: A 587 ILE cc_start: 0.4565 (mm) cc_final: 0.4133 (mm) REVERT: A 900 MET cc_start: 0.8821 (OUTLIER) cc_final: 0.8182 (mtm) REVERT: B 187 LYS cc_start: 0.3327 (OUTLIER) cc_final: 0.2338 (tttt) REVERT: B 918 GLU cc_start: 0.7758 (mt-10) cc_final: 0.7454 (mt-10) REVERT: B 1116 THR cc_start: 0.8429 (OUTLIER) cc_final: 0.8172 (m) REVERT: C 28 TYR cc_start: 0.6350 (m-80) cc_final: 0.5322 (m-80) REVERT: C 275 PHE cc_start: 0.7600 (OUTLIER) cc_final: 0.5957 (t80) REVERT: C 336 CYS cc_start: 0.3516 (OUTLIER) cc_final: 0.3226 (m) REVERT: C 387 LEU cc_start: 0.8314 (pp) cc_final: 0.7989 (mp) REVERT: C 505 TYR cc_start: 0.7139 (m-80) cc_final: 0.6226 (m-80) REVERT: C 515 PHE cc_start: 0.5653 (OUTLIER) cc_final: 0.5088 (p90) REVERT: D 152 MET cc_start: 0.0375 (tpp) cc_final: -0.0814 (ttp) REVERT: D 270 MET cc_start: -0.0206 (tmm) cc_final: -0.0518 (tmm) REVERT: D 364 VAL cc_start: 0.2990 (OUTLIER) cc_final: 0.2696 (p) REVERT: D 366 MET cc_start: 0.2793 (pmm) cc_final: 0.2267 (pmm) REVERT: D 455 MET cc_start: 0.4873 (ppp) cc_final: 0.4139 (tpp) REVERT: D 479 GLU cc_start: 0.4418 (OUTLIER) cc_final: 0.4178 (pp20) REVERT: D 480 MET cc_start: 0.0874 (tmm) cc_final: -0.0481 (tpp) REVERT: D 481 LYS cc_start: 0.3939 (OUTLIER) cc_final: 0.3637 (tmtt) REVERT: D 594 TRP cc_start: 0.4079 (t60) cc_final: 0.2854 (m-10) outliers start: 157 outliers final: 88 residues processed: 318 average time/residue: 0.1681 time to fit residues: 85.7602 Evaluate side-chains 259 residues out of total 2669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 161 time to evaluate : 1.061 ------------------------------------------------------------------------------- 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 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 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 869 MET 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 190 ARG Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 276 LEU 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 982 SER Chi-restraints excluded: chain B residue 1024 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 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 286 THR Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 355 ARG 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 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 806 LEU 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 993 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 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 259 THR Chi-restraints excluded: chain D residue 364 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 140 optimal weight: 2.9990 chunk 248 optimal weight: 10.0000 chunk 90 optimal weight: 4.9990 chunk 259 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 188 optimal weight: 10.0000 chunk 184 optimal weight: 10.0000 chunk 71 optimal weight: 0.9980 chunk 219 optimal weight: 2.9990 chunk 72 optimal weight: 5.9990 chunk 192 optimal weight: 3.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- 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 764 ASN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 953 ASN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1142 GLN ** D 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 416 ASN D 472 GLN ** 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.115151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.086385 restraints weight = 115499.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.087219 restraints weight = 78258.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.087513 restraints weight = 48724.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.087724 restraints weight = 42666.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.087732 restraints weight = 37076.486| |-----------------------------------------------------------------------------| r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.5335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.112 24550 Z= 0.322 Angle : 1.033 15.153 33420 Z= 0.554 Chirality : 0.055 0.463 3765 Planarity : 0.007 0.087 4320 Dihedral : 7.944 71.917 3243 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 23.94 Ramachandran Plot: Outliers : 0.27 % Allowed : 12.99 % Favored : 86.75 % Rotamer: Outliers : 6.14 % Allowed : 24.92 % Favored : 68.94 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.11 % Twisted General : 0.91 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.74 (0.14), residues: 2988 helix: -0.31 (0.17), residues: 940 sheet: -1.11 (0.30), residues: 289 loop : -2.98 (0.13), residues: 1759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 255 TYR 0.034 0.003 TYR A 266 PHE 0.026 0.002 PHE A 32 TRP 0.016 0.002 TRP B 104 HIS 0.010 0.002 HIS C 49 Details of bonding type rmsd covalent geometry : bond 0.00649 (24521) covalent geometry : angle 1.02814 (33362) SS BOND : bond 0.01206 ( 29) SS BOND : angle 2.61508 ( 58) hydrogen bonds : bond 0.10245 ( 882) hydrogen bonds : angle 7.33344 ( 2550) *********************** 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 324 residues out of total 2669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 164 poor density : 160 time to evaluate : 1.009 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: A 38 TYR cc_start: 0.6158 (m-10) cc_final: 0.5945 (m-10) REVERT: A 117 LEU cc_start: 0.7818 (tp) cc_final: 0.7434 (pt) REVERT: A 201 PHE cc_start: 0.7190 (OUTLIER) cc_final: 0.6472 (m-80) REVERT: A 239 GLN cc_start: 0.4843 (OUTLIER) cc_final: 0.4578 (pt0) REVERT: A 900 MET cc_start: 0.8916 (OUTLIER) cc_final: 0.8305 (mtm) REVERT: A 979 ASP cc_start: 0.8211 (m-30) cc_final: 0.7896 (p0) REVERT: B 187 LYS cc_start: 0.2845 (OUTLIER) cc_final: 0.1936 (tttm) REVERT: B 189 LEU cc_start: 0.4412 (OUTLIER) cc_final: 0.4211 (mm) REVERT: C 28 TYR cc_start: 0.6463 (m-80) cc_final: 0.5420 (m-80) REVERT: C 275 PHE cc_start: 0.7802 (OUTLIER) cc_final: 0.6578 (t80) REVERT: C 276 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.7866 (tp) REVERT: C 505 TYR cc_start: 0.6811 (m-80) cc_final: 0.5850 (m-80) REVERT: C 515 PHE cc_start: 0.5645 (OUTLIER) cc_final: 0.5137 (p90) REVERT: D 32 PHE cc_start: 0.7289 (t80) cc_final: 0.7051 (t80) REVERT: D 220 ASN cc_start: 0.3925 (p0) cc_final: 0.3444 (t0) REVERT: D 232 GLN cc_start: 0.2668 (mp10) cc_final: 0.2168 (pp30) REVERT: D 249 MET cc_start: 0.5573 (mtt) cc_final: 0.4983 (ppp) REVERT: D 455 MET cc_start: 0.4817 (OUTLIER) cc_final: 0.4074 (tpp) REVERT: D 479 GLU cc_start: 0.4719 (OUTLIER) cc_final: 0.4488 (pp20) REVERT: D 480 MET cc_start: 0.0823 (tmm) cc_final: -0.0627 (tpp) REVERT: D 594 TRP cc_start: 0.4032 (t60) cc_final: 0.2683 (m-10) outliers start: 164 outliers final: 110 residues processed: 301 average time/residue: 0.1588 time to fit residues: 77.3903 Evaluate side-chains 265 residues out of total 2669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 145 time to evaluate : 0.953 ------------------------------------------------------------------------------- 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 106 PHE Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 201 PHE Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 239 GLN 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 586 ASP Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 761 THR 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 818 ILE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 869 MET 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 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 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 65 PHE 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 276 LEU Chi-restraints excluded: chain B residue 289 VAL 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 947 LYS 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 1068 VAL 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 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 390 LEU Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 439 ASN 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 519 HIS Chi-restraints excluded: chain C residue 569 ILE 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 666 ILE Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 806 LEU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 993 ILE 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 100 LEU Chi-restraints excluded: chain D residue 119 ILE Chi-restraints excluded: chain D residue 158 TYR 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 303 ASP Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 436 ILE 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 497 TYR 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 271 optimal weight: 5.9990 chunk 210 optimal weight: 5.9990 chunk 261 optimal weight: 2.9990 chunk 184 optimal weight: 0.4980 chunk 101 optimal weight: 3.9990 chunk 250 optimal weight: 20.0000 chunk 217 optimal weight: 2.9990 chunk 224 optimal weight: 0.7980 chunk 86 optimal weight: 10.0000 chunk 43 optimal weight: 0.0060 chunk 113 optimal weight: 0.6980 overall best weight: 0.9998 ------------------------------------------------------------------------------- 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 965 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 416 ASN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.117953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.088589 restraints weight = 115166.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.090220 restraints weight = 75679.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.090305 restraints weight = 43012.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.090467 restraints weight = 40040.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.090537 restraints weight = 33580.924| |-----------------------------------------------------------------------------| r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.5503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.114 24550 Z= 0.244 Angle : 0.954 14.392 33420 Z= 0.507 Chirality : 0.052 0.553 3765 Planarity : 0.006 0.087 4320 Dihedral : 7.601 73.356 3243 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 19.21 Ramachandran Plot: Outliers : 0.23 % Allowed : 11.35 % Favored : 88.42 % Rotamer: Outliers : 4.23 % Allowed : 26.53 % Favored : 69.24 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.48 % Twisted General : 0.74 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.53 (0.14), residues: 2988 helix: -0.03 (0.17), residues: 929 sheet: -1.25 (0.28), residues: 322 loop : -2.87 (0.13), residues: 1737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1000 TYR 0.028 0.002 TYR D 516 PHE 0.019 0.001 PHE A 32 TRP 0.014 0.002 TRP D 478 HIS 0.009 0.001 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00433 (24521) covalent geometry : angle 0.94897 (33362) SS BOND : bond 0.00629 ( 29) SS BOND : angle 2.55763 ( 58) hydrogen bonds : bond 0.08721 ( 882) hydrogen bonds : angle 6.96573 ( 2550) *********************** 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 279 residues out of total 2669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 166 time to evaluate : 0.852 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 166 CYS cc_start: 0.4563 (OUTLIER) cc_final: 0.4346 (m) REVERT: A 194 PHE cc_start: 0.7949 (t80) cc_final: 0.7667 (t80) REVERT: A 201 PHE cc_start: 0.6693 (OUTLIER) cc_final: 0.5957 (m-80) REVERT: A 900 MET cc_start: 0.8846 (OUTLIER) cc_final: 0.8152 (mtm) REVERT: B 40 ASP cc_start: 0.7126 (p0) cc_final: 0.6698 (t0) REVERT: B 187 LYS cc_start: 0.2632 (OUTLIER) cc_final: 0.1783 (tttt) REVERT: B 918 GLU cc_start: 0.7820 (mt-10) cc_final: 0.7520 (mt-10) REVERT: C 28 TYR cc_start: 0.6113 (m-80) cc_final: 0.5160 (m-80) REVERT: C 275 PHE cc_start: 0.7766 (OUTLIER) cc_final: 0.6462 (t80) REVERT: C 276 LEU cc_start: 0.8506 (OUTLIER) cc_final: 0.7939 (tp) REVERT: C 505 TYR cc_start: 0.7180 (m-80) cc_final: 0.6139 (m-80) REVERT: C 515 PHE cc_start: 0.5831 (OUTLIER) cc_final: 0.5358 (p90) REVERT: D 32 PHE cc_start: 0.7322 (t80) cc_final: 0.7105 (t80) REVERT: D 152 MET cc_start: 0.0545 (tpp) cc_final: -0.0768 (ttp) REVERT: D 220 ASN cc_start: 0.3865 (p0) cc_final: 0.3545 (t0) REVERT: D 436 ILE cc_start: 0.4961 (OUTLIER) cc_final: 0.4754 (mm) REVERT: D 455 MET cc_start: 0.5068 (OUTLIER) cc_final: 0.4406 (tpp) REVERT: D 479 GLU cc_start: 0.4320 (OUTLIER) cc_final: 0.3986 (pp20) REVERT: D 480 MET cc_start: 0.0710 (tmm) cc_final: -0.0680 (tpp) REVERT: D 481 LYS cc_start: 0.6064 (tmmt) cc_final: 0.5749 (pptt) REVERT: D 531 GLN cc_start: 0.3648 (tm-30) cc_final: 0.3117 (tm-30) REVERT: D 542 CYS cc_start: -0.0093 (OUTLIER) cc_final: -0.0444 (m) REVERT: D 594 TRP cc_start: 0.3962 (t60) cc_final: 0.2797 (m-10) outliers start: 113 outliers final: 84 residues processed: 261 average time/residue: 0.1282 time to fit residues: 54.6318 Evaluate side-chains 246 residues out of total 2669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 151 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 59 PHE Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 106 PHE Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 201 PHE Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 239 GLN 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 761 THR Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 805 ILE 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 869 MET 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 1145 LEU Chi-restraints excluded: chain B residue 47 VAL 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 237 ARG Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 777 ASN Chi-restraints excluded: chain B residue 825 LYS Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 948 LEU 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 1137 VAL Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 106 PHE 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 390 LEU Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 452 LEU 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 916 LEU Chi-restraints excluded: chain C residue 1001 LEU 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 119 ILE Chi-restraints excluded: chain D residue 158 TYR 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 259 THR Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain D residue 416 ASN Chi-restraints excluded: chain D residue 436 ILE 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 530 CYS Chi-restraints excluded: chain D residue 542 CYS Chi-restraints excluded: chain D residue 595 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 32 optimal weight: 0.3980 chunk 121 optimal weight: 2.9990 chunk 107 optimal weight: 4.9990 chunk 260 optimal weight: 0.4980 chunk 182 optimal weight: 10.0000 chunk 81 optimal weight: 20.0000 chunk 251 optimal weight: 8.9990 chunk 270 optimal weight: 7.9990 chunk 262 optimal weight: 0.0670 chunk 245 optimal weight: 0.9990 chunk 217 optimal weight: 2.9990 overall best weight: 0.9922 ------------------------------------------------------------------------------- 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 134 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 416 ASN ** D 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 546 ASN ** 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 = 0.4255 r_free = 0.4255 target = 0.118050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.088947 restraints weight = 115241.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.089736 restraints weight = 74410.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.090263 restraints weight = 52017.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.090676 restraints weight = 33925.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.091187 restraints weight = 30271.317| |-----------------------------------------------------------------------------| r_work (final): 0.3719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.5712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.114 24550 Z= 0.243 Angle : 0.952 14.787 33420 Z= 0.504 Chirality : 0.052 0.616 3765 Planarity : 0.006 0.088 4320 Dihedral : 7.454 73.255 3243 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 19.23 Ramachandran Plot: Outliers : 0.20 % Allowed : 12.38 % Favored : 87.42 % Rotamer: Outliers : 4.31 % Allowed : 26.49 % Favored : 69.20 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.86 % Twisted General : 0.67 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.42 (0.15), residues: 2988 helix: 0.05 (0.17), residues: 934 sheet: -1.23 (0.29), residues: 325 loop : -2.79 (0.13), residues: 1729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 190 TYR 0.025 0.002 TYR A 38 PHE 0.019 0.001 PHE A 32 TRP 0.024 0.002 TRP C 436 HIS 0.008 0.001 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00436 (24521) covalent geometry : angle 0.94712 (33362) SS BOND : bond 0.00611 ( 29) SS BOND : angle 2.40872 ( 58) hydrogen bonds : bond 0.08518 ( 882) hydrogen bonds : angle 6.89807 ( 2550) *********************** 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 280 residues out of total 2669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 165 time to evaluate : 0.785 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 194 PHE cc_start: 0.7929 (t80) cc_final: 0.7712 (t80) REVERT: A 201 PHE cc_start: 0.7430 (OUTLIER) cc_final: 0.6299 (m-80) REVERT: A 781 VAL cc_start: 0.7413 (OUTLIER) cc_final: 0.7167 (p) REVERT: A 900 MET cc_start: 0.8886 (OUTLIER) cc_final: 0.8200 (mtm) REVERT: B 40 ASP cc_start: 0.7163 (p0) cc_final: 0.6757 (t0) REVERT: B 187 LYS cc_start: 0.2041 (OUTLIER) cc_final: 0.1345 (tttm) REVERT: B 918 GLU cc_start: 0.7873 (mt-10) cc_final: 0.7587 (mt-10) REVERT: C 28 TYR cc_start: 0.6026 (m-80) cc_final: 0.5135 (m-80) REVERT: C 275 PHE cc_start: 0.7721 (OUTLIER) cc_final: 0.6366 (t80) REVERT: C 505 TYR cc_start: 0.7061 (m-80) cc_final: 0.5985 (m-80) REVERT: D 22 GLU cc_start: 0.1860 (OUTLIER) cc_final: 0.1417 (mp0) REVERT: D 152 MET cc_start: 0.0813 (tpp) cc_final: -0.0584 (ttp) REVERT: D 220 ASN cc_start: 0.3939 (p0) cc_final: 0.3657 (t0) REVERT: D 454 TYR cc_start: 0.1433 (OUTLIER) cc_final: 0.1200 (t80) REVERT: D 455 MET cc_start: 0.4932 (OUTLIER) cc_final: 0.4302 (tpp) REVERT: D 480 MET cc_start: 0.0903 (tmm) cc_final: -0.0463 (tpp) REVERT: D 481 LYS cc_start: 0.6041 (tmmt) cc_final: 0.5696 (pptt) REVERT: D 593 THR cc_start: 0.4639 (p) cc_final: 0.4402 (m) REVERT: D 594 TRP cc_start: 0.4355 (t60) cc_final: 0.3236 (m-10) outliers start: 115 outliers final: 90 residues processed: 262 average time/residue: 0.1477 time to fit residues: 62.7139 Evaluate side-chains 256 residues out of total 2669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 158 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 59 PHE Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 131 CYS 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 239 GLN 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 781 VAL Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 805 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 869 MET 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 997 ILE Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 47 VAL 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 237 ARG Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 666 ILE Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 777 ASN Chi-restraints excluded: chain B residue 825 LYS Chi-restraints excluded: chain B residue 858 LEU 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 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 47 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 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 418 ILE Chi-restraints excluded: chain C residue 452 LEU 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 617 CYS 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 916 LEU Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1084 ASP Chi-restraints excluded: chain D residue 22 GLU Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain D residue 119 ILE Chi-restraints excluded: chain D residue 158 TYR 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 259 THR Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain D residue 416 ASN 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 530 CYS Chi-restraints excluded: chain D residue 546 ASN Chi-restraints excluded: chain D residue 595 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 203 optimal weight: 4.9990 chunk 73 optimal weight: 0.0970 chunk 22 optimal weight: 6.9990 chunk 205 optimal weight: 0.9980 chunk 42 optimal weight: 5.9990 chunk 107 optimal weight: 4.9990 chunk 183 optimal weight: 0.0050 chunk 299 optimal weight: 4.9990 chunk 88 optimal weight: 9.9990 chunk 74 optimal weight: 10.0000 chunk 280 optimal weight: 7.9990 overall best weight: 2.2196 ------------------------------------------------------------------------------- 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** C 439 ASN ** D 58 ASN ** 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 546 ASN ** 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 = 0.4230 r_free = 0.4230 target = 0.116632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.087303 restraints weight = 115328.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.089031 restraints weight = 74189.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.089195 restraints weight = 42344.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.089312 restraints weight = 36302.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.089247 restraints weight = 30315.022| |-----------------------------------------------------------------------------| r_work (final): 0.3675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.5894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.130 24550 Z= 0.277 Angle : 0.977 14.557 33420 Z= 0.519 Chirality : 0.053 0.566 3765 Planarity : 0.006 0.090 4320 Dihedral : 7.529 72.901 3243 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 20.58 Ramachandran Plot: Outliers : 0.17 % Allowed : 12.92 % Favored : 86.91 % Rotamer: Outliers : 4.20 % Allowed : 26.86 % Favored : 68.94 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.48 % Twisted General : 0.74 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.50 (0.15), residues: 2988 helix: -0.05 (0.17), residues: 942 sheet: -1.28 (0.28), residues: 325 loop : -2.84 (0.13), residues: 1721 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 190 TYR 0.041 0.002 TYR A 38 PHE 0.016 0.002 PHE A 133 TRP 0.020 0.002 TRP C 436 HIS 0.008 0.001 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00542 (24521) covalent geometry : angle 0.97155 (33362) SS BOND : bond 0.00652 ( 29) SS BOND : angle 2.68737 ( 58) hydrogen bonds : bond 0.08921 ( 882) hydrogen bonds : angle 6.95031 ( 2550) ********************** 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 267 residues out of total 2669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 155 time to evaluate : 1.065 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: A 194 PHE cc_start: 0.8054 (t80) cc_final: 0.7783 (t80) REVERT: A 201 PHE cc_start: 0.7355 (OUTLIER) cc_final: 0.6151 (m-80) REVERT: A 900 MET cc_start: 0.8901 (OUTLIER) cc_final: 0.8252 (mtm) REVERT: A 1146 ASP cc_start: 0.6638 (t0) cc_final: 0.5881 (p0) REVERT: B 40 ASP cc_start: 0.7167 (p0) cc_final: 0.6790 (t0) REVERT: B 187 LYS cc_start: 0.2020 (OUTLIER) cc_final: 0.1322 (tttm) REVERT: C 28 TYR cc_start: 0.6070 (m-80) cc_final: 0.5202 (m-80) REVERT: C 275 PHE cc_start: 0.7761 (OUTLIER) cc_final: 0.6425 (t80) REVERT: C 276 LEU cc_start: 0.8585 (OUTLIER) cc_final: 0.8071 (tp) REVERT: C 505 TYR cc_start: 0.7068 (m-80) cc_final: 0.6136 (m-80) REVERT: C 515 PHE cc_start: 0.5491 (OUTLIER) cc_final: 0.5070 (p90) REVERT: D 22 GLU cc_start: 0.1710 (OUTLIER) cc_final: 0.1294 (mp0) REVERT: D 152 MET cc_start: 0.0807 (tpp) cc_final: -0.0587 (ttp) REVERT: D 220 ASN cc_start: 0.3759 (p0) cc_final: 0.3450 (t0) REVERT: D 455 MET cc_start: 0.4948 (OUTLIER) cc_final: 0.4273 (tpp) REVERT: D 480 MET cc_start: 0.0443 (tmm) cc_final: -0.0626 (tpp) REVERT: D 481 LYS cc_start: 0.5946 (tmmt) cc_final: 0.5655 (pptt) REVERT: D 593 THR cc_start: 0.4648 (p) cc_final: 0.4402 (m) REVERT: D 594 TRP cc_start: 0.4298 (t60) cc_final: 0.3146 (m-10) outliers start: 112 outliers final: 97 residues processed: 247 average time/residue: 0.1510 time to fit residues: 60.2552 Evaluate side-chains 257 residues out of total 2669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 152 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 59 PHE Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 130 VAL 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 239 GLN 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 781 VAL Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 805 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 866 THR Chi-restraints excluded: chain A residue 869 MET 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 997 ILE Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 47 VAL 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 187 LYS Chi-restraints excluded: chain B residue 237 ARG Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 666 ILE Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 777 ASN Chi-restraints excluded: chain B residue 825 LYS Chi-restraints excluded: chain B residue 858 LEU 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 959 LEU Chi-restraints excluded: chain B residue 961 THR 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 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 106 PHE Chi-restraints excluded: chain C residue 192 PHE Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 238 PHE 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 390 LEU Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 439 ASN Chi-restraints excluded: chain C residue 452 LEU 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 617 CYS 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 916 LEU Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1084 ASP Chi-restraints excluded: chain D residue 22 GLU Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain D residue 119 ILE Chi-restraints excluded: chain D residue 158 TYR 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 259 THR Chi-restraints excluded: chain D residue 324 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 530 CYS Chi-restraints excluded: chain D residue 546 ASN Chi-restraints excluded: chain D residue 595 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 279 optimal weight: 3.9990 chunk 119 optimal weight: 7.9990 chunk 218 optimal weight: 0.9990 chunk 89 optimal weight: 7.9990 chunk 176 optimal weight: 0.4980 chunk 299 optimal weight: 2.9990 chunk 3 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 chunk 282 optimal weight: 6.9990 chunk 70 optimal weight: 3.9990 chunk 108 optimal weight: 2.9990 overall best weight: 1.8988 ------------------------------------------------------------------------------- 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** C 439 ASN ** D 58 ASN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.116303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.087378 restraints weight = 114222.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.088323 restraints weight = 75987.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.088174 restraints weight = 54520.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.088973 restraints weight = 40398.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.088824 restraints weight = 32009.039| |-----------------------------------------------------------------------------| r_work (final): 0.3669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.6181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.112 24550 Z= 0.263 Angle : 0.968 16.202 33420 Z= 0.514 Chirality : 0.052 0.519 3765 Planarity : 0.006 0.090 4320 Dihedral : 7.500 73.017 3243 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 19.90 Ramachandran Plot: Outliers : 0.17 % Allowed : 13.02 % Favored : 86.81 % Rotamer: Outliers : 4.42 % Allowed : 26.64 % Favored : 68.94 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.48 % Twisted General : 0.70 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.50 (0.15), residues: 2988 helix: -0.01 (0.17), residues: 932 sheet: -1.24 (0.28), residues: 330 loop : -2.86 (0.13), residues: 1726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 115 TYR 0.032 0.002 TYR A 38 PHE 0.015 0.002 PHE A 32 TRP 0.023 0.002 TRP C 436 HIS 0.008 0.001 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00502 (24521) covalent geometry : angle 0.96313 (33362) SS BOND : bond 0.00663 ( 29) SS BOND : angle 2.55036 ( 58) hydrogen bonds : bond 0.08981 ( 882) hydrogen bonds : angle 6.93057 ( 2550) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4827.58 seconds wall clock time: 84 minutes 27.59 seconds (5067.59 seconds total)