Starting phenix.real_space_refine on Sat Sep 12 07:36:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/3jb7_6404/09_2026/3jb7_6404.cif Found real_map, /net/cci-nas-00/data/ceres_data/3jb7_6404/09_2026/3jb7_6404.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/3jb7_6404/09_2026/3jb7_6404.map" default_real_map = "/net/cci-nas-00/data/ceres_data/3jb7_6404/09_2026/3jb7_6404.map" restraint_files = "/net/cci-nas-00/data/ceres_data/3jb7_6404/09_2026/3jb7_6404.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/3jb7_6404/09_2026/3jb7_6404.cif" model { file = "/net/cci-nas-00/data/ceres_data/3jb7_6404/09_2026/3jb7_6404.cif" } default_model = "/net/cci-nas-00/data/ceres_data/3jb7_6404/09_2026/3jb7_6404.cif" } resolution = 4.0 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 ------------------------------------------------------------------------------- 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= 0.004 sd= 0.095 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 20 5.49 5 S 54 5.16 5 C 8939 2.51 5 N 2430 2.21 5 O 2733 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14176 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 9561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1198, 9561 Classifications: {'peptide': 1198} Link IDs: {'CIS': 15, 'PCIS': 2, 'PTRANS': 35, 'TRANS': 1145} Chain breaks: 1 Chain: "B" Number of atoms: 3985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 498, 3985 Classifications: {'peptide': 498} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 17, 'TRANS': 478} Chain breaks: 2 Chain: "C" Number of atoms: 170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 170 Classifications: {'peptide': 21} Link IDs: {'PTRANS': 1, 'TRANS': 19} Chain: "t" Number of atoms: 138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 138 Classifications: {'RNAv2': 6} Modifications used: {'rna3p_pur': 6} Link IDs: {'rna3p': 5} Chain: "m" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 100 Classifications: {'RNAv2': 5} Modifications used: {'rna3p_pyr': 5} Link IDs: {'rna3p': 4} Chain: "D" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 129 Classifications: {'peptide': 16} Link IDs: {'TRANS': 15} Chain: "A" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 61 Unusual residues: {'CTP': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.15, per 1000 atoms: 0.22 Number of scatterers: 14176 At special positions: 0 Unit cell: (103.36, 133.28, 108.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 54 16.00 P 20 15.00 O 2733 8.00 N 2430 7.00 C 8939 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.09 Conformation dependent library (CDL) restraints added in 627.8 milliseconds 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3284 Finding SS restraints... Secondary structure from input PDB file: 91 helices and 16 sheets defined 53.9% alpha, 7.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'A' and resid 6 through 9 Processing helix chain 'A' and resid 10 through 16 removed outlier: 3.553A pdb=" N GLU A 14 " --> pdb=" O THR A 10 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 36 removed outlier: 3.599A pdb=" N HIS A 28 " --> pdb=" O LYS A 24 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ASP A 36 " --> pdb=" O ARG A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 45 removed outlier: 3.574A pdb=" N ARG A 40 " --> pdb=" O ASP A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 77 removed outlier: 4.192A pdb=" N ILE A 76 " --> pdb=" O PRO A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 86 removed outlier: 3.605A pdb=" N TYR A 86 " --> pdb=" O PRO A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 112 removed outlier: 3.552A pdb=" N LEU A 112 " --> pdb=" O ALA A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 134 removed outlier: 3.571A pdb=" N HIS A 134 " --> pdb=" O ASP A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 161 Processing helix chain 'A' and resid 165 through 175 removed outlier: 4.349A pdb=" N THR A 169 " --> pdb=" O TYR A 165 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N TYR A 170 " --> pdb=" O PRO A 166 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL A 171 " --> pdb=" O LEU A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 220 removed outlier: 3.860A pdb=" N PHE A 206 " --> pdb=" O ILE A 202 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL A 207 " --> pdb=" O LEU A 203 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N TYR A 208 " --> pdb=" O PRO A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 238 removed outlier: 3.716A pdb=" N ILE A 228 " --> pdb=" O HIS A 224 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL A 229 " --> pdb=" O VAL A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 255 removed outlier: 3.876A pdb=" N LYS A 246 " --> pdb=" O TYR A 242 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N GLY A 251 " --> pdb=" O LEU A 247 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N ILE A 252 " --> pdb=" O LYS A 248 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG A 254 " --> pdb=" O LYS A 250 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N SER A 255 " --> pdb=" O GLY A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 265 removed outlier: 3.584A pdb=" N ALA A 260 " --> pdb=" O TRP A 256 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL A 264 " --> pdb=" O ALA A 260 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N CYS A 265 " --> pdb=" O LEU A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 304 removed outlier: 3.739A pdb=" N THR A 295 " --> pdb=" O PHE A 291 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N PHE A 296 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ILE A 297 " --> pdb=" O SER A 293 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N SER A 298 " --> pdb=" O SER A 294 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU A 299 " --> pdb=" O THR A 295 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA A 301 " --> pdb=" O ILE A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 322 removed outlier: 3.669A pdb=" N SER A 322 " --> pdb=" O ALA A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 339 removed outlier: 3.607A pdb=" N ALA A 337 " --> pdb=" O ALA A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 358 removed outlier: 4.026A pdb=" N ASP A 354 " --> pdb=" O GLU A 350 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N ALA A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA A 356 " --> pdb=" O SER A 352 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL A 357 " --> pdb=" O LEU A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 398 removed outlier: 3.890A pdb=" N TYR A 396 " --> pdb=" O ILE A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 409 removed outlier: 3.619A pdb=" N ALA A 405 " --> pdb=" O THR A 401 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LYS A 406 " --> pdb=" O ASP A 402 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ARG A 407 " --> pdb=" O GLU A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 423 removed outlier: 3.619A pdb=" N THR A 422 " --> pdb=" O LEU A 418 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR A 423 " --> pdb=" O ASN A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 446 removed outlier: 4.035A pdb=" N ALA A 443 " --> pdb=" O GLY A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 456 Processing helix chain 'A' and resid 463 through 470 removed outlier: 4.146A pdb=" N PHE A 467 " --> pdb=" O PRO A 463 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER A 469 " --> pdb=" O ARG A 465 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU A 470 " --> pdb=" O ILE A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 510 removed outlier: 4.476A pdb=" N SER A 500 " --> pdb=" O ARG A 496 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N MET A 502 " --> pdb=" O PHE A 498 " (cutoff:3.500A) Proline residue: A 503 - end of helix removed outlier: 3.647A pdb=" N GLN A 509 " --> pdb=" O THR A 505 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ILE A 510 " --> pdb=" O ILE A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 514 removed outlier: 3.581A pdb=" N ASN A 514 " --> pdb=" O TYR A 511 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 511 through 514' Processing helix chain 'A' and resid 525 through 528 Processing helix chain 'A' and resid 529 through 538 removed outlier: 3.649A pdb=" N TYR A 534 " --> pdb=" O GLY A 530 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER A 537 " --> pdb=" O LEU A 533 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLN A 538 " --> pdb=" O TYR A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 574 removed outlier: 4.063A pdb=" N ASP A 561 " --> pdb=" O THR A 557 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ILE A 562 " --> pdb=" O ASN A 558 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N TYR A 563 " --> pdb=" O THR A 559 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N PHE A 566 " --> pdb=" O ILE A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 615 removed outlier: 3.545A pdb=" N GLN A 607 " --> pdb=" O ASN A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 645 through 666 removed outlier: 3.556A pdb=" N VAL A 650 " --> pdb=" O THR A 646 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASN A 659 " --> pdb=" O LEU A 655 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU A 661 " --> pdb=" O ARG A 657 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASP A 666 " --> pdb=" O LYS A 662 " (cutoff:3.500A) Processing helix chain 'A' and resid 689 through 707 removed outlier: 3.646A pdb=" N TYR A 694 " --> pdb=" O GLU A 690 " (cutoff:3.500A) Processing helix chain 'A' and resid 752 through 765 removed outlier: 3.702A pdb=" N ALA A 756 " --> pdb=" O ARG A 752 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU A 759 " --> pdb=" O LEU A 755 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA A 762 " --> pdb=" O MET A 758 " (cutoff:3.500A) Processing helix chain 'A' and resid 773 through 788 removed outlier: 3.930A pdb=" N LEU A 777 " --> pdb=" O ARG A 773 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LYS A 778 " --> pdb=" O PRO A 774 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N MET A 779 " --> pdb=" O GLU A 775 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N PHE A 783 " --> pdb=" O MET A 779 " (cutoff:3.500A) Processing helix chain 'A' and resid 800 through 809 removed outlier: 3.821A pdb=" N THR A 804 " --> pdb=" O LEU A 800 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N TYR A 805 " --> pdb=" O TYR A 801 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N ASN A 806 " --> pdb=" O ASP A 802 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N ASN A 807 " --> pdb=" O SER A 803 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU A 808 " --> pdb=" O THR A 804 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N SER A 809 " --> pdb=" O TYR A 805 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 800 through 809' Processing helix chain 'A' and resid 833 through 838 Processing helix chain 'A' and resid 867 through 871 removed outlier: 4.109A pdb=" N TYR A 870 " --> pdb=" O ARG A 867 " (cutoff:3.500A) Processing helix chain 'A' and resid 872 through 879 removed outlier: 4.042A pdb=" N TYR A 876 " --> pdb=" O ARG A 872 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N SER A 879 " --> pdb=" O LEU A 875 " (cutoff:3.500A) Processing helix chain 'A' and resid 880 through 887 removed outlier: 4.001A pdb=" N GLN A 886 " --> pdb=" O GLY A 882 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN A 887 " --> pdb=" O GLU A 883 " (cutoff:3.500A) Processing helix chain 'A' and resid 893 through 901 removed outlier: 3.922A pdb=" N LEU A 897 " --> pdb=" O ASP A 893 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLU A 899 " --> pdb=" O ASP A 895 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N TYR A 900 " --> pdb=" O LEU A 896 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 910 removed outlier: 3.832A pdb=" N LEU A 907 " --> pdb=" O THR A 903 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU A 908 " --> pdb=" O GLY A 904 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE A 909 " --> pdb=" O ALA A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 925 removed outlier: 3.906A pdb=" N ASP A 918 " --> pdb=" O LEU A 914 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LYS A 921 " --> pdb=" O ILE A 917 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU A 923 " --> pdb=" O GLU A 919 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ASP A 924 " --> pdb=" O VAL A 920 " (cutoff:3.500A) Processing helix chain 'A' and resid 928 through 940 removed outlier: 4.430A pdb=" N THR A 935 " --> pdb=" O SER A 931 " (cutoff:3.500A) Processing helix chain 'A' and resid 948 through 954 removed outlier: 3.726A pdb=" N ALA A 952 " --> pdb=" O LYS A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 955 through 957 No H-bonds generated for 'chain 'A' and resid 955 through 957' Processing helix chain 'A' and resid 969 through 971 No H-bonds generated for 'chain 'A' and resid 969 through 971' Processing helix chain 'A' and resid 972 through 978 removed outlier: 4.210A pdb=" N LYS A 976 " --> pdb=" O GLY A 972 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLN A 978 " --> pdb=" O GLN A 974 " (cutoff:3.500A) Processing helix chain 'A' and resid 984 through 986 No H-bonds generated for 'chain 'A' and resid 984 through 986' Processing helix chain 'A' and resid 987 through 992 Processing helix chain 'A' and resid 993 through 997 removed outlier: 3.557A pdb=" N ARG A 997 " --> pdb=" O VAL A 994 " (cutoff:3.500A) Processing helix chain 'A' and resid 999 through 1004 removed outlier: 3.798A pdb=" N VAL A1003 " --> pdb=" O HIS A 999 " (cutoff:3.500A) Processing helix chain 'A' and resid 1013 through 1021 removed outlier: 3.621A pdb=" N ALA A1017 " --> pdb=" O PRO A1014 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU A1018 " --> pdb=" O ALA A1015 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N HIS A1019 " --> pdb=" O ASP A1016 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N HIS A1021 " --> pdb=" O LEU A1018 " (cutoff:3.500A) Processing helix chain 'A' and resid 1034 through 1040 removed outlier: 3.839A pdb=" N HIS A1038 " --> pdb=" O PRO A1034 " (cutoff:3.500A) Processing helix chain 'A' and resid 1045 through 1049 removed outlier: 4.006A pdb=" N SER A1049 " --> pdb=" O TYR A1046 " (cutoff:3.500A) Processing helix chain 'A' and resid 1052 through 1062 removed outlier: 3.774A pdb=" N PHE A1058 " --> pdb=" O GLY A1054 " (cutoff:3.500A) Processing helix chain 'A' and resid 1065 through 1080 removed outlier: 3.797A pdb=" N ASN A1069 " --> pdb=" O ASP A1065 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ASP A1074 " --> pdb=" O LEU A1070 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N VAL A1075 " --> pdb=" O LEU A1071 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ALA A1076 " --> pdb=" O ARG A1072 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE A1078 " --> pdb=" O ASP A1074 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ARG A1079 " --> pdb=" O VAL A1075 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLY A1080 " --> pdb=" O ALA A1076 " (cutoff:3.500A) Processing helix chain 'A' and resid 1091 through 1095 Processing helix chain 'A' and resid 1095 through 1101 removed outlier: 3.797A pdb=" N TYR A1099 " --> pdb=" O GLY A1095 " (cutoff:3.500A) Processing helix chain 'A' and resid 1102 through 1104 No H-bonds generated for 'chain 'A' and resid 1102 through 1104' Processing helix chain 'A' and resid 1105 through 1114 removed outlier: 3.621A pdb=" N THR A1111 " --> pdb=" O ASN A1107 " (cutoff:3.500A) Processing helix chain 'A' and resid 1116 through 1126 removed outlier: 3.643A pdb=" N LEU A1123 " --> pdb=" O GLU A1119 " (cutoff:3.500A) Processing helix chain 'A' and resid 1153 through 1159 removed outlier: 3.917A pdb=" N ARG A1159 " --> pdb=" O SER A1156 " (cutoff:3.500A) Processing helix chain 'A' and resid 1164 through 1168 removed outlier: 3.590A pdb=" N TYR A1167 " --> pdb=" O PRO A1164 " (cutoff:3.500A) Processing helix chain 'A' and resid 1173 through 1175 No H-bonds generated for 'chain 'A' and resid 1173 through 1175' Processing helix chain 'A' and resid 1176 through 1188 removed outlier: 3.755A pdb=" N HIS A1184 " --> pdb=" O PHE A1180 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU A1186 " --> pdb=" O TYR A1182 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N SER A1188 " --> pdb=" O HIS A1184 " (cutoff:3.500A) Processing helix chain 'A' and resid 1202 through 1211 removed outlier: 3.619A pdb=" N ILE A1206 " --> pdb=" O HIS A1202 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ALA A1207 " --> pdb=" O PRO A1203 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLY A1211 " --> pdb=" O ALA A1207 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 17 removed outlier: 3.650A pdb=" N TYR B 16 " --> pdb=" O LEU B 12 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 61 removed outlier: 3.634A pdb=" N LYS B 47 " --> pdb=" O ILE B 43 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N TYR B 48 " --> pdb=" O ARG B 44 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ALA B 61 " --> pdb=" O ALA B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 64 No H-bonds generated for 'chain 'B' and resid 62 through 64' Processing helix chain 'B' and resid 69 through 78 Processing helix chain 'B' and resid 132 through 147 removed outlier: 5.366A pdb=" N ALA B 137 " --> pdb=" O VAL B 133 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N LEU B 138 " --> pdb=" O THR B 134 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU B 144 " --> pdb=" O GLU B 140 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N SER B 147 " --> pdb=" O THR B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 167 removed outlier: 3.700A pdb=" N LEU B 167 " --> pdb=" O LYS B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 177 removed outlier: 3.602A pdb=" N ASN B 173 " --> pdb=" O PRO B 169 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLN B 174 " --> pdb=" O ASN B 170 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU B 175 " --> pdb=" O TYR B 171 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ALA B 177 " --> pdb=" O ASN B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 202 removed outlier: 3.605A pdb=" N SER B 200 " --> pdb=" O THR B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 243 Processing helix chain 'B' and resid 244 through 248 removed outlier: 4.010A pdb=" N GLU B 247 " --> pdb=" O GLY B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 296 removed outlier: 3.737A pdb=" N PHE B 295 " --> pdb=" O LYS B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 341 removed outlier: 3.616A pdb=" N ALA B 330 " --> pdb=" O GLY B 326 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA B 338 " --> pdb=" O LYS B 334 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER B 341 " --> pdb=" O GLU B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 375 removed outlier: 4.230A pdb=" N THR B 365 " --> pdb=" O SER B 361 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLU B 368 " --> pdb=" O SER B 364 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA B 373 " --> pdb=" O GLN B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 394 removed outlier: 3.601A pdb=" N ALA B 391 " --> pdb=" O GLY B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 409 removed outlier: 3.523A pdb=" N LEU B 409 " --> pdb=" O TYR B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 429 removed outlier: 3.776A pdb=" N HIS B 429 " --> pdb=" O LEU B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 440 removed outlier: 3.658A pdb=" N LEU B 440 " --> pdb=" O GLN B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 461 removed outlier: 3.527A pdb=" N MET B 448 " --> pdb=" O LYS B 444 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLU B 451 " --> pdb=" O LYS B 447 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N GLN B 459 " --> pdb=" O VAL B 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 467 through 477 Processing helix chain 'B' and resid 491 through 496 removed outlier: 3.873A pdb=" N ALA B 496 " --> pdb=" O ALA B 493 " (cutoff:3.500A) Processing helix chain 'B' and resid 512 through 520 removed outlier: 3.614A pdb=" N ARG B 518 " --> pdb=" O THR B 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 536 removed outlier: 3.534A pdb=" N ASP B 532 " --> pdb=" O LEU B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 557 removed outlier: 3.705A pdb=" N MET B 550 " --> pdb=" O TYR B 546 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG B 555 " --> pdb=" O LEU B 551 " (cutoff:3.500A) Processing helix chain 'C' and resid 120 through 131 Processing helix chain 'D' and resid 112 through 126 removed outlier: 3.546A pdb=" N GLN D 124 " --> pdb=" O VAL D 120 " (cutoff:3.500A) Processing sheet with id=A, first strand: chain 'A' and resid 54 through 58 Processing sheet with id=B, first strand: chain 'A' and resid 183 through 186 removed outlier: 3.657A pdb=" N ARG A 191 " --> pdb=" O SER A 186 " (cutoff:3.500A) Processing sheet with id=C, first strand: chain 'A' and resid 266 through 272 removed outlier: 3.700A pdb=" N GLY A 280 " --> pdb=" O VAL A 271 " (cutoff:3.500A) Processing sheet with id=D, first strand: chain 'A' and resid 380 through 384 removed outlier: 6.978A pdb=" N SER A 380 " --> pdb=" O SER A 374 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N SER A 374 " --> pdb=" O SER A 380 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N LYS A 382 " --> pdb=" O LEU A 372 " (cutoff:3.500A) Processing sheet with id=E, first strand: chain 'A' and resid 476 through 479 removed outlier: 3.829A pdb=" N ARG A 487 " --> pdb=" O ARG A 479 " (cutoff:3.500A) Processing sheet with id=F, first strand: chain 'A' and resid 541 through 544 Processing sheet with id=G, first strand: chain 'A' and resid 547 through 548 removed outlier: 4.424A pdb=" N ASP A 547 " --> pdb=" O THR A 712 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N THR A 712 " --> pdb=" O ASP A 547 " (cutoff:3.500A) No H-bonds generated for sheet with id=G Processing sheet with id=H, first strand: chain 'A' and resid 621 through 624 removed outlier: 3.665A pdb=" N GLY A 628 " --> pdb=" O SER A 624 " (cutoff:3.500A) Processing sheet with id=I, first strand: chain 'A' and resid 719 through 720 Processing sheet with id=J, first strand: chain 'A' and resid 795 through 797 removed outlier: 3.630A pdb=" N VAL A 796 " --> pdb=" O THR A 826 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N SER A 829 " --> pdb=" O THR A 815 " (cutoff:3.500A) Processing sheet with id=K, first strand: chain 'A' and resid 1022 through 1025 removed outlier: 3.578A pdb=" N GLU A1022 " --> pdb=" O VAL A1200 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N MET A1199 " --> pdb=" O ARG A1162 " (cutoff:3.500A) Processing sheet with id=L, first strand: chain 'B' and resid 157 through 159 removed outlier: 6.833A pdb=" N ILE B 158 " --> pdb=" O ILE B 184 " (cutoff:3.500A) No H-bonds generated for sheet with id=L Processing sheet with id=M, first strand: chain 'B' and resid 204 through 208 removed outlier: 5.827A pdb=" N ARG B 204 " --> pdb=" O SER B 227 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N PHE B 229 " --> pdb=" O ARG B 204 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N PHE B 206 " --> pdb=" O PHE B 229 " (cutoff:3.500A) No H-bonds generated for sheet with id=M Processing sheet with id=N, first strand: chain 'B' and resid 266 through 267 Processing sheet with id=O, first strand: chain 'B' and resid 266 through 267 removed outlier: 3.590A pdb=" N SER B 317 " --> pdb=" O LEU B 257 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LYS B 315 " --> pdb=" O THR B 259 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N THR B 261 " --> pdb=" O ILE B 313 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ILE B 313 " --> pdb=" O THR B 261 " (cutoff:3.500A) Processing sheet with id=P, first strand: chain 'B' and resid 485 through 489 removed outlier: 6.385A pdb=" N LEU B 349 " --> pdb=" O VAL B 487 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N GLY B 489 " --> pdb=" O LEU B 349 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N VAL B 351 " --> pdb=" O GLY B 489 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N VAL B 545 " --> pdb=" O THR B 504 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N LEU B 506 " --> pdb=" O VAL B 545 " (cutoff:3.500A) 492 hydrogen bonds defined for protein. 1389 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: 2.60 Time building geometry restraints manager: 1.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.09 - 1.23: 730 1.23 - 1.38: 4749 1.38 - 1.53: 8094 1.53 - 1.68: 832 1.68 - 1.83: 95 Bond restraints: 14500 Sorted by residual: bond pdb=" N PRO D 111 " pdb=" CA PRO D 111 " ideal model delta sigma weight residual 1.466 1.114 0.352 1.50e-02 4.44e+03 5.52e+02 bond pdb=" C PRO C 132 " pdb=" O PRO C 132 " ideal model delta sigma weight residual 1.233 1.087 0.146 1.13e-02 7.83e+03 1.67e+02 bond pdb=" CA VAL C 120 " pdb=" CB VAL C 120 " ideal model delta sigma weight residual 1.540 1.401 0.138 1.10e-02 8.26e+03 1.59e+02 bond pdb=" CA PRO C 132 " pdb=" C PRO C 132 " ideal model delta sigma weight residual 1.522 1.383 0.139 1.16e-02 7.43e+03 1.43e+02 bond pdb=" N PRO D 111 " pdb=" CD PRO D 111 " ideal model delta sigma weight residual 1.473 1.638 -0.165 1.40e-02 5.10e+03 1.39e+02 ... (remaining 14495 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.03: 19621 4.03 - 8.06: 76 8.06 - 12.09: 5 12.09 - 16.12: 2 16.12 - 20.15: 2 Bond angle restraints: 19706 Sorted by residual: angle pdb=" N LEU C 130 " pdb=" CA LEU C 130 " pdb=" C LEU C 130 " ideal model delta sigma weight residual 113.61 133.76 -20.15 1.50e+00 4.44e-01 1.80e+02 angle pdb=" N THR C 118 " pdb=" CA THR C 118 " pdb=" C THR C 118 " ideal model delta sigma weight residual 111.14 121.30 -10.16 1.08e+00 8.57e-01 8.84e+01 angle pdb=" CG1 VAL C 120 " pdb=" CB VAL C 120 " pdb=" CG2 VAL C 120 " ideal model delta sigma weight residual 110.80 95.30 15.50 2.20e+00 2.07e-01 4.97e+01 angle pdb=" N PRO D 111 " pdb=" CD PRO D 111 " pdb=" CG PRO D 111 " ideal model delta sigma weight residual 103.20 93.05 10.15 1.50e+00 4.44e-01 4.58e+01 angle pdb=" CA PRO C 132 " pdb=" N PRO C 132 " pdb=" CD PRO C 132 " ideal model delta sigma weight residual 112.00 102.63 9.37 1.40e+00 5.10e-01 4.48e+01 ... (remaining 19701 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.40: 8242 18.40 - 36.79: 338 36.79 - 55.19: 60 55.19 - 73.59: 12 73.59 - 91.98: 3 Dihedral angle restraints: 8655 sinusoidal: 3555 harmonic: 5100 Sorted by residual: dihedral pdb=" N LEU C 130 " pdb=" C LEU C 130 " pdb=" CA LEU C 130 " pdb=" CB LEU C 130 " ideal model delta harmonic sigma weight residual 122.80 145.09 -22.29 0 2.50e+00 1.60e-01 7.95e+01 dihedral pdb=" C LEU C 130 " pdb=" N LEU C 130 " pdb=" CA LEU C 130 " pdb=" CB LEU C 130 " ideal model delta harmonic sigma weight residual -122.60 -144.35 21.75 0 2.50e+00 1.60e-01 7.57e+01 dihedral pdb=" CA TYR A 971 " pdb=" C TYR A 971 " pdb=" N GLY A 972 " pdb=" CA GLY A 972 " ideal model delta harmonic sigma weight residual 180.00 153.85 26.15 0 5.00e+00 4.00e-02 2.73e+01 ... (remaining 8652 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.219: 2191 0.219 - 0.439: 15 0.439 - 0.658: 1 0.658 - 0.877: 1 0.877 - 1.096: 1 Chirality restraints: 2209 Sorted by residual: chirality pdb=" CA LEU C 130 " pdb=" N LEU C 130 " pdb=" C LEU C 130 " pdb=" CB LEU C 130 " both_signs ideal model delta sigma weight residual False 2.51 1.41 1.10 2.00e-01 2.50e+01 3.00e+01 chirality pdb=" CA PRO D 111 " pdb=" N PRO D 111 " pdb=" C PRO D 111 " pdb=" CB PRO D 111 " both_signs ideal model delta sigma weight residual False 2.72 1.94 0.78 2.00e-01 2.50e+01 1.53e+01 chirality pdb=" CA PRO C 132 " pdb=" N PRO C 132 " pdb=" C PRO C 132 " pdb=" CB PRO C 132 " both_signs ideal model delta sigma weight residual False 2.72 2.28 0.44 2.00e-01 2.50e+01 4.85e+00 ... (remaining 2206 not shown) Planarity restraints: 2461 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG C 117 " 0.018 2.00e-02 2.50e+03 3.68e-02 1.36e+01 pdb=" C ARG C 117 " -0.064 2.00e-02 2.50e+03 pdb=" O ARG C 117 " 0.024 2.00e-02 2.50e+03 pdb=" N THR C 118 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 125 " -0.015 2.00e-02 2.50e+03 1.33e-02 3.09e+00 pdb=" CG PHE C 125 " 0.025 2.00e-02 2.50e+03 pdb=" CD1 PHE C 125 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE C 125 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE C 125 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 PHE C 125 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE C 125 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER C 116 " 0.008 2.00e-02 2.50e+03 1.55e-02 2.40e+00 pdb=" C SER C 116 " -0.027 2.00e-02 2.50e+03 pdb=" O SER C 116 " 0.010 2.00e-02 2.50e+03 pdb=" N ARG C 117 " 0.009 2.00e-02 2.50e+03 ... (remaining 2458 not shown) Histogram of nonbonded interaction distances: 0.79 - 1.61: 2 1.61 - 2.44: 42 2.44 - 3.26: 15142 3.26 - 4.08: 34042 4.08 - 4.90: 62597 Warning: very small nonbonded interaction distances. Nonbonded interactions: 111825 Sorted by model distance: nonbonded pdb=" OD1 ASP A1053 " pdb=" NH1 ARG D 117 " model vdw 0.793 3.120 nonbonded pdb=" OD1 ASP A1053 " pdb=" CZ ARG D 117 " model vdw 1.553 3.270 nonbonded pdb=" NH1 ARG B 518 " pdb=" NE2 GLN C 115 " model vdw 1.917 3.200 nonbonded pdb=" OH TYR B 264 " pdb=" O SER C 116 " model vdw 1.936 3.040 nonbonded pdb=" CD ARG A1193 " pdb=" OG SER D 116 " model vdw 1.970 3.440 ... (remaining 111820 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 1.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 13.990 Find NCS groups from input model: 0.060 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:1.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 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 : 0.007 0.352 14502 Z= 0.476 Angle : 0.767 20.148 19706 Z= 0.447 Chirality : 0.056 1.096 2209 Planarity : 0.004 0.038 2461 Dihedral : 10.890 91.984 5371 Min Nonbonded Distance : 0.793 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.23 % Allowed : 3.90 % Favored : 95.87 % Rotamer: Outliers : 1.13 % Allowed : 3.05 % Favored : 95.82 % Cbeta Deviations : 0.18 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.96 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.17 (0.19), residues: 1719 helix: -3.31 (0.11), residues: 727 sheet: -1.82 (0.35), residues: 155 loop : 0.78 (0.22), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 377 TYR 0.017 0.001 TYR A1133 PHE 0.025 0.002 PHE C 125 TRP 0.015 0.002 TRP A 742 HIS 0.013 0.001 HIS C 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00709 / 0.46 (14500) covalent geometry : angle 0.76704 / 0.45 (19706) hydrogen bonds : bond 0.30469 / 20.46 ( 490) hydrogen bonds : angle 9.57494 / 6.66 ( 1389) Misc. bond : bond 0.09813 / 4.92 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 456 time to evaluate : 0.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 HIS cc_start: 0.8916 (t70) cc_final: 0.8634 (t-170) REVERT: A 49 ILE cc_start: 0.9030 (mt) cc_final: 0.8783 (mt) REVERT: A 74 GLU cc_start: 0.9089 (mt-10) cc_final: 0.8888 (mm-30) REVERT: A 91 ASP cc_start: 0.8768 (t0) cc_final: 0.8491 (m-30) REVERT: A 102 ASP cc_start: 0.9379 (m-30) cc_final: 0.8746 (t0) REVERT: A 106 THR cc_start: 0.9783 (m) cc_final: 0.9563 (p) REVERT: A 133 MET cc_start: 0.9243 (ptm) cc_final: 0.8981 (ptp) REVERT: A 137 GLN cc_start: 0.8964 (mt0) cc_final: 0.8594 (mt0) REVERT: A 150 CYS cc_start: 0.9696 (m) cc_final: 0.9440 (m) REVERT: A 172 LYS cc_start: 0.9497 (tttt) cc_final: 0.9224 (ttmm) REVERT: A 179 ASP cc_start: 0.9132 (t70) cc_final: 0.8304 (t0) REVERT: A 218 MET cc_start: 0.9682 (mmm) cc_final: 0.9237 (mmm) REVERT: A 310 GLU cc_start: 0.9330 (tt0) cc_final: 0.8998 (tp30) REVERT: A 349 THR cc_start: 0.9488 (OUTLIER) cc_final: 0.9173 (t) REVERT: A 372 LEU cc_start: 0.9562 (mt) cc_final: 0.9288 (mt) REVERT: A 373 MET cc_start: 0.9365 (ttm) cc_final: 0.9101 (ttm) REVERT: A 381 LEU cc_start: 0.9540 (mt) cc_final: 0.9123 (mt) REVERT: A 483 ASP cc_start: 0.9188 (p0) cc_final: 0.8956 (p0) REVERT: A 502 MET cc_start: 0.9789 (tpp) cc_final: 0.9513 (tpp) REVERT: A 542 LEU cc_start: 0.9583 (tp) cc_final: 0.9257 (tt) REVERT: A 547 ASP cc_start: 0.9228 (p0) cc_final: 0.8922 (m-30) REVERT: A 596 GLN cc_start: 0.8942 (mt0) cc_final: 0.8637 (pm20) REVERT: A 609 CYS cc_start: 0.9577 (m) cc_final: 0.9187 (m) REVERT: A 618 THR cc_start: 0.9005 (m) cc_final: 0.8606 (p) REVERT: A 623 GLU cc_start: 0.9146 (tm-30) cc_final: 0.8945 (mm-30) REVERT: A 634 GLU cc_start: 0.8875 (tt0) cc_final: 0.8619 (tp30) REVERT: A 653 GLN cc_start: 0.9570 (pt0) cc_final: 0.9302 (tt0) REVERT: A 683 MET cc_start: 0.9279 (ttp) cc_final: 0.8877 (tmm) REVERT: A 685 ILE cc_start: 0.9659 (OUTLIER) cc_final: 0.9384 (mp) REVERT: A 714 GLU cc_start: 0.9127 (mt-10) cc_final: 0.8896 (mp0) REVERT: A 731 THR cc_start: 0.9401 (m) cc_final: 0.9009 (p) REVERT: A 759 GLU cc_start: 0.9327 (tm-30) cc_final: 0.8593 (tm-30) REVERT: A 784 CYS cc_start: 0.9728 (t) cc_final: 0.9147 (t) REVERT: A 788 CYS cc_start: 0.9546 (m) cc_final: 0.9241 (m) REVERT: A 799 LYS cc_start: 0.9151 (mmtp) cc_final: 0.8771 (tptt) REVERT: A 834 LEU cc_start: 0.9795 (mt) cc_final: 0.9533 (mt) REVERT: A 844 GLU cc_start: 0.9513 (mt-10) cc_final: 0.8983 (mp0) REVERT: A 890 MET cc_start: 0.8724 (mtp) cc_final: 0.7981 (tmm) REVERT: A 899 GLU cc_start: 0.9490 (mm-30) cc_final: 0.9183 (mp0) REVERT: A 918 ASP cc_start: 0.8822 (m-30) cc_final: 0.8589 (m-30) REVERT: A 937 LEU cc_start: 0.9185 (tp) cc_final: 0.8842 (tt) REVERT: A 939 GLN cc_start: 0.9460 (tp40) cc_final: 0.9014 (tp40) REVERT: A 961 HIS cc_start: 0.7988 (m90) cc_final: 0.7755 (m-70) REVERT: A 997 ARG cc_start: 0.8380 (mmt-90) cc_final: 0.8155 (ttt180) REVERT: A 1000 ASP cc_start: 0.9196 (t0) cc_final: 0.8921 (m-30) REVERT: A 1007 ASP cc_start: 0.8741 (m-30) cc_final: 0.8510 (t0) REVERT: A 1009 LYS cc_start: 0.9098 (mmtp) cc_final: 0.8469 (mmtt) REVERT: A 1033 LEU cc_start: 0.9187 (pp) cc_final: 0.8946 (pp) REVERT: A 1035 HIS cc_start: 0.9422 (m170) cc_final: 0.9219 (m170) REVERT: A 1170 SER cc_start: 0.3283 (OUTLIER) cc_final: 0.1337 (p) REVERT: A 1187 ARG cc_start: 0.9036 (ttp-170) cc_final: 0.8666 (ttm170) REVERT: B 73 TYR cc_start: 0.9223 (m-80) cc_final: 0.9004 (m-80) REVERT: B 162 GLU cc_start: 0.9461 (tt0) cc_final: 0.9160 (tm-30) REVERT: B 178 TYR cc_start: 0.9112 (m-80) cc_final: 0.8680 (m-10) REVERT: B 183 ILE cc_start: 0.9386 (mt) cc_final: 0.9148 (tp) REVERT: B 199 ARG cc_start: 0.8945 (ttt180) cc_final: 0.8535 (ttt-90) REVERT: B 212 ASN cc_start: 0.9221 (t0) cc_final: 0.8922 (t0) REVERT: B 267 VAL cc_start: 0.9279 (t) cc_final: 0.8873 (p) REVERT: B 289 GLU cc_start: 0.9559 (mm-30) cc_final: 0.8690 (mm-30) REVERT: B 337 GLU cc_start: 0.9341 (mt-10) cc_final: 0.9118 (tp30) REVERT: B 354 GLU cc_start: 0.9140 (mt-10) cc_final: 0.8780 (tt0) REVERT: B 398 GLU cc_start: 0.9000 (mt-10) cc_final: 0.8794 (tm-30) REVERT: B 427 ILE cc_start: 0.9674 (mt) cc_final: 0.9470 (pt) REVERT: B 442 VAL cc_start: 0.9458 (t) cc_final: 0.9099 (p) REVERT: B 451 GLU cc_start: 0.9266 (mt-10) cc_final: 0.9015 (tp30) REVERT: B 474 MET cc_start: 0.9444 (mmm) cc_final: 0.9240 (mmm) REVERT: B 501 THR cc_start: 0.9112 (p) cc_final: 0.8824 (t) REVERT: B 554 ILE cc_start: 0.9728 (mt) cc_final: 0.9506 (mt) REVERT: C 120 VAL cc_start: 0.7905 (t) cc_final: 0.7662 (t) REVERT: C 128 GLU cc_start: 0.6071 (OUTLIER) cc_final: 0.5434 (mm-30) outliers start: 17 outliers final: 5 residues processed: 469 average time/residue: 0.1391 time to fit residues: 91.7903 Evaluate side-chains 268 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 259 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 685 ILE Chi-restraints excluded: chain A residue 1170 SER Chi-restraints excluded: chain A residue 1183 LEU Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain C residue 130 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.0170 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 0.7980 overall best weight: 0.7422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 276 ASN A 413 HIS A 519 GLN ** A 603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 617 GLN A 939 GLN B 231 ASN B 436 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.101501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.083160 restraints weight = 33520.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.085972 restraints weight = 18028.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.087952 restraints weight = 11803.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.089208 restraints weight = 8744.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.090166 restraints weight = 7099.238| |-----------------------------------------------------------------------------| r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.2827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 14502 Z= 0.152 Angle : 0.650 11.179 19706 Z= 0.335 Chirality : 0.042 0.168 2209 Planarity : 0.004 0.037 2461 Dihedral : 8.300 84.221 2100 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.56 % Favored : 97.38 % Rotamer: Outliers : 2.72 % Allowed : 12.14 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.96 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.19), residues: 1719 helix: -1.21 (0.16), residues: 757 sheet: -1.58 (0.39), residues: 141 loop : 0.33 (0.22), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 443 TYR 0.019 0.001 TYR A 805 PHE 0.021 0.001 PHE A 527 TRP 0.009 0.001 TRP A 742 HIS 0.005 0.001 HIS A 999 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.15 (14500) covalent geometry : angle 0.64999 / 0.33 (19706) hydrogen bonds : bond 0.05071 / 3.35 ( 490) hydrogen bonds : angle 5.63520 / 3.89 ( 1389) Misc. bond : bond 0.00425 / 0.20 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 308 time to evaluate : 0.534 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: A 28 HIS cc_start: 0.8228 (t70) cc_final: 0.7962 (t-170) REVERT: A 91 ASP cc_start: 0.8071 (t0) cc_final: 0.7865 (m-30) REVERT: A 218 MET cc_start: 0.9321 (mmm) cc_final: 0.8877 (tpp) REVERT: A 237 CYS cc_start: 0.9427 (OUTLIER) cc_final: 0.8942 (t) REVERT: A 350 GLU cc_start: 0.9044 (OUTLIER) cc_final: 0.8838 (mp0) REVERT: A 354 ASP cc_start: 0.8393 (t0) cc_final: 0.8101 (t0) REVERT: A 361 ILE cc_start: 0.9349 (OUTLIER) cc_final: 0.8676 (mp) REVERT: A 539 ARG cc_start: 0.4910 (ptt90) cc_final: 0.4424 (ptt-90) REVERT: A 542 LEU cc_start: 0.9358 (tp) cc_final: 0.9097 (tt) REVERT: A 609 CYS cc_start: 0.9138 (m) cc_final: 0.8875 (m) REVERT: A 684 GLU cc_start: 0.8876 (mt-10) cc_final: 0.8442 (pm20) REVERT: A 731 THR cc_start: 0.9195 (m) cc_final: 0.8867 (p) REVERT: A 759 GLU cc_start: 0.8624 (tm-30) cc_final: 0.7301 (tm-30) REVERT: A 779 MET cc_start: 0.9198 (OUTLIER) cc_final: 0.8818 (tpp) REVERT: A 784 CYS cc_start: 0.9374 (t) cc_final: 0.8622 (t) REVERT: A 788 CYS cc_start: 0.8996 (m) cc_final: 0.8702 (m) REVERT: A 799 LYS cc_start: 0.9108 (mmtp) cc_final: 0.8888 (tptt) REVERT: A 877 ASP cc_start: 0.8903 (t0) cc_final: 0.8231 (t0) REVERT: A 918 ASP cc_start: 0.8671 (m-30) cc_final: 0.8450 (m-30) REVERT: A 939 GLN cc_start: 0.9114 (tp-100) cc_final: 0.8757 (tp40) REVERT: A 1008 TYR cc_start: 0.8126 (t80) cc_final: 0.7664 (t80) REVERT: A 1009 LYS cc_start: 0.9003 (mmtp) cc_final: 0.8746 (mmmm) REVERT: A 1046 TYR cc_start: 0.9143 (m-10) cc_final: 0.8902 (m-10) REVERT: A 1072 ARG cc_start: 0.6409 (ttp80) cc_final: 0.5910 (tpt90) REVERT: A 1174 ARG cc_start: 0.6569 (ttp-170) cc_final: 0.6361 (ttt180) REVERT: B 81 ASN cc_start: 0.8794 (p0) cc_final: 0.8198 (t0) REVERT: B 180 GLN cc_start: 0.8742 (mt0) cc_final: 0.8529 (mt0) REVERT: B 207 GLU cc_start: 0.8551 (mt-10) cc_final: 0.8325 (tt0) REVERT: B 212 ASN cc_start: 0.8822 (t0) cc_final: 0.8608 (t0) REVERT: B 289 GLU cc_start: 0.8437 (mm-30) cc_final: 0.7698 (mm-30) REVERT: B 322 MET cc_start: 0.7824 (mtm) cc_final: 0.6178 (mtp) REVERT: B 512 ASP cc_start: 0.7942 (t0) cc_final: 0.7663 (t0) REVERT: B 522 ARG cc_start: 0.8174 (mmm-85) cc_final: 0.7679 (ttm110) REVERT: B 532 ASP cc_start: 0.8831 (m-30) cc_final: 0.8420 (m-30) REVERT: B 549 GLU cc_start: 0.8480 (mt-10) cc_final: 0.7892 (mm-30) REVERT: C 122 ASN cc_start: 0.9031 (m-40) cc_final: 0.8823 (m-40) REVERT: C 124 GLN cc_start: 0.8587 (mt0) cc_final: 0.8179 (mt0) REVERT: C 125 PHE cc_start: 0.9195 (OUTLIER) cc_final: 0.8963 (t80) REVERT: C 128 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.7829 (mm-30) outliers start: 41 outliers final: 16 residues processed: 332 average time/residue: 0.1269 time to fit residues: 60.7383 Evaluate side-chains 259 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 237 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 237 CYS Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 350 GLU Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 495 ASP Chi-restraints excluded: chain A residue 569 ASP Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 779 MET Chi-restraints excluded: chain A residue 812 MET Chi-restraints excluded: chain A residue 1078 ILE Chi-restraints excluded: chain A residue 1183 LEU Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain B residue 498 ILE Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain C residue 125 PHE Chi-restraints excluded: chain C residue 128 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 92 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 132 optimal weight: 3.9990 chunk 129 optimal weight: 0.9980 chunk 84 optimal weight: 0.0030 chunk 41 optimal weight: 0.7980 chunk 108 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 overall best weight: 0.9392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 519 GLN ** A 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 974 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 231 ASN ** B 515 GLN ** 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 = 0.3336 r_free = 0.3336 target = 0.101541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.083320 restraints weight = 34335.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.086098 restraints weight = 18722.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.087952 restraints weight = 12351.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.089256 restraints weight = 9261.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.090197 restraints weight = 7503.265| |-----------------------------------------------------------------------------| r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.3662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14502 Z= 0.146 Angle : 0.595 7.958 19706 Z= 0.305 Chirality : 0.041 0.147 2209 Planarity : 0.004 0.039 2461 Dihedral : 7.684 83.643 2089 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.68 % Favored : 97.27 % Rotamer: Outliers : 4.05 % Allowed : 13.60 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.96 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.19), residues: 1719 helix: -0.38 (0.18), residues: 764 sheet: -1.21 (0.34), residues: 173 loop : 0.30 (0.22), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 138 TYR 0.010 0.001 TYR B 243 PHE 0.018 0.001 PHE D 121 TRP 0.008 0.001 TRP A 445 HIS 0.007 0.001 HIS A 999 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.15 (14500) covalent geometry : angle 0.59532 / 0.30 (19706) hydrogen bonds : bond 0.03861 / 2.59 ( 490) hydrogen bonds : angle 5.00777 / 3.45 ( 1389) Misc. bond : bond 0.00230 / 0.11 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 251 time to evaluate : 0.570 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: A 156 LEU cc_start: 0.9467 (mt) cc_final: 0.9024 (tt) REVERT: A 237 CYS cc_start: 0.9348 (m) cc_final: 0.8943 (t) REVERT: A 354 ASP cc_start: 0.8401 (t0) cc_final: 0.8100 (t0) REVERT: A 539 ARG cc_start: 0.3721 (ptt90) cc_final: 0.2994 (ptt-90) REVERT: A 542 LEU cc_start: 0.9320 (tp) cc_final: 0.9104 (tt) REVERT: A 731 THR cc_start: 0.9235 (m) cc_final: 0.8958 (p) REVERT: A 758 MET cc_start: 0.8583 (tmm) cc_final: 0.7837 (tmm) REVERT: A 759 GLU cc_start: 0.8528 (tm-30) cc_final: 0.7444 (tm-30) REVERT: A 779 MET cc_start: 0.9128 (OUTLIER) cc_final: 0.8743 (tpp) REVERT: A 788 CYS cc_start: 0.9039 (m) cc_final: 0.8733 (m) REVERT: A 789 LEU cc_start: 0.9311 (OUTLIER) cc_final: 0.9041 (pp) REVERT: A 828 MET cc_start: 0.6290 (ppp) cc_final: 0.6007 (ppp) REVERT: A 877 ASP cc_start: 0.8878 (t0) cc_final: 0.8241 (t0) REVERT: A 918 ASP cc_start: 0.8769 (m-30) cc_final: 0.8447 (m-30) REVERT: A 922 LYS cc_start: 0.7877 (tppt) cc_final: 0.7551 (mmmt) REVERT: A 938 GLU cc_start: 0.8149 (tm-30) cc_final: 0.7884 (tm-30) REVERT: A 939 GLN cc_start: 0.9047 (tp-100) cc_final: 0.8741 (tp40) REVERT: A 1072 ARG cc_start: 0.6471 (ttp80) cc_final: 0.5916 (tpt90) REVERT: A 1092 PHE cc_start: 0.7611 (t80) cc_final: 0.7392 (t80) REVERT: B 56 LEU cc_start: 0.9551 (OUTLIER) cc_final: 0.9241 (mm) REVERT: B 73 TYR cc_start: 0.8973 (m-80) cc_final: 0.8708 (m-80) REVERT: B 81 ASN cc_start: 0.8815 (p0) cc_final: 0.8189 (t0) REVERT: B 165 GLN cc_start: 0.9284 (mt0) cc_final: 0.8875 (mp10) REVERT: B 207 GLU cc_start: 0.8572 (mt-10) cc_final: 0.8316 (tt0) REVERT: B 289 GLU cc_start: 0.8397 (mm-30) cc_final: 0.7622 (mm-30) REVERT: B 449 MET cc_start: 0.8889 (mtp) cc_final: 0.8366 (mmm) REVERT: B 488 GLU cc_start: 0.8209 (mt-10) cc_final: 0.7861 (mt-10) REVERT: B 522 ARG cc_start: 0.8257 (mmm-85) cc_final: 0.7757 (ttm110) REVERT: B 532 ASP cc_start: 0.8854 (m-30) cc_final: 0.8644 (m-30) REVERT: C 124 GLN cc_start: 0.8661 (mt0) cc_final: 0.8235 (mt0) REVERT: C 128 GLU cc_start: 0.8483 (OUTLIER) cc_final: 0.7743 (tm-30) outliers start: 61 outliers final: 30 residues processed: 285 average time/residue: 0.1206 time to fit residues: 49.6320 Evaluate side-chains 245 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 211 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 259 GLU Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 495 ASP Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 583 TYR Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 755 LEU Chi-restraints excluded: chain A residue 777 LEU Chi-restraints excluded: chain A residue 779 MET Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain A residue 862 SER Chi-restraints excluded: chain A residue 1044 LEU Chi-restraints excluded: chain A residue 1078 ILE Chi-restraints excluded: chain A residue 1183 LEU Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain B residue 498 ILE Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain C residue 128 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 151 optimal weight: 3.9990 chunk 106 optimal weight: 6.9990 chunk 91 optimal weight: 0.8980 chunk 13 optimal weight: 3.9990 chunk 147 optimal weight: 4.9990 chunk 135 optimal weight: 5.9990 chunk 48 optimal weight: 3.9990 chunk 1 optimal weight: 0.9980 chunk 74 optimal weight: 4.9990 chunk 34 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 519 GLN ** A 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 974 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 9 HIS B 188 GLN ** B 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 231 ASN ** B 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 122 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.098749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.080861 restraints weight = 34748.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.083512 restraints weight = 18840.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.085165 restraints weight = 12426.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.086489 restraints weight = 9488.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.087320 restraints weight = 7697.108| |-----------------------------------------------------------------------------| r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.4022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 14502 Z= 0.221 Angle : 0.647 9.339 19706 Z= 0.329 Chirality : 0.043 0.161 2209 Planarity : 0.004 0.042 2461 Dihedral : 7.651 84.615 2089 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.32 % Favored : 96.63 % Rotamer: Outliers : 4.31 % Allowed : 14.13 % Favored : 81.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.96 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.20), residues: 1719 helix: 0.00 (0.19), residues: 762 sheet: -0.80 (0.37), residues: 158 loop : 0.02 (0.22), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 117 TYR 0.016 0.002 TYR A1182 PHE 0.013 0.001 PHE B 401 TRP 0.010 0.001 TRP A 445 HIS 0.010 0.001 HIS A 999 Details of bonding type rmsd/Z covalent geometry : bond 0.00490 / 0.22 (14500) covalent geometry : angle 0.64695 / 0.33 (19706) hydrogen bonds : bond 0.03962 / 2.65 ( 490) hydrogen bonds : angle 5.09928 / 3.54 ( 1389) Misc. bond : bond 0.00433 / 0.21 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 215 time to evaluate : 0.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 LEU cc_start: 0.9324 (mt) cc_final: 0.8955 (tt) REVERT: A 237 CYS cc_start: 0.9402 (m) cc_final: 0.9020 (t) REVERT: A 240 ASP cc_start: 0.8143 (OUTLIER) cc_final: 0.7828 (p0) REVERT: A 266 GLN cc_start: 0.8341 (pp30) cc_final: 0.8085 (pp30) REVERT: A 354 ASP cc_start: 0.8457 (t0) cc_final: 0.8181 (t0) REVERT: A 468 LYS cc_start: 0.9256 (tppt) cc_final: 0.9051 (tptp) REVERT: A 539 ARG cc_start: 0.3323 (ptt90) cc_final: 0.2215 (ptt-90) REVERT: A 542 LEU cc_start: 0.9419 (tp) cc_final: 0.9173 (tt) REVERT: A 563 TYR cc_start: 0.9135 (t80) cc_final: 0.8915 (t80) REVERT: A 662 LYS cc_start: 0.9105 (tptm) cc_final: 0.8891 (tttt) REVERT: A 683 MET cc_start: 0.8281 (tmm) cc_final: 0.7940 (tmm) REVERT: A 731 THR cc_start: 0.9287 (m) cc_final: 0.9027 (p) REVERT: A 758 MET cc_start: 0.8662 (tmm) cc_final: 0.7923 (tmm) REVERT: A 759 GLU cc_start: 0.8643 (tm-30) cc_final: 0.7572 (tm-30) REVERT: A 778 LYS cc_start: 0.9345 (ttpt) cc_final: 0.8844 (tttp) REVERT: A 779 MET cc_start: 0.9049 (tpp) cc_final: 0.8641 (tpp) REVERT: A 789 LEU cc_start: 0.9426 (OUTLIER) cc_final: 0.9216 (pp) REVERT: A 828 MET cc_start: 0.6492 (ppp) cc_final: 0.6048 (ppp) REVERT: A 877 ASP cc_start: 0.8942 (t0) cc_final: 0.8424 (t0) REVERT: A 918 ASP cc_start: 0.8783 (m-30) cc_final: 0.8459 (m-30) REVERT: A 922 LYS cc_start: 0.7872 (tppt) cc_final: 0.7636 (mmmt) REVERT: A 938 GLU cc_start: 0.8167 (tm-30) cc_final: 0.7860 (tm-30) REVERT: A 939 GLN cc_start: 0.9166 (tp-100) cc_final: 0.8819 (tp40) REVERT: A 1072 ARG cc_start: 0.6509 (ttp80) cc_final: 0.5942 (tpt90) REVERT: A 1092 PHE cc_start: 0.7670 (t80) cc_final: 0.7463 (t80) REVERT: B 56 LEU cc_start: 0.9563 (OUTLIER) cc_final: 0.9294 (mm) REVERT: B 81 ASN cc_start: 0.8827 (p0) cc_final: 0.8181 (t0) REVERT: B 188 GLN cc_start: 0.8421 (mm-40) cc_final: 0.8084 (mm110) REVERT: B 199 ARG cc_start: 0.5673 (ttt-90) cc_final: 0.5291 (ptt-90) REVERT: B 488 GLU cc_start: 0.8313 (mt-10) cc_final: 0.8064 (mt-10) REVERT: B 522 ARG cc_start: 0.8293 (mmm-85) cc_final: 0.7790 (ttm110) REVERT: B 532 ASP cc_start: 0.9012 (m-30) cc_final: 0.8533 (m-30) REVERT: B 552 GLU cc_start: 0.8599 (tp30) cc_final: 0.8262 (tp30) REVERT: C 124 GLN cc_start: 0.8626 (mt0) cc_final: 0.8308 (mt0) REVERT: C 128 GLU cc_start: 0.8585 (OUTLIER) cc_final: 0.7831 (tm-30) outliers start: 65 outliers final: 37 residues processed: 260 average time/residue: 0.1203 time to fit residues: 45.5692 Evaluate side-chains 237 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 196 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain A residue 259 GLU Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 583 TYR Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 707 SER Chi-restraints excluded: chain A residue 777 LEU Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain A residue 862 SER Chi-restraints excluded: chain A residue 1044 LEU Chi-restraints excluded: chain A residue 1078 ILE Chi-restraints excluded: chain A residue 1104 THR Chi-restraints excluded: chain A residue 1133 TYR Chi-restraints excluded: chain A residue 1151 SER Chi-restraints excluded: chain A residue 1183 LEU Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 76 MET Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 498 ILE Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain C residue 128 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 18 optimal weight: 3.9990 chunk 164 optimal weight: 4.9990 chunk 88 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 136 optimal weight: 0.0370 chunk 95 optimal weight: 0.0970 chunk 37 optimal weight: 0.5980 chunk 117 optimal weight: 3.9990 chunk 55 optimal weight: 0.7980 chunk 27 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 overall best weight: 0.4656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 378 HIS ** A 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 519 GLN ** A 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 974 GLN ** B 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 231 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.102547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.084463 restraints weight = 34028.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.087242 restraints weight = 18270.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.089121 restraints weight = 11982.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.090486 restraints weight = 8889.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.091359 restraints weight = 7116.620| |-----------------------------------------------------------------------------| r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.4318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.067 14502 Z= 0.107 Angle : 0.575 11.634 19706 Z= 0.287 Chirality : 0.040 0.204 2209 Planarity : 0.003 0.039 2461 Dihedral : 7.314 83.711 2089 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.73 % Favored : 97.21 % Rotamer: Outliers : 2.79 % Allowed : 16.52 % Favored : 80.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.96 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.20), residues: 1719 helix: 0.43 (0.19), residues: 756 sheet: -0.83 (0.36), residues: 164 loop : 0.04 (0.22), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 252 TYR 0.023 0.001 TYR A 805 PHE 0.010 0.001 PHE C 125 TRP 0.009 0.001 TRP A 417 HIS 0.010 0.001 HIS A 28 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 (14500) covalent geometry : angle 0.57525 / 0.29 (19706) hydrogen bonds : bond 0.03082 / 2.08 ( 490) hydrogen bonds : angle 4.62176 / 3.19 ( 1389) Misc. bond : bond 0.00301 / 0.14 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 240 time to evaluate : 0.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.8355 (tp) REVERT: A 156 LEU cc_start: 0.9252 (mt) cc_final: 0.8987 (tt) REVERT: A 237 CYS cc_start: 0.9310 (m) cc_final: 0.8936 (t) REVERT: A 354 ASP cc_start: 0.8371 (t0) cc_final: 0.8115 (t0) REVERT: A 468 LYS cc_start: 0.9403 (tppt) cc_final: 0.9156 (tptp) REVERT: A 539 ARG cc_start: 0.3250 (ptt90) cc_final: 0.2791 (ptt90) REVERT: A 542 LEU cc_start: 0.9384 (tp) cc_final: 0.9180 (tt) REVERT: A 563 TYR cc_start: 0.9112 (t80) cc_final: 0.8855 (t80) REVERT: A 662 LYS cc_start: 0.9067 (tptm) cc_final: 0.8843 (ttmt) REVERT: A 731 THR cc_start: 0.9248 (m) cc_final: 0.8941 (p) REVERT: A 758 MET cc_start: 0.8576 (tmm) cc_final: 0.7858 (tmm) REVERT: A 759 GLU cc_start: 0.8515 (tm-30) cc_final: 0.7488 (tm-30) REVERT: A 779 MET cc_start: 0.9094 (tpp) cc_final: 0.8711 (tpp) REVERT: A 828 MET cc_start: 0.6031 (ppp) cc_final: 0.5626 (ppp) REVERT: A 844 GLU cc_start: 0.8465 (mp0) cc_final: 0.8121 (mp0) REVERT: A 877 ASP cc_start: 0.8911 (t0) cc_final: 0.8383 (t0) REVERT: A 918 ASP cc_start: 0.8775 (m-30) cc_final: 0.8513 (m-30) REVERT: A 939 GLN cc_start: 0.9029 (tp-100) cc_final: 0.8769 (tp40) REVERT: A 1056 PHE cc_start: 0.9559 (t80) cc_final: 0.9271 (t80) REVERT: A 1072 ARG cc_start: 0.6541 (ttp80) cc_final: 0.5919 (tpt90) REVERT: A 1182 TYR cc_start: 0.9091 (t80) cc_final: 0.8851 (t80) REVERT: B 56 LEU cc_start: 0.9548 (OUTLIER) cc_final: 0.9259 (mm) REVERT: B 81 ASN cc_start: 0.8779 (p0) cc_final: 0.8251 (t0) REVERT: B 488 GLU cc_start: 0.8147 (mt-10) cc_final: 0.7845 (mt-10) REVERT: B 522 ARG cc_start: 0.8259 (mmm-85) cc_final: 0.7769 (ttm110) REVERT: C 119 ASP cc_start: 0.8502 (m-30) cc_final: 0.8254 (m-30) REVERT: C 124 GLN cc_start: 0.7853 (mt0) cc_final: 0.7467 (mt0) REVERT: C 125 PHE cc_start: 0.9078 (t80) cc_final: 0.8853 (t80) REVERT: C 128 GLU cc_start: 0.8478 (OUTLIER) cc_final: 0.7770 (tm-30) outliers start: 42 outliers final: 22 residues processed: 267 average time/residue: 0.1185 time to fit residues: 46.3379 Evaluate side-chains 230 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 205 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 583 TYR Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 862 SER Chi-restraints excluded: chain A residue 1044 LEU Chi-restraints excluded: chain A residue 1078 ILE Chi-restraints excluded: chain A residue 1133 TYR Chi-restraints excluded: chain A residue 1151 SER Chi-restraints excluded: chain A residue 1183 LEU Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 498 ILE Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain C residue 128 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 106 optimal weight: 5.9990 chunk 127 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 135 optimal weight: 5.9990 chunk 23 optimal weight: 0.6980 chunk 162 optimal weight: 4.9990 chunk 52 optimal weight: 0.6980 chunk 158 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 5 optimal weight: 6.9990 chunk 155 optimal weight: 0.2980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 519 GLN ** A 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 978 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.101168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.083213 restraints weight = 34260.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 19)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.085868 restraints weight = 18502.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.087755 restraints weight = 12242.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.088971 restraints weight = 9074.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.089863 restraints weight = 7372.245| |-----------------------------------------------------------------------------| r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.4478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14502 Z= 0.161 Angle : 0.614 8.771 19706 Z= 0.309 Chirality : 0.042 0.159 2209 Planarity : 0.004 0.049 2461 Dihedral : 7.263 83.468 2089 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.91 % Favored : 97.03 % Rotamer: Outliers : 3.38 % Allowed : 17.58 % Favored : 79.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.96 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.20), residues: 1719 helix: 0.47 (0.19), residues: 780 sheet: -0.52 (0.36), residues: 174 loop : -0.09 (0.22), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 252 TYR 0.011 0.001 TYR B 352 PHE 0.029 0.001 PHE A 142 TRP 0.009 0.001 TRP A 417 HIS 0.008 0.001 HIS A 28 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.16 (14500) covalent geometry : angle 0.61443 / 0.31 (19706) hydrogen bonds : bond 0.03337 / 2.24 ( 490) hydrogen bonds : angle 4.67215 / 3.23 ( 1389) Misc. bond : bond 0.00324 / 0.15 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 210 time to evaluate : 0.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 LEU cc_start: 0.9325 (mt) cc_final: 0.8877 (tt) REVERT: A 237 CYS cc_start: 0.9329 (m) cc_final: 0.9004 (t) REVERT: A 354 ASP cc_start: 0.8389 (t0) cc_final: 0.8143 (t0) REVERT: A 539 ARG cc_start: 0.3696 (ptt90) cc_final: 0.3146 (ptt90) REVERT: A 542 LEU cc_start: 0.9334 (tp) cc_final: 0.9132 (tt) REVERT: A 731 THR cc_start: 0.9262 (m) cc_final: 0.8993 (p) REVERT: A 758 MET cc_start: 0.8557 (tmm) cc_final: 0.7873 (tmm) REVERT: A 759 GLU cc_start: 0.8631 (tm-30) cc_final: 0.7749 (tm-30) REVERT: A 779 MET cc_start: 0.9083 (tpp) cc_final: 0.8649 (tpp) REVERT: A 828 MET cc_start: 0.6187 (ppp) cc_final: 0.5511 (ppp) REVERT: A 844 GLU cc_start: 0.8489 (mp0) cc_final: 0.8176 (mp0) REVERT: A 877 ASP cc_start: 0.8943 (t0) cc_final: 0.8438 (t0) REVERT: A 922 LYS cc_start: 0.7917 (tppt) cc_final: 0.7557 (mmmt) REVERT: A 939 GLN cc_start: 0.9342 (tp-100) cc_final: 0.8713 (tp40) REVERT: A 1056 PHE cc_start: 0.9552 (t80) cc_final: 0.9315 (t80) REVERT: A 1072 ARG cc_start: 0.6574 (ttp80) cc_final: 0.6001 (tpt90) REVERT: A 1182 TYR cc_start: 0.9119 (t80) cc_final: 0.8863 (t80) REVERT: B 56 LEU cc_start: 0.9565 (OUTLIER) cc_final: 0.9294 (mm) REVERT: B 81 ASN cc_start: 0.8799 (p0) cc_final: 0.8262 (t0) REVERT: B 165 GLN cc_start: 0.9310 (mt0) cc_final: 0.8798 (mp10) REVERT: B 460 LEU cc_start: 0.8875 (mt) cc_final: 0.8666 (mt) REVERT: B 488 GLU cc_start: 0.8226 (mt-10) cc_final: 0.7912 (mt-10) REVERT: B 522 ARG cc_start: 0.8333 (mmm-85) cc_final: 0.7699 (ttm110) REVERT: C 124 GLN cc_start: 0.7911 (mt0) cc_final: 0.7474 (mt0) REVERT: C 128 GLU cc_start: 0.8551 (OUTLIER) cc_final: 0.7839 (tm-30) outliers start: 51 outliers final: 33 residues processed: 246 average time/residue: 0.1207 time to fit residues: 43.6593 Evaluate side-chains 232 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 197 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 527 PHE Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 583 TYR Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 755 LEU Chi-restraints excluded: chain A residue 862 SER Chi-restraints excluded: chain A residue 1044 LEU Chi-restraints excluded: chain A residue 1078 ILE Chi-restraints excluded: chain A residue 1104 THR Chi-restraints excluded: chain A residue 1133 TYR Chi-restraints excluded: chain A residue 1151 SER Chi-restraints excluded: chain A residue 1183 LEU Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 465 THR Chi-restraints excluded: chain B residue 467 SER Chi-restraints excluded: chain B residue 498 ILE Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain C residue 128 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 91 optimal weight: 0.5980 chunk 87 optimal weight: 4.9990 chunk 79 optimal weight: 9.9990 chunk 40 optimal weight: 3.9990 chunk 110 optimal weight: 0.5980 chunk 124 optimal weight: 0.3980 chunk 94 optimal weight: 5.9990 chunk 101 optimal weight: 0.8980 chunk 3 optimal weight: 0.7980 chunk 66 optimal weight: 0.4980 chunk 9 optimal weight: 3.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 519 GLN ** A 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 978 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 212 ASN B 515 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.102963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.084815 restraints weight = 33917.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.087537 restraints weight = 18499.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.089449 restraints weight = 12258.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.090809 restraints weight = 9092.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.091554 restraints weight = 7282.001| |-----------------------------------------------------------------------------| r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.4694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 14502 Z= 0.112 Angle : 0.589 10.961 19706 Z= 0.293 Chirality : 0.041 0.214 2209 Planarity : 0.003 0.048 2461 Dihedral : 7.073 82.680 2089 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.73 % Favored : 97.21 % Rotamer: Outliers : 2.72 % Allowed : 18.18 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.96 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.20), residues: 1719 helix: 0.63 (0.19), residues: 783 sheet: -0.39 (0.40), residues: 160 loop : -0.11 (0.22), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 252 TYR 0.025 0.001 TYR A 805 PHE 0.020 0.001 PHE A 142 TRP 0.009 0.001 TRP A 445 HIS 0.011 0.001 HIS A 28 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 (14500) covalent geometry : angle 0.58852 / 0.29 (19706) hydrogen bonds : bond 0.02987 / 2.01 ( 490) hydrogen bonds : angle 4.43207 / 3.06 ( 1389) Misc. bond : bond 0.00296 / 0.14 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 226 time to evaluate : 0.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 LEU cc_start: 0.9316 (mt) cc_final: 0.9018 (tt) REVERT: A 237 CYS cc_start: 0.9269 (OUTLIER) cc_final: 0.8979 (t) REVERT: A 502 MET cc_start: 0.8906 (tpp) cc_final: 0.7963 (tmm) REVERT: A 539 ARG cc_start: 0.3819 (ptt90) cc_final: 0.3263 (ptt90) REVERT: A 683 MET cc_start: 0.8148 (tmm) cc_final: 0.7900 (tmm) REVERT: A 731 THR cc_start: 0.9250 (m) cc_final: 0.8971 (p) REVERT: A 758 MET cc_start: 0.8480 (tmm) cc_final: 0.7836 (tmm) REVERT: A 759 GLU cc_start: 0.8559 (tm-30) cc_final: 0.7661 (tm-30) REVERT: A 779 MET cc_start: 0.9080 (tpp) cc_final: 0.8724 (tpp) REVERT: A 828 MET cc_start: 0.5922 (ppp) cc_final: 0.5232 (ppp) REVERT: A 844 GLU cc_start: 0.8482 (mp0) cc_final: 0.8143 (mp0) REVERT: A 845 TYR cc_start: 0.8928 (t80) cc_final: 0.8631 (t80) REVERT: A 877 ASP cc_start: 0.8896 (t0) cc_final: 0.8386 (t0) REVERT: A 922 LYS cc_start: 0.7980 (tppt) cc_final: 0.7736 (mmmt) REVERT: A 939 GLN cc_start: 0.9277 (tp-100) cc_final: 0.8732 (tp40) REVERT: A 1048 MET cc_start: 0.9112 (tpp) cc_final: 0.8236 (mmm) REVERT: A 1056 PHE cc_start: 0.9509 (t80) cc_final: 0.9229 (t80) REVERT: A 1072 ARG cc_start: 0.6526 (ttp80) cc_final: 0.5960 (tpt90) REVERT: A 1125 ARG cc_start: 0.8785 (ttm110) cc_final: 0.8426 (ptm-80) REVERT: B 56 LEU cc_start: 0.9538 (OUTLIER) cc_final: 0.9288 (mm) REVERT: B 81 ASN cc_start: 0.8845 (p0) cc_final: 0.8357 (t0) REVERT: B 165 GLN cc_start: 0.9309 (mt0) cc_final: 0.8791 (mp10) REVERT: B 276 ARG cc_start: 0.8546 (ptt180) cc_final: 0.8263 (ptt90) REVERT: B 436 GLN cc_start: 0.8532 (mt0) cc_final: 0.8032 (mt0) REVERT: B 488 GLU cc_start: 0.7974 (mt-10) cc_final: 0.7704 (mt-10) REVERT: B 522 ARG cc_start: 0.8315 (mmm-85) cc_final: 0.7723 (ttm110) REVERT: C 124 GLN cc_start: 0.8014 (mt0) cc_final: 0.7570 (mt0) REVERT: C 128 GLU cc_start: 0.8532 (OUTLIER) cc_final: 0.7819 (tm-30) REVERT: D 121 PHE cc_start: 0.8242 (t80) cc_final: 0.7758 (t80) outliers start: 41 outliers final: 28 residues processed: 248 average time/residue: 0.1191 time to fit residues: 43.7011 Evaluate side-chains 240 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 209 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 237 CYS Chi-restraints excluded: chain A residue 259 GLU Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 519 GLN Chi-restraints excluded: chain A residue 527 PHE Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 755 LEU Chi-restraints excluded: chain A residue 862 SER Chi-restraints excluded: chain A residue 938 GLU Chi-restraints excluded: chain A residue 1044 LEU Chi-restraints excluded: chain A residue 1078 ILE Chi-restraints excluded: chain A residue 1133 TYR Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 212 ASN Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 467 SER Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain C residue 128 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 2 optimal weight: 1.9990 chunk 166 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 161 optimal weight: 2.9990 chunk 60 optimal weight: 0.5980 chunk 91 optimal weight: 3.9990 chunk 69 optimal weight: 0.9990 chunk 97 optimal weight: 2.9990 chunk 147 optimal weight: 0.9990 chunk 50 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 519 GLN ** A 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 978 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1192 ASN ** B 212 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 = 0.3329 r_free = 0.3329 target = 0.101407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.083305 restraints weight = 34293.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.085934 restraints weight = 18807.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.087796 restraints weight = 12539.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.089035 restraints weight = 9345.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.089963 restraints weight = 7605.064| |-----------------------------------------------------------------------------| r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.4737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14502 Z= 0.153 Angle : 0.613 10.426 19706 Z= 0.306 Chirality : 0.042 0.189 2209 Planarity : 0.004 0.061 2461 Dihedral : 6.937 82.777 2087 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.26 % Favored : 96.68 % Rotamer: Outliers : 3.05 % Allowed : 18.98 % Favored : 77.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.96 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.20), residues: 1719 helix: 0.60 (0.19), residues: 787 sheet: -0.34 (0.37), residues: 172 loop : -0.04 (0.22), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 252 TYR 0.021 0.001 TYR A1182 PHE 0.023 0.001 PHE A 142 TRP 0.010 0.001 TRP A 445 HIS 0.011 0.001 HIS A 28 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 (14500) covalent geometry : angle 0.61313 / 0.31 (19706) hydrogen bonds : bond 0.03212 / 2.17 ( 490) hydrogen bonds : angle 4.53742 / 3.14 ( 1389) Misc. bond : bond 0.00301 / 0.14 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 206 time to evaluate : 0.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 GLU cc_start: 0.8565 (mm-30) cc_final: 0.8090 (tp30) REVERT: A 156 LEU cc_start: 0.9351 (mt) cc_final: 0.8922 (tt) REVERT: A 237 CYS cc_start: 0.9290 (OUTLIER) cc_final: 0.9012 (t) REVERT: A 539 ARG cc_start: 0.3662 (ptt90) cc_final: 0.3145 (ptt90) REVERT: A 731 THR cc_start: 0.9274 (m) cc_final: 0.9009 (p) REVERT: A 758 MET cc_start: 0.8579 (tmm) cc_final: 0.7915 (tmm) REVERT: A 759 GLU cc_start: 0.8645 (tm-30) cc_final: 0.7734 (tm-30) REVERT: A 779 MET cc_start: 0.9058 (tpp) cc_final: 0.8609 (tpp) REVERT: A 828 MET cc_start: 0.6029 (ppp) cc_final: 0.5195 (ppp) REVERT: A 844 GLU cc_start: 0.8500 (mp0) cc_final: 0.8162 (mp0) REVERT: A 877 ASP cc_start: 0.8914 (t0) cc_final: 0.8334 (t0) REVERT: A 922 LYS cc_start: 0.7894 (tppt) cc_final: 0.7682 (mmmt) REVERT: A 939 GLN cc_start: 0.9322 (tp-100) cc_final: 0.8722 (tp40) REVERT: A 1048 MET cc_start: 0.9100 (tpp) cc_final: 0.8224 (mmm) REVERT: A 1056 PHE cc_start: 0.9538 (t80) cc_final: 0.9250 (t80) REVERT: A 1072 ARG cc_start: 0.6539 (ttp80) cc_final: 0.5978 (tpt90) REVERT: A 1125 ARG cc_start: 0.8792 (ttm110) cc_final: 0.8418 (ptm-80) REVERT: B 56 LEU cc_start: 0.9557 (OUTLIER) cc_final: 0.9176 (mm) REVERT: B 81 ASN cc_start: 0.8852 (p0) cc_final: 0.8291 (t0) REVERT: B 165 GLN cc_start: 0.9308 (mt0) cc_final: 0.8810 (mp10) REVERT: B 276 ARG cc_start: 0.8579 (ptt180) cc_final: 0.8286 (ptt90) REVERT: B 436 GLN cc_start: 0.8443 (mt0) cc_final: 0.7953 (mt0) REVERT: B 488 GLU cc_start: 0.8135 (mt-10) cc_final: 0.7835 (mt-10) REVERT: B 522 ARG cc_start: 0.8359 (mmm-85) cc_final: 0.7860 (ttm110) REVERT: C 124 GLN cc_start: 0.8133 (mt0) cc_final: 0.7907 (mt0) REVERT: C 128 GLU cc_start: 0.8553 (OUTLIER) cc_final: 0.7844 (tm-30) REVERT: D 121 PHE cc_start: 0.8246 (t80) cc_final: 0.7706 (t80) outliers start: 46 outliers final: 34 residues processed: 232 average time/residue: 0.1247 time to fit residues: 42.7628 Evaluate side-chains 235 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 198 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 237 CYS Chi-restraints excluded: chain A residue 259 GLU Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 383 GLN Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 519 GLN Chi-restraints excluded: chain A residue 527 PHE Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 583 TYR Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 755 LEU Chi-restraints excluded: chain A residue 777 LEU Chi-restraints excluded: chain A residue 862 SER Chi-restraints excluded: chain A residue 938 GLU Chi-restraints excluded: chain A residue 1044 LEU Chi-restraints excluded: chain A residue 1078 ILE Chi-restraints excluded: chain A residue 1133 TYR Chi-restraints excluded: chain A residue 1151 SER Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain C residue 128 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 33 optimal weight: 0.9980 chunk 158 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 chunk 140 optimal weight: 0.8980 chunk 106 optimal weight: 2.9990 chunk 143 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 110 optimal weight: 0.9990 chunk 44 optimal weight: 0.8980 chunk 79 optimal weight: 0.9990 chunk 163 optimal weight: 0.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 99 HIS A 413 HIS ** A 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 519 GLN ** A 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 978 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 212 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 = 0.3335 r_free = 0.3335 target = 0.101608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.083527 restraints weight = 34331.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.086244 restraints weight = 18802.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.088096 restraints weight = 12390.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.089272 restraints weight = 9232.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.090240 restraints weight = 7562.025| |-----------------------------------------------------------------------------| r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.4815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 14502 Z= 0.139 Angle : 0.620 11.673 19706 Z= 0.307 Chirality : 0.041 0.186 2209 Planarity : 0.004 0.064 2461 Dihedral : 6.905 82.314 2087 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.08 % Favored : 96.86 % Rotamer: Outliers : 2.72 % Allowed : 19.58 % Favored : 77.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.96 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.20), residues: 1719 helix: 0.63 (0.19), residues: 785 sheet: -0.26 (0.37), residues: 172 loop : -0.05 (0.22), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 252 TYR 0.025 0.001 TYR A 805 PHE 0.020 0.001 PHE A 142 TRP 0.009 0.001 TRP A 445 HIS 0.012 0.001 HIS A 28 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 (14500) covalent geometry : angle 0.61983 / 0.31 (19706) hydrogen bonds : bond 0.03140 / 2.12 ( 490) hydrogen bonds : angle 4.49935 / 3.11 ( 1389) Misc. bond : bond 0.00306 / 0.15 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 203 time to evaluate : 0.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 GLU cc_start: 0.8562 (mm-30) cc_final: 0.8054 (tp30) REVERT: A 156 LEU cc_start: 0.9351 (mt) cc_final: 0.8903 (tt) REVERT: A 237 CYS cc_start: 0.9288 (OUTLIER) cc_final: 0.8993 (t) REVERT: A 502 MET cc_start: 0.9005 (tpp) cc_final: 0.7936 (tmm) REVERT: A 539 ARG cc_start: 0.3716 (ptt90) cc_final: 0.3205 (ptt90) REVERT: A 731 THR cc_start: 0.9266 (m) cc_final: 0.8985 (p) REVERT: A 758 MET cc_start: 0.8615 (tmm) cc_final: 0.7982 (tmm) REVERT: A 759 GLU cc_start: 0.8629 (tm-30) cc_final: 0.7720 (tm-30) REVERT: A 778 LYS cc_start: 0.9401 (ttpt) cc_final: 0.9031 (tttp) REVERT: A 779 MET cc_start: 0.9025 (tpp) cc_final: 0.8554 (tpp) REVERT: A 828 MET cc_start: 0.5816 (ppp) cc_final: 0.5039 (ppp) REVERT: A 844 GLU cc_start: 0.8500 (mp0) cc_final: 0.8151 (mp0) REVERT: A 877 ASP cc_start: 0.8914 (t0) cc_final: 0.8329 (t0) REVERT: A 922 LYS cc_start: 0.7929 (tppt) cc_final: 0.7681 (mmmt) REVERT: A 939 GLN cc_start: 0.9330 (tp-100) cc_final: 0.8785 (tp40) REVERT: A 1041 TYR cc_start: 0.9068 (OUTLIER) cc_final: 0.8643 (p90) REVERT: A 1048 MET cc_start: 0.9100 (tpp) cc_final: 0.8248 (mmm) REVERT: A 1056 PHE cc_start: 0.9533 (t80) cc_final: 0.9271 (t80) REVERT: A 1072 ARG cc_start: 0.6525 (ttp80) cc_final: 0.5978 (tpt90) REVERT: A 1125 ARG cc_start: 0.8793 (ttm110) cc_final: 0.8423 (ptm-80) REVERT: B 56 LEU cc_start: 0.9564 (OUTLIER) cc_final: 0.9250 (mm) REVERT: B 81 ASN cc_start: 0.8849 (p0) cc_final: 0.8298 (t0) REVERT: B 165 GLN cc_start: 0.9305 (mt0) cc_final: 0.8812 (mp10) REVERT: B 276 ARG cc_start: 0.8567 (ptt180) cc_final: 0.8269 (ptt90) REVERT: B 321 MET cc_start: 0.8628 (mmm) cc_final: 0.8195 (mmm) REVERT: B 436 GLN cc_start: 0.8464 (mt0) cc_final: 0.8120 (mt0) REVERT: B 488 GLU cc_start: 0.8136 (mt-10) cc_final: 0.7879 (mt-10) REVERT: B 522 ARG cc_start: 0.8407 (mmm-85) cc_final: 0.7864 (ttm110) REVERT: C 124 GLN cc_start: 0.7949 (mt0) cc_final: 0.7733 (mt0) REVERT: C 128 GLU cc_start: 0.8529 (OUTLIER) cc_final: 0.7842 (tm-30) REVERT: D 121 PHE cc_start: 0.8753 (t80) cc_final: 0.8209 (t80) outliers start: 41 outliers final: 34 residues processed: 227 average time/residue: 0.1338 time to fit residues: 44.4285 Evaluate side-chains 237 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 199 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 237 CYS Chi-restraints excluded: chain A residue 259 GLU Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 383 GLN Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 527 PHE Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 583 TYR Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 755 LEU Chi-restraints excluded: chain A residue 777 LEU Chi-restraints excluded: chain A residue 862 SER Chi-restraints excluded: chain A residue 1041 TYR Chi-restraints excluded: chain A residue 1044 LEU Chi-restraints excluded: chain A residue 1133 TYR Chi-restraints excluded: chain A residue 1151 SER Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain C residue 128 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 16 optimal weight: 0.9990 chunk 169 optimal weight: 0.8980 chunk 48 optimal weight: 5.9990 chunk 15 optimal weight: 0.9980 chunk 43 optimal weight: 9.9990 chunk 90 optimal weight: 0.8980 chunk 58 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 147 optimal weight: 0.7980 chunk 140 optimal weight: 2.9990 chunk 72 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 519 GLN ** A 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 632 ASN B 212 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.101196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.082872 restraints weight = 34780.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 19)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.085501 restraints weight = 19238.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.087388 restraints weight = 12917.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.088611 restraints weight = 9671.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.089562 restraints weight = 7905.202| |-----------------------------------------------------------------------------| r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.4888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14502 Z= 0.138 Angle : 0.624 11.533 19706 Z= 0.310 Chirality : 0.041 0.156 2209 Planarity : 0.004 0.066 2461 Dihedral : 6.840 81.997 2087 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.43 % Favored : 96.51 % Rotamer: Outliers : 2.72 % Allowed : 19.84 % Favored : 77.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.96 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.20), residues: 1719 helix: 0.63 (0.19), residues: 787 sheet: -0.21 (0.38), residues: 172 loop : -0.06 (0.22), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 252 TYR 0.024 0.001 TYR A1182 PHE 0.019 0.001 PHE A 142 TRP 0.009 0.001 TRP A 445 HIS 0.012 0.001 HIS A 28 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 (14500) covalent geometry : angle 0.62396 / 0.31 (19706) hydrogen bonds : bond 0.03189 / 2.17 ( 490) hydrogen bonds : angle 4.48238 / 3.09 ( 1389) Misc. bond : bond 0.00303 / 0.14 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 206 time to evaluate : 0.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 GLU cc_start: 0.8625 (mm-30) cc_final: 0.8122 (tp30) REVERT: A 156 LEU cc_start: 0.9363 (mt) cc_final: 0.8920 (tt) REVERT: A 237 CYS cc_start: 0.9269 (OUTLIER) cc_final: 0.8981 (t) REVERT: A 502 MET cc_start: 0.9041 (tpp) cc_final: 0.7951 (tmm) REVERT: A 539 ARG cc_start: 0.3620 (ptt90) cc_final: 0.3015 (ptt90) REVERT: A 731 THR cc_start: 0.9274 (m) cc_final: 0.8997 (p) REVERT: A 758 MET cc_start: 0.8601 (tmm) cc_final: 0.7974 (tmm) REVERT: A 759 GLU cc_start: 0.8613 (tm-30) cc_final: 0.7687 (tm-30) REVERT: A 779 MET cc_start: 0.9028 (tpp) cc_final: 0.8571 (tpp) REVERT: A 828 MET cc_start: 0.5799 (ppp) cc_final: 0.4968 (ppp) REVERT: A 844 GLU cc_start: 0.8535 (mp0) cc_final: 0.8174 (mp0) REVERT: A 877 ASP cc_start: 0.8899 (t0) cc_final: 0.8323 (t0) REVERT: A 918 ASP cc_start: 0.8472 (m-30) cc_final: 0.8113 (m-30) REVERT: A 922 LYS cc_start: 0.7920 (tppt) cc_final: 0.7662 (mmmt) REVERT: A 1041 TYR cc_start: 0.9069 (OUTLIER) cc_final: 0.8647 (p90) REVERT: A 1048 MET cc_start: 0.9117 (tpp) cc_final: 0.8286 (mmm) REVERT: A 1056 PHE cc_start: 0.9535 (t80) cc_final: 0.9261 (t80) REVERT: A 1072 ARG cc_start: 0.6507 (ttp80) cc_final: 0.5989 (tpt90) REVERT: A 1125 ARG cc_start: 0.8813 (ttm110) cc_final: 0.8448 (ptm-80) REVERT: B 56 LEU cc_start: 0.9581 (OUTLIER) cc_final: 0.9237 (mm) REVERT: B 81 ASN cc_start: 0.8883 (p0) cc_final: 0.8342 (t0) REVERT: B 165 GLN cc_start: 0.9260 (mt0) cc_final: 0.8771 (mp10) REVERT: B 276 ARG cc_start: 0.8572 (ptt180) cc_final: 0.8281 (ptt90) REVERT: B 321 MET cc_start: 0.8651 (mmm) cc_final: 0.8209 (mmm) REVERT: B 436 GLN cc_start: 0.8459 (mt0) cc_final: 0.8057 (mt0) REVERT: B 447 LYS cc_start: 0.9576 (ttpt) cc_final: 0.9332 (mtmm) REVERT: B 522 ARG cc_start: 0.8457 (mmm-85) cc_final: 0.7833 (ttm110) REVERT: C 124 GLN cc_start: 0.7958 (mt0) cc_final: 0.7744 (mt0) REVERT: D 121 PHE cc_start: 0.8751 (t80) cc_final: 0.8195 (t80) outliers start: 41 outliers final: 37 residues processed: 230 average time/residue: 0.1258 time to fit residues: 42.7476 Evaluate side-chains 239 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 199 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 237 CYS Chi-restraints excluded: chain A residue 259 GLU Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 383 GLN Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 519 GLN Chi-restraints excluded: chain A residue 527 PHE Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 583 TYR Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 755 LEU Chi-restraints excluded: chain A residue 777 LEU Chi-restraints excluded: chain A residue 862 SER Chi-restraints excluded: chain A residue 1041 TYR Chi-restraints excluded: chain A residue 1044 LEU Chi-restraints excluded: chain A residue 1078 ILE Chi-restraints excluded: chain A residue 1133 TYR Chi-restraints excluded: chain A residue 1151 SER Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 212 ASN Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 541 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 26 optimal weight: 0.2980 chunk 2 optimal weight: 0.8980 chunk 99 optimal weight: 0.8980 chunk 152 optimal weight: 0.0570 chunk 6 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 163 optimal weight: 2.9990 chunk 164 optimal weight: 0.8980 chunk 156 optimal weight: 0.4980 chunk 40 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 266 GLN ** A 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.101833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.083775 restraints weight = 34265.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.086479 restraints weight = 18722.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.088307 restraints weight = 12364.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.089483 restraints weight = 9234.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.090429 restraints weight = 7569.892| |-----------------------------------------------------------------------------| r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.4880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.229 14502 Z= 0.182 Angle : 0.948 59.199 19706 Z= 0.552 Chirality : 0.053 1.553 2209 Planarity : 0.004 0.085 2461 Dihedral : 6.716 81.983 2084 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.08 % Favored : 96.80 % Rotamer: Outliers : 2.52 % Allowed : 20.04 % Favored : 77.44 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.96 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.20), residues: 1719 helix: 0.65 (0.19), residues: 787 sheet: -0.21 (0.38), residues: 172 loop : -0.08 (0.22), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 252 TYR 0.020 0.001 TYR A1182 PHE 0.015 0.001 PHE A 142 TRP 0.008 0.001 TRP A 445 HIS 0.011 0.001 HIS A 28 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.18 (14500) covalent geometry : angle 0.94774 / 0.55 (19706) hydrogen bonds : bond 0.03187 / 2.17 ( 490) hydrogen bonds : angle 4.47930 / 3.09 ( 1389) Misc. bond : bond 0.00303 / 0.14 ( 2) =============================================================================== Job complete usr+sys time: 2077.57 seconds wall clock time: 37 minutes 1.69 seconds (2221.69 seconds total)