Starting phenix.real_space_refine on Thu Aug 6 09:44:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9m1k_63574/08_2026/9m1k_63574.cif Found real_map, /net/cci-nas-00/data/ceres_data/9m1k_63574/08_2026/9m1k_63574.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9m1k_63574/08_2026/9m1k_63574.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9m1k_63574/08_2026/9m1k_63574.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9m1k_63574/08_2026/9m1k_63574.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9m1k_63574/08_2026/9m1k_63574.map" } resolution = 2.45 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.020 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 89 5.16 5 C 9036 2.51 5 N 2483 2.21 5 O 2665 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14281 Number of models: 1 Model: "" Number of chains: 6 Chain: "E" Number of atoms: 722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 722 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 5, 'TRANS': 83} Chain: "D" Number of atoms: 8647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1103, 8647 Classifications: {'peptide': 1103} Link IDs: {'PCIS': 1, 'PTRANS': 45, 'TRANS': 1056} Chain breaks: 2 Chain: "G" Number of atoms: 1466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1466 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 3, 'TRANS': 180} Chain: "b" Number of atoms: 3380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3380 Classifications: {'peptide': 431} Link IDs: {'PTRANS': 20, 'TRANS': 410} Chain: "G" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "b" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.35, per 1000 atoms: 0.16 Number of scatterers: 14281 At special positions: 0 Unit cell: (91.2975, 115.579, 143.745, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 89 16.00 P 6 15.00 Mg 2 11.99 O 2665 8.00 N 2483 7.00 C 9036 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=0, symmetry=0 Time building additional restraints: 0.93 Conformation dependent library (CDL) restraints added in 480.2 milliseconds 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3384 Finding SS restraints... Secondary structure from input PDB file: 99 helices and 6 sheets defined 64.7% alpha, 5.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'E' and resid 470 through 483 Processing helix chain 'D' and resid 32 through 42 Processing helix chain 'D' and resid 50 through 66 removed outlier: 3.902A pdb=" N LYS D 66 " --> pdb=" O VAL D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 76 Proline residue: D 76 - end of helix Processing helix chain 'D' and resid 77 through 87 removed outlier: 4.092A pdb=" N MET D 81 " --> pdb=" O HIS D 77 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N MET D 82 " --> pdb=" O LEU D 78 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASN D 83 " --> pdb=" O GLU D 79 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ASP D 87 " --> pdb=" O ASN D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 113 Processing helix chain 'D' and resid 114 through 119 Processing helix chain 'D' and resid 129 through 134 Processing helix chain 'D' and resid 135 through 139 removed outlier: 3.774A pdb=" N GLN D 139 " --> pdb=" O VAL D 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 161 removed outlier: 3.700A pdb=" N LEU D 153 " --> pdb=" O THR D 149 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N LEU D 154 " --> pdb=" O ARG D 150 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU D 155 " --> pdb=" O TYR D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 184 through 197 Processing helix chain 'D' and resid 202 through 216 removed outlier: 4.049A pdb=" N ALA D 206 " --> pdb=" O LYS D 202 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N THR D 216 " --> pdb=" O SER D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 217 through 222 removed outlier: 3.998A pdb=" N GLN D 222 " --> pdb=" O PRO D 218 " (cutoff:3.500A) Processing helix chain 'D' and resid 225 through 237 Processing helix chain 'D' and resid 243 through 263 Processing helix chain 'D' and resid 269 through 282 removed outlier: 3.797A pdb=" N ALA D 274 " --> pdb=" O LEU D 270 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N THR D 275 " --> pdb=" O PRO D 271 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLY D 282 " --> pdb=" O ARG D 278 " (cutoff:3.500A) Processing helix chain 'D' and resid 290 through 309 removed outlier: 3.591A pdb=" N ARG D 294 " --> pdb=" O GLN D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 357 through 369 Processing helix chain 'D' and resid 373 through 389 removed outlier: 3.941A pdb=" N ARG D 377 " --> pdb=" O ASP D 373 " (cutoff:3.500A) Processing helix chain 'D' and resid 392 through 406 removed outlier: 3.637A pdb=" N CYS D 406 " --> pdb=" O SER D 402 " (cutoff:3.500A) Processing helix chain 'D' and resid 412 through 430 removed outlier: 3.923A pdb=" N ARG D 429 " --> pdb=" O GLU D 425 " (cutoff:3.500A) Processing helix chain 'D' and resid 433 through 435 No H-bonds generated for 'chain 'D' and resid 433 through 435' Processing helix chain 'D' and resid 436 through 446 removed outlier: 3.507A pdb=" N VAL D 441 " --> pdb=" O LEU D 437 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N ALA D 442 " --> pdb=" O VAL D 438 " (cutoff:3.500A) Processing helix chain 'D' and resid 460 through 478 removed outlier: 3.596A pdb=" N ALA D 475 " --> pdb=" O CYS D 471 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N ARG D 476 " --> pdb=" O TRP D 472 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N TYR D 478 " --> pdb=" O PHE D 474 " (cutoff:3.500A) Processing helix chain 'D' and resid 479 through 484 Processing helix chain 'D' and resid 487 through 498 removed outlier: 3.976A pdb=" N ALA D 493 " --> pdb=" O ALA D 489 " (cutoff:3.500A) Processing helix chain 'D' and resid 503 through 521 Processing helix chain 'D' and resid 526 through 534 Processing helix chain 'D' and resid 541 through 546 Processing helix chain 'D' and resid 547 through 555 Processing helix chain 'D' and resid 556 through 559 Processing helix chain 'D' and resid 560 through 570 removed outlier: 3.774A pdb=" N ILE D 564 " --> pdb=" O THR D 560 " (cutoff:3.500A) Processing helix chain 'D' and resid 571 through 574 removed outlier: 3.618A pdb=" N HIS D 574 " --> pdb=" O LYS D 571 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 571 through 574' Processing helix chain 'D' and resid 576 through 592 removed outlier: 3.992A pdb=" N GLN D 592 " --> pdb=" O HIS D 588 " (cutoff:3.500A) Processing helix chain 'D' and resid 596 through 601 removed outlier: 3.511A pdb=" N GLN D 601 " --> pdb=" O PHE D 597 " (cutoff:3.500A) Processing helix chain 'D' and resid 602 through 609 Processing helix chain 'D' and resid 610 through 612 No H-bonds generated for 'chain 'D' and resid 610 through 612' Processing helix chain 'D' and resid 614 through 639 removed outlier: 3.538A pdb=" N ARG D 618 " --> pdb=" O ASP D 614 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU D 639 " --> pdb=" O LEU D 635 " (cutoff:3.500A) Processing helix chain 'D' and resid 642 through 646 removed outlier: 3.538A pdb=" N HIS D 646 " --> pdb=" O VAL D 643 " (cutoff:3.500A) Processing helix chain 'D' and resid 648 through 656 Processing helix chain 'D' and resid 657 through 665 Processing helix chain 'D' and resid 669 through 690 removed outlier: 3.537A pdb=" N GLN D 674 " --> pdb=" O GLY D 670 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU D 675 " --> pdb=" O LEU D 671 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N MET D 676 " --> pdb=" O GLY D 672 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N CYS D 681 " --> pdb=" O ARG D 677 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N VAL D 682 " --> pdb=" O GLN D 678 " (cutoff:3.500A) Processing helix chain 'D' and resid 697 through 713 removed outlier: 3.938A pdb=" N ASP D 701 " --> pdb=" O ASP D 697 " (cutoff:3.500A) Processing helix chain 'D' and resid 721 through 740 removed outlier: 3.937A pdb=" N MET D 725 " --> pdb=" O SER D 721 " (cutoff:3.500A) Processing helix chain 'D' and resid 749 through 763 removed outlier: 3.708A pdb=" N GLN D 759 " --> pdb=" O GLU D 755 " (cutoff:3.500A) Processing helix chain 'D' and resid 764 through 766 No H-bonds generated for 'chain 'D' and resid 764 through 766' Processing helix chain 'D' and resid 768 through 781 Processing helix chain 'D' and resid 790 through 802 removed outlier: 3.540A pdb=" N VAL D 794 " --> pdb=" O ARG D 790 " (cutoff:3.500A) Processing helix chain 'D' and resid 811 through 830 removed outlier: 3.701A pdb=" N ARG D 815 " --> pdb=" O PHE D 811 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLY D 830 " --> pdb=" O CYS D 826 " (cutoff:3.500A) Processing helix chain 'D' and resid 844 through 857 removed outlier: 3.716A pdb=" N ASP D 857 " --> pdb=" O LEU D 853 " (cutoff:3.500A) Processing helix chain 'D' and resid 867 through 887 removed outlier: 4.040A pdb=" N VAL D 871 " --> pdb=" O VAL D 867 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ALA D 874 " --> pdb=" O TRP D 870 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LEU D 885 " --> pdb=" O ASP D 881 " (cutoff:3.500A) Processing helix chain 'D' and resid 888 through 889 No H-bonds generated for 'chain 'D' and resid 888 through 889' Processing helix chain 'D' and resid 890 through 894 Processing helix chain 'D' and resid 895 through 911 removed outlier: 3.538A pdb=" N CYS D 899 " --> pdb=" O GLU D 895 " (cutoff:3.500A) Processing helix chain 'D' and resid 914 through 930 Processing helix chain 'D' and resid 941 through 949 Processing helix chain 'D' and resid 961 through 964 Processing helix chain 'D' and resid 965 through 970 Processing helix chain 'D' and resid 971 through 975 Processing helix chain 'D' and resid 976 through 978 No H-bonds generated for 'chain 'D' and resid 976 through 978' Processing helix chain 'D' and resid 979 through 991 removed outlier: 4.181A pdb=" N VAL D 988 " --> pdb=" O LEU D 984 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N SER D 989 " --> pdb=" O GLY D 985 " (cutoff:3.500A) Processing helix chain 'D' and resid 994 through 1011 removed outlier: 4.019A pdb=" N GLY D1011 " --> pdb=" O GLU D1007 " (cutoff:3.500A) Processing helix chain 'D' and resid 1015 through 1032 removed outlier: 3.726A pdb=" N LEU D1019 " --> pdb=" O ASP D1015 " (cutoff:3.500A) Processing helix chain 'D' and resid 1036 through 1054 removed outlier: 3.778A pdb=" N VAL D1041 " --> pdb=" O GLU D1037 " (cutoff:3.500A) Proline residue: D1042 - end of helix Processing helix chain 'D' and resid 1057 through 1061 Processing helix chain 'D' and resid 1065 through 1080 removed outlier: 3.628A pdb=" N LEU D1071 " --> pdb=" O PHE D1067 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LEU D1072 " --> pdb=" O ALA D1068 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LYS D1077 " --> pdb=" O ALA D1073 " (cutoff:3.500A) Processing helix chain 'D' and resid 1084 through 1098 removed outlier: 3.619A pdb=" N SER D1090 " --> pdb=" O GLN D1086 " (cutoff:3.500A) Processing helix chain 'D' and resid 1099 through 1102 Proline residue: D1102 - end of helix No H-bonds generated for 'chain 'D' and resid 1099 through 1102' Processing helix chain 'D' and resid 1103 through 1117 removed outlier: 3.562A pdb=" N ARG D1107 " --> pdb=" O GLY D1103 " (cutoff:3.500A) Processing helix chain 'D' and resid 1121 through 1139 Processing helix chain 'D' and resid 1144 through 1157 removed outlier: 3.922A pdb=" N ASP D1149 " --> pdb=" O ALA D1145 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N GLU D1150 " --> pdb=" O ASP D1146 " (cutoff:3.500A) Processing helix chain 'D' and resid 1163 through 1179 removed outlier: 3.502A pdb=" N VAL D1167 " --> pdb=" O GLU D1163 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N GLU D1169 " --> pdb=" O ALA D1165 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLN D1170 " --> pdb=" O VAL D1166 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 15 removed outlier: 4.590A pdb=" N LYS G 8 " --> pdb=" O LEU G 4 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS G 9 " --> pdb=" O THR G 5 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLN G 12 " --> pdb=" O LYS G 8 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 38 removed outlier: 3.514A pdb=" N ASN G 37 " --> pdb=" O LEU G 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 70 through 75 removed outlier: 4.083A pdb=" N SER G 75 " --> pdb=" O LYS G 71 " (cutoff:3.500A) Processing helix chain 'G' and resid 76 through 81 removed outlier: 3.814A pdb=" N PHE G 81 " --> pdb=" O ARG G 78 " (cutoff:3.500A) Processing helix chain 'G' and resid 98 through 112 removed outlier: 3.600A pdb=" N CYS G 102 " --> pdb=" O ARG G 98 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU G 109 " --> pdb=" O GLU G 105 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LEU G 110 " --> pdb=" O LEU G 106 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL G 111 " --> pdb=" O GLN G 107 " (cutoff:3.500A) Processing helix chain 'G' and resid 134 through 142 removed outlier: 3.700A pdb=" N GLU G 140 " --> pdb=" O ASN G 136 " (cutoff:3.500A) Processing helix chain 'G' and resid 164 through 180 removed outlier: 3.804A pdb=" N GLY G 168 " --> pdb=" O ASN G 164 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TRP G 171 " --> pdb=" O PRO G 167 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ARG G 179 " --> pdb=" O ASP G 175 " (cutoff:3.500A) Processing helix chain 'b' and resid 10 through 26 Processing helix chain 'b' and resid 46 through 49 Processing helix chain 'b' and resid 69 through 78 removed outlier: 4.392A pdb=" N MET b 73 " --> pdb=" O GLU b 69 " (cutoff:3.500A) Processing helix chain 'b' and resid 86 through 88 No H-bonds generated for 'chain 'b' and resid 86 through 88' Processing helix chain 'b' and resid 100 through 106 Processing helix chain 'b' and resid 108 through 127 removed outlier: 3.876A pdb=" N ASP b 114 " --> pdb=" O ALA b 110 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N SER b 115 " --> pdb=" O GLU b 111 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ASP b 118 " --> pdb=" O ASP b 114 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL b 119 " --> pdb=" O SER b 115 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N SER b 126 " --> pdb=" O LYS b 122 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N CYS b 127 " --> pdb=" O GLU b 123 " (cutoff:3.500A) Processing helix chain 'b' and resid 142 through 159 Processing helix chain 'b' and resid 180 through 185 Processing helix chain 'b' and resid 186 through 195 Processing helix chain 'b' and resid 204 through 214 removed outlier: 3.548A pdb=" N TYR b 208 " --> pdb=" O ASN b 204 " (cutoff:3.500A) Processing helix chain 'b' and resid 221 through 237 removed outlier: 3.539A pdb=" N LEU b 228 " --> pdb=" O ASP b 224 " (cutoff:3.500A) Processing helix chain 'b' and resid 237 through 242 removed outlier: 3.540A pdb=" N ARG b 241 " --> pdb=" O THR b 237 " (cutoff:3.500A) Processing helix chain 'b' and resid 249 through 258 Processing helix chain 'b' and resid 285 through 294 removed outlier: 3.804A pdb=" N PHE b 294 " --> pdb=" O THR b 290 " (cutoff:3.500A) Processing helix chain 'b' and resid 295 through 299 Processing helix chain 'b' and resid 322 through 334 Processing helix chain 'b' and resid 371 through 373 No H-bonds generated for 'chain 'b' and resid 371 through 373' Processing helix chain 'b' and resid 374 through 390 removed outlier: 3.515A pdb=" N PHE b 378 " --> pdb=" O ILE b 374 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N GLN b 384 " --> pdb=" O ARG b 380 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ALA b 387 " --> pdb=" O GLU b 383 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N MET b 388 " --> pdb=" O GLN b 384 " (cutoff:3.500A) Processing helix chain 'b' and resid 394 through 400 removed outlier: 4.225A pdb=" N TYR b 398 " --> pdb=" O PHE b 394 " (cutoff:3.500A) Processing helix chain 'b' and resid 404 through 427 removed outlier: 4.055A pdb=" N ASP b 427 " --> pdb=" O GLN b 423 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 461 through 465 removed outlier: 3.927A pdb=" N LEU E 461 " --> pdb=" O ILE E 450 " (cutoff:3.500A) removed outlier: 8.122A pdb=" N LEU E 523 " --> pdb=" O THR E 447 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N LYS E 449 " --> pdb=" O LEU E 523 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N VAL E 525 " --> pdb=" O LYS E 449 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N LYS E 451 " --> pdb=" O VAL E 525 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE E 503 " --> pdb=" O TYR E 493 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 452 through 453 removed outlier: 3.569A pdb=" N GLU D 452 " --> pdb=" O VAL D 459 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 50 through 57 removed outlier: 7.133A pdb=" N LEU G 17 " --> pdb=" O ASN G 63 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N TRP G 65 " --> pdb=" O LEU G 17 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N LEU G 19 " --> pdb=" O TRP G 65 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N VAL G 67 " --> pdb=" O LEU G 19 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N MET G 21 " --> pdb=" O VAL G 67 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLY G 86 " --> pdb=" O ARG G 18 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL G 90 " --> pdb=" O LEU G 22 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'b' and resid 90 through 91 removed outlier: 8.246A pdb=" N VAL b 91 " --> pdb=" O ALA b 63 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N LEU b 65 " --> pdb=" O VAL b 91 " (cutoff:3.500A) removed outlier: 8.286A pdb=" N ILE b 64 " --> pdb=" O ILE b 4 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N HIS b 6 " --> pdb=" O ILE b 64 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N VAL b 66 " --> pdb=" O HIS b 6 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N GLN b 8 " --> pdb=" O VAL b 66 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N GLU b 3 " --> pdb=" O LEU b 130 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N GLY b 132 " --> pdb=" O GLU b 3 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL b 5 " --> pdb=" O GLY b 132 " (cutoff:3.500A) removed outlier: 9.611A pdb=" N ILE b 163 " --> pdb=" O CYS b 129 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N GLN b 131 " --> pdb=" O ILE b 163 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N ASN b 165 " --> pdb=" O GLN b 131 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N PHE b 133 " --> pdb=" O ASN b 165 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU b 198 " --> pdb=" O MET b 164 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N THR b 199 " --> pdb=" O PHE b 266 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLY b 369 " --> pdb=" O MET b 267 " (cutoff:3.500A) removed outlier: 8.821A pdb=" N ALA b 352 " --> pdb=" O VAL b 313 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ALA b 315 " --> pdb=" O ALA b 352 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N CYS b 354 " --> pdb=" O ALA b 315 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N PHE b 317 " --> pdb=" O CYS b 354 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'b' and resid 51 through 53 Processing sheet with id=AA6, first strand: chain 'b' and resid 169 through 170 741 hydrogen bonds defined for protein. 2157 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: 2.24 Time building geometry restraints manager: 1.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2485 1.32 - 1.44: 3634 1.44 - 1.57: 8295 1.57 - 1.69: 10 1.69 - 1.81: 137 Bond restraints: 14561 Sorted by residual: bond pdb=" C GLN D 302 " pdb=" N ARG D 303 " ideal model delta sigma weight residual 1.335 1.400 -0.065 1.36e-02 5.41e+03 2.29e+01 bond pdb=" C ASP D 501 " pdb=" N ARG D 502 " ideal model delta sigma weight residual 1.335 1.269 0.066 1.42e-02 4.96e+03 2.18e+01 bond pdb=" N ILE b 356 " pdb=" CA ILE b 356 " ideal model delta sigma weight residual 1.460 1.494 -0.034 7.60e-03 1.73e+04 1.97e+01 bond pdb=" N VAL b 60 " pdb=" CA VAL b 60 " ideal model delta sigma weight residual 1.457 1.495 -0.037 9.00e-03 1.23e+04 1.72e+01 bond pdb=" O1G GTP b1500 " pdb=" PG GTP b1500 " ideal model delta sigma weight residual 1.510 1.439 0.071 2.00e-02 2.50e+03 1.25e+01 ... (remaining 14556 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.19: 19620 4.19 - 8.37: 108 8.37 - 12.56: 7 12.56 - 16.74: 3 16.74 - 20.93: 2 Bond angle restraints: 19740 Sorted by residual: angle pdb=" CA SER D 933 " pdb=" C SER D 933 " pdb=" N PRO D 934 " ideal model delta sigma weight residual 117.44 123.98 -6.54 9.20e-01 1.18e+00 5.06e+01 angle pdb=" PA GTP G1500 " pdb=" O3A GTP G1500 " pdb=" PB GTP G1500 " ideal model delta sigma weight residual 120.50 141.43 -20.93 3.00e+00 1.11e-01 4.87e+01 angle pdb=" PB GTP b1500 " pdb=" O3B GTP b1500 " pdb=" PG GTP b1500 " ideal model delta sigma weight residual 120.50 140.70 -20.20 3.00e+00 1.11e-01 4.53e+01 angle pdb=" PB GTP G1500 " pdb=" O3B GTP G1500 " pdb=" PG GTP G1500 " ideal model delta sigma weight residual 120.50 136.62 -16.12 3.00e+00 1.11e-01 2.89e+01 angle pdb=" PA GTP b1500 " pdb=" O3A GTP b1500 " pdb=" PB GTP b1500 " ideal model delta sigma weight residual 120.50 136.49 -15.99 3.00e+00 1.11e-01 2.84e+01 ... (remaining 19735 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.18: 8545 34.18 - 68.36: 221 68.36 - 102.55: 20 102.55 - 136.73: 4 136.73 - 170.91: 5 Dihedral angle restraints: 8795 sinusoidal: 3564 harmonic: 5231 Sorted by residual: dihedral pdb=" C8 GTP G1500 " pdb=" C1' GTP G1500 " pdb=" N9 GTP G1500 " pdb=" O4' GTP G1500 " ideal model delta sinusoidal sigma weight residual 104.59 -66.32 170.91 1 2.00e+01 2.50e-03 4.77e+01 dihedral pdb=" O3B GTP G1500 " pdb=" O3A GTP G1500 " pdb=" PB GTP G1500 " pdb=" PA GTP G1500 " ideal model delta sinusoidal sigma weight residual 291.08 129.67 161.41 1 2.00e+01 2.50e-03 4.67e+01 dihedral pdb=" C4' GTP b1500 " pdb=" C5' GTP b1500 " pdb=" O5' GTP b1500 " pdb=" PA GTP b1500 " ideal model delta sinusoidal sigma weight residual 260.87 103.67 157.20 1 2.00e+01 2.50e-03 4.61e+01 ... (remaining 8792 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1671 0.044 - 0.087: 305 0.087 - 0.131: 188 0.131 - 0.175: 67 0.175 - 0.219: 16 Chirality restraints: 2247 Sorted by residual: chirality pdb=" CA VAL b 91 " pdb=" N VAL b 91 " pdb=" C VAL b 91 " pdb=" CB VAL b 91 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CA ILE D1085 " pdb=" N ILE D1085 " pdb=" C ILE D1085 " pdb=" CB ILE D1085 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" C3' GTP G1500 " pdb=" C2' GTP G1500 " pdb=" C4' GTP G1500 " pdb=" O3' GTP G1500 " both_signs ideal model delta sigma weight residual False -2.47 -2.69 0.21 2.00e-01 2.50e+01 1.14e+00 ... (remaining 2244 not shown) Planarity restraints: 2532 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN D1036 " -0.014 2.00e-02 2.50e+03 2.93e-02 8.61e+00 pdb=" C ASN D1036 " 0.051 2.00e-02 2.50e+03 pdb=" O ASN D1036 " -0.019 2.00e-02 2.50e+03 pdb=" N GLU D1037 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS b 190 " -0.013 2.00e-02 2.50e+03 2.71e-02 7.32e+00 pdb=" C HIS b 190 " 0.047 2.00e-02 2.50e+03 pdb=" O HIS b 190 " -0.017 2.00e-02 2.50e+03 pdb=" N GLN b 191 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER b 25 " 0.011 2.00e-02 2.50e+03 2.24e-02 5.02e+00 pdb=" C SER b 25 " -0.039 2.00e-02 2.50e+03 pdb=" O SER b 25 " 0.015 2.00e-02 2.50e+03 pdb=" N ASP b 26 " 0.013 2.00e-02 2.50e+03 ... (remaining 2529 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1403 2.75 - 3.28: 14552 3.28 - 3.82: 23440 3.82 - 4.36: 28554 4.36 - 4.90: 48153 Nonbonded interactions: 116102 Sorted by model distance: nonbonded pdb=" OG1 THR G 30 " pdb="MG MG G1501 " model vdw 2.207 2.170 nonbonded pdb=" OD1 ASP D 134 " pdb=" NH2 ARG D 188 " model vdw 2.249 3.120 nonbonded pdb=" OE1 GLN b 15 " pdb=" O6 GTP b1500 " model vdw 2.394 3.040 nonbonded pdb=" O1B GTP G1500 " pdb="MG MG G1501 " model vdw 2.455 2.170 nonbonded pdb=" OD1 ASP b 31 " pdb=" O THR b 35 " model vdw 2.497 3.040 ... (remaining 116097 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 11.610 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 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: 0.010 Load rotamer database and sin/cos tables:7.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7141 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 : 0.006 0.071 14561 Z= 0.448 Angle : 0.908 20.929 19740 Z= 0.606 Chirality : 0.052 0.219 2247 Planarity : 0.003 0.029 2532 Dihedral : 15.893 170.910 5411 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 0.06 % Allowed : 8.82 % Favored : 91.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.87 (0.19), residues: 1795 helix: -0.38 (0.16), residues: 1047 sheet: -2.12 (0.40), residues: 130 loop : -2.42 (0.24), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 641 TYR 0.015 0.001 TYR D 196 PHE 0.012 0.001 PHE D 486 TRP 0.007 0.000 TRP b 101 HIS 0.008 0.000 HIS D 619 Details of bonding type rmsd/Z covalent geometry : bond 0.00611 / 0.45 (14561) covalent geometry : angle 0.90818 / 0.61 (19740) hydrogen bonds : bond 0.18671 / 12.35 ( 741) hydrogen bonds : angle 7.12648 / 5.06 ( 2157) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 479 time to evaluate : 0.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 510 LYS cc_start: 0.8243 (mmtt) cc_final: 0.8005 (mmmm) REVERT: D 165 PHE cc_start: 0.7219 (m-80) cc_final: 0.6990 (m-80) REVERT: D 565 ASP cc_start: 0.6939 (m-30) cc_final: 0.6665 (m-30) REVERT: D 736 LEU cc_start: 0.7216 (tp) cc_final: 0.6987 (tt) REVERT: D 892 GLU cc_start: 0.7356 (pm20) cc_final: 0.7095 (mp0) REVERT: D 1032 ASP cc_start: 0.6626 (p0) cc_final: 0.5926 (p0) REVERT: G 14 GLU cc_start: 0.7272 (mt-10) cc_final: 0.7060 (mt-10) REVERT: G 56 GLU cc_start: 0.7427 (tp30) cc_final: 0.7201 (tp30) REVERT: b 200 TYR cc_start: 0.8466 (m-80) cc_final: 0.8230 (m-80) REVERT: b 304 ASP cc_start: 0.8083 (t0) cc_final: 0.7813 (t70) outliers start: 1 outliers final: 1 residues processed: 479 average time/residue: 0.5234 time to fit residues: 273.5013 Evaluate side-chains 388 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 387 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 65 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.0770 chunk 124 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 62.8885 > 50:) chunk 103 optimal weight: 0.5980 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 0.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 444 GLN E 472 GLN D 83 ASN D 302 GLN D 521 GLN ** D 619 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 640 ASN D 704 GLN D 759 GLN D 792 GLN D 803 HIS D 941 HIS D1013 GLN D1081 ASN D1172 ASN G 26 ASN G 150 HIS G 155 GLN b 15 GLN b 43 GLN b 94 GLN ** b 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 256 ASN b 291 GLN b 292 GLN b 307 HIS ** b 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 335 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.147421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.130124 restraints weight = 17254.859| |-----------------------------------------------------------------------------| r_work (start): 0.3661 rms_B_bonded: 1.42 r_work: 0.3534 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3382 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.4212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14561 Z= 0.178 Angle : 0.659 10.370 19740 Z= 0.334 Chirality : 0.044 0.183 2247 Planarity : 0.005 0.038 2532 Dihedral : 9.554 163.862 1988 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 3.73 % Allowed : 15.06 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.20), residues: 1795 helix: 0.57 (0.16), residues: 1054 sheet: -1.05 (0.41), residues: 139 loop : -1.02 (0.27), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 386 TYR 0.024 0.003 TYR D 115 PHE 0.018 0.002 PHE b 367 TRP 0.013 0.002 TRP G 152 HIS 0.012 0.002 HIS D 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.18 (14561) covalent geometry : angle 0.65852 / 0.33 (19740) hydrogen bonds : bond 0.04799 / 3.09 ( 741) hydrogen bonds : angle 4.15610 / 2.97 ( 2157) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 401 time to evaluate : 0.491 Fit side-chains revert: symmetry clash REVERT: D 59 ARG cc_start: 0.7469 (tpt170) cc_final: 0.7040 (tpt170) REVERT: D 75 ASP cc_start: 0.7757 (m-30) cc_final: 0.7530 (m-30) REVERT: D 135 LEU cc_start: 0.7087 (tp) cc_final: 0.6765 (tp) REVERT: D 617 MET cc_start: 0.7961 (ttm) cc_final: 0.7752 (ttm) REVERT: D 847 GLN cc_start: 0.8017 (mp10) cc_final: 0.7782 (mp10) REVERT: D 892 GLU cc_start: 0.7503 (pm20) cc_final: 0.7294 (mp0) REVERT: D 986 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8609 (mp) REVERT: D 1092 ILE cc_start: 0.7634 (pt) cc_final: 0.7364 (mt) REVERT: D 1171 ARG cc_start: 0.8445 (tmm160) cc_final: 0.7956 (ttp-110) REVERT: G 25 ASP cc_start: 0.7902 (OUTLIER) cc_final: 0.7571 (p0) REVERT: G 175 ASP cc_start: 0.7632 (t0) cc_final: 0.7423 (t0) REVERT: b 1 MET cc_start: 0.5116 (mtt) cc_final: 0.4818 (mtt) REVERT: b 3 GLU cc_start: 0.7817 (mp0) cc_final: 0.7555 (mp0) REVERT: b 48 SER cc_start: 0.8071 (p) cc_final: 0.7827 (p) REVERT: b 73 MET cc_start: 0.8573 (mmp) cc_final: 0.8350 (mmp) REVERT: b 323 MET cc_start: 0.7275 (tpt) cc_final: 0.6661 (tpt) REVERT: b 327 ASP cc_start: 0.7388 (m-30) cc_final: 0.7182 (m-30) REVERT: b 375 GLN cc_start: 0.8002 (OUTLIER) cc_final: 0.7498 (pp30) REVERT: b 379 LYS cc_start: 0.8578 (mtpp) cc_final: 0.8365 (mtmt) REVERT: b 406 MET cc_start: 0.6105 (mmm) cc_final: 0.5783 (mmm) outliers start: 58 outliers final: 17 residues processed: 429 average time/residue: 0.5410 time to fit residues: 252.7724 Evaluate side-chains 388 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 368 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 449 LYS Chi-restraints excluded: chain E residue 470 THR Chi-restraints excluded: chain D residue 187 ASP Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain D residue 359 GLU Chi-restraints excluded: chain D residue 439 ASP Chi-restraints excluded: chain D residue 490 ILE Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 669 ARG Chi-restraints excluded: chain D residue 986 LEU Chi-restraints excluded: chain D residue 1149 ASP Chi-restraints excluded: chain G residue 25 ASP Chi-restraints excluded: chain G residue 119 THR Chi-restraints excluded: chain b residue 291 GLN Chi-restraints excluded: chain b residue 293 VAL Chi-restraints excluded: chain b residue 333 VAL Chi-restraints excluded: chain b residue 375 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 157 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 chunk 125 optimal weight: 0.9990 chunk 111 optimal weight: 0.9990 chunk 99 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 64 optimal weight: 0.1980 chunk 40 optimal weight: 1.9990 overall best weight: 1.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 472 GLN D 47 HIS D 124 HIS D 640 ASN D 792 GLN D1081 ASN G 57 HIS G 155 GLN b 52 ASN ** b 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 329 GLN b 332 ASN b 334 GLN b 335 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.139589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.121846 restraints weight = 17225.607| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 1.43 r_work: 0.3416 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3260 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.5160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 14561 Z= 0.218 Angle : 0.650 10.488 19740 Z= 0.330 Chirality : 0.045 0.202 2247 Planarity : 0.005 0.050 2532 Dihedral : 9.634 163.411 1986 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 4.31 % Allowed : 16.28 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.20), residues: 1795 helix: 0.87 (0.16), residues: 1066 sheet: -0.51 (0.41), residues: 143 loop : -0.66 (0.27), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 386 TYR 0.023 0.002 TYR b 425 PHE 0.028 0.002 PHE D 775 TRP 0.016 0.002 TRP b 101 HIS 0.009 0.002 HIS D 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00530 / 0.22 (14561) covalent geometry : angle 0.65000 / 0.33 (19740) hydrogen bonds : bond 0.05682 / 3.68 ( 741) hydrogen bonds : angle 4.11055 / 2.93 ( 2157) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 377 time to evaluate : 0.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 69 GLU cc_start: 0.6720 (mp0) cc_final: 0.6474 (mp0) REVERT: D 75 ASP cc_start: 0.7936 (m-30) cc_final: 0.7721 (m-30) REVERT: D 986 LEU cc_start: 0.8823 (OUTLIER) cc_final: 0.8606 (mp) REVERT: D 1120 ARG cc_start: 0.7544 (ptp90) cc_final: 0.7223 (ptt-90) REVERT: G 25 ASP cc_start: 0.7942 (OUTLIER) cc_final: 0.7627 (p0) REVERT: G 127 GLN cc_start: 0.8438 (OUTLIER) cc_final: 0.7382 (mp10) REVERT: b 323 MET cc_start: 0.7454 (tpt) cc_final: 0.6445 (tpt) REVERT: b 327 ASP cc_start: 0.7455 (m-30) cc_final: 0.7233 (m-30) REVERT: b 379 LYS cc_start: 0.8664 (mtpp) cc_final: 0.8407 (mtmt) outliers start: 67 outliers final: 28 residues processed: 410 average time/residue: 0.5676 time to fit residues: 253.1542 Evaluate side-chains 395 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 364 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 449 LYS Chi-restraints excluded: chain E residue 470 THR Chi-restraints excluded: chain E residue 479 SER Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 212 SER Chi-restraints excluded: chain D residue 488 THR Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 706 LEU Chi-restraints excluded: chain D residue 759 GLN Chi-restraints excluded: chain D residue 837 ASP Chi-restraints excluded: chain D residue 855 CYS Chi-restraints excluded: chain D residue 986 LEU Chi-restraints excluded: chain D residue 995 GLU Chi-restraints excluded: chain D residue 1043 LEU Chi-restraints excluded: chain D residue 1177 LEU Chi-restraints excluded: chain G residue 25 ASP Chi-restraints excluded: chain G residue 114 ARG Chi-restraints excluded: chain G residue 119 THR Chi-restraints excluded: chain G residue 127 GLN Chi-restraints excluded: chain b residue 53 GLU Chi-restraints excluded: chain b residue 66 VAL Chi-restraints excluded: chain b residue 95 SER Chi-restraints excluded: chain b residue 134 GLN Chi-restraints excluded: chain b residue 293 VAL Chi-restraints excluded: chain b residue 313 VAL Chi-restraints excluded: chain b residue 333 VAL Chi-restraints excluded: chain b residue 382 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 158 optimal weight: 0.9980 chunk 171 optimal weight: 0.8980 chunk 111 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 chunk 127 optimal weight: 1.9990 chunk 143 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 93 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 chunk 54 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 472 GLN D 574 HIS D 792 GLN D 827 GLN D1100 GLN D1172 ASN b 52 ASN ** b 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 191 GLN b 195 ASN b 329 GLN b 332 ASN b 334 GLN b 337 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.138729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.121058 restraints weight = 17110.417| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 1.43 r_work: 0.3403 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3247 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.5473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 14561 Z= 0.180 Angle : 0.591 10.100 19740 Z= 0.301 Chirality : 0.043 0.187 2247 Planarity : 0.005 0.042 2532 Dihedral : 9.514 162.507 1986 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 4.50 % Allowed : 17.12 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.20), residues: 1795 helix: 1.04 (0.16), residues: 1074 sheet: -0.21 (0.41), residues: 143 loop : -0.56 (0.27), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG b 309 TYR 0.019 0.002 TYR b 425 PHE 0.025 0.002 PHE D 775 TRP 0.015 0.002 TRP D 231 HIS 0.008 0.001 HIS D 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.18 (14561) covalent geometry : angle 0.59143 / 0.30 (19740) hydrogen bonds : bond 0.05061 / 3.27 ( 741) hydrogen bonds : angle 4.02473 / 2.89 ( 2157) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 366 time to evaluate : 0.462 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 451 LYS cc_start: 0.8202 (mttm) cc_final: 0.7969 (mtmm) REVERT: D 69 GLU cc_start: 0.6709 (mp0) cc_final: 0.6460 (mp0) REVERT: D 75 ASP cc_start: 0.7971 (m-30) cc_final: 0.7754 (m-30) REVERT: D 360 ARG cc_start: 0.7408 (tpp80) cc_final: 0.7178 (tpp80) REVERT: D 1150 GLU cc_start: 0.7585 (tm-30) cc_final: 0.7173 (tm-30) REVERT: D 1171 ARG cc_start: 0.8558 (OUTLIER) cc_final: 0.7623 (tmm-80) REVERT: G 25 ASP cc_start: 0.7944 (OUTLIER) cc_final: 0.7654 (p0) REVERT: G 76 TYR cc_start: 0.8124 (m-80) cc_final: 0.7882 (m-80) REVERT: G 127 GLN cc_start: 0.8425 (OUTLIER) cc_final: 0.7354 (mp10) REVERT: b 73 MET cc_start: 0.8887 (mmp) cc_final: 0.8591 (mmp) REVERT: b 147 MET cc_start: 0.8441 (OUTLIER) cc_final: 0.7918 (tpp) REVERT: b 323 MET cc_start: 0.7468 (tpt) cc_final: 0.6526 (tpt) REVERT: b 327 ASP cc_start: 0.7472 (m-30) cc_final: 0.7236 (m-30) REVERT: b 330 MET cc_start: 0.7979 (OUTLIER) cc_final: 0.7690 (mmm) REVERT: b 379 LYS cc_start: 0.8641 (mtpp) cc_final: 0.8401 (mtmt) outliers start: 70 outliers final: 34 residues processed: 397 average time/residue: 0.5692 time to fit residues: 245.8738 Evaluate side-chains 401 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 362 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 449 LYS Chi-restraints excluded: chain E residue 470 THR Chi-restraints excluded: chain E residue 479 SER Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 145 GLU Chi-restraints excluded: chain D residue 187 ASP Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 212 SER Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain D residue 443 VAL Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 573 SER Chi-restraints excluded: chain D residue 706 LEU Chi-restraints excluded: chain D residue 788 LYS Chi-restraints excluded: chain D residue 824 ARG Chi-restraints excluded: chain D residue 855 CYS Chi-restraints excluded: chain D residue 1043 LEU Chi-restraints excluded: chain D residue 1060 THR Chi-restraints excluded: chain D residue 1149 ASP Chi-restraints excluded: chain D residue 1171 ARG Chi-restraints excluded: chain G residue 17 LEU Chi-restraints excluded: chain G residue 25 ASP Chi-restraints excluded: chain G residue 114 ARG Chi-restraints excluded: chain G residue 119 THR Chi-restraints excluded: chain G residue 127 GLN Chi-restraints excluded: chain G residue 142 LEU Chi-restraints excluded: chain b residue 53 GLU Chi-restraints excluded: chain b residue 66 VAL Chi-restraints excluded: chain b residue 95 SER Chi-restraints excluded: chain b residue 147 MET Chi-restraints excluded: chain b residue 293 VAL Chi-restraints excluded: chain b residue 313 VAL Chi-restraints excluded: chain b residue 330 MET Chi-restraints excluded: chain b residue 333 VAL Chi-restraints excluded: chain b residue 371 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 126 optimal weight: 1.9990 chunk 142 optimal weight: 0.8980 chunk 90 optimal weight: 0.6980 chunk 131 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 80 optimal weight: 0.9980 chunk 122 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 133 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 472 GLN D 640 ASN D 792 GLN D1049 HIS b 52 ASN ** b 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 191 GLN b 195 ASN b 298 ASN b 329 GLN b 332 ASN b 334 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.136217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.118437 restraints weight = 17012.975| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 1.43 r_work: 0.3366 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3208 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.5831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 14561 Z= 0.257 Angle : 0.687 11.707 19740 Z= 0.347 Chirality : 0.047 0.245 2247 Planarity : 0.005 0.045 2532 Dihedral : 9.718 163.262 1986 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 4.18 % Allowed : 17.70 % Favored : 78.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.20), residues: 1795 helix: 0.87 (0.16), residues: 1075 sheet: -0.26 (0.40), residues: 145 loop : -0.47 (0.26), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 386 TYR 0.019 0.003 TYR b 425 PHE 0.026 0.002 PHE D 775 TRP 0.016 0.003 TRP D 231 HIS 0.008 0.002 HIS D 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00632 / 0.26 (14561) covalent geometry : angle 0.68682 / 0.35 (19740) hydrogen bonds : bond 0.06232 / 4.03 ( 741) hydrogen bonds : angle 4.25006 / 3.05 ( 2157) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 367 time to evaluate : 0.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 451 LYS cc_start: 0.8250 (mttm) cc_final: 0.7843 (mtmm) REVERT: D 69 GLU cc_start: 0.6757 (mp0) cc_final: 0.6539 (mp0) REVERT: D 128 ASP cc_start: 0.6870 (m-30) cc_final: 0.6639 (m-30) REVERT: D 653 GLN cc_start: 0.8332 (mm-40) cc_final: 0.8121 (tp40) REVERT: D 660 GLN cc_start: 0.8369 (tp40) cc_final: 0.8155 (tm-30) REVERT: D 1030 PHE cc_start: 0.8780 (t80) cc_final: 0.8572 (t80) REVERT: D 1083 LYS cc_start: 0.8093 (mmmt) cc_final: 0.7881 (mmtt) REVERT: G 25 ASP cc_start: 0.7970 (OUTLIER) cc_final: 0.7684 (p0) REVERT: G 76 TYR cc_start: 0.8087 (m-80) cc_final: 0.7763 (m-80) REVERT: G 127 GLN cc_start: 0.8404 (OUTLIER) cc_final: 0.7187 (mp10) REVERT: b 147 MET cc_start: 0.8532 (OUTLIER) cc_final: 0.8069 (tpp) REVERT: b 323 MET cc_start: 0.7463 (tpt) cc_final: 0.6479 (tpt) REVERT: b 327 ASP cc_start: 0.7480 (m-30) cc_final: 0.7243 (m-30) REVERT: b 330 MET cc_start: 0.7994 (OUTLIER) cc_final: 0.7759 (mmm) REVERT: b 394 PHE cc_start: 0.7052 (m-80) cc_final: 0.6814 (m-80) REVERT: b 414 ASN cc_start: 0.7288 (t0) cc_final: 0.6899 (t0) outliers start: 65 outliers final: 40 residues processed: 399 average time/residue: 0.5495 time to fit residues: 238.5122 Evaluate side-chains 403 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 359 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 449 LYS Chi-restraints excluded: chain E residue 470 THR Chi-restraints excluded: chain E residue 479 SER Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 145 GLU Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 212 SER Chi-restraints excluded: chain D residue 443 VAL Chi-restraints excluded: chain D residue 446 LYS Chi-restraints excluded: chain D residue 488 THR Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 529 ASP Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 573 SER Chi-restraints excluded: chain D residue 611 LEU Chi-restraints excluded: chain D residue 669 ARG Chi-restraints excluded: chain D residue 706 LEU Chi-restraints excluded: chain D residue 788 LYS Chi-restraints excluded: chain D residue 824 ARG Chi-restraints excluded: chain D residue 837 ASP Chi-restraints excluded: chain D residue 855 CYS Chi-restraints excluded: chain D residue 995 GLU Chi-restraints excluded: chain D residue 1043 LEU Chi-restraints excluded: chain D residue 1149 ASP Chi-restraints excluded: chain G residue 6 ILE Chi-restraints excluded: chain G residue 25 ASP Chi-restraints excluded: chain G residue 114 ARG Chi-restraints excluded: chain G residue 119 THR Chi-restraints excluded: chain G residue 127 GLN Chi-restraints excluded: chain G residue 144 LEU Chi-restraints excluded: chain b residue 53 GLU Chi-restraints excluded: chain b residue 66 VAL Chi-restraints excluded: chain b residue 95 SER Chi-restraints excluded: chain b residue 147 MET Chi-restraints excluded: chain b residue 293 VAL Chi-restraints excluded: chain b residue 313 VAL Chi-restraints excluded: chain b residue 330 MET Chi-restraints excluded: chain b residue 333 VAL Chi-restraints excluded: chain b residue 382 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 3 optimal weight: 0.5980 chunk 66 optimal weight: 0.8980 chunk 37 optimal weight: 0.0970 chunk 54 optimal weight: 1.9990 chunk 138 optimal weight: 0.9980 chunk 59 optimal weight: 0.0370 chunk 155 optimal weight: 1.9990 chunk 163 optimal weight: 0.0370 chunk 47 optimal weight: 0.6980 chunk 85 optimal weight: 0.7980 chunk 114 optimal weight: 0.3980 overall best weight: 0.2334 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 472 GLN D 640 ASN D 827 GLN D1131 GLN ** b 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 191 GLN b 329 GLN b 332 ASN b 334 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.140701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.123292 restraints weight = 17164.919| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 1.41 r_work: 0.3442 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3290 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.5665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 14561 Z= 0.100 Angle : 0.493 8.360 19740 Z= 0.249 Chirality : 0.038 0.134 2247 Planarity : 0.004 0.045 2532 Dihedral : 9.262 162.256 1986 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 3.02 % Allowed : 19.18 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.21), residues: 1795 helix: 1.54 (0.16), residues: 1067 sheet: -0.03 (0.41), residues: 150 loop : -0.23 (0.27), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 916 TYR 0.014 0.001 TYR b 425 PHE 0.017 0.001 PHE D 552 TRP 0.016 0.001 TRP D 231 HIS 0.005 0.001 HIS D 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00216 / 0.10 (14561) covalent geometry : angle 0.49306 / 0.25 (19740) hydrogen bonds : bond 0.03614 / 2.32 ( 741) hydrogen bonds : angle 3.75502 / 2.68 ( 2157) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 360 time to evaluate : 0.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 451 LYS cc_start: 0.8187 (mttm) cc_final: 0.7968 (mtmm) REVERT: D 75 ASP cc_start: 0.7971 (m-30) cc_final: 0.7757 (m-30) REVERT: D 563 MET cc_start: 0.8780 (mtp) cc_final: 0.8526 (mtm) REVERT: D 656 LYS cc_start: 0.8550 (mtpt) cc_final: 0.8228 (ttmm) REVERT: D 876 MET cc_start: 0.8854 (mtm) cc_final: 0.8575 (mtm) REVERT: D 888 ARG cc_start: 0.7293 (mtm-85) cc_final: 0.6989 (mtt180) REVERT: D 1083 LYS cc_start: 0.8052 (mmmt) cc_final: 0.7609 (mmtt) REVERT: D 1120 ARG cc_start: 0.7436 (ptt90) cc_final: 0.6988 (ptt90) REVERT: G 76 TYR cc_start: 0.7978 (m-80) cc_final: 0.7729 (m-80) REVERT: b 73 MET cc_start: 0.8988 (mmp) cc_final: 0.8552 (mmp) REVERT: b 147 MET cc_start: 0.8333 (OUTLIER) cc_final: 0.7761 (tpp) REVERT: b 323 MET cc_start: 0.7413 (tpt) cc_final: 0.6535 (tpt) REVERT: b 379 LYS cc_start: 0.8600 (OUTLIER) cc_final: 0.8386 (mtmt) outliers start: 47 outliers final: 20 residues processed: 381 average time/residue: 0.6021 time to fit residues: 248.8171 Evaluate side-chains 383 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 361 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 470 THR Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 145 GLU Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 443 VAL Chi-restraints excluded: chain D residue 446 LYS Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 669 ARG Chi-restraints excluded: chain D residue 788 LYS Chi-restraints excluded: chain D residue 855 CYS Chi-restraints excluded: chain D residue 995 GLU Chi-restraints excluded: chain G residue 123 PHE Chi-restraints excluded: chain b residue 66 VAL Chi-restraints excluded: chain b residue 147 MET Chi-restraints excluded: chain b residue 293 VAL Chi-restraints excluded: chain b residue 313 VAL Chi-restraints excluded: chain b residue 331 LEU Chi-restraints excluded: chain b residue 333 VAL Chi-restraints excluded: chain b residue 379 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 98 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 127 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 146 optimal weight: 2.9990 chunk 35 optimal weight: 0.0050 chunk 149 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 chunk 107 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 overall best weight: 0.7596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 472 GLN D 640 ASN D 792 GLN D 897 HIS b 52 ASN ** b 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 165 ASN b 191 GLN b 329 GLN b 332 ASN b 334 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.138079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.120442 restraints weight = 16966.874| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 1.39 r_work: 0.3394 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3239 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.5846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 14561 Z= 0.167 Angle : 0.578 11.122 19740 Z= 0.291 Chirality : 0.042 0.197 2247 Planarity : 0.005 0.045 2532 Dihedral : 9.418 162.689 1986 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 3.47 % Allowed : 18.60 % Favored : 77.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.19 (0.20), residues: 1795 helix: 1.46 (0.16), residues: 1071 sheet: 0.13 (0.41), residues: 143 loop : -0.18 (0.27), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 150 TYR 0.021 0.002 TYR b 425 PHE 0.021 0.002 PHE D 775 TRP 0.014 0.002 TRP D 231 HIS 0.004 0.001 HIS D 897 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.17 (14561) covalent geometry : angle 0.57804 / 0.29 (19740) hydrogen bonds : bond 0.04913 / 3.17 ( 741) hydrogen bonds : angle 3.95106 / 2.83 ( 2157) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 350 time to evaluate : 0.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 451 LYS cc_start: 0.8236 (mttm) cc_final: 0.7987 (mtmm) REVERT: D 43 LEU cc_start: 0.6435 (OUTLIER) cc_final: 0.6067 (mp) REVERT: D 502 ARG cc_start: 0.8463 (OUTLIER) cc_final: 0.8088 (ttt90) REVERT: D 563 MET cc_start: 0.8839 (mtp) cc_final: 0.8598 (mtm) REVERT: D 1083 LYS cc_start: 0.8076 (mmmt) cc_final: 0.7668 (mmtt) REVERT: D 1120 ARG cc_start: 0.7480 (ptt90) cc_final: 0.6875 (ptt90) REVERT: G 25 ASP cc_start: 0.7938 (OUTLIER) cc_final: 0.7668 (p0) REVERT: G 76 TYR cc_start: 0.8059 (m-80) cc_final: 0.7764 (m-80) REVERT: G 127 GLN cc_start: 0.8421 (OUTLIER) cc_final: 0.7357 (mp10) REVERT: b 147 MET cc_start: 0.8472 (OUTLIER) cc_final: 0.7962 (tpp) REVERT: b 195 ASN cc_start: 0.8094 (m-40) cc_final: 0.7850 (m110) REVERT: b 323 MET cc_start: 0.7401 (tpt) cc_final: 0.6729 (tpt) REVERT: b 377 LEU cc_start: 0.8758 (tp) cc_final: 0.8554 (mt) REVERT: b 379 LYS cc_start: 0.8700 (OUTLIER) cc_final: 0.8408 (mtmt) outliers start: 54 outliers final: 33 residues processed: 376 average time/residue: 0.5557 time to fit residues: 226.1576 Evaluate side-chains 391 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 352 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 449 LYS Chi-restraints excluded: chain E residue 470 THR Chi-restraints excluded: chain D residue 43 LEU Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 212 SER Chi-restraints excluded: chain D residue 438 VAL Chi-restraints excluded: chain D residue 443 VAL Chi-restraints excluded: chain D residue 446 LYS Chi-restraints excluded: chain D residue 488 THR Chi-restraints excluded: chain D residue 495 VAL Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 502 ARG Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 573 SER Chi-restraints excluded: chain D residue 669 ARG Chi-restraints excluded: chain D residue 706 LEU Chi-restraints excluded: chain D residue 788 LYS Chi-restraints excluded: chain D residue 824 ARG Chi-restraints excluded: chain D residue 837 ASP Chi-restraints excluded: chain D residue 855 CYS Chi-restraints excluded: chain D residue 861 THR Chi-restraints excluded: chain D residue 995 GLU Chi-restraints excluded: chain D residue 1043 LEU Chi-restraints excluded: chain G residue 25 ASP Chi-restraints excluded: chain G residue 114 ARG Chi-restraints excluded: chain G residue 123 PHE Chi-restraints excluded: chain G residue 127 GLN Chi-restraints excluded: chain G residue 144 LEU Chi-restraints excluded: chain G residue 163 GLU Chi-restraints excluded: chain b residue 31 ASP Chi-restraints excluded: chain b residue 66 VAL Chi-restraints excluded: chain b residue 147 MET Chi-restraints excluded: chain b residue 293 VAL Chi-restraints excluded: chain b residue 313 VAL Chi-restraints excluded: chain b residue 333 VAL Chi-restraints excluded: chain b residue 379 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 75 optimal weight: 1.9990 chunk 132 optimal weight: 0.0970 chunk 162 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 147 optimal weight: 0.8980 chunk 47 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 chunk 55 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 169 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 472 GLN D 646 HIS D 792 GLN D1028 GLN b 52 ASN ** b 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 191 GLN b 329 GLN b 332 ASN b 334 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.138054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.120482 restraints weight = 17101.251| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 1.39 r_work: 0.3397 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3242 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.5901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 14561 Z= 0.163 Angle : 0.579 11.229 19740 Z= 0.293 Chirality : 0.042 0.183 2247 Planarity : 0.005 0.047 2532 Dihedral : 9.456 162.519 1986 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.41 % Allowed : 18.60 % Favored : 77.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.20), residues: 1795 helix: 1.46 (0.16), residues: 1071 sheet: 0.14 (0.41), residues: 143 loop : -0.12 (0.27), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 150 TYR 0.019 0.002 TYR b 425 PHE 0.022 0.002 PHE D 775 TRP 0.016 0.002 TRP D 231 HIS 0.003 0.001 HIS b 396 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.16 (14561) covalent geometry : angle 0.57943 / 0.29 (19740) hydrogen bonds : bond 0.04833 / 3.12 ( 741) hydrogen bonds : angle 3.96786 / 2.85 ( 2157) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 347 time to evaluate : 0.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 451 LYS cc_start: 0.8248 (mttm) cc_final: 0.7993 (mtmm) REVERT: D 43 LEU cc_start: 0.6427 (OUTLIER) cc_final: 0.6076 (mp) REVERT: D 502 ARG cc_start: 0.8473 (OUTLIER) cc_final: 0.8106 (ttt90) REVERT: D 563 MET cc_start: 0.8842 (mtp) cc_final: 0.8610 (mtm) REVERT: D 665 ARG cc_start: 0.7864 (OUTLIER) cc_final: 0.7099 (mtm180) REVERT: D 1083 LYS cc_start: 0.8076 (mmmt) cc_final: 0.7663 (mmtt) REVERT: D 1120 ARG cc_start: 0.7474 (ptt90) cc_final: 0.6829 (ptt90) REVERT: G 25 ASP cc_start: 0.7950 (OUTLIER) cc_final: 0.7682 (p0) REVERT: G 73 LEU cc_start: 0.8164 (mt) cc_final: 0.7928 (mp) REVERT: G 76 TYR cc_start: 0.8030 (m-80) cc_final: 0.7772 (m-80) REVERT: G 127 GLN cc_start: 0.8424 (OUTLIER) cc_final: 0.7359 (mp10) REVERT: b 1 MET cc_start: 0.5845 (mtp) cc_final: 0.5639 (mtp) REVERT: b 147 MET cc_start: 0.8467 (OUTLIER) cc_final: 0.7963 (tpp) REVERT: b 183 TYR cc_start: 0.6364 (OUTLIER) cc_final: 0.6070 (m-10) REVERT: b 195 ASN cc_start: 0.8134 (m-40) cc_final: 0.7858 (m110) REVERT: b 323 MET cc_start: 0.7350 (tpt) cc_final: 0.6898 (tpt) REVERT: b 379 LYS cc_start: 0.8707 (OUTLIER) cc_final: 0.8420 (mtmt) outliers start: 53 outliers final: 33 residues processed: 374 average time/residue: 0.5964 time to fit residues: 242.3268 Evaluate side-chains 387 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 346 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 449 LYS Chi-restraints excluded: chain E residue 470 THR Chi-restraints excluded: chain D residue 43 LEU Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 145 GLU Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 212 SER Chi-restraints excluded: chain D residue 443 VAL Chi-restraints excluded: chain D residue 488 THR Chi-restraints excluded: chain D residue 495 VAL Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 502 ARG Chi-restraints excluded: chain D residue 529 ASP Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 573 SER Chi-restraints excluded: chain D residue 665 ARG Chi-restraints excluded: chain D residue 669 ARG Chi-restraints excluded: chain D residue 706 LEU Chi-restraints excluded: chain D residue 788 LYS Chi-restraints excluded: chain D residue 824 ARG Chi-restraints excluded: chain D residue 837 ASP Chi-restraints excluded: chain D residue 855 CYS Chi-restraints excluded: chain D residue 861 THR Chi-restraints excluded: chain D residue 995 GLU Chi-restraints excluded: chain D residue 1043 LEU Chi-restraints excluded: chain G residue 25 ASP Chi-restraints excluded: chain G residue 114 ARG Chi-restraints excluded: chain G residue 123 PHE Chi-restraints excluded: chain G residue 127 GLN Chi-restraints excluded: chain G residue 144 LEU Chi-restraints excluded: chain b residue 66 VAL Chi-restraints excluded: chain b residue 147 MET Chi-restraints excluded: chain b residue 183 TYR Chi-restraints excluded: chain b residue 257 MET Chi-restraints excluded: chain b residue 293 VAL Chi-restraints excluded: chain b residue 313 VAL Chi-restraints excluded: chain b residue 333 VAL Chi-restraints excluded: chain b residue 379 LYS Chi-restraints excluded: chain b residue 382 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 7 optimal weight: 0.8980 chunk 165 optimal weight: 0.9990 chunk 43 optimal weight: 0.5980 chunk 149 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 159 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 173 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 472 GLN D 792 GLN b 52 ASN ** b 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 191 GLN b 329 GLN b 332 ASN b 334 GLN ** b 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.137579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.119854 restraints weight = 17083.057| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 1.41 r_work: 0.3385 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3227 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.5978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 14561 Z= 0.179 Angle : 0.595 12.064 19740 Z= 0.301 Chirality : 0.043 0.210 2247 Planarity : 0.005 0.047 2532 Dihedral : 9.510 162.321 1986 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 3.60 % Allowed : 18.92 % Favored : 77.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.19 (0.20), residues: 1795 helix: 1.40 (0.16), residues: 1072 sheet: 0.18 (0.41), residues: 143 loop : -0.06 (0.27), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 150 TYR 0.019 0.002 TYR b 425 PHE 0.022 0.002 PHE D 775 TRP 0.016 0.002 TRP D 231 HIS 0.004 0.001 HIS D 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.18 (14561) covalent geometry : angle 0.59469 / 0.30 (19740) hydrogen bonds : bond 0.05114 / 3.31 ( 741) hydrogen bonds : angle 4.02906 / 2.90 ( 2157) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 344 time to evaluate : 0.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 451 LYS cc_start: 0.8256 (mttm) cc_final: 0.8004 (mtmm) REVERT: D 502 ARG cc_start: 0.8492 (OUTLIER) cc_final: 0.8125 (ttt90) REVERT: D 563 MET cc_start: 0.8861 (mtp) cc_final: 0.8648 (mtm) REVERT: D 653 GLN cc_start: 0.8360 (mm-40) cc_final: 0.8124 (tp40) REVERT: D 665 ARG cc_start: 0.7884 (OUTLIER) cc_final: 0.7113 (mtm180) REVERT: D 1083 LYS cc_start: 0.8086 (mmmt) cc_final: 0.7665 (mmtt) REVERT: D 1120 ARG cc_start: 0.7489 (ptt90) cc_final: 0.6904 (ptt90) REVERT: G 25 ASP cc_start: 0.7946 (OUTLIER) cc_final: 0.7676 (p0) REVERT: G 76 TYR cc_start: 0.8049 (m-80) cc_final: 0.7805 (m-80) REVERT: G 127 GLN cc_start: 0.8438 (OUTLIER) cc_final: 0.7349 (mp10) REVERT: b 1 MET cc_start: 0.5961 (mtp) cc_final: 0.5757 (mtp) REVERT: b 147 MET cc_start: 0.8540 (OUTLIER) cc_final: 0.8062 (tpp) REVERT: b 183 TYR cc_start: 0.6370 (OUTLIER) cc_final: 0.6072 (m-10) REVERT: b 323 MET cc_start: 0.7357 (tpt) cc_final: 0.6863 (tpt) REVERT: b 330 MET cc_start: 0.7939 (OUTLIER) cc_final: 0.7610 (mmm) REVERT: b 379 LYS cc_start: 0.8706 (OUTLIER) cc_final: 0.8413 (mtpp) REVERT: b 406 MET cc_start: 0.5982 (mmm) cc_final: 0.5585 (tmm) outliers start: 56 outliers final: 40 residues processed: 372 average time/residue: 0.5784 time to fit residues: 233.9575 Evaluate side-chains 386 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 338 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 449 LYS Chi-restraints excluded: chain E residue 470 THR Chi-restraints excluded: chain E residue 492 SER Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 145 GLU Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 212 SER Chi-restraints excluded: chain D residue 438 VAL Chi-restraints excluded: chain D residue 443 VAL Chi-restraints excluded: chain D residue 488 THR Chi-restraints excluded: chain D residue 495 VAL Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 502 ARG Chi-restraints excluded: chain D residue 529 ASP Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 573 SER Chi-restraints excluded: chain D residue 665 ARG Chi-restraints excluded: chain D residue 669 ARG Chi-restraints excluded: chain D residue 706 LEU Chi-restraints excluded: chain D residue 788 LYS Chi-restraints excluded: chain D residue 824 ARG Chi-restraints excluded: chain D residue 837 ASP Chi-restraints excluded: chain D residue 855 CYS Chi-restraints excluded: chain D residue 861 THR Chi-restraints excluded: chain D residue 995 GLU Chi-restraints excluded: chain D residue 1043 LEU Chi-restraints excluded: chain G residue 25 ASP Chi-restraints excluded: chain G residue 114 ARG Chi-restraints excluded: chain G residue 123 PHE Chi-restraints excluded: chain G residue 127 GLN Chi-restraints excluded: chain G residue 144 LEU Chi-restraints excluded: chain b residue 31 ASP Chi-restraints excluded: chain b residue 66 VAL Chi-restraints excluded: chain b residue 147 MET Chi-restraints excluded: chain b residue 183 TYR Chi-restraints excluded: chain b residue 230 SER Chi-restraints excluded: chain b residue 257 MET Chi-restraints excluded: chain b residue 267 MET Chi-restraints excluded: chain b residue 293 VAL Chi-restraints excluded: chain b residue 313 VAL Chi-restraints excluded: chain b residue 330 MET Chi-restraints excluded: chain b residue 333 VAL Chi-restraints excluded: chain b residue 379 LYS Chi-restraints excluded: chain b residue 382 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 132 optimal weight: 0.0000 chunk 140 optimal weight: 1.9990 chunk 142 optimal weight: 0.0970 chunk 52 optimal weight: 0.8980 chunk 130 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 115 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 7 optimal weight: 0.5980 chunk 105 optimal weight: 0.8980 chunk 73 optimal weight: 0.7980 overall best weight: 0.4782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 472 GLN D 792 GLN b 52 ASN ** b 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 191 GLN b 329 GLN b 332 ASN b 334 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.139124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.121404 restraints weight = 17057.022| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 1.43 r_work: 0.3409 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3253 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.5919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14561 Z= 0.127 Angle : 0.540 11.648 19740 Z= 0.272 Chirality : 0.040 0.181 2247 Planarity : 0.004 0.048 2532 Dihedral : 9.353 162.420 1986 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.96 % Allowed : 19.88 % Favored : 77.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.51 (0.21), residues: 1795 helix: 1.69 (0.16), residues: 1061 sheet: 0.32 (0.42), residues: 142 loop : 0.03 (0.27), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 150 TYR 0.016 0.002 TYR b 425 PHE 0.018 0.001 PHE D 775 TRP 0.017 0.002 TRP D 231 HIS 0.004 0.001 HIS D 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (14561) covalent geometry : angle 0.54032 / 0.27 (19740) hydrogen bonds : bond 0.04221 / 2.71 ( 741) hydrogen bonds : angle 3.86879 / 2.78 ( 2157) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 345 time to evaluate : 0.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 451 LYS cc_start: 0.8230 (mttm) cc_final: 0.7989 (mtmm) REVERT: D 59 ARG cc_start: 0.7474 (tpt170) cc_final: 0.7171 (tpt170) REVERT: D 502 ARG cc_start: 0.8459 (OUTLIER) cc_final: 0.8112 (ttt90) REVERT: D 563 MET cc_start: 0.8822 (mtp) cc_final: 0.8622 (mtm) REVERT: D 653 GLN cc_start: 0.8364 (mm-40) cc_final: 0.8118 (tp40) REVERT: D 665 ARG cc_start: 0.7874 (OUTLIER) cc_final: 0.7100 (mtm180) REVERT: D 1083 LYS cc_start: 0.8063 (mmmt) cc_final: 0.7846 (mmtt) REVERT: G 76 TYR cc_start: 0.7998 (m-80) cc_final: 0.7761 (m-80) REVERT: b 73 MET cc_start: 0.8994 (mmp) cc_final: 0.8716 (mmp) REVERT: b 147 MET cc_start: 0.8478 (OUTLIER) cc_final: 0.7957 (tpp) REVERT: b 183 TYR cc_start: 0.6378 (OUTLIER) cc_final: 0.6102 (m-10) REVERT: b 323 MET cc_start: 0.7360 (tpt) cc_final: 0.6873 (tpt) REVERT: b 379 LYS cc_start: 0.8699 (OUTLIER) cc_final: 0.8410 (mtmt) REVERT: b 388 MET cc_start: 0.7489 (mtm) cc_final: 0.7157 (mtt) REVERT: b 406 MET cc_start: 0.5978 (mmm) cc_final: 0.5574 (tmm) outliers start: 46 outliers final: 31 residues processed: 367 average time/residue: 0.5930 time to fit residues: 236.3193 Evaluate side-chains 384 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 348 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 463 LYS Chi-restraints excluded: chain E residue 470 THR Chi-restraints excluded: chain E residue 492 SER Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 438 VAL Chi-restraints excluded: chain D residue 443 VAL Chi-restraints excluded: chain D residue 495 VAL Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 502 ARG Chi-restraints excluded: chain D residue 529 ASP Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 665 ARG Chi-restraints excluded: chain D residue 669 ARG Chi-restraints excluded: chain D residue 706 LEU Chi-restraints excluded: chain D residue 788 LYS Chi-restraints excluded: chain D residue 824 ARG Chi-restraints excluded: chain D residue 837 ASP Chi-restraints excluded: chain D residue 855 CYS Chi-restraints excluded: chain D residue 1043 LEU Chi-restraints excluded: chain G residue 114 ARG Chi-restraints excluded: chain G residue 123 PHE Chi-restraints excluded: chain G residue 144 LEU Chi-restraints excluded: chain b residue 31 ASP Chi-restraints excluded: chain b residue 66 VAL Chi-restraints excluded: chain b residue 147 MET Chi-restraints excluded: chain b residue 183 TYR Chi-restraints excluded: chain b residue 230 SER Chi-restraints excluded: chain b residue 257 MET Chi-restraints excluded: chain b residue 293 VAL Chi-restraints excluded: chain b residue 313 VAL Chi-restraints excluded: chain b residue 333 VAL Chi-restraints excluded: chain b residue 379 LYS Chi-restraints excluded: chain b residue 382 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 98 optimal weight: 0.9980 chunk 57 optimal weight: 0.2980 chunk 33 optimal weight: 1.9990 chunk 28 optimal weight: 0.0970 chunk 153 optimal weight: 0.8980 chunk 162 optimal weight: 0.8980 chunk 19 optimal weight: 0.4980 chunk 172 optimal weight: 1.9990 chunk 87 optimal weight: 0.5980 chunk 20 optimal weight: 0.9990 chunk 106 optimal weight: 0.0370 overall best weight: 0.3056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 472 GLN D 640 ASN D 792 GLN b 52 ASN ** b 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 191 GLN ** b 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 332 ASN b 334 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.140675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.122999 restraints weight = 17085.210| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 1.45 r_work: 0.3437 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3283 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.5859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 14561 Z= 0.105 Angle : 0.506 10.974 19740 Z= 0.254 Chirality : 0.039 0.165 2247 Planarity : 0.004 0.048 2532 Dihedral : 9.148 162.685 1986 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.57 % Allowed : 20.33 % Favored : 77.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.71 (0.21), residues: 1795 helix: 1.84 (0.16), residues: 1070 sheet: 0.25 (0.41), residues: 149 loop : 0.14 (0.28), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 150 TYR 0.014 0.001 TYR b 425 PHE 0.015 0.001 PHE D 552 TRP 0.016 0.001 TRP D 231 HIS 0.004 0.001 HIS D 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.10 (14561) covalent geometry : angle 0.50563 / 0.25 (19740) hydrogen bonds : bond 0.03668 / 2.35 ( 741) hydrogen bonds : angle 3.72462 / 2.67 ( 2157) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5926.38 seconds wall clock time: 101 minutes 10.11 seconds (6070.11 seconds total)