Starting phenix.real_space_refine on Thu Feb 5 20:17:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9m1n_63577/02_2026/9m1n_63577.cif Found real_map, /net/cci-nas-00/data/ceres_data/9m1n_63577/02_2026/9m1n_63577.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9m1n_63577/02_2026/9m1n_63577.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9m1n_63577/02_2026/9m1n_63577.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9m1n_63577/02_2026/9m1n_63577.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9m1n_63577/02_2026/9m1n_63577.map" } resolution = 2.24 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= 0.025 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: 8 Type Number sf(0) Gaussians Al 1 5.89 5 P 8 5.49 5 Mg 3 5.21 5 S 118 5.16 5 C 12340 2.51 5 N 3430 2.21 5 O 3682 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19585 Number of models: 1 Model: "" Number of chains: 9 Chain: "C" Number of atoms: 2347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2347 Classifications: {'peptide': 288} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 279} Chain breaks: 1 Chain: "D" Number of atoms: 8885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1133, 8885 Classifications: {'peptide': 1133} Link IDs: {'PCIS': 1, 'PTRANS': 46, 'TRANS': 1085} Chain breaks: 1 Chain: "G" Number of atoms: 1467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1467 Classifications: {'peptide': 184} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 180} Chain: "a" Number of atoms: 3416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3416 Classifications: {'peptide': 437} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 416} Chain: "b" Number of atoms: 3371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3371 Classifications: {'peptide': 430} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 409} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 5 Unusual residues: {' MG': 1, 'AF3': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "a" 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: 4.33, per 1000 atoms: 0.22 Number of scatterers: 19585 At special positions: 0 Unit cell: (150.493, 120.231, 160.307, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 118 16.00 P 8 15.00 Al 1 13.00 Mg 3 11.99 F 3 9.00 O 3682 8.00 N 3430 7.00 C 12340 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: 1.57 Conformation dependent library (CDL) restraints added in 853.9 milliseconds 4916 Ramachandran restraints generated. 2458 Oldfield, 0 Emsley, 2458 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4632 Finding SS restraints... Secondary structure from input PDB file: 124 helices and 9 sheets defined 60.3% alpha, 8.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.66 Creating SS restraints... Processing helix chain 'C' and resid 21 through 25 Processing helix chain 'C' and resid 26 through 51 removed outlier: 3.689A pdb=" N GLN C 30 " --> pdb=" O PRO C 26 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG C 32 " --> pdb=" O ARG C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 52 through 56 removed outlier: 3.772A pdb=" N ASN C 56 " --> pdb=" O GLU C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 77 Processing helix chain 'C' and resid 80 through 100 removed outlier: 3.660A pdb=" N LEU C 91 " --> pdb=" O ALA C 87 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N GLN C 92 " --> pdb=" O ALA C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 132 Processing helix chain 'C' and resid 197 through 201 Processing helix chain 'C' and resid 298 through 304 removed outlier: 3.546A pdb=" N GLU C 304 " --> pdb=" O ASP C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 307 No H-bonds generated for 'chain 'C' and resid 305 through 307' Processing helix chain 'C' and resid 337 through 341 removed outlier: 3.619A pdb=" N ARG C 341 " --> pdb=" O GLU C 338 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 41 removed outlier: 3.504A pdb=" N THR D 36 " --> pdb=" O GLU D 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 66 removed outlier: 3.963A pdb=" N LYS D 66 " --> pdb=" O VAL D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 75 Processing helix chain 'D' and resid 79 through 90 removed outlier: 3.697A pdb=" N ILE D 88 " --> pdb=" O LEU D 84 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL D 89 " --> pdb=" O LEU D 85 " (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 120 through 122 No H-bonds generated for 'chain 'D' and resid 120 through 122' Processing helix chain 'D' and resid 129 through 138 removed outlier: 3.658A pdb=" N LEU D 133 " --> pdb=" O VAL D 129 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 145 No H-bonds generated for 'chain 'D' and resid 143 through 145' Processing helix chain 'D' and resid 146 through 160 removed outlier: 3.661A pdb=" N ARG D 150 " --> pdb=" O ALA D 146 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU D 154 " --> pdb=" O ARG D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 172 removed outlier: 3.782A pdb=" N LEU D 170 " --> pdb=" O ASP D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 184 through 197 Processing helix chain 'D' and resid 202 through 215 removed outlier: 3.611A pdb=" N ALA D 206 " --> pdb=" O LYS D 202 " (cutoff:3.500A) Processing helix chain 'D' and resid 217 through 225 removed outlier: 3.570A pdb=" N GLN D 222 " --> pdb=" O PRO D 218 " (cutoff:3.500A) Processing helix chain 'D' and resid 225 through 238 Processing helix chain 'D' and resid 243 through 264 removed outlier: 3.589A pdb=" N VAL D 247 " --> pdb=" O THR D 243 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 283 removed outlier: 3.508A pdb=" N CYS D 269 " --> pdb=" O LYS D 265 " (cutoff:3.500A) Proline residue: D 271 - end of helix removed outlier: 4.550A pdb=" N ALA D 274 " --> pdb=" O LEU D 270 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N THR D 275 " --> pdb=" O PRO D 271 " (cutoff:3.500A) Processing helix chain 'D' and resid 284 through 288 removed outlier: 3.758A pdb=" N GLU D 287 " --> pdb=" O ARG D 284 " (cutoff:3.500A) Processing helix chain 'D' and resid 290 through 307 Processing helix chain 'D' and resid 356 through 370 removed outlier: 3.797A pdb=" N ARG D 360 " --> pdb=" O GLU D 356 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LYS D 370 " --> pdb=" O LEU D 366 " (cutoff:3.500A) Processing helix chain 'D' and resid 373 through 389 Processing helix chain 'D' and resid 394 through 405 removed outlier: 3.953A pdb=" N ASP D 398 " --> pdb=" O ALA D 394 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N VAL D 399 " --> pdb=" O LEU D 395 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL D 400 " --> pdb=" O ALA D 396 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N SER D 402 " --> pdb=" O ASP D 398 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ASP D 405 " --> pdb=" O GLY D 401 " (cutoff:3.500A) Processing helix chain 'D' and resid 406 through 408 No H-bonds generated for 'chain 'D' and resid 406 through 408' Processing helix chain 'D' and resid 412 through 429 removed outlier: 3.815A 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 448 removed outlier: 3.784A pdb=" N ALA D 442 " --> pdb=" O VAL D 438 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL D 443 " --> pdb=" O ASP D 439 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LYS D 446 " --> pdb=" O ALA D 442 " (cutoff:3.500A) Processing helix chain 'D' and resid 460 through 478 removed outlier: 3.679A pdb=" N ALA D 475 " --> pdb=" O CYS D 471 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N ARG D 476 " --> pdb=" O TRP D 472 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N TYR D 478 " --> pdb=" O PHE D 474 " (cutoff:3.500A) Processing helix chain 'D' and resid 483 through 485 No H-bonds generated for 'chain 'D' and resid 483 through 485' Processing helix chain 'D' and resid 486 through 501 removed outlier: 3.547A pdb=" N ASP D 501 " --> pdb=" O ALA D 497 " (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 537 through 540 Processing helix chain 'D' and resid 541 through 555 removed outlier: 4.662A pdb=" N ILE D 549 " --> pdb=" O CYS D 545 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N SER D 550 " --> pdb=" O PHE D 546 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N VAL D 551 " --> pdb=" O LEU D 547 " (cutoff:3.500A) Processing helix chain 'D' and resid 560 through 570 Processing helix chain 'D' and resid 571 through 574 Processing helix chain 'D' and resid 576 through 590 Processing helix chain 'D' and resid 594 through 601 Processing helix chain 'D' and resid 602 through 610 removed outlier: 3.670A pdb=" N MET D 609 " --> pdb=" O ARG D 605 " (cutoff:3.500A) Processing helix chain 'D' and resid 614 through 638 removed outlier: 3.602A pdb=" N GLN D 638 " --> pdb=" O LYS D 634 " (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 670 through 690 removed outlier: 3.745A pdb=" N LEU D 675 " --> pdb=" O LEU D 671 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N MET D 676 " --> pdb=" O GLY D 672 " (cutoff:3.500A) Processing helix chain 'D' and resid 697 through 713 removed outlier: 3.816A pdb=" N ASP D 701 " --> pdb=" O ASP D 697 " (cutoff:3.500A) Processing helix chain 'D' and resid 714 through 717 Processing helix chain 'D' and resid 718 through 720 No H-bonds generated for 'chain 'D' and resid 718 through 720' Processing helix chain 'D' and resid 721 through 737 removed outlier: 3.807A pdb=" N MET D 725 " --> pdb=" O SER D 721 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N SER D 731 " --> pdb=" O ASP D 727 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA D 732 " --> pdb=" O ALA D 728 " (cutoff:3.500A) Processing helix chain 'D' and resid 749 through 762 removed outlier: 3.506A pdb=" N THR D 758 " --> pdb=" O GLU D 754 " (cutoff:3.500A) Processing helix chain 'D' and resid 768 through 780 Processing helix chain 'D' and resid 790 through 802 removed outlier: 3.775A pdb=" N VAL D 794 " --> pdb=" O ARG D 790 " (cutoff:3.500A) Processing helix chain 'D' and resid 811 through 830 removed outlier: 3.900A pdb=" N ARG D 815 " --> pdb=" O PHE D 811 " (cutoff:3.500A) Processing helix chain 'D' and resid 844 through 855 removed outlier: 3.561A pdb=" N ILE D 848 " --> pdb=" O ASN D 844 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N CYS D 855 " --> pdb=" O ALA D 851 " (cutoff:3.500A) Processing helix chain 'D' and resid 867 through 888 removed outlier: 3.937A pdb=" N VAL D 871 " --> pdb=" O VAL D 867 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N MET D 876 " --> pdb=" O ARG D 872 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N LEU D 884 " --> pdb=" O MET D 880 " (cutoff:3.500A) Processing helix chain 'D' and resid 889 through 894 removed outlier: 6.068A pdb=" N GLU D 892 " --> pdb=" O SER D 889 " (cutoff:3.500A) Processing helix chain 'D' and resid 895 through 910 Processing helix chain 'D' and resid 914 through 930 Processing helix chain 'D' and resid 941 through 949 Processing helix chain 'D' and resid 965 through 970 Processing helix chain 'D' and resid 971 through 974 removed outlier: 3.526A pdb=" N GLY D 974 " --> pdb=" O GLN D 971 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 971 through 974' Processing helix chain 'D' and resid 975 through 991 removed outlier: 4.479A pdb=" N TYR D 980 " --> pdb=" O PRO D 976 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N HIS D 981 " --> pdb=" O THR D 977 " (cutoff:3.500A) Processing helix chain 'D' and resid 994 through 1014 removed outlier: 3.524A pdb=" N LYS D1010 " --> pdb=" O PHE D1006 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N GLY D1011 " --> pdb=" O GLU D1007 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ILE D1012 " --> pdb=" O TYR D1008 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N SER D1014 " --> pdb=" O LYS D1010 " (cutoff:3.500A) Processing helix chain 'D' and resid 1015 through 1020 Processing helix chain 'D' and resid 1021 through 1033 Processing helix chain 'D' and resid 1039 through 1054 Processing helix chain 'D' and resid 1065 through 1080 removed outlier: 3.537A pdb=" N ALA D1073 " --> pdb=" O VAL D1069 " (cutoff:3.500A) Processing helix chain 'D' and resid 1084 through 1099 removed outlier: 3.692A pdb=" N LEU D1088 " --> pdb=" O ASP D1084 " (cutoff:3.500A) Processing helix chain 'D' and resid 1103 through 1118 removed outlier: 3.548A pdb=" N ARG D1107 " --> pdb=" O GLY D1103 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N CYS D1118 " --> pdb=" O CYS D1114 " (cutoff:3.500A) Processing helix chain 'D' and resid 1121 through 1139 Processing helix chain 'D' and resid 1147 through 1158 Processing helix chain 'D' and resid 1163 through 1179 removed outlier: 3.558A pdb=" N VAL D1167 " --> pdb=" O GLU D1163 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N GLU D1169 " --> pdb=" O ALA D1165 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N GLN D1170 " --> pdb=" O VAL D1166 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 15 Processing helix chain 'G' and resid 28 through 38 Processing helix chain 'G' and resid 70 through 75 removed outlier: 4.477A pdb=" N SER G 75 " --> pdb=" O LYS G 71 " (cutoff:3.500A) Processing helix chain 'G' and resid 76 through 81 removed outlier: 3.598A pdb=" N PHE G 81 " --> pdb=" O ARG G 78 " (cutoff:3.500A) Processing helix chain 'G' and resid 98 through 109 Processing helix chain 'G' and resid 134 through 142 Processing helix chain 'G' and resid 165 through 179 removed outlier: 3.528A pdb=" N ILE G 169 " --> pdb=" O LEU G 165 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ARG G 179 " --> pdb=" O ASP G 175 " (cutoff:3.500A) Processing helix chain 'a' and resid 10 through 29 removed outlier: 3.553A pdb=" N ALA a 19 " --> pdb=" O GLN a 15 " (cutoff:3.500A) Processing helix chain 'a' and resid 48 through 52 removed outlier: 3.515A pdb=" N THR a 51 " --> pdb=" O SER a 48 " (cutoff:3.500A) Processing helix chain 'a' and resid 73 through 80 removed outlier: 3.563A pdb=" N GLU a 77 " --> pdb=" O THR a 73 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL a 78 " --> pdb=" O VAL a 74 " (cutoff:3.500A) Processing helix chain 'a' and resid 102 through 108 Processing helix chain 'a' and resid 114 through 128 removed outlier: 3.598A pdb=" N ALA a 126 " --> pdb=" O ILE a 122 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLN a 128 " --> pdb=" O LYS a 124 " (cutoff:3.500A) Processing helix chain 'a' and resid 143 through 161 removed outlier: 4.130A pdb=" N THR a 150 " --> pdb=" O GLY a 146 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N SER a 151 " --> pdb=" O SER a 147 " (cutoff:3.500A) Processing helix chain 'a' and resid 182 through 195 Processing helix chain 'a' and resid 205 through 216 Processing helix chain 'a' and resid 223 through 239 removed outlier: 3.731A pdb=" N GLN a 233 " --> pdb=" O ARG a 229 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE a 234 " --> pdb=" O LEU a 230 " (cutoff:3.500A) Processing helix chain 'a' and resid 251 through 260 removed outlier: 3.623A pdb=" N PHE a 255 " --> pdb=" O ASP a 251 " (cutoff:3.500A) Processing helix chain 'a' and resid 287 through 294 removed outlier: 3.592A pdb=" N ALA a 294 " --> pdb=" O GLU a 290 " (cutoff:3.500A) Processing helix chain 'a' and resid 295 through 297 No H-bonds generated for 'chain 'a' and resid 295 through 297' Processing helix chain 'a' and resid 324 through 339 Processing helix chain 'a' and resid 384 through 400 removed outlier: 3.939A pdb=" N TRP a 388 " --> pdb=" O ILE a 384 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LEU a 391 " --> pdb=" O ALA a 387 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU a 397 " --> pdb=" O HIS a 393 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N MET a 398 " --> pdb=" O LYS a 394 " (cutoff:3.500A) Processing helix chain 'a' and resid 405 through 410 Processing helix chain 'a' and resid 415 through 436 removed outlier: 4.036A pdb=" N SER a 419 " --> pdb=" O GLU a 415 " (cutoff:3.500A) Processing helix chain 'b' and resid 9 through 29 removed outlier: 3.509A pdb=" N GLY b 13 " --> pdb=" O ALA b 9 " (cutoff:3.500A) Processing helix chain 'b' and resid 41 through 46 removed outlier: 3.892A pdb=" N ARG b 46 " --> pdb=" O LEU b 42 " (cutoff:3.500A) Processing helix chain 'b' and resid 47 through 49 No H-bonds generated for 'chain 'b' and resid 47 through 49' Processing helix chain 'b' and resid 55 through 57 No H-bonds generated for 'chain 'b' and resid 55 through 57' Processing helix chain 'b' and resid 70 through 78 Processing helix chain 'b' and resid 81 through 85 removed outlier: 3.529A pdb=" N PHE b 85 " --> pdb=" O GLY b 82 " (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 107 through 126 removed outlier: 4.812A pdb=" N ASP b 114 " --> pdb=" O ALA b 110 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N SER b 115 " --> pdb=" O GLU b 111 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ARG b 121 " --> pdb=" O LEU b 117 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER b 126 " --> pdb=" O LYS b 122 " (cutoff:3.500A) Processing helix chain 'b' and resid 141 through 159 removed outlier: 3.995A pdb=" N GLY b 148 " --> pdb=" O GLY b 144 " (cutoff:3.500A) Processing helix chain 'b' and resid 180 through 193 removed outlier: 4.007A pdb=" N SER b 188 " --> pdb=" O ASN b 184 " (cutoff:3.500A) Processing helix chain 'b' and resid 203 through 213 removed outlier: 3.589A pdb=" N LEU b 207 " --> pdb=" O ASP b 203 " (cutoff:3.500A) Processing helix chain 'b' and resid 221 through 237 removed outlier: 3.822A pdb=" N ALA b 231 " --> pdb=" O HIS b 227 " (cutoff:3.500A) Processing helix chain 'b' and resid 237 through 242 removed outlier: 3.526A pdb=" N PHE b 242 " --> pdb=" O THR b 238 " (cutoff:3.500A) Processing helix chain 'b' and resid 249 through 258 Processing helix chain 'b' and resid 285 through 294 removed outlier: 3.785A 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 337 removed outlier: 3.521A pdb=" N VAL b 326 " --> pdb=" O SER b 322 " (cutoff:3.500A) 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: 3.936A pdb=" N PHE b 378 " --> pdb=" O ILE b 374 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ILE b 381 " --> pdb=" O LEU b 377 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLN b 384 " --> pdb=" O ARG b 380 " (cutoff:3.500A) Processing helix chain 'b' and resid 395 through 400 Processing helix chain 'b' and resid 404 through 427 removed outlier: 3.788A pdb=" N PHE b 408 " --> pdb=" O ASP b 404 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 187 through 190 removed outlier: 7.315A pdb=" N LEU C 211 " --> pdb=" O ASN C 188 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N GLU C 190 " --> pdb=" O LEU C 211 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLU C 210 " --> pdb=" O THR C 228 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N ALA C 230 " --> pdb=" O GLU C 210 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N SER C 212 " --> pdb=" O ALA C 230 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N CYS C 249 " --> pdb=" O LYS C 229 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N HIS C 231 " --> pdb=" O CYS C 249 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N ASP C 251 " --> pdb=" O HIS C 231 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N VAL C 244 " --> pdb=" O ARG C 262 " (cutoff:3.500A) removed outlier: 8.088A pdb=" N HIS C 264 " --> pdb=" O VAL C 244 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N LEU C 246 " --> pdb=" O HIS C 264 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N THR C 266 " --> pdb=" O LEU C 246 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N ASP C 248 " --> pdb=" O THR C 266 " (cutoff:3.500A) removed outlier: 10.332A pdb=" N ASP C 268 " --> pdb=" O ASP C 248 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N SER C 250 " --> pdb=" O ASP C 268 " (cutoff:3.500A) removed outlier: 8.338A pdb=" N ARG C 270 " --> pdb=" O SER C 250 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N CYS C 252 " --> pdb=" O ARG C 270 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N PHE C 272 " --> pdb=" O CYS C 252 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N LEU C 254 " --> pdb=" O PHE C 272 " (cutoff:3.500A) removed outlier: 11.958A pdb=" N ALA C 257 " --> pdb=" O THR C 276 " (cutoff:3.500A) removed outlier: 11.330A pdb=" N ARG C 278 " --> pdb=" O ALA C 257 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N GLN C 259 " --> pdb=" O ARG C 278 " (cutoff:3.500A) removed outlier: 8.240A pdb=" N ILE C 280 " --> pdb=" O GLN C 259 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N LEU C 261 " --> pdb=" O ILE C 280 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N GLU C 282 " --> pdb=" O LEU C 261 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ILE C 263 " --> pdb=" O GLU C 282 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N CYS C 284 " --> pdb=" O ILE C 263 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N SER C 265 " --> pdb=" O CYS C 284 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 215 through 218 removed outlier: 6.703A pdb=" N VAL C 216 " --> pdb=" O LEU C 236 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N CYS C 237 " --> pdb=" O ALA C 255 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N VAL C 244 " --> pdb=" O ARG C 262 " (cutoff:3.500A) removed outlier: 8.088A pdb=" N HIS C 264 " --> pdb=" O VAL C 244 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N LEU C 246 " --> pdb=" O HIS C 264 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N THR C 266 " --> pdb=" O LEU C 246 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N ASP C 248 " --> pdb=" O THR C 266 " (cutoff:3.500A) removed outlier: 10.332A pdb=" N ASP C 268 " --> pdb=" O ASP C 248 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N SER C 250 " --> pdb=" O ASP C 268 " (cutoff:3.500A) removed outlier: 8.338A pdb=" N ARG C 270 " --> pdb=" O SER C 250 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N CYS C 252 " --> pdb=" O ARG C 270 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N PHE C 272 " --> pdb=" O CYS C 252 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N LEU C 254 " --> pdb=" O PHE C 272 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLN C 288 " --> pdb=" O THR C 269 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 452 through 453 Processing sheet with id=AA4, first strand: chain 'D' and resid 861 through 862 Processing sheet with id=AA5, first strand: chain 'G' and resid 50 through 57 removed outlier: 3.584A pdb=" N ASN G 63 " --> pdb=" O LEU G 17 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N GLY G 23 " --> pdb=" O VAL G 67 " (cutoff:3.500A) removed outlier: 9.075A pdb=" N GLY G 86 " --> pdb=" O GLU G 16 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ARG G 18 " --> pdb=" O GLY G 86 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N ILE G 88 " --> pdb=" O ARG G 18 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N LEU G 20 " --> pdb=" O ILE G 88 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N VAL G 90 " --> pdb=" O LEU G 20 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N LEU G 22 " --> pdb=" O VAL G 90 " (cutoff:3.500A) removed outlier: 8.522A pdb=" N ASP G 92 " --> pdb=" O LEU G 22 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N GLN G 155 " --> pdb=" O LEU G 120 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N ILE G 122 " --> pdb=" O GLN G 155 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'a' and resid 92 through 94 removed outlier: 6.279A pdb=" N PHE a 67 " --> pdb=" O ILE a 93 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N VAL a 68 " --> pdb=" O SER a 6 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N HIS a 8 " --> pdb=" O VAL a 68 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N GLU a 3 " --> pdb=" O LEU a 132 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N GLY a 134 " --> pdb=" O GLU a 3 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ILE a 5 " --> pdb=" O GLY a 134 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU a 136 " --> pdb=" O ILE a 5 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'a' and resid 269 through 273 removed outlier: 4.115A pdb=" N ALA a 314 " --> pdb=" O ASN a 380 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'b' and resid 90 through 91 removed outlier: 8.641A pdb=" N VAL b 91 " --> pdb=" O ALA b 63 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N LEU b 65 " --> pdb=" O VAL b 91 " (cutoff:3.500A) removed outlier: 8.484A pdb=" N ILE b 64 " --> pdb=" O ILE b 4 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N HIS b 6 " --> pdb=" O ILE b 64 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N VAL b 66 " --> pdb=" O HIS b 6 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N GLN b 8 " --> pdb=" O VAL b 66 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N GLU b 3 " --> pdb=" O GLN b 131 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N PHE b 133 " --> pdb=" O GLU b 3 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N VAL b 5 " --> pdb=" O PHE b 133 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N LEU b 135 " --> pdb=" O VAL b 5 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ILE b 7 " --> pdb=" O LEU b 135 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ILE b 163 " --> pdb=" O GLN b 131 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N MET b 164 " --> pdb=" O GLU b 198 " (cutoff:3.500A) removed outlier: 8.386A pdb=" N TYR b 200 " --> pdb=" O MET b 164 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N THR b 166 " --> pdb=" O TYR b 200 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N THR b 199 " --> pdb=" O PHE b 266 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N VAL b 313 " --> pdb=" O LYS b 350 " (cutoff:3.500A) removed outlier: 8.180A pdb=" N ALA b 352 " --> pdb=" O VAL b 313 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ALA b 315 " --> pdb=" O ALA b 352 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N CYS b 354 " --> pdb=" O ALA b 315 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N PHE b 317 " --> pdb=" O CYS b 354 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'b' and resid 51 through 54 988 hydrogen bonds defined for protein. 2877 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: 3.70 Time building geometry restraints manager: 1.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3307 1.31 - 1.43: 5182 1.43 - 1.56: 11292 1.56 - 1.69: 15 1.69 - 1.82: 178 Bond restraints: 19974 Sorted by residual: bond pdb=" F2 AF3 G1501 " pdb="AL AF3 G1501 " ideal model delta sigma weight residual 1.637 1.795 -0.158 2.00e-02 2.50e+03 6.24e+01 bond pdb=" F1 AF3 G1501 " pdb="AL AF3 G1501 " ideal model delta sigma weight residual 1.637 1.784 -0.147 2.00e-02 2.50e+03 5.39e+01 bond pdb=" F3 AF3 G1501 " pdb="AL AF3 G1501 " ideal model delta sigma weight residual 1.637 1.772 -0.135 2.00e-02 2.50e+03 4.58e+01 bond pdb=" C HIS C 231 " pdb=" N SER C 232 " ideal model delta sigma weight residual 1.333 1.396 -0.064 1.29e-02 6.01e+03 2.43e+01 bond pdb=" C VAL D 499 " pdb=" O VAL D 499 " ideal model delta sigma weight residual 1.241 1.189 0.052 1.06e-02 8.90e+03 2.43e+01 ... (remaining 19969 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.82: 26763 3.82 - 7.63: 290 7.63 - 11.45: 24 11.45 - 15.26: 1 15.26 - 19.08: 2 Bond angle restraints: 27080 Sorted by residual: angle pdb=" PB GTP a1500 " pdb=" O3B GTP a1500 " pdb=" PG GTP a1500 " ideal model delta sigma weight residual 120.50 139.58 -19.08 3.00e+00 1.11e-01 4.04e+01 angle pdb=" PA GTP a1500 " pdb=" O3A GTP a1500 " pdb=" PB GTP a1500 " ideal model delta sigma weight residual 120.50 136.00 -15.50 3.00e+00 1.11e-01 2.67e+01 angle pdb=" C ALA D 315 " pdb=" N TRP D 316 " pdb=" CA TRP D 316 " ideal model delta sigma weight residual 122.56 114.06 8.50 1.72e+00 3.38e-01 2.44e+01 angle pdb=" C ALA b 97 " pdb=" N GLY b 98 " pdb=" CA GLY b 98 " ideal model delta sigma weight residual 120.11 127.52 -7.41 1.51e+00 4.39e-01 2.41e+01 angle pdb=" C SER a 170 " pdb=" N ILE a 171 " pdb=" CA ILE a 171 " ideal model delta sigma weight residual 123.10 129.59 -6.49 1.33e+00 5.65e-01 2.38e+01 ... (remaining 27075 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.29: 11804 35.29 - 70.57: 209 70.57 - 105.86: 15 105.86 - 141.14: 4 141.14 - 176.43: 6 Dihedral angle restraints: 12038 sinusoidal: 4875 harmonic: 7163 Sorted by residual: dihedral pdb=" C5' GTP a1500 " pdb=" O5' GTP a1500 " pdb=" PA GTP a1500 " pdb=" O3A GTP a1500 " ideal model delta sinusoidal sigma weight residual 69.27 -107.16 176.43 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" O2B GDP G1500 " pdb=" O3A GDP G1500 " pdb=" PB GDP G1500 " pdb=" PA GDP G1500 " ideal model delta sinusoidal sigma weight residual 180.00 18.68 161.32 1 2.00e+01 2.50e-03 4.67e+01 dihedral pdb=" C8 GTP a1500 " pdb=" C1' GTP a1500 " pdb=" N9 GTP a1500 " pdb=" O4' GTP a1500 " ideal model delta sinusoidal sigma weight residual 104.59 -56.41 161.01 1 2.00e+01 2.50e-03 4.67e+01 ... (remaining 12035 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 2099 0.048 - 0.095: 514 0.095 - 0.143: 310 0.143 - 0.191: 106 0.191 - 0.238: 16 Chirality restraints: 3045 Sorted by residual: chirality pdb=" CA ILE b 345 " pdb=" N ILE b 345 " pdb=" C ILE b 345 " pdb=" CB ILE b 345 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" CA ASP C 302 " pdb=" N ASP C 302 " pdb=" C ASP C 302 " pdb=" CB ASP C 302 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" CA VAL D 831 " pdb=" N VAL D 831 " pdb=" C VAL D 831 " pdb=" CB VAL D 831 " both_signs ideal model delta sigma weight residual False 2.44 2.67 -0.22 2.00e-01 2.50e+01 1.25e+00 ... (remaining 3042 not shown) Planarity restraints: 3502 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG D 266 " -0.021 2.00e-02 2.50e+03 4.44e-02 1.97e+01 pdb=" C ARG D 266 " 0.077 2.00e-02 2.50e+03 pdb=" O ARG D 266 " -0.029 2.00e-02 2.50e+03 pdb=" N GLU D 267 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL b 119 " -0.017 2.00e-02 2.50e+03 3.41e-02 1.16e+01 pdb=" C VAL b 119 " 0.059 2.00e-02 2.50e+03 pdb=" O VAL b 119 " -0.022 2.00e-02 2.50e+03 pdb=" N VAL b 120 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' GTP a1500 " 0.034 2.00e-02 2.50e+03 1.80e-02 9.67e+00 pdb=" C2 GTP a1500 " -0.008 2.00e-02 2.50e+03 pdb=" C4 GTP a1500 " -0.010 2.00e-02 2.50e+03 pdb=" C5 GTP a1500 " -0.022 2.00e-02 2.50e+03 pdb=" C6 GTP a1500 " -0.013 2.00e-02 2.50e+03 pdb=" C8 GTP a1500 " 0.008 2.00e-02 2.50e+03 pdb=" N1 GTP a1500 " 0.021 2.00e-02 2.50e+03 pdb=" N2 GTP a1500 " -0.003 2.00e-02 2.50e+03 pdb=" N3 GTP a1500 " -0.006 2.00e-02 2.50e+03 pdb=" N7 GTP a1500 " -0.016 2.00e-02 2.50e+03 pdb=" N9 GTP a1500 " -0.015 2.00e-02 2.50e+03 pdb=" O6 GTP a1500 " 0.030 2.00e-02 2.50e+03 ... (remaining 3499 not shown) Histogram of nonbonded interaction distances: 1.82 - 2.43: 4 2.43 - 3.05: 12233 3.05 - 3.67: 29151 3.67 - 4.28: 44448 4.28 - 4.90: 73402 Nonbonded interactions: 159238 Sorted by model distance: nonbonded pdb=" OG1 THR G 30 " pdb="MG MG G1502 " model vdw 1.818 2.170 nonbonded pdb=" O1B GTP b1500 " pdb="MG MG b1501 " model vdw 2.141 2.170 nonbonded pdb=" O2B GTP a1500 " pdb="MG MG a1501 " model vdw 2.206 2.170 nonbonded pdb=" O GLU a 183 " pdb=" OG SER a 187 " model vdw 2.322 3.040 nonbonded pdb=" O GLY b 141 " pdb=" OG SER b 145 " model vdw 2.443 3.040 ... (remaining 159233 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: 4.550 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: 0.030 Extract box with map and model: 0.330 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 18.460 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.030 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:7.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7013 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.158 19974 Z= 0.582 Angle : 1.059 19.079 27080 Z= 0.744 Chirality : 0.060 0.238 3045 Planarity : 0.004 0.072 3502 Dihedral : 14.510 176.428 7406 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 0.05 % Allowed : 6.61 % Favored : 93.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.06 % 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: -2.33 (0.16), residues: 2458 helix: -0.80 (0.14), residues: 1343 sheet: -2.83 (0.30), residues: 213 loop : -2.21 (0.19), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 712 TYR 0.032 0.001 TYR a 172 PHE 0.021 0.001 PHE D 785 TRP 0.013 0.001 TRP b 344 HIS 0.006 0.001 HIS a 61 Details of bonding type rmsd covalent geometry : bond 0.00798 (19974) covalent geometry : angle 1.05874 (27080) hydrogen bonds : bond 0.20548 ( 988) hydrogen bonds : angle 7.08806 ( 2877) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4916 Ramachandran restraints generated. 2458 Oldfield, 0 Emsley, 2458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4916 Ramachandran restraints generated. 2458 Oldfield, 0 Emsley, 2458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 660 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 659 time to evaluate : 0.779 Fit side-chains REVERT: C 34 GLN cc_start: 0.6274 (mt0) cc_final: 0.6018 (mt0) REVERT: C 92 GLN cc_start: 0.6646 (mt0) cc_final: 0.6419 (mt0) REVERT: D 194 GLU cc_start: 0.7343 (mt-10) cc_final: 0.6732 (mt-10) REVERT: D 304 LEU cc_start: 0.8487 (mt) cc_final: 0.8135 (mt) REVERT: D 425 GLU cc_start: 0.8017 (mm-30) cc_final: 0.7401 (mm-30) REVERT: D 516 GLU cc_start: 0.7950 (tp30) cc_final: 0.7005 (tp30) REVERT: D 724 GLN cc_start: 0.7429 (tt0) cc_final: 0.7113 (tt0) REVERT: D 1098 MET cc_start: 0.6318 (ttm) cc_final: 0.6106 (ttm) REVERT: D 1172 ASN cc_start: 0.6317 (m-40) cc_final: 0.6059 (m-40) REVERT: G 37 ASN cc_start: 0.6865 (t0) cc_final: 0.6634 (t0) REVERT: G 55 LEU cc_start: 0.8017 (pp) cc_final: 0.7755 (pp) REVERT: a 3 GLU cc_start: 0.5926 (pm20) cc_final: 0.5663 (pm20) REVERT: a 313 MET cc_start: 0.8355 (mtm) cc_final: 0.8084 (mtm) outliers start: 1 outliers final: 1 residues processed: 660 average time/residue: 0.6117 time to fit residues: 451.7920 Evaluate side-chains 550 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 549 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 33 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 216 optimal weight: 0.6980 chunk 98 optimal weight: 0.5980 chunk 194 optimal weight: 0.3980 chunk 227 optimal weight: 0.5980 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 2.9990 chunk 235 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 95 GLN C 112 GLN C 132 GLN C 223 ASN C 259 GLN D 90 GLN D 100 HIS D 505 ASN D 640 ASN D 657 GLN G 107 GLN a 15 GLN a 50 ASN a 91 GLN a 133 GLN a 139 HIS a 186 ASN a 249 ASN a 256 GLN a 293 ASN a 380 ASN b 28 HIS b 83 GLN b 99 ASN b 191 GLN b 226 ASN b 245 GLN b 335 ASN b 396 HIS b 414 ASN b 423 GLN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.158422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.140974 restraints weight = 22839.139| |-----------------------------------------------------------------------------| r_work (start): 0.3829 rms_B_bonded: 1.35 r_work: 0.3728 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3596 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.3028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 19974 Z= 0.168 Angle : 0.596 6.999 27080 Z= 0.303 Chirality : 0.042 0.239 3045 Planarity : 0.005 0.055 3502 Dihedral : 9.458 176.148 2736 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.74 % Allowed : 13.56 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.06 % 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: -0.26 (0.17), residues: 2458 helix: 0.77 (0.15), residues: 1333 sheet: -1.66 (0.31), residues: 228 loop : -1.11 (0.21), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG b 309 TYR 0.020 0.002 TYR D 107 PHE 0.019 0.002 PHE D 214 TRP 0.013 0.002 TRP D 80 HIS 0.007 0.001 HIS a 266 Details of bonding type rmsd covalent geometry : bond 0.00367 (19974) covalent geometry : angle 0.59570 (27080) hydrogen bonds : bond 0.04901 ( 988) hydrogen bonds : angle 3.91349 ( 2877) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4916 Ramachandran restraints generated. 2458 Oldfield, 0 Emsley, 2458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4916 Ramachandran restraints generated. 2458 Oldfield, 0 Emsley, 2458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 644 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 586 time to evaluate : 0.682 Fit side-chains revert: symmetry clash REVERT: C 34 GLN cc_start: 0.6417 (mt0) cc_final: 0.6175 (mt0) REVERT: D 425 GLU cc_start: 0.8183 (mm-30) cc_final: 0.7925 (mm-30) REVERT: D 516 GLU cc_start: 0.8231 (tp30) cc_final: 0.7762 (tp30) REVERT: D 843 GLU cc_start: 0.6971 (mp0) cc_final: 0.6622 (mp0) REVERT: D 884 LEU cc_start: 0.7549 (mt) cc_final: 0.7317 (mm) REVERT: G 53 LYS cc_start: 0.7906 (OUTLIER) cc_final: 0.7569 (ttmm) REVERT: G 55 LEU cc_start: 0.8184 (pp) cc_final: 0.7971 (pp) REVERT: G 105 GLU cc_start: 0.7795 (OUTLIER) cc_final: 0.7490 (mp0) REVERT: a 351 PHE cc_start: 0.7784 (m-80) cc_final: 0.7246 (m-80) REVERT: a 363 VAL cc_start: 0.7676 (m) cc_final: 0.7464 (t) REVERT: b 62 ARG cc_start: 0.7921 (ttm-80) cc_final: 0.7560 (ttm-80) REVERT: b 162 ARG cc_start: 0.8291 (OUTLIER) cc_final: 0.6110 (mpt-90) REVERT: b 379 LYS cc_start: 0.8136 (mtpt) cc_final: 0.7931 (mttt) outliers start: 58 outliers final: 17 residues processed: 612 average time/residue: 0.6827 time to fit residues: 465.7145 Evaluate side-chains 580 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 560 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 374 THR Chi-restraints excluded: chain D residue 404 LEU Chi-restraints excluded: chain D residue 465 ASP Chi-restraints excluded: chain D residue 520 ARG Chi-restraints excluded: chain D residue 610 THR Chi-restraints excluded: chain D residue 1152 VAL Chi-restraints excluded: chain G residue 53 LYS Chi-restraints excluded: chain G residue 75 SER Chi-restraints excluded: chain G residue 105 GLU Chi-restraints excluded: chain G residue 135 SER Chi-restraints excluded: chain a residue 3 GLU Chi-restraints excluded: chain a residue 9 VAL Chi-restraints excluded: chain a residue 66 VAL Chi-restraints excluded: chain a residue 78 VAL Chi-restraints excluded: chain a residue 170 SER Chi-restraints excluded: chain a residue 236 SER Chi-restraints excluded: chain a residue 277 SER Chi-restraints excluded: chain a residue 361 THR Chi-restraints excluded: chain b residue 35 THR Chi-restraints excluded: chain b residue 162 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 34 optimal weight: 1.9990 chunk 190 optimal weight: 0.5980 chunk 195 optimal weight: 2.9990 chunk 194 optimal weight: 0.8980 chunk 4 optimal weight: 0.6980 chunk 46 optimal weight: 0.5980 chunk 18 optimal weight: 0.5980 chunk 221 optimal weight: 0.9990 chunk 236 optimal weight: 0.0170 chunk 155 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 overall best weight: 0.5018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 112 GLN C 114 GLN C 203 GLN C 221 ASN C 223 ASN C 259 GLN D 90 GLN D 235 ASN D 263 HIS D 544 ASN D 588 HIS D 759 GLN D 920 HIS a 31 GLN a 61 HIS a 91 GLN a 206 ASN a 249 ASN ** a 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 11 GLN b 14 ASN b 134 GLN b 165 ASN b 384 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.153372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.136132 restraints weight = 22786.214| |-----------------------------------------------------------------------------| r_work (start): 0.3758 rms_B_bonded: 1.29 r_work: 0.3656 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3522 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.3895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19974 Z= 0.130 Angle : 0.524 6.716 27080 Z= 0.267 Chirality : 0.040 0.153 3045 Planarity : 0.004 0.041 3502 Dihedral : 9.291 177.730 2734 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.98 % Allowed : 15.82 % Favored : 81.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.06 % 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: 0.56 (0.17), residues: 2458 helix: 1.33 (0.15), residues: 1354 sheet: -0.87 (0.34), residues: 224 loop : -0.72 (0.21), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG b 309 TYR 0.015 0.002 TYR a 83 PHE 0.018 0.002 PHE D1006 TRP 0.014 0.001 TRP b 344 HIS 0.005 0.001 HIS a 393 Details of bonding type rmsd covalent geometry : bond 0.00296 (19974) covalent geometry : angle 0.52394 (27080) hydrogen bonds : bond 0.04481 ( 988) hydrogen bonds : angle 3.69795 ( 2877) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4916 Ramachandran restraints generated. 2458 Oldfield, 0 Emsley, 2458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4916 Ramachandran restraints generated. 2458 Oldfield, 0 Emsley, 2458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 638 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 575 time to evaluate : 0.810 Fit side-chains revert: symmetry clash REVERT: C 34 GLN cc_start: 0.6334 (mt0) cc_final: 0.6100 (mt0) REVERT: D 44 ARG cc_start: 0.8380 (mtt-85) cc_final: 0.8118 (mtt180) REVERT: D 425 GLU cc_start: 0.8227 (mm-30) cc_final: 0.8017 (mm-30) REVERT: D 516 GLU cc_start: 0.8346 (tp30) cc_final: 0.7774 (tp30) REVERT: D 843 GLU cc_start: 0.7052 (mp0) cc_final: 0.6814 (mp0) REVERT: D 884 LEU cc_start: 0.7497 (mt) cc_final: 0.7294 (mm) REVERT: G 39 GLU cc_start: 0.6923 (OUTLIER) cc_final: 0.6474 (mp0) REVERT: G 53 LYS cc_start: 0.8037 (OUTLIER) cc_final: 0.7742 (ttmm) REVERT: G 105 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.7552 (mp0) REVERT: G 114 ARG cc_start: 0.8492 (mtt-85) cc_final: 0.8286 (mtt180) REVERT: a 3 GLU cc_start: 0.7989 (pm20) cc_final: 0.7476 (pm20) REVERT: a 71 GLU cc_start: 0.7468 (pp20) cc_final: 0.6950 (pp20) REVERT: a 125 LEU cc_start: 0.8095 (OUTLIER) cc_final: 0.7882 (mt) REVERT: a 361 THR cc_start: 0.7597 (OUTLIER) cc_final: 0.7287 (t) REVERT: b 11 GLN cc_start: 0.8006 (tt0) cc_final: 0.7758 (tt0) REVERT: b 162 ARG cc_start: 0.8231 (OUTLIER) cc_final: 0.6491 (mpt-90) REVERT: b 328 GLU cc_start: 0.7179 (mt-10) cc_final: 0.6889 (mp0) REVERT: b 379 LYS cc_start: 0.8113 (mtpt) cc_final: 0.7889 (mttt) outliers start: 63 outliers final: 26 residues processed: 603 average time/residue: 0.7337 time to fit residues: 491.3125 Evaluate side-chains 582 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 550 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 474 PHE Chi-restraints excluded: chain D residue 502 ARG Chi-restraints excluded: chain D residue 532 THR Chi-restraints excluded: chain D residue 572 ILE Chi-restraints excluded: chain D residue 610 THR Chi-restraints excluded: chain D residue 698 THR Chi-restraints excluded: chain D residue 880 MET Chi-restraints excluded: chain D residue 928 LEU Chi-restraints excluded: chain D residue 954 VAL Chi-restraints excluded: chain D residue 963 SER Chi-restraints excluded: chain D residue 1075 CYS Chi-restraints excluded: chain D residue 1152 VAL Chi-restraints excluded: chain G residue 39 GLU Chi-restraints excluded: chain G residue 53 LYS Chi-restraints excluded: chain G residue 75 SER Chi-restraints excluded: chain G residue 105 GLU Chi-restraints excluded: chain G residue 123 PHE Chi-restraints excluded: chain G residue 135 SER Chi-restraints excluded: chain a residue 78 VAL Chi-restraints excluded: chain a residue 109 THR Chi-restraints excluded: chain a residue 125 LEU Chi-restraints excluded: chain a residue 147 SER Chi-restraints excluded: chain a residue 236 SER Chi-restraints excluded: chain a residue 277 SER Chi-restraints excluded: chain a residue 311 LYS Chi-restraints excluded: chain a residue 361 THR Chi-restraints excluded: chain b residue 35 THR Chi-restraints excluded: chain b residue 48 SER Chi-restraints excluded: chain b residue 155 ILE Chi-restraints excluded: chain b residue 162 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 212 optimal weight: 2.9990 chunk 130 optimal weight: 0.6980 chunk 32 optimal weight: 0.4980 chunk 46 optimal weight: 0.5980 chunk 95 optimal weight: 0.9980 chunk 135 optimal weight: 0.8980 chunk 181 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 230 optimal weight: 2.9990 chunk 152 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 112 GLN C 114 GLN C 259 GLN D 70 GLN D 90 GLN D 263 HIS D 971 GLN ** a 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 91 GLN a 293 ASN a 301 GLN a 329 ASN b 134 GLN b 424 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.147757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.130059 restraints weight = 22254.526| |-----------------------------------------------------------------------------| r_work (start): 0.3703 rms_B_bonded: 1.31 r_work: 0.3598 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3463 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.4470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 19974 Z= 0.160 Angle : 0.568 7.365 27080 Z= 0.290 Chirality : 0.042 0.153 3045 Planarity : 0.005 0.045 3502 Dihedral : 9.457 178.125 2734 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 3.92 % Allowed : 16.06 % Favored : 80.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.06 % 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: 0.80 (0.17), residues: 2458 helix: 1.45 (0.15), residues: 1353 sheet: -0.33 (0.35), residues: 217 loop : -0.60 (0.21), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 968 TYR 0.019 0.002 TYR D 107 PHE 0.021 0.002 PHE D1006 TRP 0.015 0.002 TRP b 344 HIS 0.006 0.001 HIS a 266 Details of bonding type rmsd covalent geometry : bond 0.00379 (19974) covalent geometry : angle 0.56813 (27080) hydrogen bonds : bond 0.05053 ( 988) hydrogen bonds : angle 3.77083 ( 2877) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4916 Ramachandran restraints generated. 2458 Oldfield, 0 Emsley, 2458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4916 Ramachandran restraints generated. 2458 Oldfield, 0 Emsley, 2458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 649 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 566 time to evaluate : 0.811 Fit side-chains REVERT: C 34 GLN cc_start: 0.6427 (mt0) cc_final: 0.6202 (mt0) REVERT: D 516 GLU cc_start: 0.8436 (tp30) cc_final: 0.7723 (tp30) REVERT: D 843 GLU cc_start: 0.7115 (mp0) cc_final: 0.6728 (mp0) REVERT: D 880 MET cc_start: 0.7607 (OUTLIER) cc_final: 0.7300 (ttp) REVERT: D 884 LEU cc_start: 0.7595 (mt) cc_final: 0.7377 (mm) REVERT: D 1100 GLN cc_start: 0.6941 (pt0) cc_final: 0.6644 (pt0) REVERT: D 1139 TYR cc_start: 0.7291 (m-10) cc_final: 0.6264 (m-80) REVERT: G 39 GLU cc_start: 0.6990 (OUTLIER) cc_final: 0.6586 (mp0) REVERT: G 53 LYS cc_start: 0.8146 (OUTLIER) cc_final: 0.7878 (ttmm) REVERT: G 114 ARG cc_start: 0.8566 (mtt-85) cc_final: 0.8235 (mtt180) REVERT: a 3 GLU cc_start: 0.8141 (OUTLIER) cc_final: 0.7620 (pm20) REVERT: a 22 GLU cc_start: 0.8204 (tt0) cc_final: 0.8002 (tt0) REVERT: a 35 GLN cc_start: 0.8426 (OUTLIER) cc_final: 0.7176 (mp10) REVERT: a 71 GLU cc_start: 0.7706 (pp20) cc_final: 0.7222 (pp20) REVERT: a 91 GLN cc_start: 0.8609 (OUTLIER) cc_final: 0.8400 (mt0) REVERT: a 361 THR cc_start: 0.7503 (OUTLIER) cc_final: 0.7210 (t) REVERT: b 147 MET cc_start: 0.8803 (ttt) cc_final: 0.8529 (ttt) REVERT: b 237 THR cc_start: 0.8196 (m) cc_final: 0.7600 (p) REVERT: b 379 LYS cc_start: 0.8087 (mtpt) cc_final: 0.7863 (mttt) REVERT: b 394 PHE cc_start: 0.7951 (m-80) cc_final: 0.7679 (m-80) outliers start: 83 outliers final: 37 residues processed: 599 average time/residue: 0.7359 time to fit residues: 487.0406 Evaluate side-chains 592 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 548 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 191 SER Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 226 ARG Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 267 LYS Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 457 CYS Chi-restraints excluded: chain D residue 502 ARG Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 572 ILE Chi-restraints excluded: chain D residue 610 THR Chi-restraints excluded: chain D residue 649 GLU Chi-restraints excluded: chain D residue 675 LEU Chi-restraints excluded: chain D residue 683 LEU Chi-restraints excluded: chain D residue 754 GLU Chi-restraints excluded: chain D residue 880 MET Chi-restraints excluded: chain D residue 892 GLU Chi-restraints excluded: chain D residue 903 MET Chi-restraints excluded: chain D residue 928 LEU Chi-restraints excluded: chain D residue 954 VAL Chi-restraints excluded: chain D residue 1152 VAL Chi-restraints excluded: chain G residue 39 GLU Chi-restraints excluded: chain G residue 53 LYS Chi-restraints excluded: chain G residue 75 SER Chi-restraints excluded: chain G residue 129 LEU Chi-restraints excluded: chain G residue 135 SER Chi-restraints excluded: chain a residue 3 GLU Chi-restraints excluded: chain a residue 35 GLN Chi-restraints excluded: chain a residue 78 VAL Chi-restraints excluded: chain a residue 91 GLN Chi-restraints excluded: chain a residue 92 LEU Chi-restraints excluded: chain a residue 94 THR Chi-restraints excluded: chain a residue 109 THR Chi-restraints excluded: chain a residue 147 SER Chi-restraints excluded: chain a residue 170 SER Chi-restraints excluded: chain a residue 194 THR Chi-restraints excluded: chain a residue 236 SER Chi-restraints excluded: chain a residue 311 LYS Chi-restraints excluded: chain a residue 361 THR Chi-restraints excluded: chain a residue 391 LEU Chi-restraints excluded: chain b residue 35 THR Chi-restraints excluded: chain b residue 48 SER Chi-restraints excluded: chain b residue 162 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 155 optimal weight: 0.8980 chunk 131 optimal weight: 1.9990 chunk 29 optimal weight: 0.1980 chunk 53 optimal weight: 0.3980 chunk 119 optimal weight: 0.1980 chunk 108 optimal weight: 0.9990 chunk 42 optimal weight: 0.7980 chunk 97 optimal weight: 0.4980 chunk 104 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 151 optimal weight: 0.9990 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 259 GLN D 263 HIS D 646 HIS D 661 GLN D 827 GLN D 971 GLN a 11 GLN a 18 ASN a 91 GLN a 258 ASN b 134 GLN b 424 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.149221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.131597 restraints weight = 22031.414| |-----------------------------------------------------------------------------| r_work (start): 0.3722 rms_B_bonded: 1.31 r_work: 0.3619 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3484 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.4560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19974 Z= 0.116 Angle : 0.501 6.432 27080 Z= 0.256 Chirality : 0.039 0.132 3045 Planarity : 0.004 0.041 3502 Dihedral : 9.296 179.959 2734 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 2.88 % Allowed : 17.52 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.06 % 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: 1.13 (0.18), residues: 2458 helix: 1.67 (0.15), residues: 1361 sheet: -0.02 (0.35), residues: 223 loop : -0.45 (0.21), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 968 TYR 0.013 0.001 TYR D 107 PHE 0.016 0.001 PHE D1006 TRP 0.014 0.001 TRP D 80 HIS 0.003 0.001 HIS a 266 Details of bonding type rmsd covalent geometry : bond 0.00263 (19974) covalent geometry : angle 0.50054 (27080) hydrogen bonds : bond 0.04168 ( 988) hydrogen bonds : angle 3.62280 ( 2877) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4916 Ramachandran restraints generated. 2458 Oldfield, 0 Emsley, 2458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4916 Ramachandran restraints generated. 2458 Oldfield, 0 Emsley, 2458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 604 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 543 time to evaluate : 0.742 Fit side-chains revert: symmetry clash REVERT: C 34 GLN cc_start: 0.6276 (mt0) cc_final: 0.6042 (mt0) REVERT: C 194 LEU cc_start: 0.8393 (OUTLIER) cc_final: 0.8043 (mt) REVERT: D 843 GLU cc_start: 0.7106 (mp0) cc_final: 0.6710 (mp0) REVERT: D 880 MET cc_start: 0.7612 (OUTLIER) cc_final: 0.7302 (ttm) REVERT: D 884 LEU cc_start: 0.7574 (mt) cc_final: 0.7336 (mm) REVERT: D 1139 TYR cc_start: 0.7265 (m-10) cc_final: 0.6230 (m-10) REVERT: D 1167 VAL cc_start: 0.7410 (OUTLIER) cc_final: 0.7104 (m) REVERT: G 53 LYS cc_start: 0.8128 (OUTLIER) cc_final: 0.7875 (ttmm) REVERT: G 114 ARG cc_start: 0.8556 (mtt-85) cc_final: 0.8185 (mtt180) REVERT: G 173 LEU cc_start: 0.8282 (mt) cc_final: 0.7950 (mp) REVERT: a 3 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.7486 (pm20) REVERT: a 71 GLU cc_start: 0.7689 (pp20) cc_final: 0.7254 (pp20) REVERT: a 91 GLN cc_start: 0.8644 (OUTLIER) cc_final: 0.8392 (mt0) REVERT: a 361 THR cc_start: 0.7311 (OUTLIER) cc_final: 0.7078 (t) REVERT: b 289 LEU cc_start: 0.7967 (OUTLIER) cc_final: 0.7730 (mt) REVERT: b 328 GLU cc_start: 0.7142 (mt-10) cc_final: 0.6900 (mp0) REVERT: b 379 LYS cc_start: 0.8084 (mtpt) cc_final: 0.7872 (mttt) outliers start: 61 outliers final: 33 residues processed: 572 average time/residue: 0.7468 time to fit residues: 472.5190 Evaluate side-chains 577 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 536 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 226 ARG Chi-restraints excluded: chain D residue 251 ASP Chi-restraints excluded: chain D residue 474 PHE Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 548 VAL Chi-restraints excluded: chain D residue 572 ILE Chi-restraints excluded: chain D residue 610 THR Chi-restraints excluded: chain D residue 649 GLU Chi-restraints excluded: chain D residue 675 LEU Chi-restraints excluded: chain D residue 683 LEU Chi-restraints excluded: chain D residue 754 GLU Chi-restraints excluded: chain D residue 827 GLN Chi-restraints excluded: chain D residue 880 MET Chi-restraints excluded: chain D residue 903 MET Chi-restraints excluded: chain D residue 928 LEU Chi-restraints excluded: chain D residue 954 VAL Chi-restraints excluded: chain D residue 1152 VAL Chi-restraints excluded: chain D residue 1167 VAL Chi-restraints excluded: chain G residue 53 LYS Chi-restraints excluded: chain G residue 75 SER Chi-restraints excluded: chain G residue 123 PHE Chi-restraints excluded: chain G residue 129 LEU Chi-restraints excluded: chain G residue 135 SER Chi-restraints excluded: chain a residue 3 GLU Chi-restraints excluded: chain a residue 18 ASN Chi-restraints excluded: chain a residue 78 VAL Chi-restraints excluded: chain a residue 91 GLN Chi-restraints excluded: chain a residue 94 THR Chi-restraints excluded: chain a residue 109 THR Chi-restraints excluded: chain a residue 147 SER Chi-restraints excluded: chain a residue 237 SER Chi-restraints excluded: chain a residue 311 LYS Chi-restraints excluded: chain a residue 349 THR Chi-restraints excluded: chain a residue 361 THR Chi-restraints excluded: chain a residue 391 LEU Chi-restraints excluded: chain b residue 35 THR Chi-restraints excluded: chain b residue 48 SER Chi-restraints excluded: chain b residue 162 ARG Chi-restraints excluded: chain b residue 256 ASN Chi-restraints excluded: chain b residue 289 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 88 optimal weight: 0.7980 chunk 209 optimal weight: 0.3980 chunk 59 optimal weight: 2.9990 chunk 118 optimal weight: 3.9990 chunk 195 optimal weight: 3.9990 chunk 75 optimal weight: 0.7980 chunk 33 optimal weight: 0.1980 chunk 244 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 185 optimal weight: 0.3980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 132 GLN C 259 GLN D 263 HIS D 653 GLN D 661 GLN D 971 GLN a 11 GLN a 18 ASN a 91 GLN a 258 ASN a 293 ASN b 134 GLN b 416 ASN b 423 GLN b 424 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.148677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.131022 restraints weight = 22101.060| |-----------------------------------------------------------------------------| r_work (start): 0.3714 rms_B_bonded: 1.31 r_work: 0.3610 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3474 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.4668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 19974 Z= 0.127 Angle : 0.512 6.978 27080 Z= 0.261 Chirality : 0.040 0.132 3045 Planarity : 0.004 0.043 3502 Dihedral : 9.213 179.275 2734 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 3.07 % Allowed : 17.48 % Favored : 79.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.06 % 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: 1.23 (0.17), residues: 2458 helix: 1.75 (0.15), residues: 1365 sheet: 0.14 (0.35), residues: 223 loop : -0.44 (0.21), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 968 TYR 0.014 0.001 TYR D 107 PHE 0.012 0.001 PHE D1006 TRP 0.014 0.001 TRP b 344 HIS 0.004 0.001 HIS a 266 Details of bonding type rmsd covalent geometry : bond 0.00296 (19974) covalent geometry : angle 0.51227 (27080) hydrogen bonds : bond 0.04337 ( 988) hydrogen bonds : angle 3.62589 ( 2877) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4916 Ramachandran restraints generated. 2458 Oldfield, 0 Emsley, 2458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4916 Ramachandran restraints generated. 2458 Oldfield, 0 Emsley, 2458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 610 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 545 time to evaluate : 0.813 Fit side-chains REVERT: C 34 GLN cc_start: 0.6289 (mt0) cc_final: 0.6053 (mt0) REVERT: C 194 LEU cc_start: 0.8398 (OUTLIER) cc_final: 0.8067 (mt) REVERT: D 685 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.7409 (tm-30) REVERT: D 843 GLU cc_start: 0.7119 (mp0) cc_final: 0.6723 (mp0) REVERT: D 880 MET cc_start: 0.7683 (OUTLIER) cc_final: 0.7389 (ttm) REVERT: D 884 LEU cc_start: 0.7588 (mt) cc_final: 0.7363 (mm) REVERT: D 1139 TYR cc_start: 0.7253 (m-10) cc_final: 0.6253 (m-80) REVERT: D 1167 VAL cc_start: 0.7418 (OUTLIER) cc_final: 0.7108 (m) REVERT: G 39 GLU cc_start: 0.6984 (OUTLIER) cc_final: 0.6654 (mp0) REVERT: G 53 LYS cc_start: 0.8143 (OUTLIER) cc_final: 0.7887 (ttmm) REVERT: G 114 ARG cc_start: 0.8573 (mtt-85) cc_final: 0.8177 (mtt-85) REVERT: G 173 LEU cc_start: 0.8363 (mt) cc_final: 0.8042 (mp) REVERT: a 3 GLU cc_start: 0.8078 (OUTLIER) cc_final: 0.7516 (pm20) REVERT: a 35 GLN cc_start: 0.8436 (OUTLIER) cc_final: 0.7174 (mp10) REVERT: a 71 GLU cc_start: 0.7706 (pp20) cc_final: 0.7259 (pp20) REVERT: a 91 GLN cc_start: 0.8509 (OUTLIER) cc_final: 0.8240 (mt0) REVERT: b 237 THR cc_start: 0.7987 (m) cc_final: 0.7519 (p) REVERT: b 289 LEU cc_start: 0.7993 (OUTLIER) cc_final: 0.7748 (mt) REVERT: b 328 GLU cc_start: 0.7171 (mt-10) cc_final: 0.6904 (mp0) REVERT: b 379 LYS cc_start: 0.8091 (mtpt) cc_final: 0.7880 (mttt) outliers start: 65 outliers final: 40 residues processed: 579 average time/residue: 0.7670 time to fit residues: 491.8894 Evaluate side-chains 584 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 534 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 226 ARG Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 251 ASP Chi-restraints excluded: chain D residue 474 PHE Chi-restraints excluded: chain D residue 482 GLU Chi-restraints excluded: chain D residue 495 VAL Chi-restraints excluded: chain D residue 502 ARG Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 572 ILE Chi-restraints excluded: chain D residue 649 GLU Chi-restraints excluded: chain D residue 675 LEU Chi-restraints excluded: chain D residue 683 LEU Chi-restraints excluded: chain D residue 685 GLU Chi-restraints excluded: chain D residue 698 THR Chi-restraints excluded: chain D residue 754 GLU Chi-restraints excluded: chain D residue 827 GLN Chi-restraints excluded: chain D residue 880 MET Chi-restraints excluded: chain D residue 903 MET Chi-restraints excluded: chain D residue 928 LEU Chi-restraints excluded: chain D residue 954 VAL Chi-restraints excluded: chain D residue 971 GLN Chi-restraints excluded: chain D residue 1152 VAL Chi-restraints excluded: chain D residue 1167 VAL Chi-restraints excluded: chain G residue 39 GLU Chi-restraints excluded: chain G residue 53 LYS Chi-restraints excluded: chain G residue 75 SER Chi-restraints excluded: chain G residue 123 PHE Chi-restraints excluded: chain G residue 129 LEU Chi-restraints excluded: chain G residue 135 SER Chi-restraints excluded: chain a residue 3 GLU Chi-restraints excluded: chain a residue 18 ASN Chi-restraints excluded: chain a residue 35 GLN Chi-restraints excluded: chain a residue 78 VAL Chi-restraints excluded: chain a residue 91 GLN Chi-restraints excluded: chain a residue 94 THR Chi-restraints excluded: chain a residue 109 THR Chi-restraints excluded: chain a residue 124 LYS Chi-restraints excluded: chain a residue 147 SER Chi-restraints excluded: chain a residue 194 THR Chi-restraints excluded: chain a residue 237 SER Chi-restraints excluded: chain a residue 349 THR Chi-restraints excluded: chain a residue 391 LEU Chi-restraints excluded: chain b residue 35 THR Chi-restraints excluded: chain b residue 48 SER Chi-restraints excluded: chain b residue 162 ARG Chi-restraints excluded: chain b residue 256 ASN Chi-restraints excluded: chain b residue 289 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 18 optimal weight: 0.0270 chunk 213 optimal weight: 0.9990 chunk 68 optimal weight: 0.9980 chunk 118 optimal weight: 1.9990 chunk 181 optimal weight: 0.0370 chunk 187 optimal weight: 0.0170 chunk 166 optimal weight: 0.6980 chunk 77 optimal weight: 0.9990 chunk 75 optimal weight: 0.6980 chunk 205 optimal weight: 0.9980 chunk 122 optimal weight: 2.9990 overall best weight: 0.2954 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 259 GLN D 263 HIS D 319 GLN D 653 GLN D 661 GLN D 827 GLN D 971 GLN a 11 GLN a 18 ASN a 91 GLN a 258 ASN a 293 ASN b 134 GLN b 424 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.149712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.131790 restraints weight = 22294.639| |-----------------------------------------------------------------------------| r_work (start): 0.3728 rms_B_bonded: 1.36 r_work: 0.3622 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3485 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.4701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 19974 Z= 0.104 Angle : 0.483 7.914 27080 Z= 0.247 Chirality : 0.039 0.134 3045 Planarity : 0.004 0.040 3502 Dihedral : 9.051 178.269 2734 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 2.83 % Allowed : 17.81 % Favored : 79.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.06 % 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: 1.42 (0.18), residues: 2458 helix: 1.88 (0.15), residues: 1372 sheet: 0.22 (0.35), residues: 223 loop : -0.35 (0.21), residues: 863 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 968 TYR 0.012 0.001 TYR D 107 PHE 0.011 0.001 PHE D1006 TRP 0.014 0.001 TRP b 344 HIS 0.003 0.001 HIS b 105 Details of bonding type rmsd covalent geometry : bond 0.00228 (19974) covalent geometry : angle 0.48344 (27080) hydrogen bonds : bond 0.03821 ( 988) hydrogen bonds : angle 3.53758 ( 2877) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4916 Ramachandran restraints generated. 2458 Oldfield, 0 Emsley, 2458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4916 Ramachandran restraints generated. 2458 Oldfield, 0 Emsley, 2458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 605 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 545 time to evaluate : 0.764 Fit side-chains REVERT: C 34 GLN cc_start: 0.6254 (mt0) cc_final: 0.6000 (mt0) REVERT: D 713 HIS cc_start: 0.8124 (m90) cc_final: 0.7913 (m90) REVERT: D 843 GLU cc_start: 0.7109 (mp0) cc_final: 0.6795 (mp0) REVERT: D 880 MET cc_start: 0.7649 (OUTLIER) cc_final: 0.7343 (ttm) REVERT: D 884 LEU cc_start: 0.7552 (mt) cc_final: 0.7330 (mm) REVERT: D 1139 TYR cc_start: 0.7233 (m-10) cc_final: 0.6278 (m-80) REVERT: D 1167 VAL cc_start: 0.7386 (OUTLIER) cc_final: 0.7081 (m) REVERT: G 39 GLU cc_start: 0.7003 (OUTLIER) cc_final: 0.6666 (mp0) REVERT: G 55 LEU cc_start: 0.7969 (pp) cc_final: 0.7766 (pt) REVERT: G 114 ARG cc_start: 0.8579 (mtt-85) cc_final: 0.8157 (mtt-85) REVERT: G 173 LEU cc_start: 0.8348 (mt) cc_final: 0.8048 (mp) REVERT: a 3 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.7586 (pm20) REVERT: a 71 GLU cc_start: 0.7708 (pp20) cc_final: 0.7214 (pp20) REVERT: a 91 GLN cc_start: 0.8448 (OUTLIER) cc_final: 0.8246 (mt0) REVERT: b 121 ARG cc_start: 0.8285 (OUTLIER) cc_final: 0.7756 (ptp90) REVERT: b 237 THR cc_start: 0.7821 (m) cc_final: 0.7381 (p) REVERT: b 289 LEU cc_start: 0.7918 (OUTLIER) cc_final: 0.7646 (mt) REVERT: b 328 GLU cc_start: 0.7184 (mt-10) cc_final: 0.6886 (mp0) REVERT: b 379 LYS cc_start: 0.8067 (mtpt) cc_final: 0.7850 (mttt) outliers start: 60 outliers final: 34 residues processed: 573 average time/residue: 0.7330 time to fit residues: 463.7545 Evaluate side-chains 580 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 539 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 251 ASP Chi-restraints excluded: chain D residue 474 PHE Chi-restraints excluded: chain D residue 495 VAL Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 548 VAL Chi-restraints excluded: chain D residue 572 ILE Chi-restraints excluded: chain D residue 649 GLU Chi-restraints excluded: chain D residue 675 LEU Chi-restraints excluded: chain D residue 683 LEU Chi-restraints excluded: chain D residue 698 THR Chi-restraints excluded: chain D residue 754 GLU Chi-restraints excluded: chain D residue 827 GLN Chi-restraints excluded: chain D residue 880 MET Chi-restraints excluded: chain D residue 903 MET Chi-restraints excluded: chain D residue 928 LEU Chi-restraints excluded: chain D residue 954 VAL Chi-restraints excluded: chain D residue 1152 VAL Chi-restraints excluded: chain D residue 1167 VAL Chi-restraints excluded: chain G residue 39 GLU Chi-restraints excluded: chain G residue 75 SER Chi-restraints excluded: chain G residue 123 PHE Chi-restraints excluded: chain G residue 135 SER Chi-restraints excluded: chain a residue 3 GLU Chi-restraints excluded: chain a residue 18 ASN Chi-restraints excluded: chain a residue 78 VAL Chi-restraints excluded: chain a residue 91 GLN Chi-restraints excluded: chain a residue 109 THR Chi-restraints excluded: chain a residue 124 LYS Chi-restraints excluded: chain a residue 128 GLN Chi-restraints excluded: chain a residue 147 SER Chi-restraints excluded: chain a residue 170 SER Chi-restraints excluded: chain a residue 194 THR Chi-restraints excluded: chain a residue 391 LEU Chi-restraints excluded: chain a residue 411 GLU Chi-restraints excluded: chain b residue 35 THR Chi-restraints excluded: chain b residue 48 SER Chi-restraints excluded: chain b residue 121 ARG Chi-restraints excluded: chain b residue 256 ASN Chi-restraints excluded: chain b residue 289 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 218 optimal weight: 1.9990 chunk 214 optimal weight: 0.0970 chunk 71 optimal weight: 0.0870 chunk 117 optimal weight: 0.9980 chunk 3 optimal weight: 3.9990 chunk 36 optimal weight: 0.6980 chunk 98 optimal weight: 4.9990 chunk 127 optimal weight: 0.6980 chunk 48 optimal weight: 0.7980 chunk 221 optimal weight: 0.4980 chunk 175 optimal weight: 0.9980 overall best weight: 0.4156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 259 GLN D 319 GLN D 561 GLN D 653 GLN D 661 GLN D 827 GLN a 11 GLN a 18 ASN a 91 GLN a 258 ASN a 293 ASN b 134 GLN b 423 GLN b 424 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.149299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.131318 restraints weight = 22261.783| |-----------------------------------------------------------------------------| r_work (start): 0.3720 rms_B_bonded: 1.37 r_work: 0.3615 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3476 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.4761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 19974 Z= 0.115 Angle : 0.499 11.226 27080 Z= 0.254 Chirality : 0.039 0.136 3045 Planarity : 0.004 0.041 3502 Dihedral : 9.053 178.161 2734 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 2.36 % Allowed : 18.04 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.06 % 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: 1.45 (0.17), residues: 2458 helix: 1.89 (0.15), residues: 1372 sheet: 0.30 (0.35), residues: 223 loop : -0.31 (0.21), residues: 863 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 968 TYR 0.013 0.001 TYR D 107 PHE 0.011 0.001 PHE D 966 TRP 0.013 0.001 TRP b 344 HIS 0.003 0.001 HIS a 266 Details of bonding type rmsd covalent geometry : bond 0.00264 (19974) covalent geometry : angle 0.49880 (27080) hydrogen bonds : bond 0.04015 ( 988) hydrogen bonds : angle 3.54132 ( 2877) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4916 Ramachandran restraints generated. 2458 Oldfield, 0 Emsley, 2458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4916 Ramachandran restraints generated. 2458 Oldfield, 0 Emsley, 2458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 598 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 548 time to evaluate : 0.793 Fit side-chains REVERT: C 34 GLN cc_start: 0.6252 (mt0) cc_final: 0.6002 (mt0) REVERT: C 194 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.8073 (mt) REVERT: D 713 HIS cc_start: 0.8118 (m90) cc_final: 0.7893 (m90) REVERT: D 843 GLU cc_start: 0.7118 (mp0) cc_final: 0.6799 (mp0) REVERT: D 880 MET cc_start: 0.7676 (OUTLIER) cc_final: 0.7379 (ttm) REVERT: D 884 LEU cc_start: 0.7566 (mt) cc_final: 0.7329 (mm) REVERT: D 1139 TYR cc_start: 0.7256 (m-10) cc_final: 0.6334 (m-80) REVERT: D 1167 VAL cc_start: 0.7396 (OUTLIER) cc_final: 0.7074 (m) REVERT: G 39 GLU cc_start: 0.7016 (OUTLIER) cc_final: 0.6679 (mp0) REVERT: G 55 LEU cc_start: 0.7991 (pp) cc_final: 0.7786 (pt) REVERT: G 114 ARG cc_start: 0.8597 (mtt-85) cc_final: 0.8173 (mtt-85) REVERT: G 173 LEU cc_start: 0.8361 (mt) cc_final: 0.7975 (mp) REVERT: a 3 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7565 (pm20) REVERT: a 35 GLN cc_start: 0.8456 (OUTLIER) cc_final: 0.7160 (mp10) REVERT: a 71 GLU cc_start: 0.7727 (pp20) cc_final: 0.7312 (pp20) REVERT: a 91 GLN cc_start: 0.8347 (OUTLIER) cc_final: 0.8145 (mt0) REVERT: b 237 THR cc_start: 0.7908 (m) cc_final: 0.7439 (p) REVERT: b 289 LEU cc_start: 0.7942 (OUTLIER) cc_final: 0.7673 (mt) REVERT: b 328 GLU cc_start: 0.7197 (mt-10) cc_final: 0.6895 (mp0) REVERT: b 379 LYS cc_start: 0.8089 (mtpt) cc_final: 0.7872 (mttt) outliers start: 50 outliers final: 36 residues processed: 571 average time/residue: 0.6971 time to fit residues: 440.4952 Evaluate side-chains 581 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 537 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 226 ARG Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 457 CYS Chi-restraints excluded: chain D residue 474 PHE Chi-restraints excluded: chain D residue 495 VAL Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 548 VAL Chi-restraints excluded: chain D residue 572 ILE Chi-restraints excluded: chain D residue 649 GLU Chi-restraints excluded: chain D residue 675 LEU Chi-restraints excluded: chain D residue 683 LEU Chi-restraints excluded: chain D residue 698 THR Chi-restraints excluded: chain D residue 827 GLN Chi-restraints excluded: chain D residue 880 MET Chi-restraints excluded: chain D residue 903 MET Chi-restraints excluded: chain D residue 928 LEU Chi-restraints excluded: chain D residue 954 VAL Chi-restraints excluded: chain D residue 1115 LEU Chi-restraints excluded: chain D residue 1152 VAL Chi-restraints excluded: chain D residue 1167 VAL Chi-restraints excluded: chain G residue 39 GLU Chi-restraints excluded: chain G residue 75 SER Chi-restraints excluded: chain G residue 123 PHE Chi-restraints excluded: chain G residue 129 LEU Chi-restraints excluded: chain G residue 135 SER Chi-restraints excluded: chain a residue 3 GLU Chi-restraints excluded: chain a residue 18 ASN Chi-restraints excluded: chain a residue 35 GLN Chi-restraints excluded: chain a residue 78 VAL Chi-restraints excluded: chain a residue 91 GLN Chi-restraints excluded: chain a residue 109 THR Chi-restraints excluded: chain a residue 124 LYS Chi-restraints excluded: chain a residue 128 GLN Chi-restraints excluded: chain a residue 147 SER Chi-restraints excluded: chain a residue 170 SER Chi-restraints excluded: chain a residue 194 THR Chi-restraints excluded: chain a residue 311 LYS Chi-restraints excluded: chain a residue 391 LEU Chi-restraints excluded: chain b residue 35 THR Chi-restraints excluded: chain b residue 48 SER Chi-restraints excluded: chain b residue 256 ASN Chi-restraints excluded: chain b residue 289 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 70 optimal weight: 0.0870 chunk 123 optimal weight: 0.8980 chunk 13 optimal weight: 0.1980 chunk 11 optimal weight: 0.9980 chunk 27 optimal weight: 0.0170 chunk 65 optimal weight: 0.6980 chunk 116 optimal weight: 2.9990 chunk 118 optimal weight: 0.9980 chunk 47 optimal weight: 0.0870 chunk 188 optimal weight: 0.0770 chunk 214 optimal weight: 0.0010 overall best weight: 0.0538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 112 GLN C 259 GLN D 255 GLN D 319 GLN D 653 GLN D 661 GLN a 11 GLN ** a 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 91 GLN a 258 ASN a 293 ASN b 134 GLN b 424 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.155089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.137782 restraints weight = 22375.202| |-----------------------------------------------------------------------------| r_work (start): 0.3769 rms_B_bonded: 1.32 r_work: 0.3668 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3536 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.4747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 19974 Z= 0.089 Angle : 0.461 11.525 27080 Z= 0.234 Chirality : 0.038 0.134 3045 Planarity : 0.004 0.039 3502 Dihedral : 8.686 170.690 2734 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 1.42 % Allowed : 19.60 % Favored : 78.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.06 % 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: 1.69 (0.18), residues: 2458 helix: 2.09 (0.15), residues: 1368 sheet: 0.37 (0.35), residues: 223 loop : -0.20 (0.21), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 968 TYR 0.013 0.001 TYR D 115 PHE 0.012 0.001 PHE C 104 TRP 0.018 0.001 TRP D 705 HIS 0.003 0.000 HIS a 88 Details of bonding type rmsd covalent geometry : bond 0.00182 (19974) covalent geometry : angle 0.46091 (27080) hydrogen bonds : bond 0.03125 ( 988) hydrogen bonds : angle 3.41463 ( 2877) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4916 Ramachandran restraints generated. 2458 Oldfield, 0 Emsley, 2458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4916 Ramachandran restraints generated. 2458 Oldfield, 0 Emsley, 2458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 561 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 531 time to evaluate : 0.833 Fit side-chains REVERT: C 34 GLN cc_start: 0.6260 (mt0) cc_final: 0.6019 (mt0) REVERT: D 675 LEU cc_start: 0.8339 (OUTLIER) cc_final: 0.8100 (mp) REVERT: D 843 GLU cc_start: 0.7109 (mp0) cc_final: 0.6709 (mp0) REVERT: D 880 MET cc_start: 0.7623 (OUTLIER) cc_final: 0.7364 (ttm) REVERT: D 884 LEU cc_start: 0.7639 (mt) cc_final: 0.7436 (mm) REVERT: D 1139 TYR cc_start: 0.7129 (m-10) cc_final: 0.6331 (m-80) REVERT: D 1167 VAL cc_start: 0.7347 (OUTLIER) cc_final: 0.7058 (m) REVERT: G 39 GLU cc_start: 0.6986 (OUTLIER) cc_final: 0.6684 (mp0) REVERT: G 173 LEU cc_start: 0.8337 (mt) cc_final: 0.8017 (mp) REVERT: a 3 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.7704 (pm20) REVERT: b 289 LEU cc_start: 0.7823 (OUTLIER) cc_final: 0.7565 (mt) REVERT: b 379 LYS cc_start: 0.8074 (mtpt) cc_final: 0.7762 (mttt) outliers start: 30 outliers final: 14 residues processed: 546 average time/residue: 0.7455 time to fit residues: 451.0756 Evaluate side-chains 543 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 523 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain D residue 251 ASP Chi-restraints excluded: chain D residue 474 PHE Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 675 LEU Chi-restraints excluded: chain D residue 827 GLN Chi-restraints excluded: chain D residue 880 MET Chi-restraints excluded: chain D residue 928 LEU Chi-restraints excluded: chain D residue 954 VAL Chi-restraints excluded: chain D residue 1167 VAL Chi-restraints excluded: chain G residue 39 GLU Chi-restraints excluded: chain G residue 140 GLU Chi-restraints excluded: chain a residue 3 GLU Chi-restraints excluded: chain a residue 78 VAL Chi-restraints excluded: chain a residue 128 GLN Chi-restraints excluded: chain a residue 170 SER Chi-restraints excluded: chain a residue 194 THR Chi-restraints excluded: chain a residue 391 LEU Chi-restraints excluded: chain b residue 48 SER Chi-restraints excluded: chain b residue 289 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 42 optimal weight: 0.6980 chunk 82 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 146 optimal weight: 4.9990 chunk 94 optimal weight: 4.9990 chunk 4 optimal weight: 0.5980 chunk 115 optimal weight: 0.9990 chunk 7 optimal weight: 0.7980 chunk 56 optimal weight: 0.8980 chunk 206 optimal weight: 0.0870 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 112 GLN C 259 GLN D 140 ASN D 255 GLN D 319 GLN D 827 GLN D1033 ASN a 11 GLN ** a 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 91 GLN a 258 ASN a 293 ASN b 52 ASN b 99 ASN b 134 GLN b 256 ASN b 423 GLN b 424 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.148305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.130653 restraints weight = 22216.050| |-----------------------------------------------------------------------------| r_work (start): 0.3712 rms_B_bonded: 1.31 r_work: 0.3607 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3471 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.4891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 19974 Z= 0.142 Angle : 0.537 9.915 27080 Z= 0.274 Chirality : 0.041 0.159 3045 Planarity : 0.004 0.050 3502 Dihedral : 9.035 178.105 2734 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.65 % Allowed : 19.89 % Favored : 78.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.06 % 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: 1.57 (0.17), residues: 2458 helix: 1.93 (0.15), residues: 1372 sheet: 0.51 (0.35), residues: 214 loop : -0.20 (0.21), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 968 TYR 0.016 0.002 TYR D 107 PHE 0.013 0.001 PHE D 966 TRP 0.027 0.002 TRP D 705 HIS 0.005 0.001 HIS D 713 Details of bonding type rmsd covalent geometry : bond 0.00337 (19974) covalent geometry : angle 0.53696 (27080) hydrogen bonds : bond 0.04459 ( 988) hydrogen bonds : angle 3.58165 ( 2877) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4916 Ramachandran restraints generated. 2458 Oldfield, 0 Emsley, 2458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4916 Ramachandran restraints generated. 2458 Oldfield, 0 Emsley, 2458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 566 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 531 time to evaluate : 0.718 Fit side-chains revert: symmetry clash REVERT: C 34 GLN cc_start: 0.6275 (mt0) cc_final: 0.6028 (mt0) REVERT: D 563 MET cc_start: 0.8278 (mtt) cc_final: 0.7915 (mtp) REVERT: D 713 HIS cc_start: 0.8104 (m90) cc_final: 0.7893 (m90) REVERT: D 843 GLU cc_start: 0.7140 (mp0) cc_final: 0.6835 (mp0) REVERT: D 884 LEU cc_start: 0.7657 (mt) cc_final: 0.7452 (mm) REVERT: D 1139 TYR cc_start: 0.7334 (m-10) cc_final: 0.6430 (m-80) REVERT: D 1167 VAL cc_start: 0.7429 (OUTLIER) cc_final: 0.7118 (m) REVERT: G 39 GLU cc_start: 0.6999 (OUTLIER) cc_final: 0.6703 (mp0) REVERT: G 173 LEU cc_start: 0.8366 (mt) cc_final: 0.8061 (mp) REVERT: a 3 GLU cc_start: 0.8103 (OUTLIER) cc_final: 0.7752 (pm20) REVERT: a 71 GLU cc_start: 0.7702 (pp20) cc_final: 0.7447 (pp20) REVERT: a 351 PHE cc_start: 0.7919 (m-80) cc_final: 0.7594 (m-80) REVERT: b 1 MET cc_start: 0.4443 (mmm) cc_final: 0.3988 (tmm) REVERT: b 162 ARG cc_start: 0.8190 (OUTLIER) cc_final: 0.6083 (mpt-90) REVERT: b 237 THR cc_start: 0.8134 (m) cc_final: 0.7602 (p) REVERT: b 289 LEU cc_start: 0.7979 (OUTLIER) cc_final: 0.7722 (mt) REVERT: b 379 LYS cc_start: 0.8098 (mtpt) cc_final: 0.7886 (mttt) REVERT: b 394 PHE cc_start: 0.7980 (m-80) cc_final: 0.7754 (m-80) outliers start: 35 outliers final: 23 residues processed: 549 average time/residue: 0.7144 time to fit residues: 434.4046 Evaluate side-chains 558 residues out of total 2117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 530 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 267 LYS Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 251 ASP Chi-restraints excluded: chain D residue 457 CYS Chi-restraints excluded: chain D residue 474 PHE Chi-restraints excluded: chain D residue 495 VAL Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 548 VAL Chi-restraints excluded: chain D residue 572 ILE Chi-restraints excluded: chain D residue 675 LEU Chi-restraints excluded: chain D residue 827 GLN Chi-restraints excluded: chain D residue 971 GLN Chi-restraints excluded: chain D residue 1167 VAL Chi-restraints excluded: chain G residue 39 GLU Chi-restraints excluded: chain G residue 129 LEU Chi-restraints excluded: chain a residue 3 GLU Chi-restraints excluded: chain a residue 62 VAL Chi-restraints excluded: chain a residue 78 VAL Chi-restraints excluded: chain a residue 124 LYS Chi-restraints excluded: chain a residue 170 SER Chi-restraints excluded: chain a residue 194 THR Chi-restraints excluded: chain a residue 236 SER Chi-restraints excluded: chain a residue 391 LEU Chi-restraints excluded: chain b residue 53 GLU Chi-restraints excluded: chain b residue 162 ARG Chi-restraints excluded: chain b residue 256 ASN Chi-restraints excluded: chain b residue 289 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 137 optimal weight: 0.9990 chunk 136 optimal weight: 0.4980 chunk 186 optimal weight: 0.7980 chunk 92 optimal weight: 0.9980 chunk 161 optimal weight: 0.9990 chunk 154 optimal weight: 1.9990 chunk 91 optimal weight: 0.0170 chunk 13 optimal weight: 0.0970 chunk 190 optimal weight: 0.5980 chunk 208 optimal weight: 0.9980 chunk 89 optimal weight: 0.7980 overall best weight: 0.4016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 112 GLN C 259 GLN D 90 GLN D 255 GLN D 653 GLN D1033 ASN a 11 GLN ** a 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 91 GLN a 128 GLN a 258 ASN a 293 ASN b 52 ASN b 134 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.148564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.130908 restraints weight = 22134.075| |-----------------------------------------------------------------------------| r_work (start): 0.3715 rms_B_bonded: 1.31 r_work: 0.3610 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3475 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.4909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.093 19974 Z= 0.165 Angle : 0.741 59.193 27080 Z= 0.422 Chirality : 0.041 0.152 3045 Planarity : 0.005 0.112 3502 Dihedral : 9.039 178.100 2734 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.56 % Allowed : 19.98 % Favored : 78.46 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 3.06 % 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: 1.56 (0.17), residues: 2458 helix: 1.93 (0.15), residues: 1372 sheet: 0.51 (0.35), residues: 214 loop : -0.20 (0.21), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 916 TYR 0.015 0.001 TYR D 107 PHE 0.013 0.001 PHE D 966 TRP 0.023 0.001 TRP D 705 HIS 0.004 0.001 HIS D 659 Details of bonding type rmsd covalent geometry : bond 0.00348 (19974) covalent geometry : angle 0.74073 (27080) hydrogen bonds : bond 0.04417 ( 988) hydrogen bonds : angle 3.58602 ( 2877) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12135.78 seconds wall clock time: 206 minutes 0.65 seconds (12360.65 seconds total)