Starting phenix.real_space_refine on Sun Sep 13 14:34:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6sjb_10214/09_2026/6sjb_10214.cif Found real_map, /net/cci-nas-00/data/ceres_data/6sjb_10214/09_2026/6sjb_10214.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6sjb_10214/09_2026/6sjb_10214.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6sjb_10214/09_2026/6sjb_10214.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6sjb_10214/09_2026/6sjb_10214.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6sjb_10214/09_2026/6sjb_10214.map" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 68 5.49 5 S 101 5.16 5 C 15036 2.51 5 N 4236 2.21 5 O 4674 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 105 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 24115 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 9047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1129, 9047 Classifications: {'peptide': 1129} Link IDs: {'PTRANS': 51, 'TRANS': 1077} Chain breaks: 2 Chain: "C" Number of atoms: 9078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1121, 9078 Classifications: {'peptide': 1121} Link IDs: {'PCIS': 1, 'PTRANS': 66, 'TRANS': 1053} Chain: "D" Number of atoms: 4603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4603 Classifications: {'peptide': 597} Link IDs: {'PTRANS': 25, 'TRANS': 571} Chain: "X" Number of atoms: 1387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 1387 Classifications: {'DNA': 68} Link IDs: {'rna3p': 67} Chain breaks: 1 Time building chain proxies: 4.17, per 1000 atoms: 0.17 Number of scatterers: 24115 At special positions: 0 Unit cell: (151.815, 150.768, 123.546, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 101 16.00 P 68 15.00 O 4674 8.00 N 4236 7.00 C 15036 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: 1.77 Conformation dependent library (CDL) restraints added in 938.0 milliseconds 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5372 Finding SS restraints... Secondary structure from input PDB file: 126 helices and 16 sheets defined 53.2% alpha, 9.6% beta 17 base pairs and 39 stacking pairs defined. Time for finding SS restraints: 2.58 Creating SS restraints... Processing helix chain 'B' and resid 28 through 43 Processing helix chain 'B' and resid 45 through 49 removed outlier: 3.527A pdb=" N ALA B 49 " --> pdb=" O GLY B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 59 removed outlier: 3.691A pdb=" N LEU B 59 " --> pdb=" O VAL B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 90 Processing helix chain 'B' and resid 94 through 104 removed outlier: 3.762A pdb=" N ILE B 104 " --> pdb=" O LEU B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 120 Processing helix chain 'B' and resid 121 through 124 Processing helix chain 'B' and resid 128 through 140 Processing helix chain 'B' and resid 140 through 145 removed outlier: 3.538A pdb=" N SER B 144 " --> pdb=" O ASN B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 173 removed outlier: 3.800A pdb=" N TYR B 173 " --> pdb=" O ARG B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 187 removed outlier: 4.333A pdb=" N VAL B 182 " --> pdb=" O GLU B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 202 removed outlier: 3.707A pdb=" N LEU B 193 " --> pdb=" O GLY B 189 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N ARG B 199 " --> pdb=" O ARG B 195 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N TYR B 200 " --> pdb=" O ASP B 196 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLN B 202 " --> pdb=" O ASN B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 239 removed outlier: 3.562A pdb=" N VAL B 232 " --> pdb=" O ARG B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 266 removed outlier: 3.559A pdb=" N ASN B 258 " --> pdb=" O ARG B 254 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ILE B 266 " --> pdb=" O GLN B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 281 removed outlier: 3.610A pdb=" N ASN B 278 " --> pdb=" O GLU B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 289 removed outlier: 3.844A pdb=" N LYS B 288 " --> pdb=" O GLU B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 317 removed outlier: 4.349A pdb=" N GLU B 311 " --> pdb=" O HIS B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 347 removed outlier: 4.504A pdb=" N ARG B 336 " --> pdb=" O LEU B 332 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N GLU B 337 " --> pdb=" O ALA B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 364 removed outlier: 3.506A pdb=" N MET B 354 " --> pdb=" O GLY B 350 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LEU B 355 " --> pdb=" O PHE B 351 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER B 364 " --> pdb=" O SER B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 378 Processing helix chain 'B' and resid 390 through 401 Processing helix chain 'B' and resid 414 through 418 removed outlier: 3.816A pdb=" N ALA B 418 " --> pdb=" O PRO B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 437 removed outlier: 3.780A pdb=" N TYR B 430 " --> pdb=" O ASP B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 461 Processing helix chain 'B' and resid 511 through 534 removed outlier: 3.511A pdb=" N GLN B 534 " --> pdb=" O LEU B 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 572 removed outlier: 3.552A pdb=" N ALA B 564 " --> pdb=" O SER B 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 589 removed outlier: 3.643A pdb=" N GLU B 589 " --> pdb=" O SER B 586 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 586 through 589' Processing helix chain 'B' and resid 590 through 605 removed outlier: 3.944A pdb=" N GLN B 594 " --> pdb=" O THR B 590 " (cutoff:3.500A) Processing helix chain 'B' and resid 608 through 617 removed outlier: 3.941A pdb=" N LEU B 612 " --> pdb=" O ARG B 608 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA B 617 " --> pdb=" O ARG B 613 " (cutoff:3.500A) Processing helix chain 'B' and resid 624 through 634 Processing helix chain 'B' and resid 634 through 655 removed outlier: 3.542A pdb=" N TRP B 638 " --> pdb=" O ASP B 634 " (cutoff:3.500A) Processing helix chain 'B' and resid 657 through 668 Processing helix chain 'B' and resid 669 through 677 removed outlier: 3.551A pdb=" N ASN B 673 " --> pdb=" O ASN B 669 " (cutoff:3.500A) Processing helix chain 'B' and resid 679 through 699 removed outlier: 4.376A pdb=" N ARG B 683 " --> pdb=" O GLY B 679 " (cutoff:3.500A) Processing helix chain 'B' and resid 704 through 717 removed outlier: 3.851A pdb=" N VAL B 708 " --> pdb=" O GLU B 704 " (cutoff:3.500A) Processing helix chain 'B' and resid 742 through 745 removed outlier: 3.909A pdb=" N LYS B 745 " --> pdb=" O HIS B 742 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 742 through 745' Processing helix chain 'B' and resid 783 through 807 removed outlier: 3.611A pdb=" N GLU B 793 " --> pdb=" O LEU B 789 " (cutoff:3.500A) Processing helix chain 'B' and resid 832 through 836 Processing helix chain 'B' and resid 838 through 843 Processing helix chain 'B' and resid 849 through 860 removed outlier: 3.909A pdb=" N LEU B 860 " --> pdb=" O CYS B 856 " (cutoff:3.500A) Processing helix chain 'B' and resid 941 through 945 Processing helix chain 'B' and resid 948 through 962 Processing helix chain 'B' and resid 969 through 981 Processing helix chain 'B' and resid 986 through 1000 removed outlier: 3.702A pdb=" N GLU B 992 " --> pdb=" O PRO B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1032 through 1044 removed outlier: 3.747A pdb=" N THR B1038 " --> pdb=" O SER B1034 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N LEU B1039 " --> pdb=" O GLN B1035 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N PHE B1043 " --> pdb=" O LEU B1039 " (cutoff:3.500A) Processing helix chain 'B' and resid 1045 through 1048 removed outlier: 3.858A pdb=" N ALA B1048 " --> pdb=" O PRO B1045 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1045 through 1048' Processing helix chain 'B' and resid 1094 through 1106 Processing helix chain 'B' and resid 1107 through 1126 Processing helix chain 'B' and resid 1130 through 1134 Processing helix chain 'B' and resid 1144 through 1146 No H-bonds generated for 'chain 'B' and resid 1144 through 1146' Processing helix chain 'B' and resid 1163 through 1174 removed outlier: 3.661A pdb=" N LEU B1167 " --> pdb=" O GLY B1163 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 24 removed outlier: 3.937A pdb=" N LEU C 13 " --> pdb=" O ARG C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 39 through 55 Processing helix chain 'C' and resid 64 through 77 Processing helix chain 'C' and resid 87 through 102 removed outlier: 3.641A pdb=" N THR C 97 " --> pdb=" O TRP C 93 " (cutoff:3.500A) Proline residue: C 100 - end of helix Processing helix chain 'C' and resid 108 through 116 removed outlier: 3.928A pdb=" N HIS C 113 " --> pdb=" O THR C 109 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N TYR C 114 " --> pdb=" O LEU C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 142 Processing helix chain 'C' and resid 142 through 152 removed outlier: 3.691A pdb=" N LEU C 146 " --> pdb=" O ARG C 142 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N THR C 151 " --> pdb=" O ALA C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 179 Processing helix chain 'C' and resid 185 through 199 Processing helix chain 'C' and resid 223 through 231 Processing helix chain 'C' and resid 253 through 263 removed outlier: 3.573A pdb=" N ALA C 258 " --> pdb=" O PRO C 254 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LYS C 259 " --> pdb=" O ALA C 255 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ARG C 263 " --> pdb=" O LYS C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 287 Processing helix chain 'C' and resid 297 through 304 Processing helix chain 'C' and resid 304 through 316 Processing helix chain 'C' and resid 333 through 344 Processing helix chain 'C' and resid 354 through 360 Processing helix chain 'C' and resid 381 through 400 Processing helix chain 'C' and resid 404 through 406 No H-bonds generated for 'chain 'C' and resid 404 through 406' Processing helix chain 'C' and resid 418 through 428 Processing helix chain 'C' and resid 447 through 459 removed outlier: 3.528A pdb=" N LEU C 451 " --> pdb=" O SER C 447 " (cutoff:3.500A) Processing helix chain 'C' and resid 466 through 475 Processing helix chain 'C' and resid 476 through 483 removed outlier: 3.696A pdb=" N PHE C 483 " --> pdb=" O LEU C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 486 through 500 removed outlier: 3.850A pdb=" N GLN C 495 " --> pdb=" O ARG C 491 " (cutoff:3.500A) Processing helix chain 'C' and resid 507 through 514 removed outlier: 3.517A pdb=" N LEU C 514 " --> pdb=" O ASN C 510 " (cutoff:3.500A) Processing helix chain 'C' and resid 523 through 537 Processing helix chain 'C' and resid 555 through 557 No H-bonds generated for 'chain 'C' and resid 555 through 557' Processing helix chain 'C' and resid 558 through 574 removed outlier: 3.773A pdb=" N MET C 569 " --> pdb=" O ALA C 565 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N GLN C 570 " --> pdb=" O SER C 566 " (cutoff:3.500A) Processing helix chain 'C' and resid 587 through 599 removed outlier: 4.417A pdb=" N CYS C 591 " --> pdb=" O TRP C 587 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N ARG C 592 " --> pdb=" O LEU C 588 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASP C 593 " --> pdb=" O PRO C 589 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA C 597 " --> pdb=" O ASP C 593 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHE C 599 " --> pdb=" O LEU C 595 " (cutoff:3.500A) Processing helix chain 'C' and resid 605 through 625 Processing helix chain 'C' and resid 633 through 644 removed outlier: 4.014A pdb=" N LEU C 637 " --> pdb=" O PRO C 633 " (cutoff:3.500A) Processing helix chain 'C' and resid 695 through 700 removed outlier: 3.803A pdb=" N GLN C 699 " --> pdb=" O ASP C 695 " (cutoff:3.500A) Processing helix chain 'C' and resid 707 through 723 removed outlier: 3.571A pdb=" N LEU C 717 " --> pdb=" O ARG C 713 " (cutoff:3.500A) Processing helix chain 'C' and resid 745 through 758 Processing helix chain 'C' and resid 769 through 780 Processing helix chain 'C' and resid 806 through 812 Processing helix chain 'C' and resid 833 through 843 removed outlier: 3.551A pdb=" N LEU C 837 " --> pdb=" O PRO C 833 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N HIS C 843 " --> pdb=" O ARG C 839 " (cutoff:3.500A) Processing helix chain 'C' and resid 843 through 851 Processing helix chain 'C' and resid 874 through 889 Processing helix chain 'C' and resid 893 through 904 removed outlier: 3.721A pdb=" N LEU C 897 " --> pdb=" O ASP C 893 " (cutoff:3.500A) Processing helix chain 'C' and resid 910 through 932 removed outlier: 4.024A pdb=" N GLU C 914 " --> pdb=" O GLY C 910 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ARG C 930 " --> pdb=" O GLN C 926 " (cutoff:3.500A) Processing helix chain 'C' and resid 973 through 989 removed outlier: 3.595A pdb=" N GLY C 977 " --> pdb=" O SER C 973 " (cutoff:3.500A) Processing helix chain 'C' and resid 1012 through 1033 removed outlier: 4.082A pdb=" N SER C1032 " --> pdb=" O ARG C1028 " (cutoff:3.500A) Processing helix chain 'C' and resid 1038 through 1050 Processing helix chain 'C' and resid 1060 through 1076 removed outlier: 3.668A pdb=" N ARG C1068 " --> pdb=" O LEU C1064 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR C1069 " --> pdb=" O GLN C1065 " (cutoff:3.500A) Processing helix chain 'C' and resid 1098 through 1113 Processing helix chain 'C' and resid 1113 through 1119 removed outlier: 3.802A pdb=" N PHE C1117 " --> pdb=" O LEU C1113 " (cutoff:3.500A) Processing helix chain 'D' and resid 11 through 15 removed outlier: 3.565A pdb=" N GLN D 15 " --> pdb=" O VAL D 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 11 through 15' Processing helix chain 'D' and resid 17 through 28 Processing helix chain 'D' and resid 32 through 49 Processing helix chain 'D' and resid 55 through 61 Processing helix chain 'D' and resid 64 through 72 removed outlier: 3.513A pdb=" N VAL D 72 " --> pdb=" O LEU D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 88 removed outlier: 3.891A pdb=" N SER D 88 " --> pdb=" O CYS D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 125 Processing helix chain 'D' and resid 133 through 145 removed outlier: 3.576A pdb=" N LEU D 137 " --> pdb=" O ASP D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 164 removed outlier: 3.602A pdb=" N ARG D 164 " --> pdb=" O VAL D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 192 Processing helix chain 'D' and resid 205 through 221 Processing helix chain 'D' and resid 240 through 244 Processing helix chain 'D' and resid 270 through 274 removed outlier: 3.631A pdb=" N MET D 273 " --> pdb=" O GLU D 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 284 Processing helix chain 'D' and resid 308 through 315 removed outlier: 3.980A pdb=" N ASP D 312 " --> pdb=" O ALA D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 316 through 319 removed outlier: 3.540A pdb=" N ALA D 319 " --> pdb=" O TYR D 316 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 316 through 319' Processing helix chain 'D' and resid 322 through 334 removed outlier: 3.547A pdb=" N ARG D 327 " --> pdb=" O ALA D 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 352 Processing helix chain 'D' and resid 365 through 375 removed outlier: 4.004A pdb=" N GLN D 369 " --> pdb=" O SER D 365 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ASN D 375 " --> pdb=" O ALA D 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 377 through 387 removed outlier: 3.651A pdb=" N ALA D 381 " --> pdb=" O GLY D 377 " (cutoff:3.500A) Processing helix chain 'D' and resid 388 through 391 removed outlier: 3.890A pdb=" N THR D 391 " --> pdb=" O GLN D 388 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 388 through 391' Processing helix chain 'D' and resid 400 through 415 Processing helix chain 'D' and resid 415 through 424 Processing helix chain 'D' and resid 427 through 436 removed outlier: 3.525A pdb=" N ILE D 431 " --> pdb=" O GLU D 427 " (cutoff:3.500A) Processing helix chain 'D' and resid 450 through 465 Processing helix chain 'D' and resid 523 through 527 Processing helix chain 'D' and resid 562 through 572 Processing helix chain 'D' and resid 582 through 592 removed outlier: 3.738A pdb=" N ILE D 590 " --> pdb=" O LEU D 586 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ALA D 591 " --> pdb=" O SER D 587 " (cutoff:3.500A) Processing helix chain 'D' and resid 599 through 604 Processing sheet with id=AA1, first strand: chain 'B' and resid 6 through 7 removed outlier: 6.410A pdb=" N GLU B 6 " --> pdb=" O THR B 442 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N ALA B 439 " --> pdb=" O GLU B 18 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU B 20 " --> pdb=" O ALA B 439 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N GLY B 17 " --> pdb=" O LEU B 409 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N LEU B 411 " --> pdb=" O GLY B 17 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ARG B 19 " --> pdb=" O LEU B 411 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N GLY B 413 " --> pdb=" O ARG B 19 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N ILE B 21 " --> pdb=" O GLY B 413 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ALA B 381 " --> pdb=" O LEU B 410 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N ILE B 412 " --> pdb=" O ALA B 381 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N ILE B 383 " --> pdb=" O ILE B 412 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N VAL B 62 " --> pdb=" O ASP B 384 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N VAL B 61 " --> pdb=" O PHE B 127 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 151 through 152 removed outlier: 6.461A pdb=" N GLN B 151 " --> pdb=" O LEU B 349 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 207 through 208 removed outlier: 6.352A pdb=" N VAL B 207 " --> pdb=" O LEU B 778 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 445 through 446 Processing sheet with id=AA5, first strand: chain 'B' and resid 487 through 490 Processing sheet with id=AA6, first strand: chain 'B' and resid 578 through 580 removed outlier: 6.711A pdb=" N VAL B 579 " --> pdb=" O ILE B 738 " (cutoff:3.500A) removed outlier: 8.702A pdb=" N THR B 740 " --> pdb=" O VAL B 579 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N ILE B 554 " --> pdb=" O GLN B 737 " (cutoff:3.500A) removed outlier: 8.176A pdb=" N VAL B 739 " --> pdb=" O ILE B 554 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N VAL B 556 " --> pdb=" O VAL B 739 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N MET B 499 " --> pdb=" O ALA B 866 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N GLN B 868 " --> pdb=" O MET B 499 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N MET B 501 " --> pdb=" O GLN B 868 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 901 through 904 removed outlier: 5.993A pdb=" N ARG B 902 " --> pdb=" O MET B1061 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N LYS B1063 " --> pdb=" O ARG B 902 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N THR B 904 " --> pdb=" O LYS B1063 " (cutoff:3.500A) removed outlier: 8.488A pdb=" N PHE B1065 " --> pdb=" O THR B 904 " (cutoff:3.500A) removed outlier: 10.217A pdb=" N ILE B1066 " --> pdb=" O TYR B1081 " (cutoff:3.500A) removed outlier: 8.439A pdb=" N TYR B1081 " --> pdb=" O ILE B1066 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N TYR B1076 " --> pdb=" O PHE B1135 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLY B1137 " --> pdb=" O TYR B1076 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 901 through 904 removed outlier: 5.993A pdb=" N ARG B 902 " --> pdb=" O MET B1061 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N LYS B1063 " --> pdb=" O ARG B 902 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N THR B 904 " --> pdb=" O LYS B1063 " (cutoff:3.500A) removed outlier: 8.488A pdb=" N PHE B1065 " --> pdb=" O THR B 904 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N LEU B1068 " --> pdb=" O VAL B1019 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N VAL B1019 " --> pdb=" O LEU B1068 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N PHE B1070 " --> pdb=" O LYS B1017 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N LYS B1017 " --> pdb=" O PHE B1070 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA C 57 " --> pdb=" O TYR B1024 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 60 through 61 removed outlier: 4.639A pdb=" N MET C 34 " --> pdb=" O ARG C 210 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ARG C 3 " --> pdb=" O LEU C 238 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N PHE C 240 " --> pdb=" O ARG C 3 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N TYR C 5 " --> pdb=" O PHE C 240 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ARG C 266 " --> pdb=" O GLU C 322 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ASP C 324 " --> pdb=" O ARG C 266 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 365 through 366 removed outlier: 5.972A pdb=" N ARG C 365 " --> pdb=" O TYR C 760 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 437 through 439 removed outlier: 7.379A pdb=" N ILE C 408 " --> pdb=" O ASN C 660 " (cutoff:3.500A) removed outlier: 8.236A pdb=" N CYS C 662 " --> pdb=" O ILE C 408 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N VAL C 410 " --> pdb=" O CYS C 662 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ILE C 409 " --> pdb=" O CYS C 676 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N LEU C 678 " --> pdb=" O ILE C 409 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N MET C 411 " --> pdb=" O LEU C 678 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N VAL C 675 " --> pdb=" O TYR C 728 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N SER C 730 " --> pdb=" O VAL C 675 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N LEU C 677 " --> pdb=" O SER C 730 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N ILE C 732 " --> pdb=" O LEU C 677 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N THR C 375 " --> pdb=" O ILE C 729 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N TYR C 731 " --> pdb=" O THR C 375 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N HIS C 377 " --> pdb=" O TYR C 731 " (cutoff:3.500A) removed outlier: 8.734A pdb=" N CYS C 782 " --> pdb=" O ILE C 374 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N PHE C 376 " --> pdb=" O CYS C 782 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 939 through 947 removed outlier: 5.507A pdb=" N GLN C 939 " --> pdb=" O GLN C 958 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLN C 958 " --> pdb=" O GLN C 939 " (cutoff:3.500A) removed outlier: 15.623A pdb=" N LEU C 956 " --> pdb=" O TRP C 967 " (cutoff:3.500A) removed outlier: 13.231A pdb=" N TRP C 967 " --> pdb=" O LEU C 956 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N GLN C 958 " --> pdb=" O LEU C 965 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N LEU C 965 " --> pdb=" O GLN C 958 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N LEU C 964 " --> pdb=" O ARG C 997 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N PHE C 999 " --> pdb=" O LEU C 964 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N ARG C 966 " --> pdb=" O PHE C 999 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 53 through 54 removed outlier: 6.046A pdb=" N SER D 92 " --> pdb=" O LEU D 102 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 167 through 170 removed outlier: 3.576A pdb=" N GLY D 296 " --> pdb=" O ILE D 169 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ARG D 200 " --> pdb=" O VAL D 267 " (cutoff:3.500A) removed outlier: 8.933A pdb=" N SER D 238 " --> pdb=" O ILE D 199 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N LEU D 201 " --> pdb=" O SER D 238 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 393 through 396 removed outlier: 7.246A pdb=" N ASP D 547 " --> pdb=" O ARG D 574 " (cutoff:3.500A) removed outlier: 8.658A pdb=" N MET D 536 " --> pdb=" O TYR D 438 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N LEU D 440 " --> pdb=" O MET D 536 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 519 through 522 removed outlier: 4.450A pdb=" N ALA D 513 " --> pdb=" O ILE D 498 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ILE D 498 " --> pdb=" O ALA D 513 " (cutoff:3.500A) 1048 hydrogen bonds defined for protein. 3075 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 42 hydrogen bonds 80 hydrogen bond angles 0 basepair planarities 17 basepair parallelities 39 stacking parallelities Total time for adding SS restraints: 4.68 Time building geometry restraints manager: 2.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6774 1.34 - 1.45: 4450 1.45 - 1.57: 13247 1.57 - 1.69: 134 1.69 - 1.81: 169 Bond restraints: 24774 Sorted by residual: bond pdb=" O3' DC X 80 " pdb=" P DT X 81 " ideal model delta sigma weight residual 1.607 1.679 -0.072 1.20e-02 6.94e+03 3.64e+01 bond pdb=" C4' DT X 81 " pdb=" O4' DT X 81 " ideal model delta sigma weight residual 1.446 1.393 0.053 1.00e-02 1.00e+04 2.80e+01 bond pdb=" P DT X 81 " pdb=" OP1 DT X 81 " ideal model delta sigma weight residual 1.480 1.551 -0.071 2.00e-02 2.50e+03 1.26e+01 bond pdb=" C3' DT X 87 " pdb=" C2' DT X 87 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.07e+01 bond pdb=" C2' DG X 79 " pdb=" C1' DG X 79 " ideal model delta sigma weight residual 1.518 1.549 -0.031 1.00e-02 1.00e+04 9.50e+00 ... (remaining 24769 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.32: 33509 2.32 - 4.63: 359 4.63 - 6.95: 27 6.95 - 9.27: 10 9.27 - 11.59: 3 Bond angle restraints: 33908 Sorted by residual: angle pdb=" N LEU C 664 " pdb=" CA LEU C 664 " pdb=" C LEU C 664 " ideal model delta sigma weight residual 111.28 122.87 -11.59 1.09e+00 8.42e-01 1.13e+02 angle pdb=" O5' DC X 80 " pdb=" C5' DC X 80 " pdb=" C4' DC X 80 " ideal model delta sigma weight residual 109.40 115.80 -6.40 8.00e-01 1.56e+00 6.40e+01 angle pdb=" N MET C 665 " pdb=" CA MET C 665 " pdb=" C MET C 665 " ideal model delta sigma weight residual 113.16 123.90 -10.74 1.42e+00 4.96e-01 5.72e+01 angle pdb=" N ILE B 323 " pdb=" CA ILE B 323 " pdb=" C ILE B 323 " ideal model delta sigma weight residual 112.29 107.22 5.07 9.40e-01 1.13e+00 2.91e+01 angle pdb=" O4' DT X 5 " pdb=" C4' DT X 5 " pdb=" C3' DT X 5 " ideal model delta sigma weight residual 106.00 103.22 2.78 6.00e-01 2.78e+00 2.15e+01 ... (remaining 33903 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 13594 17.86 - 35.71: 776 35.71 - 53.57: 322 53.57 - 71.42: 54 71.42 - 89.28: 9 Dihedral angle restraints: 14755 sinusoidal: 6466 harmonic: 8289 Sorted by residual: dihedral pdb=" N MET C 665 " pdb=" C MET C 665 " pdb=" CA MET C 665 " pdb=" CB MET C 665 " ideal model delta harmonic sigma weight residual 122.80 131.57 -8.77 0 2.50e+00 1.60e-01 1.23e+01 dihedral pdb=" C MET C 665 " pdb=" N MET C 665 " pdb=" CA MET C 665 " pdb=" CB MET C 665 " ideal model delta harmonic sigma weight residual -122.60 -131.28 8.68 0 2.50e+00 1.60e-01 1.21e+01 dihedral pdb=" CA SER C 419 " pdb=" C SER C 419 " pdb=" N PRO C 420 " pdb=" CA PRO C 420 " ideal model delta harmonic sigma weight residual 180.00 163.74 16.26 0 5.00e+00 4.00e-02 1.06e+01 ... (remaining 14752 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 3550 0.093 - 0.187: 170 0.187 - 0.280: 5 0.280 - 0.373: 2 0.373 - 0.466: 2 Chirality restraints: 3729 Sorted by residual: chirality pdb=" CA MET C 665 " pdb=" N MET C 665 " pdb=" C MET C 665 " pdb=" CB MET C 665 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.44e+00 chirality pdb=" C4' DT X 81 " pdb=" C5' DT X 81 " pdb=" O4' DT X 81 " pdb=" C3' DT X 81 " both_signs ideal model delta sigma weight residual False -2.53 -2.10 -0.43 2.00e-01 2.50e+01 4.64e+00 chirality pdb=" CA LEU C 664 " pdb=" N LEU C 664 " pdb=" C LEU C 664 " pdb=" CB LEU C 664 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.26e+00 ... (remaining 3726 not shown) Planarity restraints: 4219 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG X 79 " -0.021 2.00e-02 2.50e+03 1.57e-02 7.44e+00 pdb=" N9 DG X 79 " -0.014 2.00e-02 2.50e+03 pdb=" C8 DG X 79 " 0.043 2.00e-02 2.50e+03 pdb=" N7 DG X 79 " -0.002 2.00e-02 2.50e+03 pdb=" C5 DG X 79 " 0.000 2.00e-02 2.50e+03 pdb=" C6 DG X 79 " -0.001 2.00e-02 2.50e+03 pdb=" O6 DG X 79 " -0.018 2.00e-02 2.50e+03 pdb=" N1 DG X 79 " -0.002 2.00e-02 2.50e+03 pdb=" C2 DG X 79 " 0.007 2.00e-02 2.50e+03 pdb=" N2 DG X 79 " 0.012 2.00e-02 2.50e+03 pdb=" N3 DG X 79 " -0.001 2.00e-02 2.50e+03 pdb=" C4 DG X 79 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER C 419 " -0.040 5.00e-02 4.00e+02 5.93e-02 5.63e+00 pdb=" N PRO C 420 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO C 420 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO C 420 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 304 " 0.036 5.00e-02 4.00e+02 5.41e-02 4.68e+00 pdb=" N PRO B 305 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO B 305 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 305 " 0.031 5.00e-02 4.00e+02 ... (remaining 4216 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 3238 2.76 - 3.30: 21004 3.30 - 3.83: 40288 3.83 - 4.37: 45781 4.37 - 4.90: 78345 Nonbonded interactions: 188656 Sorted by model distance: nonbonded pdb=" NH2 ARG C 668 " pdb=" OD1 ASP C 711 " model vdw 2.227 3.120 nonbonded pdb=" O ILE C 670 " pdb=" OG SER C 722 " model vdw 2.271 3.040 nonbonded pdb=" O2 DC X 27 " pdb=" N2 DG X 59 " model vdw 2.304 2.496 nonbonded pdb=" O THR D 533 " pdb=" OG1 THR D 533 " model vdw 2.314 3.040 nonbonded pdb=" O TYR C 754 " pdb=" OG SER C 758 " model vdw 2.329 3.040 ... (remaining 188651 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.280 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: 0.000 Extract box with map and model: 0.280 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 21.240 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.050 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:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 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 : 0.003 0.072 24774 Z= 0.242 Angle : 0.609 11.586 33908 Z= 0.428 Chirality : 0.043 0.466 3729 Planarity : 0.005 0.059 4219 Dihedral : 13.428 89.279 9383 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.57 % Allowed : 5.38 % Favored : 92.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % 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: -3.60 (0.12), residues: 2837 helix: -2.56 (0.09), residues: 1389 sheet: -1.02 (0.28), residues: 301 loop : -2.35 (0.14), residues: 1147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 761 TYR 0.012 0.001 TYR C 190 PHE 0.015 0.001 PHE B1023 TRP 0.012 0.001 TRP B 652 HIS 0.004 0.000 HIS D 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.24 (24774) covalent geometry : angle 0.60892 / 0.43 (33908) hydrogen bonds : bond 0.14289 / 9.73 ( 1090) hydrogen bonds : angle 6.19066 / 4.43 ( 3155) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 730 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 668 time to evaluate : 0.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 159 LEU cc_start: 0.8762 (mp) cc_final: 0.8142 (mt) REVERT: B 234 GLN cc_start: 0.8943 (tt0) cc_final: 0.8688 (mm110) REVERT: B 610 ASN cc_start: 0.8781 (t0) cc_final: 0.8493 (t0) REVERT: B 646 ASP cc_start: 0.8629 (t0) cc_final: 0.8366 (t0) REVERT: B 832 ASP cc_start: 0.7810 (m-30) cc_final: 0.7418 (m-30) REVERT: B 1053 LEU cc_start: 0.5128 (OUTLIER) cc_final: 0.4515 (mp) REVERT: B 1079 LEU cc_start: 0.9064 (tp) cc_final: 0.8716 (tp) REVERT: C 509 ASP cc_start: 0.7973 (t0) cc_final: 0.7457 (t0) REVERT: C 548 LEU cc_start: 0.9305 (tp) cc_final: 0.9074 (tp) REVERT: C 554 SER cc_start: 0.8234 (p) cc_final: 0.7935 (t) REVERT: C 978 MET cc_start: 0.8942 (tpp) cc_final: 0.8555 (tpp) REVERT: D 68 LEU cc_start: 0.6554 (pp) cc_final: 0.6197 (mt) REVERT: D 116 GLU cc_start: 0.8494 (tp30) cc_final: 0.8282 (tp30) REVERT: D 350 ASP cc_start: 0.7248 (OUTLIER) cc_final: 0.6881 (t70) REVERT: D 404 TYR cc_start: 0.8411 (t80) cc_final: 0.7035 (t80) REVERT: D 462 MET cc_start: 0.8349 (mmt) cc_final: 0.7922 (mmp) outliers start: 62 outliers final: 14 residues processed: 708 average time/residue: 0.1782 time to fit residues: 190.6958 Evaluate side-chains 343 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 327 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 758 THR Chi-restraints excluded: chain B residue 947 ARG Chi-restraints excluded: chain B residue 1002 LEU Chi-restraints excluded: chain B residue 1027 ILE Chi-restraints excluded: chain B residue 1053 LEU Chi-restraints excluded: chain B residue 1111 TYR Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 506 ILE Chi-restraints excluded: chain C residue 853 LEU Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 350 ASP Chi-restraints excluded: chain D residue 502 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 3.9990 chunk 111 optimal weight: 30.0000 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 120 GLN B 181 GLN B 191 GLN B 222 HIS B 261 ASN B 278 ASN B 402 HIS B 455 ASN B 458 ASN B 463 GLN B 594 GLN B 610 ASN ** B 705 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 713 GLN B 765 GLN B 834 HIS B 848 GLN B 900 ASN B 943 HIS B 944 GLN B1072 HIS B1134 HIS C 6 HIS C 8 ASN ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 52 GLN C 162 GLN C 181 GLN C 264 GLN C 570 GLN C 660 ASN C 749 GLN C 759 HIS C 822 GLN C 843 HIS C 883 GLN C 925 GLN C 951 GLN ** C 958 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1110 GLN D 22 GLN D 89 GLN D 115 ASN D 128 HIS D 251 GLN D 455 ASN D 469 HIS D 542 GLN Total number of N/Q/H flips: 45 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.089934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.070687 restraints weight = 72624.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.072869 restraints weight = 38032.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.074312 restraints weight = 24862.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.075264 restraints weight = 18695.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.075831 restraints weight = 15471.965| |-----------------------------------------------------------------------------| r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.2793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 24774 Z= 0.203 Angle : 0.660 12.115 33908 Z= 0.342 Chirality : 0.043 0.222 3729 Planarity : 0.005 0.059 4219 Dihedral : 14.653 84.521 3874 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 3.64 % Allowed : 11.55 % Favored : 84.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % 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: -1.34 (0.14), residues: 2837 helix: -0.16 (0.13), residues: 1409 sheet: -0.44 (0.29), residues: 284 loop : -1.88 (0.16), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 254 TYR 0.025 0.002 TYR B1111 PHE 0.017 0.001 PHE D 145 TRP 0.014 0.001 TRP B 901 HIS 0.006 0.001 HIS C 390 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.20 (24774) covalent geometry : angle 0.66007 / 0.34 (33908) hydrogen bonds : bond 0.04010 / 2.54 ( 1090) hydrogen bonds : angle 4.29266 / 3.01 ( 3155) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 304 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 146 MET cc_start: 0.7579 (mmm) cc_final: 0.7327 (mmm) REVERT: B 234 GLN cc_start: 0.9014 (tt0) cc_final: 0.8705 (mm110) REVERT: B 491 PHE cc_start: 0.6840 (OUTLIER) cc_final: 0.4742 (m-80) REVERT: B 646 ASP cc_start: 0.8759 (t0) cc_final: 0.8390 (t0) REVERT: B 1053 LEU cc_start: 0.4789 (OUTLIER) cc_final: 0.4144 (mp) REVERT: C 42 MET cc_start: 0.8472 (tmm) cc_final: 0.8052 (tmm) REVERT: C 569 MET cc_start: 0.7499 (tpp) cc_final: 0.7175 (tpp) REVERT: C 573 ILE cc_start: 0.9227 (mm) cc_final: 0.9002 (mm) REVERT: C 665 MET cc_start: 0.8338 (mtp) cc_final: 0.7966 (ttm) REVERT: D 68 LEU cc_start: 0.6363 (pp) cc_final: 0.5937 (mt) REVERT: D 100 MET cc_start: 0.8937 (mtm) cc_final: 0.8731 (mtm) REVERT: D 279 MET cc_start: 0.9068 (tpp) cc_final: 0.8843 (tpp) REVERT: D 329 LEU cc_start: 0.8967 (mp) cc_final: 0.8756 (tp) REVERT: D 408 LEU cc_start: 0.8867 (mt) cc_final: 0.8656 (mt) REVERT: D 449 PHE cc_start: 0.8268 (m-10) cc_final: 0.7964 (m-80) REVERT: D 462 MET cc_start: 0.8438 (mmt) cc_final: 0.8203 (mmp) REVERT: D 504 ARG cc_start: 0.8201 (tpt90) cc_final: 0.7835 (tpp80) REVERT: D 564 GLU cc_start: 0.8285 (mp0) cc_final: 0.7925 (mp0) outliers start: 88 outliers final: 46 residues processed: 366 average time/residue: 0.1631 time to fit residues: 95.2582 Evaluate side-chains 279 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 231 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 382 MET Chi-restraints excluded: chain B residue 491 PHE Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 582 SER Chi-restraints excluded: chain B residue 605 THR Chi-restraints excluded: chain B residue 699 THR Chi-restraints excluded: chain B residue 727 MET Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 752 VAL Chi-restraints excluded: chain B residue 753 TRP Chi-restraints excluded: chain B residue 982 PHE Chi-restraints excluded: chain B residue 998 LEU Chi-restraints excluded: chain B residue 1002 LEU Chi-restraints excluded: chain B residue 1019 VAL Chi-restraints excluded: chain B residue 1027 ILE Chi-restraints excluded: chain B residue 1053 LEU Chi-restraints excluded: chain B residue 1069 VAL Chi-restraints excluded: chain B residue 1111 TYR Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 178 GLN Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 484 ASP Chi-restraints excluded: chain C residue 499 GLU Chi-restraints excluded: chain C residue 506 ILE Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 853 LEU Chi-restraints excluded: chain C residue 889 VAL Chi-restraints excluded: chain C residue 1036 LEU Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 65 HIS Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 350 ASP Chi-restraints excluded: chain D residue 493 LEU Chi-restraints excluded: chain D residue 537 THR Chi-restraints excluded: chain D residue 538 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 48 optimal weight: 10.0000 chunk 233 optimal weight: 4.9990 chunk 158 optimal weight: 7.9990 chunk 26 optimal weight: 8.9990 chunk 138 optimal weight: 20.0000 chunk 47 optimal weight: 1.9990 chunk 209 optimal weight: 1.9990 chunk 279 optimal weight: 0.9980 chunk 150 optimal weight: 0.9990 chunk 179 optimal weight: 5.9990 chunk 60 optimal weight: 1.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 150 GLN B 162 GLN B 191 GLN ** B 689 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 705 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 GLN C 614 GLN C 724 GLN ** C 958 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 979 GLN C1110 GLN D 423 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.089580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.070246 restraints weight = 72783.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.072413 restraints weight = 38572.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.073839 restraints weight = 25408.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.074770 restraints weight = 19212.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.075329 restraints weight = 15919.930| |-----------------------------------------------------------------------------| r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.3203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 24774 Z= 0.132 Angle : 0.557 9.854 33908 Z= 0.291 Chirality : 0.040 0.155 3729 Planarity : 0.004 0.037 4219 Dihedral : 14.571 89.482 3861 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.31 % Allowed : 12.05 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % 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: -0.48 (0.15), residues: 2837 helix: 0.72 (0.14), residues: 1405 sheet: -0.29 (0.29), residues: 286 loop : -1.63 (0.16), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C1082 TYR 0.029 0.001 TYR D 415 PHE 0.018 0.001 PHE B1070 TRP 0.014 0.001 TRP B 972 HIS 0.005 0.001 HIS D 539 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 (24774) covalent geometry : angle 0.55737 / 0.29 (33908) hydrogen bonds : bond 0.03573 / 2.27 ( 1090) hydrogen bonds : angle 4.01159 / 2.80 ( 3155) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 262 time to evaluate : 0.980 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 129 ILE cc_start: 0.8734 (mt) cc_final: 0.8484 (mt) REVERT: B 146 MET cc_start: 0.7673 (mmm) cc_final: 0.7337 (mmm) REVERT: B 234 GLN cc_start: 0.9028 (tt0) cc_final: 0.8744 (mm110) REVERT: B 491 PHE cc_start: 0.6831 (OUTLIER) cc_final: 0.5337 (m-80) REVERT: B 646 ASP cc_start: 0.8734 (t0) cc_final: 0.8376 (t0) REVERT: B 1053 LEU cc_start: 0.4959 (OUTLIER) cc_final: 0.4465 (mp) REVERT: C 42 MET cc_start: 0.8631 (tmm) cc_final: 0.8171 (tmm) REVERT: C 383 GLN cc_start: 0.7907 (tm-30) cc_final: 0.7454 (tt0) REVERT: C 475 ASP cc_start: 0.7963 (m-30) cc_final: 0.7645 (m-30) REVERT: C 665 MET cc_start: 0.8399 (mtp) cc_final: 0.7994 (ttm) REVERT: C 1031 MET cc_start: 0.9254 (mmt) cc_final: 0.9022 (mmm) REVERT: C 1072 LEU cc_start: 0.8507 (mt) cc_final: 0.8183 (mt) REVERT: D 279 MET cc_start: 0.9173 (tpp) cc_final: 0.8890 (tpp) REVERT: D 408 LEU cc_start: 0.8869 (mt) cc_final: 0.8625 (mt) REVERT: D 431 ILE cc_start: 0.9230 (mt) cc_final: 0.9015 (tp) REVERT: D 449 PHE cc_start: 0.8312 (m-10) cc_final: 0.7901 (m-80) REVERT: D 462 MET cc_start: 0.8517 (mmt) cc_final: 0.8232 (mmp) REVERT: D 504 ARG cc_start: 0.8232 (tpt90) cc_final: 0.7897 (tpp80) REVERT: D 564 GLU cc_start: 0.8466 (mp0) cc_final: 0.8045 (mp0) REVERT: D 594 THR cc_start: 0.8936 (OUTLIER) cc_final: 0.7976 (p) outliers start: 80 outliers final: 47 residues processed: 319 average time/residue: 0.1520 time to fit residues: 79.8837 Evaluate side-chains 284 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 234 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 382 MET Chi-restraints excluded: chain B residue 426 ASP Chi-restraints excluded: chain B residue 491 PHE Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 582 SER Chi-restraints excluded: chain B residue 605 THR Chi-restraints excluded: chain B residue 699 THR Chi-restraints excluded: chain B residue 727 MET Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 752 VAL Chi-restraints excluded: chain B residue 753 TRP Chi-restraints excluded: chain B residue 982 PHE Chi-restraints excluded: chain B residue 998 LEU Chi-restraints excluded: chain B residue 1002 LEU Chi-restraints excluded: chain B residue 1019 VAL Chi-restraints excluded: chain B residue 1027 ILE Chi-restraints excluded: chain B residue 1053 LEU Chi-restraints excluded: chain B residue 1069 VAL Chi-restraints excluded: chain B residue 1111 TYR Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 178 GLN Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 479 LEU Chi-restraints excluded: chain C residue 506 ILE Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 853 LEU Chi-restraints excluded: chain C residue 889 VAL Chi-restraints excluded: chain C residue 1036 LEU Chi-restraints excluded: chain C residue 1114 LEU Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 236 ASP Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 265 VAL Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 324 GLU Chi-restraints excluded: chain D residue 350 ASP Chi-restraints excluded: chain D residue 493 LEU Chi-restraints excluded: chain D residue 537 THR Chi-restraints excluded: chain D residue 594 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 277 optimal weight: 9.9990 chunk 267 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 99 optimal weight: 20.0000 chunk 141 optimal weight: 10.0000 chunk 153 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 chunk 227 optimal weight: 10.0000 chunk 197 optimal weight: 6.9990 chunk 196 optimal weight: 0.8980 chunk 171 optimal weight: 6.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 689 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 900 ASN C 8 ASN C 137 GLN C 614 GLN ** C 984 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1108 GLN D 229 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.087091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.067431 restraints weight = 73574.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.069545 restraints weight = 39351.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.070934 restraints weight = 26125.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.071843 restraints weight = 19911.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.072412 restraints weight = 16646.245| |-----------------------------------------------------------------------------| r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.3642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 24774 Z= 0.172 Angle : 0.580 9.571 33908 Z= 0.299 Chirality : 0.041 0.173 3729 Planarity : 0.004 0.058 4219 Dihedral : 14.646 89.968 3861 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 3.73 % Allowed : 12.26 % Favored : 84.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % 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: 0.16 (0.16), residues: 2837 helix: 1.28 (0.14), residues: 1411 sheet: -0.08 (0.30), residues: 273 loop : -1.34 (0.17), residues: 1153 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C1082 TYR 0.018 0.001 TYR B1111 PHE 0.015 0.001 PHE C1117 TRP 0.013 0.001 TRP B 901 HIS 0.005 0.001 HIS B 705 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.17 (24774) covalent geometry : angle 0.58030 / 0.30 (33908) hydrogen bonds : bond 0.03546 / 2.25 ( 1090) hydrogen bonds : angle 3.90105 / 2.73 ( 3155) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 250 time to evaluate : 0.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 129 ILE cc_start: 0.8873 (mt) cc_final: 0.8598 (mt) REVERT: B 146 MET cc_start: 0.7747 (mmm) cc_final: 0.7341 (mmm) REVERT: B 234 GLN cc_start: 0.9014 (tt0) cc_final: 0.8708 (mm110) REVERT: B 304 THR cc_start: 0.7220 (OUTLIER) cc_final: 0.6981 (p) REVERT: B 491 PHE cc_start: 0.6827 (OUTLIER) cc_final: 0.5663 (m-80) REVERT: B 1021 MET cc_start: 0.8482 (tpp) cc_final: 0.8107 (tpp) REVERT: B 1053 LEU cc_start: 0.4810 (OUTLIER) cc_final: 0.4230 (mp) REVERT: C 42 MET cc_start: 0.8727 (tmm) cc_final: 0.8427 (tmm) REVERT: C 475 ASP cc_start: 0.8002 (m-30) cc_final: 0.7684 (m-30) REVERT: C 665 MET cc_start: 0.8449 (mtp) cc_final: 0.8089 (ttm) REVERT: C 817 HIS cc_start: 0.8489 (OUTLIER) cc_final: 0.8263 (m90) REVERT: C 1072 LEU cc_start: 0.8606 (mt) cc_final: 0.8309 (mt) REVERT: D 35 VAL cc_start: 0.9575 (OUTLIER) cc_final: 0.9322 (p) REVERT: D 279 MET cc_start: 0.9199 (tpp) cc_final: 0.8986 (tpp) REVERT: D 408 LEU cc_start: 0.8865 (mt) cc_final: 0.8616 (mt) REVERT: D 462 MET cc_start: 0.8560 (mmt) cc_final: 0.8200 (mmp) REVERT: D 504 ARG cc_start: 0.8297 (tpt90) cc_final: 0.7964 (tpp80) REVERT: D 564 GLU cc_start: 0.8510 (mp0) cc_final: 0.7995 (mp0) REVERT: D 594 THR cc_start: 0.8922 (OUTLIER) cc_final: 0.8127 (p) outliers start: 90 outliers final: 49 residues processed: 311 average time/residue: 0.1451 time to fit residues: 75.6672 Evaluate side-chains 278 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 223 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 382 MET Chi-restraints excluded: chain B residue 491 PHE Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 582 SER Chi-restraints excluded: chain B residue 605 THR Chi-restraints excluded: chain B residue 619 SER Chi-restraints excluded: chain B residue 699 THR Chi-restraints excluded: chain B residue 727 MET Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 752 VAL Chi-restraints excluded: chain B residue 753 TRP Chi-restraints excluded: chain B residue 758 THR Chi-restraints excluded: chain B residue 982 PHE Chi-restraints excluded: chain B residue 998 LEU Chi-restraints excluded: chain B residue 1002 LEU Chi-restraints excluded: chain B residue 1019 VAL Chi-restraints excluded: chain B residue 1027 ILE Chi-restraints excluded: chain B residue 1053 LEU Chi-restraints excluded: chain B residue 1069 VAL Chi-restraints excluded: chain B residue 1109 LEU Chi-restraints excluded: chain B residue 1111 TYR Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 38 GLN Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 178 GLN Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 479 LEU Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 817 HIS Chi-restraints excluded: chain C residue 853 LEU Chi-restraints excluded: chain C residue 889 VAL Chi-restraints excluded: chain C residue 1036 LEU Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 65 HIS Chi-restraints excluded: chain D residue 108 TYR Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 265 VAL Chi-restraints excluded: chain D residue 303 SER Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 350 ASP Chi-restraints excluded: chain D residue 493 LEU Chi-restraints excluded: chain D residue 594 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 172 optimal weight: 0.4980 chunk 81 optimal weight: 4.9990 chunk 130 optimal weight: 6.9990 chunk 169 optimal weight: 2.9990 chunk 224 optimal weight: 0.5980 chunk 25 optimal weight: 9.9990 chunk 48 optimal weight: 9.9990 chunk 252 optimal weight: 2.9990 chunk 158 optimal weight: 0.8980 chunk 63 optimal weight: 8.9990 chunk 248 optimal weight: 4.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 689 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 769 HIS B1035 GLN C 8 ASN C 614 GLN D 530 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.087199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.067441 restraints weight = 72803.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.069594 restraints weight = 38298.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.071016 restraints weight = 25237.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.071945 restraints weight = 19087.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.072565 restraints weight = 15882.158| |-----------------------------------------------------------------------------| r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.3787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 24774 Z= 0.127 Angle : 0.551 13.372 33908 Z= 0.283 Chirality : 0.040 0.202 3729 Planarity : 0.003 0.040 4219 Dihedral : 14.660 89.392 3859 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 3.27 % Allowed : 13.29 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % 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: 0.38 (0.16), residues: 2837 helix: 1.46 (0.14), residues: 1412 sheet: 0.06 (0.30), residues: 279 loop : -1.26 (0.17), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 728 TYR 0.016 0.001 TYR B1111 PHE 0.012 0.001 PHE B 428 TRP 0.014 0.001 TRP B 265 HIS 0.004 0.001 HIS B 705 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.13 (24774) covalent geometry : angle 0.55096 / 0.28 (33908) hydrogen bonds : bond 0.03360 / 2.13 ( 1090) hydrogen bonds : angle 3.83005 / 2.68 ( 3155) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 241 time to evaluate : 0.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 146 MET cc_start: 0.7716 (mmm) cc_final: 0.7296 (mmm) REVERT: B 234 GLN cc_start: 0.9030 (tt0) cc_final: 0.8727 (mm110) REVERT: B 304 THR cc_start: 0.7189 (OUTLIER) cc_final: 0.6933 (p) REVERT: B 491 PHE cc_start: 0.6819 (OUTLIER) cc_final: 0.5634 (m-80) REVERT: B 947 ARG cc_start: 0.6559 (OUTLIER) cc_final: 0.6146 (ptp-170) REVERT: B 976 LYS cc_start: 0.8083 (pptt) cc_final: 0.7401 (mmtm) REVERT: B 1021 MET cc_start: 0.8456 (tpp) cc_final: 0.8026 (tpp) REVERT: B 1053 LEU cc_start: 0.4970 (OUTLIER) cc_final: 0.4441 (mp) REVERT: C 42 MET cc_start: 0.8712 (tmm) cc_final: 0.8347 (tmm) REVERT: C 46 LEU cc_start: 0.9194 (mm) cc_final: 0.8964 (mm) REVERT: C 47 GLN cc_start: 0.8850 (tt0) cc_final: 0.8588 (tt0) REVERT: C 665 MET cc_start: 0.8456 (mtp) cc_final: 0.8111 (ttm) REVERT: C 718 GLU cc_start: 0.7902 (tt0) cc_final: 0.7700 (tt0) REVERT: C 817 HIS cc_start: 0.8433 (OUTLIER) cc_final: 0.8191 (m90) REVERT: C 1031 MET cc_start: 0.9286 (mmt) cc_final: 0.9015 (mmm) REVERT: D 35 VAL cc_start: 0.9572 (OUTLIER) cc_final: 0.9332 (p) REVERT: D 100 MET cc_start: 0.8936 (mtm) cc_final: 0.8617 (mtm) REVERT: D 279 MET cc_start: 0.9209 (tpp) cc_final: 0.8938 (tpp) REVERT: D 408 LEU cc_start: 0.8939 (mt) cc_final: 0.8654 (mt) REVERT: D 449 PHE cc_start: 0.8506 (m-10) cc_final: 0.7962 (m-80) REVERT: D 462 MET cc_start: 0.8608 (mmt) cc_final: 0.8277 (mmp) REVERT: D 564 GLU cc_start: 0.8564 (mp0) cc_final: 0.7900 (mp0) outliers start: 79 outliers final: 50 residues processed: 296 average time/residue: 0.1440 time to fit residues: 70.8149 Evaluate side-chains 275 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 219 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 382 MET Chi-restraints excluded: chain B residue 491 PHE Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 582 SER Chi-restraints excluded: chain B residue 605 THR Chi-restraints excluded: chain B residue 699 THR Chi-restraints excluded: chain B residue 727 MET Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 752 VAL Chi-restraints excluded: chain B residue 753 TRP Chi-restraints excluded: chain B residue 758 THR Chi-restraints excluded: chain B residue 853 LEU Chi-restraints excluded: chain B residue 947 ARG Chi-restraints excluded: chain B residue 982 PHE Chi-restraints excluded: chain B residue 998 LEU Chi-restraints excluded: chain B residue 1002 LEU Chi-restraints excluded: chain B residue 1019 VAL Chi-restraints excluded: chain B residue 1027 ILE Chi-restraints excluded: chain B residue 1053 LEU Chi-restraints excluded: chain B residue 1066 ILE Chi-restraints excluded: chain B residue 1069 VAL Chi-restraints excluded: chain B residue 1109 LEU Chi-restraints excluded: chain B residue 1111 TYR Chi-restraints excluded: chain B residue 1155 ILE Chi-restraints excluded: chain B residue 1171 MET Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 38 GLN Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 479 LEU Chi-restraints excluded: chain C residue 506 ILE Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 817 HIS Chi-restraints excluded: chain C residue 853 LEU Chi-restraints excluded: chain C residue 889 VAL Chi-restraints excluded: chain C residue 1046 LEU Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 65 HIS Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 143 LYS Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 265 VAL Chi-restraints excluded: chain D residue 303 SER Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 324 GLU Chi-restraints excluded: chain D residue 350 ASP Chi-restraints excluded: chain D residue 493 LEU Chi-restraints excluded: chain D residue 532 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 90 optimal weight: 0.5980 chunk 246 optimal weight: 8.9990 chunk 47 optimal weight: 6.9990 chunk 27 optimal weight: 7.9990 chunk 67 optimal weight: 3.9990 chunk 204 optimal weight: 10.0000 chunk 49 optimal weight: 8.9990 chunk 135 optimal weight: 6.9990 chunk 93 optimal weight: 7.9990 chunk 260 optimal weight: 0.9990 chunk 284 optimal weight: 30.0000 overall best weight: 3.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 402 HIS B 624 ASN ** B 689 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1003 ASN B1035 GLN C 614 GLN C 886 ASN ** C 984 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 530 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.083875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.064033 restraints weight = 73522.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.066062 restraints weight = 39383.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.067423 restraints weight = 26300.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.068326 restraints weight = 20088.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.068870 restraints weight = 16798.318| |-----------------------------------------------------------------------------| r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.4210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 24774 Z= 0.220 Angle : 0.627 13.567 33908 Z= 0.318 Chirality : 0.042 0.196 3729 Planarity : 0.004 0.043 4219 Dihedral : 14.797 89.582 3859 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.27 % Allowed : 14.12 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % 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: 0.47 (0.16), residues: 2837 helix: 1.54 (0.14), residues: 1414 sheet: -0.12 (0.30), residues: 282 loop : -1.15 (0.18), residues: 1141 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 728 TYR 0.016 0.002 TYR C 190 PHE 0.030 0.002 PHE D 386 TRP 0.016 0.001 TRP B 901 HIS 0.006 0.001 HIS C 233 Details of bonding type rmsd/Z covalent geometry : bond 0.00489 / 0.22 (24774) covalent geometry : angle 0.62655 / 0.32 (33908) hydrogen bonds : bond 0.03731 / 2.36 ( 1090) hydrogen bonds : angle 4.00673 / 2.81 ( 3155) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 227 time to evaluate : 0.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 146 MET cc_start: 0.7857 (mmm) cc_final: 0.7412 (mmm) REVERT: B 234 GLN cc_start: 0.9012 (tt0) cc_final: 0.8684 (mm110) REVERT: B 259 ARG cc_start: 0.8135 (ttt180) cc_final: 0.7874 (ttt180) REVERT: B 304 THR cc_start: 0.7100 (OUTLIER) cc_final: 0.6846 (p) REVERT: B 491 PHE cc_start: 0.6862 (OUTLIER) cc_final: 0.5560 (m-80) REVERT: B 947 ARG cc_start: 0.6693 (OUTLIER) cc_final: 0.6411 (ptp-170) REVERT: B 976 LYS cc_start: 0.8103 (pptt) cc_final: 0.7453 (mmtm) REVERT: B 1021 MET cc_start: 0.8524 (tpp) cc_final: 0.8059 (tpp) REVERT: C 42 MET cc_start: 0.8745 (tmm) cc_final: 0.8499 (tmm) REVERT: C 665 MET cc_start: 0.8568 (mtp) cc_final: 0.8120 (ttm) REVERT: C 718 GLU cc_start: 0.8087 (tt0) cc_final: 0.7673 (tm-30) REVERT: C 817 HIS cc_start: 0.8550 (OUTLIER) cc_final: 0.8336 (m90) REVERT: C 1031 MET cc_start: 0.9298 (mmt) cc_final: 0.9035 (mmm) REVERT: D 279 MET cc_start: 0.9287 (tpp) cc_final: 0.9055 (tpp) REVERT: D 408 LEU cc_start: 0.8979 (mt) cc_final: 0.8710 (mt) REVERT: D 462 MET cc_start: 0.8582 (mmt) cc_final: 0.8306 (mmp) REVERT: D 564 GLU cc_start: 0.8653 (mp0) cc_final: 0.7900 (mp0) outliers start: 79 outliers final: 61 residues processed: 284 average time/residue: 0.1541 time to fit residues: 71.4384 Evaluate side-chains 270 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 205 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 457 VAL Chi-restraints excluded: chain B residue 491 PHE Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 582 SER Chi-restraints excluded: chain B residue 605 THR Chi-restraints excluded: chain B residue 619 SER Chi-restraints excluded: chain B residue 699 THR Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 752 VAL Chi-restraints excluded: chain B residue 753 TRP Chi-restraints excluded: chain B residue 758 THR Chi-restraints excluded: chain B residue 853 LEU Chi-restraints excluded: chain B residue 947 ARG Chi-restraints excluded: chain B residue 982 PHE Chi-restraints excluded: chain B residue 998 LEU Chi-restraints excluded: chain B residue 1002 LEU Chi-restraints excluded: chain B residue 1019 VAL Chi-restraints excluded: chain B residue 1027 ILE Chi-restraints excluded: chain B residue 1053 LEU Chi-restraints excluded: chain B residue 1066 ILE Chi-restraints excluded: chain B residue 1069 VAL Chi-restraints excluded: chain B residue 1111 TYR Chi-restraints excluded: chain B residue 1155 ILE Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 38 GLN Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 178 GLN Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 479 LEU Chi-restraints excluded: chain C residue 506 ILE Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 569 MET Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 817 HIS Chi-restraints excluded: chain C residue 853 LEU Chi-restraints excluded: chain C residue 889 VAL Chi-restraints excluded: chain C residue 1036 LEU Chi-restraints excluded: chain C residue 1046 LEU Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 65 HIS Chi-restraints excluded: chain D residue 108 TYR Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 265 VAL Chi-restraints excluded: chain D residue 280 SER Chi-restraints excluded: chain D residue 303 SER Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 324 GLU Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain D residue 350 ASP Chi-restraints excluded: chain D residue 493 LEU Chi-restraints excluded: chain D residue 532 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 43 optimal weight: 9.9990 chunk 206 optimal weight: 9.9990 chunk 115 optimal weight: 8.9990 chunk 122 optimal weight: 0.9990 chunk 152 optimal weight: 7.9990 chunk 38 optimal weight: 2.9990 chunk 11 optimal weight: 7.9990 chunk 214 optimal weight: 5.9990 chunk 117 optimal weight: 9.9990 chunk 71 optimal weight: 0.0770 chunk 236 optimal weight: 10.0000 overall best weight: 3.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 689 HIS B1133 HIS C 510 ASN C 614 GLN ** C 984 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 530 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.083529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.063668 restraints weight = 73529.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.065713 restraints weight = 39267.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.067060 restraints weight = 26144.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.067953 restraints weight = 19996.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.068554 restraints weight = 16742.607| |-----------------------------------------------------------------------------| r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.4422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 24774 Z= 0.194 Angle : 0.595 12.751 33908 Z= 0.305 Chirality : 0.042 0.368 3729 Planarity : 0.004 0.034 4219 Dihedral : 14.874 89.817 3859 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.94 % Allowed : 15.07 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % 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 (0.16), residues: 2837 helix: 1.62 (0.14), residues: 1412 sheet: -0.05 (0.31), residues: 267 loop : -1.12 (0.18), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 592 TYR 0.024 0.002 TYR B1093 PHE 0.035 0.001 PHE D 386 TRP 0.035 0.001 TRP B1085 HIS 0.005 0.001 HIS B 689 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.19 (24774) covalent geometry : angle 0.59485 / 0.30 (33908) hydrogen bonds : bond 0.03614 / 2.28 ( 1090) hydrogen bonds : angle 3.93933 / 2.77 ( 3155) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 223 time to evaluate : 0.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 146 MET cc_start: 0.7854 (mmm) cc_final: 0.7452 (mmm) REVERT: B 234 GLN cc_start: 0.9015 (tt0) cc_final: 0.8697 (mm110) REVERT: B 259 ARG cc_start: 0.8114 (ttt180) cc_final: 0.7841 (ttt180) REVERT: B 274 GLU cc_start: 0.7942 (pm20) cc_final: 0.7287 (pp20) REVERT: B 304 THR cc_start: 0.7042 (OUTLIER) cc_final: 0.6793 (p) REVERT: B 947 ARG cc_start: 0.6705 (OUTLIER) cc_final: 0.6457 (ptp-170) REVERT: B 976 LYS cc_start: 0.8118 (pptt) cc_final: 0.7461 (mmtm) REVERT: B 1021 MET cc_start: 0.8515 (tpp) cc_final: 0.8013 (tpp) REVERT: B 1061 MET cc_start: 0.7078 (mpp) cc_final: 0.6842 (mmt) REVERT: B 1070 PHE cc_start: 0.8988 (p90) cc_final: 0.8745 (p90) REVERT: C 17 MET cc_start: 0.9074 (tmm) cc_final: 0.8366 (ptp) REVERT: C 42 MET cc_start: 0.8796 (OUTLIER) cc_final: 0.8593 (tmm) REVERT: C 46 LEU cc_start: 0.9267 (OUTLIER) cc_final: 0.9047 (tp) REVERT: C 665 MET cc_start: 0.8582 (mtp) cc_final: 0.8103 (ttm) REVERT: C 718 GLU cc_start: 0.8123 (tt0) cc_final: 0.7752 (tm-30) REVERT: C 817 HIS cc_start: 0.8561 (OUTLIER) cc_final: 0.8345 (m90) REVERT: C 1031 MET cc_start: 0.9305 (mmt) cc_final: 0.9019 (mmm) REVERT: D 35 VAL cc_start: 0.9617 (OUTLIER) cc_final: 0.9395 (p) REVERT: D 408 LEU cc_start: 0.8939 (mt) cc_final: 0.8666 (mt) REVERT: D 449 PHE cc_start: 0.8494 (m-10) cc_final: 0.8130 (m-80) REVERT: D 462 MET cc_start: 0.8563 (mmt) cc_final: 0.8272 (mmp) REVERT: D 504 ARG cc_start: 0.8393 (tpt90) cc_final: 0.7954 (tpp80) outliers start: 71 outliers final: 54 residues processed: 272 average time/residue: 0.1498 time to fit residues: 66.9872 Evaluate side-chains 259 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 199 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 582 SER Chi-restraints excluded: chain B residue 605 THR Chi-restraints excluded: chain B residue 619 SER Chi-restraints excluded: chain B residue 699 THR Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 752 VAL Chi-restraints excluded: chain B residue 753 TRP Chi-restraints excluded: chain B residue 757 ILE Chi-restraints excluded: chain B residue 758 THR Chi-restraints excluded: chain B residue 853 LEU Chi-restraints excluded: chain B residue 947 ARG Chi-restraints excluded: chain B residue 982 PHE Chi-restraints excluded: chain B residue 998 LEU Chi-restraints excluded: chain B residue 1002 LEU Chi-restraints excluded: chain B residue 1019 VAL Chi-restraints excluded: chain B residue 1027 ILE Chi-restraints excluded: chain B residue 1053 LEU Chi-restraints excluded: chain B residue 1111 TYR Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 38 GLN Chi-restraints excluded: chain C residue 42 MET Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 178 GLN Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 236 ILE Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 479 LEU Chi-restraints excluded: chain C residue 506 ILE Chi-restraints excluded: chain C residue 591 CYS Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 817 HIS Chi-restraints excluded: chain C residue 853 LEU Chi-restraints excluded: chain C residue 1046 LEU Chi-restraints excluded: chain C residue 1076 GLU Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 65 HIS Chi-restraints excluded: chain D residue 108 TYR Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 265 VAL Chi-restraints excluded: chain D residue 280 SER Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 324 GLU Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain D residue 350 ASP Chi-restraints excluded: chain D residue 493 LEU Chi-restraints excluded: chain D residue 532 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 72 optimal weight: 3.9990 chunk 170 optimal weight: 7.9990 chunk 231 optimal weight: 10.0000 chunk 22 optimal weight: 8.9990 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 10.0000 chunk 71 optimal weight: 5.9990 chunk 166 optimal weight: 2.9990 chunk 21 optimal weight: 6.9990 chunk 82 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 614 GLN C 958 GLN D 530 HIS D 542 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.083044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.063443 restraints weight = 72735.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.065453 restraints weight = 38505.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.066780 restraints weight = 25560.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.067661 restraints weight = 19480.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.068138 restraints weight = 16297.510| |-----------------------------------------------------------------------------| r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.4624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 24774 Z= 0.190 Angle : 0.600 12.450 33908 Z= 0.307 Chirality : 0.041 0.196 3729 Planarity : 0.004 0.035 4219 Dihedral : 14.932 89.926 3859 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 3.19 % Allowed : 15.49 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % 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: 0.64 (0.16), residues: 2837 helix: 1.71 (0.14), residues: 1409 sheet: -0.14 (0.31), residues: 262 loop : -1.06 (0.18), residues: 1166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 442 TYR 0.021 0.002 TYR B1093 PHE 0.040 0.001 PHE D 386 TRP 0.015 0.001 TRP B1085 HIS 0.005 0.001 HIS C 233 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.19 (24774) covalent geometry : angle 0.60013 / 0.31 (33908) hydrogen bonds : bond 0.03685 / 2.32 ( 1090) hydrogen bonds : angle 3.94506 / 2.77 ( 3155) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 214 time to evaluate : 0.954 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 146 MET cc_start: 0.7791 (mmm) cc_final: 0.7427 (mmm) REVERT: B 234 GLN cc_start: 0.9018 (tt0) cc_final: 0.8704 (mm110) REVERT: B 274 GLU cc_start: 0.7938 (pm20) cc_final: 0.7291 (pp20) REVERT: B 304 THR cc_start: 0.7159 (OUTLIER) cc_final: 0.6900 (p) REVERT: B 976 LYS cc_start: 0.8220 (pptt) cc_final: 0.7595 (mmtm) REVERT: B 1021 MET cc_start: 0.8537 (tpp) cc_final: 0.8048 (tpp) REVERT: C 17 MET cc_start: 0.9017 (tmm) cc_final: 0.8282 (ptp) REVERT: C 42 MET cc_start: 0.8818 (OUTLIER) cc_final: 0.8614 (tmm) REVERT: C 46 LEU cc_start: 0.9266 (OUTLIER) cc_final: 0.9044 (tp) REVERT: C 665 MET cc_start: 0.8614 (mtp) cc_final: 0.8139 (ttm) REVERT: C 680 MET cc_start: 0.9282 (mmm) cc_final: 0.9050 (mmt) REVERT: C 718 GLU cc_start: 0.8153 (tt0) cc_final: 0.7775 (tm-30) REVERT: C 817 HIS cc_start: 0.8551 (OUTLIER) cc_final: 0.8335 (m90) REVERT: C 1031 MET cc_start: 0.9336 (mmt) cc_final: 0.9040 (mmm) REVERT: D 35 VAL cc_start: 0.9624 (OUTLIER) cc_final: 0.9407 (p) REVERT: D 252 ARG cc_start: 0.7688 (OUTLIER) cc_final: 0.7263 (ptp-170) REVERT: D 408 LEU cc_start: 0.8925 (mt) cc_final: 0.8667 (mt) REVERT: D 462 MET cc_start: 0.8552 (mmt) cc_final: 0.8256 (mmp) REVERT: D 504 ARG cc_start: 0.8317 (tpt90) cc_final: 0.7896 (tpp80) REVERT: D 564 GLU cc_start: 0.8710 (mp0) cc_final: 0.7934 (mp0) outliers start: 77 outliers final: 60 residues processed: 266 average time/residue: 0.1430 time to fit residues: 62.8435 Evaluate side-chains 271 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 205 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 582 SER Chi-restraints excluded: chain B residue 605 THR Chi-restraints excluded: chain B residue 619 SER Chi-restraints excluded: chain B residue 699 THR Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 752 VAL Chi-restraints excluded: chain B residue 753 TRP Chi-restraints excluded: chain B residue 757 ILE Chi-restraints excluded: chain B residue 758 THR Chi-restraints excluded: chain B residue 982 PHE Chi-restraints excluded: chain B residue 998 LEU Chi-restraints excluded: chain B residue 1002 LEU Chi-restraints excluded: chain B residue 1019 VAL Chi-restraints excluded: chain B residue 1027 ILE Chi-restraints excluded: chain B residue 1053 LEU Chi-restraints excluded: chain B residue 1066 ILE Chi-restraints excluded: chain B residue 1111 TYR Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 38 GLN Chi-restraints excluded: chain C residue 42 MET Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 178 GLN Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 236 ILE Chi-restraints excluded: chain C residue 374 ILE Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 479 LEU Chi-restraints excluded: chain C residue 506 ILE Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 591 CYS Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 752 ILE Chi-restraints excluded: chain C residue 817 HIS Chi-restraints excluded: chain C residue 853 LEU Chi-restraints excluded: chain C residue 958 GLN Chi-restraints excluded: chain C residue 1036 LEU Chi-restraints excluded: chain C residue 1046 LEU Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 65 HIS Chi-restraints excluded: chain D residue 108 TYR Chi-restraints excluded: chain D residue 143 LYS Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 252 ARG Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 324 GLU Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain D residue 350 ASP Chi-restraints excluded: chain D residue 493 LEU Chi-restraints excluded: chain D residue 532 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 104 optimal weight: 20.0000 chunk 172 optimal weight: 1.9990 chunk 263 optimal weight: 7.9990 chunk 207 optimal weight: 10.0000 chunk 45 optimal weight: 5.9990 chunk 232 optimal weight: 4.9990 chunk 229 optimal weight: 8.9990 chunk 241 optimal weight: 9.9990 chunk 19 optimal weight: 4.9990 chunk 86 optimal weight: 5.9990 chunk 129 optimal weight: 10.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 614 GLN C 793 ASN ** C 984 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1053 GLN D 530 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.081599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.062062 restraints weight = 73533.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.064060 restraints weight = 38664.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.065377 restraints weight = 25547.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.066261 restraints weight = 19448.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.066778 restraints weight = 16222.893| |-----------------------------------------------------------------------------| r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.4865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.086 24774 Z= 0.254 Angle : 0.664 12.454 33908 Z= 0.337 Chirality : 0.043 0.315 3729 Planarity : 0.004 0.084 4219 Dihedral : 15.041 89.037 3859 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 3.19 % Allowed : 15.49 % Favored : 81.33 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.70 % 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: 0.59 (0.16), residues: 2837 helix: 1.63 (0.14), residues: 1409 sheet: -0.05 (0.31), residues: 281 loop : -1.07 (0.18), residues: 1147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 423 TYR 0.020 0.002 TYR D 580 PHE 0.041 0.002 PHE D 386 TRP 0.016 0.002 TRP C 248 HIS 0.005 0.001 HIS C 233 Details of bonding type rmsd/Z covalent geometry : bond 0.00567 / 0.25 (24774) covalent geometry : angle 0.66359 / 0.34 (33908) hydrogen bonds : bond 0.03934 / 2.47 ( 1090) hydrogen bonds : angle 4.09415 / 2.88 ( 3155) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 217 time to evaluate : 0.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 146 MET cc_start: 0.7823 (mmm) cc_final: 0.7443 (mmm) REVERT: B 234 GLN cc_start: 0.9021 (tt0) cc_final: 0.8694 (mm110) REVERT: B 259 ARG cc_start: 0.8123 (ttt180) cc_final: 0.7878 (ttt180) REVERT: B 274 GLU cc_start: 0.8015 (pm20) cc_final: 0.7351 (pp20) REVERT: B 304 THR cc_start: 0.7098 (OUTLIER) cc_final: 0.6847 (p) REVERT: B 976 LYS cc_start: 0.8319 (pptt) cc_final: 0.7686 (mmtm) REVERT: B 1021 MET cc_start: 0.8554 (tpp) cc_final: 0.8043 (tpt) REVERT: C 17 MET cc_start: 0.9008 (tmm) cc_final: 0.8572 (ptp) REVERT: C 42 MET cc_start: 0.8842 (OUTLIER) cc_final: 0.8612 (tmm) REVERT: C 46 LEU cc_start: 0.9325 (OUTLIER) cc_final: 0.9112 (tp) REVERT: C 239 LEU cc_start: 0.9355 (mp) cc_final: 0.9013 (mp) REVERT: C 362 ASP cc_start: 0.7698 (OUTLIER) cc_final: 0.7467 (m-30) REVERT: C 383 GLN cc_start: 0.7870 (tm-30) cc_final: 0.7331 (tm-30) REVERT: C 665 MET cc_start: 0.8658 (mtp) cc_final: 0.8430 (ttp) REVERT: C 680 MET cc_start: 0.9333 (mmm) cc_final: 0.9120 (mmt) REVERT: C 718 GLU cc_start: 0.8170 (tt0) cc_final: 0.7787 (tm-30) REVERT: C 817 HIS cc_start: 0.8595 (OUTLIER) cc_final: 0.8259 (m90) REVERT: D 408 LEU cc_start: 0.8942 (mt) cc_final: 0.8679 (mt) REVERT: D 449 PHE cc_start: 0.8495 (m-10) cc_final: 0.8072 (m-80) REVERT: D 462 MET cc_start: 0.8560 (mmt) cc_final: 0.8235 (mmp) REVERT: D 504 ARG cc_start: 0.8327 (tpt90) cc_final: 0.7906 (tpp80) outliers start: 77 outliers final: 58 residues processed: 267 average time/residue: 0.1521 time to fit residues: 67.3660 Evaluate side-chains 273 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 210 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 582 SER Chi-restraints excluded: chain B residue 605 THR Chi-restraints excluded: chain B residue 699 THR Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 752 VAL Chi-restraints excluded: chain B residue 753 TRP Chi-restraints excluded: chain B residue 757 ILE Chi-restraints excluded: chain B residue 758 THR Chi-restraints excluded: chain B residue 982 PHE Chi-restraints excluded: chain B residue 998 LEU Chi-restraints excluded: chain B residue 1002 LEU Chi-restraints excluded: chain B residue 1019 VAL Chi-restraints excluded: chain B residue 1027 ILE Chi-restraints excluded: chain B residue 1053 LEU Chi-restraints excluded: chain B residue 1111 TYR Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 38 GLN Chi-restraints excluded: chain C residue 42 MET Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 178 GLN Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 236 ILE Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 362 ASP Chi-restraints excluded: chain C residue 374 ILE Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain C residue 479 LEU Chi-restraints excluded: chain C residue 506 ILE Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 569 MET Chi-restraints excluded: chain C residue 591 CYS Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 752 ILE Chi-restraints excluded: chain C residue 817 HIS Chi-restraints excluded: chain C residue 853 LEU Chi-restraints excluded: chain C residue 1036 LEU Chi-restraints excluded: chain C residue 1046 LEU Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 65 HIS Chi-restraints excluded: chain D residue 143 LYS Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 303 SER Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 324 GLU Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain D residue 341 THR Chi-restraints excluded: chain D residue 350 ASP Chi-restraints excluded: chain D residue 404 TYR Chi-restraints excluded: chain D residue 493 LEU Chi-restraints excluded: chain D residue 532 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 130 optimal weight: 4.9990 chunk 127 optimal weight: 5.9990 chunk 161 optimal weight: 0.9980 chunk 279 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 134 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 132 optimal weight: 0.0170 chunk 62 optimal weight: 2.9990 chunk 248 optimal weight: 5.9990 chunk 70 optimal weight: 3.9990 overall best weight: 0.8018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 843 GLN B1003 ASN C 614 GLN D 61 ASN D 530 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.084165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.064308 restraints weight = 72757.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.066393 restraints weight = 38352.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.067767 restraints weight = 25377.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.068684 restraints weight = 19318.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.069170 restraints weight = 16090.081| |-----------------------------------------------------------------------------| r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.4787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 24774 Z= 0.114 Angle : 0.590 12.601 33908 Z= 0.298 Chirality : 0.040 0.178 3729 Planarity : 0.004 0.097 4219 Dihedral : 14.971 89.504 3859 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.19 % Allowed : 16.73 % Favored : 81.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % 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: 0.77 (0.16), residues: 2837 helix: 1.81 (0.14), residues: 1410 sheet: -0.03 (0.31), residues: 275 loop : -1.02 (0.18), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 423 TYR 0.029 0.001 TYR B 906 PHE 0.027 0.001 PHE B 64 TRP 0.011 0.001 TRP C 841 HIS 0.004 0.001 HIS B 705 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 (24774) covalent geometry : angle 0.59032 / 0.30 (33908) hydrogen bonds : bond 0.03525 / 2.22 ( 1090) hydrogen bonds : angle 3.87549 / 2.72 ( 3155) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 232 time to evaluate : 0.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 146 MET cc_start: 0.7748 (mmm) cc_final: 0.7383 (mmm) REVERT: B 234 GLN cc_start: 0.9025 (tt0) cc_final: 0.8708 (mm110) REVERT: B 259 ARG cc_start: 0.8128 (ttt180) cc_final: 0.7877 (ttt180) REVERT: B 304 THR cc_start: 0.7113 (OUTLIER) cc_final: 0.6858 (p) REVERT: B 384 ASP cc_start: 0.8468 (t0) cc_final: 0.8203 (t0) REVERT: B 385 GLU cc_start: 0.7599 (mm-30) cc_final: 0.7322 (mm-30) REVERT: B 414 ASP cc_start: 0.8126 (t0) cc_final: 0.7851 (t0) REVERT: B 976 LYS cc_start: 0.8320 (pptt) cc_final: 0.7689 (mmtm) REVERT: B 1021 MET cc_start: 0.8514 (tpp) cc_final: 0.7997 (tpt) REVERT: C 17 MET cc_start: 0.9112 (tmm) cc_final: 0.8553 (ptp) REVERT: C 42 MET cc_start: 0.8843 (OUTLIER) cc_final: 0.8638 (tmm) REVERT: C 46 LEU cc_start: 0.9228 (OUTLIER) cc_final: 0.8983 (tp) REVERT: C 362 ASP cc_start: 0.7677 (OUTLIER) cc_final: 0.7445 (m-30) REVERT: C 665 MET cc_start: 0.8623 (mtp) cc_final: 0.8206 (ttm) REVERT: C 718 GLU cc_start: 0.8111 (tt0) cc_final: 0.7694 (tm-30) REVERT: C 817 HIS cc_start: 0.8509 (OUTLIER) cc_final: 0.8243 (m90) REVERT: D 35 VAL cc_start: 0.9627 (OUTLIER) cc_final: 0.9415 (p) REVERT: D 408 LEU cc_start: 0.8865 (mt) cc_final: 0.8599 (mt) REVERT: D 462 MET cc_start: 0.8588 (mmt) cc_final: 0.8279 (mmp) REVERT: D 504 ARG cc_start: 0.8275 (tpt90) cc_final: 0.7842 (tpp80) REVERT: D 564 GLU cc_start: 0.8724 (mp0) cc_final: 0.7949 (mp0) outliers start: 53 outliers final: 39 residues processed: 267 average time/residue: 0.1482 time to fit residues: 65.6781 Evaluate side-chains 268 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 223 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 582 SER Chi-restraints excluded: chain B residue 605 THR Chi-restraints excluded: chain B residue 699 THR Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 752 VAL Chi-restraints excluded: chain B residue 753 TRP Chi-restraints excluded: chain B residue 758 THR Chi-restraints excluded: chain B residue 982 PHE Chi-restraints excluded: chain B residue 998 LEU Chi-restraints excluded: chain B residue 1002 LEU Chi-restraints excluded: chain B residue 1019 VAL Chi-restraints excluded: chain B residue 1027 ILE Chi-restraints excluded: chain B residue 1053 LEU Chi-restraints excluded: chain B residue 1111 TYR Chi-restraints excluded: chain B residue 1155 ILE Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 38 GLN Chi-restraints excluded: chain C residue 42 MET Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 362 ASP Chi-restraints excluded: chain C residue 479 LEU Chi-restraints excluded: chain C residue 817 HIS Chi-restraints excluded: chain C residue 853 LEU Chi-restraints excluded: chain C residue 1046 LEU Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 65 HIS Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 265 VAL Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 324 GLU Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain D residue 350 ASP Chi-restraints excluded: chain D residue 404 TYR Chi-restraints excluded: chain D residue 493 LEU Chi-restraints excluded: chain D residue 532 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 286 optimal weight: 50.0000 chunk 198 optimal weight: 1.9990 chunk 135 optimal weight: 0.8980 chunk 17 optimal weight: 8.9990 chunk 9 optimal weight: 0.8980 chunk 108 optimal weight: 9.9990 chunk 277 optimal weight: 9.9990 chunk 238 optimal weight: 9.9990 chunk 26 optimal weight: 0.9990 chunk 202 optimal weight: 0.5980 chunk 142 optimal weight: 7.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 237 HIS C 614 GLN D 61 ASN D 530 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.084271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.064383 restraints weight = 72720.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.066485 restraints weight = 38239.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.067863 restraints weight = 25222.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.068772 restraints weight = 19168.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.069316 restraints weight = 15984.649| |-----------------------------------------------------------------------------| r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.4799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 24774 Z= 0.117 Angle : 0.587 12.536 33908 Z= 0.296 Chirality : 0.041 0.244 3729 Planarity : 0.004 0.088 4219 Dihedral : 14.933 89.300 3859 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.11 % Allowed : 16.81 % Favored : 81.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % 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: 0.84 (0.16), residues: 2837 helix: 1.88 (0.14), residues: 1410 sheet: -0.02 (0.31), residues: 275 loop : -0.99 (0.18), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 423 TYR 0.028 0.001 TYR D 580 PHE 0.038 0.001 PHE D 386 TRP 0.026 0.001 TRP D 534 HIS 0.003 0.001 HIS B 705 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 (24774) covalent geometry : angle 0.58720 / 0.30 (33908) hydrogen bonds : bond 0.03453 / 2.16 ( 1090) hydrogen bonds : angle 3.84538 / 2.70 ( 3155) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3647.82 seconds wall clock time: 63 minutes 46.92 seconds (3826.92 seconds total)