Starting phenix.real_space_refine on Thu Mar 5 16:57:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6sjb_10214/03_2026/6sjb_10214.cif Found real_map, /net/cci-nas-00/data/ceres_data/6sjb_10214/03_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_10214/03_2026/6sjb_10214.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6sjb_10214/03_2026/6sjb_10214.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6sjb_10214/03_2026/6sjb_10214.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6sjb_10214/03_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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/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: 4.84, per 1000 atoms: 0.20 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: 1.94 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 2.78 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: 5.16 Time building geometry restraints manager: 2.50 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 1.50e-02 4.44e+03 2.33e+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=" CA LEU C 664 " pdb=" C LEU C 664 " ideal model delta sigma weight residual 1.523 1.561 -0.037 1.30e-02 5.92e+03 8.32e+00 bond pdb=" C4' DT X 81 " pdb=" O4' DT X 81 " ideal model delta sigma weight residual 1.450 1.393 0.057 2.00e-02 2.50e+03 8.09e+00 bond pdb=" O3' DG X 79 " pdb=" P DC X 80 " ideal model delta sigma weight residual 1.607 1.643 -0.036 1.50e-02 4.44e+03 5.78e+00 ... (remaining 24769 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.32: 33579 2.32 - 4.63: 289 4.63 - 6.95: 28 6.95 - 9.27: 10 9.27 - 11.59: 2 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=" 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=" O3' DG X 79 " pdb=" C3' DG X 79 " pdb=" C2' DG X 79 " ideal model delta sigma weight residual 111.50 120.53 -9.03 1.50e+00 4.44e-01 3.62e+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=" O3' DC X 80 " pdb=" C3' DC X 80 " pdb=" C2' DC X 80 " ideal model delta sigma weight residual 111.50 118.07 -6.57 1.50e+00 4.44e-01 1.92e+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: 3556 0.093 - 0.187: 165 0.187 - 0.280: 4 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 -0.42 2.00e-01 2.50e+01 4.51e+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: 0.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.360 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 23.670 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:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 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= 0.159 Angle : 0.580 11.586 33908 Z= 0.355 Chirality : 0.042 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 covalent geometry : bond 0.00280 (24774) covalent geometry : angle 0.58023 (33908) hydrogen bonds : bond 0.14289 ( 1090) hydrogen bonds : angle 6.19066 ( 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 : 0.936 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: 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: 0.8689 (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: 0.8367 (t0) REVERT: B 832 ASP cc_start: 0.7810 (m-30) cc_final: 0.7417 (m-30) REVERT: B 1053 LEU cc_start: 0.5128 (OUTLIER) cc_final: 0.4508 (mp) REVERT: B 1079 LEU cc_start: 0.9064 (tp) cc_final: 0.8715 (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: 0.8281 (tp30) REVERT: D 350 ASP cc_start: 0.7248 (OUTLIER) cc_final: 0.6880 (t70) REVERT: D 404 TYR cc_start: 0.8411 (t80) cc_final: 0.7034 (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: 0.1806 time to fit residues: 190.9604 Evaluate side-chains 344 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 328 time to evaluate : 0.908 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: B 120 GLN B 181 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 689 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 705 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 713 GLN B 765 GLN B 834 HIS B 848 GLN 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 510 ASN C 570 GLN C 596 ASN C 660 ASN C 724 GLN 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** ** C 984 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1110 GLN D 22 GLN D 44 HIS 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: 47 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.088732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.069480 restraints weight = 71939.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.071662 restraints weight = 37486.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.073106 restraints weight = 24407.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.074045 restraints weight = 18268.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.074528 restraints weight = 15095.569| |-----------------------------------------------------------------------------| r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.3061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 24774 Z= 0.198 Angle : 0.654 11.569 33908 Z= 0.333 Chirality : 0.042 0.238 3729 Planarity : 0.005 0.043 4219 Dihedral : 14.520 88.705 3874 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 3.69 % Allowed : 11.51 % 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: -1.17 (0.14), residues: 2837 helix: -0.04 (0.13), residues: 1410 sheet: -0.36 (0.30), residues: 274 loop : -1.76 (0.16), residues: 1153 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 254 TYR 0.019 0.002 TYR B1111 PHE 0.018 0.001 PHE B 386 TRP 0.018 0.002 TRP C 574 HIS 0.007 0.001 HIS C 390 Details of bonding type rmsd covalent geometry : bond 0.00444 (24774) covalent geometry : angle 0.65396 (33908) hydrogen bonds : bond 0.03884 ( 1090) hydrogen bonds : angle 4.16911 ( 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 391 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 302 time to evaluate : 0.830 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: B 123 GLU cc_start: 0.7771 (tp30) cc_final: 0.7525 (tm-30) REVERT: B 146 MET cc_start: 0.7696 (mmm) cc_final: 0.7368 (mmm) REVERT: B 234 GLN cc_start: 0.9006 (tt0) cc_final: 0.8727 (mm110) REVERT: B 491 PHE cc_start: 0.6816 (OUTLIER) cc_final: 0.5349 (m-80) REVERT: B 646 ASP cc_start: 0.8820 (t0) cc_final: 0.8450 (t0) REVERT: B 728 ARG cc_start: 0.8214 (mmm-85) cc_final: 0.7788 (ttt-90) REVERT: B 1081 TYR cc_start: 0.8806 (m-10) cc_final: 0.8532 (m-10) REVERT: B 1093 TYR cc_start: 0.3010 (OUTLIER) cc_final: 0.2569 (p90) REVERT: C 230 LEU cc_start: 0.9618 (OUTLIER) cc_final: 0.9250 (tt) REVERT: C 475 ASP cc_start: 0.8319 (m-30) cc_final: 0.8041 (m-30) REVERT: C 528 LEU cc_start: 0.9498 (OUTLIER) cc_final: 0.9219 (mm) REVERT: C 569 MET cc_start: 0.7721 (tpp) cc_final: 0.7486 (tpt) REVERT: C 665 MET cc_start: 0.8387 (mtp) cc_final: 0.7988 (ttm) REVERT: D 35 VAL cc_start: 0.9533 (OUTLIER) cc_final: 0.9270 (p) REVERT: D 45 ASP cc_start: 0.8866 (m-30) cc_final: 0.8660 (m-30) REVERT: D 68 LEU cc_start: 0.6416 (pp) cc_final: 0.5958 (mt) REVERT: D 332 LEU cc_start: 0.8826 (mt) cc_final: 0.8399 (mt) REVERT: D 449 PHE cc_start: 0.8365 (m-10) cc_final: 0.7988 (m-80) REVERT: D 462 MET cc_start: 0.8481 (mmt) cc_final: 0.8239 (mmp) REVERT: D 483 MET cc_start: 0.7845 (ttp) cc_final: 0.7449 (ttp) REVERT: D 504 ARG cc_start: 0.8279 (tpt90) cc_final: 0.7877 (tpp80) REVERT: D 564 GLU cc_start: 0.8311 (mp0) cc_final: 0.7904 (mp0) outliers start: 89 outliers final: 46 residues processed: 368 average time/residue: 0.1649 time to fit residues: 96.4318 Evaluate side-chains 286 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 235 time to evaluate : 0.863 ------------------------------------------------------------------------------- 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 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 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 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 1093 TYR Chi-restraints excluded: chain B residue 1111 TYR Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 178 GLN Chi-restraints excluded: chain C residue 230 LEU 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 484 ASP Chi-restraints excluded: chain C residue 506 ILE Chi-restraints excluded: chain C residue 528 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 236 ASP 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 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: 5.9990 chunk 158 optimal weight: 6.9990 chunk 26 optimal weight: 10.0000 chunk 138 optimal weight: 20.0000 chunk 47 optimal weight: 10.0000 chunk 209 optimal weight: 3.9990 chunk 279 optimal weight: 8.9990 chunk 150 optimal weight: 0.5980 chunk 179 optimal weight: 7.9990 chunk 60 optimal weight: 0.9980 overall best weight: 3.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 150 GLN B 162 GLN B 402 HIS ** B 689 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 742 HIS B 769 HIS ** B1150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 8 ASN ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 137 GLN C 596 ASN C 886 ASN C1108 GLN C1110 GLN D 229 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.085183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.065387 restraints weight = 73331.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.067469 restraints weight = 39050.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.068849 restraints weight = 25993.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.069754 restraints weight = 19877.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.070306 restraints weight = 16652.075| |-----------------------------------------------------------------------------| r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.3853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 24774 Z= 0.216 Angle : 0.617 9.170 33908 Z= 0.317 Chirality : 0.041 0.197 3729 Planarity : 0.004 0.037 4219 Dihedral : 14.611 88.935 3861 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 3.64 % Allowed : 11.93 % Favored : 84.43 % 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: -0.20 (0.15), residues: 2837 helix: 0.90 (0.14), residues: 1410 sheet: -0.26 (0.30), residues: 287 loop : -1.40 (0.17), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 265 TYR 0.023 0.002 TYR C 434 PHE 0.018 0.001 PHE B1070 TRP 0.016 0.001 TRP B 901 HIS 0.010 0.001 HIS B1133 Details of bonding type rmsd covalent geometry : bond 0.00475 (24774) covalent geometry : angle 0.61714 (33908) hydrogen bonds : bond 0.03753 ( 1090) hydrogen bonds : angle 4.02273 ( 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 346 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 258 time to evaluate : 0.751 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: 0.7764 (mmm) cc_final: 0.7362 (mmm) REVERT: B 234 GLN cc_start: 0.9027 (tt0) cc_final: 0.8702 (mm110) REVERT: B 304 THR cc_start: 0.7261 (OUTLIER) cc_final: 0.7028 (p) REVERT: B 491 PHE cc_start: 0.6902 (OUTLIER) cc_final: 0.5720 (m-80) REVERT: B 959 PHE cc_start: 0.8646 (OUTLIER) cc_final: 0.8411 (t80) REVERT: B 976 LYS cc_start: 0.8275 (pptt) cc_final: 0.7790 (mmtm) REVERT: B 1021 MET cc_start: 0.8380 (tpp) cc_final: 0.8072 (tpp) REVERT: B 1024 TYR cc_start: 0.7272 (m-10) cc_final: 0.6569 (m-10) REVERT: B 1102 MET cc_start: 0.7808 (tpt) cc_final: 0.7582 (tmm) REVERT: C 42 MET cc_start: 0.8768 (OUTLIER) cc_final: 0.8009 (tmm) REVERT: C 47 GLN cc_start: 0.8842 (tt0) cc_final: 0.8376 (tt0) REVERT: C 383 GLN cc_start: 0.8268 (tm-30) cc_final: 0.7906 (tt0) REVERT: C 475 ASP cc_start: 0.8315 (m-30) cc_final: 0.8065 (m-30) REVERT: C 665 MET cc_start: 0.8564 (mtp) cc_final: 0.8201 (ttm) REVERT: D 462 MET cc_start: 0.8598 (mmt) cc_final: 0.8242 (mmp) REVERT: D 504 ARG cc_start: 0.8302 (tpt90) cc_final: 0.7929 (tpp80) REVERT: D 530 HIS cc_start: 0.8686 (OUTLIER) cc_final: 0.8481 (p-80) REVERT: D 594 THR cc_start: 0.8976 (OUTLIER) cc_final: 0.8319 (p) outliers start: 88 outliers final: 54 residues processed: 321 average time/residue: 0.1491 time to fit residues: 78.5595 Evaluate side-chains 276 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 216 time to evaluate : 0.892 ------------------------------------------------------------------------------- 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 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 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 959 PHE 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 B residue 1155 ILE Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 42 MET 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 327 VAL 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 484 ASP Chi-restraints excluded: chain C residue 506 ILE Chi-restraints excluded: chain C residue 533 LEU 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 1097 LEU Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 65 HIS Chi-restraints excluded: chain D residue 67 LEU 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 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 350 ASP Chi-restraints excluded: chain D residue 493 LEU Chi-restraints excluded: chain D residue 530 HIS 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: 10.0000 chunk 267 optimal weight: 4.9990 chunk 60 optimal weight: 0.9990 chunk 99 optimal weight: 7.9990 chunk 141 optimal weight: 9.9990 chunk 153 optimal weight: 0.9990 chunk 82 optimal weight: 6.9990 chunk 227 optimal weight: 10.0000 chunk 197 optimal weight: 0.9980 chunk 196 optimal weight: 0.9980 chunk 171 optimal weight: 0.9980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 689 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 742 HIS C 8 ASN ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 137 GLN C 614 GLN ** C 958 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.086641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.066769 restraints weight = 73003.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.068913 restraints weight = 38262.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.070356 restraints weight = 25192.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.071303 restraints weight = 19008.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.071841 restraints weight = 15804.498| |-----------------------------------------------------------------------------| r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.3946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 24774 Z= 0.113 Angle : 0.545 12.144 33908 Z= 0.278 Chirality : 0.039 0.170 3729 Planarity : 0.003 0.035 4219 Dihedral : 14.568 89.124 3861 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.73 % Allowed : 13.37 % Favored : 83.89 % 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: 0.24 (0.16), residues: 2837 helix: 1.33 (0.14), residues: 1411 sheet: -0.32 (0.30), residues: 277 loop : -1.21 (0.17), residues: 1149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 491 TYR 0.025 0.001 TYR B1093 PHE 0.013 0.001 PHE B 386 TRP 0.021 0.001 TRP B 265 HIS 0.003 0.001 HIS D 44 Details of bonding type rmsd covalent geometry : bond 0.00255 (24774) covalent geometry : angle 0.54466 (33908) hydrogen bonds : bond 0.03276 ( 1090) hydrogen bonds : angle 3.80949 ( 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 314 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 248 time to evaluate : 0.932 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 146 MET cc_start: 0.7774 (mmm) cc_final: 0.7387 (mmm) REVERT: B 234 GLN cc_start: 0.9042 (tt0) cc_final: 0.8735 (mm110) REVERT: B 304 THR cc_start: 0.7174 (OUTLIER) cc_final: 0.6918 (p) REVERT: B 491 PHE cc_start: 0.6732 (OUTLIER) cc_final: 0.5719 (m-80) REVERT: B 976 LYS cc_start: 0.8147 (pptt) cc_final: 0.7518 (mmtm) REVERT: B 1024 TYR cc_start: 0.7329 (m-10) cc_final: 0.6655 (m-10) REVERT: B 1102 MET cc_start: 0.7775 (tpt) cc_final: 0.7486 (tmm) REVERT: C 47 GLN cc_start: 0.8912 (tt0) cc_final: 0.8504 (tt0) REVERT: C 528 LEU cc_start: 0.9566 (OUTLIER) cc_final: 0.9359 (mm) REVERT: C 665 MET cc_start: 0.8578 (mtp) cc_final: 0.8138 (ttt) REVERT: C 817 HIS cc_start: 0.8463 (OUTLIER) cc_final: 0.8245 (m90) REVERT: C 924 MET cc_start: 0.8713 (mmp) cc_final: 0.8507 (mmp) REVERT: D 35 VAL cc_start: 0.9602 (OUTLIER) cc_final: 0.9370 (p) REVERT: D 449 PHE cc_start: 0.8496 (m-10) cc_final: 0.8104 (m-80) REVERT: D 462 MET cc_start: 0.8570 (mmt) cc_final: 0.8233 (mmp) REVERT: D 530 HIS cc_start: 0.8660 (OUTLIER) cc_final: 0.8448 (p-80) outliers start: 66 outliers final: 37 residues processed: 293 average time/residue: 0.1501 time to fit residues: 72.7939 Evaluate side-chains 260 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 217 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 304 THR 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 729 LEU Chi-restraints excluded: chain B residue 752 VAL Chi-restraints excluded: chain B residue 753 TRP Chi-restraints excluded: chain B residue 780 LEU Chi-restraints excluded: chain B residue 853 LEU 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 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 B residue 1155 ILE Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 479 LEU Chi-restraints excluded: chain C residue 528 LEU Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 614 GLN Chi-restraints excluded: chain C residue 817 HIS Chi-restraints excluded: chain C residue 853 LEU Chi-restraints excluded: chain D residue 13 HIS 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 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 350 ASP Chi-restraints excluded: chain D residue 493 LEU Chi-restraints excluded: chain D residue 530 HIS 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: 3.9990 chunk 81 optimal weight: 9.9990 chunk 130 optimal weight: 9.9990 chunk 169 optimal weight: 7.9990 chunk 224 optimal weight: 0.5980 chunk 25 optimal weight: 10.0000 chunk 48 optimal weight: 8.9990 chunk 252 optimal weight: 9.9990 chunk 158 optimal weight: 5.9990 chunk 63 optimal weight: 7.9990 chunk 248 optimal weight: 20.0000 overall best weight: 5.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 689 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 742 HIS B1003 ASN B1133 HIS C 8 ASN C 38 GLN C 228 GLN ** C 984 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.081606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.061811 restraints weight = 73732.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.063806 restraints weight = 39252.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.065130 restraints weight = 26176.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.065947 restraints weight = 20024.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.066544 restraints weight = 16904.280| |-----------------------------------------------------------------------------| r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.4642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.097 24774 Z= 0.289 Angle : 0.683 11.533 33908 Z= 0.345 Chirality : 0.044 0.181 3729 Planarity : 0.004 0.043 4219 Dihedral : 14.858 88.335 3859 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 3.52 % Allowed : 14.24 % Favored : 82.24 % 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: 0.32 (0.16), residues: 2837 helix: 1.37 (0.14), residues: 1407 sheet: -0.14 (0.30), residues: 275 loop : -1.16 (0.18), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 119 TYR 0.026 0.002 TYR C 434 PHE 0.016 0.002 PHE B1070 TRP 0.018 0.002 TRP C 248 HIS 0.006 0.001 HIS C 390 Details of bonding type rmsd covalent geometry : bond 0.00649 (24774) covalent geometry : angle 0.68341 (33908) hydrogen bonds : bond 0.04130 ( 1090) hydrogen bonds : angle 4.17284 ( 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 302 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 217 time to evaluate : 0.945 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: 0.7822 (mmm) cc_final: 0.7416 (mmm) REVERT: B 234 GLN cc_start: 0.9029 (tt0) cc_final: 0.8683 (mm110) REVERT: B 288 LYS cc_start: 0.7499 (ttmt) cc_final: 0.7179 (tptp) REVERT: B 304 THR cc_start: 0.7041 (OUTLIER) cc_final: 0.6788 (p) REVERT: B 384 ASP cc_start: 0.8511 (t0) cc_final: 0.8226 (t0) REVERT: B 385 GLU cc_start: 0.7565 (mm-30) cc_final: 0.7264 (mm-30) REVERT: B 491 PHE cc_start: 0.7014 (OUTLIER) cc_final: 0.5208 (m-80) REVERT: B 728 ARG cc_start: 0.8322 (mmm-85) cc_final: 0.7967 (ttt-90) REVERT: B 976 LYS cc_start: 0.8279 (pptt) cc_final: 0.7633 (mmtm) REVERT: B 1061 MET cc_start: 0.7248 (mpp) cc_final: 0.6995 (mmt) REVERT: C 8 ASN cc_start: 0.9111 (OUTLIER) cc_final: 0.8804 (m110) REVERT: C 17 MET cc_start: 0.9073 (tmm) cc_final: 0.8520 (ptp) REVERT: C 42 MET cc_start: 0.8882 (OUTLIER) cc_final: 0.7980 (tmm) REVERT: C 383 GLN cc_start: 0.8155 (tm-30) cc_final: 0.7648 (tm-30) REVERT: C 665 MET cc_start: 0.8656 (mtp) cc_final: 0.8273 (ttm) REVERT: C 667 MET cc_start: 0.8602 (mtm) cc_final: 0.8221 (mtt) REVERT: C 1076 GLU cc_start: 0.8078 (pm20) cc_final: 0.7726 (pm20) REVERT: D 35 VAL cc_start: 0.9634 (OUTLIER) cc_final: 0.9429 (p) REVERT: D 462 MET cc_start: 0.8555 (mmt) cc_final: 0.8242 (mmp) outliers start: 85 outliers final: 58 residues processed: 277 average time/residue: 0.1456 time to fit residues: 66.7017 Evaluate side-chains 268 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 205 time to evaluate : 0.809 ------------------------------------------------------------------------------- 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 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 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 780 LEU Chi-restraints excluded: chain B residue 958 LEU 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 8 ASN 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 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 374 ILE Chi-restraints excluded: chain C residue 479 LEU Chi-restraints excluded: chain C residue 484 ASP Chi-restraints excluded: chain C residue 506 ILE Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 853 LEU 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 67 LEU 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 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 341 THR Chi-restraints excluded: chain D residue 350 ASP Chi-restraints excluded: chain D residue 425 ARG Chi-restraints excluded: chain D residue 493 LEU Chi-restraints excluded: chain D residue 532 THR Chi-restraints excluded: chain D residue 594 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 90 optimal weight: 6.9990 chunk 246 optimal weight: 8.9990 chunk 47 optimal weight: 0.7980 chunk 27 optimal weight: 0.6980 chunk 67 optimal weight: 2.9990 chunk 204 optimal weight: 8.9990 chunk 49 optimal weight: 0.0570 chunk 135 optimal weight: 6.9990 chunk 93 optimal weight: 6.9990 chunk 260 optimal weight: 1.9990 chunk 284 optimal weight: 10.0000 overall best weight: 1.3102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 624 ASN B 689 HIS B 843 GLN B1003 ASN C 8 ASN C 228 GLN C 237 HIS ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1053 GLN D 61 ASN D 530 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.084226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.064459 restraints weight = 72525.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.066539 restraints weight = 38152.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.067922 restraints weight = 25163.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.068823 restraints weight = 19078.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.069287 restraints weight = 15930.664| |-----------------------------------------------------------------------------| r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.4602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 24774 Z= 0.118 Angle : 0.555 11.920 33908 Z= 0.281 Chirality : 0.039 0.149 3729 Planarity : 0.003 0.041 4219 Dihedral : 14.779 89.957 3859 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.73 % Allowed : 15.36 % Favored : 81.90 % 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: 1.67 (0.14), residues: 1411 sheet: -0.11 (0.31), residues: 266 loop : -1.02 (0.18), residues: 1160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 259 TYR 0.022 0.001 TYR C 434 PHE 0.021 0.001 PHE D 386 TRP 0.009 0.001 TRP C 841 HIS 0.004 0.001 HIS B 689 Details of bonding type rmsd covalent geometry : bond 0.00267 (24774) covalent geometry : angle 0.55525 (33908) hydrogen bonds : bond 0.03381 ( 1090) hydrogen bonds : angle 3.85121 ( 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 300 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 234 time to evaluate : 0.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 146 MET cc_start: 0.7824 (mmm) cc_final: 0.7484 (mmm) REVERT: B 234 GLN cc_start: 0.9031 (tt0) cc_final: 0.8701 (mm110) REVERT: B 304 THR cc_start: 0.7003 (OUTLIER) cc_final: 0.6744 (p) REVERT: B 342 GLU cc_start: 0.8122 (tm-30) cc_final: 0.7867 (tm-30) REVERT: B 385 GLU cc_start: 0.7623 (mm-30) cc_final: 0.7400 (mm-30) REVERT: B 414 ASP cc_start: 0.8187 (t0) cc_final: 0.7900 (t0) REVERT: B 728 ARG cc_start: 0.8335 (mmm-85) cc_final: 0.8021 (ttt-90) REVERT: B 947 ARG cc_start: 0.6802 (OUTLIER) cc_final: 0.6528 (ptp-170) REVERT: B 976 LYS cc_start: 0.8316 (pptt) cc_final: 0.7688 (mmtm) REVERT: B 1070 PHE cc_start: 0.8942 (p90) cc_final: 0.8695 (p90) REVERT: C 8 ASN cc_start: 0.9203 (OUTLIER) cc_final: 0.8926 (m110) REVERT: C 17 MET cc_start: 0.9112 (tmm) cc_final: 0.8498 (ptp) REVERT: C 383 GLN cc_start: 0.7830 (tm-30) cc_final: 0.7277 (tm-30) REVERT: C 665 MET cc_start: 0.8671 (mtp) cc_final: 0.8230 (ttm) REVERT: C 667 MET cc_start: 0.8616 (mtm) cc_final: 0.8278 (mtt) REVERT: C 773 GLU cc_start: 0.8719 (OUTLIER) cc_final: 0.8280 (pt0) REVERT: C 817 HIS cc_start: 0.8520 (OUTLIER) cc_final: 0.8234 (m90) REVERT: D 35 VAL cc_start: 0.9615 (OUTLIER) cc_final: 0.9402 (p) REVERT: D 449 PHE cc_start: 0.8509 (m-10) cc_final: 0.8130 (m-80) REVERT: D 462 MET cc_start: 0.8557 (mmt) cc_final: 0.8241 (mmp) outliers start: 66 outliers final: 44 residues processed: 280 average time/residue: 0.1413 time to fit residues: 65.6278 Evaluate side-chains 261 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 211 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 780 LEU Chi-restraints excluded: chain B residue 853 LEU Chi-restraints excluded: chain B residue 947 ARG Chi-restraints excluded: chain B residue 958 LEU 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 8 ASN Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain C residue 506 ILE Chi-restraints excluded: chain C residue 752 ILE Chi-restraints excluded: chain C residue 773 GLU Chi-restraints excluded: chain C residue 817 HIS Chi-restraints excluded: chain C residue 853 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 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 502 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: 5.9990 chunk 206 optimal weight: 10.0000 chunk 115 optimal weight: 5.9990 chunk 122 optimal weight: 10.0000 chunk 152 optimal weight: 5.9990 chunk 38 optimal weight: 7.9990 chunk 11 optimal weight: 9.9990 chunk 214 optimal weight: 7.9990 chunk 117 optimal weight: 0.8980 chunk 71 optimal weight: 10.0000 chunk 236 optimal weight: 6.9990 overall best weight: 5.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 8 ASN ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 228 GLN C 545 GLN C1053 GLN D 61 ASN D 542 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.081325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.061834 restraints weight = 73182.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.063854 restraints weight = 38491.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.065196 restraints weight = 25362.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.066061 restraints weight = 19248.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.066644 restraints weight = 16064.000| |-----------------------------------------------------------------------------| r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.5038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.089 24774 Z= 0.273 Angle : 0.667 11.971 33908 Z= 0.335 Chirality : 0.043 0.156 3729 Planarity : 0.004 0.043 4219 Dihedral : 14.955 89.316 3859 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.98 % Allowed : 15.16 % Favored : 81.86 % 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: 0.49 (0.16), residues: 2837 helix: 1.53 (0.14), residues: 1413 sheet: -0.13 (0.31), residues: 285 loop : -1.10 (0.18), residues: 1139 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 9 TYR 0.022 0.002 TYR B1093 PHE 0.013 0.002 PHE B 428 TRP 0.022 0.002 TRP D 534 HIS 0.007 0.001 HIS C 6 Details of bonding type rmsd covalent geometry : bond 0.00617 (24774) covalent geometry : angle 0.66703 (33908) hydrogen bonds : bond 0.03999 ( 1090) hydrogen bonds : angle 4.11937 ( 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 286 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 214 time to evaluate : 0.839 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 146 MET cc_start: 0.7802 (mmm) cc_final: 0.7408 (mmm) REVERT: B 234 GLN cc_start: 0.9030 (tt0) cc_final: 0.8702 (mm110) REVERT: B 304 THR cc_start: 0.7096 (OUTLIER) cc_final: 0.6835 (p) REVERT: B 342 GLU cc_start: 0.8210 (tm-30) cc_final: 0.7895 (tm-30) REVERT: B 976 LYS cc_start: 0.8391 (pptt) cc_final: 0.7779 (mmtm) REVERT: B 978 GLU cc_start: 0.8400 (mm-30) cc_final: 0.8089 (mm-30) REVERT: C 42 MET cc_start: 0.8889 (tmm) cc_final: 0.8584 (tmm) REVERT: C 47 GLN cc_start: 0.9115 (tt0) cc_final: 0.8768 (tt0) REVERT: C 96 MET cc_start: 0.8838 (OUTLIER) cc_final: 0.8608 (ttp) REVERT: C 362 ASP cc_start: 0.7710 (OUTLIER) cc_final: 0.7423 (m-30) REVERT: C 383 GLN cc_start: 0.8184 (tm-30) cc_final: 0.7701 (tm-30) REVERT: C 665 MET cc_start: 0.8699 (mtp) cc_final: 0.8441 (ttp) REVERT: C 773 GLU cc_start: 0.8762 (OUTLIER) cc_final: 0.8345 (pt0) REVERT: D 35 VAL cc_start: 0.9641 (OUTLIER) cc_final: 0.9434 (p) REVERT: D 449 PHE cc_start: 0.8494 (m-10) cc_final: 0.8035 (m-80) REVERT: D 462 MET cc_start: 0.8568 (mmt) cc_final: 0.8236 (mmp) REVERT: D 504 ARG cc_start: 0.8295 (tpt90) cc_final: 0.7916 (tpp80) outliers start: 72 outliers final: 57 residues processed: 267 average time/residue: 0.1399 time to fit residues: 62.2157 Evaluate side-chains 262 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 200 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 780 LEU Chi-restraints excluded: chain B residue 958 LEU 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 1058 VAL Chi-restraints excluded: chain B residue 1066 ILE Chi-restraints excluded: chain B residue 1111 TYR Chi-restraints excluded: chain B residue 1138 VAL 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 96 MET Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 362 ASP Chi-restraints excluded: chain C residue 374 ILE 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 561 VAL Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 752 ILE Chi-restraints excluded: chain C residue 773 GLU Chi-restraints excluded: chain C residue 853 LEU Chi-restraints excluded: chain C residue 1053 GLN Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 65 HIS Chi-restraints excluded: chain D residue 107 LEU 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 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 341 THR Chi-restraints excluded: chain D residue 350 ASP Chi-restraints excluded: chain D residue 502 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: 0.7980 chunk 170 optimal weight: 2.9990 chunk 231 optimal weight: 9.9990 chunk 22 optimal weight: 9.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 9.9990 chunk 71 optimal weight: 2.9990 chunk 166 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 82 optimal weight: 0.9990 chunk 60 optimal weight: 8.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.082635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.062850 restraints weight = 73016.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.064918 restraints weight = 38485.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.066270 restraints weight = 25438.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.067186 restraints weight = 19357.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.067705 restraints weight = 16124.953| |-----------------------------------------------------------------------------| r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.5016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 24774 Z= 0.145 Angle : 0.585 11.944 33908 Z= 0.294 Chirality : 0.040 0.192 3729 Planarity : 0.003 0.037 4219 Dihedral : 14.913 89.648 3859 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.90 % Allowed : 15.73 % Favored : 81.37 % 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: 0.67 (0.16), residues: 2837 helix: 1.70 (0.14), residues: 1416 sheet: -0.03 (0.31), residues: 281 loop : -1.07 (0.18), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 265 TYR 0.019 0.001 TYR B1093 PHE 0.027 0.001 PHE D 386 TRP 0.018 0.001 TRP D 534 HIS 0.004 0.001 HIS C 233 Details of bonding type rmsd covalent geometry : bond 0.00332 (24774) covalent geometry : angle 0.58503 (33908) hydrogen bonds : bond 0.03533 ( 1090) hydrogen bonds : angle 3.92603 ( 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 297 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 227 time to evaluate : 0.855 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 146 MET cc_start: 0.7810 (mmm) cc_final: 0.7440 (mmm) REVERT: B 234 GLN cc_start: 0.9042 (tt0) cc_final: 0.8680 (mm110) REVERT: B 304 THR cc_start: 0.7009 (OUTLIER) cc_final: 0.6738 (p) REVERT: B 342 GLU cc_start: 0.8164 (tm-30) cc_final: 0.7827 (tm-30) REVERT: B 414 ASP cc_start: 0.8164 (t0) cc_final: 0.7889 (t0) REVERT: B 595 GLU cc_start: 0.8352 (mt-10) cc_final: 0.8124 (mt-10) REVERT: B 976 LYS cc_start: 0.8395 (pptt) cc_final: 0.7808 (mmtm) REVERT: B 978 GLU cc_start: 0.8399 (mm-30) cc_final: 0.8058 (mm-30) REVERT: B 1070 PHE cc_start: 0.8988 (p90) cc_final: 0.8695 (p90) REVERT: C 17 MET cc_start: 0.9092 (tmm) cc_final: 0.8536 (ptp) REVERT: C 42 MET cc_start: 0.8923 (OUTLIER) cc_final: 0.8656 (tmm) REVERT: C 47 GLN cc_start: 0.9087 (tt0) cc_final: 0.8751 (tt0) REVERT: C 362 ASP cc_start: 0.7778 (OUTLIER) cc_final: 0.7416 (m-30) REVERT: C 383 GLN cc_start: 0.7961 (tm-30) cc_final: 0.7381 (tm-30) REVERT: C 665 MET cc_start: 0.8673 (mtp) cc_final: 0.8425 (ttp) REVERT: C 773 GLU cc_start: 0.8769 (OUTLIER) cc_final: 0.8349 (pt0) REVERT: C 817 HIS cc_start: 0.8591 (OUTLIER) cc_final: 0.8292 (m90) REVERT: D 35 VAL cc_start: 0.9639 (OUTLIER) cc_final: 0.9437 (p) REVERT: D 449 PHE cc_start: 0.8495 (m-10) cc_final: 0.8041 (m-80) REVERT: D 462 MET cc_start: 0.8595 (mmt) cc_final: 0.8259 (mmp) REVERT: D 493 LEU cc_start: 0.9219 (OUTLIER) cc_final: 0.8990 (pp) REVERT: D 504 ARG cc_start: 0.8250 (tpt90) cc_final: 0.7918 (tpp80) outliers start: 70 outliers final: 51 residues processed: 276 average time/residue: 0.1455 time to fit residues: 68.3133 Evaluate side-chains 279 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 221 time to evaluate : 0.907 ------------------------------------------------------------------------------- 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 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 757 ILE Chi-restraints excluded: chain B residue 758 THR Chi-restraints excluded: chain B residue 780 LEU Chi-restraints excluded: chain B residue 853 LEU 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 1058 VAL Chi-restraints excluded: chain B residue 1111 TYR Chi-restraints excluded: chain B residue 1138 VAL Chi-restraints excluded: chain B residue 1155 ILE Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 42 MET Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 72 MET Chi-restraints excluded: chain C residue 97 THR 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 389 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 752 ILE Chi-restraints excluded: chain C residue 773 GLU Chi-restraints excluded: chain C residue 817 HIS Chi-restraints excluded: chain C residue 853 LEU Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 65 HIS Chi-restraints excluded: chain D residue 67 LEU 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 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 502 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: 5.9990 chunk 263 optimal weight: 9.9990 chunk 207 optimal weight: 9.9990 chunk 45 optimal weight: 1.9990 chunk 232 optimal weight: 0.3980 chunk 229 optimal weight: 7.9990 chunk 241 optimal weight: 10.0000 chunk 19 optimal weight: 5.9990 chunk 86 optimal weight: 0.1980 chunk 129 optimal weight: 1.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 448 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.082844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.063098 restraints weight = 73357.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.065164 restraints weight = 38577.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.066532 restraints weight = 25461.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.067440 restraints weight = 19330.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.067905 restraints weight = 16137.488| |-----------------------------------------------------------------------------| r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.5059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 24774 Z= 0.145 Angle : 0.593 11.924 33908 Z= 0.296 Chirality : 0.041 0.198 3729 Planarity : 0.003 0.042 4219 Dihedral : 14.896 89.950 3859 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.73 % Allowed : 16.19 % 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: 0.75 (0.16), residues: 2837 helix: 1.77 (0.14), residues: 1418 sheet: -0.00 (0.31), residues: 281 loop : -1.03 (0.18), residues: 1138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 728 TYR 0.022 0.001 TYR D 580 PHE 0.023 0.001 PHE D 386 TRP 0.020 0.001 TRP D 534 HIS 0.004 0.001 HIS C 233 Details of bonding type rmsd covalent geometry : bond 0.00334 (24774) covalent geometry : angle 0.59259 (33908) hydrogen bonds : bond 0.03483 ( 1090) hydrogen bonds : angle 3.91828 ( 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: 66 poor density : 228 time to evaluate : 0.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 146 MET cc_start: 0.7801 (mmm) cc_final: 0.7506 (mmm) REVERT: B 234 GLN cc_start: 0.9017 (tt0) cc_final: 0.8651 (mm110) REVERT: B 304 THR cc_start: 0.6996 (OUTLIER) cc_final: 0.6719 (p) REVERT: B 342 GLU cc_start: 0.8163 (tm-30) cc_final: 0.7826 (tm-30) REVERT: B 414 ASP cc_start: 0.8188 (t0) cc_final: 0.7923 (t0) REVERT: B 595 GLU cc_start: 0.8352 (mt-10) cc_final: 0.8117 (mt-10) REVERT: B 976 LYS cc_start: 0.8419 (pptt) cc_final: 0.7834 (mmtm) REVERT: B 978 GLU cc_start: 0.8424 (mm-30) cc_final: 0.8088 (mm-30) REVERT: B 1070 PHE cc_start: 0.8946 (p90) cc_final: 0.8716 (p90) REVERT: C 17 MET cc_start: 0.9150 (tmm) cc_final: 0.8747 (ptp) REVERT: C 42 MET cc_start: 0.8913 (OUTLIER) cc_final: 0.8665 (tmm) REVERT: C 47 GLN cc_start: 0.9071 (tt0) cc_final: 0.8743 (tt0) REVERT: C 383 GLN cc_start: 0.7953 (tm-30) cc_final: 0.7425 (tm-30) REVERT: C 665 MET cc_start: 0.8604 (mtp) cc_final: 0.8366 (ttp) REVERT: C 773 GLU cc_start: 0.8747 (OUTLIER) cc_final: 0.8356 (pt0) REVERT: C 817 HIS cc_start: 0.8550 (OUTLIER) cc_final: 0.8236 (m90) REVERT: D 35 VAL cc_start: 0.9638 (OUTLIER) cc_final: 0.9431 (p) REVERT: D 449 PHE cc_start: 0.8470 (m-10) cc_final: 0.8014 (m-80) REVERT: D 462 MET cc_start: 0.8578 (mmt) cc_final: 0.8248 (mmp) outliers start: 66 outliers final: 54 residues processed: 276 average time/residue: 0.1397 time to fit residues: 64.0092 Evaluate side-chains 275 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 216 time to evaluate : 0.892 ------------------------------------------------------------------------------- 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 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 757 ILE Chi-restraints excluded: chain B residue 758 THR Chi-restraints excluded: chain B residue 780 LEU Chi-restraints excluded: chain B residue 853 LEU Chi-restraints excluded: chain B residue 958 LEU 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 1058 VAL Chi-restraints excluded: chain B residue 1111 TYR Chi-restraints excluded: chain B residue 1138 VAL Chi-restraints excluded: chain B residue 1155 ILE Chi-restraints excluded: chain C residue 42 MET Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 72 MET Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 286 LEU 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 632 VAL Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 752 ILE Chi-restraints excluded: chain C residue 773 GLU Chi-restraints excluded: chain C residue 817 HIS Chi-restraints excluded: chain C residue 853 LEU Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 65 HIS Chi-restraints excluded: chain D residue 67 LEU 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 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 502 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: 5.9990 chunk 127 optimal weight: 9.9990 chunk 161 optimal weight: 0.5980 chunk 279 optimal weight: 10.0000 chunk 47 optimal weight: 0.7980 chunk 134 optimal weight: 0.7980 chunk 13 optimal weight: 5.9990 chunk 132 optimal weight: 0.2980 chunk 62 optimal weight: 5.9990 chunk 248 optimal weight: 10.0000 chunk 70 optimal weight: 10.0000 overall best weight: 1.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.083427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.063694 restraints weight = 73027.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.065762 restraints weight = 38432.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.067136 restraints weight = 25382.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.068045 restraints weight = 19290.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.068618 restraints weight = 16089.530| |-----------------------------------------------------------------------------| r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.5064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 24774 Z= 0.129 Angle : 0.586 13.850 33908 Z= 0.291 Chirality : 0.040 0.327 3729 Planarity : 0.003 0.039 4219 Dihedral : 14.857 89.234 3859 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.61 % Allowed : 16.48 % Favored : 80.91 % 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: 1.86 (0.14), residues: 1418 sheet: 0.06 (0.31), residues: 280 loop : -1.00 (0.18), residues: 1139 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 728 TYR 0.025 0.001 TYR D 580 PHE 0.009 0.001 PHE B 386 TRP 0.018 0.001 TRP D 534 HIS 0.003 0.001 HIS B 705 Details of bonding type rmsd covalent geometry : bond 0.00296 (24774) covalent geometry : angle 0.58623 (33908) hydrogen bonds : bond 0.03376 ( 1090) hydrogen bonds : angle 3.87885 ( 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 294 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 231 time to evaluate : 0.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 146 MET cc_start: 0.7800 (mmm) cc_final: 0.7498 (mmm) REVERT: B 234 GLN cc_start: 0.9019 (tt0) cc_final: 0.8673 (mm110) REVERT: B 304 THR cc_start: 0.6988 (OUTLIER) cc_final: 0.6702 (p) REVERT: B 342 GLU cc_start: 0.8163 (tm-30) cc_final: 0.7818 (tm-30) REVERT: B 414 ASP cc_start: 0.8194 (t0) cc_final: 0.7908 (t0) REVERT: B 595 GLU cc_start: 0.8329 (mt-10) cc_final: 0.8059 (mt-10) REVERT: B 976 LYS cc_start: 0.8430 (pptt) cc_final: 0.7840 (mmtm) REVERT: B 978 GLU cc_start: 0.8442 (mm-30) cc_final: 0.8116 (mm-30) REVERT: B 1070 PHE cc_start: 0.8924 (p90) cc_final: 0.8706 (p90) REVERT: C 17 MET cc_start: 0.9137 (tmm) cc_final: 0.8616 (ptp) REVERT: C 42 MET cc_start: 0.8908 (OUTLIER) cc_final: 0.8668 (tmm) REVERT: C 47 GLN cc_start: 0.9055 (tt0) cc_final: 0.8720 (tt0) REVERT: C 383 GLN cc_start: 0.7931 (tm-30) cc_final: 0.7371 (tm-30) REVERT: C 665 MET cc_start: 0.8652 (mtp) cc_final: 0.8405 (ttp) REVERT: C 773 GLU cc_start: 0.8745 (OUTLIER) cc_final: 0.8365 (pt0) REVERT: C 817 HIS cc_start: 0.8532 (OUTLIER) cc_final: 0.8261 (m90) REVERT: D 35 VAL cc_start: 0.9623 (OUTLIER) cc_final: 0.9411 (p) REVERT: D 449 PHE cc_start: 0.8462 (m-10) cc_final: 0.8012 (m-80) REVERT: D 462 MET cc_start: 0.8592 (mmt) cc_final: 0.8259 (mmp) outliers start: 63 outliers final: 49 residues processed: 276 average time/residue: 0.1430 time to fit residues: 66.1460 Evaluate side-chains 271 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 217 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 THR 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 757 ILE Chi-restraints excluded: chain B residue 758 THR Chi-restraints excluded: chain B residue 780 LEU Chi-restraints excluded: chain B residue 853 LEU Chi-restraints excluded: chain B residue 958 LEU 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 1058 VAL Chi-restraints excluded: chain B residue 1111 TYR Chi-restraints excluded: chain B residue 1138 VAL Chi-restraints excluded: chain C residue 42 MET Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 72 MET Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain C residue 479 LEU Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 632 VAL Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 773 GLU Chi-restraints excluded: chain C residue 817 HIS Chi-restraints excluded: chain C residue 853 LEU Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 65 HIS Chi-restraints excluded: chain D residue 67 LEU 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 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 493 LEU Chi-restraints excluded: chain D residue 502 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: 20.0000 chunk 198 optimal weight: 2.9990 chunk 135 optimal weight: 8.9990 chunk 17 optimal weight: 7.9990 chunk 9 optimal weight: 0.8980 chunk 108 optimal weight: 9.9990 chunk 277 optimal weight: 10.0000 chunk 238 optimal weight: 8.9990 chunk 26 optimal weight: 9.9990 chunk 202 optimal weight: 1.9990 chunk 142 optimal weight: 0.9980 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 109 GLN ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.082842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.063226 restraints weight = 73221.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.065276 restraints weight = 38611.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.066645 restraints weight = 25566.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.067553 restraints weight = 19432.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.068079 restraints weight = 16199.237| |-----------------------------------------------------------------------------| r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.5195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 24774 Z= 0.176 Angle : 0.612 12.475 33908 Z= 0.305 Chirality : 0.041 0.312 3729 Planarity : 0.003 0.038 4219 Dihedral : 14.891 89.088 3859 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.53 % Allowed : 16.85 % Favored : 80.62 % 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: 0.82 (0.16), residues: 2837 helix: 1.85 (0.14), residues: 1418 sheet: -0.04 (0.31), residues: 283 loop : -1.01 (0.18), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 728 TYR 0.025 0.001 TYR D 580 PHE 0.017 0.001 PHE D 386 TRP 0.021 0.001 TRP D 534 HIS 0.004 0.001 HIS C 390 Details of bonding type rmsd covalent geometry : bond 0.00404 (24774) covalent geometry : angle 0.61228 (33908) hydrogen bonds : bond 0.03553 ( 1090) hydrogen bonds : angle 3.94646 ( 3155) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3528.40 seconds wall clock time: 61 minutes 49.65 seconds (3709.65 seconds total)