Starting phenix.real_space_refine on Tue Oct 27 04:27:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6sjg_10217/10_2026/6sjg_10217.cif Found real_map, /net/cci-nas-00/data/ceres_data/6sjg_10217/10_2026/6sjg_10217.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6sjg_10217/10_2026/6sjg_10217.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6sjg_10217/10_2026/6sjg_10217.map" model { file = "/net/cci-nas-00/data/ceres_data/6sjg_10217/10_2026/6sjg_10217.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6sjg_10217/10_2026/6sjg_10217.cif" } resolution = 3.8 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 54 5.49 5 S 101 5.16 5 C 14897 2.51 5 N 4192 2.21 5 O 4582 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 106 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 23826 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: 1098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 1098 Classifications: {'DNA': 54} Link IDs: {'rna3p': 53} Chain breaks: 1 Time building chain proxies: 4.92, per 1000 atoms: 0.21 Number of scatterers: 23826 At special positions: 0 Unit cell: (150.912, 149.864, 129.952, 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 54 15.00 O 4582 8.00 N 4192 7.00 C 14897 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: 1.81 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: 125 helices and 16 sheets defined 53.5% alpha, 9.2% beta 17 base pairs and 33 stacking pairs defined. Time for finding SS restraints: 2.93 Creating SS restraints... Processing helix chain 'B' and resid 28 through 43 Processing helix chain 'B' and resid 45 through 49 removed outlier: 3.516A pdb=" N ALA B 49 " --> pdb=" O GLY B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 58 removed outlier: 3.527A pdb=" N GLU B 58 " --> pdb=" O THR B 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 55 through 58' Processing helix chain 'B' and resid 65 through 90 Processing helix chain 'B' and resid 94 through 104 removed outlier: 3.780A 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: 3.810A pdb=" N SER B 144 " --> pdb=" O ASN B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 173 removed outlier: 3.797A pdb=" N TYR B 173 " --> pdb=" O ARG B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 187 removed outlier: 4.326A pdb=" N VAL B 182 " --> pdb=" O GLU B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 202 removed outlier: 3.661A pdb=" N LEU B 193 " --> pdb=" O GLY B 189 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N ARG B 199 " --> pdb=" O ARG B 195 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N TYR B 200 " --> pdb=" O ASP B 196 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLN B 202 " --> pdb=" O ASN B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 239 removed outlier: 3.572A pdb=" N VAL B 232 " --> pdb=" O ARG B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 264 Processing helix chain 'B' and resid 275 through 281 removed outlier: 3.734A pdb=" N ASN B 278 " --> pdb=" O GLU B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 289 removed outlier: 3.724A pdb=" N LYS B 288 " --> pdb=" O GLU B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 317 Processing helix chain 'B' and resid 323 through 347 removed outlier: 4.522A pdb=" N ARG B 336 " --> pdb=" O LEU B 332 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N GLU B 337 " --> pdb=" O ALA B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 364 removed outlier: 3.550A pdb=" N MET B 354 " --> pdb=" O GLY B 350 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LEU B 355 " --> pdb=" O PHE B 351 " (cutoff:3.500A) removed outlier: 3.528A 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: 3.770A pdb=" N ALA B 418 " --> pdb=" O PRO B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 437 removed outlier: 3.737A 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: 3.556A pdb=" N GLN B 534 " --> pdb=" O LEU B 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 573 removed outlier: 3.532A pdb=" N ALA B 564 " --> pdb=" O SER B 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 589 removed outlier: 3.595A 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: 3.927A pdb=" N GLN B 594 " --> pdb=" O THR B 590 " (cutoff:3.500A) Processing helix chain 'B' and resid 608 through 617 removed outlier: 3.882A pdb=" N LEU B 612 " --> pdb=" O ARG B 608 " (cutoff:3.500A) removed outlier: 3.548A 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 Processing helix chain 'B' and resid 656 through 668 removed outlier: 3.759A pdb=" N MET B 660 " --> pdb=" O GLY B 656 " (cutoff:3.500A) Processing helix chain 'B' and resid 669 through 677 removed outlier: 3.574A pdb=" N ASN B 673 " --> pdb=" O ASN B 669 " (cutoff:3.500A) Processing helix chain 'B' and resid 680 through 699 removed outlier: 3.530A pdb=" N THR B 699 " --> pdb=" O GLN B 695 " (cutoff:3.500A) Processing helix chain 'B' and resid 704 through 717 removed outlier: 3.969A pdb=" N VAL B 708 " --> pdb=" O GLU B 704 " (cutoff:3.500A) Processing helix chain 'B' and resid 783 through 807 removed outlier: 3.599A 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 837 through 843 removed outlier: 3.820A pdb=" N LEU B 841 " --> pdb=" O ALA B 837 " (cutoff:3.500A) Processing helix chain 'B' and resid 849 through 860 removed outlier: 3.971A pdb=" N LEU B 860 " --> pdb=" O CYS B 856 " (cutoff:3.500A) 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: 3.724A pdb=" N GLU B 992 " --> pdb=" O PRO B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1008 through 1012 removed outlier: 3.755A pdb=" N GLN B1011 " --> pdb=" O SER B1008 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU B1012 " --> pdb=" O LEU B1009 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1008 through 1012' Processing helix chain 'B' and resid 1032 through 1044 removed outlier: 3.698A pdb=" N THR B1038 " --> pdb=" O SER B1034 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N LEU B1039 " --> pdb=" O GLN B1035 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N PHE B1043 " --> pdb=" O LEU B1039 " (cutoff:3.500A) Processing helix chain 'B' and resid 1045 through 1048 removed outlier: 3.888A 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: 3.638A pdb=" N LEU B1167 " --> pdb=" O GLY B1163 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 24 removed outlier: 4.041A 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: 3.730A 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 Processing helix chain 'C' and resid 122 through 142 Processing helix chain 'C' and resid 142 through 152 removed outlier: 3.789A pdb=" N LEU C 146 " --> pdb=" O ARG C 142 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N THR C 151 " --> pdb=" O ALA C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 161 through 179 Proline residue: C 167 - end of helix removed outlier: 3.509A pdb=" N LYS C 170 " --> pdb=" O ALA C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 199 removed outlier: 3.798A pdb=" N LEU C 189 " --> pdb=" O HIS C 185 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N TYR C 190 " --> pdb=" O ARG C 186 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N GLN C 191 " --> pdb=" O ALA C 187 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N ARG C 192 " --> pdb=" O ASN C 188 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU C 197 " --> pdb=" O PHE C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 232 removed outlier: 3.510A pdb=" N ALA C 229 " --> pdb=" O GLN C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 263 removed outlier: 3.553A pdb=" N ALA C 258 " --> pdb=" O PRO C 254 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LYS C 259 " --> pdb=" O ALA C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 287 removed outlier: 3.758A pdb=" N LEU C 286 " --> pdb=" O ASN C 282 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N PHE C 287 " --> pdb=" O ALA C 283 " (cutoff:3.500A) No H-bonds generated for '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 removed outlier: 3.546A pdb=" N TYR C 312 " --> pdb=" O ARG C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 344 Processing helix chain 'C' and resid 354 through 360 removed outlier: 3.516A pdb=" N ARG C 360 " --> pdb=" O GLU C 356 " (cutoff:3.500A) Processing helix chain 'C' and resid 381 through 400 removed outlier: 3.561A pdb=" N VAL C 386 " --> pdb=" O PRO C 382 " (cutoff:3.500A) 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 414 through 428 removed outlier: 3.744A pdb=" N TYR C 418 " --> pdb=" O ASP C 414 " (cutoff:3.500A) Proline residue: C 420 - end of helix Processing helix chain 'C' and resid 447 through 459 removed outlier: 4.040A pdb=" N ALA C 453 " --> pdb=" O PRO C 449 " (cutoff:3.500A) Processing helix chain 'C' and resid 466 through 475 removed outlier: 3.502A pdb=" N LEU C 473 " --> pdb=" O ASP C 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 483 removed outlier: 3.702A pdb=" N PHE C 483 " --> pdb=" O LEU C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 486 through 501 removed outlier: 3.884A pdb=" N GLN C 495 " --> pdb=" O ARG C 491 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLY C 501 " --> pdb=" O VAL C 497 " (cutoff:3.500A) Processing helix chain 'C' and resid 507 through 514 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 578 removed outlier: 3.657A pdb=" N MET C 569 " --> pdb=" O ALA C 565 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N GLN C 570 " --> pdb=" O SER C 566 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ARG C 575 " --> pdb=" O LEU C 571 " (cutoff:3.500A) Processing helix chain 'C' and resid 587 through 599 removed outlier: 4.363A pdb=" N CYS C 591 " --> pdb=" O TRP C 587 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ARG C 592 " --> pdb=" O LEU C 588 " (cutoff:3.500A) Processing helix chain 'C' and resid 605 through 625 Processing helix chain 'C' and resid 633 through 646 removed outlier: 3.732A pdb=" N LEU C 637 " --> pdb=" O PRO C 633 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ASP C 646 " --> pdb=" O ALA C 642 " (cutoff:3.500A) Processing helix chain 'C' and resid 707 through 722 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: 3.541A pdb=" N LEU C 837 " --> pdb=" O PRO C 833 " (cutoff:3.500A) removed outlier: 3.734A 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: 3.672A pdb=" N LEU C 897 " --> pdb=" O ASP C 893 " (cutoff:3.500A) Processing helix chain 'C' and resid 910 through 932 removed outlier: 3.872A pdb=" N GLU C 914 " --> pdb=" O GLY C 910 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ARG C 930 " --> pdb=" O GLN C 926 " (cutoff:3.500A) Processing helix chain 'C' and resid 933 through 935 No H-bonds generated for 'chain 'C' and resid 933 through 935' Processing helix chain 'C' and resid 973 through 989 removed outlier: 3.565A pdb=" N GLY C 977 " --> pdb=" O SER C 973 " (cutoff:3.500A) Processing helix chain 'C' and resid 1012 through 1033 removed outlier: 3.911A 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: 3.602A pdb=" N GLU C1076 " --> pdb=" O LEU C1072 " (cutoff:3.500A) Processing helix chain 'C' and resid 1098 through 1113 Processing helix chain 'C' and resid 1113 through 1119 removed outlier: 3.800A pdb=" N PHE C1117 " --> pdb=" O LEU C1113 " (cutoff:3.500A) Processing helix chain 'D' and resid 11 through 15 removed outlier: 3.716A 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 Processing helix chain 'D' and resid 80 through 88 removed outlier: 3.922A 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 Processing helix chain 'D' and resid 152 through 164 removed outlier: 3.508A pdb=" N VAL D 156 " --> pdb=" O ASN D 152 " (cutoff:3.500A) removed outlier: 3.548A 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 removed outlier: 3.591A pdb=" N ARG D 221 " --> pdb=" O GLY D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 240 through 244 removed outlier: 3.515A pdb=" N LEU D 244 " --> pdb=" O LEU D 240 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 240 through 244' Processing helix chain 'D' and resid 270 through 274 removed outlier: 3.655A pdb=" N MET D 273 " --> pdb=" O GLU D 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 285 removed outlier: 3.536A pdb=" N ALA D 285 " --> pdb=" O ARG D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 315 removed outlier: 3.822A pdb=" N ASP D 312 " --> pdb=" O ALA D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 316 through 319 removed outlier: 3.552A 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: 3.543A 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: 3.977A pdb=" N GLN D 369 " --> pdb=" O SER D 365 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ASN D 375 " --> pdb=" O ALA D 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 377 through 387 removed outlier: 3.595A pdb=" N ALA D 381 " --> pdb=" O GLY D 377 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN D 387 " --> pdb=" O LYS D 383 " (cutoff:3.500A) Processing helix chain 'D' and resid 388 through 391 removed outlier: 3.884A 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: 3.553A 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 removed outlier: 3.522A pdb=" N LEU D 527 " --> pdb=" O PRO D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 562 through 572 Processing helix chain 'D' and resid 582 through 592 removed outlier: 3.762A pdb=" N ILE D 590 " --> pdb=" O LEU D 586 " (cutoff:3.500A) removed outlier: 3.902A 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: 6.428A pdb=" N GLU B 6 " --> pdb=" O THR B 442 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N ALA B 439 " --> pdb=" O GLU B 18 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU B 20 " --> pdb=" O ALA B 439 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N GLY B 17 " --> pdb=" O LEU B 409 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N LEU B 411 " --> pdb=" O GLY B 17 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ARG B 19 " --> pdb=" O LEU B 411 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N GLY B 413 " --> pdb=" O ARG B 19 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ILE B 21 " --> pdb=" O GLY B 413 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N LEU B 60 " --> pdb=" O MET B 382 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N ASP B 384 " --> pdb=" O LEU B 60 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N VAL B 62 " --> pdb=" O ASP B 384 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 151 through 152 removed outlier: 6.230A 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: 6.517A 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: 6.718A pdb=" N VAL B 579 " --> pdb=" O ILE B 738 " (cutoff:3.500A) removed outlier: 8.696A pdb=" N THR B 740 " --> pdb=" O VAL B 579 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N ILE B 554 " --> pdb=" O GLN B 737 " (cutoff:3.500A) removed outlier: 8.288A pdb=" N VAL B 739 " --> pdb=" O ILE B 554 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N VAL B 556 " --> pdb=" O VAL B 739 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N MET B 499 " --> pdb=" O ALA B 866 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N GLN B 868 " --> pdb=" O MET B 499 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N MET B 501 " --> pdb=" O GLN B 868 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 1017 through 1027 removed outlier: 6.688A pdb=" N ASP B1067 " --> pdb=" O GLU B1020 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N GLU B1022 " --> pdb=" O PHE B1065 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N PHE B1065 " --> pdb=" O GLU B1022 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N TYR B1024 " --> pdb=" O LYS B1063 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N LYS B1063 " --> pdb=" O TYR B1024 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N MET B1061 " --> pdb=" O PRO B1026 " (cutoff:3.500A) removed outlier: 10.060A pdb=" N ILE B1066 " --> pdb=" O TYR B1081 " (cutoff:3.500A) removed outlier: 8.335A pdb=" N TYR B1081 " --> pdb=" O ILE B1066 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N TYR B1076 " --> pdb=" O PHE B1135 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N GLY B1137 " --> pdb=" O TYR B1076 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 60 through 61 removed outlier: 6.215A pdb=" N VAL C 211 " --> pdb=" O HIS C 237 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N LEU C 239 " --> pdb=" O VAL C 211 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N ILE C 213 " --> pdb=" O LEU C 239 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N THR C 241 " --> pdb=" O ILE C 213 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ARG C 3 " --> pdb=" O LEU C 238 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N PHE C 240 " --> pdb=" O ARG C 3 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N TYR C 5 " --> pdb=" O PHE C 240 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ARG C 266 " --> pdb=" O GLU C 322 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP C 324 " --> pdb=" O ARG C 266 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 365 through 366 removed outlier: 6.001A pdb=" N ARG C 365 " --> pdb=" O TYR C 760 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'C' and resid 437 through 439 removed outlier: 3.661A pdb=" N ASN C 660 " --> pdb=" O ILE C 408 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N LYS C 673 " --> pdb=" O LYS C 726 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N TYR C 728 " --> pdb=" O LYS C 673 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N VAL C 675 " --> pdb=" O TYR C 728 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N SER C 730 " --> pdb=" O VAL C 675 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N LEU C 677 " --> pdb=" O SER C 730 " (cutoff:3.500A) removed outlier: 8.252A pdb=" N ILE C 732 " --> pdb=" O LEU C 677 " (cutoff:3.500A) removed outlier: 8.988A pdb=" N CYS C 782 " --> pdb=" O ILE C 374 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N PHE C 376 " --> pdb=" O CYS C 782 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 442 through 443 removed outlier: 4.060A pdb=" N ARG C 442 " --> pdb=" O ILE C 650 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ILE C 650 " --> pdb=" O ARG C 442 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 939 through 947 removed outlier: 5.602A pdb=" N GLN C 939 " --> pdb=" O GLN C 958 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLN C 958 " --> pdb=" O GLN C 939 " (cutoff:3.500A) removed outlier: 15.508A pdb=" N LEU C 956 " --> pdb=" O TRP C 967 " (cutoff:3.500A) removed outlier: 13.186A pdb=" N TRP C 967 " --> pdb=" O LEU C 956 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N GLN C 958 " --> pdb=" O LEU C 965 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N LEU C 965 " --> pdb=" O GLN C 958 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N LEU C 964 " --> pdb=" O ARG C 997 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N PHE C 999 " --> pdb=" O LEU C 964 " (cutoff:3.500A) removed outlier: 7.326A 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: 5.993A 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: 6.886A pdb=" N SER D 167 " --> pdb=" O PHE D 294 " (cutoff:3.500A) removed outlier: 8.544A pdb=" N GLY D 296 " --> pdb=" O SER D 167 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N ILE D 169 " --> pdb=" O GLY D 296 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ARG D 200 " --> pdb=" O VAL D 267 " (cutoff:3.500A) removed outlier: 8.890A pdb=" N SER D 238 " --> pdb=" O ILE D 199 " (cutoff:3.500A) removed outlier: 6.574A 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: 7.248A pdb=" N ASP D 547 " --> pdb=" O ARG D 574 " (cutoff:3.500A) removed outlier: 8.725A pdb=" N MET D 536 " --> pdb=" O TYR D 438 " (cutoff:3.500A) removed outlier: 6.512A 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: 4.419A pdb=" N ALA D 513 " --> pdb=" O ILE D 498 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ILE D 498 " --> pdb=" O ALA D 513 " (cutoff:3.500A) 1052 hydrogen bonds defined for protein. 3102 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 42 hydrogen bonds 80 hydrogen bond angles 0 basepair planarities 17 basepair parallelities 33 stacking parallelities Total time for adding SS restraints: 5.57 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: 6697 1.34 - 1.45: 4289 1.45 - 1.57: 13191 1.57 - 1.69: 106 1.69 - 1.81: 169 Bond restraints: 24452 Sorted by residual: bond pdb=" C3' DG X 59 " pdb=" C2' DG X 59 " ideal model delta sigma weight residual 1.516 1.537 -0.021 8.00e-03 1.56e+04 6.91e+00 bond pdb=" C3' DG X 20 " pdb=" C2' DG X 20 " ideal model delta sigma weight residual 1.516 1.536 -0.020 8.00e-03 1.56e+04 6.47e+00 bond pdb=" C1' DT X 74 " pdb=" N1 DT X 74 " ideal model delta sigma weight residual 1.468 1.502 -0.034 1.40e-02 5.10e+03 5.99e+00 bond pdb=" C1' DC X 70 " pdb=" N1 DC X 70 " ideal model delta sigma weight residual 1.468 1.502 -0.034 1.40e-02 5.10e+03 5.88e+00 bond pdb=" C3' DT X 8 " pdb=" C2' DT X 8 " ideal model delta sigma weight residual 1.516 1.535 -0.019 8.00e-03 1.56e+04 5.79e+00 ... (remaining 24447 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.62: 32607 1.62 - 3.24: 705 3.24 - 4.86: 68 4.86 - 6.47: 20 6.47 - 8.09: 9 Bond angle restraints: 33409 Sorted by residual: angle pdb=" N3 DT X 54 " pdb=" C4 DT X 54 " pdb=" O4 DT X 54 " ideal model delta sigma weight residual 119.90 122.45 -2.55 6.00e-01 2.78e+00 1.80e+01 angle pdb=" N3 DT X 65 " pdb=" C4 DT X 65 " pdb=" O4 DT X 65 " ideal model delta sigma weight residual 119.90 122.42 -2.52 6.00e-01 2.78e+00 1.76e+01 angle pdb=" N3 DT X 5 " pdb=" C4 DT X 5 " pdb=" O4 DT X 5 " ideal model delta sigma weight residual 119.90 122.41 -2.51 6.00e-01 2.78e+00 1.75e+01 angle pdb=" N3 DT X 60 " pdb=" C4 DT X 60 " pdb=" O4 DT X 60 " ideal model delta sigma weight residual 119.90 122.39 -2.49 6.00e-01 2.78e+00 1.72e+01 angle pdb=" N3 DT X 9 " pdb=" C4 DT X 9 " pdb=" O4 DT X 9 " ideal model delta sigma weight residual 119.90 122.38 -2.48 6.00e-01 2.78e+00 1.71e+01 ... (remaining 33404 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.78: 13492 16.78 - 33.57: 730 33.57 - 50.35: 307 50.35 - 67.14: 79 67.14 - 83.92: 7 Dihedral angle restraints: 14615 sinusoidal: 6326 harmonic: 8289 Sorted by residual: dihedral pdb=" CA ILE B 400 " pdb=" C ILE B 400 " pdb=" N TRP B 401 " pdb=" CA TRP B 401 " ideal model delta harmonic sigma weight residual -180.00 -163.37 -16.63 0 5.00e+00 4.00e-02 1.11e+01 dihedral pdb=" CA GLY C 657 " pdb=" C GLY C 657 " pdb=" N PRO C 658 " pdb=" CA PRO C 658 " ideal model delta harmonic sigma weight residual 180.00 164.04 15.96 0 5.00e+00 4.00e-02 1.02e+01 dihedral pdb=" N ASN C 768 " pdb=" CA ASN C 768 " pdb=" CB ASN C 768 " pdb=" CG ASN C 768 " ideal model delta sinusoidal sigma weight residual -60.00 -118.97 58.97 3 1.50e+01 4.44e-03 9.47e+00 ... (remaining 14612 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 2541 0.034 - 0.069: 784 0.069 - 0.103: 257 0.103 - 0.137: 81 0.137 - 0.171: 10 Chirality restraints: 3673 Sorted by residual: chirality pdb=" CA LEU C 588 " pdb=" N LEU C 588 " pdb=" C LEU C 588 " pdb=" CB LEU C 588 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.35e-01 chirality pdb=" CA TYR B 173 " pdb=" N TYR B 173 " pdb=" C TYR B 173 " pdb=" CB TYR B 173 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.98e-01 chirality pdb=" CA LEU C 99 " pdb=" N LEU C 99 " pdb=" C LEU C 99 " pdb=" CB LEU C 99 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.65e-01 ... (remaining 3670 not shown) Planarity restraints: 4205 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY C 657 " 0.050 5.00e-02 4.00e+02 7.51e-02 9.02e+00 pdb=" N PRO C 658 " -0.130 5.00e-02 4.00e+02 pdb=" CA PRO C 658 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO C 658 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER C 419 " -0.036 5.00e-02 4.00e+02 5.40e-02 4.66e+00 pdb=" N PRO C 420 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO C 420 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 420 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 99 " 0.036 5.00e-02 4.00e+02 5.32e-02 4.52e+00 pdb=" N PRO C 100 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO C 100 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO C 100 " 0.030 5.00e-02 4.00e+02 ... (remaining 4202 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.82: 6709 2.82 - 3.34: 19747 3.34 - 3.86: 39494 3.86 - 4.38: 44353 4.38 - 4.90: 76387 Nonbonded interactions: 186690 Sorted by model distance: nonbonded pdb=" O LEU C 115 " pdb=" OG SER C 119 " model vdw 2.294 3.040 nonbonded pdb=" O THR D 533 " pdb=" OG1 THR D 533 " model vdw 2.321 3.040 nonbonded pdb=" OH TYR C 794 " pdb=" O ALA C 803 " model vdw 2.332 3.040 nonbonded pdb=" O TYR C 754 " pdb=" OG SER C 758 " model vdw 2.333 3.040 nonbonded pdb=" O2 DC X 27 " pdb=" N2 DG X 59 " model vdw 2.334 2.496 ... (remaining 186685 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.460 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 24.290 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7300 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 0.045 24452 Z= 0.214 Angle : 0.583 8.094 33409 Z= 0.398 Chirality : 0.040 0.171 3673 Planarity : 0.005 0.075 4205 Dihedral : 12.823 83.921 9243 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.90 % Allowed : 4.89 % Favored : 92.22 % 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: -3.61 (0.11), residues: 2837 helix: -2.53 (0.09), residues: 1384 sheet: -0.89 (0.27), residues: 284 loop : -2.43 (0.14), residues: 1169 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 399 TYR 0.012 0.001 TYR B1111 PHE 0.014 0.001 PHE B1023 TRP 0.011 0.001 TRP B 652 HIS 0.004 0.000 HIS D 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.21 (24452) covalent geometry : angle 0.58265 / 0.40 (33409) hydrogen bonds : bond 0.14036 / 9.52 ( 1094) hydrogen bonds : angle 6.49909 / 4.57 ( 3182) *********************** 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 647 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 577 time to evaluate : 0.795 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: B 66 GLU cc_start: 0.7112 (tt0) cc_final: 0.6740 (tp30) REVERT: B 137 LEU cc_start: 0.9029 (mt) cc_final: 0.8822 (mt) REVERT: B 304 THR cc_start: 0.2275 (OUTLIER) cc_final: 0.1069 (p) REVERT: B 354 MET cc_start: 0.8311 (mtt) cc_final: 0.7979 (mtm) REVERT: B 735 LEU cc_start: 0.5925 (mt) cc_final: 0.5488 (mp) REVERT: B 756 PHE cc_start: 0.7654 (m-80) cc_final: 0.7350 (m-80) REVERT: B 842 LEU cc_start: 0.8491 (mt) cc_final: 0.8275 (mt) REVERT: B 860 LEU cc_start: 0.8178 (OUTLIER) cc_final: 0.7912 (pt) REVERT: B 940 LEU cc_start: 0.6118 (mt) cc_final: 0.5763 (mm) REVERT: B 1024 TYR cc_start: 0.5652 (m-80) cc_final: 0.5396 (m-10) REVERT: B 1058 VAL cc_start: 0.7867 (t) cc_final: 0.7390 (m) REVERT: B 1158 THR cc_start: 0.7728 (OUTLIER) cc_final: 0.6521 (p) REVERT: C 460 LEU cc_start: 0.8937 (tp) cc_final: 0.8648 (tt) REVERT: C 697 MET cc_start: 0.7577 (mtp) cc_final: 0.6978 (mtp) REVERT: C 781 THR cc_start: 0.8165 (m) cc_final: 0.7800 (p) REVERT: C 817 HIS cc_start: 0.7393 (OUTLIER) cc_final: 0.7154 (m90) REVERT: C 1000 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8548 (mt) REVERT: D 216 LEU cc_start: 0.5196 (mt) cc_final: 0.4765 (pp) REVERT: D 407 MET cc_start: 0.6652 (ttp) cc_final: 0.5882 (ptm) REVERT: D 415 TYR cc_start: 0.2918 (m-80) cc_final: 0.2253 (m-80) REVERT: D 430 LEU cc_start: 0.8443 (mp) cc_final: 0.8062 (mp) REVERT: D 462 MET cc_start: 0.4050 (mmt) cc_final: 0.3781 (mmt) REVERT: D 493 LEU cc_start: 0.7917 (OUTLIER) cc_final: 0.7712 (pp) REVERT: D 558 THR cc_start: 0.6561 (OUTLIER) cc_final: 0.6352 (t) REVERT: D 567 TYR cc_start: 0.7747 (t80) cc_final: 0.7458 (t80) REVERT: D 571 THR cc_start: 0.7677 (p) cc_final: 0.7473 (p) outliers start: 70 outliers final: 11 residues processed: 631 average time/residue: 0.1664 time to fit residues: 160.2560 Evaluate side-chains 308 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 290 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 860 LEU Chi-restraints excluded: chain B residue 947 ARG Chi-restraints excluded: chain B residue 1002 LEU Chi-restraints excluded: chain B residue 1158 THR Chi-restraints excluded: chain C residue 506 ILE Chi-restraints excluded: chain C residue 817 HIS Chi-restraints excluded: chain C residue 821 VAL Chi-restraints excluded: chain C residue 853 LEU Chi-restraints excluded: chain C residue 1000 LEU Chi-restraints excluded: chain D residue 108 TYR Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 350 ASP Chi-restraints excluded: chain D residue 493 LEU Chi-restraints excluded: chain D residue 558 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: [197, 215, 20, 132, 261, 248, 207, 155, 244, 183, 111] chunk 197 optimal weight: 9.9990 chunk 215 optimal weight: 0.0670 chunk 20 optimal weight: 0.4980 chunk 132 optimal weight: 0.6980 chunk 261 optimal weight: 30.0000 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 20.0000 chunk 183 optimal weight: 6.9990 chunk 111 optimal weight: 0.6980 overall best weight: 0.9920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 120 GLN B 150 GLN B 181 GLN B 458 ASN B 463 GLN B 525 GLN B 650 GLN B 713 GLN B 734 HIS B 765 GLN B 834 HIS B 848 GLN B 944 GLN ** B1057 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1072 HIS C 113 HIS C 162 GLN ** C 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 HIS C 191 GLN C 570 GLN C 822 GLN C 843 HIS C 883 GLN C 925 GLN C 958 GLN C 979 GLN C1091 GLN C1108 GLN D 15 GLN D 22 GLN ** D 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 50 HIS D 79 GLN D 89 GLN D 115 ASN D 128 HIS D 251 GLN D 259 ASN D 423 GLN D 523 GLN Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.117102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.091408 restraints weight = 79658.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.093310 restraints weight = 48615.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.094491 restraints weight = 35316.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.095219 restraints weight = 28969.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.095666 restraints weight = 25608.480| |-----------------------------------------------------------------------------| r_work (final): 0.3707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.2649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 24452 Z= 0.142 Angle : 0.615 9.831 33409 Z= 0.318 Chirality : 0.041 0.291 3673 Planarity : 0.005 0.075 4205 Dihedral : 13.522 82.850 3734 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.86 % Allowed : 12.30 % Favored : 84.84 % 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: -1.70 (0.14), residues: 2837 helix: -0.47 (0.12), residues: 1408 sheet: -0.53 (0.29), residues: 286 loop : -2.07 (0.15), residues: 1143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 306 TYR 0.019 0.001 TYR C 535 PHE 0.020 0.001 PHE B 132 TRP 0.032 0.002 TRP B1085 HIS 0.011 0.001 HIS C 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.14 (24452) covalent geometry : angle 0.61492 / 0.32 (33409) hydrogen bonds : bond 0.04096 / 2.86 ( 1094) hydrogen bonds : angle 4.63330 / 3.26 ( 3182) *********************** 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 373 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 304 time to evaluate : 0.762 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 137 LEU cc_start: 0.9080 (mt) cc_final: 0.8669 (mt) REVERT: B 321 LEU cc_start: 0.8447 (mt) cc_final: 0.8187 (mp) REVERT: B 354 MET cc_start: 0.8316 (mtt) cc_final: 0.7928 (mtm) REVERT: B 753 TRP cc_start: 0.8445 (OUTLIER) cc_final: 0.8021 (t60) REVERT: B 823 ARG cc_start: 0.5426 (ttt-90) cc_final: 0.3701 (mmt90) REVERT: B 1004 GLU cc_start: 0.8513 (tm-30) cc_final: 0.7888 (pm20) REVERT: B 1088 GLU cc_start: 0.6467 (OUTLIER) cc_final: 0.5793 (tp30) REVERT: C 475 ASP cc_start: 0.7841 (m-30) cc_final: 0.7567 (m-30) REVERT: C 653 ARG cc_start: 0.7545 (mtm-85) cc_final: 0.7268 (mpp80) REVERT: C 781 THR cc_start: 0.8463 (m) cc_final: 0.8005 (p) REVERT: D 108 TYR cc_start: 0.5048 (OUTLIER) cc_final: 0.4476 (p90) REVERT: D 112 MET cc_start: 0.7508 (mmm) cc_final: 0.7205 (ttm) REVERT: D 329 LEU cc_start: 0.7461 (mm) cc_final: 0.7257 (mm) REVERT: D 415 TYR cc_start: 0.2924 (m-80) cc_final: 0.2622 (m-80) REVERT: D 430 LEU cc_start: 0.8390 (mp) cc_final: 0.8179 (mp) REVERT: D 462 MET cc_start: 0.4320 (mmt) cc_final: 0.3834 (mmt) REVERT: D 567 TYR cc_start: 0.7640 (t80) cc_final: 0.7273 (t80) outliers start: 69 outliers final: 24 residues processed: 354 average time/residue: 0.1576 time to fit residues: 87.2945 Evaluate side-chains 264 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 237 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 753 TRP Chi-restraints excluded: chain B residue 841 LEU Chi-restraints excluded: chain B residue 1002 LEU Chi-restraints excluded: chain B residue 1025 LEU Chi-restraints excluded: chain B residue 1078 LEU Chi-restraints excluded: chain B residue 1088 GLU Chi-restraints excluded: chain B residue 1116 LEU Chi-restraints excluded: chain C residue 381 SER Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 506 ILE Chi-restraints excluded: chain C residue 528 LEU Chi-restraints excluded: chain C residue 821 VAL Chi-restraints excluded: chain C residue 853 LEU Chi-restraints excluded: chain C residue 958 GLN Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 108 TYR Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 350 ASP Chi-restraints excluded: chain D residue 370 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: [248, 212, 233, 167, 232, 200, 90, 275, 101, 270, 125] chunk 248 optimal weight: 20.0000 chunk 212 optimal weight: 6.9990 chunk 233 optimal weight: 7.9990 chunk 167 optimal weight: 9.9990 chunk 232 optimal weight: 7.9990 chunk 200 optimal weight: 6.9990 chunk 90 optimal weight: 6.9990 chunk 275 optimal weight: 2.9990 chunk 101 optimal weight: 20.0000 chunk 270 optimal weight: 30.0000 chunk 125 optimal weight: 7.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 134 GLN ** B 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 463 GLN B 763 GLN B 769 HIS B 843 GLN B 868 GLN ** B1057 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1134 HIS B1150 HIS C 87 ASN ** C 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 237 HIS ** C 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 336 HIS C 390 HIS C 725 GLN C 749 GLN C 958 GLN C 984 HIS ** D 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 328 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.105096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.078825 restraints weight = 83126.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.080442 restraints weight = 52313.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.081469 restraints weight = 39019.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.082133 restraints weight = 32806.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.082544 restraints weight = 29296.335| |-----------------------------------------------------------------------------| r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.4226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.159 24452 Z= 0.322 Angle : 0.830 11.498 33409 Z= 0.419 Chirality : 0.048 0.239 3673 Planarity : 0.007 0.090 4205 Dihedral : 13.720 85.026 3715 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.28 % Favored : 96.69 % Rotamer: Outliers : 4.18 % Allowed : 12.30 % Favored : 83.52 % 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: -0.96 (0.15), residues: 2837 helix: 0.21 (0.13), residues: 1431 sheet: -0.52 (0.29), residues: 298 loop : -1.74 (0.17), residues: 1108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 561 TYR 0.021 0.003 TYR C 728 PHE 0.030 0.003 PHE B 310 TRP 0.025 0.002 TRP C 574 HIS 0.013 0.002 HIS C 817 Details of bonding type rmsd/Z covalent geometry : bond 0.00717 / 0.32 (24452) covalent geometry : angle 0.83042 / 0.42 (33409) hydrogen bonds : bond 0.04606 / 3.17 ( 1094) hydrogen bonds : angle 4.80481 / 3.38 ( 3182) *********************** 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 339 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 238 time to evaluate : 0.849 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: B 354 MET cc_start: 0.8403 (mtt) cc_final: 0.8008 (mtm) REVERT: B 426 ASP cc_start: 0.9035 (OUTLIER) cc_final: 0.8668 (p0) REVERT: B 492 LYS cc_start: 0.7424 (OUTLIER) cc_final: 0.7040 (pptt) REVERT: B 544 ASP cc_start: 0.7059 (m-30) cc_final: 0.6845 (m-30) REVERT: B 753 TRP cc_start: 0.8958 (OUTLIER) cc_final: 0.8108 (t60) REVERT: B 871 GLN cc_start: 0.5685 (tt0) cc_final: 0.5004 (mp10) REVERT: B 1002 LEU cc_start: 0.7790 (OUTLIER) cc_final: 0.7541 (pp) REVERT: B 1004 GLU cc_start: 0.8684 (tm-30) cc_final: 0.7992 (pm20) REVERT: B 1066 ILE cc_start: 0.8598 (mt) cc_final: 0.8313 (mm) REVERT: B 1098 MET cc_start: 0.6154 (OUTLIER) cc_final: 0.5931 (mpp) REVERT: B 1102 MET cc_start: 0.7759 (mmm) cc_final: 0.7382 (tpt) REVERT: C 411 MET cc_start: 0.8271 (mtp) cc_final: 0.8021 (mmm) REVERT: C 495 GLN cc_start: 0.7757 (pp30) cc_final: 0.7504 (pp30) REVERT: C 569 MET cc_start: 0.7218 (tmm) cc_final: 0.6998 (tmm) REVERT: C 653 ARG cc_start: 0.7822 (mtm-85) cc_final: 0.7408 (mpp80) REVERT: C 660 ASN cc_start: 0.7379 (OUTLIER) cc_final: 0.7085 (m110) REVERT: C 781 THR cc_start: 0.9014 (m) cc_final: 0.8755 (p) REVERT: C 1057 MET cc_start: 0.8401 (tpp) cc_final: 0.8169 (tpp) REVERT: D 191 MET cc_start: 0.8813 (mmm) cc_final: 0.8607 (mmp) REVERT: D 415 TYR cc_start: 0.3086 (m-80) cc_final: 0.2627 (m-80) REVERT: D 430 LEU cc_start: 0.8540 (mp) cc_final: 0.8079 (mp) REVERT: D 462 MET cc_start: 0.4719 (mmt) cc_final: 0.4448 (mmt) REVERT: D 511 TRP cc_start: 0.7897 (m100) cc_final: 0.7401 (m100) REVERT: D 567 TYR cc_start: 0.7870 (t80) cc_final: 0.7591 (t80) outliers start: 101 outliers final: 53 residues processed: 316 average time/residue: 0.1452 time to fit residues: 74.1638 Evaluate side-chains 257 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 198 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 289 PHE Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 426 ASP Chi-restraints excluded: chain B residue 431 MET Chi-restraints excluded: chain B residue 492 LYS Chi-restraints excluded: chain B residue 566 GLN Chi-restraints excluded: chain B residue 727 MET Chi-restraints excluded: chain B residue 735 LEU Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 753 TRP Chi-restraints excluded: chain B residue 804 VAL Chi-restraints excluded: chain B residue 813 CYS Chi-restraints excluded: chain B residue 1002 LEU Chi-restraints excluded: chain B residue 1025 LEU Chi-restraints excluded: chain B residue 1069 VAL Chi-restraints excluded: chain B residue 1088 GLU Chi-restraints excluded: chain B residue 1098 MET Chi-restraints excluded: chain B residue 1158 THR Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 96 MET Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 381 SER Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 404 THR Chi-restraints excluded: chain C residue 484 ASP Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 506 ILE Chi-restraints excluded: chain C residue 528 LEU Chi-restraints excluded: chain C residue 602 ASP Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 612 ILE Chi-restraints excluded: chain C residue 645 LEU Chi-restraints excluded: chain C residue 651 SER Chi-restraints excluded: chain C residue 660 ASN Chi-restraints excluded: chain C residue 821 VAL Chi-restraints excluded: chain C residue 853 LEU Chi-restraints excluded: chain C residue 885 LEU Chi-restraints excluded: chain C residue 965 LEU Chi-restraints excluded: chain C residue 1106 VAL Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 108 TYR Chi-restraints excluded: chain D residue 130 ILE Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 350 ASP Chi-restraints excluded: chain D residue 370 LEU Chi-restraints excluded: chain D residue 471 HIS Chi-restraints excluded: chain D residue 551 LEU Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 568 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: [137, 231, 172, 101, 259, 196, 34, 220, 25, 26, 0] chunk 137 optimal weight: 0.7980 chunk 231 optimal weight: 8.9990 chunk 172 optimal weight: 2.9990 chunk 101 optimal weight: 5.9990 chunk 259 optimal weight: 10.0000 chunk 196 optimal weight: 0.9990 chunk 34 optimal weight: 6.9990 chunk 220 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 26 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B1057 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1084 ASN ** C 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 228 GLN C 423 GLN C 660 ASN C 759 HIS D 15 GLN ** D 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 318 ASN D 328 GLN D 433 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.105683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.079473 restraints weight = 81904.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.081292 restraints weight = 49572.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.082470 restraints weight = 36031.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.083172 restraints weight = 29529.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.083525 restraints weight = 26290.629| |-----------------------------------------------------------------------------| r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.4459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 24452 Z= 0.155 Angle : 0.611 10.207 33409 Z= 0.310 Chirality : 0.042 0.262 3673 Planarity : 0.004 0.060 4205 Dihedral : 13.683 88.184 3714 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.53 % Allowed : 13.79 % Favored : 83.69 % 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: -0.39 (0.15), residues: 2837 helix: 0.83 (0.13), residues: 1421 sheet: -0.59 (0.29), residues: 297 loop : -1.58 (0.17), residues: 1119 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 306 TYR 0.020 0.002 TYR C 256 PHE 0.026 0.002 PHE B 351 TRP 0.020 0.001 TRP C 574 HIS 0.007 0.001 HIS B 222 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.16 (24452) covalent geometry : angle 0.61124 / 0.31 (33409) hydrogen bonds : bond 0.03688 / 2.55 ( 1094) hydrogen bonds : angle 4.45246 / 3.12 ( 3182) *********************** 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 285 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 224 time to evaluate : 0.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 354 MET cc_start: 0.8350 (mtt) cc_final: 0.7940 (mtm) REVERT: B 492 LYS cc_start: 0.7719 (OUTLIER) cc_final: 0.7344 (pptt) REVERT: B 499 MET cc_start: 0.7735 (tmm) cc_final: 0.7344 (tmm) REVERT: B 753 TRP cc_start: 0.8946 (OUTLIER) cc_final: 0.8081 (t60) REVERT: B 871 GLN cc_start: 0.5741 (tt0) cc_final: 0.5199 (mp10) REVERT: B 944 GLN cc_start: 0.8365 (mt0) cc_final: 0.8117 (mt0) REVERT: B 1002 LEU cc_start: 0.7774 (OUTLIER) cc_final: 0.7539 (pp) REVERT: B 1004 GLU cc_start: 0.8729 (tm-30) cc_final: 0.8057 (pm20) REVERT: B 1066 ILE cc_start: 0.8488 (OUTLIER) cc_final: 0.8212 (mm) REVERT: B 1098 MET cc_start: 0.5997 (mpp) cc_final: 0.5745 (mpp) REVERT: B 1102 MET cc_start: 0.7759 (mmm) cc_final: 0.7530 (tpt) REVERT: B 1111 TYR cc_start: 0.7512 (t80) cc_final: 0.7203 (t80) REVERT: C 238 LEU cc_start: 0.9199 (OUTLIER) cc_final: 0.8831 (tp) REVERT: C 411 MET cc_start: 0.8305 (mtp) cc_final: 0.7980 (mtp) REVERT: C 495 GLN cc_start: 0.7852 (pp30) cc_final: 0.7441 (pp30) REVERT: C 560 LEU cc_start: 0.8241 (tt) cc_final: 0.7536 (mm) REVERT: C 653 ARG cc_start: 0.7863 (mtm-85) cc_final: 0.7428 (mpp80) REVERT: C 781 THR cc_start: 0.9102 (m) cc_final: 0.8795 (p) REVERT: D 269 ASP cc_start: 0.8084 (p0) cc_final: 0.7669 (p0) REVERT: D 415 TYR cc_start: 0.3244 (m-80) cc_final: 0.2747 (m-80) REVERT: D 462 MET cc_start: 0.4560 (mmt) cc_final: 0.4347 (mmt) REVERT: D 514 MET cc_start: 0.6597 (mmt) cc_final: 0.5607 (mtt) outliers start: 61 outliers final: 37 residues processed: 270 average time/residue: 0.1490 time to fit residues: 64.7683 Evaluate side-chains 247 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 205 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 431 MET Chi-restraints excluded: chain B residue 492 LYS Chi-restraints excluded: chain B residue 566 GLN Chi-restraints excluded: chain B residue 727 MET Chi-restraints excluded: chain B residue 735 LEU Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 753 TRP Chi-restraints excluded: chain B residue 813 CYS Chi-restraints excluded: chain B residue 1002 LEU Chi-restraints excluded: chain B residue 1025 LEU Chi-restraints excluded: chain B residue 1027 ILE Chi-restraints excluded: chain B residue 1066 ILE Chi-restraints excluded: chain B residue 1069 VAL Chi-restraints excluded: chain B residue 1088 GLU Chi-restraints excluded: chain B residue 1116 LEU Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 381 SER Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 404 THR Chi-restraints excluded: chain C residue 506 ILE Chi-restraints excluded: chain C residue 528 LEU Chi-restraints excluded: chain C residue 553 SER Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 612 ILE Chi-restraints excluded: chain C residue 645 LEU Chi-restraints excluded: chain C residue 651 SER Chi-restraints excluded: chain C residue 821 VAL Chi-restraints excluded: chain C residue 853 LEU Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 108 TYR Chi-restraints excluded: chain D residue 130 ILE Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 298 ARG Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 350 ASP Chi-restraints excluded: chain D residue 370 LEU Chi-restraints excluded: chain D residue 551 LEU Chi-restraints excluded: chain D residue 553 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: [174, 99, 13, 70, 152, 113, 256, 72, 267, 115, 111] chunk 174 optimal weight: 9.9990 chunk 99 optimal weight: 20.0000 chunk 13 optimal weight: 8.9990 chunk 70 optimal weight: 0.7980 chunk 152 optimal weight: 6.9990 chunk 113 optimal weight: 2.9990 chunk 256 optimal weight: 20.0000 chunk 72 optimal weight: 7.9990 chunk 267 optimal weight: 7.9990 chunk 115 optimal weight: 0.1980 chunk 111 optimal weight: 30.0000 overall best weight: 3.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1057 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 328 GLN D 469 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.103745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.077564 restraints weight = 81768.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.079228 restraints weight = 50779.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.080243 restraints weight = 37647.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.080958 restraints weight = 31325.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.081361 restraints weight = 27900.054| |-----------------------------------------------------------------------------| r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.4934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 24452 Z= 0.200 Angle : 0.632 10.536 33409 Z= 0.318 Chirality : 0.042 0.178 3673 Planarity : 0.004 0.051 4205 Dihedral : 13.788 87.374 3714 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.02 % Allowed : 13.79 % Favored : 83.19 % 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: -0.13 (0.16), residues: 2837 helix: 1.04 (0.14), residues: 1422 sheet: -0.55 (0.30), residues: 287 loop : -1.43 (0.18), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 255 TYR 0.012 0.002 TYR C 256 PHE 0.019 0.002 PHE B 351 TRP 0.018 0.002 TRP C 574 HIS 0.009 0.001 HIS B 222 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.20 (24452) covalent geometry : angle 0.63158 / 0.32 (33409) hydrogen bonds : bond 0.03790 / 2.60 ( 1094) hydrogen bonds : angle 4.43549 / 3.10 ( 3182) *********************** 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 284 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 211 time to evaluate : 0.895 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 354 MET cc_start: 0.8422 (mtt) cc_final: 0.7891 (mtm) REVERT: B 492 LYS cc_start: 0.7875 (OUTLIER) cc_final: 0.7435 (pptt) REVERT: B 499 MET cc_start: 0.7955 (tmm) cc_final: 0.7574 (tmm) REVERT: B 518 MET cc_start: 0.8347 (mmm) cc_final: 0.7942 (mmm) REVERT: B 753 TRP cc_start: 0.8988 (OUTLIER) cc_final: 0.8236 (t60) REVERT: B 871 GLN cc_start: 0.5630 (tt0) cc_final: 0.5248 (mp10) REVERT: B 944 GLN cc_start: 0.8466 (mt0) cc_final: 0.8195 (mt0) REVERT: B 993 TRP cc_start: 0.7738 (t60) cc_final: 0.7186 (t60) REVERT: B 1066 ILE cc_start: 0.8272 (OUTLIER) cc_final: 0.8023 (mm) REVERT: B 1088 GLU cc_start: 0.6408 (OUTLIER) cc_final: 0.6079 (tp30) REVERT: B 1098 MET cc_start: 0.6113 (OUTLIER) cc_final: 0.5888 (mpp) REVERT: B 1111 TYR cc_start: 0.7572 (t80) cc_final: 0.7370 (t80) REVERT: C 475 ASP cc_start: 0.7583 (m-30) cc_final: 0.7364 (m-30) REVERT: C 495 GLN cc_start: 0.7864 (pp30) cc_final: 0.7516 (pp30) REVERT: C 569 MET cc_start: 0.6779 (tmm) cc_final: 0.6522 (tmm) REVERT: C 634 LEU cc_start: 0.9319 (tp) cc_final: 0.9095 (tp) REVERT: C 667 MET cc_start: 0.6875 (mmm) cc_final: 0.6370 (tpt) REVERT: C 781 THR cc_start: 0.9215 (m) cc_final: 0.8894 (p) REVERT: C 1079 MET cc_start: 0.7850 (mmp) cc_final: 0.7587 (mmt) REVERT: D 222 GLN cc_start: 0.8460 (OUTLIER) cc_final: 0.8217 (pp30) REVERT: D 269 ASP cc_start: 0.8043 (p0) cc_final: 0.7735 (p0) REVERT: D 415 TYR cc_start: 0.3490 (m-80) cc_final: 0.2912 (m-80) REVERT: D 514 MET cc_start: 0.6562 (mmt) cc_final: 0.5786 (mtt) REVERT: D 575 ARG cc_start: 0.7962 (tpt170) cc_final: 0.7753 (tpt170) outliers start: 73 outliers final: 48 residues processed: 264 average time/residue: 0.1461 time to fit residues: 62.4478 Evaluate side-chains 247 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 193 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 431 MET Chi-restraints excluded: chain B residue 492 LYS Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 566 GLN Chi-restraints excluded: chain B residue 735 LEU Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 753 TRP Chi-restraints excluded: chain B residue 813 CYS Chi-restraints excluded: chain B residue 1025 LEU Chi-restraints excluded: chain B residue 1027 ILE Chi-restraints excluded: chain B residue 1066 ILE Chi-restraints excluded: chain B residue 1069 VAL Chi-restraints excluded: chain B residue 1088 GLU Chi-restraints excluded: chain B residue 1098 MET Chi-restraints excluded: chain B residue 1116 LEU Chi-restraints excluded: chain B residue 1158 THR Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 381 SER Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 404 THR Chi-restraints excluded: chain C residue 455 ILE Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 484 ASP Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 506 ILE Chi-restraints excluded: chain C residue 528 LEU Chi-restraints excluded: chain C residue 553 SER Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 612 ILE Chi-restraints excluded: chain C residue 645 LEU Chi-restraints excluded: chain C residue 651 SER Chi-restraints excluded: chain C residue 821 VAL Chi-restraints excluded: chain C residue 853 LEU Chi-restraints excluded: chain C residue 885 LEU Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 108 TYR Chi-restraints excluded: chain D residue 130 ILE Chi-restraints excluded: chain D residue 222 GLN Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain D residue 350 ASP Chi-restraints excluded: chain D residue 370 LEU Chi-restraints excluded: chain D residue 471 HIS Chi-restraints excluded: chain D residue 553 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: [82, 268, 16, 219, 286, 96, 165, 195, 84, 176, 201] chunk 82 optimal weight: 10.0000 chunk 268 optimal weight: 20.0000 chunk 16 optimal weight: 1.9990 chunk 219 optimal weight: 4.9990 chunk 286 optimal weight: 50.0000 chunk 96 optimal weight: 20.0000 chunk 165 optimal weight: 9.9990 chunk 195 optimal weight: 3.9990 chunk 84 optimal weight: 6.9990 chunk 176 optimal weight: 3.9990 chunk 201 optimal weight: 3.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 134 GLN B 138 ASN ** B1057 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 423 GLN ** C 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 328 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.102212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.076002 restraints weight = 82435.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.077693 restraints weight = 51321.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.078727 restraints weight = 37927.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.079422 restraints weight = 31479.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.079762 restraints weight = 28108.513| |-----------------------------------------------------------------------------| r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.5190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 24452 Z= 0.191 Angle : 0.612 9.857 33409 Z= 0.308 Chirality : 0.042 0.199 3673 Planarity : 0.004 0.057 4205 Dihedral : 13.827 87.115 3712 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.73 % Allowed : 14.49 % Favored : 82.77 % 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: -0.05 (0.16), residues: 2837 helix: 1.15 (0.14), residues: 1421 sheet: -0.65 (0.29), residues: 289 loop : -1.39 (0.17), residues: 1127 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 298 TYR 0.021 0.002 TYR B1093 PHE 0.018 0.002 PHE B 289 TRP 0.017 0.001 TRP C 574 HIS 0.007 0.001 HIS B 222 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.19 (24452) covalent geometry : angle 0.61244 / 0.31 (33409) hydrogen bonds : bond 0.03761 / 2.57 ( 1094) hydrogen bonds : angle 4.41307 / 3.08 ( 3182) *********************** 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 263 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 197 time to evaluate : 0.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 354 MET cc_start: 0.8466 (mtt) cc_final: 0.7942 (mtm) REVERT: B 492 LYS cc_start: 0.7958 (OUTLIER) cc_final: 0.7563 (pptt) REVERT: B 499 MET cc_start: 0.7968 (tmm) cc_final: 0.7548 (tmm) REVERT: B 518 MET cc_start: 0.8383 (mmm) cc_final: 0.7897 (mmm) REVERT: B 522 CYS cc_start: 0.6394 (t) cc_final: 0.6135 (t) REVERT: B 753 TRP cc_start: 0.9028 (OUTLIER) cc_final: 0.8023 (t60) REVERT: B 871 GLN cc_start: 0.5801 (tt0) cc_final: 0.5418 (mp10) REVERT: B 993 TRP cc_start: 0.7686 (t60) cc_final: 0.7147 (t60) REVERT: B 1002 LEU cc_start: 0.7743 (OUTLIER) cc_final: 0.7445 (pp) REVERT: B 1111 TYR cc_start: 0.7587 (t80) cc_final: 0.7358 (t80) REVERT: C 1 MET cc_start: 0.5951 (tpt) cc_final: 0.5377 (tmm) REVERT: C 475 ASP cc_start: 0.7614 (m-30) cc_final: 0.7327 (m-30) REVERT: C 495 GLN cc_start: 0.7773 (pp30) cc_final: 0.7461 (pp30) REVERT: C 569 MET cc_start: 0.6678 (tmm) cc_final: 0.6381 (tmm) REVERT: C 634 LEU cc_start: 0.9272 (tp) cc_final: 0.9058 (tp) REVERT: C 653 ARG cc_start: 0.8173 (mtm-85) cc_final: 0.7785 (mpp80) REVERT: C 660 ASN cc_start: 0.7690 (OUTLIER) cc_final: 0.7307 (m110) REVERT: C 781 THR cc_start: 0.9249 (m) cc_final: 0.8935 (p) REVERT: D 100 MET cc_start: 0.8666 (mpp) cc_final: 0.8341 (mpp) REVERT: D 222 GLN cc_start: 0.8527 (OUTLIER) cc_final: 0.8232 (pp30) REVERT: D 269 ASP cc_start: 0.8113 (p0) cc_final: 0.7767 (p0) REVERT: D 415 TYR cc_start: 0.3568 (m-80) cc_final: 0.3099 (m-80) REVERT: D 462 MET cc_start: 0.4294 (mmt) cc_final: 0.3980 (mmt) REVERT: D 504 ARG cc_start: 0.8107 (ptm160) cc_final: 0.7289 (ptp-170) REVERT: D 511 TRP cc_start: 0.8144 (m100) cc_final: 0.7555 (m100) REVERT: D 514 MET cc_start: 0.6576 (mmt) cc_final: 0.5807 (mtt) outliers start: 66 outliers final: 47 residues processed: 250 average time/residue: 0.1410 time to fit residues: 57.7225 Evaluate side-chains 243 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 191 time to evaluate : 0.856 ------------------------------------------------------------------------------- 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 151 GLN Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 431 MET Chi-restraints excluded: chain B residue 492 LYS Chi-restraints excluded: chain B residue 566 GLN Chi-restraints excluded: chain B residue 727 MET Chi-restraints excluded: chain B residue 735 LEU Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 753 TRP Chi-restraints excluded: chain B residue 813 CYS Chi-restraints excluded: chain B residue 1002 LEU Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1025 LEU Chi-restraints excluded: chain B residue 1027 ILE Chi-restraints excluded: chain B residue 1069 VAL Chi-restraints excluded: chain B residue 1088 GLU Chi-restraints excluded: chain B residue 1158 THR Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 381 SER Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 404 THR Chi-restraints excluded: chain C residue 506 ILE Chi-restraints excluded: chain C residue 528 LEU Chi-restraints excluded: chain C residue 553 SER Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 612 ILE Chi-restraints excluded: chain C residue 645 LEU Chi-restraints excluded: chain C residue 660 ASN Chi-restraints excluded: chain C residue 746 VAL Chi-restraints excluded: chain C residue 821 VAL Chi-restraints excluded: chain C residue 853 LEU Chi-restraints excluded: chain C residue 945 LEU Chi-restraints excluded: chain C residue 1106 VAL Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 108 TYR Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 130 ILE Chi-restraints excluded: chain D residue 222 GLN Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain D residue 350 ASP Chi-restraints excluded: chain D residue 370 LEU Chi-restraints excluded: chain D residue 471 HIS Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 594 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: [89, 262, 10, 276, 212, 120, 170, 55, 185, 243, 238] chunk 89 optimal weight: 20.0000 chunk 262 optimal weight: 7.9990 chunk 10 optimal weight: 0.9990 chunk 276 optimal weight: 20.0000 chunk 212 optimal weight: 0.9990 chunk 120 optimal weight: 0.0870 chunk 170 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 185 optimal weight: 10.0000 chunk 243 optimal weight: 0.9990 chunk 238 optimal weight: 8.9990 overall best weight: 1.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 134 GLN B 138 ASN ** B 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 843 GLN B1057 GLN ** C 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 522 HIS D 15 GLN ** D 44 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 = 0.3931 r_free = 0.3931 target = 0.105610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.079036 restraints weight = 81443.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.080852 restraints weight = 48996.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.081985 restraints weight = 35758.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.082700 restraints weight = 29362.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.083010 restraints weight = 26289.994| |-----------------------------------------------------------------------------| r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.5178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.062 24452 Z= 0.109 Angle : 0.567 10.256 33409 Z= 0.282 Chirality : 0.040 0.246 3673 Planarity : 0.004 0.067 4205 Dihedral : 13.809 87.470 3712 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.48 % Allowed : 15.11 % Favored : 82.40 % 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: 0.14 (0.16), residues: 2837 helix: 1.30 (0.14), residues: 1432 sheet: -0.71 (0.29), residues: 289 loop : -1.29 (0.18), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 23 TYR 0.021 0.001 TYR C 256 PHE 0.024 0.001 PHE B 289 TRP 0.017 0.001 TRP D 153 HIS 0.005 0.001 HIS D 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 (24452) covalent geometry : angle 0.56702 / 0.28 (33409) hydrogen bonds : bond 0.03495 / 2.40 ( 1094) hydrogen bonds : angle 4.26167 / 2.98 ( 3182) *********************** 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 272 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 212 time to evaluate : 0.782 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: B 354 MET cc_start: 0.8400 (mtt) cc_final: 0.7884 (mtm) REVERT: B 492 LYS cc_start: 0.8130 (OUTLIER) cc_final: 0.7781 (pptt) REVERT: B 499 MET cc_start: 0.7943 (tmm) cc_final: 0.7574 (tmm) REVERT: B 518 MET cc_start: 0.8333 (mmm) cc_final: 0.7696 (mmm) REVERT: B 753 TRP cc_start: 0.8973 (OUTLIER) cc_final: 0.8518 (t60) REVERT: B 871 GLN cc_start: 0.5713 (tt0) cc_final: 0.5362 (mp10) REVERT: B 993 TRP cc_start: 0.7674 (t60) cc_final: 0.7204 (t60) REVERT: B 1002 LEU cc_start: 0.7739 (OUTLIER) cc_final: 0.7431 (pp) REVERT: B 1021 MET cc_start: 0.7423 (mtt) cc_final: 0.7201 (mtt) REVERT: C 1 MET cc_start: 0.5968 (tpt) cc_final: 0.5760 (tmm) REVERT: C 2 LEU cc_start: 0.8366 (tp) cc_final: 0.7802 (tp) REVERT: C 238 LEU cc_start: 0.9241 (OUTLIER) cc_final: 0.8878 (tp) REVERT: C 475 ASP cc_start: 0.7601 (m-30) cc_final: 0.7283 (m-30) REVERT: C 560 LEU cc_start: 0.8220 (tt) cc_final: 0.7421 (mm) REVERT: C 653 ARG cc_start: 0.8187 (mtm-85) cc_final: 0.7674 (mpp80) REVERT: C 660 ASN cc_start: 0.7675 (OUTLIER) cc_final: 0.7276 (m110) REVERT: C 781 THR cc_start: 0.9231 (m) cc_final: 0.8908 (p) REVERT: D 100 MET cc_start: 0.8705 (mpp) cc_final: 0.8457 (mpp) REVERT: D 222 GLN cc_start: 0.8500 (OUTLIER) cc_final: 0.8222 (pp30) REVERT: D 266 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.8208 (tt) REVERT: D 269 ASP cc_start: 0.8127 (p0) cc_final: 0.7845 (p0) REVERT: D 415 TYR cc_start: 0.3501 (m-80) cc_final: 0.3001 (m-80) REVERT: D 462 MET cc_start: 0.4255 (mmt) cc_final: 0.3955 (mmt) REVERT: D 514 MET cc_start: 0.6570 (mmt) cc_final: 0.5969 (mtt) outliers start: 60 outliers final: 37 residues processed: 259 average time/residue: 0.1419 time to fit residues: 59.7215 Evaluate side-chains 239 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 195 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 492 LYS Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 566 GLN Chi-restraints excluded: chain B residue 727 MET Chi-restraints excluded: chain B residue 735 LEU Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 753 TRP Chi-restraints excluded: chain B residue 813 CYS Chi-restraints excluded: chain B residue 1002 LEU Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1025 LEU Chi-restraints excluded: chain B residue 1027 ILE Chi-restraints excluded: chain B residue 1066 ILE Chi-restraints excluded: chain B residue 1069 VAL Chi-restraints excluded: chain B residue 1088 GLU Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 381 SER Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 404 THR Chi-restraints excluded: chain C residue 528 LEU Chi-restraints excluded: chain C residue 612 ILE Chi-restraints excluded: chain C residue 645 LEU Chi-restraints excluded: chain C residue 660 ASN Chi-restraints excluded: chain C residue 821 VAL Chi-restraints excluded: chain C residue 853 LEU Chi-restraints excluded: chain C residue 879 GLN Chi-restraints excluded: chain C residue 945 LEU Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 108 TYR Chi-restraints excluded: chain D residue 130 ILE Chi-restraints excluded: chain D residue 222 GLN Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain D residue 350 ASP Chi-restraints excluded: chain D residue 471 HIS Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 594 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: [274, 187, 38, 167, 108, 94, 180, 220, 57, 196, 269] chunk 274 optimal weight: 10.0000 chunk 187 optimal weight: 3.9990 chunk 38 optimal weight: 6.9990 chunk 167 optimal weight: 9.9990 chunk 108 optimal weight: 5.9990 chunk 94 optimal weight: 20.0000 chunk 180 optimal weight: 0.9980 chunk 220 optimal weight: 0.5980 chunk 57 optimal weight: 8.9990 chunk 196 optimal weight: 0.9990 chunk 269 optimal weight: 5.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 134 GLN ** B 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 843 GLN ** D 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.105000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.078481 restraints weight = 81686.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.080202 restraints weight = 50749.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.081188 restraints weight = 37626.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.081877 restraints weight = 31477.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.082315 restraints weight = 28186.318| |-----------------------------------------------------------------------------| r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.5358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 24452 Z= 0.150 Angle : 0.600 9.705 33409 Z= 0.298 Chirality : 0.041 0.227 3673 Planarity : 0.004 0.079 4205 Dihedral : 13.825 87.402 3710 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.53 % Allowed : 15.57 % 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: 0.16 (0.16), residues: 2837 helix: 1.31 (0.14), residues: 1433 sheet: -0.76 (0.29), residues: 283 loop : -1.24 (0.18), residues: 1121 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 23 TYR 0.018 0.001 TYR C 256 PHE 0.019 0.001 PHE B 289 TRP 0.019 0.001 TRP D 153 HIS 0.005 0.001 HIS D 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 (24452) covalent geometry : angle 0.60041 / 0.30 (33409) hydrogen bonds : bond 0.03563 / 2.44 ( 1094) hydrogen bonds : angle 4.28358 / 2.99 ( 3182) *********************** 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 265 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 204 time to evaluate : 0.847 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: B 306 ARG cc_start: 0.7487 (OUTLIER) cc_final: 0.7273 (mtm-85) REVERT: B 354 MET cc_start: 0.8421 (mtt) cc_final: 0.7880 (mtm) REVERT: B 492 LYS cc_start: 0.8163 (OUTLIER) cc_final: 0.7784 (pptt) REVERT: B 753 TRP cc_start: 0.8961 (OUTLIER) cc_final: 0.8516 (t60) REVERT: B 871 GLN cc_start: 0.5762 (tt0) cc_final: 0.5415 (mp10) REVERT: B 993 TRP cc_start: 0.7666 (t60) cc_final: 0.7193 (t60) REVERT: B 1002 LEU cc_start: 0.7659 (OUTLIER) cc_final: 0.7403 (pp) REVERT: C 2 LEU cc_start: 0.8308 (tp) cc_final: 0.7727 (tp) REVERT: C 360 ARG cc_start: 0.8707 (mmp-170) cc_final: 0.8276 (mmm160) REVERT: C 475 ASP cc_start: 0.7603 (m-30) cc_final: 0.7285 (m-30) REVERT: C 560 LEU cc_start: 0.8302 (tt) cc_final: 0.7420 (mm) REVERT: C 653 ARG cc_start: 0.8123 (mtm-85) cc_final: 0.7744 (mpp80) REVERT: C 660 ASN cc_start: 0.7692 (OUTLIER) cc_final: 0.7342 (m110) REVERT: C 781 THR cc_start: 0.9225 (m) cc_final: 0.8943 (p) REVERT: D 100 MET cc_start: 0.8612 (mpp) cc_final: 0.8378 (mpp) REVERT: D 222 GLN cc_start: 0.8512 (OUTLIER) cc_final: 0.8221 (pp30) REVERT: D 269 ASP cc_start: 0.8080 (p0) cc_final: 0.7847 (p0) REVERT: D 415 TYR cc_start: 0.3731 (m-80) cc_final: 0.3187 (m-80) REVERT: D 433 GLN cc_start: 0.8244 (mt0) cc_final: 0.7509 (mp10) REVERT: D 462 MET cc_start: 0.4257 (mmt) cc_final: 0.3906 (mmt) REVERT: D 514 MET cc_start: 0.6593 (mmt) cc_final: 0.5993 (mtt) REVERT: D 575 ARG cc_start: 0.7790 (tpt170) cc_final: 0.6503 (tpt90) outliers start: 61 outliers final: 41 residues processed: 249 average time/residue: 0.1448 time to fit residues: 58.5585 Evaluate side-chains 245 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 198 time to evaluate : 0.834 ------------------------------------------------------------------------------- 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 153 ILE Chi-restraints excluded: chain B residue 306 ARG Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain B residue 492 LYS Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 566 GLN Chi-restraints excluded: chain B residue 727 MET Chi-restraints excluded: chain B residue 735 LEU Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 753 TRP Chi-restraints excluded: chain B residue 813 CYS Chi-restraints excluded: chain B residue 1002 LEU Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1025 LEU Chi-restraints excluded: chain B residue 1027 ILE Chi-restraints excluded: chain B residue 1066 ILE Chi-restraints excluded: chain B residue 1069 VAL Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 381 SER Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 404 THR Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 528 LEU Chi-restraints excluded: chain C residue 553 SER Chi-restraints excluded: chain C residue 612 ILE Chi-restraints excluded: chain C residue 645 LEU Chi-restraints excluded: chain C residue 660 ASN Chi-restraints excluded: chain C residue 821 VAL Chi-restraints excluded: chain C residue 853 LEU Chi-restraints excluded: chain C residue 885 LEU Chi-restraints excluded: chain C residue 945 LEU Chi-restraints excluded: chain C residue 1106 VAL Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 108 TYR Chi-restraints excluded: chain D residue 130 ILE Chi-restraints excluded: chain D residue 222 GLN Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain D residue 350 ASP Chi-restraints excluded: chain D residue 471 HIS Chi-restraints excluded: chain D residue 551 LEU Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 594 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: [57, 241, 278, 238, 53, 29, 205, 133, 167, 150, 83] chunk 57 optimal weight: 7.9990 chunk 241 optimal weight: 0.9990 chunk 278 optimal weight: 20.0000 chunk 238 optimal weight: 8.9990 chunk 53 optimal weight: 7.9990 chunk 29 optimal weight: 9.9990 chunk 205 optimal weight: 5.9990 chunk 133 optimal weight: 10.0000 chunk 167 optimal weight: 10.0000 chunk 150 optimal weight: 3.9990 chunk 83 optimal weight: 6.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 112 GLN ** B 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 328 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.102694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.076076 restraints weight = 82763.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.077674 restraints weight = 51703.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.078667 restraints weight = 38665.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.079281 restraints weight = 32345.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.079633 restraints weight = 29203.073| |-----------------------------------------------------------------------------| r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.5854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.103 24452 Z= 0.259 Angle : 0.707 10.445 33409 Z= 0.354 Chirality : 0.044 0.307 3673 Planarity : 0.005 0.069 4205 Dihedral : 14.014 88.086 3710 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 2.36 % Allowed : 15.82 % Favored : 81.82 % 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: -0.11 (0.15), residues: 2837 helix: 1.06 (0.14), residues: 1427 sheet: -0.80 (0.29), residues: 286 loop : -1.33 (0.18), residues: 1124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 568 TYR 0.018 0.002 TYR B1140 PHE 0.055 0.002 PHE B 351 TRP 0.020 0.002 TRP D 153 HIS 0.017 0.002 HIS B 130 Details of bonding type rmsd/Z covalent geometry : bond 0.00581 / 0.26 (24452) covalent geometry : angle 0.70676 / 0.35 (33409) hydrogen bonds : bond 0.04118 / 2.78 ( 1094) hydrogen bonds : angle 4.59812 / 3.22 ( 3182) *********************** 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 247 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 190 time to evaluate : 0.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 354 MET cc_start: 0.8422 (mtt) cc_final: 0.7961 (mtm) REVERT: B 492 LYS cc_start: 0.8325 (OUTLIER) cc_final: 0.7882 (pptt) REVERT: B 753 TRP cc_start: 0.9070 (OUTLIER) cc_final: 0.8602 (t60) REVERT: B 871 GLN cc_start: 0.6149 (tt0) cc_final: 0.5728 (mp10) REVERT: B 1002 LEU cc_start: 0.7728 (OUTLIER) cc_final: 0.7502 (pp) REVERT: B 1098 MET cc_start: 0.6103 (mpp) cc_final: 0.5274 (mpp) REVERT: C 238 LEU cc_start: 0.9312 (OUTLIER) cc_final: 0.8924 (tp) REVERT: C 475 ASP cc_start: 0.7629 (m-30) cc_final: 0.7307 (m-30) REVERT: C 653 ARG cc_start: 0.8147 (mtm-85) cc_final: 0.7774 (mpp80) REVERT: C 660 ASN cc_start: 0.7779 (OUTLIER) cc_final: 0.7422 (m110) REVERT: C 781 THR cc_start: 0.9252 (m) cc_final: 0.9037 (p) REVERT: D 100 MET cc_start: 0.8686 (mpp) cc_final: 0.8442 (mpp) REVERT: D 222 GLN cc_start: 0.8555 (OUTLIER) cc_final: 0.8020 (tm-30) REVERT: D 269 ASP cc_start: 0.8001 (p0) cc_final: 0.7744 (p0) REVERT: D 415 TYR cc_start: 0.4023 (m-80) cc_final: 0.3435 (m-80) REVERT: D 462 MET cc_start: 0.4470 (mmt) cc_final: 0.4084 (mmt) REVERT: D 514 MET cc_start: 0.6800 (mmt) cc_final: 0.5970 (mtt) outliers start: 57 outliers final: 39 residues processed: 239 average time/residue: 0.1487 time to fit residues: 57.9955 Evaluate side-chains 229 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 184 time to evaluate : 0.741 ------------------------------------------------------------------------------- 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 153 ILE Chi-restraints excluded: chain B residue 492 LYS Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 566 GLN Chi-restraints excluded: chain B residue 735 LEU Chi-restraints excluded: chain B residue 753 TRP Chi-restraints excluded: chain B residue 813 CYS Chi-restraints excluded: chain B residue 1002 LEU Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1025 LEU Chi-restraints excluded: chain B residue 1027 ILE Chi-restraints excluded: chain B residue 1066 ILE Chi-restraints excluded: chain B residue 1069 VAL Chi-restraints excluded: chain B residue 1113 LEU Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 381 SER Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 404 THR Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 528 LEU Chi-restraints excluded: chain C residue 553 SER Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain C residue 612 ILE Chi-restraints excluded: chain C residue 645 LEU Chi-restraints excluded: chain C residue 660 ASN Chi-restraints excluded: chain C residue 821 VAL Chi-restraints excluded: chain C residue 853 LEU Chi-restraints excluded: chain C residue 879 GLN Chi-restraints excluded: chain C residue 885 LEU Chi-restraints excluded: chain C residue 945 LEU Chi-restraints excluded: chain C residue 1106 VAL Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 108 TYR Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 130 ILE Chi-restraints excluded: chain D residue 222 GLN Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 350 ASP Chi-restraints excluded: chain D residue 471 HIS Chi-restraints excluded: chain D residue 594 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: [184, 26, 227, 192, 220, 37, 258, 93, 223, 70, 244] chunk 184 optimal weight: 1.9990 chunk 26 optimal weight: 8.9990 chunk 227 optimal weight: 8.9990 chunk 192 optimal weight: 8.9990 chunk 220 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 258 optimal weight: 0.9980 chunk 93 optimal weight: 7.9990 chunk 223 optimal weight: 0.9980 chunk 70 optimal weight: 8.9990 chunk 244 optimal weight: 5.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 843 GLN ** D 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 328 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.104010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.077344 restraints weight = 81702.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.079083 restraints weight = 49158.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.080149 restraints weight = 36058.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.080800 restraints weight = 29900.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.081140 restraints weight = 26827.910| |-----------------------------------------------------------------------------| r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.5858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 24452 Z= 0.138 Angle : 0.619 11.100 33409 Z= 0.310 Chirality : 0.042 0.258 3673 Planarity : 0.004 0.067 4205 Dihedral : 13.994 88.582 3710 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.66 % Allowed : 16.60 % Favored : 81.74 % 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: 0.05 (0.16), residues: 2837 helix: 1.19 (0.14), residues: 1427 sheet: -0.91 (0.29), residues: 287 loop : -1.20 (0.18), residues: 1123 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 491 TYR 0.041 0.001 TYR D 404 PHE 0.016 0.001 PHE B 756 TRP 0.018 0.001 TRP D 153 HIS 0.005 0.001 HIS D 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 (24452) covalent geometry : angle 0.61905 / 0.31 (33409) hydrogen bonds : bond 0.03707 / 2.52 ( 1094) hydrogen bonds : angle 4.42915 / 3.11 ( 3182) ********************** 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 242 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 202 time to evaluate : 0.833 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 354 MET cc_start: 0.8362 (mtt) cc_final: 0.7871 (mtm) REVERT: B 492 LYS cc_start: 0.8447 (OUTLIER) cc_final: 0.8083 (pptt) REVERT: B 660 MET cc_start: 0.8454 (ppp) cc_final: 0.7861 (ppp) REVERT: B 735 LEU cc_start: 0.4954 (OUTLIER) cc_final: 0.4440 (mp) REVERT: B 753 TRP cc_start: 0.9004 (OUTLIER) cc_final: 0.8629 (t60) REVERT: B 871 GLN cc_start: 0.6016 (tt0) cc_final: 0.5712 (mp10) REVERT: B 1002 LEU cc_start: 0.7724 (OUTLIER) cc_final: 0.7513 (pp) REVERT: B 1098 MET cc_start: 0.6225 (mpp) cc_final: 0.5378 (mpp) REVERT: C 2 LEU cc_start: 0.7889 (tt) cc_final: 0.7589 (tp) REVERT: C 238 LEU cc_start: 0.9239 (OUTLIER) cc_final: 0.8849 (tp) REVERT: C 411 MET cc_start: 0.8221 (tpt) cc_final: 0.7778 (tpt) REVERT: C 475 ASP cc_start: 0.7594 (m-30) cc_final: 0.7263 (m-30) REVERT: C 571 LEU cc_start: 0.9394 (mt) cc_final: 0.9175 (mt) REVERT: C 660 ASN cc_start: 0.7659 (OUTLIER) cc_final: 0.7305 (m110) REVERT: C 781 THR cc_start: 0.9236 (m) cc_final: 0.9026 (p) REVERT: D 100 MET cc_start: 0.8597 (mpp) cc_final: 0.8346 (mpp) REVERT: D 222 GLN cc_start: 0.8568 (OUTLIER) cc_final: 0.8306 (pp30) REVERT: D 269 ASP cc_start: 0.7978 (p0) cc_final: 0.7656 (p0) REVERT: D 415 TYR cc_start: 0.4068 (m-80) cc_final: 0.3469 (m-80) REVERT: D 433 GLN cc_start: 0.8231 (mt0) cc_final: 0.7588 (mp10) REVERT: D 462 MET cc_start: 0.4309 (mmt) cc_final: 0.3957 (mmt) REVERT: D 514 MET cc_start: 0.6823 (mmt) cc_final: 0.5995 (mtt) outliers start: 40 outliers final: 30 residues processed: 236 average time/residue: 0.1400 time to fit residues: 53.9166 Evaluate side-chains 232 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 195 time to evaluate : 0.717 ------------------------------------------------------------------------------- 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 153 ILE Chi-restraints excluded: chain B residue 492 LYS Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 566 GLN Chi-restraints excluded: chain B residue 735 LEU Chi-restraints excluded: chain B residue 753 TRP Chi-restraints excluded: chain B residue 813 CYS Chi-restraints excluded: chain B residue 1002 LEU Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1025 LEU Chi-restraints excluded: chain B residue 1027 ILE Chi-restraints excluded: chain B residue 1066 ILE Chi-restraints excluded: chain B residue 1069 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 381 SER Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 404 THR Chi-restraints excluded: chain C residue 528 LEU Chi-restraints excluded: chain C residue 612 ILE Chi-restraints excluded: chain C residue 645 LEU Chi-restraints excluded: chain C residue 660 ASN Chi-restraints excluded: chain C residue 821 VAL Chi-restraints excluded: chain C residue 853 LEU Chi-restraints excluded: chain C residue 879 GLN Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 108 TYR Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 130 ILE Chi-restraints excluded: chain D residue 222 GLN Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 350 ASP Chi-restraints excluded: chain D residue 471 HIS Chi-restraints excluded: chain D residue 594 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: [68, 98, 271, 77, 277, 48, 182, 120, 156, 50, 235] chunk 68 optimal weight: 9.9990 chunk 98 optimal weight: 9.9990 chunk 271 optimal weight: 5.9990 chunk 77 optimal weight: 3.9990 chunk 277 optimal weight: 20.0000 chunk 48 optimal weight: 2.9990 chunk 182 optimal weight: 10.0000 chunk 120 optimal weight: 0.9980 chunk 156 optimal weight: 9.9990 chunk 50 optimal weight: 9.9990 chunk 235 optimal weight: 9.9990 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 328 GLN D 433 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.102880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.076250 restraints weight = 81585.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.077836 restraints weight = 51474.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.078806 restraints weight = 38621.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.079388 restraints weight = 32301.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.079644 restraints weight = 29318.116| |-----------------------------------------------------------------------------| r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.6185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 24452 Z= 0.242 Angle : 0.709 10.107 33409 Z= 0.353 Chirality : 0.044 0.246 3673 Planarity : 0.005 0.060 4205 Dihedral : 14.079 88.939 3710 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 1.95 % Allowed : 16.77 % Favored : 81.28 % 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: -0.08 (0.16), residues: 2837 helix: 1.07 (0.14), residues: 1436 sheet: -0.88 (0.29), residues: 293 loop : -1.28 (0.18), residues: 1108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 491 TYR 0.014 0.002 TYR B 37 PHE 0.025 0.002 PHE B 428 TRP 0.019 0.002 TRP C 248 HIS 0.007 0.001 HIS C 233 Details of bonding type rmsd/Z covalent geometry : bond 0.00548 / 0.24 (24452) covalent geometry : angle 0.70876 / 0.35 (33409) hydrogen bonds : bond 0.04081 / 2.75 ( 1094) hydrogen bonds : angle 4.60976 / 3.24 ( 3182) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3759.15 seconds wall clock time: 65 minutes 35.87 seconds (3935.87 seconds total)