Starting phenix.real_space_refine on Sun Sep 13 13:34:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6sjf_10216/09_2026/6sjf_10216.cif Found real_map, /net/cci-nas-00/data/ceres_data/6sjf_10216/09_2026/6sjf_10216.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6sjf_10216/09_2026/6sjf_10216.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6sjf_10216/09_2026/6sjf_10216.map" model { file = "/net/cci-nas-00/data/ceres_data/6sjf_10216/09_2026/6sjf_10216.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6sjf_10216/09_2026/6sjf_10216.cif" } resolution = 3.9 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= 0.002 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 103 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: 5.06, per 1000 atoms: 0.21 Number of scatterers: 23826 At special positions: 0 Unit cell: (151.815, 151.815, 123.546, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 101 16.00 P 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: 1.90 Conformation dependent library (CDL) restraints added in 1.2 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 53.4% alpha, 9.1% beta 17 base pairs and 35 stacking pairs defined. Time for finding SS restraints: 2.85 Creating SS restraints... Processing helix chain 'B' and resid 28 through 43 Processing helix chain 'B' and resid 45 through 49 Processing helix chain 'B' and resid 55 through 59 removed outlier: 3.553A pdb=" N GLU B 58 " --> pdb=" O THR B 55 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU B 59 " --> pdb=" O VAL B 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 55 through 59' Processing helix chain 'B' and resid 65 through 90 Processing helix chain 'B' and resid 94 through 104 removed outlier: 3.720A 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 128 through 140 Processing helix chain 'B' and resid 140 through 145 removed outlier: 3.607A pdb=" N SER B 144 " --> pdb=" O ASN B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 173 removed outlier: 3.794A pdb=" N TYR B 173 " --> pdb=" O ARG B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 187 removed outlier: 4.278A pdb=" N VAL B 182 " --> pdb=" O GLU B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 202 removed outlier: 3.667A pdb=" N LEU B 193 " --> pdb=" O GLY B 189 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N ARG B 199 " --> pdb=" O ARG B 195 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N TYR B 200 " --> pdb=" O ASP B 196 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLN B 202 " --> pdb=" O ASN B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 239 removed outlier: 3.565A 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: 3.632A pdb=" N ASN B 278 " --> pdb=" O GLU B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 289 removed outlier: 3.854A pdb=" N LYS B 288 " --> pdb=" O GLU B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 317 removed outlier: 4.333A pdb=" N GLU B 311 " --> pdb=" O HIS B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 347 removed outlier: 4.518A pdb=" N ARG B 336 " --> pdb=" O LEU B 332 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N GLU B 337 " --> pdb=" O ALA B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 364 removed outlier: 3.538A pdb=" N MET B 354 " --> pdb=" O GLY B 350 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N LEU B 355 " --> pdb=" O PHE B 351 " (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: 3.755A pdb=" N ALA B 418 " --> pdb=" O PRO B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 437 removed outlier: 3.811A 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 Processing helix chain 'B' and resid 560 through 573 removed outlier: 3.515A pdb=" N LEU B 573 " --> pdb=" O ASP B 569 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 589 Processing helix chain 'B' and resid 590 through 605 removed outlier: 3.905A pdb=" N GLN B 594 " --> pdb=" O THR B 590 " (cutoff:3.500A) Processing helix chain 'B' and resid 608 through 617 removed outlier: 3.867A pdb=" N LEU B 612 " --> pdb=" O ARG B 608 " (cutoff:3.500A) Processing helix chain 'B' and resid 624 through 634 Processing helix chain 'B' and resid 634 through 655 removed outlier: 3.581A pdb=" N TRP B 638 " --> pdb=" O ASP B 634 " (cutoff:3.500A) Processing helix chain 'B' and resid 656 through 668 removed outlier: 3.903A pdb=" N MET B 660 " --> pdb=" O GLY B 656 " (cutoff:3.500A) Processing helix chain 'B' and resid 669 through 677 removed outlier: 3.541A pdb=" N ASN B 673 " --> pdb=" O ASN B 669 " (cutoff:3.500A) Processing helix chain 'B' and resid 680 through 699 removed outlier: 3.539A pdb=" N THR B 699 " --> pdb=" O GLN B 695 " (cutoff:3.500A) Processing helix chain 'B' and resid 704 through 717 removed outlier: 3.833A pdb=" N VAL B 708 " --> pdb=" O GLU B 704 " (cutoff:3.500A) Processing helix chain 'B' and resid 783 through 807 removed outlier: 3.543A pdb=" N GLU B 793 " --> pdb=" O LEU B 789 " (cutoff:3.500A) Processing helix chain 'B' and resid 831 through 836 removed outlier: 4.539A pdb=" N HIS B 834 " --> pdb=" O THR B 831 " (cutoff:3.500A) Processing helix chain 'B' and resid 837 through 843 removed outlier: 3.787A pdb=" N LEU B 841 " --> pdb=" O ALA B 837 " (cutoff:3.500A) Processing helix chain 'B' and resid 849 through 860 removed outlier: 3.928A 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: 3.705A pdb=" N GLU B 992 " --> pdb=" O PRO B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1008 through 1012 removed outlier: 3.703A pdb=" N GLN B1011 " --> pdb=" O SER B1008 " (cutoff:3.500A) removed outlier: 3.511A 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: 3.650A pdb=" N THR B1038 " --> pdb=" O SER B1034 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LEU B1039 " --> pdb=" O GLN B1035 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N PHE B1043 " --> pdb=" O LEU B1039 " (cutoff:3.500A) Processing helix chain 'B' and resid 1045 through 1048 removed outlier: 3.789A 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 Processing helix chain 'C' and resid 9 through 24 removed outlier: 4.153A 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: 3.716A 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: 3.850A pdb=" N LEU C 146 " --> pdb=" O ARG C 142 " (cutoff:3.500A) removed outlier: 3.841A 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 Processing helix chain 'C' and resid 189 through 199 removed outlier: 3.551A pdb=" N LEU C 197 " --> pdb=" O PHE C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 232 removed outlier: 3.627A pdb=" N ALA C 229 " --> pdb=" O GLN C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 263 removed outlier: 3.673A pdb=" N LYS C 259 " --> pdb=" O ALA C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 304 Processing helix chain 'C' and resid 304 through 316 Processing helix chain 'C' and resid 333 through 344 Processing helix chain 'C' and resid 354 through 360 removed outlier: 3.509A pdb=" N ARG C 360 " --> pdb=" O GLU C 356 " (cutoff:3.500A) Processing helix chain 'C' and resid 381 through 400 removed outlier: 3.665A pdb=" N VAL C 386 " --> pdb=" O PRO C 382 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASP C 391 " --> pdb=" O GLU C 387 " (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: 3.723A 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: 3.926A pdb=" N ALA C 453 " --> pdb=" O PRO C 449 " (cutoff:3.500A) Processing helix chain 'C' and resid 466 through 475 Processing helix chain 'C' and resid 476 through 483 removed outlier: 3.639A pdb=" N PHE C 483 " --> pdb=" O LEU C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 486 through 501 removed outlier: 3.763A pdb=" N GLN C 495 " --> pdb=" O ARG C 491 " (cutoff:3.500A) removed outlier: 3.793A 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: 3.683A pdb=" N MET C 569 " --> pdb=" O ALA C 565 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLN C 570 " --> pdb=" O SER C 566 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ARG C 575 " --> pdb=" O LEU C 571 " (cutoff:3.500A) Processing helix chain 'C' and resid 587 through 599 removed outlier: 4.493A pdb=" N CYS C 591 " --> pdb=" O TRP C 587 " (cutoff:3.500A) removed outlier: 4.504A 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: 3.773A pdb=" N LEU C 637 " --> pdb=" O PRO C 633 " (cutoff:3.500A) removed outlier: 3.796A 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 803 through 805 No H-bonds generated for 'chain 'C' and resid 803 through 805' Processing helix chain 'C' and resid 806 through 812 Processing helix chain 'C' and resid 833 through 843 removed outlier: 3.515A pdb=" N LEU C 837 " --> pdb=" O PRO C 833 " (cutoff:3.500A) removed outlier: 3.760A 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: 3.629A pdb=" N LEU C 897 " --> pdb=" O ASP C 893 " (cutoff:3.500A) Processing helix chain 'C' and resid 910 through 932 removed outlier: 3.748A pdb=" N GLU C 914 " --> pdb=" O GLY C 910 " (cutoff:3.500A) removed outlier: 3.822A 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: 3.562A pdb=" N GLY C 977 " --> pdb=" O SER C 973 " (cutoff:3.500A) Processing helix chain 'C' and resid 1012 through 1033 removed outlier: 3.940A pdb=" N SER C1032 " --> pdb=" O ARG C1028 " (cutoff:3.500A) Processing helix chain 'C' and resid 1038 through 1049 Processing helix chain 'C' and resid 1060 through 1076 removed outlier: 3.532A pdb=" N ARG C1068 " --> pdb=" O LEU C1064 " (cutoff:3.500A) Processing helix chain 'C' and resid 1089 through 1094 removed outlier: 4.288A pdb=" N LEU C1093 " --> pdb=" O TRP C1089 " (cutoff:3.500A) Processing helix chain 'C' and resid 1098 through 1113 Processing helix chain 'C' and resid 1113 through 1119 removed outlier: 3.873A pdb=" N PHE C1117 " --> pdb=" O LEU C1113 " (cutoff:3.500A) Processing helix chain 'D' and resid 11 through 15 removed outlier: 3.688A 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: 3.972A 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: 3.605A 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: 3.603A pdb=" N ARG D 221 " --> pdb=" O GLY D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 240 through 244 Processing helix chain 'D' and resid 270 through 274 removed outlier: 3.594A pdb=" N MET D 273 " --> pdb=" O GLU D 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 285 removed outlier: 3.579A pdb=" N ALA D 285 " --> pdb=" O ARG D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 315 removed outlier: 3.829A pdb=" N ASP D 312 " --> pdb=" O ALA D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 316 through 319 removed outlier: 3.536A 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: 3.557A 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: 3.905A pdb=" N GLN D 369 " --> pdb=" O SER D 365 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ASN D 375 " --> pdb=" O ALA D 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 377 through 387 removed outlier: 3.586A pdb=" N ALA D 381 " --> pdb=" O GLY D 377 " (cutoff:3.500A) Processing helix chain 'D' and resid 388 through 391 removed outlier: 3.889A 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: 3.528A 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: 3.503A 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: 3.678A pdb=" N ILE D 590 " --> pdb=" O LEU D 586 " (cutoff:3.500A) removed outlier: 3.776A 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: 6.380A pdb=" N GLU B 6 " --> pdb=" O THR B 442 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N ALA B 439 " --> pdb=" O GLU B 18 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU B 20 " --> pdb=" O ALA B 439 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N GLY B 17 " --> pdb=" O LEU B 409 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N LEU B 411 " --> pdb=" O GLY B 17 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ARG B 19 " --> pdb=" O LEU B 411 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N GLY B 413 " --> pdb=" O ARG B 19 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N ILE B 21 " --> pdb=" O GLY B 413 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N VAL B 62 " --> pdb=" O ASP B 384 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N VAL B 61 " --> pdb=" O PHE B 127 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 151 through 152 removed outlier: 6.366A 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: 6.433A 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: 6.603A pdb=" N VAL B 579 " --> pdb=" O ILE B 738 " (cutoff:3.500A) removed outlier: 8.598A pdb=" N THR B 740 " --> pdb=" O VAL B 579 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N ILE B 554 " --> pdb=" O GLN B 737 " (cutoff:3.500A) removed outlier: 8.233A pdb=" N VAL B 739 " --> pdb=" O ILE B 554 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N VAL B 556 " --> pdb=" O VAL B 739 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N MET B 499 " --> pdb=" O ALA B 866 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N GLN B 868 " --> pdb=" O MET B 499 " (cutoff:3.500A) removed outlier: 6.230A 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: 6.656A pdb=" N ASP B1067 " --> pdb=" O GLU B1020 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N GLU B1022 " --> pdb=" O PHE B1065 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N PHE B1065 " --> pdb=" O GLU B1022 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N TYR B1024 " --> pdb=" O LYS B1063 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N LYS B1063 " --> pdb=" O TYR B1024 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N MET B1061 " --> pdb=" O PRO B1026 " (cutoff:3.500A) removed outlier: 10.028A pdb=" N ILE B1066 " --> pdb=" O TYR B1081 " (cutoff:3.500A) removed outlier: 8.268A pdb=" N TYR B1081 " --> pdb=" O ILE B1066 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N TYR B1076 " --> pdb=" O GLY B1137 " (cutoff:3.500A) removed outlier: 8.522A pdb=" N ILE B1139 " --> pdb=" O TYR B1076 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N LEU B1078 " --> pdb=" O ILE B1139 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N LEU B1141 " --> pdb=" O LEU B1078 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ALA B1080 " --> pdb=" O LEU B1141 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 60 through 61 removed outlier: 6.007A pdb=" N ARG C 266 " --> pdb=" O ASP C 324 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 365 through 366 removed outlier: 6.000A 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: 3.591A pdb=" N ASN C 660 " --> pdb=" O ILE C 408 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N LYS C 673 " --> pdb=" O LYS C 726 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N TYR C 728 " --> pdb=" O LYS C 673 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N VAL C 675 " --> pdb=" O TYR C 728 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N SER C 730 " --> pdb=" O VAL C 675 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N LEU C 677 " --> pdb=" O SER C 730 " (cutoff:3.500A) removed outlier: 8.197A pdb=" N ILE C 732 " --> pdb=" O LEU C 677 " (cutoff:3.500A) removed outlier: 9.095A pdb=" N CYS C 782 " --> pdb=" O ILE C 374 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N PHE C 376 " --> pdb=" O CYS C 782 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 939 through 947 removed outlier: 5.633A pdb=" N GLN C 939 " --> pdb=" O GLN C 958 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLN C 958 " --> pdb=" O GLN C 939 " (cutoff:3.500A) removed outlier: 15.501A pdb=" N LEU C 956 " --> pdb=" O TRP C 967 " (cutoff:3.500A) removed outlier: 13.137A pdb=" N TRP C 967 " --> pdb=" O LEU C 956 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N GLN C 958 " --> pdb=" O LEU C 965 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N LEU C 965 " --> pdb=" O GLN C 958 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N LEU C 964 " --> pdb=" O ARG C 997 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N PHE C 999 " --> pdb=" O LEU C 964 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N ARG C 966 " --> pdb=" O PHE C 999 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 1050 through 1051 removed outlier: 3.531A pdb=" N ALA C1056 " --> pdb=" O ASP C1051 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 53 through 54 removed outlier: 6.042A pdb=" N SER D 92 " --> pdb=" O LEU D 102 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 167 through 170 removed outlier: 3.579A pdb=" N GLY D 296 " --> pdb=" O ILE D 169 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N LEU D 266 " --> pdb=" O ILE D 293 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N LEU D 295 " --> pdb=" O LEU D 266 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N VAL D 268 " --> pdb=" O LEU D 295 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ARG D 200 " --> pdb=" O VAL D 267 " (cutoff:3.500A) removed outlier: 8.861A pdb=" N SER D 238 " --> pdb=" O ILE D 199 " (cutoff:3.500A) removed outlier: 6.527A 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: 7.251A pdb=" N ASP D 547 " --> pdb=" O ARG D 574 " (cutoff:3.500A) removed outlier: 8.621A pdb=" N MET D 536 " --> pdb=" O TYR D 438 " (cutoff:3.500A) removed outlier: 6.391A 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: 4.447A pdb=" N ALA D 513 " --> pdb=" O ILE D 498 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ILE D 498 " --> pdb=" O ALA D 513 " (cutoff:3.500A) 1062 hydrogen bonds defined for protein. 3126 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 42 hydrogen bonds 80 hydrogen bond angles 0 basepair planarities 17 basepair parallelities 35 stacking parallelities Total time for adding SS restraints: 5.66 Time building geometry restraints manager: 2.59 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: 6864 1.34 - 1.45: 4231 1.45 - 1.57: 13082 1.57 - 1.69: 106 1.69 - 1.81: 169 Bond restraints: 24452 Sorted by residual: bond pdb=" C3' DT X 8 " pdb=" C2' DT X 8 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.09e+01 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 6.83e+00 bond pdb=" C3' DT X 13 " pdb=" C2' DT X 13 " ideal model delta sigma weight residual 1.516 1.537 -0.021 8.00e-03 1.56e+04 6.69e+00 bond pdb=" C1' DT X 69 " pdb=" N1 DT X 69 " ideal model delta sigma weight residual 1.468 1.503 -0.035 1.40e-02 5.10e+03 6.26e+00 bond pdb=" C1' DT X 6 " pdb=" N1 DT X 6 " ideal model delta sigma weight residual 1.468 1.502 -0.034 1.40e-02 5.10e+03 6.00e+00 ... (remaining 24447 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.68: 32617 1.68 - 3.36: 707 3.36 - 5.04: 57 5.04 - 6.72: 18 6.72 - 8.41: 10 Bond angle restraints: 33409 Sorted by residual: angle pdb=" C PHE B 468 " pdb=" N MET B 469 " pdb=" CA MET B 469 " ideal model delta sigma weight residual 121.54 129.95 -8.41 1.91e+00 2.74e-01 1.94e+01 angle pdb=" N3 DT X 60 " pdb=" C4 DT X 60 " pdb=" O4 DT X 60 " ideal model delta sigma weight residual 119.90 122.43 -2.53 6.00e-01 2.78e+00 1.77e+01 angle pdb=" N3 DT X 54 " pdb=" C4 DT X 54 " pdb=" O4 DT X 54 " ideal model delta sigma weight residual 119.90 122.41 -2.51 6.00e-01 2.78e+00 1.75e+01 angle pdb=" N3 DT X 28 " pdb=" C4 DT X 28 " pdb=" O4 DT X 28 " ideal model delta sigma weight residual 119.90 122.40 -2.50 6.00e-01 2.78e+00 1.74e+01 angle pdb=" N3 DT X 74 " pdb=" C4 DT X 74 " pdb=" O4 DT X 74 " ideal model delta sigma weight residual 119.90 122.39 -2.49 6.00e-01 2.78e+00 1.72e+01 ... (remaining 33404 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.85: 13327 15.85 - 31.70: 824 31.70 - 47.54: 330 47.54 - 63.39: 123 63.39 - 79.24: 11 Dihedral angle restraints: 14615 sinusoidal: 6326 harmonic: 8289 Sorted by residual: dihedral pdb=" CA PRO B1051 " pdb=" C PRO B1051 " pdb=" N PRO B1052 " pdb=" CA PRO B1052 " ideal model delta harmonic sigma weight residual 180.00 -160.49 -19.51 0 5.00e+00 4.00e-02 1.52e+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 180.00 162.72 17.28 0 5.00e+00 4.00e-02 1.19e+01 dihedral pdb=" CA THR B 304 " pdb=" C THR B 304 " pdb=" N PRO B 305 " pdb=" CA PRO B 305 " ideal model delta harmonic sigma weight residual 180.00 163.78 16.22 0 5.00e+00 4.00e-02 1.05e+01 ... (remaining 14612 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 2520 0.034 - 0.069: 809 0.069 - 0.103: 246 0.103 - 0.138: 87 0.138 - 0.172: 11 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 7.40e-01 chirality pdb=" CA MET B 469 " pdb=" N MET B 469 " pdb=" C MET B 469 " pdb=" CB MET B 469 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.12e-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 5.70e-01 ... (remaining 3670 not shown) Planarity restraints: 4205 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY C 657 " -0.052 5.00e-02 4.00e+02 7.88e-02 9.93e+00 pdb=" N PRO C 658 " 0.136 5.00e-02 4.00e+02 pdb=" CA PRO C 658 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO C 658 " -0.043 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 5.41e-02 4.69e+00 pdb=" N PRO C 420 " 0.094 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 THR B 304 " 0.036 5.00e-02 4.00e+02 5.33e-02 4.55e+00 pdb=" N PRO B 305 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO B 305 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 305 " 0.030 5.00e-02 4.00e+02 ... (remaining 4202 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 7111 2.83 - 3.34: 19854 3.34 - 3.86: 39686 3.86 - 4.38: 44623 4.38 - 4.90: 76485 Nonbonded interactions: 187759 Sorted by model distance: nonbonded pdb=" O THR D 533 " pdb=" OG1 THR D 533 " model vdw 2.307 3.040 nonbonded pdb=" O2 DC X 27 " pdb=" N2 DG X 59 " model vdw 2.308 2.496 nonbonded pdb=" O LEU C 115 " pdb=" OG SER C 119 " model vdw 2.324 3.040 nonbonded pdb=" O LEU D 67 " pdb=" OG1 THR D 70 " model vdw 2.336 3.040 nonbonded pdb=" OH TYR C 794 " pdb=" O ALA C 803 " model vdw 2.338 3.040 ... (remaining 187754 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: 1.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.420 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 25.000 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 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 0.046 24452 Z= 0.217 Angle : 0.598 8.406 33409 Z= 0.405 Chirality : 0.040 0.172 3673 Planarity : 0.005 0.079 4205 Dihedral : 13.121 79.239 9243 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.98 % Allowed : 4.89 % Favored : 92.13 % 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: -3.64 (0.11), residues: 2837 helix: -2.57 (0.09), residues: 1397 sheet: -0.77 (0.29), residues: 276 loop : -2.47 (0.14), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 761 TYR 0.014 0.001 TYR B1093 PHE 0.015 0.001 PHE B1023 TRP 0.011 0.001 TRP C 164 HIS 0.004 0.000 HIS D 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.22 (24452) covalent geometry : angle 0.59790 / 0.41 (33409) hydrogen bonds : bond 0.15143 / 9.86 ( 1104) hydrogen bonds : angle 6.63332 / 4.64 ( 3206) *********************** 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 711 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 639 time to evaluate : 0.874 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 137 LEU cc_start: 0.8882 (mt) cc_final: 0.8599 (mp) REVERT: B 138 ASN cc_start: 0.8379 (m-40) cc_final: 0.7944 (m110) REVERT: B 351 PHE cc_start: 0.7831 (m-80) cc_final: 0.6842 (m-10) REVERT: B 354 MET cc_start: 0.7846 (mtt) cc_final: 0.7624 (mtm) REVERT: B 491 PHE cc_start: 0.8000 (OUTLIER) cc_final: 0.7593 (t80) REVERT: B 501 MET cc_start: 0.8652 (mtm) cc_final: 0.8258 (mtt) REVERT: B 582 SER cc_start: 0.8875 (m) cc_final: 0.8540 (t) REVERT: B 595 GLU cc_start: 0.8393 (mt-10) cc_final: 0.7452 (mt-10) REVERT: B 753 TRP cc_start: 0.9163 (OUTLIER) cc_final: 0.7810 (t60) REVERT: B 758 THR cc_start: 0.9292 (OUTLIER) cc_final: 0.8992 (p) REVERT: B 1111 TYR cc_start: 0.8546 (OUTLIER) cc_final: 0.8063 (p90) REVERT: C 2 LEU cc_start: 0.7036 (tp) cc_final: 0.6802 (tp) REVERT: C 103 LEU cc_start: 0.8679 (mt) cc_final: 0.8276 (mt) REVERT: C 133 ASP cc_start: 0.7700 (t0) cc_final: 0.7316 (t0) REVERT: C 906 ASP cc_start: 0.8047 (m-30) cc_final: 0.7801 (m-30) REVERT: C 916 PHE cc_start: 0.8137 (m-80) cc_final: 0.7631 (m-80) REVERT: C 965 LEU cc_start: 0.8815 (tp) cc_final: 0.8343 (tp) REVERT: D 236 ASP cc_start: 0.6962 (OUTLIER) cc_final: 0.6127 (t0) REVERT: D 405 ILE cc_start: 0.8762 (mt) cc_final: 0.8447 (mm) REVERT: D 407 MET cc_start: 0.8947 (ttp) cc_final: 0.8718 (ppp) REVERT: D 436 ASN cc_start: 0.8254 (m-40) cc_final: 0.7248 (t0) REVERT: D 515 PRO cc_start: 0.7674 (Cg_exo) cc_final: 0.7151 (Cg_endo) outliers start: 72 outliers final: 12 residues processed: 690 average time/residue: 0.1725 time to fit residues: 179.9095 Evaluate side-chains 306 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 289 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 491 PHE Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 753 TRP Chi-restraints excluded: chain B residue 758 THR Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 947 ARG Chi-restraints excluded: chain B residue 1111 TYR Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 591 CYS Chi-restraints excluded: chain C residue 853 LEU Chi-restraints excluded: chain C residue 974 VAL Chi-restraints excluded: chain D residue 108 TYR Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 236 ASP Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 493 LEU Chi-restraints excluded: chain D residue 538 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 8.9990 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 5.9990 chunk 111 optimal weight: 4.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 120 GLN B 150 GLN B 181 GLN ** B 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 458 ASN B 463 GLN B 566 GLN B 594 GLN B 601 GLN B 650 GLN B 765 GLN B 843 GLN B 848 GLN B 943 HIS B 944 GLN B1072 HIS B1084 ASN B1134 HIS B1161 ASN C 113 HIS C 126 GLN C 162 GLN C 185 HIS C 191 GLN C 336 HIS C 570 GLN C 614 GLN C 725 GLN C 759 HIS ** C 817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 822 GLN C 843 HIS C 856 ASN C 883 GLN C 925 GLN ** C 958 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 979 GLN ** C 984 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 993 ASN C1108 GLN ** C1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 89 GLN D 115 ASN D 128 HIS D 222 GLN D 251 GLN D 469 HIS D 523 GLN D 542 GLN Total number of N/Q/H flips: 44 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.081889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.063834 restraints weight = 85105.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.065674 restraints weight = 46369.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.066882 restraints weight = 30789.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.067702 restraints weight = 23267.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.068229 restraints weight = 19335.310| |-----------------------------------------------------------------------------| r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.3104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.101 24452 Z= 0.254 Angle : 0.736 12.091 33409 Z= 0.371 Chirality : 0.044 0.206 3673 Planarity : 0.005 0.062 4205 Dihedral : 13.758 84.608 3732 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.60 % Allowed : 12.09 % Favored : 84.31 % 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: -1.30 (0.14), residues: 2837 helix: -0.07 (0.13), residues: 1421 sheet: -0.42 (0.29), residues: 279 loop : -1.96 (0.16), residues: 1137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 804 TYR 0.015 0.002 TYR C 728 PHE 0.029 0.002 PHE B 397 TRP 0.020 0.002 TRP B 598 HIS 0.009 0.001 HIS D 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00562 / 0.25 (24452) covalent geometry : angle 0.73614 / 0.37 (33409) hydrogen bonds : bond 0.04275 / 2.71 ( 1104) hydrogen bonds : angle 4.65655 / 3.29 ( 3206) *********************** 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 369 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 282 time to evaluate : 0.726 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 137 LEU cc_start: 0.8956 (mt) cc_final: 0.8456 (tp) REVERT: B 342 GLU cc_start: 0.7779 (OUTLIER) cc_final: 0.7553 (tt0) REVERT: B 351 PHE cc_start: 0.7903 (m-80) cc_final: 0.6996 (m-10) REVERT: B 354 MET cc_start: 0.7957 (mtt) cc_final: 0.7632 (mtm) REVERT: B 393 GLN cc_start: 0.8859 (mt0) cc_final: 0.8537 (mt0) REVERT: B 491 PHE cc_start: 0.8326 (OUTLIER) cc_final: 0.8064 (t80) REVERT: B 753 TRP cc_start: 0.9244 (OUTLIER) cc_final: 0.7590 (t60) REVERT: B 758 THR cc_start: 0.9461 (OUTLIER) cc_final: 0.9252 (p) REVERT: B 1082 LYS cc_start: 0.7999 (mmtt) cc_final: 0.6756 (tmtt) REVERT: B 1111 TYR cc_start: 0.8608 (OUTLIER) cc_final: 0.8033 (p90) REVERT: C 2 LEU cc_start: 0.7991 (tp) cc_final: 0.7772 (tp) REVERT: C 103 LEU cc_start: 0.8934 (mt) cc_final: 0.8642 (mt) REVERT: C 133 ASP cc_start: 0.8028 (t0) cc_final: 0.7721 (t0) REVERT: C 499 GLU cc_start: 0.7762 (mp0) cc_final: 0.7524 (mp0) REVERT: C 736 ILE cc_start: 0.8973 (tp) cc_final: 0.8741 (tp) REVERT: C 856 ASN cc_start: 0.8437 (OUTLIER) cc_final: 0.8216 (p0) REVERT: C 965 LEU cc_start: 0.9092 (tp) cc_final: 0.8843 (tp) REVERT: C 971 LEU cc_start: 0.8633 (mt) cc_final: 0.8418 (mt) REVERT: C 1075 TYR cc_start: 0.8568 (t80) cc_final: 0.8241 (t80) REVERT: D 100 MET cc_start: 0.8687 (mtm) cc_final: 0.8360 (mtp) REVERT: D 143 LYS cc_start: 0.9185 (mmmt) cc_final: 0.8753 (mmtm) REVERT: D 236 ASP cc_start: 0.7416 (OUTLIER) cc_final: 0.7189 (m-30) REVERT: D 407 MET cc_start: 0.9013 (ttp) cc_final: 0.8666 (tmm) REVERT: D 420 ASP cc_start: 0.8277 (t0) cc_final: 0.7884 (t0) outliers start: 87 outliers final: 49 residues processed: 351 average time/residue: 0.1476 time to fit residues: 82.7244 Evaluate side-chains 274 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 218 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 491 PHE Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 569 ASP Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 666 SER Chi-restraints excluded: chain B residue 721 ASN Chi-restraints excluded: chain B residue 753 TRP Chi-restraints excluded: chain B residue 758 THR Chi-restraints excluded: chain B residue 777 VAL Chi-restraints excluded: chain B residue 788 ASP Chi-restraints excluded: chain B residue 843 GLN Chi-restraints excluded: chain B residue 853 LEU Chi-restraints excluded: chain B residue 860 LEU Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 1002 LEU Chi-restraints excluded: chain B residue 1027 ILE Chi-restraints excluded: chain B residue 1063 LYS Chi-restraints excluded: chain B residue 1111 TYR Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 368 ASP Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 495 GLN Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain C residue 591 CYS Chi-restraints excluded: chain C residue 595 LEU Chi-restraints excluded: chain C residue 853 LEU Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 953 THR Chi-restraints excluded: chain C residue 1017 LEU Chi-restraints excluded: chain C residue 1116 LEU Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 80 ASN Chi-restraints excluded: chain D residue 108 TYR Chi-restraints excluded: chain D residue 218 LYS Chi-restraints excluded: chain D residue 236 ASP Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 265 VAL Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain D residue 303 SER Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 430 LEU Chi-restraints excluded: chain D residue 498 ILE Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain D residue 561 VAL Chi-restraints excluded: chain D residue 562 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 248 optimal weight: 0.8980 chunk 212 optimal weight: 0.0470 chunk 233 optimal weight: 6.9990 chunk 167 optimal weight: 7.9990 chunk 232 optimal weight: 8.9990 chunk 200 optimal weight: 4.9990 chunk 90 optimal weight: 4.9990 chunk 275 optimal weight: 5.9990 chunk 101 optimal weight: 20.0000 chunk 270 optimal weight: 4.9990 chunk 125 optimal weight: 5.9990 overall best weight: 3.1884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 222 HIS ** B 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 843 GLN ** B 876 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 126 GLN C 237 HIS C 510 ASN ** C 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 749 GLN C 792 GLN ** C 958 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1110 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.081092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.063419 restraints weight = 85147.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.065101 restraints weight = 48107.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.066226 restraints weight = 32693.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.066979 restraints weight = 25164.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.067401 restraints weight = 21121.466| |-----------------------------------------------------------------------------| r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.3560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 24452 Z= 0.179 Angle : 0.621 11.149 33409 Z= 0.315 Chirality : 0.041 0.180 3673 Planarity : 0.004 0.055 4205 Dihedral : 13.712 86.340 3719 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 3.40 % Allowed : 12.96 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.15), residues: 2837 helix: 0.75 (0.14), residues: 1419 sheet: -0.24 (0.30), residues: 279 loop : -1.66 (0.16), residues: 1139 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 504 TYR 0.012 0.001 TYR C 5 PHE 0.028 0.001 PHE C 19 TRP 0.016 0.001 TRP C 574 HIS 0.004 0.001 HIS C 817 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.18 (24452) covalent geometry : angle 0.62137 / 0.31 (33409) hydrogen bonds : bond 0.03778 / 2.39 ( 1104) hydrogen bonds : angle 4.36791 / 3.06 ( 3206) *********************** 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 320 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 238 time to evaluate : 0.886 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 137 LEU cc_start: 0.8999 (mt) cc_final: 0.8683 (tp) REVERT: B 351 PHE cc_start: 0.8002 (m-80) cc_final: 0.7572 (m-10) REVERT: B 354 MET cc_start: 0.7886 (mtt) cc_final: 0.7600 (mtm) REVERT: B 471 ARG cc_start: 0.7197 (OUTLIER) cc_final: 0.6678 (tmm-80) REVERT: B 753 TRP cc_start: 0.9243 (OUTLIER) cc_final: 0.7788 (t60) REVERT: B 1093 TYR cc_start: 0.3493 (OUTLIER) cc_final: 0.2561 (p90) REVERT: B 1098 MET cc_start: 0.7071 (mpp) cc_final: 0.6693 (mpp) REVERT: B 1111 TYR cc_start: 0.8436 (OUTLIER) cc_final: 0.7942 (p90) REVERT: C 133 ASP cc_start: 0.7747 (t0) cc_final: 0.7518 (t0) REVERT: C 499 GLU cc_start: 0.7681 (mp0) cc_final: 0.7439 (mp0) REVERT: C 660 ASN cc_start: 0.8470 (OUTLIER) cc_final: 0.8172 (m-40) REVERT: C 736 ILE cc_start: 0.8948 (tp) cc_final: 0.8729 (tp) REVERT: C 965 LEU cc_start: 0.8979 (tp) cc_final: 0.8774 (tp) REVERT: C 1075 TYR cc_start: 0.8334 (t80) cc_final: 0.7675 (t80) REVERT: D 143 LYS cc_start: 0.9175 (mmmt) cc_final: 0.8742 (mmtm) REVERT: D 239 THR cc_start: 0.8905 (OUTLIER) cc_final: 0.8703 (p) REVERT: D 407 MET cc_start: 0.8856 (ttp) cc_final: 0.8624 (tmm) REVERT: D 420 ASP cc_start: 0.8310 (t0) cc_final: 0.7896 (t0) outliers start: 82 outliers final: 57 residues processed: 298 average time/residue: 0.1383 time to fit residues: 67.7914 Evaluate side-chains 269 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 206 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 146 MET Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 471 ARG Chi-restraints excluded: chain B residue 569 ASP Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 721 ASN Chi-restraints excluded: chain B residue 753 TRP Chi-restraints excluded: chain B residue 777 VAL Chi-restraints excluded: chain B residue 853 LEU Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 947 ARG Chi-restraints excluded: chain B residue 1027 ILE Chi-restraints excluded: chain B residue 1063 LYS Chi-restraints excluded: chain B residue 1093 TYR Chi-restraints excluded: chain B residue 1111 TYR Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 387 GLU Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain C residue 495 GLN Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 590 VAL Chi-restraints excluded: chain C residue 591 CYS Chi-restraints excluded: chain C residue 595 LEU Chi-restraints excluded: chain C residue 660 ASN Chi-restraints excluded: chain C residue 853 LEU Chi-restraints excluded: chain C residue 906 ASP Chi-restraints excluded: chain C residue 953 THR Chi-restraints excluded: chain C residue 1017 LEU Chi-restraints excluded: chain C residue 1088 ILE Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 80 ASN Chi-restraints excluded: chain D residue 108 TYR Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 218 LYS Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 265 VAL Chi-restraints excluded: chain D residue 303 SER Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 430 LEU Chi-restraints excluded: chain D residue 484 ILE Chi-restraints excluded: chain D residue 493 LEU Chi-restraints excluded: chain D residue 498 ILE Chi-restraints excluded: chain D residue 537 THR Chi-restraints excluded: chain D residue 561 VAL Chi-restraints excluded: chain D residue 562 THR Chi-restraints excluded: chain D residue 579 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 137 optimal weight: 6.9990 chunk 231 optimal weight: 9.9990 chunk 172 optimal weight: 4.9990 chunk 101 optimal weight: 5.9990 chunk 259 optimal weight: 20.0000 chunk 196 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 220 optimal weight: 0.0970 chunk 25 optimal weight: 8.9990 chunk 26 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 overall best weight: 3.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 393 GLN ** B 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 876 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 956 HIS C 891 GLN C 958 GLN D 22 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.080077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.061813 restraints weight = 86498.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.063608 restraints weight = 47931.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.064738 restraints weight = 32206.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.065564 restraints weight = 24733.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.066096 restraints weight = 20650.105| |-----------------------------------------------------------------------------| r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.3930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 24452 Z= 0.191 Angle : 0.618 14.341 33409 Z= 0.310 Chirality : 0.041 0.235 3673 Planarity : 0.004 0.052 4205 Dihedral : 13.725 88.091 3713 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 3.64 % Allowed : 12.59 % Favored : 83.77 % 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: -0.04 (0.16), residues: 2837 helix: 1.14 (0.14), residues: 1416 sheet: -0.22 (0.30), residues: 293 loop : -1.49 (0.17), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 709 TYR 0.014 0.001 TYR C 878 PHE 0.015 0.001 PHE C 19 TRP 0.021 0.001 TRP C 574 HIS 0.004 0.001 HIS C 377 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.19 (24452) covalent geometry : angle 0.61788 / 0.31 (33409) hydrogen bonds : bond 0.03661 / 2.33 ( 1104) hydrogen bonds : angle 4.31112 / 3.03 ( 3206) *********************** 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 313 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 225 time to evaluate : 0.861 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: 0.7946 (mtt) cc_final: 0.7603 (mtm) REVERT: B 471 ARG cc_start: 0.7437 (OUTLIER) cc_final: 0.7040 (tmm-80) REVERT: B 753 TRP cc_start: 0.9293 (OUTLIER) cc_final: 0.7663 (t60) REVERT: B 1093 TYR cc_start: 0.3694 (OUTLIER) cc_final: 0.3057 (p90) REVERT: B 1102 MET cc_start: 0.8129 (tpp) cc_final: 0.7853 (tpp) REVERT: B 1111 TYR cc_start: 0.8615 (OUTLIER) cc_final: 0.8078 (p90) REVERT: C 133 ASP cc_start: 0.7895 (t0) cc_final: 0.7655 (t0) REVERT: C 499 GLU cc_start: 0.7796 (mp0) cc_final: 0.7514 (mp0) REVERT: C 660 ASN cc_start: 0.8595 (OUTLIER) cc_final: 0.8277 (m-40) REVERT: C 736 ILE cc_start: 0.9068 (tp) cc_final: 0.8758 (tp) REVERT: C 790 ASP cc_start: 0.8842 (OUTLIER) cc_final: 0.8388 (t0) REVERT: C 851 MET cc_start: 0.7734 (mtp) cc_final: 0.7452 (mtp) REVERT: C 916 PHE cc_start: 0.8329 (OUTLIER) cc_final: 0.7708 (t80) REVERT: C 965 LEU cc_start: 0.9155 (tp) cc_final: 0.8945 (tp) REVERT: C 1075 TYR cc_start: 0.8399 (t80) cc_final: 0.8126 (t80) REVERT: C 1080 MET cc_start: 0.7934 (ppp) cc_final: 0.7414 (tmm) REVERT: D 100 MET cc_start: 0.8274 (mtp) cc_final: 0.8061 (mtp) REVERT: D 143 LYS cc_start: 0.9171 (mmmt) cc_final: 0.8735 (mmtm) REVERT: D 239 THR cc_start: 0.9004 (OUTLIER) cc_final: 0.8762 (p) REVERT: D 407 MET cc_start: 0.9025 (ttp) cc_final: 0.8714 (tmm) REVERT: D 420 ASP cc_start: 0.8437 (t0) cc_final: 0.7974 (t0) REVERT: D 466 ARG cc_start: 0.6620 (mmp-170) cc_final: 0.6353 (mmm160) outliers start: 88 outliers final: 64 residues processed: 292 average time/residue: 0.1470 time to fit residues: 70.1460 Evaluate side-chains 272 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 200 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 471 ARG Chi-restraints excluded: chain B residue 569 ASP Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 721 ASN Chi-restraints excluded: chain B residue 753 TRP Chi-restraints excluded: chain B residue 777 VAL Chi-restraints excluded: chain B residue 788 ASP Chi-restraints excluded: chain B residue 853 LEU Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 947 ARG Chi-restraints excluded: chain B residue 1027 ILE Chi-restraints excluded: chain B residue 1063 LYS Chi-restraints excluded: chain B residue 1079 LEU Chi-restraints excluded: chain B residue 1086 LEU Chi-restraints excluded: chain B residue 1093 TYR Chi-restraints excluded: chain B residue 1111 TYR Chi-restraints excluded: chain B residue 1158 THR Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 387 GLU Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 495 GLN Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain C residue 590 VAL Chi-restraints excluded: chain C residue 591 CYS Chi-restraints excluded: chain C residue 595 LEU Chi-restraints excluded: chain C residue 660 ASN Chi-restraints excluded: chain C residue 790 ASP Chi-restraints excluded: chain C residue 853 LEU Chi-restraints excluded: chain C residue 855 VAL Chi-restraints excluded: chain C residue 906 ASP Chi-restraints excluded: chain C residue 916 PHE Chi-restraints excluded: chain C residue 953 THR Chi-restraints excluded: chain C residue 1017 LEU Chi-restraints excluded: chain C residue 1088 ILE Chi-restraints excluded: chain C residue 1098 THR Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 80 ASN Chi-restraints excluded: chain D residue 108 TYR Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 218 LYS Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 265 VAL Chi-restraints excluded: chain D residue 303 SER Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 484 ILE Chi-restraints excluded: chain D residue 493 LEU Chi-restraints excluded: chain D residue 498 ILE Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain D residue 561 VAL Chi-restraints excluded: chain D residue 562 THR Chi-restraints excluded: chain D residue 579 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 174 optimal weight: 6.9990 chunk 99 optimal weight: 6.9990 chunk 13 optimal weight: 2.9990 chunk 70 optimal weight: 0.4980 chunk 152 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 chunk 256 optimal weight: 9.9990 chunk 72 optimal weight: 0.8980 chunk 267 optimal weight: 6.9990 chunk 115 optimal weight: 4.9990 chunk 111 optimal weight: 20.0000 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 876 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 660 ASN C 891 GLN D 387 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.080559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.062440 restraints weight = 85570.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.064241 restraints weight = 47144.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.065450 restraints weight = 31562.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.066229 restraints weight = 24040.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.066685 restraints weight = 20068.918| |-----------------------------------------------------------------------------| r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.4083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 24452 Z= 0.133 Angle : 0.573 12.037 33409 Z= 0.287 Chirality : 0.040 0.280 3673 Planarity : 0.003 0.051 4205 Dihedral : 13.747 87.705 3713 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 3.11 % Allowed : 13.37 % 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: 0.21 (0.16), residues: 2837 helix: 1.33 (0.14), residues: 1416 sheet: -0.20 (0.30), residues: 297 loop : -1.32 (0.17), residues: 1124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 360 TYR 0.012 0.001 TYR B 394 PHE 0.013 0.001 PHE B 428 TRP 0.015 0.001 TRP B 993 HIS 0.003 0.001 HIS C 377 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (24452) covalent geometry : angle 0.57304 / 0.29 (33409) hydrogen bonds : bond 0.03467 / 2.19 ( 1104) hydrogen bonds : angle 4.18248 / 2.93 ( 3206) *********************** 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 290 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 215 time to evaluate : 0.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 354 MET cc_start: 0.7944 (mtt) cc_final: 0.7568 (mtm) REVERT: B 753 TRP cc_start: 0.9258 (OUTLIER) cc_final: 0.7708 (t60) REVERT: B 1093 TYR cc_start: 0.3003 (OUTLIER) cc_final: 0.2255 (p90) REVERT: B 1098 MET cc_start: 0.7364 (mpp) cc_final: 0.6896 (mpp) REVERT: B 1102 MET cc_start: 0.8378 (tpp) cc_final: 0.8169 (tpp) REVERT: B 1111 TYR cc_start: 0.8604 (OUTLIER) cc_final: 0.8054 (p90) REVERT: C 133 ASP cc_start: 0.7885 (t0) cc_final: 0.7642 (t0) REVERT: C 499 GLU cc_start: 0.7788 (mp0) cc_final: 0.7489 (mp0) REVERT: C 569 MET cc_start: 0.8508 (OUTLIER) cc_final: 0.8284 (ttm) REVERT: C 736 ILE cc_start: 0.9032 (tp) cc_final: 0.8738 (tp) REVERT: C 790 ASP cc_start: 0.8808 (OUTLIER) cc_final: 0.8412 (t0) REVERT: C 851 MET cc_start: 0.7751 (mtp) cc_final: 0.7550 (mtp) REVERT: C 916 PHE cc_start: 0.8300 (OUTLIER) cc_final: 0.7697 (t80) REVERT: C 1031 MET cc_start: 0.8556 (mmt) cc_final: 0.8093 (tpp) REVERT: C 1075 TYR cc_start: 0.8321 (t80) cc_final: 0.8039 (t80) REVERT: C 1080 MET cc_start: 0.7770 (ppp) cc_final: 0.7353 (tmm) REVERT: D 112 MET cc_start: 0.8333 (mtp) cc_final: 0.8053 (ttt) REVERT: D 143 LYS cc_start: 0.9170 (mmmt) cc_final: 0.8717 (mmtm) REVERT: D 239 THR cc_start: 0.8964 (OUTLIER) cc_final: 0.8701 (p) REVERT: D 407 MET cc_start: 0.9016 (ttp) cc_final: 0.8711 (tmm) REVERT: D 420 ASP cc_start: 0.8438 (t0) cc_final: 0.7954 (t0) REVERT: D 466 ARG cc_start: 0.6583 (mmp-170) cc_final: 0.6344 (mmm160) outliers start: 75 outliers final: 55 residues processed: 273 average time/residue: 0.1427 time to fit residues: 63.5726 Evaluate side-chains 267 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 205 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 569 ASP Chi-restraints excluded: chain B residue 582 SER Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 753 TRP Chi-restraints excluded: chain B residue 777 VAL Chi-restraints excluded: chain B residue 788 ASP Chi-restraints excluded: chain B residue 853 LEU Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 947 ARG Chi-restraints excluded: chain B residue 1027 ILE Chi-restraints excluded: chain B residue 1063 LYS Chi-restraints excluded: chain B residue 1079 LEU Chi-restraints excluded: chain B residue 1086 LEU Chi-restraints excluded: chain B residue 1093 TYR Chi-restraints excluded: chain B residue 1111 TYR Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 387 GLU Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 495 GLN Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 569 MET Chi-restraints excluded: chain C residue 595 LEU Chi-restraints excluded: chain C residue 790 ASP Chi-restraints excluded: chain C residue 853 LEU Chi-restraints excluded: chain C residue 916 PHE Chi-restraints excluded: chain C residue 953 THR Chi-restraints excluded: chain C residue 1017 LEU Chi-restraints excluded: chain C residue 1088 ILE Chi-restraints excluded: chain C residue 1098 THR Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 80 ASN Chi-restraints excluded: chain D residue 108 TYR Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 265 VAL Chi-restraints excluded: chain D residue 303 SER Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 387 GLN Chi-restraints excluded: chain D residue 493 LEU Chi-restraints excluded: chain D residue 498 ILE Chi-restraints excluded: chain D residue 502 LEU Chi-restraints excluded: chain D residue 522 VAL Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain D residue 561 VAL Chi-restraints excluded: chain D residue 579 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 82 optimal weight: 9.9990 chunk 268 optimal weight: 20.0000 chunk 16 optimal weight: 1.9990 chunk 219 optimal weight: 9.9990 chunk 286 optimal weight: 50.0000 chunk 96 optimal weight: 20.0000 chunk 165 optimal weight: 4.9990 chunk 195 optimal weight: 9.9990 chunk 84 optimal weight: 2.9990 chunk 176 optimal weight: 6.9990 chunk 201 optimal weight: 7.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 262 GLN ** B 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 594 GLN ** B 876 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1096 GLN C 891 GLN D 388 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.078047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.059788 restraints weight = 87522.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.061524 restraints weight = 49265.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.062677 restraints weight = 33493.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.063452 restraints weight = 25789.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.063925 restraints weight = 21668.121| |-----------------------------------------------------------------------------| r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.4503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.102 24452 Z= 0.245 Angle : 0.671 12.841 33409 Z= 0.334 Chirality : 0.042 0.231 3673 Planarity : 0.004 0.047 4205 Dihedral : 13.835 89.902 3712 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.85 % Allowed : 13.79 % Favored : 82.36 % 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: 0.25 (0.16), residues: 2837 helix: 1.35 (0.14), residues: 1419 sheet: -0.16 (0.30), residues: 296 loop : -1.29 (0.18), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1125 TYR 0.016 0.002 TYR C 878 PHE 0.016 0.002 PHE B 475 TRP 0.016 0.002 TRP C 248 HIS 0.005 0.001 HIS B 812 Details of bonding type rmsd/Z covalent geometry : bond 0.00544 / 0.24 (24452) covalent geometry : angle 0.67050 / 0.33 (33409) hydrogen bonds : bond 0.03893 / 2.46 ( 1104) hydrogen bonds : angle 4.33054 / 3.04 ( 3206) *********************** 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 296 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 203 time to evaluate : 0.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 354 MET cc_start: 0.7919 (mtt) cc_final: 0.7557 (mtm) REVERT: B 753 TRP cc_start: 0.9275 (OUTLIER) cc_final: 0.7725 (t60) REVERT: B 1093 TYR cc_start: 0.3282 (OUTLIER) cc_final: 0.2202 (p90) REVERT: B 1098 MET cc_start: 0.7250 (mpp) cc_final: 0.6751 (mpp) REVERT: B 1102 MET cc_start: 0.8381 (tpp) cc_final: 0.8177 (tpp) REVERT: B 1111 TYR cc_start: 0.8593 (OUTLIER) cc_final: 0.8045 (p90) REVERT: C 133 ASP cc_start: 0.7897 (t0) cc_final: 0.7634 (t0) REVERT: C 230 LEU cc_start: 0.9532 (OUTLIER) cc_final: 0.9271 (tt) REVERT: C 499 GLU cc_start: 0.7804 (mp0) cc_final: 0.7509 (mp0) REVERT: C 790 ASP cc_start: 0.8870 (OUTLIER) cc_final: 0.8435 (t0) REVERT: C 916 PHE cc_start: 0.8314 (OUTLIER) cc_final: 0.8013 (m-80) REVERT: C 1075 TYR cc_start: 0.8345 (t80) cc_final: 0.8100 (t80) REVERT: C 1080 MET cc_start: 0.7661 (ppp) cc_final: 0.7288 (tmm) REVERT: D 239 THR cc_start: 0.8960 (OUTLIER) cc_final: 0.8696 (p) REVERT: D 407 MET cc_start: 0.8997 (ttp) cc_final: 0.8686 (ppp) REVERT: D 420 ASP cc_start: 0.8543 (t0) cc_final: 0.8038 (t0) REVERT: D 466 ARG cc_start: 0.6552 (mmp-170) cc_final: 0.6319 (mmm160) outliers start: 93 outliers final: 69 residues processed: 273 average time/residue: 0.1449 time to fit residues: 64.1207 Evaluate side-chains 266 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 190 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 133 CYS Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 383 ILE Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 569 ASP Chi-restraints excluded: chain B residue 582 SER Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 595 GLU Chi-restraints excluded: chain B residue 721 ASN Chi-restraints excluded: chain B residue 753 TRP Chi-restraints excluded: chain B residue 777 VAL Chi-restraints excluded: chain B residue 788 ASP Chi-restraints excluded: chain B residue 853 LEU Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 947 ARG Chi-restraints excluded: chain B residue 1027 ILE Chi-restraints excluded: chain B residue 1063 LYS Chi-restraints excluded: chain B residue 1069 VAL Chi-restraints excluded: chain B residue 1079 LEU Chi-restraints excluded: chain B residue 1086 LEU Chi-restraints excluded: chain B residue 1093 TYR Chi-restraints excluded: chain B residue 1111 TYR Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 387 GLU Chi-restraints excluded: chain C residue 422 ILE Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 495 GLN Chi-restraints excluded: chain C residue 506 ILE Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain C residue 591 CYS Chi-restraints excluded: chain C residue 595 LEU Chi-restraints excluded: chain C residue 692 LEU Chi-restraints excluded: chain C residue 790 ASP Chi-restraints excluded: chain C residue 853 LEU Chi-restraints excluded: chain C residue 855 VAL Chi-restraints excluded: chain C residue 906 ASP Chi-restraints excluded: chain C residue 916 PHE Chi-restraints excluded: chain C residue 953 THR Chi-restraints excluded: chain C residue 1017 LEU Chi-restraints excluded: chain C residue 1088 ILE Chi-restraints excluded: chain C residue 1098 THR Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 80 ASN Chi-restraints excluded: chain D residue 108 TYR Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 265 VAL Chi-restraints excluded: chain D residue 303 SER Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 484 ILE Chi-restraints excluded: chain D residue 493 LEU Chi-restraints excluded: chain D residue 502 LEU Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain D residue 561 VAL Chi-restraints excluded: chain D residue 562 THR Chi-restraints excluded: chain D residue 579 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 89 optimal weight: 3.9990 chunk 262 optimal weight: 4.9990 chunk 10 optimal weight: 8.9990 chunk 276 optimal weight: 10.0000 chunk 212 optimal weight: 0.0170 chunk 120 optimal weight: 0.0370 chunk 170 optimal weight: 6.9990 chunk 55 optimal weight: 5.9990 chunk 185 optimal weight: 0.9990 chunk 243 optimal weight: 1.9990 chunk 238 optimal weight: 20.0000 overall best weight: 1.4102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 876 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.079746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.061840 restraints weight = 85518.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.063556 restraints weight = 48943.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.064674 restraints weight = 33429.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.065417 restraints weight = 25888.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.065845 restraints weight = 21789.481| |-----------------------------------------------------------------------------| r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.4491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 24452 Z= 0.122 Angle : 0.588 12.602 33409 Z= 0.290 Chirality : 0.040 0.194 3673 Planarity : 0.004 0.090 4205 Dihedral : 13.845 88.675 3712 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.65 % Allowed : 15.36 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.16), residues: 2837 helix: 1.54 (0.14), residues: 1423 sheet: -0.17 (0.31), residues: 295 loop : -1.13 (0.18), residues: 1119 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D 360 TYR 0.014 0.001 TYR B 394 PHE 0.013 0.001 PHE B 428 TRP 0.015 0.001 TRP C 496 HIS 0.004 0.001 HIS B 689 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (24452) covalent geometry : angle 0.58786 / 0.29 (33409) hydrogen bonds : bond 0.03416 / 2.16 ( 1104) hydrogen bonds : angle 4.10435 / 2.88 ( 3206) *********************** 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 273 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 209 time to evaluate : 0.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 264 LYS cc_start: 0.8935 (pttm) cc_final: 0.8502 (pttm) REVERT: B 354 MET cc_start: 0.7824 (mtt) cc_final: 0.7525 (mtm) REVERT: B 753 TRP cc_start: 0.9200 (OUTLIER) cc_final: 0.7823 (t60) REVERT: B 1093 TYR cc_start: 0.3349 (OUTLIER) cc_final: 0.2423 (p90) REVERT: B 1098 MET cc_start: 0.6846 (mpp) cc_final: 0.6381 (mpp) REVERT: B 1111 TYR cc_start: 0.8478 (OUTLIER) cc_final: 0.7961 (p90) REVERT: C 133 ASP cc_start: 0.7716 (t0) cc_final: 0.7489 (t0) REVERT: C 499 GLU cc_start: 0.7735 (mp0) cc_final: 0.7446 (mp0) REVERT: C 790 ASP cc_start: 0.8740 (OUTLIER) cc_final: 0.8482 (t0) REVERT: C 1057 MET cc_start: 0.8386 (tpt) cc_final: 0.7799 (tpt) REVERT: C 1075 TYR cc_start: 0.8167 (t80) cc_final: 0.7922 (t80) REVERT: C 1080 MET cc_start: 0.7641 (ppp) cc_final: 0.7298 (tmm) REVERT: D 407 MET cc_start: 0.8873 (ttp) cc_final: 0.8639 (ppp) REVERT: D 420 ASP cc_start: 0.8558 (t0) cc_final: 0.8062 (t0) REVERT: D 466 ARG cc_start: 0.6336 (mmp-170) cc_final: 0.6130 (mmm160) REVERT: D 514 MET cc_start: 0.7285 (OUTLIER) cc_final: 0.7010 (mpp) outliers start: 64 outliers final: 50 residues processed: 256 average time/residue: 0.1483 time to fit residues: 62.4862 Evaluate side-chains 247 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 192 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 569 ASP Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 595 GLU Chi-restraints excluded: chain B residue 753 TRP Chi-restraints excluded: chain B residue 777 VAL Chi-restraints excluded: chain B residue 788 ASP Chi-restraints excluded: chain B residue 853 LEU Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 947 ARG Chi-restraints excluded: chain B residue 1027 ILE Chi-restraints excluded: chain B residue 1063 LYS Chi-restraints excluded: chain B residue 1079 LEU Chi-restraints excluded: chain B residue 1086 LEU Chi-restraints excluded: chain B residue 1093 TYR Chi-restraints excluded: chain B residue 1111 TYR Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 387 GLU Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain C residue 495 GLN Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain C residue 595 LEU Chi-restraints excluded: chain C residue 790 ASP Chi-restraints excluded: chain C residue 853 LEU Chi-restraints excluded: chain C residue 855 VAL Chi-restraints excluded: chain C residue 953 THR Chi-restraints excluded: chain C residue 1017 LEU Chi-restraints excluded: chain C residue 1088 ILE Chi-restraints excluded: chain C residue 1098 THR Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 108 TYR Chi-restraints excluded: chain D residue 303 SER Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 493 LEU Chi-restraints excluded: chain D residue 498 ILE Chi-restraints excluded: chain D residue 502 LEU Chi-restraints excluded: chain D residue 514 MET Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain D residue 561 VAL Chi-restraints excluded: chain D residue 562 THR Chi-restraints excluded: chain D residue 579 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 274 optimal weight: 4.9990 chunk 187 optimal weight: 0.9990 chunk 38 optimal weight: 7.9990 chunk 167 optimal weight: 10.0000 chunk 108 optimal weight: 0.9980 chunk 94 optimal weight: 10.0000 chunk 180 optimal weight: 7.9990 chunk 220 optimal weight: 0.0070 chunk 57 optimal weight: 5.9990 chunk 196 optimal weight: 3.9990 chunk 269 optimal weight: 9.9990 overall best weight: 2.2004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 198 ASN ** B 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 876 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.079362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.061520 restraints weight = 85671.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.063201 restraints weight = 49199.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.064319 restraints weight = 33722.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.065048 restraints weight = 26106.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.065479 restraints weight = 22027.559| |-----------------------------------------------------------------------------| r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.4614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 24452 Z= 0.140 Angle : 0.597 12.854 33409 Z= 0.293 Chirality : 0.040 0.251 3673 Planarity : 0.003 0.053 4205 Dihedral : 13.845 88.990 3711 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 3.15 % Allowed : 14.82 % Favored : 82.03 % 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: 0.57 (0.16), residues: 2837 helix: 1.58 (0.14), residues: 1430 sheet: -0.08 (0.31), residues: 295 loop : -1.09 (0.18), residues: 1112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1125 TYR 0.011 0.001 TYR B 394 PHE 0.021 0.001 PHE C 376 TRP 0.025 0.001 TRP C 496 HIS 0.003 0.001 HIS B 689 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 (24452) covalent geometry : angle 0.59650 / 0.29 (33409) hydrogen bonds : bond 0.03459 / 2.18 ( 1104) hydrogen bonds : angle 4.10443 / 2.88 ( 3206) *********************** 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 273 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 197 time to evaluate : 0.834 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 264 LYS cc_start: 0.9002 (pttm) cc_final: 0.8584 (pttm) REVERT: B 354 MET cc_start: 0.7854 (mtt) cc_final: 0.7506 (mtm) REVERT: B 453 MET cc_start: 0.6345 (ttm) cc_final: 0.6077 (ttm) REVERT: B 753 TRP cc_start: 0.9186 (OUTLIER) cc_final: 0.7835 (t60) REVERT: B 1093 TYR cc_start: 0.3403 (OUTLIER) cc_final: 0.2321 (p90) REVERT: B 1098 MET cc_start: 0.6950 (mpp) cc_final: 0.6356 (mpp) REVERT: B 1111 TYR cc_start: 0.8492 (OUTLIER) cc_final: 0.7968 (p90) REVERT: C 133 ASP cc_start: 0.7725 (t0) cc_final: 0.7498 (t0) REVERT: C 396 MET cc_start: 0.7736 (OUTLIER) cc_final: 0.7470 (mtp) REVERT: C 499 GLU cc_start: 0.7731 (mp0) cc_final: 0.7464 (mp0) REVERT: C 790 ASP cc_start: 0.8744 (OUTLIER) cc_final: 0.8492 (t0) REVERT: C 916 PHE cc_start: 0.8078 (OUTLIER) cc_final: 0.7603 (t80) REVERT: C 1075 TYR cc_start: 0.8162 (t80) cc_final: 0.7933 (t80) REVERT: C 1080 MET cc_start: 0.7553 (ppp) cc_final: 0.7283 (tmm) REVERT: D 100 MET cc_start: 0.8810 (mmm) cc_final: 0.8519 (mmm) REVERT: D 407 MET cc_start: 0.8854 (ttp) cc_final: 0.8618 (ppp) REVERT: D 420 ASP cc_start: 0.8651 (t0) cc_final: 0.8147 (t0) REVERT: D 514 MET cc_start: 0.7287 (OUTLIER) cc_final: 0.6872 (mpp) outliers start: 76 outliers final: 55 residues processed: 254 average time/residue: 0.1392 time to fit residues: 57.9095 Evaluate side-chains 251 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 189 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 133 CYS Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 569 ASP Chi-restraints excluded: chain B residue 582 SER Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 595 GLU Chi-restraints excluded: chain B residue 753 TRP Chi-restraints excluded: chain B residue 777 VAL Chi-restraints excluded: chain B residue 788 ASP Chi-restraints excluded: chain B residue 853 LEU Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 947 ARG Chi-restraints excluded: chain B residue 1027 ILE Chi-restraints excluded: chain B residue 1063 LYS Chi-restraints excluded: chain B residue 1079 LEU Chi-restraints excluded: chain B residue 1086 LEU Chi-restraints excluded: chain B residue 1093 TYR Chi-restraints excluded: chain B residue 1111 TYR Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 387 GLU Chi-restraints excluded: chain C residue 396 MET Chi-restraints excluded: chain C residue 404 THR Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain C residue 495 GLN Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain C residue 569 MET Chi-restraints excluded: chain C residue 595 LEU Chi-restraints excluded: chain C residue 790 ASP Chi-restraints excluded: chain C residue 853 LEU Chi-restraints excluded: chain C residue 855 VAL Chi-restraints excluded: chain C residue 916 PHE Chi-restraints excluded: chain C residue 953 THR Chi-restraints excluded: chain C residue 1017 LEU Chi-restraints excluded: chain C residue 1088 ILE Chi-restraints excluded: chain C residue 1098 THR Chi-restraints excluded: chain C residue 1116 LEU Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 108 TYR Chi-restraints excluded: chain D residue 303 SER Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 493 LEU Chi-restraints excluded: chain D residue 498 ILE Chi-restraints excluded: chain D residue 502 LEU Chi-restraints excluded: chain D residue 514 MET Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain D residue 561 VAL Chi-restraints excluded: chain D residue 562 THR Chi-restraints excluded: chain D residue 579 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 57 optimal weight: 4.9990 chunk 241 optimal weight: 9.9990 chunk 278 optimal weight: 30.0000 chunk 238 optimal weight: 8.9990 chunk 53 optimal weight: 1.9990 chunk 29 optimal weight: 9.9990 chunk 205 optimal weight: 9.9990 chunk 133 optimal weight: 2.9990 chunk 167 optimal weight: 7.9990 chunk 150 optimal weight: 0.9990 chunk 83 optimal weight: 0.8980 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 876 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.079378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.061536 restraints weight = 86220.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.063228 restraints weight = 49415.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.064340 restraints weight = 33781.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.065078 restraints weight = 26076.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.065507 restraints weight = 22023.134| |-----------------------------------------------------------------------------| r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.4716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 24452 Z= 0.144 Angle : 0.604 12.661 33409 Z= 0.296 Chirality : 0.040 0.237 3673 Planarity : 0.003 0.052 4205 Dihedral : 13.865 89.010 3711 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.57 % Allowed : 15.69 % 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: 0.59 (0.16), residues: 2837 helix: 1.59 (0.14), residues: 1428 sheet: -0.05 (0.31), residues: 280 loop : -1.06 (0.18), residues: 1129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B1125 TYR 0.012 0.001 TYR B 394 PHE 0.011 0.001 PHE B 428 TRP 0.027 0.001 TRP C 496 HIS 0.004 0.001 HIS B1124 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 (24452) covalent geometry : angle 0.60428 / 0.30 (33409) hydrogen bonds : bond 0.03463 / 2.18 ( 1104) hydrogen bonds : angle 4.12007 / 2.89 ( 3206) *********************** 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 258 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 196 time to evaluate : 0.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 264 LYS cc_start: 0.9080 (pttm) cc_final: 0.8575 (pttm) REVERT: B 354 MET cc_start: 0.7899 (mtt) cc_final: 0.7547 (mtm) REVERT: B 402 HIS cc_start: 0.6276 (t70) cc_final: 0.5845 (t70) REVERT: B 753 TRP cc_start: 0.9190 (OUTLIER) cc_final: 0.7770 (t60) REVERT: B 1093 TYR cc_start: 0.3437 (OUTLIER) cc_final: 0.3038 (p90) REVERT: B 1111 TYR cc_start: 0.8544 (OUTLIER) cc_final: 0.7954 (p90) REVERT: C 133 ASP cc_start: 0.7810 (t0) cc_final: 0.7563 (t0) REVERT: C 499 GLU cc_start: 0.7760 (mp0) cc_final: 0.7455 (mp0) REVERT: C 790 ASP cc_start: 0.8819 (OUTLIER) cc_final: 0.8496 (t0) REVERT: C 1075 TYR cc_start: 0.8229 (t80) cc_final: 0.8008 (t80) REVERT: D 100 MET cc_start: 0.8897 (mmm) cc_final: 0.8526 (mmm) REVERT: D 407 MET cc_start: 0.8923 (ttp) cc_final: 0.8658 (ppp) REVERT: D 420 ASP cc_start: 0.8720 (t0) cc_final: 0.8251 (t0) REVERT: D 514 MET cc_start: 0.7179 (OUTLIER) cc_final: 0.6845 (mpp) outliers start: 62 outliers final: 53 residues processed: 242 average time/residue: 0.1462 time to fit residues: 57.7587 Evaluate side-chains 251 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 193 time to evaluate : 1.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 133 CYS Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 569 ASP Chi-restraints excluded: chain B residue 582 SER Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 595 GLU Chi-restraints excluded: chain B residue 753 TRP Chi-restraints excluded: chain B residue 777 VAL Chi-restraints excluded: chain B residue 788 ASP Chi-restraints excluded: chain B residue 853 LEU Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 1027 ILE Chi-restraints excluded: chain B residue 1063 LYS Chi-restraints excluded: chain B residue 1079 LEU Chi-restraints excluded: chain B residue 1086 LEU Chi-restraints excluded: chain B residue 1093 TYR Chi-restraints excluded: chain B residue 1111 TYR Chi-restraints excluded: chain B residue 1158 THR Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 387 GLU Chi-restraints excluded: chain C residue 404 THR Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain C residue 495 GLN Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain C residue 595 LEU Chi-restraints excluded: chain C residue 790 ASP Chi-restraints excluded: chain C residue 855 VAL Chi-restraints excluded: chain C residue 953 THR Chi-restraints excluded: chain C residue 1017 LEU Chi-restraints excluded: chain C residue 1088 ILE Chi-restraints excluded: chain C residue 1098 THR Chi-restraints excluded: chain D residue 13 HIS Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 108 TYR Chi-restraints excluded: chain D residue 303 SER Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 493 LEU Chi-restraints excluded: chain D residue 498 ILE Chi-restraints excluded: chain D residue 502 LEU Chi-restraints excluded: chain D residue 514 MET Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain D residue 561 VAL Chi-restraints excluded: chain D residue 562 THR Chi-restraints excluded: chain D residue 579 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 184 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 chunk 227 optimal weight: 6.9990 chunk 192 optimal weight: 3.9990 chunk 220 optimal weight: 0.9990 chunk 37 optimal weight: 7.9990 chunk 258 optimal weight: 20.0000 chunk 93 optimal weight: 30.0000 chunk 223 optimal weight: 1.9990 chunk 70 optimal weight: 0.0170 chunk 244 optimal weight: 7.9990 overall best weight: 2.0026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 876 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.079591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.061624 restraints weight = 86648.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.063324 restraints weight = 49937.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.064444 restraints weight = 34222.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.065187 restraints weight = 26502.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.065644 restraints weight = 22375.228| |-----------------------------------------------------------------------------| r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.4775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 24452 Z= 0.134 Angle : 0.611 13.366 33409 Z= 0.298 Chirality : 0.040 0.237 3673 Planarity : 0.003 0.053 4205 Dihedral : 13.876 88.882 3709 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.77 % Allowed : 15.57 % Favored : 81.66 % 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: 0.63 (0.16), residues: 2837 helix: 1.62 (0.14), residues: 1427 sheet: -0.08 (0.31), residues: 285 loop : -1.03 (0.18), residues: 1125 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B1125 TYR 0.012 0.001 TYR C1027 PHE 0.069 0.001 PHE C 125 TRP 0.030 0.001 TRP C 496 HIS 0.003 0.001 HIS C 377 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (24452) covalent geometry : angle 0.61130 / 0.30 (33409) hydrogen bonds : bond 0.03451 / 2.17 ( 1104) hydrogen bonds : angle 4.10197 / 2.85 ( 3206) ********************** 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 267 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 200 time to evaluate : 0.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 264 LYS cc_start: 0.9055 (pttm) cc_final: 0.8764 (pttm) REVERT: B 354 MET cc_start: 0.7877 (mtt) cc_final: 0.7544 (mtm) REVERT: B 402 HIS cc_start: 0.6106 (t70) cc_final: 0.5772 (t70) REVERT: B 753 TRP cc_start: 0.9124 (OUTLIER) cc_final: 0.7870 (t60) REVERT: B 1111 TYR cc_start: 0.8479 (OUTLIER) cc_final: 0.7921 (p90) REVERT: C 133 ASP cc_start: 0.7714 (t0) cc_final: 0.7474 (t0) REVERT: C 499 GLU cc_start: 0.7716 (mp0) cc_final: 0.7444 (mp0) REVERT: C 790 ASP cc_start: 0.8791 (OUTLIER) cc_final: 0.8514 (t0) REVERT: C 916 PHE cc_start: 0.8089 (OUTLIER) cc_final: 0.7587 (t80) REVERT: C 1075 TYR cc_start: 0.8166 (t80) cc_final: 0.7963 (t80) REVERT: D 100 MET cc_start: 0.8837 (mmm) cc_final: 0.8497 (mmm) REVERT: D 407 MET cc_start: 0.8866 (ttp) cc_final: 0.8639 (ppp) REVERT: D 420 ASP cc_start: 0.8709 (t0) cc_final: 0.8233 (t0) REVERT: D 514 MET cc_start: 0.7131 (OUTLIER) cc_final: 0.6804 (mpp) outliers start: 67 outliers final: 54 residues processed: 250 average time/residue: 0.1466 time to fit residues: 59.9341 Evaluate side-chains 252 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 193 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 133 CYS Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 569 ASP Chi-restraints excluded: chain B residue 582 SER Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 595 GLU Chi-restraints excluded: chain B residue 753 TRP Chi-restraints excluded: chain B residue 777 VAL Chi-restraints excluded: chain B residue 788 ASP Chi-restraints excluded: chain B residue 853 LEU Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 947 ARG Chi-restraints excluded: chain B residue 1027 ILE Chi-restraints excluded: chain B residue 1063 LYS Chi-restraints excluded: chain B residue 1079 LEU Chi-restraints excluded: chain B residue 1086 LEU Chi-restraints excluded: chain B residue 1111 TYR Chi-restraints excluded: chain B residue 1158 THR Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 404 THR Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain C residue 495 GLN Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain C residue 569 MET Chi-restraints excluded: chain C residue 595 LEU Chi-restraints excluded: chain C residue 790 ASP Chi-restraints excluded: chain C residue 855 VAL Chi-restraints excluded: chain C residue 916 PHE Chi-restraints excluded: chain C residue 953 THR Chi-restraints excluded: chain C residue 1017 LEU Chi-restraints excluded: chain C residue 1088 ILE Chi-restraints excluded: chain C residue 1098 THR Chi-restraints excluded: chain D residue 13 HIS Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 108 TYR Chi-restraints excluded: chain D residue 136 LEU Chi-restraints excluded: chain D residue 303 SER Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 493 LEU Chi-restraints excluded: chain D residue 498 ILE Chi-restraints excluded: chain D residue 502 LEU Chi-restraints excluded: chain D residue 514 MET Chi-restraints excluded: chain D residue 561 VAL Chi-restraints excluded: chain D residue 562 THR Chi-restraints excluded: chain D residue 579 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 68 optimal weight: 4.9990 chunk 98 optimal weight: 50.0000 chunk 271 optimal weight: 9.9990 chunk 77 optimal weight: 10.0000 chunk 277 optimal weight: 20.0000 chunk 48 optimal weight: 8.9990 chunk 182 optimal weight: 2.9990 chunk 120 optimal weight: 5.9990 chunk 156 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 235 optimal weight: 10.0000 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 261 ASN ** B 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 876 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 47 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.078257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.060299 restraints weight = 86315.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.061939 restraints weight = 49960.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.063037 restraints weight = 34473.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.063762 restraints weight = 26779.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.064169 restraints weight = 22707.100| |-----------------------------------------------------------------------------| r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.4973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 24452 Z= 0.187 Angle : 0.648 13.024 33409 Z= 0.317 Chirality : 0.041 0.235 3673 Planarity : 0.004 0.049 4205 Dihedral : 13.913 89.830 3709 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.73 % Allowed : 15.78 % Favored : 81.49 % 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: 0.57 (0.16), residues: 2837 helix: 1.56 (0.14), residues: 1431 sheet: -0.11 (0.31), residues: 288 loop : -1.04 (0.18), residues: 1118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B1125 TYR 0.017 0.001 TYR B1093 PHE 0.054 0.002 PHE C 125 TRP 0.033 0.002 TRP C 496 HIS 0.005 0.001 HIS B 689 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.19 (24452) covalent geometry : angle 0.64807 / 0.32 (33409) hydrogen bonds : bond 0.03616 / 2.29 ( 1104) hydrogen bonds : angle 4.20089 / 2.93 ( 3206) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3577.56 seconds wall clock time: 62 minutes 40.61 seconds (3760.61 seconds total)