Starting phenix.real_space_refine on Sun Sep 13 14:03:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6t2v_10370/09_2026/6t2v_10370.cif Found real_map, /net/cci-nas-00/data/ceres_data/6t2v_10370/09_2026/6t2v_10370.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6t2v_10370/09_2026/6t2v_10370.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6t2v_10370/09_2026/6t2v_10370.map" model { file = "/net/cci-nas-00/data/ceres_data/6t2v_10370/09_2026/6t2v_10370.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6t2v_10370/09_2026/6t2v_10370.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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 102 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: 5.08, per 1000 atoms: 0.21 Number of scatterers: 23826 At special positions: 0 Unit cell: (152.985, 150.815, 131.285, 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: 2.32 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: 124 helices and 16 sheets defined 53.1% alpha, 9.2% beta 18 base pairs and 34 stacking pairs defined. Time for finding SS restraints: 2.97 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: 3.556A pdb=" N GLU B 58 " --> pdb=" O THR B 55 " (cutoff:3.500A) removed outlier: 3.611A 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: 3.642A 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: 3.622A pdb=" N SER B 144 " --> pdb=" O ASN B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 173 removed outlier: 3.820A pdb=" N TYR B 173 " --> pdb=" O ARG B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 187 removed outlier: 4.256A pdb=" N VAL B 182 " --> pdb=" O GLU B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 202 removed outlier: 3.678A pdb=" N LEU B 193 " --> pdb=" O GLY B 189 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N ARG B 199 " --> pdb=" O ARG B 195 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N TYR B 200 " --> pdb=" O ASP B 196 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLN B 202 " --> pdb=" O ASN B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 239 removed outlier: 3.559A 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: 3.625A pdb=" N ASN B 278 " --> pdb=" O GLU B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 289 removed outlier: 3.760A pdb=" N LYS B 288 " --> pdb=" O GLU B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 317 removed outlier: 4.251A pdb=" N GLU B 311 " --> pdb=" O HIS B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 347 removed outlier: 4.469A pdb=" N ARG B 336 " --> pdb=" O LEU B 332 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N GLU B 337 " --> pdb=" O ALA B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 364 removed outlier: 3.529A pdb=" N MET B 354 " --> pdb=" O GLY B 350 " (cutoff:3.500A) removed outlier: 4.065A 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: 3.756A pdb=" N ALA B 418 " --> pdb=" O PRO B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 437 removed outlier: 3.829A 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 Processing helix chain 'B' and resid 586 through 589 Processing helix chain 'B' and resid 590 through 605 removed outlier: 3.953A pdb=" N GLN B 594 " --> pdb=" O THR B 590 " (cutoff:3.500A) Processing helix chain 'B' and resid 608 through 617 removed outlier: 3.801A 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: 3.613A pdb=" N TRP B 638 " --> pdb=" O ASP B 634 " (cutoff:3.500A) Processing helix chain 'B' and resid 656 through 668 removed outlier: 3.806A pdb=" N MET B 660 " --> pdb=" O GLY B 656 " (cutoff:3.500A) Processing helix chain 'B' and resid 669 through 677 removed outlier: 3.607A pdb=" N ASN B 673 " --> pdb=" O ASN B 669 " (cutoff:3.500A) Processing helix chain 'B' and resid 680 through 699 removed outlier: 3.619A pdb=" N THR B 699 " --> pdb=" O GLN B 695 " (cutoff:3.500A) Processing helix chain 'B' and resid 703 through 717 removed outlier: 4.103A pdb=" N LEU B 707 " --> pdb=" O SER B 703 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL B 708 " --> pdb=" O GLU B 704 " (cutoff:3.500A) Processing helix chain 'B' and resid 783 through 807 removed outlier: 3.514A pdb=" N GLU B 793 " --> pdb=" O LEU B 789 " (cutoff:3.500A) Processing helix chain 'B' and resid 832 through 836 Processing helix chain 'B' and resid 837 through 843 removed outlier: 3.764A pdb=" N LEU B 841 " --> pdb=" O ALA B 837 " (cutoff:3.500A) Processing helix chain 'B' and resid 849 through 860 removed outlier: 3.900A 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: 3.880A pdb=" N GLU B 992 " --> pdb=" O PRO B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1008 through 1012 removed outlier: 3.707A pdb=" N GLN B1011 " --> pdb=" O SER B1008 " (cutoff:3.500A) Processing helix chain 'B' and resid 1032 through 1044 removed outlier: 3.633A pdb=" N THR B1038 " --> pdb=" O SER B1034 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU B1039 " --> pdb=" O GLN B1035 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N PHE B1043 " --> pdb=" O LEU B1039 " (cutoff:3.500A) Processing helix chain 'B' and resid 1045 through 1048 removed outlier: 3.800A pdb=" N ALA B1048 " --> pdb=" O PRO B1045 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1045 through 1048' Processing helix chain 'B' and resid 1094 through 1106 Processing helix chain 'B' and resid 1107 through 1126 Processing helix chain 'B' and resid 1130 through 1134 Processing helix chain 'B' and resid 1144 through 1146 No H-bonds generated for 'chain 'B' and resid 1144 through 1146' Processing helix chain 'B' and resid 1163 through 1174 removed outlier: 3.563A pdb=" N LEU B1167 " --> pdb=" O GLY B1163 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 24 removed outlier: 4.139A 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: 3.741A 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: 3.898A pdb=" N LEU C 146 " --> pdb=" O ARG C 142 " (cutoff:3.500A) removed outlier: 3.840A 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 Processing helix chain 'C' and resid 220 through 232 removed outlier: 3.568A pdb=" N ALA C 229 " --> pdb=" O GLN C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 263 Processing helix chain 'C' and resid 297 through 304 Processing helix chain 'C' and resid 304 through 316 Processing helix chain 'C' and resid 333 through 344 Processing helix chain 'C' and resid 354 through 360 Processing helix chain 'C' and resid 381 through 400 removed outlier: 3.605A pdb=" N VAL C 386 " --> pdb=" O PRO C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 406 No H-bonds generated for 'chain 'C' and resid 404 through 406' Processing helix chain 'C' and resid 414 through 428 removed outlier: 3.667A 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: 3.868A pdb=" N ALA C 453 " --> pdb=" O PRO C 449 " (cutoff:3.500A) Processing helix chain 'C' and resid 466 through 474 Processing helix chain 'C' and resid 476 through 483 removed outlier: 3.593A pdb=" N PHE C 483 " --> pdb=" O LEU C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 486 through 500 removed outlier: 3.786A pdb=" N GLN C 495 " --> pdb=" O ARG C 491 " (cutoff:3.500A) Processing helix chain 'C' and resid 507 through 514 removed outlier: 3.575A pdb=" N LEU C 514 " --> pdb=" O ASN C 510 " (cutoff:3.500A) Processing helix chain 'C' and resid 523 through 537 Processing helix chain 'C' and resid 555 through 557 No H-bonds generated for 'chain 'C' and resid 555 through 557' Processing helix chain 'C' and resid 558 through 574 removed outlier: 3.726A pdb=" N MET C 569 " --> pdb=" O ALA C 565 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLN C 570 " --> pdb=" O SER C 566 " (cutoff:3.500A) Processing helix chain 'C' and resid 587 through 599 removed outlier: 4.590A pdb=" N CYS C 591 " --> pdb=" O TRP C 587 " (cutoff:3.500A) removed outlier: 4.555A 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: 3.849A pdb=" N LEU C 637 " --> pdb=" O PRO C 633 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ASP C 646 " --> pdb=" O ALA C 642 " (cutoff:3.500A) Processing helix chain 'C' and resid 707 through 722 Processing helix chain 'C' and resid 745 through 758 Processing helix chain 'C' and resid 769 through 780 Processing helix chain 'C' and resid 806 through 812 removed outlier: 3.546A pdb=" N GLN C 812 " --> pdb=" O PRO C 808 " (cutoff:3.500A) Processing helix chain 'C' and resid 833 through 843 removed outlier: 3.521A pdb=" N LEU C 837 " --> pdb=" O PRO C 833 " (cutoff:3.500A) removed outlier: 3.833A 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: 3.621A pdb=" N LEU C 897 " --> pdb=" O ASP C 893 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA C 904 " --> pdb=" O ARG C 900 " (cutoff:3.500A) Processing helix chain 'C' and resid 910 through 932 removed outlier: 3.767A pdb=" N GLU C 914 " --> pdb=" O GLY C 910 " (cutoff:3.500A) removed outlier: 3.838A 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: 3.575A pdb=" N GLY C 977 " --> pdb=" O SER C 973 " (cutoff:3.500A) Processing helix chain 'C' and resid 1012 through 1033 removed outlier: 3.696A 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: 3.571A pdb=" N ARG C1068 " --> pdb=" O LEU C1064 " (cutoff:3.500A) Processing helix chain 'C' and resid 1089 through 1094 removed outlier: 4.266A 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: 3.924A pdb=" N PHE C1117 " --> pdb=" O LEU C1113 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N PHE C1119 " --> pdb=" O PRO C1115 " (cutoff:3.500A) Processing helix chain 'D' and resid 11 through 15 removed outlier: 3.766A 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: 3.970A pdb=" N SER D 88 " --> pdb=" O CYS D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 125 Processing helix chain 'D' and resid 133 through 145 removed outlier: 3.547A pdb=" N LEU D 137 " --> pdb=" O ASP D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 164 removed outlier: 3.515A 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: 3.647A 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: 3.563A pdb=" N MET D 273 " --> pdb=" O GLU D 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 286 removed outlier: 3.569A pdb=" N ALA D 285 " --> pdb=" O ARG D 281 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU D 286 " --> pdb=" O LEU D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 315 removed outlier: 3.739A pdb=" N ASP D 312 " --> pdb=" O ALA D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 316 through 319 Processing helix chain 'D' and resid 322 through 334 removed outlier: 3.519A 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: 3.813A pdb=" N GLN D 369 " --> pdb=" O SER D 365 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ASN D 375 " --> pdb=" O ALA D 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 377 through 387 removed outlier: 3.537A pdb=" N ALA D 381 " --> pdb=" O GLY D 377 " (cutoff:3.500A) Processing helix chain 'D' and resid 388 through 391 removed outlier: 3.539A 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 Processing helix chain 'D' and resid 450 through 465 Processing helix chain 'D' and resid 523 through 527 removed outlier: 3.534A 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: 3.661A pdb=" N ILE D 590 " --> pdb=" O LEU D 586 " (cutoff:3.500A) removed outlier: 3.749A 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: 6.497A pdb=" N GLU B 6 " --> pdb=" O THR B 442 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N ALA B 439 " --> pdb=" O GLU B 18 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU B 20 " --> pdb=" O ALA B 439 " (cutoff:3.500A) removed outlier: 6.112A 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: 6.778A pdb=" N ARG B 19 " --> pdb=" O LEU B 411 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N GLY B 413 " --> pdb=" O ARG B 19 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N ILE B 21 " --> pdb=" O GLY B 413 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N ALA B 381 " --> pdb=" O LEU B 410 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N ILE B 412 " --> pdb=" O ALA B 381 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N ILE B 383 " --> pdb=" O ILE B 412 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N VAL B 62 " --> pdb=" O ASP B 384 " (cutoff:3.500A) removed outlier: 5.777A 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: 6.294A 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: 6.591A pdb=" N VAL B 207 " --> pdb=" O LEU B 778 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 487 through 490 Processing sheet with id=AA5, first strand: chain 'B' and resid 578 through 580 removed outlier: 6.643A pdb=" N VAL B 579 " --> pdb=" O ILE B 738 " (cutoff:3.500A) removed outlier: 8.645A pdb=" N THR B 740 " --> pdb=" O VAL B 579 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N ILE B 554 " --> pdb=" O GLN B 737 " (cutoff:3.500A) removed outlier: 8.329A pdb=" N VAL B 739 " --> pdb=" O ILE B 554 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N VAL B 556 " --> pdb=" O VAL B 739 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N MET B 499 " --> pdb=" O ALA B 866 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N GLN B 868 " --> pdb=" O MET B 499 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N MET B 501 " --> pdb=" O GLN B 868 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 1155 through 1158 removed outlier: 7.225A pdb=" N TYR B1076 " --> pdb=" O GLY B1137 " (cutoff:3.500A) removed outlier: 8.371A pdb=" N ILE B1139 " --> pdb=" O TYR B1076 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N LEU B1078 " --> pdb=" O ILE B1139 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N LEU B1141 " --> pdb=" O LEU B1078 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ALA B1080 " --> pdb=" O LEU B1141 " (cutoff:3.500A) removed outlier: 8.270A pdb=" N TYR B1081 " --> pdb=" O ILE B1066 " (cutoff:3.500A) removed outlier: 10.123A pdb=" N ILE B1066 " --> pdb=" O TYR B1081 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N MET B1061 " --> pdb=" O PRO B1026 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N LYS B1063 " --> pdb=" O TYR B1024 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N TYR B1024 " --> pdb=" O LYS B1063 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N PHE B1065 " --> pdb=" O GLU B1022 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N GLU B1022 " --> pdb=" O PHE B1065 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ASP B1067 " --> pdb=" O GLU B1020 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA C 57 " --> pdb=" O TYR B1024 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 60 through 61 removed outlier: 6.370A pdb=" N VAL C 211 " --> pdb=" O HIS C 237 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N LEU C 239 " --> pdb=" O VAL C 211 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N ILE C 213 " --> pdb=" O LEU C 239 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N THR C 241 " --> pdb=" O ILE C 213 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ARG C 3 " --> pdb=" O LEU C 238 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N PHE C 240 " --> pdb=" O ARG C 3 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N TYR C 5 " --> pdb=" O PHE C 240 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ARG C 266 " --> pdb=" O GLU C 322 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ASP C 324 " --> pdb=" O ARG C 266 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 365 through 366 removed outlier: 5.928A pdb=" N ARG C 365 " --> pdb=" O TYR C 760 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'C' and resid 437 through 439 removed outlier: 3.645A pdb=" N ASN C 660 " --> pdb=" O ILE C 408 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N LYS C 673 " --> pdb=" O LYS C 726 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N TYR C 728 " --> pdb=" O LYS C 673 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N VAL C 675 " --> pdb=" O TYR C 728 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N SER C 730 " --> pdb=" O VAL C 675 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N LEU C 677 " --> pdb=" O SER C 730 " (cutoff:3.500A) removed outlier: 8.228A pdb=" N ILE C 732 " --> pdb=" O LEU C 677 " (cutoff:3.500A) removed outlier: 8.981A pdb=" N CYS C 782 " --> pdb=" O ILE C 374 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N PHE C 376 " --> pdb=" O CYS C 782 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 442 through 443 removed outlier: 3.723A pdb=" N ARG C 442 " --> pdb=" O ILE C 650 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 939 through 947 removed outlier: 5.653A pdb=" N GLN C 939 " --> pdb=" O GLN C 958 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLN C 958 " --> pdb=" O GLN C 939 " (cutoff:3.500A) removed outlier: 15.752A pdb=" N LEU C 956 " --> pdb=" O TRP C 967 " (cutoff:3.500A) removed outlier: 13.340A pdb=" N TRP C 967 " --> pdb=" O LEU C 956 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N GLN C 958 " --> pdb=" O LEU C 965 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N LEU C 965 " --> pdb=" O GLN C 958 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N LEU C 964 " --> pdb=" O ARG C 997 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N PHE C 999 " --> pdb=" O LEU C 964 " (cutoff:3.500A) removed outlier: 7.270A 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: 3.516A 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: 6.198A pdb=" N SER D 92 " --> pdb=" O LEU D 102 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 167 through 170 removed outlier: 6.585A pdb=" N ARG D 200 " --> pdb=" O VAL D 267 " (cutoff:3.500A) removed outlier: 8.836A pdb=" N SER D 238 " --> pdb=" O ILE D 199 " (cutoff:3.500A) removed outlier: 6.395A 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: 7.199A pdb=" N ASP D 547 " --> pdb=" O ARG D 574 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N GLN D 439 " --> pdb=" O ALA D 550 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N ILE D 552 " --> pdb=" O GLN D 439 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N LEU D 441 " --> pdb=" O ILE D 552 " (cutoff:3.500A) removed outlier: 8.677A pdb=" N MET D 536 " --> pdb=" O TYR D 438 " (cutoff:3.500A) removed outlier: 6.459A 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: 4.488A pdb=" N ALA D 513 " --> pdb=" O ILE D 498 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ILE D 498 " --> pdb=" O ALA D 513 " (cutoff:3.500A) 1051 hydrogen bonds defined for protein. 3087 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 46 hydrogen bonds 92 hydrogen bond angles 0 basepair planarities 18 basepair parallelities 34 stacking parallelities Total time for adding SS restraints: 5.28 Time building geometry restraints manager: 3.09 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: 7590 1.34 - 1.45: 3403 1.45 - 1.57: 13184 1.57 - 1.69: 106 1.69 - 1.81: 169 Bond restraints: 24452 Sorted by residual: bond pdb=" C3' DT X 5 " pdb=" C2' DT X 5 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.07e+01 bond pdb=" C3' DT X 8 " pdb=" C2' DT X 8 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.50e+00 bond pdb=" C3' DT X 23 " pdb=" C2' DT X 23 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.29e+00 bond pdb=" C3' DT X 69 " pdb=" C2' DT X 69 " ideal model delta sigma weight residual 1.516 1.537 -0.021 8.00e-03 1.56e+04 6.87e+00 bond pdb=" C3' DG X 24 " pdb=" C2' DG X 24 " ideal model delta sigma weight residual 1.516 1.536 -0.020 8.00e-03 1.56e+04 6.31e+00 ... (remaining 24447 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.39: 32597 1.39 - 2.78: 733 2.78 - 4.17: 60 4.17 - 5.56: 17 5.56 - 6.95: 2 Bond angle restraints: 33409 Sorted by residual: angle pdb=" N3 DT X 28 " pdb=" C4 DT X 28 " pdb=" O4 DT X 28 " ideal model delta sigma weight residual 119.90 122.44 -2.54 6.00e-01 2.78e+00 1.80e+01 angle pdb=" N3 DT X 57 " pdb=" C4 DT X 57 " pdb=" O4 DT X 57 " ideal model delta sigma weight residual 119.90 122.43 -2.53 6.00e-01 2.78e+00 1.78e+01 angle pdb=" N3 DT X 76 " pdb=" C4 DT X 76 " pdb=" O4 DT X 76 " ideal model delta sigma weight residual 119.90 122.41 -2.51 6.00e-01 2.78e+00 1.74e+01 angle pdb=" N3 DT X 4 " pdb=" C4 DT X 4 " pdb=" O4 DT X 4 " 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 5 " pdb=" C4 DT X 5 " pdb=" O4 DT X 5 " 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 - 15.26: 13284 15.26 - 30.53: 832 30.53 - 45.79: 325 45.79 - 61.06: 164 61.06 - 76.32: 10 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 -160.86 -19.14 0 5.00e+00 4.00e-02 1.47e+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 180.00 163.49 16.51 0 5.00e+00 4.00e-02 1.09e+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 180.00 164.26 15.74 0 5.00e+00 4.00e-02 9.90e+00 ... (remaining 14612 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 2318 0.026 - 0.052: 882 0.052 - 0.078: 261 0.078 - 0.104: 161 0.104 - 0.131: 51 Chirality restraints: 3673 Sorted by residual: chirality pdb=" CA ILE D 233 " pdb=" N ILE D 233 " pdb=" C ILE D 233 " pdb=" CB ILE D 233 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.26e-01 chirality pdb=" CA ILE C 661 " pdb=" N ILE C 661 " pdb=" C ILE C 661 " pdb=" CB ILE C 661 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.11e-01 chirality pdb=" CA VAL D 337 " pdb=" N VAL D 337 " pdb=" C VAL D 337 " pdb=" CB VAL D 337 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 3.93e-01 ... (remaining 3670 not shown) Planarity restraints: 4205 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU B 992 " 0.016 2.00e-02 2.50e+03 3.28e-02 1.08e+01 pdb=" C GLU B 992 " -0.057 2.00e-02 2.50e+03 pdb=" O GLU B 992 " 0.021 2.00e-02 2.50e+03 pdb=" N TRP B 993 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY C 657 " 0.049 5.00e-02 4.00e+02 7.36e-02 8.66e+00 pdb=" N PRO C 658 " -0.127 5.00e-02 4.00e+02 pdb=" CA PRO C 658 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO C 658 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP C 469 " 0.014 2.00e-02 2.50e+03 2.79e-02 7.76e+00 pdb=" C ASP C 469 " -0.048 2.00e-02 2.50e+03 pdb=" O ASP C 469 " 0.018 2.00e-02 2.50e+03 pdb=" N VAL C 470 " 0.016 2.00e-02 2.50e+03 ... (remaining 4202 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2695 2.75 - 3.29: 21379 3.29 - 3.83: 39009 3.83 - 4.36: 44859 4.36 - 4.90: 77256 Nonbonded interactions: 185198 Sorted by model distance: nonbonded pdb=" OD1 ASN B 759 " pdb=" NH2 ARG B 822 " model vdw 2.213 3.120 nonbonded pdb=" OG SER D 303 " pdb=" O GLY D 307 " model vdw 2.285 3.040 nonbonded pdb=" NH2 ARG B 254 " pdb=" O3' DG X 61 " model vdw 2.292 3.120 nonbonded pdb=" O LEU C 115 " pdb=" OG SER C 119 " model vdw 2.295 3.040 nonbonded pdb=" OH TYR B 394 " pdb=" OE1 GLU B 436 " model vdw 2.304 3.040 ... (remaining 185193 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.490 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 25.280 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.040 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: 0.000 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 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 : 0.002 0.045 24452 Z= 0.179 Angle : 0.481 6.953 33409 Z= 0.350 Chirality : 0.036 0.131 3673 Planarity : 0.005 0.074 4205 Dihedral : 13.085 76.320 9243 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.01 % Favored : 97.96 % Rotamer: Outliers : 3.02 % Allowed : 5.18 % Favored : 91.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.62 (0.11), residues: 2837 helix: -2.53 (0.09), residues: 1409 sheet: -0.87 (0.29), residues: 276 loop : -2.44 (0.14), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 800 TYR 0.007 0.001 TYR B1093 PHE 0.007 0.000 PHE B1023 TRP 0.009 0.001 TRP B 652 HIS 0.002 0.000 HIS C 377 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.18 (24452) covalent geometry : angle 0.48119 / 0.35 (33409) hydrogen bonds : bond 0.14798 / 9.92 ( 1097) hydrogen bonds : angle 6.30144 / 4.56 ( 3179) *********************** 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 514 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 441 time to evaluate : 0.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 166 ASP cc_start: 0.9158 (m-30) cc_final: 0.8830 (m-30) REVERT: B 269 ILE cc_start: 0.6919 (OUTLIER) cc_final: 0.5762 (mm) REVERT: B 354 MET cc_start: 0.7717 (mtt) cc_final: 0.7479 (mtm) REVERT: B 431 MET cc_start: 0.9115 (mtm) cc_final: 0.8621 (mtp) REVERT: B 499 MET cc_start: 0.8110 (ttp) cc_final: 0.7781 (tpp) REVERT: B 501 MET cc_start: 0.9116 (mtm) cc_final: 0.8339 (mpp) REVERT: B 518 MET cc_start: 0.7577 (mmm) cc_final: 0.6302 (mmm) REVERT: B 541 MET cc_start: 0.8598 (mtp) cc_final: 0.7617 (tpp) REVERT: B 588 PHE cc_start: 0.8255 (m-80) cc_final: 0.7916 (m-80) REVERT: B 594 GLN cc_start: 0.8864 (tp-100) cc_final: 0.8458 (tp-100) REVERT: B 658 MET cc_start: 0.8796 (tpp) cc_final: 0.8531 (tpt) REVERT: B 694 LEU cc_start: 0.9384 (mt) cc_final: 0.9163 (mt) REVERT: B 711 LEU cc_start: 0.9635 (tp) cc_final: 0.9396 (tp) REVERT: B 753 TRP cc_start: 0.9178 (OUTLIER) cc_final: 0.7613 (t60) REVERT: B 964 PHE cc_start: 0.8239 (m-80) cc_final: 0.7892 (m-10) REVERT: B 1021 MET cc_start: 0.9165 (ttp) cc_final: 0.8733 (ppp) REVERT: C 50 LEU cc_start: 0.9252 (mt) cc_final: 0.9007 (tt) REVERT: C 91 MET cc_start: 0.8431 (mtm) cc_final: 0.8101 (mtm) REVERT: C 133 ASP cc_start: 0.8831 (t0) cc_final: 0.8506 (m-30) REVERT: C 165 GLN cc_start: 0.9140 (mt0) cc_final: 0.8781 (mt0) REVERT: C 234 ILE cc_start: 0.7021 (OUTLIER) cc_final: 0.6813 (mm) REVERT: C 408 ILE cc_start: 0.9364 (mt) cc_final: 0.8940 (pt) REVERT: C 465 PHE cc_start: 0.8373 (m-80) cc_final: 0.7752 (m-80) REVERT: C 471 LEU cc_start: 0.8936 (mt) cc_final: 0.8544 (pp) REVERT: C 906 ASP cc_start: 0.8350 (m-30) cc_final: 0.8019 (t0) REVERT: C 980 LEU cc_start: 0.8905 (tp) cc_final: 0.8663 (tp) REVERT: D 25 LEU cc_start: 0.9307 (mt) cc_final: 0.8994 (pp) REVERT: D 100 MET cc_start: 0.9257 (mtm) cc_final: 0.8886 (mpp) REVERT: D 108 TYR cc_start: 0.6563 (OUTLIER) cc_final: 0.5915 (p90) REVERT: D 201 LEU cc_start: 0.9360 (mt) cc_final: 0.9098 (tp) REVERT: D 212 LEU cc_start: 0.9492 (tp) cc_final: 0.8917 (tp) REVERT: D 273 MET cc_start: 0.8275 (mtm) cc_final: 0.8005 (ttt) REVERT: D 280 SER cc_start: 0.7789 (p) cc_final: 0.6701 (p) REVERT: D 282 LEU cc_start: 0.9357 (tp) cc_final: 0.9063 (pp) outliers start: 73 outliers final: 13 residues processed: 508 average time/residue: 0.1674 time to fit residues: 132.0835 Evaluate side-chains 257 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 240 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 753 TRP Chi-restraints excluded: chain B residue 947 ARG Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 591 CYS Chi-restraints excluded: chain C residue 746 VAL Chi-restraints excluded: chain C residue 821 VAL Chi-restraints excluded: chain D residue 108 TYR Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 265 VAL Chi-restraints excluded: chain D residue 350 ASP Chi-restraints excluded: chain D residue 493 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 197 optimal weight: 9.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 0.0870 chunk 132 optimal weight: 0.5980 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 30.0000 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 8.9990 chunk 244 optimal weight: 9.9990 chunk 183 optimal weight: 9.9990 chunk 111 optimal weight: 6.9990 overall best weight: 3.7364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 120 GLN B 150 GLN B 162 GLN B 181 GLN B 222 HIS ** B 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 455 ASN B 458 ASN B 463 GLN B 562 GLN B 566 GLN B 594 GLN B 610 ASN B 650 GLN B 713 GLN ** B 742 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 765 GLN B 834 HIS B 848 GLN B 944 GLN ** B1112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1134 HIS B1150 HIS ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 HIS C 191 GLN C 336 HIS C 390 HIS C 570 GLN C 614 GLN C 749 GLN C 759 HIS C 793 ASN C 822 GLN C 843 HIS C 883 GLN C 925 GLN ** C 958 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 960 GLN C1091 GLN C1108 GLN D 22 GLN D 89 GLN D 110 ASN D 115 ASN D 128 HIS D 251 GLN D 300 GLN D 469 HIS D 495 ASN D 523 GLN Total number of N/Q/H flips: 46 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.074345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.054902 restraints weight = 135984.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.056786 restraints weight = 77485.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.058010 restraints weight = 53584.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.058830 restraints weight = 41936.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.059330 restraints weight = 35519.245| |-----------------------------------------------------------------------------| r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.2346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 24452 Z= 0.172 Angle : 0.650 14.335 33409 Z= 0.326 Chirality : 0.040 0.199 3673 Planarity : 0.005 0.062 4205 Dihedral : 13.492 78.861 3732 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.73 % Allowed : 10.23 % Favored : 87.04 % 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: -1.41 (0.14), residues: 2837 helix: -0.16 (0.13), residues: 1407 sheet: -0.54 (0.29), residues: 281 loop : -1.96 (0.15), residues: 1149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 974 TYR 0.016 0.002 TYR B 430 PHE 0.016 0.001 PHE C 193 TRP 0.026 0.001 TRP B 652 HIS 0.006 0.001 HIS B 956 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.17 (24452) covalent geometry : angle 0.64994 / 0.33 (33409) hydrogen bonds : bond 0.03946 / 2.64 ( 1097) hydrogen bonds : angle 4.54558 / 3.27 ( 3179) *********************** 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 296 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 230 time to evaluate : 0.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 121 MET cc_start: 0.8696 (tpp) cc_final: 0.8388 (tpp) REVERT: B 354 MET cc_start: 0.8170 (mtt) cc_final: 0.7809 (mtm) REVERT: B 431 MET cc_start: 0.8911 (mtm) cc_final: 0.8624 (mtp) REVERT: B 501 MET cc_start: 0.9019 (mtm) cc_final: 0.8210 (mtm) REVERT: B 518 MET cc_start: 0.7794 (mmm) cc_final: 0.7187 (mmm) REVERT: B 541 MET cc_start: 0.8587 (mtp) cc_final: 0.7649 (tpp) REVERT: B 594 GLN cc_start: 0.8824 (tp40) cc_final: 0.8384 (tp-100) REVERT: B 658 MET cc_start: 0.9053 (tpp) cc_final: 0.8809 (tpp) REVERT: B 694 LEU cc_start: 0.9325 (mt) cc_final: 0.9110 (mt) REVERT: B 711 LEU cc_start: 0.9668 (tp) cc_final: 0.9449 (tp) REVERT: B 753 TRP cc_start: 0.9101 (OUTLIER) cc_final: 0.7760 (t60) REVERT: B 964 PHE cc_start: 0.8299 (m-80) cc_final: 0.7866 (m-10) REVERT: B 1032 ILE cc_start: 0.9142 (mt) cc_final: 0.8893 (mm) REVERT: B 1035 GLN cc_start: 0.9273 (mt0) cc_final: 0.8897 (pp30) REVERT: B 1111 TYR cc_start: 0.8442 (OUTLIER) cc_final: 0.8175 (p90) REVERT: C 1 MET cc_start: 0.6986 (tpp) cc_final: 0.6648 (tmm) REVERT: C 50 LEU cc_start: 0.9276 (mt) cc_final: 0.9057 (tt) REVERT: C 91 MET cc_start: 0.8481 (mtm) cc_final: 0.8176 (mtp) REVERT: C 133 ASP cc_start: 0.8902 (t0) cc_final: 0.8543 (t0) REVERT: C 165 GLN cc_start: 0.9100 (mt0) cc_final: 0.8779 (mt0) REVERT: C 227 LEU cc_start: 0.9596 (mt) cc_final: 0.9148 (pp) REVERT: C 408 ILE cc_start: 0.9395 (mt) cc_final: 0.8993 (pt) REVERT: C 471 LEU cc_start: 0.8984 (mt) cc_final: 0.8610 (pp) REVERT: C 591 CYS cc_start: 0.8308 (OUTLIER) cc_final: 0.7935 (t) REVERT: C 667 MET cc_start: 0.6256 (ttm) cc_final: 0.5305 (ttm) REVERT: C 787 MET cc_start: 0.7256 (pmm) cc_final: 0.6913 (pmm) REVERT: C 906 ASP cc_start: 0.8283 (m-30) cc_final: 0.7982 (t0) REVERT: C 1102 MET cc_start: 0.9328 (ttt) cc_final: 0.9006 (ttp) REVERT: D 25 LEU cc_start: 0.9340 (mt) cc_final: 0.9125 (pp) REVERT: D 108 TYR cc_start: 0.6406 (OUTLIER) cc_final: 0.5854 (p90) REVERT: D 273 MET cc_start: 0.7785 (mtm) cc_final: 0.7274 (ttp) REVERT: D 278 MET cc_start: 0.8807 (mtm) cc_final: 0.8393 (ptp) REVERT: D 471 HIS cc_start: 0.8304 (m90) cc_final: 0.7876 (m-70) REVERT: D 533 THR cc_start: 0.9189 (OUTLIER) cc_final: 0.8906 (p) REVERT: D 536 MET cc_start: 0.5419 (tpt) cc_final: 0.4997 (tpt) REVERT: D 564 GLU cc_start: 0.6728 (mm-30) cc_final: 0.5720 (tp30) outliers start: 66 outliers final: 34 residues processed: 281 average time/residue: 0.1459 time to fit residues: 67.7902 Evaluate side-chains 231 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 192 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 614 SER Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain B residue 699 THR Chi-restraints excluded: chain B residue 753 TRP Chi-restraints excluded: chain B residue 757 ILE Chi-restraints excluded: chain B residue 954 PHE Chi-restraints excluded: chain B residue 1093 TYR Chi-restraints excluded: chain B residue 1111 TYR Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 506 ILE Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 591 CYS Chi-restraints excluded: chain C residue 632 VAL Chi-restraints excluded: chain C residue 684 VAL Chi-restraints excluded: chain C residue 821 VAL Chi-restraints excluded: chain C residue 889 VAL Chi-restraints excluded: chain C residue 970 SER Chi-restraints excluded: chain C residue 1116 LEU Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 108 TYR Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 265 VAL Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 268 VAL Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 300 GLN Chi-restraints excluded: chain D residue 350 ASP Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 533 THR Chi-restraints excluded: chain D residue 579 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 248 optimal weight: 2.9990 chunk 212 optimal weight: 10.0000 chunk 233 optimal weight: 5.9990 chunk 167 optimal weight: 0.9980 chunk 232 optimal weight: 0.3980 chunk 200 optimal weight: 8.9990 chunk 90 optimal weight: 10.0000 chunk 275 optimal weight: 8.9990 chunk 101 optimal weight: 30.0000 chunk 270 optimal weight: 6.9990 chunk 125 optimal weight: 9.9990 overall best weight: 3.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 742 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1072 HIS ** B1084 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1112 GLN C 137 GLN ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 510 ASN ** C 958 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 110 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.072280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.053052 restraints weight = 137802.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.054850 restraints weight = 78139.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.056049 restraints weight = 53909.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.056817 restraints weight = 42000.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.057320 restraints weight = 35705.971| |-----------------------------------------------------------------------------| r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.2928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 24452 Z= 0.151 Angle : 0.593 11.535 33409 Z= 0.299 Chirality : 0.039 0.145 3673 Planarity : 0.004 0.060 4205 Dihedral : 13.578 83.503 3717 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.95 % Allowed : 11.26 % Favored : 86.79 % 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 (0.15), residues: 2837 helix: 0.64 (0.14), residues: 1435 sheet: -0.37 (0.29), residues: 281 loop : -1.75 (0.16), residues: 1121 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 974 TYR 0.013 0.001 TYR C 878 PHE 0.014 0.001 PHE B 184 TRP 0.013 0.001 TRP C 169 HIS 0.004 0.001 HIS C 377 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.15 (24452) covalent geometry : angle 0.59282 / 0.30 (33409) hydrogen bonds : bond 0.03532 / 2.37 ( 1097) hydrogen bonds : angle 4.25949 / 3.05 ( 3179) *********************** 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 244 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 197 time to evaluate : 0.881 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 264 LYS cc_start: 0.9121 (pttm) cc_final: 0.8807 (pttm) REVERT: B 354 MET cc_start: 0.8192 (mtt) cc_final: 0.7821 (mtm) REVERT: B 431 MET cc_start: 0.8895 (mtm) cc_final: 0.8651 (mtp) REVERT: B 501 MET cc_start: 0.8945 (mtm) cc_final: 0.8450 (mtm) REVERT: B 518 MET cc_start: 0.8059 (mmm) cc_final: 0.7231 (mmm) REVERT: B 541 MET cc_start: 0.8545 (mtp) cc_final: 0.7573 (tpp) REVERT: B 594 GLN cc_start: 0.8880 (tp40) cc_final: 0.8486 (tp40) REVERT: B 658 MET cc_start: 0.9199 (tpp) cc_final: 0.8897 (tpp) REVERT: B 753 TRP cc_start: 0.9121 (OUTLIER) cc_final: 0.7872 (t60) REVERT: B 798 ASP cc_start: 0.8575 (t0) cc_final: 0.8273 (t0) REVERT: B 944 GLN cc_start: 0.9063 (mt0) cc_final: 0.8708 (mm-40) REVERT: B 964 PHE cc_start: 0.8339 (m-80) cc_final: 0.7996 (m-10) REVERT: B 1035 GLN cc_start: 0.9267 (mt0) cc_final: 0.8921 (pp30) REVERT: B 1111 TYR cc_start: 0.8616 (OUTLIER) cc_final: 0.8255 (p90) REVERT: B 1168 MET cc_start: 0.6224 (mmp) cc_final: 0.5886 (mmt) REVERT: B 1171 MET cc_start: 0.7282 (ptt) cc_final: 0.7079 (ppp) REVERT: C 1 MET cc_start: 0.7025 (tpp) cc_final: 0.6682 (tmm) REVERT: C 50 LEU cc_start: 0.9300 (mt) cc_final: 0.9068 (tt) REVERT: C 91 MET cc_start: 0.8559 (mtm) cc_final: 0.8205 (mtp) REVERT: C 133 ASP cc_start: 0.8901 (t0) cc_final: 0.8447 (t0) REVERT: C 227 LEU cc_start: 0.9600 (mt) cc_final: 0.9151 (pp) REVERT: C 408 ILE cc_start: 0.9455 (mt) cc_final: 0.9055 (pt) REVERT: C 471 LEU cc_start: 0.8968 (mt) cc_final: 0.8630 (pp) REVERT: C 591 CYS cc_start: 0.8377 (OUTLIER) cc_final: 0.8097 (t) REVERT: C 667 MET cc_start: 0.6257 (ttm) cc_final: 0.5420 (ttm) REVERT: C 906 ASP cc_start: 0.8306 (m-30) cc_final: 0.8032 (t0) REVERT: C 1102 MET cc_start: 0.9364 (ttt) cc_final: 0.9063 (ttp) REVERT: D 25 LEU cc_start: 0.9301 (mt) cc_final: 0.9082 (pp) REVERT: D 100 MET cc_start: 0.8454 (mpp) cc_final: 0.8179 (mpp) REVERT: D 108 TYR cc_start: 0.6455 (OUTLIER) cc_final: 0.6005 (p90) REVERT: D 112 MET cc_start: 0.8611 (ttm) cc_final: 0.8263 (ttm) REVERT: D 273 MET cc_start: 0.7847 (mtm) cc_final: 0.7485 (ttp) REVERT: D 278 MET cc_start: 0.8901 (mtm) cc_final: 0.8437 (ptp) REVERT: D 471 HIS cc_start: 0.8299 (m90) cc_final: 0.7801 (m-70) REVERT: D 514 MET cc_start: 0.7926 (mmm) cc_final: 0.7661 (mmm) REVERT: D 520 LYS cc_start: 0.8864 (tttt) cc_final: 0.8534 (mtpt) REVERT: D 536 MET cc_start: 0.4843 (tpt) cc_final: 0.4468 (tpt) REVERT: D 564 GLU cc_start: 0.6682 (mm-30) cc_final: 0.5671 (tp30) outliers start: 47 outliers final: 30 residues processed: 234 average time/residue: 0.1458 time to fit residues: 57.1304 Evaluate side-chains 206 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 172 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 614 SER Chi-restraints excluded: chain B residue 699 THR Chi-restraints excluded: chain B residue 753 TRP Chi-restraints excluded: chain B residue 954 PHE Chi-restraints excluded: chain B residue 1093 TYR Chi-restraints excluded: chain B residue 1111 TYR Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 506 ILE Chi-restraints excluded: chain C residue 591 CYS Chi-restraints excluded: chain C residue 632 VAL Chi-restraints excluded: chain C residue 660 ASN Chi-restraints excluded: chain C residue 821 VAL Chi-restraints excluded: chain C residue 970 SER Chi-restraints excluded: chain C residue 1116 LEU Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 108 TYR Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 179 THR Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 268 VAL Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 350 ASP Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 533 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: 7.9990 chunk 231 optimal weight: 20.0000 chunk 172 optimal weight: 10.0000 chunk 101 optimal weight: 30.0000 chunk 259 optimal weight: 0.7980 chunk 196 optimal weight: 9.9990 chunk 34 optimal weight: 7.9990 chunk 220 optimal weight: 0.0020 chunk 25 optimal weight: 8.9990 chunk 26 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 overall best weight: 5.1594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 742 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 725 GLN ** C 960 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 328 GLN D 471 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.069312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.050328 restraints weight = 139713.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.051980 restraints weight = 79595.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.053070 restraints weight = 55607.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.053773 restraints weight = 43951.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.054239 restraints weight = 37596.614| |-----------------------------------------------------------------------------| r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.3629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 24452 Z= 0.201 Angle : 0.631 10.829 33409 Z= 0.322 Chirality : 0.040 0.161 3673 Planarity : 0.004 0.073 4205 Dihedral : 13.805 86.823 3716 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.32 % Allowed : 10.68 % Favored : 87.00 % 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: -0.15 (0.15), residues: 2837 helix: 1.06 (0.14), residues: 1443 sheet: -0.37 (0.30), residues: 282 loop : -1.59 (0.17), residues: 1112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 947 TYR 0.015 0.002 TYR C1050 PHE 0.014 0.002 PHE B 461 TRP 0.016 0.001 TRP B 272 HIS 0.007 0.001 HIS D 289 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.20 (24452) covalent geometry : angle 0.63135 / 0.32 (33409) hydrogen bonds : bond 0.03928 / 2.59 ( 1097) hydrogen bonds : angle 4.22478 / 3.00 ( 3179) *********************** 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 232 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 176 time to evaluate : 0.914 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 264 LYS cc_start: 0.9185 (pttm) cc_final: 0.8808 (pttm) REVERT: B 354 MET cc_start: 0.8140 (mtt) cc_final: 0.7761 (mtm) REVERT: B 431 MET cc_start: 0.8996 (mtm) cc_final: 0.8757 (mtp) REVERT: B 518 MET cc_start: 0.8211 (mmm) cc_final: 0.7373 (mmm) REVERT: B 541 MET cc_start: 0.8533 (mtp) cc_final: 0.7497 (tpp) REVERT: B 594 GLN cc_start: 0.8955 (tp40) cc_final: 0.8363 (tp-100) REVERT: B 620 MET cc_start: 0.8960 (ptm) cc_final: 0.8732 (ppp) REVERT: B 658 MET cc_start: 0.9257 (tpp) cc_final: 0.8711 (tpt) REVERT: B 753 TRP cc_start: 0.9201 (OUTLIER) cc_final: 0.7954 (t60) REVERT: B 798 ASP cc_start: 0.8622 (t0) cc_final: 0.8319 (t0) REVERT: B 1061 MET cc_start: 0.6377 (tpp) cc_final: 0.6059 (tpp) REVERT: B 1111 TYR cc_start: 0.8714 (OUTLIER) cc_final: 0.8352 (p90) REVERT: B 1168 MET cc_start: 0.6818 (mmp) cc_final: 0.6323 (mmm) REVERT: B 1171 MET cc_start: 0.7618 (ptt) cc_final: 0.7323 (ppp) REVERT: C 1 MET cc_start: 0.7313 (tpp) cc_final: 0.6956 (tmm) REVERT: C 133 ASP cc_start: 0.8931 (t0) cc_final: 0.8680 (t0) REVERT: C 227 LEU cc_start: 0.9622 (mt) cc_final: 0.9197 (pp) REVERT: C 408 ILE cc_start: 0.9551 (mt) cc_final: 0.9166 (pt) REVERT: C 411 MET cc_start: 0.8188 (mmt) cc_final: 0.7893 (mmt) REVERT: C 667 MET cc_start: 0.6177 (ttm) cc_final: 0.5282 (ttm) REVERT: C 906 ASP cc_start: 0.8439 (m-30) cc_final: 0.8101 (t0) REVERT: C 1102 MET cc_start: 0.9436 (ttt) cc_final: 0.9189 (ttp) REVERT: D 25 LEU cc_start: 0.9332 (mt) cc_final: 0.9099 (pp) REVERT: D 100 MET cc_start: 0.8800 (mpp) cc_final: 0.8431 (mpp) REVERT: D 108 TYR cc_start: 0.6573 (OUTLIER) cc_final: 0.6106 (p90) REVERT: D 112 MET cc_start: 0.8587 (ttm) cc_final: 0.8240 (ttm) REVERT: D 278 MET cc_start: 0.8940 (mtm) cc_final: 0.8695 (mtm) REVERT: D 471 HIS cc_start: 0.8460 (m170) cc_final: 0.7920 (m-70) REVERT: D 536 MET cc_start: 0.5104 (tpt) cc_final: 0.4780 (tpt) outliers start: 56 outliers final: 37 residues processed: 219 average time/residue: 0.1470 time to fit residues: 53.8626 Evaluate side-chains 201 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 161 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 388 ASP Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 614 SER Chi-restraints excluded: chain B residue 699 THR Chi-restraints excluded: chain B residue 753 TRP Chi-restraints excluded: chain B residue 813 CYS Chi-restraints excluded: chain B residue 1093 TYR Chi-restraints excluded: chain B residue 1111 TYR Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 506 ILE Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 632 VAL Chi-restraints excluded: chain C residue 660 ASN Chi-restraints excluded: chain C residue 689 LEU Chi-restraints excluded: chain C residue 821 VAL Chi-restraints excluded: chain C residue 889 VAL Chi-restraints excluded: chain C residue 970 SER Chi-restraints excluded: chain C residue 1116 LEU Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 108 TYR Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 179 THR Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 265 VAL Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 268 VAL Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 350 ASP Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 533 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: 20.0000 chunk 13 optimal weight: 8.9990 chunk 70 optimal weight: 3.9990 chunk 152 optimal weight: 1.9990 chunk 113 optimal weight: 3.9990 chunk 256 optimal weight: 30.0000 chunk 72 optimal weight: 0.5980 chunk 267 optimal weight: 40.0000 chunk 115 optimal weight: 0.7980 chunk 111 optimal weight: 40.0000 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 742 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 958 GLN ** C 960 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 439 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 = 0.3835 r_free = 0.3835 target = 0.069978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.050789 restraints weight = 137993.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.052484 restraints weight = 78277.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.053608 restraints weight = 54344.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.054329 restraints weight = 42770.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.054808 restraints weight = 36552.434| |-----------------------------------------------------------------------------| r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.3757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 24452 Z= 0.113 Angle : 0.559 10.832 33409 Z= 0.278 Chirality : 0.039 0.150 3673 Planarity : 0.004 0.053 4205 Dihedral : 13.785 88.147 3715 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.82 % Allowed : 11.84 % Favored : 86.34 % 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: 0.17 (0.16), residues: 2837 helix: 1.37 (0.14), residues: 1440 sheet: -0.33 (0.30), residues: 277 loop : -1.46 (0.17), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 974 TYR 0.012 0.001 TYR B 394 PHE 0.009 0.001 PHE B 588 TRP 0.023 0.001 TRP B 972 HIS 0.004 0.001 HIS C 377 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 (24452) covalent geometry : angle 0.55899 / 0.28 (33409) hydrogen bonds : bond 0.03276 / 2.19 ( 1097) hydrogen bonds : angle 3.99528 / 2.84 ( 3179) *********************** 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 224 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 180 time to evaluate : 0.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 269 ILE cc_start: 0.7580 (OUTLIER) cc_final: 0.6636 (mm) REVERT: B 354 MET cc_start: 0.8175 (mtt) cc_final: 0.7800 (mtm) REVERT: B 431 MET cc_start: 0.8952 (mtm) cc_final: 0.8728 (mtp) REVERT: B 518 MET cc_start: 0.8250 (mmm) cc_final: 0.7860 (mmm) REVERT: B 541 MET cc_start: 0.8581 (mtp) cc_final: 0.7575 (tpp) REVERT: B 594 GLN cc_start: 0.8888 (tp40) cc_final: 0.8322 (tp-100) REVERT: B 658 MET cc_start: 0.9246 (tpp) cc_final: 0.9008 (tpp) REVERT: B 753 TRP cc_start: 0.9158 (OUTLIER) cc_final: 0.7920 (t60) REVERT: B 798 ASP cc_start: 0.8531 (t0) cc_final: 0.8292 (t0) REVERT: B 1061 MET cc_start: 0.6285 (tpp) cc_final: 0.6041 (tpp) REVERT: B 1111 TYR cc_start: 0.8670 (OUTLIER) cc_final: 0.8320 (p90) REVERT: B 1168 MET cc_start: 0.6730 (mmp) cc_final: 0.6306 (mmp) REVERT: B 1171 MET cc_start: 0.7625 (ptt) cc_final: 0.7304 (ppp) REVERT: C 1 MET cc_start: 0.7212 (tpp) cc_final: 0.6898 (tmm) REVERT: C 17 MET cc_start: 0.9086 (ptm) cc_final: 0.8854 (ptp) REVERT: C 50 LEU cc_start: 0.9303 (mm) cc_final: 0.9029 (tt) REVERT: C 91 MET cc_start: 0.8503 (mtp) cc_final: 0.8279 (mtp) REVERT: C 133 ASP cc_start: 0.8955 (t0) cc_final: 0.8628 (t0) REVERT: C 227 LEU cc_start: 0.9600 (mt) cc_final: 0.9178 (pp) REVERT: C 408 ILE cc_start: 0.9555 (mt) cc_final: 0.9192 (pt) REVERT: C 602 ASP cc_start: 0.8658 (t0) cc_final: 0.8445 (t70) REVERT: C 660 ASN cc_start: 0.7612 (OUTLIER) cc_final: 0.7076 (m-40) REVERT: C 667 MET cc_start: 0.6085 (ttm) cc_final: 0.5215 (ttm) REVERT: C 787 MET cc_start: 0.7455 (pmm) cc_final: 0.7158 (pmm) REVERT: C 906 ASP cc_start: 0.8401 (m-30) cc_final: 0.8046 (t0) REVERT: C 1102 MET cc_start: 0.9427 (ttt) cc_final: 0.9191 (ttp) REVERT: D 25 LEU cc_start: 0.9281 (mt) cc_final: 0.9053 (pp) REVERT: D 100 MET cc_start: 0.8848 (mpp) cc_final: 0.8563 (mpp) REVERT: D 108 TYR cc_start: 0.6448 (OUTLIER) cc_final: 0.6004 (p90) REVERT: D 112 MET cc_start: 0.8562 (ttm) cc_final: 0.8215 (ttm) REVERT: D 149 ASP cc_start: 0.8867 (m-30) cc_final: 0.8649 (p0) REVERT: D 273 MET cc_start: 0.8098 (OUTLIER) cc_final: 0.7862 (ptt) REVERT: D 278 MET cc_start: 0.8874 (mtm) cc_final: 0.8220 (ptp) REVERT: D 407 MET cc_start: 0.8949 (mpp) cc_final: 0.8675 (mpp) REVERT: D 471 HIS cc_start: 0.8469 (m170) cc_final: 0.7938 (m-70) REVERT: D 520 LYS cc_start: 0.8915 (tttt) cc_final: 0.8589 (mtpt) REVERT: D 536 MET cc_start: 0.5110 (tpt) cc_final: 0.4542 (tpp) outliers start: 44 outliers final: 25 residues processed: 215 average time/residue: 0.1497 time to fit residues: 53.1667 Evaluate side-chains 198 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 167 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 254 ARG Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 388 ASP Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 753 TRP Chi-restraints excluded: chain B residue 1093 TYR Chi-restraints excluded: chain B residue 1111 TYR Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 591 CYS Chi-restraints excluded: chain C residue 632 VAL Chi-restraints excluded: chain C residue 660 ASN Chi-restraints excluded: chain C residue 821 VAL Chi-restraints excluded: chain C residue 889 VAL Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 108 TYR Chi-restraints excluded: chain D residue 179 THR Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 273 MET Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 350 ASP Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 533 THR 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: 0.0070 chunk 16 optimal weight: 4.9990 chunk 219 optimal weight: 10.0000 chunk 286 optimal weight: 50.0000 chunk 96 optimal weight: 30.0000 chunk 165 optimal weight: 10.0000 chunk 195 optimal weight: 10.0000 chunk 84 optimal weight: 10.0000 chunk 176 optimal weight: 9.9990 chunk 201 optimal weight: 9.9990 overall best weight: 7.0006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 463 GLN ** B 742 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 769 HIS B 943 HIS B1133 HIS ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 822 GLN C 951 GLN ** C 960 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.066471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.047810 restraints weight = 144286.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.049377 restraints weight = 82543.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.050422 restraints weight = 57910.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.051073 restraints weight = 45793.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.051464 restraints weight = 39498.964| |-----------------------------------------------------------------------------| r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.4407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 24452 Z= 0.245 Angle : 0.690 9.999 33409 Z= 0.347 Chirality : 0.042 0.293 3673 Planarity : 0.004 0.050 4205 Dihedral : 13.938 88.577 3714 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.65 % Allowed : 11.88 % Favored : 85.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.15), residues: 2837 helix: 1.11 (0.14), residues: 1453 sheet: -0.42 (0.30), residues: 282 loop : -1.53 (0.17), residues: 1102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 974 TYR 0.027 0.002 TYR C 550 PHE 0.015 0.002 PHE B 475 TRP 0.020 0.002 TRP B 272 HIS 0.011 0.001 HIS D 289 Details of bonding type rmsd/Z covalent geometry : bond 0.00534 / 0.25 (24452) covalent geometry : angle 0.69034 / 0.35 (33409) hydrogen bonds : bond 0.04436 / 2.93 ( 1097) hydrogen bonds : angle 4.34889 / 3.09 ( 3179) *********************** 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 219 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 155 time to evaluate : 0.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 264 LYS cc_start: 0.9214 (pttp) cc_final: 0.8851 (pttm) REVERT: B 269 ILE cc_start: 0.7796 (OUTLIER) cc_final: 0.6843 (mm) REVERT: B 354 MET cc_start: 0.8152 (mtt) cc_final: 0.7733 (mtm) REVERT: B 431 MET cc_start: 0.8996 (mtm) cc_final: 0.8762 (mtp) REVERT: B 518 MET cc_start: 0.8462 (mmm) cc_final: 0.7631 (mmm) REVERT: B 541 MET cc_start: 0.8599 (mtp) cc_final: 0.7503 (tpp) REVERT: B 594 GLN cc_start: 0.8989 (tp40) cc_final: 0.8369 (tp-100) REVERT: B 753 TRP cc_start: 0.9230 (OUTLIER) cc_final: 0.7964 (t60) REVERT: B 798 ASP cc_start: 0.8565 (t0) cc_final: 0.8299 (t0) REVERT: B 1111 TYR cc_start: 0.8671 (OUTLIER) cc_final: 0.8097 (p90) REVERT: B 1114 TYR cc_start: 0.9163 (m-10) cc_final: 0.8913 (m-10) REVERT: B 1168 MET cc_start: 0.7164 (mmp) cc_final: 0.6678 (mmp) REVERT: C 1 MET cc_start: 0.7309 (tpp) cc_final: 0.6986 (tmm) REVERT: C 96 MET cc_start: 0.8855 (tpp) cc_final: 0.8444 (tpp) REVERT: C 102 LEU cc_start: 0.9081 (OUTLIER) cc_final: 0.8788 (mm) REVERT: C 133 ASP cc_start: 0.8969 (t0) cc_final: 0.8704 (t0) REVERT: C 408 ILE cc_start: 0.9613 (mt) cc_final: 0.9287 (pt) REVERT: C 537 MET cc_start: 0.7099 (tpp) cc_final: 0.6142 (tpp) REVERT: C 660 ASN cc_start: 0.7797 (OUTLIER) cc_final: 0.7217 (m-40) REVERT: C 667 MET cc_start: 0.6165 (ttm) cc_final: 0.5298 (ttm) REVERT: C 787 MET cc_start: 0.7512 (pmm) cc_final: 0.7204 (pmm) REVERT: C 906 ASP cc_start: 0.8516 (m-30) cc_final: 0.8220 (t0) REVERT: C 1102 MET cc_start: 0.9462 (ttt) cc_final: 0.9242 (ttp) REVERT: D 100 MET cc_start: 0.8957 (mpp) cc_final: 0.8750 (mpp) REVERT: D 108 TYR cc_start: 0.6727 (OUTLIER) cc_final: 0.6134 (p90) REVERT: D 112 MET cc_start: 0.8593 (ttm) cc_final: 0.8126 (ttm) REVERT: D 278 MET cc_start: 0.8833 (mtm) cc_final: 0.8560 (mtm) REVERT: D 471 HIS cc_start: 0.8646 (m170) cc_final: 0.8144 (m90) REVERT: D 483 MET cc_start: 0.1504 (tmm) cc_final: 0.0859 (tpp) REVERT: D 520 LYS cc_start: 0.9021 (tttt) cc_final: 0.8689 (mtpt) REVERT: D 536 MET cc_start: 0.5147 (tpt) cc_final: 0.4827 (tpt) outliers start: 64 outliers final: 37 residues processed: 205 average time/residue: 0.1475 time to fit residues: 50.2311 Evaluate side-chains 185 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 142 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 254 ARG Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 388 ASP Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 699 THR Chi-restraints excluded: chain B residue 739 VAL Chi-restraints excluded: chain B residue 753 TRP Chi-restraints excluded: chain B residue 813 CYS Chi-restraints excluded: chain B residue 1093 TYR Chi-restraints excluded: chain B residue 1111 TYR Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 499 GLU Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 632 VAL Chi-restraints excluded: chain C residue 660 ASN Chi-restraints excluded: chain C residue 689 LEU Chi-restraints excluded: chain C residue 821 VAL Chi-restraints excluded: chain C residue 889 VAL Chi-restraints excluded: chain C residue 970 SER Chi-restraints excluded: chain C residue 1035 LEU Chi-restraints excluded: chain C residue 1106 VAL Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 108 TYR Chi-restraints excluded: chain D residue 179 THR Chi-restraints excluded: chain D residue 191 MET Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 268 VAL Chi-restraints excluded: chain D residue 273 MET Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 350 ASP Chi-restraints excluded: chain D residue 422 LEU 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: 4.9990 chunk 262 optimal weight: 40.0000 chunk 10 optimal weight: 9.9990 chunk 276 optimal weight: 10.0000 chunk 212 optimal weight: 8.9990 chunk 120 optimal weight: 9.9990 chunk 170 optimal weight: 0.2980 chunk 55 optimal weight: 5.9990 chunk 185 optimal weight: 9.9990 chunk 243 optimal weight: 2.9990 chunk 238 optimal weight: 7.9990 overall best weight: 4.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 742 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 960 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 = 0.3777 r_free = 0.3777 target = 0.066850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.048507 restraints weight = 142207.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.050043 restraints weight = 82628.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.051051 restraints weight = 58340.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.051709 restraints weight = 46286.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.052146 restraints weight = 39821.573| |-----------------------------------------------------------------------------| r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.4592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 24452 Z= 0.162 Angle : 0.613 11.567 33409 Z= 0.310 Chirality : 0.041 0.253 3673 Planarity : 0.004 0.052 4205 Dihedral : 13.991 88.911 3714 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.82 % Allowed : 13.04 % Favored : 85.13 % 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: 0.18 (0.16), residues: 2837 helix: 1.35 (0.14), residues: 1447 sheet: -0.35 (0.30), residues: 280 loop : -1.43 (0.17), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 23 TYR 0.016 0.001 TYR B 394 PHE 0.018 0.001 PHE C 19 TRP 0.015 0.001 TRP B 272 HIS 0.005 0.001 HIS D 289 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.16 (24452) covalent geometry : angle 0.61305 / 0.31 (33409) hydrogen bonds : bond 0.03744 / 2.49 ( 1097) hydrogen bonds : angle 4.19518 / 2.97 ( 3179) *********************** 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 195 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 151 time to evaluate : 0.953 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 264 LYS cc_start: 0.9197 (pttp) cc_final: 0.8827 (pttm) REVERT: B 269 ILE cc_start: 0.7791 (OUTLIER) cc_final: 0.6866 (mm) REVERT: B 354 MET cc_start: 0.8155 (mtt) cc_final: 0.7718 (mtm) REVERT: B 501 MET cc_start: 0.8911 (mtm) cc_final: 0.8399 (mpp) REVERT: B 518 MET cc_start: 0.8492 (mmm) cc_final: 0.7595 (mmm) REVERT: B 541 MET cc_start: 0.8581 (mtp) cc_final: 0.7499 (tpp) REVERT: B 594 GLN cc_start: 0.8889 (tp40) cc_final: 0.8292 (tp-100) REVERT: B 753 TRP cc_start: 0.9157 (OUTLIER) cc_final: 0.8011 (t60) REVERT: B 798 ASP cc_start: 0.8554 (t0) cc_final: 0.8275 (t0) REVERT: B 1061 MET cc_start: 0.6528 (tpp) cc_final: 0.6237 (tpp) REVERT: B 1111 TYR cc_start: 0.8674 (OUTLIER) cc_final: 0.8288 (p90) REVERT: C 17 MET cc_start: 0.9042 (ptm) cc_final: 0.8813 (ptp) REVERT: C 408 ILE cc_start: 0.9589 (mt) cc_final: 0.9284 (pt) REVERT: C 537 MET cc_start: 0.6917 (tpp) cc_final: 0.6073 (tpp) REVERT: C 660 ASN cc_start: 0.7585 (OUTLIER) cc_final: 0.7013 (m-40) REVERT: C 667 MET cc_start: 0.6060 (ttm) cc_final: 0.5253 (ttm) REVERT: C 697 MET cc_start: 0.8228 (mtt) cc_final: 0.7087 (mtt) REVERT: C 746 VAL cc_start: 0.8595 (OUTLIER) cc_final: 0.8379 (p) REVERT: C 787 MET cc_start: 0.7664 (pmm) cc_final: 0.7380 (pmm) REVERT: C 906 ASP cc_start: 0.8348 (m-30) cc_final: 0.8049 (t0) REVERT: C 1102 MET cc_start: 0.9422 (ttt) cc_final: 0.9196 (ttp) REVERT: D 25 LEU cc_start: 0.9212 (mt) cc_final: 0.8949 (pp) REVERT: D 100 MET cc_start: 0.8893 (mpp) cc_final: 0.8692 (mpp) REVERT: D 108 TYR cc_start: 0.6564 (OUTLIER) cc_final: 0.6029 (p90) REVERT: D 112 MET cc_start: 0.8608 (ttm) cc_final: 0.8210 (ttm) REVERT: D 278 MET cc_start: 0.8782 (mtm) cc_final: 0.8093 (ptp) REVERT: D 471 HIS cc_start: 0.8713 (m170) cc_final: 0.8157 (m90) REVERT: D 483 MET cc_start: 0.0948 (tmm) cc_final: 0.0690 (tmm) REVERT: D 520 LYS cc_start: 0.9006 (tttt) cc_final: 0.8670 (mtpt) REVERT: D 536 MET cc_start: 0.5071 (tpt) cc_final: 0.4731 (tpt) outliers start: 44 outliers final: 26 residues processed: 190 average time/residue: 0.1549 time to fit residues: 48.9774 Evaluate side-chains 171 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 139 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 254 ARG Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 388 ASP Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 614 SER Chi-restraints excluded: chain B residue 753 TRP Chi-restraints excluded: chain B residue 1078 LEU Chi-restraints excluded: chain B residue 1093 TYR Chi-restraints excluded: chain B residue 1111 TYR Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 632 VAL Chi-restraints excluded: chain C residue 660 ASN Chi-restraints excluded: chain C residue 689 LEU Chi-restraints excluded: chain C residue 746 VAL Chi-restraints excluded: chain C residue 821 VAL Chi-restraints excluded: chain C residue 970 SER Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 108 TYR Chi-restraints excluded: chain D residue 179 THR Chi-restraints excluded: chain D residue 191 MET Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 273 MET Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 350 ASP 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: 10.0000 chunk 38 optimal weight: 9.9990 chunk 167 optimal weight: 3.9990 chunk 108 optimal weight: 5.9990 chunk 94 optimal weight: 20.0000 chunk 180 optimal weight: 0.0670 chunk 220 optimal weight: 10.0000 chunk 57 optimal weight: 2.9990 chunk 196 optimal weight: 7.9990 chunk 269 optimal weight: 4.9990 overall best weight: 3.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 742 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 958 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 960 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 65 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.066883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.048533 restraints weight = 141821.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.050110 restraints weight = 81760.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.051138 restraints weight = 57506.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.051799 restraints weight = 45611.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.052235 restraints weight = 39206.192| |-----------------------------------------------------------------------------| r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.4752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 24452 Z= 0.138 Angle : 0.603 15.956 33409 Z= 0.302 Chirality : 0.040 0.190 3673 Planarity : 0.004 0.131 4205 Dihedral : 13.954 87.701 3714 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.82 % Allowed : 13.42 % Favored : 84.76 % 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: 0.33 (0.16), residues: 2837 helix: 1.49 (0.14), residues: 1441 sheet: -0.29 (0.30), residues: 278 loop : -1.37 (0.17), residues: 1118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 75 TYR 0.025 0.001 TYR C 550 PHE 0.014 0.001 PHE D 512 TRP 0.014 0.001 TRP B 972 HIS 0.005 0.001 HIS D 289 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.14 (24452) covalent geometry : angle 0.60341 / 0.30 (33409) hydrogen bonds : bond 0.03630 / 2.41 ( 1097) hydrogen bonds : angle 4.07522 / 2.89 ( 3179) *********************** 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 191 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 147 time to evaluate : 0.975 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 264 LYS cc_start: 0.9216 (pttp) cc_final: 0.8860 (pttm) REVERT: B 269 ILE cc_start: 0.7824 (OUTLIER) cc_final: 0.6894 (mm) REVERT: B 354 MET cc_start: 0.8105 (mtt) cc_final: 0.7658 (mtm) REVERT: B 501 MET cc_start: 0.9098 (mtm) cc_final: 0.8420 (mpp) REVERT: B 518 MET cc_start: 0.8486 (mmm) cc_final: 0.7445 (mmm) REVERT: B 541 MET cc_start: 0.8576 (mtp) cc_final: 0.7470 (tpp) REVERT: B 594 GLN cc_start: 0.8901 (tp40) cc_final: 0.8270 (tp-100) REVERT: B 658 MET cc_start: 0.9119 (mmm) cc_final: 0.8786 (tpt) REVERT: B 753 TRP cc_start: 0.9175 (OUTLIER) cc_final: 0.8062 (t60) REVERT: B 798 ASP cc_start: 0.8580 (t0) cc_final: 0.8298 (t0) REVERT: B 1111 TYR cc_start: 0.8677 (OUTLIER) cc_final: 0.8299 (p90) REVERT: C 96 MET cc_start: 0.8673 (tpp) cc_final: 0.8232 (tpp) REVERT: C 408 ILE cc_start: 0.9595 (mt) cc_final: 0.9296 (pt) REVERT: C 537 MET cc_start: 0.6894 (tpp) cc_final: 0.6033 (tpp) REVERT: C 660 ASN cc_start: 0.7657 (OUTLIER) cc_final: 0.7099 (m-40) REVERT: C 667 MET cc_start: 0.5993 (ttm) cc_final: 0.5190 (ttm) REVERT: C 746 VAL cc_start: 0.8510 (OUTLIER) cc_final: 0.8303 (p) REVERT: C 787 MET cc_start: 0.7674 (pmm) cc_final: 0.7419 (pmm) REVERT: C 906 ASP cc_start: 0.8449 (m-30) cc_final: 0.8087 (t0) REVERT: C 1102 MET cc_start: 0.9454 (ttt) cc_final: 0.9243 (ttp) REVERT: D 25 LEU cc_start: 0.9222 (mt) cc_final: 0.8933 (pp) REVERT: D 100 MET cc_start: 0.8966 (mpp) cc_final: 0.8759 (mpp) REVERT: D 108 TYR cc_start: 0.6542 (OUTLIER) cc_final: 0.6008 (p90) REVERT: D 112 MET cc_start: 0.8587 (ttm) cc_final: 0.8187 (ttm) REVERT: D 273 MET cc_start: 0.8143 (OUTLIER) cc_final: 0.6349 (mmp) REVERT: D 278 MET cc_start: 0.8736 (mtm) cc_final: 0.8045 (ptp) REVERT: D 471 HIS cc_start: 0.8706 (m170) cc_final: 0.8150 (m90) REVERT: D 483 MET cc_start: 0.0844 (tmm) cc_final: 0.0644 (tmm) REVERT: D 504 ARG cc_start: 0.8342 (tpm170) cc_final: 0.8068 (tpm170) REVERT: D 536 MET cc_start: 0.5246 (tpt) cc_final: 0.4798 (tpt) outliers start: 44 outliers final: 28 residues processed: 184 average time/residue: 0.1476 time to fit residues: 45.7056 Evaluate side-chains 177 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 142 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 254 ARG Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 614 SER Chi-restraints excluded: chain B residue 699 THR Chi-restraints excluded: chain B residue 753 TRP Chi-restraints excluded: chain B residue 813 CYS Chi-restraints excluded: chain B residue 1093 TYR Chi-restraints excluded: chain B residue 1111 TYR Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 506 ILE Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 591 CYS Chi-restraints excluded: chain C residue 632 VAL Chi-restraints excluded: chain C residue 660 ASN Chi-restraints excluded: chain C residue 689 LEU Chi-restraints excluded: chain C residue 746 VAL Chi-restraints excluded: chain C residue 821 VAL Chi-restraints excluded: chain C residue 1035 LEU Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 108 TYR Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 179 THR Chi-restraints excluded: chain D residue 191 MET Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 273 MET Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 350 ASP 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: 6.9990 chunk 241 optimal weight: 20.0000 chunk 278 optimal weight: 5.9990 chunk 238 optimal weight: 4.9990 chunk 53 optimal weight: 6.9990 chunk 29 optimal weight: 5.9990 chunk 205 optimal weight: 0.0570 chunk 133 optimal weight: 9.9990 chunk 167 optimal weight: 9.9990 chunk 150 optimal weight: 2.9990 chunk 83 optimal weight: 30.0000 overall best weight: 4.0106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 109 GLN B 278 ASN ** B 742 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 958 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 960 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 50 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.066238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.048003 restraints weight = 143640.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.049574 restraints weight = 82936.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.050580 restraints weight = 58229.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.051240 restraints weight = 46362.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.051619 restraints weight = 39848.567| |-----------------------------------------------------------------------------| r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.4984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 24452 Z= 0.156 Angle : 0.619 15.395 33409 Z= 0.308 Chirality : 0.040 0.249 3673 Planarity : 0.004 0.063 4205 Dihedral : 13.990 89.791 3714 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.74 % Allowed : 13.62 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.16), residues: 2837 helix: 1.49 (0.14), residues: 1444 sheet: -0.26 (0.30), residues: 276 loop : -1.36 (0.18), residues: 1117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 974 TYR 0.024 0.001 TYR C 550 PHE 0.013 0.001 PHE C 19 TRP 0.013 0.001 TRP B 272 HIS 0.005 0.001 HIS D 289 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.16 (24452) covalent geometry : angle 0.61865 / 0.31 (33409) hydrogen bonds : bond 0.03679 / 2.45 ( 1097) hydrogen bonds : angle 4.09954 / 2.91 ( 3179) *********************** 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 186 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 144 time to evaluate : 0.899 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 264 LYS cc_start: 0.9208 (pttp) cc_final: 0.8838 (pttm) REVERT: B 269 ILE cc_start: 0.7986 (OUTLIER) cc_final: 0.7079 (mm) REVERT: B 354 MET cc_start: 0.8148 (mtt) cc_final: 0.7679 (mtm) REVERT: B 501 MET cc_start: 0.9028 (mtm) cc_final: 0.8387 (mpp) REVERT: B 518 MET cc_start: 0.8580 (mmm) cc_final: 0.7703 (mmm) REVERT: B 541 MET cc_start: 0.8585 (mtp) cc_final: 0.7478 (tpp) REVERT: B 594 GLN cc_start: 0.8840 (tp40) cc_final: 0.8242 (tp-100) REVERT: B 660 MET cc_start: 0.8358 (tpt) cc_final: 0.7551 (tpt) REVERT: B 753 TRP cc_start: 0.9135 (OUTLIER) cc_final: 0.8113 (t60) REVERT: B 798 ASP cc_start: 0.8513 (t0) cc_final: 0.8251 (t0) REVERT: B 1111 TYR cc_start: 0.8692 (OUTLIER) cc_final: 0.8425 (p90) REVERT: C 96 MET cc_start: 0.8747 (tpp) cc_final: 0.8335 (tpp) REVERT: C 408 ILE cc_start: 0.9580 (mt) cc_final: 0.9289 (pt) REVERT: C 537 MET cc_start: 0.6938 (tpp) cc_final: 0.6068 (tpp) REVERT: C 660 ASN cc_start: 0.7535 (OUTLIER) cc_final: 0.7011 (m-40) REVERT: C 667 MET cc_start: 0.6022 (ttm) cc_final: 0.5180 (ttm) REVERT: C 746 VAL cc_start: 0.8563 (OUTLIER) cc_final: 0.8354 (p) REVERT: C 787 MET cc_start: 0.7794 (pmm) cc_final: 0.7563 (pmm) REVERT: C 906 ASP cc_start: 0.8403 (m-30) cc_final: 0.8065 (t0) REVERT: C 1102 MET cc_start: 0.9432 (ttt) cc_final: 0.9215 (ttp) REVERT: D 25 LEU cc_start: 0.9217 (mt) cc_final: 0.8886 (pp) REVERT: D 100 MET cc_start: 0.8894 (mpp) cc_final: 0.8688 (mpp) REVERT: D 112 MET cc_start: 0.8636 (ttm) cc_final: 0.8207 (ttm) REVERT: D 273 MET cc_start: 0.8163 (OUTLIER) cc_final: 0.6324 (mmp) REVERT: D 278 MET cc_start: 0.8725 (mtm) cc_final: 0.8027 (ptp) REVERT: D 471 HIS cc_start: 0.8788 (m170) cc_final: 0.8208 (m90) REVERT: D 536 MET cc_start: 0.5240 (tpt) cc_final: 0.4776 (tpt) outliers start: 42 outliers final: 31 residues processed: 180 average time/residue: 0.1503 time to fit residues: 45.2862 Evaluate side-chains 176 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 139 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 254 ARG Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 614 SER Chi-restraints excluded: chain B residue 699 THR Chi-restraints excluded: chain B residue 753 TRP Chi-restraints excluded: chain B residue 1093 TYR Chi-restraints excluded: chain B residue 1111 TYR Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 506 ILE Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 591 CYS Chi-restraints excluded: chain C residue 632 VAL Chi-restraints excluded: chain C residue 660 ASN Chi-restraints excluded: chain C residue 689 LEU Chi-restraints excluded: chain C residue 746 VAL Chi-restraints excluded: chain C residue 821 VAL Chi-restraints excluded: chain C residue 889 VAL Chi-restraints excluded: chain C residue 970 SER Chi-restraints excluded: chain C residue 1035 LEU Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 108 TYR Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 179 THR Chi-restraints excluded: chain D residue 191 MET Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 273 MET Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 350 ASP 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: 4.9990 chunk 26 optimal weight: 9.9990 chunk 227 optimal weight: 5.9990 chunk 192 optimal weight: 5.9990 chunk 220 optimal weight: 10.0000 chunk 37 optimal weight: 10.0000 chunk 258 optimal weight: 3.9990 chunk 93 optimal weight: 0.1980 chunk 223 optimal weight: 0.1980 chunk 70 optimal weight: 20.0000 chunk 244 optimal weight: 0.7980 overall best weight: 2.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 742 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 321 GLN ** C 958 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 960 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 HIS ** 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 = 0.3779 r_free = 0.3779 target = 0.066880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.048431 restraints weight = 142060.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.050058 restraints weight = 80083.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.051112 restraints weight = 55626.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.051809 restraints weight = 43832.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.052265 restraints weight = 37436.253| |-----------------------------------------------------------------------------| r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.5031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 24452 Z= 0.116 Angle : 0.605 12.419 33409 Z= 0.302 Chirality : 0.040 0.238 3673 Planarity : 0.004 0.069 4205 Dihedral : 13.971 89.740 3714 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.24 % Allowed : 14.00 % Favored : 84.76 % 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: 1.65 (0.14), residues: 1436 sheet: -0.28 (0.30), residues: 278 loop : -1.29 (0.18), residues: 1123 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B1144 TYR 0.024 0.001 TYR B1081 PHE 0.014 0.001 PHE B 959 TRP 0.014 0.001 TRP B 972 HIS 0.003 0.001 HIS B 769 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.12 (24452) covalent geometry : angle 0.60511 / 0.30 (33409) hydrogen bonds : bond 0.03392 / 2.27 ( 1097) hydrogen bonds : angle 3.98429 / 2.83 ( 3179) ********************** 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 178 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 148 time to evaluate : 0.930 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 264 LYS cc_start: 0.9221 (pttp) cc_final: 0.8851 (pttm) REVERT: B 269 ILE cc_start: 0.7889 (OUTLIER) cc_final: 0.6963 (mm) REVERT: B 354 MET cc_start: 0.8080 (mtt) cc_final: 0.7625 (mtm) REVERT: B 431 MET cc_start: 0.9002 (mtm) cc_final: 0.8462 (pmm) REVERT: B 501 MET cc_start: 0.9074 (mtm) cc_final: 0.8393 (mpp) REVERT: B 518 MET cc_start: 0.8543 (mmm) cc_final: 0.7791 (mmm) REVERT: B 541 MET cc_start: 0.8545 (mtp) cc_final: 0.7465 (tpp) REVERT: B 568 ARG cc_start: 0.9319 (tmm-80) cc_final: 0.8686 (tmm-80) REVERT: B 594 GLN cc_start: 0.8806 (tp40) cc_final: 0.8217 (tp-100) REVERT: B 660 MET cc_start: 0.8184 (tpt) cc_final: 0.7733 (tpt) REVERT: B 753 TRP cc_start: 0.9134 (OUTLIER) cc_final: 0.8078 (t60) REVERT: B 798 ASP cc_start: 0.8560 (t0) cc_final: 0.8269 (t0) REVERT: B 1061 MET cc_start: 0.6478 (tpp) cc_final: 0.6148 (tpp) REVERT: B 1111 TYR cc_start: 0.8690 (OUTLIER) cc_final: 0.8332 (p90) REVERT: C 17 MET cc_start: 0.9073 (ptm) cc_final: 0.8858 (ptp) REVERT: C 96 MET cc_start: 0.8689 (tpp) cc_final: 0.8344 (tpp) REVERT: C 387 GLU cc_start: 0.8856 (mm-30) cc_final: 0.8628 (mm-30) REVERT: C 408 ILE cc_start: 0.9581 (mt) cc_final: 0.9284 (pt) REVERT: C 471 LEU cc_start: 0.9142 (mt) cc_final: 0.8692 (pp) REVERT: C 609 MET cc_start: 0.8341 (tpt) cc_final: 0.8058 (tpp) REVERT: C 660 ASN cc_start: 0.7485 (OUTLIER) cc_final: 0.6995 (m-40) REVERT: C 667 MET cc_start: 0.6133 (ttm) cc_final: 0.5350 (ttm) REVERT: C 787 MET cc_start: 0.7804 (pmm) cc_final: 0.7142 (ptp) REVERT: C 906 ASP cc_start: 0.8398 (m-30) cc_final: 0.8076 (t0) REVERT: C 1102 MET cc_start: 0.9442 (ttt) cc_final: 0.9233 (ttp) REVERT: D 25 LEU cc_start: 0.9221 (mt) cc_final: 0.8885 (pp) REVERT: D 100 MET cc_start: 0.9000 (mpp) cc_final: 0.8796 (mpp) REVERT: D 108 TYR cc_start: 0.6429 (OUTLIER) cc_final: 0.5900 (p90) REVERT: D 112 MET cc_start: 0.8569 (ttm) cc_final: 0.8151 (ttm) REVERT: D 273 MET cc_start: 0.7967 (OUTLIER) cc_final: 0.6122 (mmt) REVERT: D 278 MET cc_start: 0.8649 (mtm) cc_final: 0.7979 (ptp) REVERT: D 471 HIS cc_start: 0.8743 (m170) cc_final: 0.8424 (m90) REVERT: D 483 MET cc_start: 0.0362 (tmm) cc_final: -0.0270 (tpp) REVERT: D 504 ARG cc_start: 0.8609 (tpm170) cc_final: 0.8376 (tpm170) REVERT: D 536 MET cc_start: 0.5285 (tpt) cc_final: 0.4825 (tpt) outliers start: 30 outliers final: 22 residues processed: 173 average time/residue: 0.1510 time to fit residues: 43.7497 Evaluate side-chains 172 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 144 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 254 ARG Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 753 TRP Chi-restraints excluded: chain B residue 813 CYS Chi-restraints excluded: chain B residue 1093 TYR Chi-restraints excluded: chain B residue 1111 TYR Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 591 CYS Chi-restraints excluded: chain C residue 632 VAL Chi-restraints excluded: chain C residue 660 ASN Chi-restraints excluded: chain C residue 821 VAL Chi-restraints excluded: chain C residue 889 VAL Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 108 TYR Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 179 THR Chi-restraints excluded: chain D residue 191 MET Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 273 MET Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 350 ASP 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: 9.9990 chunk 98 optimal weight: 0.0270 chunk 271 optimal weight: 8.9990 chunk 77 optimal weight: 20.0000 chunk 277 optimal weight: 20.0000 chunk 48 optimal weight: 10.0000 chunk 182 optimal weight: 5.9990 chunk 120 optimal weight: 0.9990 chunk 156 optimal weight: 5.9990 chunk 50 optimal weight: 9.9990 chunk 235 optimal weight: 10.0000 overall best weight: 4.4046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 742 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 958 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 960 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 HIS ** 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 = 0.3756 r_free = 0.3756 target = 0.065952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.047943 restraints weight = 146953.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.049498 restraints weight = 84319.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.050498 restraints weight = 59160.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.051140 restraints weight = 46992.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.051561 restraints weight = 40523.687| |-----------------------------------------------------------------------------| r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.5227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 24452 Z= 0.165 Angle : 0.627 11.797 33409 Z= 0.314 Chirality : 0.041 0.231 3673 Planarity : 0.004 0.059 4205 Dihedral : 14.002 89.175 3714 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.37 % Allowed : 14.04 % Favored : 84.60 % 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: 0.46 (0.16), residues: 2837 helix: 1.58 (0.14), residues: 1438 sheet: -0.26 (0.30), residues: 278 loop : -1.26 (0.18), residues: 1121 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 75 TYR 0.014 0.001 TYR C 728 PHE 0.012 0.001 PHE B 428 TRP 0.013 0.001 TRP B 272 HIS 0.005 0.001 HIS D 289 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.16 (24452) covalent geometry : angle 0.62678 / 0.31 (33409) hydrogen bonds : bond 0.03709 / 2.46 ( 1097) hydrogen bonds : angle 4.10675 / 2.91 ( 3179) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4497.31 seconds wall clock time: 78 minutes 14.62 seconds (4694.62 seconds total)