Starting phenix.real_space_refine on Sun Aug 24 23:52:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6t2v_10370/08_2025/6t2v_10370.cif Found real_map, /net/cci-nas-00/data/ceres_data/6t2v_10370/08_2025/6t2v_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_10370/08_2025/6t2v_10370.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6t2v_10370/08_2025/6t2v_10370.map" model { file = "/net/cci-nas-00/data/ceres_data/6t2v_10370/08_2025/6t2v_10370.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6t2v_10370/08_2025/6t2v_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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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: 5.58, per 1000 atoms: 0.23 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: 1.94 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 1.4 microseconds 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: 2.93 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: 5.38 Time building geometry restraints manager: 2.65 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=" N GLU B1073 " pdb=" CA GLU B1073 " ideal model delta sigma weight residual 1.457 1.471 -0.014 1.29e-02 6.01e+03 1.19e+00 bond pdb=" C PRO C 823 " pdb=" N LEU C 824 " ideal model delta sigma weight residual 1.331 1.353 -0.022 2.07e-02 2.33e+03 1.17e+00 bond pdb=" C ILE C 670 " pdb=" O ILE C 670 " ideal model delta sigma weight residual 1.232 1.240 -0.008 8.90e-03 1.26e+04 8.47e-01 bond pdb=" C SER C 419 " pdb=" N PRO C 420 " ideal model delta sigma weight residual 1.335 1.348 -0.012 1.36e-02 5.41e+03 8.32e-01 bond pdb=" CB PRO C 63 " pdb=" CG PRO C 63 " ideal model delta sigma weight residual 1.492 1.537 -0.045 5.00e-02 4.00e+02 8.22e-01 ... (remaining 24447 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.39: 32753 1.39 - 2.78: 577 2.78 - 4.17: 60 4.17 - 5.56: 17 5.56 - 6.95: 2 Bond angle restraints: 33409 Sorted by residual: angle pdb=" C PHE B 468 " pdb=" N MET B 469 " pdb=" CA MET B 469 " ideal model delta sigma weight residual 121.54 128.49 -6.95 1.91e+00 2.74e-01 1.33e+01 angle pdb=" N GLY B 898 " pdb=" CA GLY B 898 " pdb=" C GLY B 898 " ideal model delta sigma weight residual 110.87 115.76 -4.89 1.54e+00 4.22e-01 1.01e+01 angle pdb=" N TRP B 878 " pdb=" CA TRP B 878 " pdb=" C TRP B 878 " ideal model delta sigma weight residual 107.88 112.25 -4.37 1.41e+00 5.03e-01 9.59e+00 angle pdb=" C SER C 447 " pdb=" N HIS C 448 " pdb=" CA HIS C 448 " ideal model delta sigma weight residual 119.78 123.18 -3.40 1.24e+00 6.50e-01 7.51e+00 angle pdb=" CA GLY C 938 " pdb=" C GLY C 938 " pdb=" N GLN C 939 " ideal model delta sigma weight residual 114.98 117.50 -2.52 1.14e+00 7.69e-01 4.90e+00 ... (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: 2423 0.026 - 0.052: 828 0.052 - 0.078: 240 0.078 - 0.104: 134 0.104 - 0.131: 48 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: 0.690 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: 0.410 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 25.090 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.060 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:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 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= 0.099 Angle : 0.453 6.953 33409 Z= 0.287 Chirality : 0.034 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 aren 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 covalent geometry : bond 0.00167 (24452) covalent geometry : angle 0.45276 (33409) hydrogen bonds : bond 0.14798 ( 1097) hydrogen bonds : angle 6.30144 ( 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 : 0.935 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: 0.8620 (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: 0.8885 (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: 0.1799 time to fit residues: 140.1386 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 : 0.896 ------------------------------------------------------------------------------- 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: 0.9980 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: 2.7362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 510 ASN 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 960 GLN C1091 GLN C1108 GLN D 22 GLN D 89 GLN 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 = 0.074202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.054643 restraints weight = 135964.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.056577 restraints weight = 76687.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.057830 restraints weight = 52690.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.058631 restraints weight = 41024.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.059168 restraints weight = 34807.689| |-----------------------------------------------------------------------------| r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.2485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 24452 Z= 0.139 Angle : 0.607 12.775 33409 Z= 0.301 Chirality : 0.039 0.183 3673 Planarity : 0.005 0.059 4205 Dihedral : 13.359 79.822 3732 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.48 % Allowed : 10.27 % Favored : 87.25 % 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 aren not related in a simple way. whole: -1.26 (0.14), residues: 2837 helix: -0.01 (0.13), residues: 1409 sheet: -0.51 (0.29), residues: 281 loop : -1.92 (0.16), residues: 1147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG B 974 TYR 0.017 0.001 TYR B 430 PHE 0.012 0.001 PHE B1135 TRP 0.011 0.001 TRP B 272 HIS 0.005 0.001 HIS B 956 Details of bonding type rmsd covalent geometry : bond 0.00307 (24452) covalent geometry : angle 0.60662 (33409) hydrogen bonds : bond 0.03588 ( 1097) hydrogen bonds : angle 4.31150 ( 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 290 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 230 time to evaluate : 0.714 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: B 155 ASP cc_start: 0.7992 (p0) cc_final: 0.7699 (t0) REVERT: B 264 LYS cc_start: 0.9133 (pttm) cc_final: 0.8840 (pttm) REVERT: B 354 MET cc_start: 0.8171 (mtt) cc_final: 0.7822 (mtm) REVERT: B 431 MET cc_start: 0.8898 (mtm) cc_final: 0.8639 (mtp) REVERT: B 501 MET cc_start: 0.9025 (mtm) cc_final: 0.8213 (mtm) REVERT: B 518 MET cc_start: 0.7866 (mmm) cc_final: 0.7170 (mmm) REVERT: B 541 MET cc_start: 0.8521 (mtp) cc_final: 0.7561 (tpp) REVERT: B 594 GLN cc_start: 0.8794 (tp40) cc_final: 0.8382 (tp-100) REVERT: B 657 VAL cc_start: 0.9039 (OUTLIER) cc_final: 0.8836 (t) REVERT: B 658 MET cc_start: 0.9092 (tpp) cc_final: 0.8641 (tpt) REVERT: B 711 LEU cc_start: 0.9668 (tp) cc_final: 0.9447 (tp) REVERT: B 753 TRP cc_start: 0.9028 (OUTLIER) cc_final: 0.7646 (t60) REVERT: B 944 GLN cc_start: 0.9172 (mt0) cc_final: 0.8762 (mm-40) REVERT: B 964 PHE cc_start: 0.8278 (m-80) cc_final: 0.7878 (m-10) REVERT: B 1111 TYR cc_start: 0.8415 (OUTLIER) cc_final: 0.8122 (p90) REVERT: C 1 MET cc_start: 0.6997 (tpp) cc_final: 0.6727 (tmm) REVERT: C 50 LEU cc_start: 0.9256 (mt) cc_final: 0.9032 (tt) REVERT: C 91 MET cc_start: 0.8494 (mtm) cc_final: 0.8220 (mtp) REVERT: C 133 ASP cc_start: 0.8874 (t0) cc_final: 0.8458 (t0) REVERT: C 165 GLN cc_start: 0.9125 (mt0) cc_final: 0.8860 (mt0) REVERT: C 227 LEU cc_start: 0.9593 (mt) cc_final: 0.9124 (pp) REVERT: C 387 GLU cc_start: 0.8996 (mm-30) cc_final: 0.8600 (mm-30) REVERT: C 408 ILE cc_start: 0.9423 (mt) cc_final: 0.9022 (pt) REVERT: C 471 LEU cc_start: 0.8987 (mt) cc_final: 0.8624 (pp) REVERT: C 591 CYS cc_start: 0.8291 (OUTLIER) cc_final: 0.7975 (t) REVERT: C 665 MET cc_start: 0.6991 (mtp) cc_final: 0.6760 (mtp) REVERT: C 667 MET cc_start: 0.5975 (ttm) cc_final: 0.5001 (ttm) REVERT: C 787 MET cc_start: 0.7176 (pmm) cc_final: 0.6851 (pmm) REVERT: C 882 GLN cc_start: 0.8891 (tt0) cc_final: 0.8604 (mt0) REVERT: C 906 ASP cc_start: 0.8237 (m-30) cc_final: 0.7968 (t0) REVERT: C 1102 MET cc_start: 0.9325 (ttt) cc_final: 0.9000 (ttp) REVERT: D 25 LEU cc_start: 0.9315 (mt) cc_final: 0.9038 (pp) REVERT: D 108 TYR cc_start: 0.6350 (OUTLIER) cc_final: 0.5814 (p90) REVERT: D 471 HIS cc_start: 0.8308 (m90) cc_final: 0.7873 (m-70) REVERT: D 536 MET cc_start: 0.5287 (tpt) cc_final: 0.4848 (tpt) REVERT: D 564 GLU cc_start: 0.6619 (mm-30) cc_final: 0.5689 (tp30) outliers start: 60 outliers final: 28 residues processed: 279 average time/residue: 0.1595 time to fit residues: 73.3751 Evaluate side-chains 220 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 187 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 185 GLU 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 657 VAL 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 947 ARG 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 435 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 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 266 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 248 optimal weight: 0.9980 chunk 212 optimal weight: 9.9990 chunk 233 optimal weight: 20.0000 chunk 167 optimal weight: 3.9990 chunk 232 optimal weight: 6.9990 chunk 200 optimal weight: 0.9990 chunk 90 optimal weight: 20.0000 chunk 275 optimal weight: 30.0000 chunk 101 optimal weight: 40.0000 chunk 270 optimal weight: 10.0000 chunk 125 optimal weight: 10.0000 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 689 HIS ** B 742 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1072 HIS B1112 GLN ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 725 GLN C 817 HIS ** C 960 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 328 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.068872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.049679 restraints weight = 138500.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.051304 restraints weight = 78232.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.052428 restraints weight = 54301.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.053154 restraints weight = 42901.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.053591 restraints weight = 36626.129| |-----------------------------------------------------------------------------| r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.3820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 24452 Z= 0.177 Angle : 0.634 10.702 33409 Z= 0.318 Chirality : 0.040 0.185 3673 Planarity : 0.004 0.053 4205 Dihedral : 13.663 87.568 3722 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.65 % Allowed : 10.64 % Favored : 86.71 % 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 aren not related in a simple way. whole: -0.36 (0.15), residues: 2837 helix: 0.82 (0.14), residues: 1443 sheet: -0.44 (0.29), residues: 285 loop : -1.60 (0.17), residues: 1109 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 974 TYR 0.015 0.002 TYR B 394 PHE 0.016 0.002 PHE D 512 TRP 0.019 0.002 TRP B 272 HIS 0.009 0.001 HIS D 289 Details of bonding type rmsd covalent geometry : bond 0.00386 (24452) covalent geometry : angle 0.63443 (33409) hydrogen bonds : bond 0.04143 ( 1097) hydrogen bonds : angle 4.19523 ( 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 247 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 183 time to evaluate : 0.931 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: B 264 LYS cc_start: 0.9181 (pttm) cc_final: 0.8865 (pttm) REVERT: B 354 MET cc_start: 0.8183 (mtt) cc_final: 0.7809 (mtm) REVERT: B 501 MET cc_start: 0.9159 (mtm) cc_final: 0.8915 (mtm) REVERT: B 518 MET cc_start: 0.8223 (mmm) cc_final: 0.7471 (mmm) REVERT: B 541 MET cc_start: 0.8608 (mtp) cc_final: 0.7542 (tpp) REVERT: B 594 GLN cc_start: 0.8949 (tp40) cc_final: 0.8374 (tp-100) REVERT: B 657 VAL cc_start: 0.9060 (OUTLIER) cc_final: 0.8830 (t) REVERT: B 658 MET cc_start: 0.9123 (tpp) cc_final: 0.8874 (tpp) REVERT: B 753 TRP cc_start: 0.9199 (OUTLIER) cc_final: 0.7992 (t60) REVERT: B 794 ARG cc_start: 0.8090 (OUTLIER) cc_final: 0.7872 (ttp80) REVERT: B 798 ASP cc_start: 0.8612 (t0) cc_final: 0.8303 (t0) REVERT: B 1061 MET cc_start: 0.6529 (tpp) cc_final: 0.6182 (tpp) REVERT: B 1111 TYR cc_start: 0.8689 (OUTLIER) cc_final: 0.8354 (p90) REVERT: B 1168 MET cc_start: 0.6508 (mmp) cc_final: 0.6300 (mmt) REVERT: B 1171 MET cc_start: 0.7455 (ptt) cc_final: 0.6942 (ppp) REVERT: C 1 MET cc_start: 0.7288 (tpp) cc_final: 0.6994 (tmm) REVERT: C 50 LEU cc_start: 0.9384 (mt) cc_final: 0.9151 (tt) REVERT: C 91 MET cc_start: 0.8499 (mtm) cc_final: 0.8138 (mtp) REVERT: C 133 ASP cc_start: 0.8947 (t0) cc_final: 0.8590 (t0) REVERT: C 227 LEU cc_start: 0.9610 (mt) cc_final: 0.9204 (pp) REVERT: C 408 ILE cc_start: 0.9566 (mt) cc_final: 0.9204 (pt) REVERT: C 411 MET cc_start: 0.8050 (mmt) cc_final: 0.7755 (mmt) REVERT: C 660 ASN cc_start: 0.7573 (OUTLIER) cc_final: 0.7178 (m-40) REVERT: C 665 MET cc_start: 0.7497 (mtp) cc_final: 0.7179 (mtm) REVERT: C 667 MET cc_start: 0.6059 (ttm) cc_final: 0.5234 (ttm) REVERT: C 787 MET cc_start: 0.7413 (pmm) cc_final: 0.7196 (pmm) REVERT: C 906 ASP cc_start: 0.8424 (m-30) cc_final: 0.8101 (t0) REVERT: C 980 LEU cc_start: 0.9220 (tp) cc_final: 0.9011 (tp) REVERT: C 1079 MET cc_start: 0.9121 (pmm) cc_final: 0.8882 (pmm) REVERT: C 1102 MET cc_start: 0.9416 (ttt) cc_final: 0.9156 (ttp) REVERT: D 25 LEU cc_start: 0.9288 (mt) cc_final: 0.9053 (pp) REVERT: D 100 MET cc_start: 0.8863 (mpp) cc_final: 0.8651 (mmp) REVERT: D 273 MET cc_start: 0.8140 (OUTLIER) cc_final: 0.6451 (mmp) REVERT: D 278 MET cc_start: 0.8665 (mtm) cc_final: 0.7994 (ptp) REVERT: D 471 HIS cc_start: 0.8417 (m90) cc_final: 0.7850 (m-70) REVERT: D 536 MET cc_start: 0.5311 (tpt) cc_final: 0.4564 (tpt) outliers start: 64 outliers final: 33 residues processed: 235 average time/residue: 0.1491 time to fit residues: 57.9978 Evaluate side-chains 201 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 162 time to evaluate : 0.899 ------------------------------------------------------------------------------- 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 526 ILE Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 657 VAL Chi-restraints excluded: chain B residue 699 THR Chi-restraints excluded: chain B residue 753 TRP Chi-restraints excluded: chain B residue 794 ARG 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 497 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 862 SER 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 179 THR Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 265 VAL 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 437 GLU Chi-restraints excluded: chain D residue 562 THR 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: 6.9990 chunk 101 optimal weight: 20.0000 chunk 259 optimal weight: 10.0000 chunk 196 optimal weight: 10.0000 chunk 34 optimal weight: 5.9990 chunk 220 optimal weight: 10.0000 chunk 25 optimal weight: 20.0000 chunk 26 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 overall best weight: 6.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 109 GLN ** B 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 463 GLN B 566 GLN ** B 742 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 769 HIS B 943 HIS B1133 HIS C 137 GLN ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 510 ASN C 822 GLN C 951 GLN ** C 960 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 65 HIS ** D 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 471 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.065577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.047029 restraints weight = 143905.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.048585 restraints weight = 82140.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.049598 restraints weight = 57510.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.050263 restraints weight = 45723.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.050698 restraints weight = 39304.310| |-----------------------------------------------------------------------------| r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.4790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 24452 Z= 0.233 Angle : 0.674 10.172 33409 Z= 0.341 Chirality : 0.041 0.156 3673 Planarity : 0.005 0.064 4205 Dihedral : 13.861 88.844 3714 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.90 % Allowed : 11.26 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.27 (0.15), residues: 2837 helix: 0.85 (0.13), residues: 1457 sheet: -0.31 (0.30), residues: 264 loop : -1.51 (0.17), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 974 TYR 0.019 0.002 TYR C 728 PHE 0.015 0.002 PHE C1112 TRP 0.025 0.002 TRP D 113 HIS 0.010 0.001 HIS D 289 Details of bonding type rmsd covalent geometry : bond 0.00510 (24452) covalent geometry : angle 0.67436 (33409) hydrogen bonds : bond 0.04424 ( 1097) hydrogen bonds : angle 4.37200 ( 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 233 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 163 time to evaluate : 0.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 354 MET cc_start: 0.8124 (mtt) cc_final: 0.7684 (mtm) REVERT: B 518 MET cc_start: 0.8529 (mmm) cc_final: 0.7698 (mmm) REVERT: B 541 MET cc_start: 0.8604 (mtp) cc_final: 0.7493 (tpp) REVERT: B 568 ARG cc_start: 0.9318 (tmm-80) cc_final: 0.8864 (tmm-80) REVERT: B 594 GLN cc_start: 0.9002 (tp40) cc_final: 0.8427 (tp-100) REVERT: B 658 MET cc_start: 0.9149 (tpp) cc_final: 0.8816 (tpt) REVERT: B 660 MET cc_start: 0.8445 (tpt) cc_final: 0.7673 (tpt) REVERT: B 753 TRP cc_start: 0.9184 (OUTLIER) cc_final: 0.7993 (t60) REVERT: B 794 ARG cc_start: 0.8111 (OUTLIER) cc_final: 0.7814 (ttp80) REVERT: B 798 ASP cc_start: 0.8525 (t0) cc_final: 0.8309 (t0) REVERT: B 1111 TYR cc_start: 0.8743 (OUTLIER) cc_final: 0.8390 (p90) REVERT: B 1168 MET cc_start: 0.7588 (mmp) cc_final: 0.7123 (mmt) REVERT: B 1171 MET cc_start: 0.7922 (ptt) cc_final: 0.7323 (ppp) REVERT: C 1 MET cc_start: 0.7351 (tpp) cc_final: 0.7041 (tmm) REVERT: C 72 MET cc_start: 0.9093 (mmp) cc_final: 0.8889 (mmp) REVERT: C 408 ILE cc_start: 0.9607 (mt) cc_final: 0.9364 (pt) REVERT: C 411 MET cc_start: 0.8011 (mmt) cc_final: 0.7685 (mmt) REVERT: C 665 MET cc_start: 0.7851 (mtp) cc_final: 0.7508 (mtp) REVERT: C 667 MET cc_start: 0.6088 (ttm) cc_final: 0.5298 (ttm) REVERT: C 787 MET cc_start: 0.7716 (pmm) cc_final: 0.7200 (ptp) REVERT: C 906 ASP cc_start: 0.8565 (m-30) cc_final: 0.8211 (t0) REVERT: C 1102 MET cc_start: 0.9458 (ttt) cc_final: 0.9218 (ttp) REVERT: D 100 MET cc_start: 0.8937 (mpp) cc_final: 0.8686 (mpp) REVERT: D 278 MET cc_start: 0.8790 (mtm) cc_final: 0.8104 (ptp) REVERT: D 396 ARG cc_start: 0.8112 (OUTLIER) cc_final: 0.7843 (ttm170) REVERT: D 439 GLN cc_start: 0.8534 (OUTLIER) cc_final: 0.8299 (pm20) REVERT: D 471 HIS cc_start: 0.8772 (m170) cc_final: 0.8156 (m-70) REVERT: D 483 MET cc_start: 0.2145 (tmm) cc_final: 0.1904 (tmm) REVERT: D 536 MET cc_start: 0.5540 (tpt) cc_final: 0.5035 (tpt) outliers start: 70 outliers final: 39 residues processed: 222 average time/residue: 0.1176 time to fit residues: 42.7129 Evaluate side-chains 185 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 141 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 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 696 GLU Chi-restraints excluded: chain B residue 699 THR Chi-restraints excluded: chain B residue 753 TRP Chi-restraints excluded: chain B residue 794 ARG Chi-restraints excluded: chain B residue 813 CYS Chi-restraints excluded: chain B residue 1028 SER Chi-restraints excluded: chain B residue 1093 TYR Chi-restraints excluded: chain B residue 1111 TYR Chi-restraints excluded: chain C residue 82 LYS Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 362 ASP Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 632 VAL Chi-restraints excluded: chain C residue 821 VAL Chi-restraints excluded: chain C residue 862 SER 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 126 VAL 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 282 LEU Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 350 ASP Chi-restraints excluded: chain D residue 396 ARG Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 437 GLU Chi-restraints excluded: chain D residue 439 GLN Chi-restraints excluded: chain D residue 533 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 174 optimal weight: 9.9990 chunk 99 optimal weight: 20.0000 chunk 13 optimal weight: 7.9990 chunk 70 optimal weight: 8.9990 chunk 152 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 chunk 256 optimal weight: 5.9990 chunk 72 optimal weight: 7.9990 chunk 267 optimal weight: 8.9990 chunk 115 optimal weight: 10.0000 chunk 111 optimal weight: 0.4980 overall best weight: 3.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 695 GLN ** B 742 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 137 GLN ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 817 HIS ** C 960 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 110 ASN D 300 GLN D 471 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.066032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.047556 restraints weight = 142916.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.049156 restraints weight = 81385.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.050204 restraints weight = 56759.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.050873 restraints weight = 44919.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.051311 restraints weight = 38571.394| |-----------------------------------------------------------------------------| r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.5014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 24452 Z= 0.147 Angle : 0.576 10.165 33409 Z= 0.290 Chirality : 0.039 0.168 3673 Planarity : 0.004 0.052 4205 Dihedral : 13.821 88.908 3714 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.53 % Allowed : 12.13 % Favored : 85.34 % 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 aren not related in a simple way. whole: 0.16 (0.16), residues: 2837 helix: 1.29 (0.14), residues: 1443 sheet: -0.21 (0.30), residues: 272 loop : -1.38 (0.18), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 23 TYR 0.017 0.001 TYR D 108 PHE 0.013 0.001 PHE C 19 TRP 0.015 0.001 TRP D 113 HIS 0.004 0.001 HIS D 289 Details of bonding type rmsd covalent geometry : bond 0.00325 (24452) covalent geometry : angle 0.57584 (33409) hydrogen bonds : bond 0.03660 ( 1097) hydrogen bonds : angle 4.09018 ( 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 213 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 152 time to evaluate : 0.947 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 269 ILE cc_start: 0.7763 (OUTLIER) cc_final: 0.6846 (mm) REVERT: B 354 MET cc_start: 0.8080 (mtt) cc_final: 0.7710 (mtm) REVERT: B 518 MET cc_start: 0.8564 (mmm) cc_final: 0.7651 (mmm) REVERT: B 541 MET cc_start: 0.8576 (mtp) cc_final: 0.7477 (tpp) REVERT: B 594 GLN cc_start: 0.8835 (tp40) cc_final: 0.8277 (tp-100) REVERT: B 620 MET cc_start: 0.8764 (ptt) cc_final: 0.8529 (ppp) REVERT: B 753 TRP cc_start: 0.9147 (OUTLIER) cc_final: 0.8096 (t60) REVERT: B 794 ARG cc_start: 0.8065 (OUTLIER) cc_final: 0.7763 (ttp80) REVERT: B 798 ASP cc_start: 0.8511 (t0) cc_final: 0.8252 (t0) REVERT: B 1061 MET cc_start: 0.6507 (tpp) cc_final: 0.6113 (tpp) REVERT: B 1111 TYR cc_start: 0.8752 (OUTLIER) cc_final: 0.8366 (p90) REVERT: B 1171 MET cc_start: 0.8117 (ptt) cc_final: 0.7623 (ptt) REVERT: C 18 GLU cc_start: 0.8588 (OUTLIER) cc_final: 0.8353 (tm-30) REVERT: C 42 MET cc_start: 0.8233 (tpp) cc_final: 0.7989 (tpp) REVERT: C 72 MET cc_start: 0.9123 (mmp) cc_final: 0.8909 (mmp) REVERT: C 91 MET cc_start: 0.8502 (mtp) cc_final: 0.8223 (mtp) REVERT: C 96 MET cc_start: 0.8865 (ttm) cc_final: 0.8577 (tpp) REVERT: C 408 ILE cc_start: 0.9593 (mt) cc_final: 0.9351 (pt) REVERT: C 665 MET cc_start: 0.7815 (mtp) cc_final: 0.7479 (mtm) REVERT: C 667 MET cc_start: 0.6163 (ttm) cc_final: 0.5440 (ttm) REVERT: C 817 HIS cc_start: 0.3364 (OUTLIER) cc_final: 0.1755 (m90) REVERT: C 906 ASP cc_start: 0.8494 (m-30) cc_final: 0.8132 (t0) REVERT: C 1102 MET cc_start: 0.9445 (ttt) cc_final: 0.9221 (ttp) REVERT: D 25 LEU cc_start: 0.9277 (mt) cc_final: 0.8928 (pp) REVERT: D 278 MET cc_start: 0.8707 (mtm) cc_final: 0.8029 (ptp) REVERT: D 437 GLU cc_start: 0.9441 (OUTLIER) cc_final: 0.8995 (tm-30) REVERT: D 439 GLN cc_start: 0.8587 (OUTLIER) cc_final: 0.8317 (pm20) REVERT: D 471 HIS cc_start: 0.8601 (m90) cc_final: 0.8044 (m90) REVERT: D 483 MET cc_start: 0.2045 (tmm) cc_final: 0.1839 (tmm) REVERT: D 512 PHE cc_start: 0.9329 (m-10) cc_final: 0.9128 (m-10) REVERT: D 536 MET cc_start: 0.5542 (tpt) cc_final: 0.5038 (tpt) outliers start: 61 outliers final: 33 residues processed: 206 average time/residue: 0.1232 time to fit residues: 42.8953 Evaluate side-chains 185 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 144 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 64 PHE Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 699 THR Chi-restraints excluded: chain B residue 753 TRP Chi-restraints excluded: chain B residue 794 ARG Chi-restraints excluded: chain B residue 1028 SER Chi-restraints excluded: chain B residue 1093 TYR Chi-restraints excluded: chain B residue 1111 TYR Chi-restraints excluded: chain C residue 18 GLU Chi-restraints excluded: chain C residue 82 LYS Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 362 ASP Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 559 GLU Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 632 VAL Chi-restraints excluded: chain C residue 689 LEU Chi-restraints excluded: chain C residue 817 HIS Chi-restraints excluded: chain C residue 821 VAL Chi-restraints excluded: chain C residue 862 SER 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 216 LEU Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 261 LEU 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 437 GLU Chi-restraints excluded: chain D residue 439 GLN Chi-restraints excluded: chain D residue 533 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 82 optimal weight: 2.9990 chunk 268 optimal weight: 7.9990 chunk 16 optimal weight: 9.9990 chunk 219 optimal weight: 6.9990 chunk 286 optimal weight: 20.0000 chunk 96 optimal weight: 20.0000 chunk 165 optimal weight: 10.0000 chunk 195 optimal weight: 8.9990 chunk 84 optimal weight: 0.0970 chunk 176 optimal weight: 6.9990 chunk 201 optimal weight: 10.0000 overall best weight: 5.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 742 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 228 GLN ** C 960 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 471 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.064908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.046462 restraints weight = 145967.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.048015 restraints weight = 83357.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.049028 restraints weight = 58424.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.049649 restraints weight = 46380.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.050106 restraints weight = 39987.855| |-----------------------------------------------------------------------------| r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.5395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 24452 Z= 0.181 Angle : 0.615 9.883 33409 Z= 0.311 Chirality : 0.040 0.155 3673 Planarity : 0.004 0.051 4205 Dihedral : 13.852 88.451 3714 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.69 % Allowed : 11.80 % Favored : 85.51 % 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 aren not related in a simple way. whole: 0.17 (0.16), residues: 2837 helix: 1.26 (0.14), residues: 1446 sheet: -0.31 (0.30), residues: 280 loop : -1.31 (0.18), residues: 1111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 974 TYR 0.015 0.001 TYR C 728 PHE 0.012 0.001 PHE C 19 TRP 0.013 0.001 TRP B 272 HIS 0.040 0.001 HIS C 817 Details of bonding type rmsd covalent geometry : bond 0.00401 (24452) covalent geometry : angle 0.61460 (33409) hydrogen bonds : bond 0.03967 ( 1097) hydrogen bonds : angle 4.17532 ( 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 209 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 144 time to evaluate : 0.872 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 269 ILE cc_start: 0.8004 (OUTLIER) cc_final: 0.7055 (mm) REVERT: B 354 MET cc_start: 0.8092 (mtt) cc_final: 0.7624 (mtm) REVERT: B 518 MET cc_start: 0.8642 (mmm) cc_final: 0.7908 (mmm) REVERT: B 541 MET cc_start: 0.8596 (mtp) cc_final: 0.7480 (tpp) REVERT: B 594 GLN cc_start: 0.8851 (tp40) cc_final: 0.8246 (tp-100) REVERT: B 620 MET cc_start: 0.8835 (ptt) cc_final: 0.8566 (ppp) REVERT: B 658 MET cc_start: 0.9248 (tpt) cc_final: 0.8918 (tpt) REVERT: B 753 TRP cc_start: 0.9155 (OUTLIER) cc_final: 0.8081 (t60) REVERT: B 798 ASP cc_start: 0.8481 (t0) cc_final: 0.8166 (t0) REVERT: B 1111 TYR cc_start: 0.8772 (OUTLIER) cc_final: 0.8449 (p90) REVERT: B 1171 MET cc_start: 0.8274 (ptt) cc_final: 0.7741 (ptt) REVERT: C 1 MET cc_start: 0.7515 (tpp) cc_final: 0.7119 (tmm) REVERT: C 17 MET cc_start: 0.9215 (ptp) cc_final: 0.8696 (ptp) REVERT: C 42 MET cc_start: 0.8159 (tpp) cc_final: 0.7861 (tpp) REVERT: C 46 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8714 (mm) REVERT: C 72 MET cc_start: 0.9185 (mmp) cc_final: 0.8972 (mmp) REVERT: C 89 GLN cc_start: 0.8488 (pm20) cc_final: 0.8191 (pm20) REVERT: C 96 MET cc_start: 0.8961 (ttm) cc_final: 0.8744 (tpp) REVERT: C 408 ILE cc_start: 0.9570 (mt) cc_final: 0.9321 (pt) REVERT: C 537 MET cc_start: 0.7118 (tpp) cc_final: 0.6067 (tpp) REVERT: C 665 MET cc_start: 0.7887 (mtp) cc_final: 0.7551 (mtp) REVERT: C 667 MET cc_start: 0.6212 (ttm) cc_final: 0.5405 (ttm) REVERT: C 787 MET cc_start: 0.7712 (pmm) cc_final: 0.7179 (ptt) REVERT: C 906 ASP cc_start: 0.8580 (m-30) cc_final: 0.8199 (t0) REVERT: C 1079 MET cc_start: 0.9186 (pmm) cc_final: 0.8945 (pmm) REVERT: C 1102 MET cc_start: 0.9449 (ttt) cc_final: 0.9216 (ttp) REVERT: D 25 LEU cc_start: 0.9270 (mt) cc_final: 0.8925 (pp) REVERT: D 273 MET cc_start: 0.7949 (ptm) cc_final: 0.6538 (ppp) REVERT: D 278 MET cc_start: 0.8479 (mtm) cc_final: 0.8042 (ptp) REVERT: D 396 ARG cc_start: 0.8198 (OUTLIER) cc_final: 0.7931 (ttm170) REVERT: D 437 GLU cc_start: 0.9494 (OUTLIER) cc_final: 0.9047 (tm-30) REVERT: D 439 GLN cc_start: 0.8595 (OUTLIER) cc_final: 0.8238 (pm20) REVERT: D 471 HIS cc_start: 0.8862 (m170) cc_final: 0.8455 (m-70) REVERT: D 483 MET cc_start: 0.2290 (tmm) cc_final: 0.2082 (tmm) REVERT: D 536 MET cc_start: 0.5822 (tpt) cc_final: 0.5302 (tpt) outliers start: 65 outliers final: 44 residues processed: 201 average time/residue: 0.1534 time to fit residues: 51.4672 Evaluate side-chains 191 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 140 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 64 PHE Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 382 MET 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 1028 SER Chi-restraints excluded: chain B residue 1085 TRP Chi-restraints excluded: chain B residue 1093 TYR Chi-restraints excluded: chain B residue 1111 TYR Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 82 LYS Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 362 ASP Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 506 ILE Chi-restraints excluded: chain C residue 559 GLU Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 632 VAL Chi-restraints excluded: chain C residue 689 LEU Chi-restraints excluded: chain C residue 721 ILE Chi-restraints excluded: chain C residue 821 VAL Chi-restraints excluded: chain C residue 862 SER Chi-restraints excluded: chain C residue 889 VAL Chi-restraints excluded: chain C residue 892 ASP 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 126 VAL Chi-restraints excluded: chain D residue 179 THR Chi-restraints excluded: chain D residue 191 MET Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 261 LEU 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 396 ARG Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 437 GLU Chi-restraints excluded: chain D residue 439 GLN Chi-restraints excluded: chain D residue 533 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 89 optimal weight: 3.9990 chunk 262 optimal weight: 10.0000 chunk 10 optimal weight: 0.9990 chunk 276 optimal weight: 30.0000 chunk 212 optimal weight: 5.9990 chunk 120 optimal weight: 0.6980 chunk 170 optimal weight: 4.9990 chunk 55 optimal weight: 9.9990 chunk 185 optimal weight: 9.9990 chunk 243 optimal weight: 8.9990 chunk 238 optimal weight: 3.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 742 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 817 HIS ** 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 = 0.3753 r_free = 0.3753 target = 0.065581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.047487 restraints weight = 143902.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.049028 restraints weight = 82774.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.050059 restraints weight = 58259.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.050712 restraints weight = 46168.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.051098 restraints weight = 39696.605| |-----------------------------------------------------------------------------| r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.5479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 24452 Z= 0.123 Angle : 0.563 10.055 33409 Z= 0.282 Chirality : 0.039 0.199 3673 Planarity : 0.004 0.053 4205 Dihedral : 13.809 88.531 3713 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.95 % Allowed : 13.13 % Favored : 84.93 % 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 aren not related in a simple way. whole: 0.44 (0.16), residues: 2837 helix: 1.54 (0.14), residues: 1440 sheet: -0.32 (0.30), residues: 283 loop : -1.21 (0.18), residues: 1114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 794 TYR 0.016 0.001 TYR D 108 PHE 0.014 0.001 PHE D 512 TRP 0.013 0.001 TRP B 972 HIS 0.003 0.001 HIS C 817 Details of bonding type rmsd covalent geometry : bond 0.00275 (24452) covalent geometry : angle 0.56305 (33409) hydrogen bonds : bond 0.03371 ( 1097) hydrogen bonds : angle 3.97023 ( 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 197 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 150 time to evaluate : 0.958 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 269 ILE cc_start: 0.8002 (OUTLIER) cc_final: 0.7071 (mm) REVERT: B 354 MET cc_start: 0.8098 (mtt) cc_final: 0.7614 (mtm) REVERT: B 518 MET cc_start: 0.8628 (mmm) cc_final: 0.8106 (mmm) REVERT: B 541 MET cc_start: 0.8553 (mtp) cc_final: 0.7461 (tpp) REVERT: B 594 GLN cc_start: 0.8750 (tp40) cc_final: 0.8197 (tp-100) REVERT: B 753 TRP cc_start: 0.9089 (OUTLIER) cc_final: 0.7909 (t60) REVERT: B 798 ASP cc_start: 0.8351 (t0) cc_final: 0.8131 (t0) REVERT: B 1061 MET cc_start: 0.6668 (tpp) cc_final: 0.6340 (tpp) REVERT: B 1111 TYR cc_start: 0.8762 (OUTLIER) cc_final: 0.8470 (p90) REVERT: B 1171 MET cc_start: 0.8384 (ptt) cc_final: 0.7806 (ptt) REVERT: C 1 MET cc_start: 0.7401 (tpp) cc_final: 0.7055 (tmm) REVERT: C 46 LEU cc_start: 0.9095 (OUTLIER) cc_final: 0.8881 (mm) REVERT: C 89 GLN cc_start: 0.8471 (pm20) cc_final: 0.8211 (pm20) REVERT: C 96 MET cc_start: 0.8776 (ttm) cc_final: 0.8562 (tpp) REVERT: C 408 ILE cc_start: 0.9545 (mt) cc_final: 0.9302 (pt) REVERT: C 609 MET cc_start: 0.8643 (tpt) cc_final: 0.8323 (tpt) REVERT: C 646 ASP cc_start: 0.8795 (t0) cc_final: 0.8099 (t0) REVERT: C 665 MET cc_start: 0.7775 (mtp) cc_final: 0.7451 (mtm) REVERT: C 667 MET cc_start: 0.6177 (ttm) cc_final: 0.5374 (ttm) REVERT: C 787 MET cc_start: 0.7729 (pmm) cc_final: 0.7162 (ptt) REVERT: C 906 ASP cc_start: 0.8361 (m-30) cc_final: 0.8048 (t0) REVERT: C 1102 MET cc_start: 0.9381 (ttt) cc_final: 0.9137 (ttp) REVERT: D 273 MET cc_start: 0.7879 (ptm) cc_final: 0.6676 (ppp) REVERT: D 278 MET cc_start: 0.8501 (mtm) cc_final: 0.7806 (ptp) REVERT: D 279 MET cc_start: 0.9090 (ppp) cc_final: 0.8871 (ppp) REVERT: D 396 ARG cc_start: 0.8234 (OUTLIER) cc_final: 0.7965 (ttm170) REVERT: D 437 GLU cc_start: 0.9472 (OUTLIER) cc_final: 0.9132 (tm-30) REVERT: D 439 GLN cc_start: 0.8567 (OUTLIER) cc_final: 0.8063 (pm20) REVERT: D 471 HIS cc_start: 0.8939 (m170) cc_final: 0.8367 (m-70) outliers start: 47 outliers final: 30 residues processed: 193 average time/residue: 0.1334 time to fit residues: 43.6307 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 : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 64 PHE 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 587 VAL Chi-restraints excluded: chain B residue 753 TRP Chi-restraints excluded: chain B residue 1085 TRP Chi-restraints excluded: chain B residue 1093 TYR Chi-restraints excluded: chain B residue 1111 TYR Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 82 LYS Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 362 ASP Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 559 GLU Chi-restraints excluded: chain C residue 632 VAL Chi-restraints excluded: chain C residue 689 LEU Chi-restraints excluded: chain C residue 821 VAL Chi-restraints excluded: chain C residue 862 SER Chi-restraints excluded: chain C residue 889 VAL Chi-restraints excluded: chain C residue 1035 LEU Chi-restraints excluded: chain D residue 35 VAL 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 216 LEU Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 350 ASP Chi-restraints excluded: chain D residue 396 ARG Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 437 GLU Chi-restraints excluded: chain D residue 439 GLN Chi-restraints excluded: chain D residue 533 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 274 optimal weight: 0.8980 chunk 187 optimal weight: 10.0000 chunk 38 optimal weight: 10.0000 chunk 167 optimal weight: 9.9990 chunk 108 optimal weight: 7.9990 chunk 94 optimal weight: 30.0000 chunk 180 optimal weight: 1.9990 chunk 220 optimal weight: 0.0000 chunk 57 optimal weight: 7.9990 chunk 196 optimal weight: 5.9990 chunk 269 optimal weight: 30.0000 overall best weight: 3.3790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 531 GLN ** B 742 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 580 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 D 110 ASN ** D 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.065076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.047173 restraints weight = 144085.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.048698 restraints weight = 82837.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.049697 restraints weight = 58205.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.050341 restraints weight = 46169.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.050737 restraints weight = 39689.266| |-----------------------------------------------------------------------------| r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.5672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 24452 Z= 0.137 Angle : 0.580 11.864 33409 Z= 0.289 Chirality : 0.039 0.169 3673 Planarity : 0.004 0.052 4205 Dihedral : 13.776 88.559 3713 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.07 % Allowed : 13.42 % Favored : 84.51 % 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 aren not related in a simple way. whole: 0.49 (0.16), residues: 2837 helix: 1.57 (0.14), residues: 1451 sheet: -0.27 (0.30), residues: 272 loop : -1.21 (0.18), residues: 1114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 794 TYR 0.020 0.001 TYR D 108 PHE 0.009 0.001 PHE C 193 TRP 0.012 0.001 TRP B 972 HIS 0.005 0.001 HIS B 689 Details of bonding type rmsd covalent geometry : bond 0.00308 (24452) covalent geometry : angle 0.57995 (33409) hydrogen bonds : bond 0.03500 ( 1097) hydrogen bonds : angle 3.99603 ( 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 194 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 144 time to evaluate : 0.870 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 269 ILE cc_start: 0.8024 (OUTLIER) cc_final: 0.7058 (mm) REVERT: B 354 MET cc_start: 0.8099 (mtt) cc_final: 0.7618 (mtm) REVERT: B 501 MET cc_start: 0.9011 (mtm) cc_final: 0.8398 (mpp) REVERT: B 518 MET cc_start: 0.8647 (mmm) cc_final: 0.8213 (mmm) REVERT: B 541 MET cc_start: 0.8543 (mtp) cc_final: 0.7451 (tpp) REVERT: B 753 TRP cc_start: 0.9133 (OUTLIER) cc_final: 0.7950 (t60) REVERT: B 798 ASP cc_start: 0.8355 (t0) cc_final: 0.8132 (t0) REVERT: B 1061 MET cc_start: 0.6642 (tpp) cc_final: 0.6197 (tpp) REVERT: B 1111 TYR cc_start: 0.8803 (OUTLIER) cc_final: 0.8508 (p90) REVERT: B 1171 MET cc_start: 0.8517 (ptt) cc_final: 0.7988 (ptt) REVERT: C 1 MET cc_start: 0.7552 (tpp) cc_final: 0.7202 (tmm) REVERT: C 17 MET cc_start: 0.9146 (ptp) cc_final: 0.8622 (ptp) REVERT: C 46 LEU cc_start: 0.9198 (OUTLIER) cc_final: 0.8984 (mm) REVERT: C 89 GLN cc_start: 0.8507 (pm20) cc_final: 0.8241 (pm20) REVERT: C 387 GLU cc_start: 0.8844 (mm-30) cc_final: 0.8608 (mm-30) REVERT: C 408 ILE cc_start: 0.9549 (mt) cc_final: 0.9309 (pt) REVERT: C 537 MET cc_start: 0.6777 (tpp) cc_final: 0.5953 (tpp) REVERT: C 646 ASP cc_start: 0.8811 (t0) cc_final: 0.8130 (t0) REVERT: C 665 MET cc_start: 0.7870 (mtp) cc_final: 0.7560 (mtp) REVERT: C 667 MET cc_start: 0.6174 (ttm) cc_final: 0.5335 (ttm) REVERT: C 787 MET cc_start: 0.7777 (pmm) cc_final: 0.7265 (ptt) REVERT: C 906 ASP cc_start: 0.8451 (m-30) cc_final: 0.8119 (t0) REVERT: C 1079 MET cc_start: 0.8997 (pmm) cc_final: 0.8664 (pmm) REVERT: C 1102 MET cc_start: 0.9411 (ttt) cc_final: 0.9171 (ttp) REVERT: D 273 MET cc_start: 0.7875 (ptm) cc_final: 0.6669 (ppp) REVERT: D 278 MET cc_start: 0.8475 (mtm) cc_final: 0.7738 (ptp) REVERT: D 279 MET cc_start: 0.8938 (ppp) cc_final: 0.8633 (ppp) REVERT: D 396 ARG cc_start: 0.8206 (OUTLIER) cc_final: 0.7808 (ttp80) REVERT: D 439 GLN cc_start: 0.8569 (OUTLIER) cc_final: 0.8210 (pm20) REVERT: D 471 HIS cc_start: 0.9086 (m170) cc_final: 0.8602 (m90) REVERT: D 520 LYS cc_start: 0.8935 (tttt) cc_final: 0.8668 (mtpt) REVERT: D 536 MET cc_start: 0.8870 (mpp) cc_final: 0.8428 (tpt) outliers start: 50 outliers final: 35 residues processed: 185 average time/residue: 0.1467 time to fit residues: 45.7932 Evaluate side-chains 180 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 139 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 64 PHE 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 382 MET 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 1085 TRP Chi-restraints excluded: chain B residue 1093 TYR Chi-restraints excluded: chain B residue 1111 TYR Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 362 ASP Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 559 GLU Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 632 VAL Chi-restraints excluded: chain C residue 689 LEU Chi-restraints excluded: chain C residue 721 ILE Chi-restraints excluded: chain C residue 821 VAL Chi-restraints excluded: chain C residue 862 SER 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 126 VAL Chi-restraints excluded: chain D residue 179 THR Chi-restraints excluded: chain D residue 191 MET Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 261 LEU 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 396 ARG Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 439 GLN Chi-restraints excluded: chain D residue 493 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 57 optimal weight: 8.9990 chunk 241 optimal weight: 20.0000 chunk 278 optimal weight: 30.0000 chunk 238 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 29 optimal weight: 7.9990 chunk 205 optimal weight: 10.0000 chunk 133 optimal weight: 6.9990 chunk 167 optimal weight: 9.9990 chunk 150 optimal weight: 1.9990 chunk 83 optimal weight: 30.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 742 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 580 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 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 523 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 = 0.3711 r_free = 0.3711 target = 0.063683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.045620 restraints weight = 148785.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.047105 restraints weight = 86319.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.048059 restraints weight = 60985.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.048676 restraints weight = 48813.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.049044 restraints weight = 42256.920| |-----------------------------------------------------------------------------| r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.6101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 24452 Z= 0.186 Angle : 0.635 11.693 33409 Z= 0.318 Chirality : 0.041 0.193 3673 Planarity : 0.004 0.051 4205 Dihedral : 13.934 89.104 3713 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.24 % Allowed : 13.54 % Favored : 84.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.32 (0.16), residues: 2837 helix: 1.38 (0.14), residues: 1446 sheet: -0.39 (0.31), residues: 253 loop : -1.18 (0.18), residues: 1138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 974 TYR 0.016 0.001 TYR B 394 PHE 0.012 0.002 PHE B 428 TRP 0.019 0.002 TRP B 598 HIS 0.006 0.001 HIS B 689 Details of bonding type rmsd covalent geometry : bond 0.00412 (24452) covalent geometry : angle 0.63466 (33409) hydrogen bonds : bond 0.04045 ( 1097) hydrogen bonds : angle 4.20068 ( 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 190 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 136 time to evaluate : 0.612 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 269 ILE cc_start: 0.8129 (OUTLIER) cc_final: 0.7438 (mm) REVERT: B 354 MET cc_start: 0.8117 (mtt) cc_final: 0.7633 (mtm) REVERT: B 501 MET cc_start: 0.9140 (mtm) cc_final: 0.8439 (mpp) REVERT: B 518 MET cc_start: 0.8762 (mmm) cc_final: 0.8432 (mmm) REVERT: B 541 MET cc_start: 0.8656 (mtp) cc_final: 0.7502 (tpp) REVERT: B 753 TRP cc_start: 0.9088 (OUTLIER) cc_final: 0.8029 (t60) REVERT: B 798 ASP cc_start: 0.8390 (t0) cc_final: 0.8149 (t0) REVERT: B 1061 MET cc_start: 0.6613 (tpp) cc_final: 0.6218 (tpp) REVERT: B 1111 TYR cc_start: 0.8835 (OUTLIER) cc_final: 0.8567 (p90) REVERT: B 1171 MET cc_start: 0.8647 (ptt) cc_final: 0.8338 (ppp) REVERT: C 1 MET cc_start: 0.7658 (tpp) cc_final: 0.7324 (tmm) REVERT: C 89 GLN cc_start: 0.8576 (OUTLIER) cc_final: 0.8274 (pm20) REVERT: C 387 GLU cc_start: 0.8845 (mm-30) cc_final: 0.8568 (mm-30) REVERT: C 537 MET cc_start: 0.6798 (tpp) cc_final: 0.6126 (tpp) REVERT: C 606 GLU cc_start: 0.8834 (OUTLIER) cc_final: 0.8341 (mm-30) REVERT: C 646 ASP cc_start: 0.8860 (t0) cc_final: 0.8206 (t0) REVERT: C 665 MET cc_start: 0.7839 (mtp) cc_final: 0.7506 (mtp) REVERT: C 667 MET cc_start: 0.6290 (ttm) cc_final: 0.5460 (ttm) REVERT: C 787 MET cc_start: 0.7762 (pmm) cc_final: 0.7158 (ptt) REVERT: C 851 MET cc_start: 0.8999 (mtm) cc_final: 0.8667 (mtp) REVERT: C 906 ASP cc_start: 0.8535 (m-30) cc_final: 0.8278 (t0) REVERT: C 1102 MET cc_start: 0.9431 (ttt) cc_final: 0.9191 (ttp) REVERT: D 278 MET cc_start: 0.8553 (mtm) cc_final: 0.7829 (ptp) REVERT: D 279 MET cc_start: 0.9117 (ppp) cc_final: 0.8854 (ppp) REVERT: D 396 ARG cc_start: 0.8142 (OUTLIER) cc_final: 0.7908 (ttm170) REVERT: D 437 GLU cc_start: 0.9548 (OUTLIER) cc_final: 0.9165 (tm-30) REVERT: D 439 GLN cc_start: 0.8796 (OUTLIER) cc_final: 0.8262 (pm20) REVERT: D 471 HIS cc_start: 0.9177 (m170) cc_final: 0.8884 (m90) REVERT: D 536 MET cc_start: 0.8949 (mpp) cc_final: 0.8230 (tpt) outliers start: 54 outliers final: 35 residues processed: 183 average time/residue: 0.1422 time to fit residues: 43.7334 Evaluate side-chains 178 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 135 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 64 PHE Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 382 MET 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 1085 TRP Chi-restraints excluded: chain B residue 1093 TYR Chi-restraints excluded: chain B residue 1111 TYR Chi-restraints excluded: chain C residue 89 GLN Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 362 ASP Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 606 GLU Chi-restraints excluded: chain C residue 632 VAL Chi-restraints excluded: chain C residue 689 LEU Chi-restraints excluded: chain C residue 721 ILE Chi-restraints excluded: chain C residue 821 VAL Chi-restraints excluded: chain C residue 862 SER Chi-restraints excluded: chain C residue 889 VAL Chi-restraints excluded: chain C residue 892 ASP 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 126 VAL Chi-restraints excluded: chain D residue 179 THR Chi-restraints excluded: chain D residue 191 MET Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 350 ASP Chi-restraints excluded: chain D residue 396 ARG Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 437 GLU Chi-restraints excluded: chain D residue 439 GLN Chi-restraints excluded: chain D residue 493 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 184 optimal weight: 9.9990 chunk 26 optimal weight: 8.9990 chunk 227 optimal weight: 10.0000 chunk 192 optimal weight: 1.9990 chunk 220 optimal weight: 10.0000 chunk 37 optimal weight: 3.9990 chunk 258 optimal weight: 0.5980 chunk 93 optimal weight: 6.9990 chunk 223 optimal weight: 10.0000 chunk 70 optimal weight: 0.0270 chunk 244 optimal weight: 7.9990 overall best weight: 2.7244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 262 GLN ** B 742 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 817 HIS ** C 960 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 523 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.064675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.046399 restraints weight = 145306.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.047966 restraints weight = 82712.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.048953 restraints weight = 57834.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.049628 restraints weight = 45856.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.050079 restraints weight = 39458.111| |-----------------------------------------------------------------------------| r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.6117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 24452 Z= 0.122 Angle : 0.586 11.756 33409 Z= 0.290 Chirality : 0.040 0.210 3673 Planarity : 0.004 0.058 4205 Dihedral : 13.902 88.793 3713 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.61 % Allowed : 14.53 % Favored : 83.85 % 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 aren not related in a simple way. whole: 0.53 (0.16), residues: 2837 helix: 1.61 (0.14), residues: 1445 sheet: -0.21 (0.31), residues: 262 loop : -1.18 (0.18), residues: 1130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 794 TYR 0.010 0.001 TYR C 794 PHE 0.010 0.001 PHE B1023 TRP 0.013 0.001 TRP B 972 HIS 0.005 0.001 HIS B 689 Details of bonding type rmsd covalent geometry : bond 0.00272 (24452) covalent geometry : angle 0.58613 (33409) hydrogen bonds : bond 0.03373 ( 1097) hydrogen bonds : angle 4.00162 ( 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 182 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 143 time to evaluate : 1.013 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 269 ILE cc_start: 0.8178 (OUTLIER) cc_final: 0.7422 (mm) REVERT: B 354 MET cc_start: 0.8021 (mtt) cc_final: 0.7537 (mtm) REVERT: B 501 MET cc_start: 0.9168 (mtm) cc_final: 0.8442 (mpp) REVERT: B 541 MET cc_start: 0.8748 (mtp) cc_final: 0.7667 (tpp) REVERT: B 696 GLU cc_start: 0.8889 (tm-30) cc_final: 0.8641 (mm-30) REVERT: B 753 TRP cc_start: 0.9127 (OUTLIER) cc_final: 0.7826 (t60) REVERT: B 798 ASP cc_start: 0.8376 (t0) cc_final: 0.8130 (t0) REVERT: B 1111 TYR cc_start: 0.8864 (OUTLIER) cc_final: 0.8592 (p90) REVERT: B 1171 MET cc_start: 0.8714 (ptt) cc_final: 0.8167 (ptt) REVERT: C 1 MET cc_start: 0.7768 (tpp) cc_final: 0.7411 (tmm) REVERT: C 387 GLU cc_start: 0.8886 (mm-30) cc_final: 0.8637 (mm-30) REVERT: C 537 MET cc_start: 0.6767 (tpp) cc_final: 0.5979 (tpp) REVERT: C 646 ASP cc_start: 0.8862 (t0) cc_final: 0.8210 (t0) REVERT: C 665 MET cc_start: 0.7785 (mtp) cc_final: 0.7450 (mtp) REVERT: C 667 MET cc_start: 0.6314 (ttm) cc_final: 0.5618 (ttm) REVERT: C 787 MET cc_start: 0.7672 (pmm) cc_final: 0.7090 (ptt) REVERT: C 851 MET cc_start: 0.9002 (mtm) cc_final: 0.8661 (mtp) REVERT: C 906 ASP cc_start: 0.8446 (m-30) cc_final: 0.8123 (t0) REVERT: C 1102 MET cc_start: 0.9448 (ttt) cc_final: 0.9221 (ttp) REVERT: D 273 MET cc_start: 0.7764 (ptt) cc_final: 0.6897 (ppp) REVERT: D 278 MET cc_start: 0.8429 (mtm) cc_final: 0.7638 (ptp) REVERT: D 279 MET cc_start: 0.9142 (ppp) cc_final: 0.8864 (ppp) REVERT: D 396 ARG cc_start: 0.7991 (OUTLIER) cc_final: 0.7523 (ttm170) REVERT: D 407 MET cc_start: 0.8637 (mtt) cc_final: 0.8373 (mpp) REVERT: D 439 GLN cc_start: 0.8739 (OUTLIER) cc_final: 0.8237 (pm20) REVERT: D 471 HIS cc_start: 0.9216 (m170) cc_final: 0.8823 (m-70) REVERT: D 536 MET cc_start: 0.8959 (mpp) cc_final: 0.8312 (tpt) outliers start: 39 outliers final: 28 residues processed: 176 average time/residue: 0.1335 time to fit residues: 39.8603 Evaluate side-chains 170 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 137 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 64 PHE Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 382 MET Chi-restraints excluded: chain B residue 699 THR Chi-restraints excluded: chain B residue 753 TRP Chi-restraints excluded: chain B residue 1085 TRP Chi-restraints excluded: chain B residue 1093 TYR Chi-restraints excluded: chain B residue 1111 TYR Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 362 ASP 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 689 LEU Chi-restraints excluded: chain C residue 821 VAL Chi-restraints excluded: chain C residue 862 SER Chi-restraints excluded: chain C residue 889 VAL Chi-restraints excluded: chain C residue 1035 LEU Chi-restraints excluded: chain D residue 35 VAL 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 216 LEU Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 350 ASP Chi-restraints excluded: chain D residue 396 ARG Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 439 GLN Chi-restraints excluded: chain D residue 493 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 68 optimal weight: 20.0000 chunk 98 optimal weight: 10.0000 chunk 271 optimal weight: 2.9990 chunk 77 optimal weight: 20.0000 chunk 277 optimal weight: 20.0000 chunk 48 optimal weight: 20.0000 chunk 182 optimal weight: 6.9990 chunk 120 optimal weight: 2.9990 chunk 156 optimal weight: 30.0000 chunk 50 optimal weight: 0.6980 chunk 235 optimal weight: 8.9990 overall best weight: 4.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 258 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 580 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 439 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 = 0.3715 r_free = 0.3715 target = 0.063723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.045650 restraints weight = 145394.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.047166 restraints weight = 83203.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.048145 restraints weight = 58386.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.048766 restraints weight = 46373.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.049197 restraints weight = 39933.240| |-----------------------------------------------------------------------------| r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.6307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 24452 Z= 0.168 Angle : 0.628 10.563 33409 Z= 0.312 Chirality : 0.041 0.257 3673 Planarity : 0.004 0.058 4205 Dihedral : 13.921 88.788 3713 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.61 % Allowed : 14.53 % Favored : 83.85 % 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 aren not related in a simple way. whole: 0.44 (0.16), residues: 2837 helix: 1.48 (0.14), residues: 1447 sheet: -0.21 (0.32), residues: 263 loop : -1.17 (0.18), residues: 1127 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 794 TYR 0.014 0.001 TYR B 394 PHE 0.012 0.001 PHE B 428 TRP 0.011 0.001 TRP B 272 HIS 0.005 0.001 HIS B 689 Details of bonding type rmsd covalent geometry : bond 0.00375 (24452) covalent geometry : angle 0.62751 (33409) hydrogen bonds : bond 0.03795 ( 1097) hydrogen bonds : angle 4.14770 ( 3179) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4422.54 seconds wall clock time: 76 minutes 56.67 seconds (4616.67 seconds total)