Starting phenix.real_space_refine on Fri May 23 03:15:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6sjg_10217/05_2025/6sjg_10217.cif Found real_map, /net/cci-nas-00/data/ceres_data/6sjg_10217/05_2025/6sjg_10217.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6sjg_10217/05_2025/6sjg_10217.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6sjg_10217/05_2025/6sjg_10217.map" model { file = "/net/cci-nas-00/data/ceres_data/6sjg_10217/05_2025/6sjg_10217.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6sjg_10217/05_2025/6sjg_10217.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 54 5.49 5 S 101 5.16 5 C 14897 2.51 5 N 4192 2.21 5 O 4582 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 106 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 12.67, per 1000 atoms: 0.53 Number of scatterers: 23826 At special positions: 0 Unit cell: (150.912, 149.864, 129.952, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 101 16.00 P 54 15.00 O 4582 8.00 N 4192 7.00 C 14897 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.30 Conformation dependent library (CDL) restraints added in 2.8 seconds 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5372 Finding SS restraints... Secondary structure from input PDB file: 125 helices and 16 sheets defined 53.5% alpha, 9.2% beta 17 base pairs and 33 stacking pairs defined. Time for finding SS restraints: 7.66 Creating SS restraints... Processing helix chain 'B' and resid 28 through 43 Processing helix chain 'B' and resid 45 through 49 removed outlier: 3.516A pdb=" N ALA B 49 " --> pdb=" O GLY B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 58 removed outlier: 3.527A pdb=" N GLU B 58 " --> pdb=" O THR B 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 55 through 58' Processing helix chain 'B' and resid 65 through 90 Processing helix chain 'B' and resid 94 through 104 removed outlier: 3.780A pdb=" N ILE B 104 " --> pdb=" O LEU B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 120 Processing helix chain 'B' and resid 121 through 124 Processing helix chain 'B' and resid 128 through 140 Processing helix chain 'B' and resid 140 through 145 removed outlier: 3.810A pdb=" N SER B 144 " --> pdb=" O ASN B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 173 removed outlier: 3.797A pdb=" N TYR B 173 " --> pdb=" O ARG B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 187 removed outlier: 4.326A pdb=" N VAL B 182 " --> pdb=" O GLU B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 202 removed outlier: 3.661A pdb=" N LEU B 193 " --> pdb=" O GLY B 189 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N ARG B 199 " --> pdb=" O ARG B 195 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N TYR B 200 " --> pdb=" O ASP B 196 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLN B 202 " --> pdb=" O ASN B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 239 removed outlier: 3.572A pdb=" N VAL B 232 " --> pdb=" O ARG B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 264 Processing helix chain 'B' and resid 275 through 281 removed outlier: 3.734A pdb=" N ASN B 278 " --> pdb=" O GLU B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 289 removed outlier: 3.724A pdb=" N LYS B 288 " --> pdb=" O GLU B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 317 Processing helix chain 'B' and resid 323 through 347 removed outlier: 4.522A pdb=" N ARG B 336 " --> pdb=" O LEU B 332 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N GLU B 337 " --> pdb=" O ALA B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 364 removed outlier: 3.550A pdb=" N MET B 354 " --> pdb=" O GLY B 350 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LEU B 355 " --> pdb=" O PHE B 351 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER B 364 " --> pdb=" O SER B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 378 Processing helix chain 'B' and resid 390 through 401 Processing helix chain 'B' and resid 414 through 418 removed outlier: 3.770A pdb=" N ALA B 418 " --> pdb=" O PRO B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 437 removed outlier: 3.737A pdb=" N TYR B 430 " --> pdb=" O ASP B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 461 Processing helix chain 'B' and resid 511 through 534 removed outlier: 3.556A pdb=" N GLN B 534 " --> pdb=" O LEU B 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 573 removed outlier: 3.532A pdb=" N ALA B 564 " --> pdb=" O SER B 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 589 removed outlier: 3.595A pdb=" N GLU B 589 " --> pdb=" O SER B 586 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 586 through 589' Processing helix chain 'B' and resid 590 through 605 removed outlier: 3.927A pdb=" N GLN B 594 " --> pdb=" O THR B 590 " (cutoff:3.500A) Processing helix chain 'B' and resid 608 through 617 removed outlier: 3.882A pdb=" N LEU B 612 " --> pdb=" O ARG B 608 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA B 617 " --> pdb=" O ARG B 613 " (cutoff:3.500A) Processing helix chain 'B' and resid 624 through 634 Processing helix chain 'B' and resid 634 through 655 Processing helix chain 'B' and resid 656 through 668 removed outlier: 3.759A pdb=" N MET B 660 " --> pdb=" O GLY B 656 " (cutoff:3.500A) Processing helix chain 'B' and resid 669 through 677 removed outlier: 3.574A pdb=" N ASN B 673 " --> pdb=" O ASN B 669 " (cutoff:3.500A) Processing helix chain 'B' and resid 680 through 699 removed outlier: 3.530A pdb=" N THR B 699 " --> pdb=" O GLN B 695 " (cutoff:3.500A) Processing helix chain 'B' and resid 704 through 717 removed outlier: 3.969A pdb=" N VAL B 708 " --> pdb=" O GLU B 704 " (cutoff:3.500A) Processing helix chain 'B' and resid 783 through 807 removed outlier: 3.599A pdb=" N GLU B 793 " --> pdb=" O LEU B 789 " (cutoff:3.500A) Processing helix chain 'B' and resid 832 through 836 Processing helix chain 'B' and resid 837 through 843 removed outlier: 3.820A pdb=" N LEU B 841 " --> pdb=" O ALA B 837 " (cutoff:3.500A) Processing helix chain 'B' and resid 849 through 860 removed outlier: 3.971A pdb=" N LEU B 860 " --> pdb=" O CYS B 856 " (cutoff:3.500A) Processing helix chain 'B' and resid 948 through 962 Processing helix chain 'B' and resid 969 through 981 Processing helix chain 'B' and resid 986 through 1000 removed outlier: 3.724A pdb=" N GLU B 992 " --> pdb=" O PRO B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1008 through 1012 removed outlier: 3.755A pdb=" N GLN B1011 " --> pdb=" O SER B1008 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU B1012 " --> pdb=" O LEU B1009 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1008 through 1012' Processing helix chain 'B' and resid 1032 through 1044 removed outlier: 3.698A pdb=" N THR B1038 " --> pdb=" O SER B1034 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N LEU B1039 " --> pdb=" O GLN B1035 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N PHE B1043 " --> pdb=" O LEU B1039 " (cutoff:3.500A) Processing helix chain 'B' and resid 1045 through 1048 removed outlier: 3.888A pdb=" N ALA B1048 " --> pdb=" O PRO B1045 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1045 through 1048' Processing helix chain 'B' and resid 1094 through 1106 Processing helix chain 'B' and resid 1107 through 1126 Processing helix chain 'B' and resid 1130 through 1134 Processing helix chain 'B' and resid 1144 through 1146 No H-bonds generated for 'chain 'B' and resid 1144 through 1146' Processing helix chain 'B' and resid 1163 through 1174 removed outlier: 3.638A pdb=" N LEU B1167 " --> pdb=" O GLY B1163 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 24 removed outlier: 4.041A pdb=" N LEU C 13 " --> pdb=" O ARG C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 39 through 55 Processing helix chain 'C' and resid 64 through 77 Processing helix chain 'C' and resid 87 through 102 removed outlier: 3.730A pdb=" N THR C 97 " --> pdb=" O TRP C 93 " (cutoff:3.500A) Proline residue: C 100 - end of helix Processing helix chain 'C' and resid 108 through 116 Processing helix chain 'C' and resid 122 through 142 Processing helix chain 'C' and resid 142 through 152 removed outlier: 3.789A pdb=" N LEU C 146 " --> pdb=" O ARG C 142 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N THR C 151 " --> pdb=" O ALA C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 161 through 179 Proline residue: C 167 - end of helix removed outlier: 3.509A pdb=" N LYS C 170 " --> pdb=" O ALA C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 199 removed outlier: 3.798A pdb=" N LEU C 189 " --> pdb=" O HIS C 185 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N TYR C 190 " --> pdb=" O ARG C 186 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N GLN C 191 " --> pdb=" O ALA C 187 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N ARG C 192 " --> pdb=" O ASN C 188 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU C 197 " --> pdb=" O PHE C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 232 removed outlier: 3.510A pdb=" N ALA C 229 " --> pdb=" O GLN C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 263 removed outlier: 3.553A pdb=" N ALA C 258 " --> pdb=" O PRO C 254 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LYS C 259 " --> pdb=" O ALA C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 287 removed outlier: 3.758A pdb=" N LEU C 286 " --> pdb=" O ASN C 282 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N PHE C 287 " --> pdb=" O ALA C 283 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 282 through 287' Processing helix chain 'C' and resid 297 through 304 Processing helix chain 'C' and resid 304 through 316 removed outlier: 3.546A pdb=" N TYR C 312 " --> pdb=" O ARG C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 344 Processing helix chain 'C' and resid 354 through 360 removed outlier: 3.516A pdb=" N ARG C 360 " --> pdb=" O GLU C 356 " (cutoff:3.500A) Processing helix chain 'C' and resid 381 through 400 removed outlier: 3.561A pdb=" N VAL C 386 " --> pdb=" O PRO C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 406 No H-bonds generated for 'chain 'C' and resid 404 through 406' Processing helix chain 'C' and resid 414 through 428 removed outlier: 3.744A pdb=" N TYR C 418 " --> pdb=" O ASP C 414 " (cutoff:3.500A) Proline residue: C 420 - end of helix Processing helix chain 'C' and resid 447 through 459 removed outlier: 4.040A pdb=" N ALA C 453 " --> pdb=" O PRO C 449 " (cutoff:3.500A) Processing helix chain 'C' and resid 466 through 475 removed outlier: 3.502A pdb=" N LEU C 473 " --> pdb=" O ASP C 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 483 removed outlier: 3.702A pdb=" N PHE C 483 " --> pdb=" O LEU C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 486 through 501 removed outlier: 3.884A pdb=" N GLN C 495 " --> pdb=" O ARG C 491 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLY C 501 " --> pdb=" O VAL C 497 " (cutoff:3.500A) Processing helix chain 'C' and resid 507 through 514 Processing helix chain 'C' and resid 523 through 537 Processing helix chain 'C' and resid 555 through 557 No H-bonds generated for 'chain 'C' and resid 555 through 557' Processing helix chain 'C' and resid 558 through 578 removed outlier: 3.657A pdb=" N MET C 569 " --> pdb=" O ALA C 565 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N GLN C 570 " --> pdb=" O SER C 566 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ARG C 575 " --> pdb=" O LEU C 571 " (cutoff:3.500A) Processing helix chain 'C' and resid 587 through 599 removed outlier: 4.363A pdb=" N CYS C 591 " --> pdb=" O TRP C 587 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ARG C 592 " --> pdb=" O LEU C 588 " (cutoff:3.500A) Processing helix chain 'C' and resid 605 through 625 Processing helix chain 'C' and resid 633 through 646 removed outlier: 3.732A pdb=" N LEU C 637 " --> pdb=" O PRO C 633 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ASP C 646 " --> pdb=" O ALA C 642 " (cutoff:3.500A) Processing helix chain 'C' and resid 707 through 722 Processing helix chain 'C' and resid 745 through 758 Processing helix chain 'C' and resid 769 through 780 Processing helix chain 'C' and resid 806 through 812 Processing helix chain 'C' and resid 833 through 843 removed outlier: 3.541A pdb=" N LEU C 837 " --> pdb=" O PRO C 833 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N HIS C 843 " --> pdb=" O ARG C 839 " (cutoff:3.500A) Processing helix chain 'C' and resid 843 through 851 Processing helix chain 'C' and resid 874 through 889 Processing helix chain 'C' and resid 893 through 904 removed outlier: 3.672A pdb=" N LEU C 897 " --> pdb=" O ASP C 893 " (cutoff:3.500A) Processing helix chain 'C' and resid 910 through 932 removed outlier: 3.872A pdb=" N GLU C 914 " --> pdb=" O GLY C 910 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ARG C 930 " --> pdb=" O GLN C 926 " (cutoff:3.500A) Processing helix chain 'C' and resid 933 through 935 No H-bonds generated for 'chain 'C' and resid 933 through 935' Processing helix chain 'C' and resid 973 through 989 removed outlier: 3.565A pdb=" N GLY C 977 " --> pdb=" O SER C 973 " (cutoff:3.500A) Processing helix chain 'C' and resid 1012 through 1033 removed outlier: 3.911A pdb=" N SER C1032 " --> pdb=" O ARG C1028 " (cutoff:3.500A) Processing helix chain 'C' and resid 1038 through 1050 Processing helix chain 'C' and resid 1060 through 1076 removed outlier: 3.602A pdb=" N GLU C1076 " --> pdb=" O LEU C1072 " (cutoff:3.500A) Processing helix chain 'C' and resid 1098 through 1113 Processing helix chain 'C' and resid 1113 through 1119 removed outlier: 3.800A pdb=" N PHE C1117 " --> pdb=" O LEU C1113 " (cutoff:3.500A) Processing helix chain 'D' and resid 11 through 15 removed outlier: 3.716A pdb=" N GLN D 15 " --> pdb=" O VAL D 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 11 through 15' Processing helix chain 'D' and resid 17 through 28 Processing helix chain 'D' and resid 32 through 49 Processing helix chain 'D' and resid 55 through 61 Processing helix chain 'D' and resid 64 through 72 Processing helix chain 'D' and resid 80 through 88 removed outlier: 3.922A pdb=" N SER D 88 " --> pdb=" O CYS D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 125 Processing helix chain 'D' and resid 133 through 145 Processing helix chain 'D' and resid 152 through 164 removed outlier: 3.508A pdb=" N VAL D 156 " --> pdb=" O ASN D 152 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ARG D 164 " --> pdb=" O VAL D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 192 Processing helix chain 'D' and resid 205 through 221 removed outlier: 3.591A pdb=" N ARG D 221 " --> pdb=" O GLY D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 240 through 244 removed outlier: 3.515A pdb=" N LEU D 244 " --> pdb=" O LEU D 240 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 240 through 244' Processing helix chain 'D' and resid 270 through 274 removed outlier: 3.655A pdb=" N MET D 273 " --> pdb=" O GLU D 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 285 removed outlier: 3.536A pdb=" N ALA D 285 " --> pdb=" O ARG D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 315 removed outlier: 3.822A pdb=" N ASP D 312 " --> pdb=" O ALA D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 316 through 319 removed outlier: 3.552A pdb=" N ALA D 319 " --> pdb=" O TYR D 316 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 316 through 319' Processing helix chain 'D' and resid 322 through 334 removed outlier: 3.543A pdb=" N ARG D 327 " --> pdb=" O ALA D 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 352 Processing helix chain 'D' and resid 365 through 375 removed outlier: 3.977A pdb=" N GLN D 369 " --> pdb=" O SER D 365 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ASN D 375 " --> pdb=" O ALA D 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 377 through 387 removed outlier: 3.595A pdb=" N ALA D 381 " --> pdb=" O GLY D 377 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN D 387 " --> pdb=" O LYS D 383 " (cutoff:3.500A) Processing helix chain 'D' and resid 388 through 391 removed outlier: 3.884A pdb=" N THR D 391 " --> pdb=" O GLN D 388 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 388 through 391' Processing helix chain 'D' and resid 400 through 415 Processing helix chain 'D' and resid 415 through 424 Processing helix chain 'D' and resid 427 through 436 removed outlier: 3.553A pdb=" N ILE D 431 " --> pdb=" O GLU D 427 " (cutoff:3.500A) Processing helix chain 'D' and resid 450 through 465 Processing helix chain 'D' and resid 523 through 527 removed outlier: 3.522A pdb=" N LEU D 527 " --> pdb=" O PRO D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 562 through 572 Processing helix chain 'D' and resid 582 through 592 removed outlier: 3.762A pdb=" N ILE D 590 " --> pdb=" O LEU D 586 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ALA D 591 " --> pdb=" O SER D 587 " (cutoff:3.500A) Processing helix chain 'D' and resid 599 through 604 Processing sheet with id=AA1, first strand: chain 'B' and resid 6 through 7 removed outlier: 6.428A pdb=" N GLU B 6 " --> pdb=" O THR B 442 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N ALA B 439 " --> pdb=" O GLU B 18 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU B 20 " --> pdb=" O ALA B 439 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N GLY B 17 " --> pdb=" O LEU B 409 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N LEU B 411 " --> pdb=" O GLY B 17 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ARG B 19 " --> pdb=" O LEU B 411 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N GLY B 413 " --> pdb=" O ARG B 19 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ILE B 21 " --> pdb=" O GLY B 413 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N LEU B 60 " --> pdb=" O MET B 382 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N ASP B 384 " --> pdb=" O LEU B 60 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N VAL B 62 " --> pdb=" O ASP B 384 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 151 through 152 removed outlier: 6.230A pdb=" N GLN B 151 " --> pdb=" O LEU B 349 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 207 through 208 removed outlier: 6.517A pdb=" N VAL B 207 " --> pdb=" O LEU B 778 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 445 through 446 Processing sheet with id=AA5, first strand: chain 'B' and resid 487 through 490 Processing sheet with id=AA6, first strand: chain 'B' and resid 578 through 580 removed outlier: 6.718A pdb=" N VAL B 579 " --> pdb=" O ILE B 738 " (cutoff:3.500A) removed outlier: 8.696A pdb=" N THR B 740 " --> pdb=" O VAL B 579 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N ILE B 554 " --> pdb=" O GLN B 737 " (cutoff:3.500A) removed outlier: 8.288A pdb=" N VAL B 739 " --> pdb=" O ILE B 554 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N VAL B 556 " --> pdb=" O VAL B 739 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N MET B 499 " --> pdb=" O ALA B 866 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N GLN B 868 " --> pdb=" O MET B 499 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N MET B 501 " --> pdb=" O GLN B 868 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 1017 through 1027 removed outlier: 6.688A pdb=" N ASP B1067 " --> pdb=" O GLU B1020 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N GLU B1022 " --> pdb=" O PHE B1065 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N PHE B1065 " --> pdb=" O GLU B1022 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N TYR B1024 " --> pdb=" O LYS B1063 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N LYS B1063 " --> pdb=" O TYR B1024 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N MET B1061 " --> pdb=" O PRO B1026 " (cutoff:3.500A) removed outlier: 10.060A pdb=" N ILE B1066 " --> pdb=" O TYR B1081 " (cutoff:3.500A) removed outlier: 8.335A pdb=" N TYR B1081 " --> pdb=" O ILE B1066 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N TYR B1076 " --> pdb=" O PHE B1135 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N GLY B1137 " --> pdb=" O TYR B1076 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 60 through 61 removed outlier: 6.215A pdb=" N VAL C 211 " --> pdb=" O HIS C 237 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N LEU C 239 " --> pdb=" O VAL C 211 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N ILE C 213 " --> pdb=" O LEU C 239 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N THR C 241 " --> pdb=" O ILE C 213 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ARG C 3 " --> pdb=" O LEU C 238 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N PHE C 240 " --> pdb=" O ARG C 3 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N TYR C 5 " --> pdb=" O PHE C 240 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ARG C 266 " --> pdb=" O GLU C 322 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP C 324 " --> pdb=" O ARG C 266 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 365 through 366 removed outlier: 6.001A pdb=" N ARG C 365 " --> pdb=" O TYR C 760 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'C' and resid 437 through 439 removed outlier: 3.661A pdb=" N ASN C 660 " --> pdb=" O ILE C 408 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N LYS C 673 " --> pdb=" O LYS C 726 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N TYR C 728 " --> pdb=" O LYS C 673 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N VAL C 675 " --> pdb=" O TYR C 728 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N SER C 730 " --> pdb=" O VAL C 675 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N LEU C 677 " --> pdb=" O SER C 730 " (cutoff:3.500A) removed outlier: 8.252A pdb=" N ILE C 732 " --> pdb=" O LEU C 677 " (cutoff:3.500A) removed outlier: 8.988A pdb=" N CYS C 782 " --> pdb=" O ILE C 374 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N PHE C 376 " --> pdb=" O CYS C 782 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 442 through 443 removed outlier: 4.060A pdb=" N ARG C 442 " --> pdb=" O ILE C 650 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ILE C 650 " --> pdb=" O ARG C 442 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 939 through 947 removed outlier: 5.602A pdb=" N GLN C 939 " --> pdb=" O GLN C 958 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLN C 958 " --> pdb=" O GLN C 939 " (cutoff:3.500A) removed outlier: 15.508A pdb=" N LEU C 956 " --> pdb=" O TRP C 967 " (cutoff:3.500A) removed outlier: 13.186A pdb=" N TRP C 967 " --> pdb=" O LEU C 956 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N GLN C 958 " --> pdb=" O LEU C 965 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N LEU C 965 " --> pdb=" O GLN C 958 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N LEU C 964 " --> pdb=" O ARG C 997 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N PHE C 999 " --> pdb=" O LEU C 964 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N ARG C 966 " --> pdb=" O PHE C 999 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 53 through 54 removed outlier: 5.993A pdb=" N SER D 92 " --> pdb=" O LEU D 102 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 167 through 170 removed outlier: 6.886A pdb=" N SER D 167 " --> pdb=" O PHE D 294 " (cutoff:3.500A) removed outlier: 8.544A pdb=" N GLY D 296 " --> pdb=" O SER D 167 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N ILE D 169 " --> pdb=" O GLY D 296 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ARG D 200 " --> pdb=" O VAL D 267 " (cutoff:3.500A) removed outlier: 8.890A pdb=" N SER D 238 " --> pdb=" O ILE D 199 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N LEU D 201 " --> pdb=" O SER D 238 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 393 through 396 removed outlier: 7.248A pdb=" N ASP D 547 " --> pdb=" O ARG D 574 " (cutoff:3.500A) removed outlier: 8.725A pdb=" N MET D 536 " --> pdb=" O TYR D 438 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N LEU D 440 " --> pdb=" O MET D 536 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 519 through 522 removed outlier: 4.419A pdb=" N ALA D 513 " --> pdb=" O ILE D 498 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ILE D 498 " --> pdb=" O ALA D 513 " (cutoff:3.500A) 1052 hydrogen bonds defined for protein. 3102 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 42 hydrogen bonds 80 hydrogen bond angles 0 basepair planarities 17 basepair parallelities 33 stacking parallelities Total time for adding SS restraints: 10.80 Time building geometry restraints manager: 6.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6697 1.34 - 1.45: 4289 1.45 - 1.57: 13191 1.57 - 1.69: 106 1.69 - 1.81: 169 Bond restraints: 24452 Sorted by residual: bond pdb=" N GLU B1073 " pdb=" CA GLU B1073 " ideal model delta sigma weight residual 1.457 1.483 -0.025 1.29e-02 6.01e+03 3.86e+00 bond pdb=" N PRO B1051 " pdb=" CA PRO B1051 " ideal model delta sigma weight residual 1.457 1.479 -0.022 1.31e-02 5.83e+03 2.85e+00 bond pdb=" CA THR B 304 " pdb=" C THR B 304 " ideal model delta sigma weight residual 1.525 1.558 -0.033 2.10e-02 2.27e+03 2.51e+00 bond pdb=" C MET B 658 " pdb=" N PRO B 659 " ideal model delta sigma weight residual 1.335 1.355 -0.019 1.36e-02 5.41e+03 1.99e+00 bond pdb=" CA TYR B 173 " pdb=" C TYR B 173 " ideal model delta sigma weight residual 1.521 1.537 -0.016 1.14e-02 7.69e+03 1.98e+00 ... (remaining 24447 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.62: 32749 1.62 - 3.24: 563 3.24 - 4.86: 68 4.86 - 6.47: 20 6.47 - 8.09: 9 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 121.54 128.33 -6.79 1.91e+00 2.74e-01 1.26e+01 angle pdb=" C VAL B 657 " pdb=" N MET B 658 " pdb=" CA MET B 658 " ideal model delta sigma weight residual 120.09 124.51 -4.42 1.25e+00 6.40e-01 1.25e+01 angle pdb=" C ASN B1084 " pdb=" N TRP B1085 " pdb=" CA TRP B1085 " ideal model delta sigma weight residual 122.82 127.75 -4.93 1.42e+00 4.96e-01 1.20e+01 angle pdb=" N GLY B 656 " pdb=" CA GLY B 656 " pdb=" C GLY B 656 " ideal model delta sigma weight residual 110.60 115.08 -4.48 1.46e+00 4.69e-01 9.44e+00 angle pdb=" C GLN D 387 " pdb=" N GLN D 388 " pdb=" CA GLN D 388 " ideal model delta sigma weight residual 121.54 127.40 -5.86 1.91e+00 2.74e-01 9.40e+00 ... (remaining 33404 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.78: 13492 16.78 - 33.57: 730 33.57 - 50.35: 307 50.35 - 67.14: 79 67.14 - 83.92: 7 Dihedral angle restraints: 14615 sinusoidal: 6326 harmonic: 8289 Sorted by residual: dihedral pdb=" CA ILE B 400 " pdb=" C ILE B 400 " pdb=" N TRP B 401 " pdb=" CA TRP B 401 " ideal model delta harmonic sigma weight residual -180.00 -163.37 -16.63 0 5.00e+00 4.00e-02 1.11e+01 dihedral pdb=" CA GLY C 657 " pdb=" C GLY C 657 " pdb=" N PRO C 658 " pdb=" CA PRO C 658 " ideal model delta harmonic sigma weight residual 180.00 164.04 15.96 0 5.00e+00 4.00e-02 1.02e+01 dihedral pdb=" N ASN C 768 " pdb=" CA ASN C 768 " pdb=" CB ASN C 768 " pdb=" CG ASN C 768 " ideal model delta sinusoidal sigma weight residual -60.00 -118.97 58.97 3 1.50e+01 4.44e-03 9.47e+00 ... (remaining 14612 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 2613 0.034 - 0.069: 745 0.069 - 0.103: 227 0.103 - 0.137: 78 0.137 - 0.171: 10 Chirality restraints: 3673 Sorted by residual: chirality pdb=" CA LEU C 588 " pdb=" N LEU C 588 " pdb=" C LEU C 588 " pdb=" CB LEU C 588 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.35e-01 chirality pdb=" CA TYR B 173 " pdb=" N TYR B 173 " pdb=" C TYR B 173 " pdb=" CB TYR B 173 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.98e-01 chirality pdb=" CA LEU C 99 " pdb=" N LEU C 99 " pdb=" C LEU C 99 " pdb=" CB LEU C 99 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.65e-01 ... (remaining 3670 not shown) Planarity restraints: 4205 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY C 657 " 0.050 5.00e-02 4.00e+02 7.51e-02 9.02e+00 pdb=" N PRO C 658 " -0.130 5.00e-02 4.00e+02 pdb=" CA PRO C 658 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO C 658 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER C 419 " -0.036 5.00e-02 4.00e+02 5.40e-02 4.66e+00 pdb=" N PRO C 420 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO C 420 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 420 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 99 " 0.036 5.00e-02 4.00e+02 5.32e-02 4.52e+00 pdb=" N PRO C 100 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO C 100 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO C 100 " 0.030 5.00e-02 4.00e+02 ... (remaining 4202 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.82: 6709 2.82 - 3.34: 19747 3.34 - 3.86: 39494 3.86 - 4.38: 44353 4.38 - 4.90: 76387 Nonbonded interactions: 186690 Sorted by model distance: nonbonded pdb=" O LEU C 115 " pdb=" OG SER C 119 " model vdw 2.294 3.040 nonbonded pdb=" O THR D 533 " pdb=" OG1 THR D 533 " model vdw 2.321 3.040 nonbonded pdb=" OH TYR C 794 " pdb=" O ALA C 803 " model vdw 2.332 3.040 nonbonded pdb=" O TYR C 754 " pdb=" OG SER C 758 " model vdw 2.333 3.040 nonbonded pdb=" O2 DC X 27 " pdb=" N2 DG X 59 " model vdw 2.334 2.496 ... (remaining 186685 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.800 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: 0.990 Check model and map are aligned: 0.170 Set scattering table: 0.240 Process input model: 57.170 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7249 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 24452 Z= 0.142 Angle : 0.558 8.094 33409 Z= 0.336 Chirality : 0.039 0.171 3673 Planarity : 0.005 0.075 4205 Dihedral : 12.823 83.921 9243 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.90 % Allowed : 4.89 % Favored : 92.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.61 (0.11), residues: 2837 helix: -2.53 (0.09), residues: 1384 sheet: -0.89 (0.27), residues: 284 loop : -2.43 (0.14), residues: 1169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 652 HIS 0.004 0.000 HIS D 256 PHE 0.014 0.001 PHE B1023 TYR 0.012 0.001 TYR B1111 ARG 0.004 0.000 ARG B 399 Details of bonding type rmsd hydrogen bonds : bond 0.14036 ( 1094) hydrogen bonds : angle 6.49909 ( 3182) covalent geometry : bond 0.00250 (24452) covalent geometry : angle 0.55795 (33409) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 647 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 577 time to evaluate : 2.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 66 GLU cc_start: 0.7112 (tt0) cc_final: 0.6737 (tp30) REVERT: B 137 LEU cc_start: 0.9029 (mt) cc_final: 0.8822 (mt) REVERT: B 304 THR cc_start: 0.2275 (OUTLIER) cc_final: 0.1073 (p) REVERT: B 354 MET cc_start: 0.8311 (mtt) cc_final: 0.7980 (mtm) REVERT: B 514 TYR cc_start: 0.5926 (t80) cc_final: 0.5725 (t80) REVERT: B 735 LEU cc_start: 0.5925 (mt) cc_final: 0.5497 (mp) REVERT: B 756 PHE cc_start: 0.7654 (m-80) cc_final: 0.7350 (m-80) REVERT: B 842 LEU cc_start: 0.8491 (mt) cc_final: 0.8277 (mt) REVERT: B 860 LEU cc_start: 0.8178 (OUTLIER) cc_final: 0.7913 (pt) REVERT: B 940 LEU cc_start: 0.6118 (mt) cc_final: 0.5759 (mm) REVERT: B 1024 TYR cc_start: 0.5652 (m-80) cc_final: 0.5400 (m-10) REVERT: B 1058 VAL cc_start: 0.7867 (t) cc_final: 0.7390 (m) REVERT: B 1158 THR cc_start: 0.7728 (OUTLIER) cc_final: 0.6518 (p) REVERT: C 460 LEU cc_start: 0.8937 (tp) cc_final: 0.8648 (tt) REVERT: C 697 MET cc_start: 0.7577 (mtp) cc_final: 0.6978 (mtp) REVERT: C 781 THR cc_start: 0.8165 (m) cc_final: 0.7800 (p) REVERT: C 817 HIS cc_start: 0.7393 (OUTLIER) cc_final: 0.7159 (m90) REVERT: C 1000 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8549 (mt) REVERT: D 216 LEU cc_start: 0.5196 (mt) cc_final: 0.4768 (pp) REVERT: D 407 MET cc_start: 0.6652 (ttp) cc_final: 0.5882 (ptm) REVERT: D 415 TYR cc_start: 0.2918 (m-80) cc_final: 0.2246 (m-80) REVERT: D 430 LEU cc_start: 0.8443 (mp) cc_final: 0.8061 (mp) REVERT: D 462 MET cc_start: 0.4050 (mmt) cc_final: 0.3782 (mmt) REVERT: D 493 LEU cc_start: 0.7917 (OUTLIER) cc_final: 0.7712 (pp) REVERT: D 558 THR cc_start: 0.6561 (OUTLIER) cc_final: 0.6360 (t) REVERT: D 567 TYR cc_start: 0.7747 (t80) cc_final: 0.7459 (t80) REVERT: D 571 THR cc_start: 0.7677 (p) cc_final: 0.7474 (p) outliers start: 70 outliers final: 9 residues processed: 631 average time/residue: 0.3857 time to fit residues: 365.4553 Evaluate side-chains 310 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 294 time to evaluate : 2.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 860 LEU Chi-restraints excluded: chain B residue 1002 LEU Chi-restraints excluded: chain B residue 1158 THR Chi-restraints excluded: chain C residue 506 ILE Chi-restraints excluded: chain C residue 817 HIS Chi-restraints excluded: chain C residue 821 VAL Chi-restraints excluded: chain C residue 853 LEU Chi-restraints excluded: chain C residue 1000 LEU Chi-restraints excluded: chain D residue 108 TYR Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 350 ASP Chi-restraints excluded: chain D residue 493 LEU Chi-restraints excluded: chain D residue 558 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 243 optimal weight: 20.0000 chunk 218 optimal weight: 6.9990 chunk 121 optimal weight: 8.9990 chunk 74 optimal weight: 10.0000 chunk 147 optimal weight: 8.9990 chunk 116 optimal weight: 8.9990 chunk 225 optimal weight: 6.9990 chunk 87 optimal weight: 6.9990 chunk 137 optimal weight: 9.9990 chunk 168 optimal weight: 5.9990 chunk 261 optimal weight: 30.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 109 GLN B 120 GLN B 134 GLN B 150 GLN B 181 GLN ** B 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 458 ASN ** B 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 650 GLN B 713 GLN B 765 GLN B 769 HIS B 843 GLN B 848 GLN ** B 943 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 944 GLN ** B1057 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1072 HIS B1084 ASN B1133 HIS B1134 HIS C 113 HIS ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 191 GLN ** C 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 282 ASN C 336 HIS C 390 HIS C 423 GLN C 570 GLN C 725 GLN C 749 GLN C 759 HIS C 822 GLN C 843 HIS C 883 GLN C 925 GLN C 979 GLN C 984 HIS C1091 GLN C1108 GLN ** D 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 22 GLN ** D 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 50 HIS D 79 GLN D 89 GLN D 115 ASN ** D 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 128 HIS D 251 GLN D 328 GLN D 423 GLN ** D 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 44 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.103679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.076959 restraints weight = 82869.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.078638 restraints weight = 51745.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.079703 restraints weight = 38446.239| |-----------------------------------------------------------------------------| r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.4458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.172 24452 Z= 0.368 Angle : 0.869 13.253 33409 Z= 0.447 Chirality : 0.049 0.280 3673 Planarity : 0.007 0.066 4205 Dihedral : 13.694 80.221 3729 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 4.06 % Allowed : 12.22 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.14), residues: 2837 helix: -0.48 (0.12), residues: 1430 sheet: -0.66 (0.29), residues: 291 loop : -1.96 (0.16), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP C1045 HIS 0.012 0.002 HIS C 233 PHE 0.024 0.003 PHE C 86 TYR 0.023 0.003 TYR C 728 ARG 0.011 0.001 ARG D 349 Details of bonding type rmsd hydrogen bonds : bond 0.04895 ( 1094) hydrogen bonds : angle 4.94248 ( 3182) covalent geometry : bond 0.00805 (24452) covalent geometry : angle 0.86947 (33409) *********************** 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 376 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 278 time to evaluate : 2.485 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 66 GLU cc_start: 0.8097 (tt0) cc_final: 0.7892 (tm-30) REVERT: B 146 MET cc_start: 0.7948 (tpp) cc_final: 0.7670 (tpt) REVERT: B 354 MET cc_start: 0.8468 (mtt) cc_final: 0.7991 (mtm) REVERT: B 431 MET cc_start: 0.8916 (OUTLIER) cc_final: 0.8624 (mpp) REVERT: B 492 LYS cc_start: 0.7809 (OUTLIER) cc_final: 0.7397 (pptt) REVERT: B 753 TRP cc_start: 0.8862 (OUTLIER) cc_final: 0.8379 (t60) REVERT: B 871 GLN cc_start: 0.6085 (tt0) cc_final: 0.5422 (mp10) REVERT: B 944 GLN cc_start: 0.8475 (mt0) cc_final: 0.8267 (mp10) REVERT: B 1002 LEU cc_start: 0.7827 (OUTLIER) cc_final: 0.7540 (pp) REVERT: B 1004 GLU cc_start: 0.8762 (tm-30) cc_final: 0.8029 (pm20) REVERT: B 1066 ILE cc_start: 0.8619 (mt) cc_final: 0.8370 (mm) REVERT: C 260 LEU cc_start: 0.9147 (tp) cc_final: 0.8931 (tp) REVERT: C 569 MET cc_start: 0.6996 (tmm) cc_final: 0.6705 (tmm) REVERT: C 653 ARG cc_start: 0.8000 (mtm-85) cc_final: 0.7568 (mpp80) REVERT: C 781 THR cc_start: 0.9132 (m) cc_final: 0.8883 (p) REVERT: C 817 HIS cc_start: 0.7698 (OUTLIER) cc_final: 0.6611 (m90) REVERT: C 1000 LEU cc_start: 0.9453 (OUTLIER) cc_final: 0.9217 (mt) REVERT: D 19 LEU cc_start: 0.9080 (tp) cc_final: 0.8824 (tp) REVERT: D 100 MET cc_start: 0.8788 (mpp) cc_final: 0.8318 (mmm) REVERT: D 112 MET cc_start: 0.8204 (mmm) cc_final: 0.7911 (mtm) REVERT: D 125 GLU cc_start: 0.8308 (pt0) cc_final: 0.8061 (pp20) REVERT: D 222 GLN cc_start: 0.8415 (OUTLIER) cc_final: 0.7964 (tm-30) REVERT: D 415 TYR cc_start: 0.3499 (m-80) cc_final: 0.2989 (m-80) REVERT: D 462 MET cc_start: 0.4469 (mmt) cc_final: 0.4188 (mmt) REVERT: D 484 ILE cc_start: 0.6995 (OUTLIER) cc_final: 0.6391 (tp) REVERT: D 567 TYR cc_start: 0.8019 (t80) cc_final: 0.7699 (t80) REVERT: D 580 TYR cc_start: 0.4994 (m-80) cc_final: 0.4710 (m-80) outliers start: 98 outliers final: 46 residues processed: 359 average time/residue: 0.3691 time to fit residues: 204.1823 Evaluate side-chains 259 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 205 time to evaluate : 2.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 431 MET Chi-restraints excluded: chain B residue 492 LYS Chi-restraints excluded: chain B residue 514 TYR Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 566 GLN Chi-restraints excluded: chain B residue 640 VAL Chi-restraints excluded: chain B residue 696 GLU Chi-restraints excluded: chain B residue 753 TRP Chi-restraints excluded: chain B residue 804 VAL Chi-restraints excluded: chain B residue 817 VAL Chi-restraints excluded: chain B residue 947 ARG Chi-restraints excluded: chain B residue 1002 LEU Chi-restraints excluded: chain B residue 1025 LEU Chi-restraints excluded: chain B residue 1069 VAL Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 381 SER Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 404 THR Chi-restraints excluded: chain C residue 455 ILE Chi-restraints excluded: chain C residue 456 SER Chi-restraints excluded: chain C residue 484 ASP Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 506 ILE Chi-restraints excluded: chain C residue 528 LEU Chi-restraints excluded: chain C residue 529 THR Chi-restraints excluded: chain C residue 612 ILE Chi-restraints excluded: chain C residue 651 SER Chi-restraints excluded: chain C residue 817 HIS Chi-restraints excluded: chain C residue 821 VAL Chi-restraints excluded: chain C residue 853 LEU Chi-restraints excluded: chain C residue 885 LEU Chi-restraints excluded: chain C residue 965 LEU Chi-restraints excluded: chain C residue 1000 LEU Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 108 TYR Chi-restraints excluded: chain D residue 222 GLN Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 350 ASP Chi-restraints excluded: chain D residue 471 HIS Chi-restraints excluded: chain D residue 484 ILE Chi-restraints excluded: chain D residue 493 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 3 optimal weight: 0.9990 chunk 268 optimal weight: 20.0000 chunk 253 optimal weight: 30.0000 chunk 224 optimal weight: 10.0000 chunk 244 optimal weight: 5.9990 chunk 199 optimal weight: 0.9980 chunk 64 optimal weight: 0.8980 chunk 127 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 99 optimal weight: 8.9990 chunk 200 optimal weight: 0.6980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 134 GLN B 222 HIS B 525 GLN B 843 GLN B 868 GLN ** B1057 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 228 GLN C 237 HIS C 282 ASN C 321 GLN D 15 GLN ** D 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 318 ASN D 328 GLN ** D 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.105519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.079087 restraints weight = 81314.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.080863 restraints weight = 49353.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.082007 restraints weight = 36131.178| |-----------------------------------------------------------------------------| r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.4640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 24452 Z= 0.125 Angle : 0.590 12.139 33409 Z= 0.297 Chirality : 0.040 0.187 3673 Planarity : 0.004 0.055 4205 Dihedral : 13.524 86.013 3720 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.40 % Allowed : 13.50 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.15), residues: 2837 helix: 0.58 (0.13), residues: 1417 sheet: -0.67 (0.29), residues: 285 loop : -1.61 (0.17), residues: 1135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 574 HIS 0.007 0.001 HIS B 222 PHE 0.024 0.001 PHE B 351 TYR 0.027 0.001 TYR D 404 ARG 0.010 0.001 ARG C 23 Details of bonding type rmsd hydrogen bonds : bond 0.03571 ( 1094) hydrogen bonds : angle 4.36821 ( 3182) covalent geometry : bond 0.00279 (24452) covalent geometry : angle 0.59019 (33409) *********************** 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 310 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 252 time to evaluate : 2.461 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 66 GLU cc_start: 0.7894 (tt0) cc_final: 0.7534 (tp30) REVERT: B 354 MET cc_start: 0.8406 (mtt) cc_final: 0.7812 (mtm) REVERT: B 426 ASP cc_start: 0.8852 (OUTLIER) cc_final: 0.8494 (p0) REVERT: B 492 LYS cc_start: 0.7888 (OUTLIER) cc_final: 0.7518 (pptt) REVERT: B 518 MET cc_start: 0.8252 (mmt) cc_final: 0.7563 (mmm) REVERT: B 753 TRP cc_start: 0.8930 (OUTLIER) cc_final: 0.8451 (t60) REVERT: B 871 GLN cc_start: 0.5535 (tt0) cc_final: 0.5155 (mp10) REVERT: B 944 GLN cc_start: 0.8443 (mt0) cc_final: 0.8218 (mp10) REVERT: B 1002 LEU cc_start: 0.7840 (OUTLIER) cc_final: 0.7514 (pp) REVERT: B 1004 GLU cc_start: 0.8807 (tm-30) cc_final: 0.8064 (pm20) REVERT: C 411 MET cc_start: 0.7963 (mmt) cc_final: 0.7310 (mmm) REVERT: C 653 ARG cc_start: 0.8086 (mtm-85) cc_final: 0.7767 (mpp80) REVERT: C 781 THR cc_start: 0.9198 (m) cc_final: 0.8848 (p) REVERT: C 817 HIS cc_start: 0.7683 (OUTLIER) cc_final: 0.6910 (m90) REVERT: C 1031 MET cc_start: 0.8826 (mmm) cc_final: 0.8605 (mmm) REVERT: D 269 ASP cc_start: 0.7972 (p0) cc_final: 0.7668 (p0) REVERT: D 415 TYR cc_start: 0.3320 (m-80) cc_final: 0.2732 (m-80) REVERT: D 462 MET cc_start: 0.4311 (mmt) cc_final: 0.4053 (mmt) REVERT: D 466 ARG cc_start: 0.6797 (mmt-90) cc_final: 0.6361 (tpp-160) REVERT: D 504 ARG cc_start: 0.8210 (ptm160) cc_final: 0.7426 (ptp-170) REVERT: D 511 TRP cc_start: 0.7883 (m100) cc_final: 0.7096 (m100) REVERT: D 562 THR cc_start: 0.8249 (OUTLIER) cc_final: 0.8023 (t) REVERT: D 575 ARG cc_start: 0.7640 (mmm160) cc_final: 0.7188 (tpp80) outliers start: 58 outliers final: 29 residues processed: 299 average time/residue: 0.3375 time to fit residues: 159.6438 Evaluate side-chains 246 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 211 time to evaluate : 2.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 151 GLN Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 426 ASP Chi-restraints excluded: chain B residue 492 LYS Chi-restraints excluded: chain B residue 735 LEU Chi-restraints excluded: chain B residue 753 TRP Chi-restraints excluded: chain B residue 813 CYS Chi-restraints excluded: chain B residue 1002 LEU Chi-restraints excluded: chain B residue 1025 LEU Chi-restraints excluded: chain B residue 1027 ILE Chi-restraints excluded: chain B residue 1088 GLU Chi-restraints excluded: chain B residue 1128 ASP Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 381 SER Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 404 THR Chi-restraints excluded: chain C residue 422 ILE Chi-restraints excluded: chain C residue 506 ILE Chi-restraints excluded: chain C residue 528 LEU Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 612 ILE Chi-restraints excluded: chain C residue 651 SER Chi-restraints excluded: chain C residue 817 HIS Chi-restraints excluded: chain C residue 821 VAL Chi-restraints excluded: chain C residue 853 LEU Chi-restraints excluded: chain C residue 866 ASP Chi-restraints excluded: chain C residue 945 LEU Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 108 TYR Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain D residue 350 ASP Chi-restraints excluded: chain D residue 471 HIS 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 22 optimal weight: 9.9990 chunk 94 optimal weight: 20.0000 chunk 103 optimal weight: 20.0000 chunk 150 optimal weight: 5.9990 chunk 42 optimal weight: 9.9990 chunk 223 optimal weight: 0.9980 chunk 209 optimal weight: 7.9990 chunk 111 optimal weight: 3.9990 chunk 4 optimal weight: 6.9990 chunk 255 optimal weight: 10.0000 chunk 284 optimal weight: 10.0000 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 112 GLN B 134 GLN B 843 GLN ** B1057 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 87 ASN ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 300 GLN D 328 GLN D 469 HIS ** D 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.100464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.074354 restraints weight = 82812.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.075975 restraints weight = 50379.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.077054 restraints weight = 37126.947| |-----------------------------------------------------------------------------| r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.5488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.116 24452 Z= 0.263 Angle : 0.702 9.271 33409 Z= 0.352 Chirality : 0.043 0.191 3673 Planarity : 0.005 0.052 4205 Dihedral : 13.778 85.278 3716 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 3.56 % Allowed : 13.75 % Favored : 82.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.15), residues: 2837 helix: 0.79 (0.13), residues: 1424 sheet: -0.70 (0.29), residues: 288 loop : -1.54 (0.17), residues: 1125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 574 HIS 0.007 0.001 HIS C 233 PHE 0.021 0.002 PHE B 428 TYR 0.019 0.002 TYR C 256 ARG 0.014 0.001 ARG B 947 Details of bonding type rmsd hydrogen bonds : bond 0.04118 ( 1094) hydrogen bonds : angle 4.57461 ( 3182) covalent geometry : bond 0.00596 (24452) covalent geometry : angle 0.70203 (33409) *********************** 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 304 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 218 time to evaluate : 3.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 66 GLU cc_start: 0.8014 (tt0) cc_final: 0.7762 (tp30) REVERT: B 146 MET cc_start: 0.7754 (ttp) cc_final: 0.7533 (ttt) REVERT: B 171 HIS cc_start: 0.8081 (OUTLIER) cc_final: 0.7861 (m-70) REVERT: B 354 MET cc_start: 0.8509 (mtt) cc_final: 0.7928 (mtm) REVERT: B 492 LYS cc_start: 0.8175 (OUTLIER) cc_final: 0.7813 (pptt) REVERT: B 753 TRP cc_start: 0.9083 (OUTLIER) cc_final: 0.8555 (t60) REVERT: B 871 GLN cc_start: 0.6025 (tt0) cc_final: 0.5615 (mp10) REVERT: B 944 GLN cc_start: 0.8462 (mt0) cc_final: 0.8159 (mt0) REVERT: B 1004 GLU cc_start: 0.8682 (tm-30) cc_final: 0.8289 (pm20) REVERT: C 411 MET cc_start: 0.8031 (mmt) cc_final: 0.7208 (mmm) REVERT: C 653 ARG cc_start: 0.8081 (mtm-85) cc_final: 0.7720 (mpp80) REVERT: C 660 ASN cc_start: 0.7471 (OUTLIER) cc_final: 0.7265 (m-40) REVERT: C 817 HIS cc_start: 0.7846 (OUTLIER) cc_final: 0.6620 (m90) REVERT: D 112 MET cc_start: 0.8254 (mmm) cc_final: 0.7790 (ttm) REVERT: D 212 LEU cc_start: 0.9327 (tp) cc_final: 0.9078 (tp) REVERT: D 222 GLN cc_start: 0.8483 (OUTLIER) cc_final: 0.8074 (tm-30) REVERT: D 269 ASP cc_start: 0.7992 (p0) cc_final: 0.7719 (p0) REVERT: D 415 TYR cc_start: 0.3846 (m-80) cc_final: 0.3102 (m-80) REVERT: D 462 MET cc_start: 0.4504 (mmt) cc_final: 0.4275 (mmt) REVERT: D 466 ARG cc_start: 0.6812 (mmt-90) cc_final: 0.6539 (tpp-160) REVERT: D 511 TRP cc_start: 0.7982 (m100) cc_final: 0.7514 (m100) REVERT: D 514 MET cc_start: 0.6407 (mmt) cc_final: 0.5296 (mtt) REVERT: D 562 THR cc_start: 0.8331 (OUTLIER) cc_final: 0.8121 (t) REVERT: D 575 ARG cc_start: 0.7723 (mmm160) cc_final: 0.7334 (tpp80) outliers start: 86 outliers final: 52 residues processed: 285 average time/residue: 0.3262 time to fit residues: 152.3851 Evaluate side-chains 255 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 196 time to evaluate : 2.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 151 GLN Chi-restraints excluded: chain B residue 171 HIS Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 492 LYS Chi-restraints excluded: chain B residue 514 TYR Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 566 GLN Chi-restraints excluded: chain B residue 735 LEU Chi-restraints excluded: chain B residue 753 TRP Chi-restraints excluded: chain B residue 804 VAL Chi-restraints excluded: chain B residue 813 CYS Chi-restraints excluded: chain B residue 1002 LEU Chi-restraints excluded: chain B residue 1025 LEU Chi-restraints excluded: chain B residue 1027 ILE Chi-restraints excluded: chain B residue 1056 MET Chi-restraints excluded: chain B residue 1066 ILE Chi-restraints excluded: chain B residue 1069 VAL Chi-restraints excluded: chain B residue 1128 ASP Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 404 THR Chi-restraints excluded: chain C residue 422 ILE Chi-restraints excluded: chain C residue 455 ILE Chi-restraints excluded: chain C residue 484 ASP Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 506 ILE Chi-restraints excluded: chain C residue 528 LEU Chi-restraints excluded: chain C residue 551 ASP Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 612 ILE Chi-restraints excluded: chain C residue 651 SER Chi-restraints excluded: chain C residue 660 ASN Chi-restraints excluded: chain C residue 817 HIS Chi-restraints excluded: chain C residue 821 VAL Chi-restraints excluded: chain C residue 853 LEU Chi-restraints excluded: chain C residue 879 GLN Chi-restraints excluded: chain C residue 945 LEU Chi-restraints excluded: chain C residue 965 LEU Chi-restraints excluded: chain C residue 1106 VAL Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 108 TYR Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 170 SER Chi-restraints excluded: chain D residue 222 GLN Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain D residue 350 ASP Chi-restraints excluded: chain D residue 471 HIS Chi-restraints excluded: chain D residue 484 ILE Chi-restraints excluded: chain D residue 562 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 43 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 191 optimal weight: 2.9990 chunk 108 optimal weight: 8.9990 chunk 230 optimal weight: 30.0000 chunk 149 optimal weight: 8.9990 chunk 283 optimal weight: 10.0000 chunk 76 optimal weight: 1.9990 chunk 210 optimal weight: 6.9990 chunk 259 optimal weight: 20.0000 chunk 84 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 843 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1057 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 87 ASN ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 423 GLN ** C 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 328 GLN ** D 523 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 = 0.3885 r_free = 0.3885 target = 0.101734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.075398 restraints weight = 82167.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.077158 restraints weight = 48868.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.078274 restraints weight = 35358.935| |-----------------------------------------------------------------------------| r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.5583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 24452 Z= 0.151 Angle : 0.591 10.679 33409 Z= 0.297 Chirality : 0.040 0.215 3673 Planarity : 0.004 0.054 4205 Dihedral : 13.755 88.253 3716 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.53 % Allowed : 15.40 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.16), residues: 2837 helix: 1.14 (0.14), residues: 1423 sheet: -0.82 (0.29), residues: 287 loop : -1.39 (0.18), residues: 1127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 574 HIS 0.004 0.001 HIS C 779 PHE 0.016 0.001 PHE B 351 TYR 0.029 0.002 TYR C 256 ARG 0.006 0.000 ARG B 345 Details of bonding type rmsd hydrogen bonds : bond 0.03591 ( 1094) hydrogen bonds : angle 4.31714 ( 3182) covalent geometry : bond 0.00345 (24452) covalent geometry : angle 0.59069 (33409) *********************** 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 281 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 220 time to evaluate : 2.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 66 GLU cc_start: 0.7985 (tt0) cc_final: 0.7706 (tp30) REVERT: B 354 MET cc_start: 0.8451 (mtt) cc_final: 0.7861 (mtm) REVERT: B 492 LYS cc_start: 0.8218 (OUTLIER) cc_final: 0.7919 (pptt) REVERT: B 735 LEU cc_start: 0.5035 (OUTLIER) cc_final: 0.4505 (mp) REVERT: B 753 TRP cc_start: 0.9050 (OUTLIER) cc_final: 0.8586 (t60) REVERT: B 871 GLN cc_start: 0.6051 (tt0) cc_final: 0.5657 (mp10) REVERT: B 944 GLN cc_start: 0.8458 (mt0) cc_final: 0.8137 (mt0) REVERT: B 1140 TYR cc_start: 0.7454 (m-80) cc_final: 0.6722 (m-80) REVERT: C 1 MET cc_start: 0.6454 (tpt) cc_final: 0.5860 (tmm) REVERT: C 411 MET cc_start: 0.8191 (mmt) cc_final: 0.7282 (mmm) REVERT: C 653 ARG cc_start: 0.8218 (mtm-85) cc_final: 0.7932 (mpp80) REVERT: C 781 THR cc_start: 0.9272 (m) cc_final: 0.9015 (p) REVERT: C 787 MET cc_start: 0.8698 (mmp) cc_final: 0.8407 (mmm) REVERT: C 817 HIS cc_start: 0.7700 (OUTLIER) cc_final: 0.6459 (m90) REVERT: D 112 MET cc_start: 0.8077 (mmm) cc_final: 0.7650 (ttm) REVERT: D 212 LEU cc_start: 0.9313 (tp) cc_final: 0.9064 (tp) REVERT: D 222 GLN cc_start: 0.8518 (OUTLIER) cc_final: 0.8005 (tm-30) REVERT: D 269 ASP cc_start: 0.7941 (p0) cc_final: 0.7661 (p0) REVERT: D 415 TYR cc_start: 0.3830 (m-80) cc_final: 0.3159 (m-80) REVERT: D 462 MET cc_start: 0.4635 (mmt) cc_final: 0.4355 (mmt) REVERT: D 466 ARG cc_start: 0.6885 (mmt-90) cc_final: 0.6562 (tpp-160) REVERT: D 504 ARG cc_start: 0.8327 (ptm160) cc_final: 0.7443 (ptp-170) REVERT: D 511 TRP cc_start: 0.7992 (m100) cc_final: 0.7333 (m100) REVERT: D 514 MET cc_start: 0.6501 (mmt) cc_final: 0.5624 (mtt) REVERT: D 575 ARG cc_start: 0.7697 (mmm160) cc_final: 0.7328 (tpp80) outliers start: 61 outliers final: 40 residues processed: 267 average time/residue: 0.3461 time to fit residues: 148.9255 Evaluate side-chains 246 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 201 time to evaluate : 2.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 151 GLN Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 492 LYS Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 566 GLN Chi-restraints excluded: chain B residue 735 LEU Chi-restraints excluded: chain B residue 753 TRP Chi-restraints excluded: chain B residue 813 CYS Chi-restraints excluded: chain B residue 1002 LEU Chi-restraints excluded: chain B residue 1025 LEU Chi-restraints excluded: chain B residue 1027 ILE Chi-restraints excluded: chain B residue 1066 ILE Chi-restraints excluded: chain B residue 1069 VAL Chi-restraints excluded: chain B residue 1128 ASP Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 404 THR Chi-restraints excluded: chain C residue 422 ILE Chi-restraints excluded: chain C residue 492 TYR Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 506 ILE Chi-restraints excluded: chain C residue 528 LEU Chi-restraints excluded: chain C residue 551 ASP Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 612 ILE Chi-restraints excluded: chain C residue 651 SER Chi-restraints excluded: chain C residue 817 HIS Chi-restraints excluded: chain C residue 821 VAL Chi-restraints excluded: chain C residue 853 LEU Chi-restraints excluded: chain C residue 885 LEU Chi-restraints excluded: chain C residue 945 LEU Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 108 TYR Chi-restraints excluded: chain D residue 222 GLN Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain D residue 350 ASP Chi-restraints excluded: chain D residue 471 HIS Chi-restraints excluded: chain D residue 484 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 134 optimal weight: 2.9990 chunk 162 optimal weight: 9.9990 chunk 110 optimal weight: 3.9990 chunk 208 optimal weight: 0.7980 chunk 26 optimal weight: 10.0000 chunk 277 optimal weight: 20.0000 chunk 203 optimal weight: 1.9990 chunk 89 optimal weight: 30.0000 chunk 194 optimal weight: 10.0000 chunk 182 optimal weight: 5.9990 chunk 144 optimal weight: 10.0000 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 134 GLN ** B 843 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1057 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1091 GLN ** D 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 328 GLN ** D 523 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 = 0.3875 r_free = 0.3875 target = 0.101227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.074782 restraints weight = 81674.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.076485 restraints weight = 49282.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.077592 restraints weight = 36149.680| |-----------------------------------------------------------------------------| r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.5836 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= 0.172 Angle : 0.607 9.178 33409 Z= 0.304 Chirality : 0.040 0.162 3673 Planarity : 0.004 0.052 4205 Dihedral : 13.791 88.816 3716 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.73 % Allowed : 15.20 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.16), residues: 2837 helix: 1.26 (0.14), residues: 1424 sheet: -0.79 (0.29), residues: 285 loop : -1.32 (0.18), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 153 HIS 0.005 0.001 HIS B 130 PHE 0.019 0.001 PHE C 86 TYR 0.025 0.002 TYR C 256 ARG 0.006 0.000 ARG B 345 Details of bonding type rmsd hydrogen bonds : bond 0.03651 ( 1094) hydrogen bonds : angle 4.30532 ( 3182) covalent geometry : bond 0.00389 (24452) covalent geometry : angle 0.60672 (33409) *********************** 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 281 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 215 time to evaluate : 2.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 66 GLU cc_start: 0.7966 (tt0) cc_final: 0.7732 (tp30) REVERT: B 354 MET cc_start: 0.8428 (mtt) cc_final: 0.7868 (mtm) REVERT: B 492 LYS cc_start: 0.8335 (OUTLIER) cc_final: 0.7995 (pptt) REVERT: B 735 LEU cc_start: 0.5352 (OUTLIER) cc_final: 0.4882 (mp) REVERT: B 753 TRP cc_start: 0.9039 (OUTLIER) cc_final: 0.8610 (t60) REVERT: B 842 LEU cc_start: 0.8702 (mt) cc_final: 0.8366 (tp) REVERT: B 871 GLN cc_start: 0.6055 (tt0) cc_final: 0.5789 (mp10) REVERT: B 944 GLN cc_start: 0.8555 (mt0) cc_final: 0.8217 (mt0) REVERT: B 1088 GLU cc_start: 0.6829 (OUTLIER) cc_final: 0.6485 (tp30) REVERT: B 1140 TYR cc_start: 0.7489 (m-80) cc_final: 0.6837 (m-80) REVERT: C 1 MET cc_start: 0.6440 (tpt) cc_final: 0.5648 (tmm) REVERT: C 411 MET cc_start: 0.8232 (mmt) cc_final: 0.7502 (mmm) REVERT: C 817 HIS cc_start: 0.7752 (OUTLIER) cc_final: 0.6534 (m90) REVERT: D 212 LEU cc_start: 0.9332 (tp) cc_final: 0.9110 (tp) REVERT: D 222 GLN cc_start: 0.8521 (OUTLIER) cc_final: 0.8024 (tm-30) REVERT: D 269 ASP cc_start: 0.8004 (p0) cc_final: 0.7786 (p0) REVERT: D 415 TYR cc_start: 0.3809 (m-80) cc_final: 0.3102 (m-80) REVERT: D 462 MET cc_start: 0.4680 (mmt) cc_final: 0.4466 (mmt) REVERT: D 466 ARG cc_start: 0.6599 (mmt-90) cc_final: 0.6331 (tpp-160) REVERT: D 484 ILE cc_start: 0.6490 (OUTLIER) cc_final: 0.6206 (tp) REVERT: D 504 ARG cc_start: 0.8290 (ptm160) cc_final: 0.7440 (ptp-170) REVERT: D 511 TRP cc_start: 0.7962 (m100) cc_final: 0.7334 (m100) REVERT: D 514 MET cc_start: 0.6518 (mmt) cc_final: 0.5733 (mtt) REVERT: D 575 ARG cc_start: 0.7725 (mmm160) cc_final: 0.7385 (tpp80) outliers start: 66 outliers final: 42 residues processed: 264 average time/residue: 0.3136 time to fit residues: 134.4372 Evaluate side-chains 247 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 198 time to evaluate : 2.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 492 LYS Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 563 GLU Chi-restraints excluded: chain B residue 566 GLN Chi-restraints excluded: chain B residue 735 LEU Chi-restraints excluded: chain B residue 753 TRP Chi-restraints excluded: chain B residue 813 CYS Chi-restraints excluded: chain B residue 1002 LEU Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1025 LEU Chi-restraints excluded: chain B residue 1027 ILE Chi-restraints excluded: chain B residue 1066 ILE Chi-restraints excluded: chain B residue 1069 VAL Chi-restraints excluded: chain B residue 1088 GLU Chi-restraints excluded: chain B residue 1128 ASP Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 404 THR Chi-restraints excluded: chain C residue 422 ILE Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 506 ILE Chi-restraints excluded: chain C residue 528 LEU Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 551 ASP Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 612 ILE Chi-restraints excluded: chain C residue 651 SER Chi-restraints excluded: chain C residue 817 HIS Chi-restraints excluded: chain C residue 821 VAL Chi-restraints excluded: chain C residue 853 LEU Chi-restraints excluded: chain C residue 885 LEU Chi-restraints excluded: chain C residue 945 LEU Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 108 TYR Chi-restraints excluded: chain D residue 170 SER Chi-restraints excluded: chain D residue 222 GLN Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain D residue 350 ASP Chi-restraints excluded: chain D residue 471 HIS Chi-restraints excluded: chain D residue 484 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 180 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 212 optimal weight: 0.0370 chunk 273 optimal weight: 10.0000 chunk 28 optimal weight: 20.0000 chunk 127 optimal weight: 10.0000 chunk 185 optimal weight: 9.9990 chunk 120 optimal weight: 0.7980 chunk 4 optimal weight: 0.0040 chunk 55 optimal weight: 0.9990 chunk 136 optimal weight: 9.9990 overall best weight: 0.5672 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 843 GLN B1057 GLN ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 522 HIS C 984 HIS ** D 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 328 GLN ** D 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.102894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.076836 restraints weight = 82199.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.078659 restraints weight = 48799.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.079802 restraints weight = 35080.518| |-----------------------------------------------------------------------------| r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.5779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 24452 Z= 0.103 Angle : 0.562 9.534 33409 Z= 0.278 Chirality : 0.039 0.173 3673 Planarity : 0.004 0.056 4205 Dihedral : 13.720 86.045 3716 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.86 % Allowed : 16.31 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.16), residues: 2837 helix: 1.45 (0.14), residues: 1428 sheet: -0.83 (0.29), residues: 296 loop : -1.21 (0.18), residues: 1113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 153 HIS 0.006 0.001 HIS D 241 PHE 0.017 0.001 PHE B 351 TYR 0.020 0.001 TYR C 256 ARG 0.006 0.000 ARG C 491 Details of bonding type rmsd hydrogen bonds : bond 0.03402 ( 1094) hydrogen bonds : angle 4.07145 ( 3182) covalent geometry : bond 0.00225 (24452) covalent geometry : angle 0.56217 (33409) *********************** 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 271 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 226 time to evaluate : 2.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 66 GLU cc_start: 0.7957 (tt0) cc_final: 0.7649 (tp30) REVERT: B 354 MET cc_start: 0.8391 (mtt) cc_final: 0.7864 (mtm) REVERT: B 735 LEU cc_start: 0.5688 (OUTLIER) cc_final: 0.5243 (mp) REVERT: B 753 TRP cc_start: 0.9006 (OUTLIER) cc_final: 0.8596 (t60) REVERT: B 842 LEU cc_start: 0.8735 (mt) cc_final: 0.8505 (tp) REVERT: B 871 GLN cc_start: 0.6051 (tt0) cc_final: 0.5646 (mp10) REVERT: B 1140 TYR cc_start: 0.7530 (m-80) cc_final: 0.6709 (m-10) REVERT: C 1 MET cc_start: 0.6464 (tpt) cc_final: 0.5529 (tmm) REVERT: C 411 MET cc_start: 0.8260 (mmt) cc_final: 0.7688 (mmm) REVERT: C 781 THR cc_start: 0.9256 (m) cc_final: 0.8954 (p) REVERT: C 817 HIS cc_start: 0.7702 (OUTLIER) cc_final: 0.6387 (m90) REVERT: D 112 MET cc_start: 0.7965 (mmm) cc_final: 0.7557 (ttm) REVERT: D 222 GLN cc_start: 0.8575 (OUTLIER) cc_final: 0.8053 (tm-30) REVERT: D 266 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.8393 (tt) REVERT: D 269 ASP cc_start: 0.8033 (p0) cc_final: 0.7757 (p0) REVERT: D 350 ASP cc_start: 0.6889 (OUTLIER) cc_final: 0.6517 (p0) REVERT: D 415 TYR cc_start: 0.3868 (m-80) cc_final: 0.3193 (m-80) REVERT: D 462 MET cc_start: 0.4607 (mmt) cc_final: 0.4280 (mmt) REVERT: D 466 ARG cc_start: 0.6509 (mmt-90) cc_final: 0.6205 (tpp-160) REVERT: D 504 ARG cc_start: 0.8224 (ptm160) cc_final: 0.7405 (ptp-170) REVERT: D 511 TRP cc_start: 0.7954 (m100) cc_final: 0.7218 (m100) REVERT: D 514 MET cc_start: 0.6517 (mmt) cc_final: 0.5879 (mtt) outliers start: 45 outliers final: 26 residues processed: 259 average time/residue: 0.3219 time to fit residues: 135.1475 Evaluate side-chains 239 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 207 time to evaluate : 2.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 563 GLU Chi-restraints excluded: chain B residue 604 MET Chi-restraints excluded: chain B residue 735 LEU Chi-restraints excluded: chain B residue 753 TRP Chi-restraints excluded: chain B residue 1002 LEU Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1025 LEU Chi-restraints excluded: chain B residue 1027 ILE Chi-restraints excluded: chain B residue 1066 ILE Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 404 THR Chi-restraints excluded: chain C residue 422 ILE Chi-restraints excluded: chain C residue 551 ASP Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 801 SER Chi-restraints excluded: chain C residue 817 HIS Chi-restraints excluded: chain C residue 821 VAL Chi-restraints excluded: chain C residue 853 LEU Chi-restraints excluded: chain C residue 945 LEU Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 108 TYR Chi-restraints excluded: chain D residue 170 SER Chi-restraints excluded: chain D residue 222 GLN Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain D residue 350 ASP Chi-restraints excluded: chain D residue 471 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 212 optimal weight: 10.0000 chunk 121 optimal weight: 8.9990 chunk 154 optimal weight: 0.8980 chunk 33 optimal weight: 10.0000 chunk 6 optimal weight: 0.9990 chunk 250 optimal weight: 10.0000 chunk 188 optimal weight: 10.0000 chunk 94 optimal weight: 20.0000 chunk 255 optimal weight: 10.0000 chunk 183 optimal weight: 5.9990 chunk 95 optimal weight: 5.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 134 GLN ** B 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 843 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 264 GLN C 288 ASN C 984 HIS ** D 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 328 GLN ** D 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.101452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.075824 restraints weight = 82555.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.077405 restraints weight = 51243.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.078354 restraints weight = 38220.464| |-----------------------------------------------------------------------------| r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.6300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 24452 Z= 0.233 Angle : 0.672 10.023 33409 Z= 0.337 Chirality : 0.043 0.229 3673 Planarity : 0.004 0.048 4205 Dihedral : 13.848 87.147 3714 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 2.48 % Allowed : 16.27 % Favored : 81.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.16), residues: 2837 helix: 1.22 (0.14), residues: 1433 sheet: -0.85 (0.29), residues: 295 loop : -1.26 (0.18), residues: 1109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 153 HIS 0.006 0.001 HIS C 779 PHE 0.016 0.002 PHE B 428 TYR 0.018 0.002 TYR C 256 ARG 0.006 0.001 ARG D 164 Details of bonding type rmsd hydrogen bonds : bond 0.03975 ( 1094) hydrogen bonds : angle 4.43253 ( 3182) covalent geometry : bond 0.00526 (24452) covalent geometry : angle 0.67225 (33409) *********************** 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 267 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 207 time to evaluate : 2.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 735 LEU cc_start: 0.5956 (OUTLIER) cc_final: 0.5488 (mp) REVERT: B 753 TRP cc_start: 0.9010 (OUTLIER) cc_final: 0.8597 (t60) REVERT: B 871 GLN cc_start: 0.6063 (tt0) cc_final: 0.5841 (mp10) REVERT: B 944 GLN cc_start: 0.8632 (mt0) cc_final: 0.8318 (mp10) REVERT: B 1102 MET cc_start: 0.7677 (mmm) cc_final: 0.7114 (tpt) REVERT: B 1140 TYR cc_start: 0.7498 (m-80) cc_final: 0.6724 (m-10) REVERT: C 230 LEU cc_start: 0.9056 (OUTLIER) cc_final: 0.8856 (tt) REVERT: C 411 MET cc_start: 0.8367 (mmt) cc_final: 0.7385 (mmm) REVERT: C 653 ARG cc_start: 0.8185 (mtm-85) cc_final: 0.7387 (ptp90) REVERT: C 817 HIS cc_start: 0.7821 (OUTLIER) cc_final: 0.6602 (m90) REVERT: C 1000 LEU cc_start: 0.9522 (OUTLIER) cc_final: 0.9277 (mt) REVERT: D 112 MET cc_start: 0.7973 (mmm) cc_final: 0.7696 (ttm) REVERT: D 222 GLN cc_start: 0.8639 (OUTLIER) cc_final: 0.8129 (tm-30) REVERT: D 415 TYR cc_start: 0.3867 (m-80) cc_final: 0.3056 (m-80) REVERT: D 461 PHE cc_start: 0.7302 (OUTLIER) cc_final: 0.6708 (t80) REVERT: D 466 ARG cc_start: 0.6417 (mmt-90) cc_final: 0.6153 (tpp-160) REVERT: D 483 MET cc_start: 0.7360 (ttm) cc_final: 0.6513 (mtp) REVERT: D 511 TRP cc_start: 0.7989 (m100) cc_final: 0.7566 (m100) REVERT: D 514 MET cc_start: 0.6454 (mmt) cc_final: 0.5781 (mtt) outliers start: 60 outliers final: 36 residues processed: 255 average time/residue: 0.3232 time to fit residues: 133.5063 Evaluate side-chains 237 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 194 time to evaluate : 2.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 476 ILE Chi-restraints excluded: chain B residue 563 GLU Chi-restraints excluded: chain B residue 566 GLN Chi-restraints excluded: chain B residue 604 MET Chi-restraints excluded: chain B residue 735 LEU Chi-restraints excluded: chain B residue 753 TRP Chi-restraints excluded: chain B residue 813 CYS Chi-restraints excluded: chain B residue 1002 LEU Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1019 VAL Chi-restraints excluded: chain B residue 1025 LEU Chi-restraints excluded: chain B residue 1027 ILE Chi-restraints excluded: chain B residue 1069 VAL Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 404 THR Chi-restraints excluded: chain C residue 422 ILE Chi-restraints excluded: chain C residue 528 LEU Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 551 ASP Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 801 SER Chi-restraints excluded: chain C residue 817 HIS Chi-restraints excluded: chain C residue 821 VAL Chi-restraints excluded: chain C residue 853 LEU Chi-restraints excluded: chain C residue 879 GLN Chi-restraints excluded: chain C residue 945 LEU Chi-restraints excluded: chain C residue 1000 LEU Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 108 TYR Chi-restraints excluded: chain D residue 170 SER Chi-restraints excluded: chain D residue 222 GLN Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain D residue 350 ASP Chi-restraints excluded: chain D residue 461 PHE Chi-restraints excluded: chain D residue 471 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 69.9968 > 50: distance: 29 - 35: 20.924 distance: 35 - 36: 36.670 distance: 36 - 37: 51.678 distance: 36 - 39: 23.243 distance: 37 - 38: 51.126 distance: 37 - 46: 27.690 distance: 39 - 40: 40.922 distance: 40 - 41: 40.711 distance: 40 - 42: 42.190 distance: 41 - 43: 40.598 distance: 42 - 44: 37.595 distance: 43 - 45: 44.148 distance: 44 - 45: 40.994 distance: 46 - 47: 19.238 distance: 47 - 48: 52.334 distance: 47 - 50: 17.650 distance: 48 - 49: 7.336 distance: 48 - 53: 30.779 distance: 50 - 51: 35.905 distance: 50 - 52: 45.065 distance: 53 - 54: 42.475 distance: 54 - 55: 41.341 distance: 54 - 57: 45.627 distance: 55 - 62: 42.920 distance: 57 - 58: 34.097 distance: 58 - 59: 54.045 distance: 59 - 60: 11.392 distance: 59 - 61: 45.495 distance: 62 - 63: 33.854 distance: 62 - 68: 35.681 distance: 63 - 64: 47.967 distance: 63 - 66: 21.842 distance: 64 - 65: 54.119 distance: 64 - 69: 22.069 distance: 66 - 67: 8.538 distance: 67 - 68: 6.559 distance: 69 - 70: 17.848 distance: 70 - 71: 57.400 distance: 70 - 73: 67.465 distance: 71 - 72: 39.079 distance: 71 - 77: 39.770 distance: 73 - 74: 22.941 distance: 74 - 75: 43.758 distance: 74 - 76: 51.260 distance: 77 - 78: 49.007 distance: 77 - 83: 39.444 distance: 78 - 79: 30.120 distance: 78 - 81: 37.126 distance: 79 - 84: 49.186 distance: 81 - 82: 23.639 distance: 82 - 83: 22.341 distance: 84 - 85: 40.721 distance: 85 - 86: 49.878 distance: 85 - 88: 24.162 distance: 86 - 95: 54.682 distance: 88 - 89: 40.219 distance: 89 - 90: 19.505 distance: 89 - 91: 40.886 distance: 90 - 92: 14.918 distance: 91 - 93: 47.225 distance: 92 - 94: 24.412 distance: 93 - 94: 36.699 distance: 95 - 96: 6.769 distance: 96 - 97: 51.119 distance: 96 - 99: 7.023 distance: 97 - 98: 39.762 distance: 97 - 102: 19.629 distance: 99 - 100: 13.277 distance: 99 - 101: 21.705 distance: 102 - 103: 40.221 distance: 103 - 104: 63.574 distance: 103 - 106: 18.562 distance: 104 - 105: 46.155 distance: 104 - 110: 56.690 distance: 106 - 107: 25.199 distance: 107 - 108: 52.851 distance: 107 - 109: 39.495 distance: 110 - 111: 69.554 distance: 110 - 116: 55.373 distance: 111 - 112: 40.787 distance: 112 - 113: 4.451 distance: 112 - 117: 29.553 distance: 114 - 115: 41.181 distance: 115 - 116: 48.576