Starting phenix.real_space_refine on Fri Jun 20 14:53:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6t2u_10369/06_2025/6t2u_10369.cif Found real_map, /net/cci-nas-00/data/ceres_data/6t2u_10369/06_2025/6t2u_10369.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6t2u_10369/06_2025/6t2u_10369.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6t2u_10369/06_2025/6t2u_10369.map" model { file = "/net/cci-nas-00/data/ceres_data/6t2u_10369/06_2025/6t2u_10369.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6t2u_10369/06_2025/6t2u_10369.cif" } resolution = 3.6 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= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 54 5.49 5 S 101 5.16 5 C 14897 2.51 5 N 4192 2.21 5 O 4582 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 103 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 13.58, per 1000 atoms: 0.57 Number of scatterers: 23826 At special positions: 0 Unit cell: (151.9, 151.9, 131.285, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 101 16.00 P 54 15.00 O 4582 8.00 N 4192 7.00 C 14897 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.10 Conformation dependent library (CDL) restraints added in 2.9 seconds 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5372 Finding SS restraints... Secondary structure from input PDB file: 124 helices and 17 sheets defined 53.1% alpha, 9.1% beta 17 base pairs and 33 stacking pairs defined. Time for finding SS restraints: 8.51 Creating SS restraints... Processing helix chain 'B' and resid 28 through 43 Processing helix chain 'B' and resid 45 through 49 Processing helix chain 'B' and resid 55 through 59 removed outlier: 3.543A pdb=" N GLU B 58 " --> pdb=" O THR B 55 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU B 59 " --> pdb=" O VAL B 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 55 through 59' Processing helix chain 'B' and resid 65 through 90 Processing helix chain 'B' and resid 94 through 104 removed outlier: 3.677A pdb=" N ILE B 104 " --> pdb=" O LEU B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 120 Processing helix chain 'B' and resid 128 through 140 Processing helix chain 'B' and resid 140 through 145 removed outlier: 3.535A pdb=" N SER B 144 " --> pdb=" O ASN B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 173 removed outlier: 3.773A pdb=" N TYR B 173 " --> pdb=" O ARG B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 187 removed outlier: 4.320A pdb=" N VAL B 182 " --> pdb=" O GLU B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 202 removed outlier: 3.650A pdb=" N LEU B 193 " --> pdb=" O GLY B 189 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N ARG B 199 " --> pdb=" O ARG B 195 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N TYR B 200 " --> pdb=" O ASP B 196 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLN B 202 " --> pdb=" O ASN B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 239 removed outlier: 3.546A 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: 3.612A pdb=" N ASN B 278 " --> pdb=" O GLU B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 289 removed outlier: 3.683A pdb=" N LYS B 288 " --> pdb=" O GLU B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 317 removed outlier: 4.256A pdb=" N GLU B 311 " --> pdb=" O HIS B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 347 removed outlier: 3.519A pdb=" N VAL B 327 " --> pdb=" O ILE B 323 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N ARG B 336 " --> pdb=" O LEU B 332 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N GLU B 337 " --> pdb=" O ALA B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 364 removed outlier: 3.643A pdb=" N MET B 354 " --> pdb=" O GLY B 350 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N LEU B 355 " --> pdb=" O PHE B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 378 Processing helix chain 'B' and resid 390 through 401 Processing helix chain 'B' and resid 414 through 418 removed outlier: 3.747A pdb=" N ALA B 418 " --> pdb=" O PRO B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 437 removed outlier: 3.792A pdb=" N TYR B 430 " --> pdb=" O ASP B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 461 Processing helix chain 'B' and resid 511 through 534 Processing helix chain 'B' and resid 560 through 573 Processing helix chain 'B' and resid 586 through 589 Processing helix chain 'B' and resid 590 through 605 removed outlier: 3.948A pdb=" N GLN B 594 " --> pdb=" O THR B 590 " (cutoff:3.500A) Processing helix chain 'B' and resid 608 through 617 removed outlier: 3.810A pdb=" N LEU B 612 " --> pdb=" O ARG B 608 " (cutoff:3.500A) Processing helix chain 'B' and resid 624 through 634 Processing helix chain 'B' and resid 634 through 655 removed outlier: 3.654A pdb=" N TRP B 638 " --> pdb=" O ASP B 634 " (cutoff:3.500A) Processing helix chain 'B' and resid 656 through 668 removed outlier: 3.794A pdb=" N MET B 660 " --> pdb=" O GLY B 656 " (cutoff:3.500A) Processing helix chain 'B' and resid 669 through 677 removed outlier: 3.568A pdb=" N ASN B 673 " --> pdb=" O ASN B 669 " (cutoff:3.500A) Processing helix chain 'B' and resid 680 through 699 removed outlier: 3.608A pdb=" N THR B 699 " --> pdb=" O GLN B 695 " (cutoff:3.500A) Processing helix chain 'B' and resid 703 through 717 removed outlier: 4.132A pdb=" N LEU B 707 " --> pdb=" O SER B 703 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL B 708 " --> pdb=" O GLU B 704 " (cutoff:3.500A) Processing helix chain 'B' and resid 783 through 807 removed outlier: 3.522A pdb=" N GLU B 793 " --> pdb=" O LEU B 789 " (cutoff:3.500A) Processing helix chain 'B' and resid 831 through 836 removed outlier: 4.529A pdb=" N HIS B 834 " --> pdb=" O THR B 831 " (cutoff:3.500A) Processing helix chain 'B' and resid 837 through 843 removed outlier: 3.794A pdb=" N LEU B 841 " --> pdb=" O ALA B 837 " (cutoff:3.500A) Processing helix chain 'B' and resid 849 through 860 removed outlier: 3.875A 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: 3.847A pdb=" N GLU B 992 " --> pdb=" O PRO B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1008 through 1012 removed outlier: 3.686A pdb=" N GLN B1011 " --> pdb=" O SER B1008 " (cutoff:3.500A) Processing helix chain 'B' and resid 1032 through 1044 removed outlier: 3.652A pdb=" N THR B1038 " --> pdb=" O SER B1034 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LEU B1039 " --> pdb=" O GLN B1035 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N PHE B1043 " --> pdb=" O LEU B1039 " (cutoff:3.500A) Processing helix chain 'B' and resid 1045 through 1048 removed outlier: 3.785A 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: 3.595A pdb=" N LEU B1167 " --> pdb=" O GLY B1163 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 24 removed outlier: 4.126A 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: 3.749A 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: 3.901A pdb=" N LEU C 146 " --> pdb=" O ARG C 142 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N THR C 151 " --> pdb=" O ALA C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 161 through 179 Proline residue: C 167 - end of helix Processing helix chain 'C' and resid 189 through 199 Processing helix chain 'C' and resid 220 through 232 removed outlier: 3.593A pdb=" N ALA C 229 " --> pdb=" O GLN C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 263 Processing helix chain 'C' and resid 297 through 304 Processing helix chain 'C' and resid 304 through 316 removed outlier: 3.505A 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: 3.522A pdb=" N ARG C 360 " --> pdb=" O GLU C 356 " (cutoff:3.500A) Processing helix chain 'C' and resid 381 through 400 removed outlier: 3.599A pdb=" N VAL C 386 " --> pdb=" O PRO C 382 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASP C 391 " --> pdb=" O GLU C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 406 No H-bonds generated for 'chain 'C' and resid 404 through 406' Processing helix chain 'C' and resid 414 through 428 removed outlier: 3.677A pdb=" N TYR C 418 " --> pdb=" O ASP C 414 " (cutoff:3.500A) Proline residue: C 420 - end of helix Processing helix chain 'C' and resid 447 through 459 removed outlier: 3.874A pdb=" N ALA C 453 " --> pdb=" O PRO C 449 " (cutoff:3.500A) Processing helix chain 'C' and resid 466 through 475 Processing helix chain 'C' and resid 476 through 483 removed outlier: 3.605A pdb=" N PHE C 483 " --> pdb=" O LEU C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 486 through 500 removed outlier: 3.848A pdb=" N GLN C 495 " --> pdb=" O ARG C 491 " (cutoff:3.500A) Processing helix chain 'C' and resid 507 through 514 removed outlier: 3.516A pdb=" N LEU C 514 " --> pdb=" O ASN C 510 " (cutoff:3.500A) Processing helix chain 'C' and resid 523 through 537 Processing helix chain 'C' and resid 555 through 557 No H-bonds generated for 'chain 'C' and resid 555 through 557' Processing helix chain 'C' and resid 558 through 574 removed outlier: 3.692A pdb=" N MET C 569 " --> pdb=" O ALA C 565 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLN C 570 " --> pdb=" O SER C 566 " (cutoff:3.500A) Processing helix chain 'C' and resid 587 through 599 removed outlier: 4.588A pdb=" N CYS C 591 " --> pdb=" O TRP C 587 " (cutoff:3.500A) removed outlier: 4.578A 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: 3.860A pdb=" N LEU C 637 " --> pdb=" O PRO C 633 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ASP C 646 " --> pdb=" O ALA C 642 " (cutoff:3.500A) Processing helix chain 'C' and resid 707 through 722 Processing helix chain 'C' and resid 745 through 758 Processing helix chain 'C' and resid 769 through 780 Processing helix chain 'C' and resid 803 through 805 No H-bonds generated for 'chain 'C' and resid 803 through 805' Processing helix chain 'C' and resid 806 through 812 removed outlier: 3.552A pdb=" N GLN C 812 " --> pdb=" O PRO C 808 " (cutoff:3.500A) Processing helix chain 'C' and resid 833 through 843 removed outlier: 3.536A pdb=" N LEU C 837 " --> pdb=" O PRO C 833 " (cutoff:3.500A) removed outlier: 3.776A 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: 3.688A pdb=" N LEU C 897 " --> pdb=" O ASP C 893 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA C 904 " --> pdb=" O ARG C 900 " (cutoff:3.500A) Processing helix chain 'C' and resid 910 through 932 removed outlier: 3.759A pdb=" N GLU C 914 " --> pdb=" O GLY C 910 " (cutoff:3.500A) removed outlier: 3.863A 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: 3.606A pdb=" N GLY C 977 " --> pdb=" O SER C 973 " (cutoff:3.500A) Processing helix chain 'C' and resid 1012 through 1033 removed outlier: 3.723A pdb=" N SER C1032 " --> pdb=" O ARG C1028 " (cutoff:3.500A) Processing helix chain 'C' and resid 1038 through 1049 Processing helix chain 'C' and resid 1060 through 1076 removed outlier: 3.582A pdb=" N ARG C1068 " --> pdb=" O LEU C1064 " (cutoff:3.500A) Processing helix chain 'C' and resid 1098 through 1113 Processing helix chain 'C' and resid 1113 through 1119 removed outlier: 3.916A pdb=" N PHE C1117 " --> pdb=" O LEU C1113 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N PHE C1119 " --> pdb=" O PRO C1115 " (cutoff:3.500A) Processing helix chain 'D' and resid 11 through 15 removed outlier: 3.751A 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: 3.964A pdb=" N SER D 88 " --> pdb=" O CYS D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 125 Processing helix chain 'D' and resid 133 through 145 removed outlier: 3.560A pdb=" N LEU D 137 " --> pdb=" O ASP D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 164 removed outlier: 3.638A 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: 3.597A pdb=" N ARG D 221 " --> pdb=" O GLY D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 240 through 244 Processing helix chain 'D' and resid 270 through 274 removed outlier: 3.599A pdb=" N MET D 273 " --> pdb=" O GLU D 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 286 removed outlier: 3.573A pdb=" N ALA D 285 " --> pdb=" O ARG D 281 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU D 286 " --> pdb=" O LEU D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 315 removed outlier: 3.789A pdb=" N ASP D 312 " --> pdb=" O ALA D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 316 through 319 removed outlier: 3.511A 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: 3.560A 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: 3.868A pdb=" N GLN D 369 " --> pdb=" O SER D 365 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ASN D 375 " --> pdb=" O ALA D 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 377 through 387 removed outlier: 3.574A pdb=" N ALA D 381 " --> pdb=" O GLY D 377 " (cutoff:3.500A) Processing helix chain 'D' and resid 388 through 391 removed outlier: 3.599A pdb=" N THR D 391 " --> pdb=" O GLN D 388 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 388 through 391' Processing helix chain 'D' and resid 400 through 415 Processing helix chain 'D' and resid 415 through 424 Processing helix chain 'D' and resid 427 through 436 Processing helix chain 'D' and resid 450 through 465 Processing helix chain 'D' and resid 523 through 527 removed outlier: 3.526A 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: 3.718A pdb=" N ILE D 590 " --> pdb=" O LEU D 586 " (cutoff:3.500A) removed outlier: 3.769A 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: 6.510A pdb=" N GLU B 6 " --> pdb=" O THR B 442 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N ALA B 439 " --> pdb=" O GLU B 18 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU B 20 " --> pdb=" O ALA B 439 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N GLY B 17 " --> pdb=" O LEU B 409 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N LEU B 411 " --> pdb=" O GLY B 17 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ARG B 19 " --> pdb=" O LEU B 411 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N GLY B 413 " --> pdb=" O ARG B 19 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N ILE B 21 " --> pdb=" O GLY B 413 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ALA B 381 " --> pdb=" O LEU B 410 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N ILE B 412 " --> pdb=" O ALA B 381 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N ILE B 383 " --> pdb=" O ILE B 412 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N VAL B 62 " --> pdb=" O ASP B 384 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N VAL B 61 " --> pdb=" O PHE B 127 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 151 through 152 removed outlier: 6.252A 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: 6.519A pdb=" N VAL B 207 " --> pdb=" O LEU B 778 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 487 through 490 Processing sheet with id=AA5, first strand: chain 'B' and resid 578 through 580 removed outlier: 6.588A pdb=" N VAL B 579 " --> pdb=" O ILE B 738 " (cutoff:3.500A) removed outlier: 8.554A pdb=" N THR B 740 " --> pdb=" O VAL B 579 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N ILE B 554 " --> pdb=" O GLN B 737 " (cutoff:3.500A) removed outlier: 8.367A pdb=" N VAL B 739 " --> pdb=" O ILE B 554 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N VAL B 556 " --> pdb=" O VAL B 739 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N MET B 499 " --> pdb=" O ALA B 866 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N GLN B 868 " --> pdb=" O MET B 499 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N MET B 501 " --> pdb=" O GLN B 868 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 1017 through 1027 removed outlier: 6.664A pdb=" N ASP B1067 " --> pdb=" O GLU B1020 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N GLU B1022 " --> pdb=" O PHE B1065 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N PHE B1065 " --> pdb=" O GLU B1022 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N TYR B1024 " --> pdb=" O LYS B1063 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N LYS B1063 " --> pdb=" O TYR B1024 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N MET B1061 " --> pdb=" O PRO B1026 " (cutoff:3.500A) removed outlier: 10.150A pdb=" N ILE B1066 " --> pdb=" O TYR B1081 " (cutoff:3.500A) removed outlier: 8.294A pdb=" N TYR B1081 " --> pdb=" O ILE B1066 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N TYR B1076 " --> pdb=" O GLY B1137 " (cutoff:3.500A) removed outlier: 8.374A pdb=" N ILE B1139 " --> pdb=" O TYR B1076 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N LEU B1078 " --> pdb=" O ILE B1139 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N LEU B1141 " --> pdb=" O LEU B1078 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ALA B1080 " --> pdb=" O LEU B1141 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 60 through 61 removed outlier: 6.397A pdb=" N ARG C 3 " --> pdb=" O LEU C 238 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N PHE C 240 " --> pdb=" O ARG C 3 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N TYR C 5 " --> pdb=" O PHE C 240 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 265 through 266 Processing sheet with id=AA9, first strand: chain 'C' and resid 365 through 366 removed outlier: 5.977A 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: 3.556A pdb=" N ASN C 660 " --> pdb=" O ILE C 408 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N LYS C 673 " --> pdb=" O LYS C 726 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N TYR C 728 " --> pdb=" O LYS C 673 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N VAL C 675 " --> pdb=" O TYR C 728 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N SER C 730 " --> pdb=" O VAL C 675 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N LEU C 677 " --> pdb=" O SER C 730 " (cutoff:3.500A) removed outlier: 8.229A pdb=" N ILE C 732 " --> pdb=" O LEU C 677 " (cutoff:3.500A) removed outlier: 8.922A pdb=" N CYS C 782 " --> pdb=" O ILE C 374 " (cutoff:3.500A) removed outlier: 7.256A 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: 3.793A pdb=" N ARG C 442 " --> pdb=" O ILE C 650 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 939 through 947 removed outlier: 5.698A pdb=" N GLN C 939 " --> pdb=" O GLN C 958 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLN C 958 " --> pdb=" O GLN C 939 " (cutoff:3.500A) removed outlier: 15.867A pdb=" N LEU C 956 " --> pdb=" O TRP C 967 " (cutoff:3.500A) removed outlier: 13.382A pdb=" N TRP C 967 " --> pdb=" O LEU C 956 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N GLN C 958 " --> pdb=" O LEU C 965 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N LEU C 965 " --> pdb=" O GLN C 958 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N LEU C 964 " --> pdb=" O ARG C 997 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N PHE C 999 " --> pdb=" O LEU C 964 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N ARG C 966 " --> pdb=" O PHE C 999 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 1050 through 1051 Processing sheet with id=AB5, first strand: chain 'D' and resid 53 through 54 removed outlier: 6.066A pdb=" N SER D 92 " --> pdb=" O LEU D 102 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 167 through 170 removed outlier: 3.605A pdb=" N GLY D 296 " --> pdb=" O ILE D 169 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N LEU D 266 " --> pdb=" O ILE D 293 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N LEU D 295 " --> pdb=" O LEU D 266 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N VAL D 268 " --> pdb=" O LEU D 295 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ARG D 200 " --> pdb=" O VAL D 267 " (cutoff:3.500A) removed outlier: 8.989A pdb=" N SER D 238 " --> pdb=" O ILE D 199 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N LEU D 201 " --> pdb=" O SER D 238 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 393 through 396 removed outlier: 7.397A pdb=" N ASP D 547 " --> pdb=" O ARG D 574 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N GLN D 439 " --> pdb=" O ALA D 550 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N ILE D 552 " --> pdb=" O GLN D 439 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N LEU D 441 " --> pdb=" O ILE D 552 " (cutoff:3.500A) removed outlier: 8.604A pdb=" N MET D 536 " --> pdb=" O TYR D 438 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N LEU D 440 " --> pdb=" O MET D 536 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 519 through 522 removed outlier: 4.460A pdb=" N ALA D 513 " --> pdb=" O ILE D 498 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ILE D 498 " --> pdb=" O ALA D 513 " (cutoff:3.500A) 1044 hydrogen bonds defined for protein. 3066 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 43 hydrogen bonds 86 hydrogen bond angles 0 basepair planarities 17 basepair parallelities 33 stacking parallelities Total time for adding SS restraints: 10.61 Time building geometry restraints manager: 7.22 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: 7521 1.34 - 1.45: 3467 1.45 - 1.57: 13188 1.57 - 1.69: 107 1.69 - 1.81: 169 Bond restraints: 24452 Sorted by residual: bond pdb=" CD LYS D 383 " pdb=" CE LYS D 383 " ideal model delta sigma weight residual 1.520 1.580 -0.060 3.00e-02 1.11e+03 3.97e+00 bond pdb=" C THR B 304 " pdb=" N PRO B 305 " ideal model delta sigma weight residual 1.333 1.350 -0.017 1.01e-02 9.80e+03 2.74e+00 bond pdb=" N ILE B 266 " pdb=" CA ILE B 266 " ideal model delta sigma weight residual 1.474 1.458 0.016 1.57e-02 4.06e+03 1.10e+00 bond pdb=" C PRO C 823 " pdb=" N LEU C 824 " ideal model delta sigma weight residual 1.331 1.353 -0.022 2.07e-02 2.33e+03 1.09e+00 bond pdb=" CD GLN D 433 " pdb=" NE2 GLN D 433 " ideal model delta sigma weight residual 1.328 1.307 0.021 2.10e-02 2.27e+03 1.02e+00 ... (remaining 24447 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.16: 33157 2.16 - 4.32: 233 4.32 - 6.48: 16 6.48 - 8.64: 2 8.64 - 10.80: 1 Bond angle restraints: 33409 Sorted by residual: angle pdb=" CG LYS D 383 " pdb=" CD LYS D 383 " pdb=" CE LYS D 383 " ideal model delta sigma weight residual 111.30 100.50 10.80 2.30e+00 1.89e-01 2.21e+01 angle pdb=" C LYS D 383 " pdb=" CA LYS D 383 " pdb=" CB LYS D 383 " ideal model delta sigma weight residual 110.67 118.66 -7.99 1.92e+00 2.71e-01 1.73e+01 angle pdb=" N GLY B 898 " pdb=" CA GLY B 898 " pdb=" C GLY B 898 " ideal model delta sigma weight residual 110.87 116.01 -5.14 1.54e+00 4.22e-01 1.12e+01 angle pdb=" N TRP B 878 " pdb=" CA TRP B 878 " pdb=" C TRP B 878 " ideal model delta sigma weight residual 107.88 112.37 -4.49 1.41e+00 5.03e-01 1.01e+01 angle pdb=" C SER C 447 " pdb=" N HIS C 448 " pdb=" CA HIS C 448 " ideal model delta sigma weight residual 119.78 123.60 -3.82 1.24e+00 6.50e-01 9.48e+00 ... (remaining 33404 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.82: 13443 16.82 - 33.64: 773 33.64 - 50.45: 304 50.45 - 67.27: 89 67.27 - 84.09: 6 Dihedral angle restraints: 14615 sinusoidal: 6326 harmonic: 8289 Sorted by residual: dihedral pdb=" C LYS D 383 " pdb=" N LYS D 383 " pdb=" CA LYS D 383 " pdb=" CB LYS D 383 " ideal model delta harmonic sigma weight residual -122.60 -134.09 11.49 0 2.50e+00 1.60e-01 2.11e+01 dihedral pdb=" CA PRO B1051 " pdb=" C PRO B1051 " pdb=" N PRO B1052 " pdb=" CA PRO B1052 " ideal model delta harmonic sigma weight residual -180.00 -160.75 -19.25 0 5.00e+00 4.00e-02 1.48e+01 dihedral pdb=" CA GLY C 657 " pdb=" C GLY C 657 " pdb=" N PRO C 658 " pdb=" CA PRO C 658 " ideal model delta harmonic sigma weight residual 180.00 163.49 16.51 0 5.00e+00 4.00e-02 1.09e+01 ... (remaining 14612 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 3468 0.076 - 0.151: 204 0.151 - 0.227: 0 0.227 - 0.303: 0 0.303 - 0.378: 1 Chirality restraints: 3673 Sorted by residual: chirality pdb=" CA LYS D 383 " pdb=" N LYS D 383 " pdb=" C LYS D 383 " pdb=" CB LYS D 383 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.58e+00 chirality pdb=" CA ILE C 864 " pdb=" N ILE C 864 " pdb=" C ILE C 864 " pdb=" CB ILE C 864 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.65e-01 chirality pdb=" CA ILE D 233 " pdb=" N ILE D 233 " pdb=" C ILE D 233 " pdb=" CB ILE D 233 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.42e-01 ... (remaining 3670 not shown) Planarity restraints: 4205 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN D 433 " -0.016 2.00e-02 2.50e+03 3.27e-02 1.07e+01 pdb=" CD GLN D 433 " 0.057 2.00e-02 2.50e+03 pdb=" OE1 GLN D 433 " -0.021 2.00e-02 2.50e+03 pdb=" NE2 GLN D 433 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY C 657 " 0.049 5.00e-02 4.00e+02 7.40e-02 8.77e+00 pdb=" N PRO C 658 " -0.128 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=" CA ASP C 469 " 0.014 2.00e-02 2.50e+03 2.78e-02 7.74e+00 pdb=" C ASP C 469 " -0.048 2.00e-02 2.50e+03 pdb=" O ASP C 469 " 0.018 2.00e-02 2.50e+03 pdb=" N VAL C 470 " 0.016 2.00e-02 2.50e+03 ... (remaining 4202 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2630 2.75 - 3.29: 21339 3.29 - 3.82: 38961 3.82 - 4.36: 44805 4.36 - 4.90: 77124 Nonbonded interactions: 184859 Sorted by model distance: nonbonded pdb=" OD1 ASN B 759 " pdb=" NH2 ARG B 822 " model vdw 2.211 3.120 nonbonded pdb=" O LEU C 115 " pdb=" OG SER C 119 " model vdw 2.283 3.040 nonbonded pdb=" O HIS B1124 " pdb=" NH2 ARG C 25 " model vdw 2.288 3.120 nonbonded pdb=" NZ LYS C 121 " pdb=" O ALA C 631 " model vdw 2.299 3.120 nonbonded pdb=" OH TYR B 394 " pdb=" OE1 GLU B 436 " model vdw 2.311 3.040 ... (remaining 184854 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: 0.610 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: 0.970 Check model and map are aligned: 0.190 Set scattering table: 0.250 Process input model: 61.850 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7049 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.060 24452 Z= 0.105 Angle : 0.479 10.801 33409 Z= 0.301 Chirality : 0.035 0.378 3673 Planarity : 0.005 0.074 4205 Dihedral : 13.105 84.089 9243 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.97 % Favored : 97.99 % Rotamer: Outliers : 2.98 % Allowed : 4.97 % Favored : 92.05 % Cbeta Deviations : 0.04 % 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: -3.59 (0.11), residues: 2837 helix: -2.51 (0.09), residues: 1400 sheet: -1.02 (0.28), residues: 301 loop : -2.39 (0.14), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 164 HIS 0.002 0.000 HIS C 377 PHE 0.007 0.001 PHE B1023 TYR 0.006 0.001 TYR D 108 ARG 0.003 0.000 ARG B 800 Details of bonding type rmsd hydrogen bonds : bond 0.14020 ( 1087) hydrogen bonds : angle 6.13571 ( 3152) covalent geometry : bond 0.00181 (24452) covalent geometry : angle 0.47870 (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 515 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 443 time to evaluate : 2.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 21 ILE cc_start: 0.8504 (mt) cc_final: 0.8272 (mt) REVERT: B 491 PHE cc_start: 0.4682 (OUTLIER) cc_final: 0.4280 (t80) REVERT: B 518 MET cc_start: 0.5790 (mmm) cc_final: 0.5573 (mmm) REVERT: B 526 ILE cc_start: 0.8364 (mt) cc_final: 0.8033 (mm) REVERT: B 665 MET cc_start: 0.8853 (mtp) cc_final: 0.7922 (tmm) REVERT: B 666 SER cc_start: 0.9017 (t) cc_final: 0.8778 (m) REVERT: B 753 TRP cc_start: 0.7965 (OUTLIER) cc_final: 0.6043 (t60) REVERT: B 966 GLN cc_start: 0.8517 (mt0) cc_final: 0.7983 (pp30) REVERT: B 1053 LEU cc_start: 0.2111 (OUTLIER) cc_final: 0.1818 (mt) REVERT: B 1069 VAL cc_start: 0.8922 (t) cc_final: 0.7784 (t) REVERT: C 96 MET cc_start: 0.8777 (ttt) cc_final: 0.8408 (ttm) REVERT: C 414 ASP cc_start: 0.7664 (t70) cc_final: 0.7434 (t0) REVERT: C 514 LEU cc_start: 0.8805 (mt) cc_final: 0.8452 (mp) REVERT: C 580 GLN cc_start: 0.7375 (tt0) cc_final: 0.7142 (pm20) REVERT: C 591 CYS cc_start: 0.6683 (OUTLIER) cc_final: 0.5829 (t) REVERT: C 665 MET cc_start: 0.7625 (tpp) cc_final: 0.7373 (tpt) REVERT: C 968 ARG cc_start: 0.7864 (mtp180) cc_final: 0.7605 (mtp85) REVERT: D 108 TYR cc_start: 0.5667 (OUTLIER) cc_final: 0.4011 (p90) REVERT: D 273 MET cc_start: 0.7582 (mtm) cc_final: 0.7202 (mtm) REVERT: D 393 ILE cc_start: 0.8271 (OUTLIER) cc_final: 0.7855 (mp) REVERT: D 407 MET cc_start: 0.8726 (ttp) cc_final: 0.8358 (tmm) REVERT: D 433 GLN cc_start: 0.9589 (tt0) cc_final: 0.9301 (tm-30) outliers start: 72 outliers final: 10 residues processed: 503 average time/residue: 0.3772 time to fit residues: 289.2027 Evaluate side-chains 210 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 194 time to evaluate : 2.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 491 PHE Chi-restraints excluded: chain B residue 753 TRP Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 1053 LEU Chi-restraints excluded: chain B residue 1159 ARG Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 479 LEU Chi-restraints excluded: chain C residue 591 CYS Chi-restraints excluded: chain C residue 821 VAL Chi-restraints excluded: chain D residue 108 TYR Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 393 ILE Chi-restraints excluded: chain D residue 533 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 243 optimal weight: 4.9990 chunk 218 optimal weight: 7.9990 chunk 121 optimal weight: 2.9990 chunk 74 optimal weight: 10.0000 chunk 147 optimal weight: 20.0000 chunk 116 optimal weight: 8.9990 chunk 225 optimal weight: 10.0000 chunk 87 optimal weight: 10.0000 chunk 137 optimal weight: 8.9990 chunk 168 optimal weight: 10.0000 chunk 261 optimal weight: 10.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- 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 B 234 GLN B 417 GLN B 458 ASN B 463 GLN B 520 GLN B 566 GLN B 594 GLN B 601 GLN B 650 GLN B 713 GLN B 734 HIS B 765 GLN B 769 HIS B 848 GLN B 943 HIS B1035 GLN B1072 HIS B1084 ASN B1133 HIS B1134 HIS B1150 HIS C 126 GLN C 137 GLN ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 HIS C 191 GLN C 390 HIS C 510 ASN C 570 GLN C 614 GLN C 725 GLN C 749 GLN C 759 HIS C 793 ASN C 817 HIS C 822 GLN C 843 HIS C 883 GLN C 925 GLN ** C 958 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 976 GLN C1091 GLN C1108 GLN D 22 GLN ** D 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 89 GLN D 124 ASN ** D 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 241 HIS D 251 GLN D 328 GLN D 469 HIS ** D 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 54 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.084604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.061829 restraints weight = 97311.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.063923 restraints weight = 51317.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.065290 restraints weight = 34534.351| |-----------------------------------------------------------------------------| r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.3428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.087 24452 Z= 0.283 Angle : 0.765 12.202 33409 Z= 0.389 Chirality : 0.045 0.153 3673 Planarity : 0.006 0.060 4205 Dihedral : 13.663 86.470 3732 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.89 % Allowed : 10.02 % Favored : 86.09 % 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: -1.29 (0.14), residues: 2837 helix: -0.10 (0.13), residues: 1415 sheet: -0.34 (0.29), residues: 284 loop : -1.91 (0.16), residues: 1138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 638 HIS 0.011 0.002 HIS C 233 PHE 0.020 0.003 PHE B 428 TYR 0.022 0.003 TYR B 37 ARG 0.051 0.001 ARG B 974 Details of bonding type rmsd hydrogen bonds : bond 0.05279 ( 1087) hydrogen bonds : angle 4.54702 ( 3152) covalent geometry : bond 0.00645 (24452) covalent geometry : angle 0.76535 (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 287 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 193 time to evaluate : 3.040 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 185 GLU cc_start: 0.8714 (tp30) cc_final: 0.8420 (tm-30) REVERT: B 518 MET cc_start: 0.6205 (mmm) cc_final: 0.5948 (mmm) REVERT: B 596 MET cc_start: 0.8825 (mmm) cc_final: 0.8624 (mtp) REVERT: B 665 MET cc_start: 0.8706 (mtp) cc_final: 0.8096 (tmm) REVERT: B 753 TRP cc_start: 0.8103 (OUTLIER) cc_final: 0.6106 (t60) REVERT: B 1053 LEU cc_start: 0.2226 (OUTLIER) cc_final: 0.1882 (mt) REVERT: C 34 MET cc_start: 0.8141 (mmm) cc_final: 0.7669 (mmp) REVERT: C 96 MET cc_start: 0.8760 (ttt) cc_final: 0.8434 (ttm) REVERT: C 411 MET cc_start: 0.7422 (mmm) cc_final: 0.7070 (mmt) REVERT: C 414 ASP cc_start: 0.8196 (t70) cc_final: 0.7303 (p0) REVERT: C 528 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8743 (tt) REVERT: C 580 GLN cc_start: 0.7608 (tt0) cc_final: 0.7380 (pm20) REVERT: D 112 MET cc_start: 0.7497 (ttm) cc_final: 0.7031 (ttm) REVERT: D 407 MET cc_start: 0.8634 (ttp) cc_final: 0.8236 (tmm) REVERT: D 433 GLN cc_start: 0.9565 (tt0) cc_final: 0.9314 (tm-30) outliers start: 94 outliers final: 56 residues processed: 271 average time/residue: 0.3528 time to fit residues: 151.2258 Evaluate side-chains 218 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 159 time to evaluate : 2.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 234 GLN Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 352 ASP Chi-restraints excluded: chain B residue 491 PHE Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 582 SER Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 614 SER Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 696 GLU Chi-restraints excluded: chain B residue 753 TRP Chi-restraints excluded: chain B residue 860 LEU Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 1053 LEU Chi-restraints excluded: chain B residue 1093 TYR Chi-restraints excluded: chain B residue 1159 ARG Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 419 SER Chi-restraints excluded: chain C residue 434 TYR Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 479 LEU Chi-restraints excluded: chain C residue 506 ILE Chi-restraints excluded: chain C residue 528 LEU Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain C residue 674 VAL Chi-restraints excluded: chain C residue 698 SER Chi-restraints excluded: chain C residue 801 SER Chi-restraints excluded: chain C residue 821 VAL Chi-restraints excluded: chain C residue 853 LEU Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 889 VAL Chi-restraints excluded: chain C residue 976 GLN Chi-restraints excluded: chain C residue 1106 VAL Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 108 TYR Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 293 ILE Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 350 ASP Chi-restraints excluded: chain D residue 384 THR Chi-restraints excluded: chain D residue 393 ILE Chi-restraints excluded: chain D residue 484 ILE Chi-restraints excluded: chain D residue 493 LEU Chi-restraints excluded: chain D residue 498 ILE Chi-restraints excluded: chain D residue 537 THR Chi-restraints excluded: chain D residue 592 THR 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: 30.0000 chunk 253 optimal weight: 1.9990 chunk 224 optimal weight: 5.9990 chunk 244 optimal weight: 0.0020 chunk 199 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 127 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 99 optimal weight: 8.9990 chunk 200 optimal weight: 4.9990 overall best weight: 2.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 463 GLN B 520 GLN B 601 GLN B 834 HIS ** B 985 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 958 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 976 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 979 GLN ** D 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 50 HIS D 128 HIS D 523 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.086185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.064064 restraints weight = 96983.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.066164 restraints weight = 51404.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.067511 restraints weight = 34658.616| |-----------------------------------------------------------------------------| r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.3672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 24452 Z= 0.123 Angle : 0.550 11.727 33409 Z= 0.278 Chirality : 0.039 0.167 3673 Planarity : 0.004 0.059 4205 Dihedral : 13.618 87.682 3730 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.65 % Allowed : 11.84 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.24 (0.15), residues: 2837 helix: 0.99 (0.14), residues: 1419 sheet: -0.19 (0.29), residues: 296 loop : -1.67 (0.17), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 972 HIS 0.005 0.001 HIS D 65 PHE 0.010 0.001 PHE B 982 TYR 0.016 0.001 TYR C 437 ARG 0.013 0.000 ARG B 974 Details of bonding type rmsd hydrogen bonds : bond 0.03603 ( 1087) hydrogen bonds : angle 4.01201 ( 3152) covalent geometry : bond 0.00278 (24452) covalent geometry : angle 0.55029 (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 247 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 183 time to evaluate : 2.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 185 GLU cc_start: 0.8609 (tp30) cc_final: 0.8280 (tm-30) REVERT: B 499 MET cc_start: 0.7607 (tpt) cc_final: 0.7384 (tpt) REVERT: B 518 MET cc_start: 0.6213 (mmm) cc_final: 0.5903 (mmm) REVERT: B 596 MET cc_start: 0.8791 (mmm) cc_final: 0.8579 (mtp) REVERT: B 621 MET cc_start: 0.8119 (mtt) cc_final: 0.7904 (mtt) REVERT: B 665 MET cc_start: 0.8580 (mtp) cc_final: 0.8139 (tmm) REVERT: B 666 SER cc_start: 0.8963 (t) cc_final: 0.8734 (m) REVERT: B 753 TRP cc_start: 0.7982 (OUTLIER) cc_final: 0.6017 (t60) REVERT: B 1053 LEU cc_start: 0.2331 (OUTLIER) cc_final: 0.2054 (mt) REVERT: C 96 MET cc_start: 0.8597 (ttt) cc_final: 0.8302 (ttm) REVERT: C 414 ASP cc_start: 0.8082 (t70) cc_final: 0.7575 (p0) REVERT: C 422 ILE cc_start: 0.8520 (tp) cc_final: 0.8214 (tp) REVERT: D 112 MET cc_start: 0.7348 (ttm) cc_final: 0.7016 (ttm) REVERT: D 407 MET cc_start: 0.8520 (ttp) cc_final: 0.8192 (tmm) REVERT: D 433 GLN cc_start: 0.9552 (tt0) cc_final: 0.9299 (tm-30) REVERT: D 502 LEU cc_start: 0.3772 (OUTLIER) cc_final: 0.3475 (pp) REVERT: D 536 MET cc_start: 0.6693 (mmm) cc_final: 0.6467 (mmt) outliers start: 64 outliers final: 42 residues processed: 239 average time/residue: 0.3335 time to fit residues: 129.2846 Evaluate side-chains 202 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 157 time to evaluate : 2.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 198 ASN Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 352 ASP Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 491 PHE Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 582 SER Chi-restraints excluded: chain B residue 753 TRP Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 1053 LEU Chi-restraints excluded: chain B residue 1093 TYR Chi-restraints excluded: chain B residue 1159 ARG Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 419 SER Chi-restraints excluded: chain C residue 434 TYR Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 479 LEU Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain C residue 612 ILE Chi-restraints excluded: chain C residue 698 SER Chi-restraints excluded: chain C residue 801 SER Chi-restraints excluded: chain C residue 802 TYR Chi-restraints excluded: chain C residue 821 VAL Chi-restraints excluded: chain C residue 889 VAL Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 108 TYR Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 293 ILE Chi-restraints excluded: chain D residue 350 ASP Chi-restraints excluded: chain D residue 393 ILE Chi-restraints excluded: chain D residue 493 LEU Chi-restraints excluded: chain D residue 498 ILE Chi-restraints excluded: chain D residue 502 LEU Chi-restraints excluded: chain D residue 537 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: 30.0000 chunk 103 optimal weight: 30.0000 chunk 150 optimal weight: 10.0000 chunk 42 optimal weight: 5.9990 chunk 223 optimal weight: 9.9990 chunk 209 optimal weight: 1.9990 chunk 111 optimal weight: 20.0000 chunk 4 optimal weight: 5.9990 chunk 255 optimal weight: 5.9990 chunk 284 optimal weight: 10.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 234 GLN ** B 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 278 ASN B 534 GLN B 566 GLN B 601 GLN B 610 ASN ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 522 HIS C 951 GLN C 976 GLN ** D 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.082185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.060321 restraints weight = 100361.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.062267 restraints weight = 53826.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.063533 restraints weight = 36704.394| |-----------------------------------------------------------------------------| r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.4601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 24452 Z= 0.243 Angle : 0.681 13.365 33409 Z= 0.345 Chirality : 0.043 0.162 3673 Planarity : 0.005 0.054 4205 Dihedral : 13.698 89.411 3730 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 3.77 % Allowed : 12.13 % 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: -0.13 (0.15), residues: 2837 helix: 1.02 (0.14), residues: 1420 sheet: -0.10 (0.30), residues: 284 loop : -1.52 (0.17), residues: 1133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 841 HIS 0.009 0.001 HIS C 233 PHE 0.016 0.002 PHE C 193 TYR 0.017 0.002 TYR B 37 ARG 0.017 0.001 ARG B 254 Details of bonding type rmsd hydrogen bonds : bond 0.04800 ( 1087) hydrogen bonds : angle 4.36736 ( 3152) covalent geometry : bond 0.00558 (24452) covalent geometry : angle 0.68053 (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 245 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 154 time to evaluate : 2.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 264 LYS cc_start: 0.9320 (pttp) cc_final: 0.9019 (pttp) REVERT: B 665 MET cc_start: 0.8577 (mtp) cc_final: 0.8154 (tmm) REVERT: B 753 TRP cc_start: 0.7933 (OUTLIER) cc_final: 0.6359 (t60) REVERT: B 1053 LEU cc_start: 0.2010 (OUTLIER) cc_final: 0.1478 (mt) REVERT: B 1061 MET cc_start: 0.8762 (mmm) cc_final: 0.8545 (mmm) REVERT: C 17 MET cc_start: 0.8440 (tmm) cc_final: 0.7870 (ttm) REVERT: C 96 MET cc_start: 0.8691 (ttt) cc_final: 0.8268 (ttm) REVERT: C 253 ASP cc_start: 0.8832 (p0) cc_final: 0.8303 (p0) REVERT: C 414 ASP cc_start: 0.8112 (t70) cc_final: 0.7766 (p0) REVERT: C 422 ILE cc_start: 0.8611 (tp) cc_final: 0.8311 (tp) REVERT: C 802 TYR cc_start: 0.6552 (OUTLIER) cc_final: 0.5481 (t80) REVERT: C 817 HIS cc_start: 0.5246 (OUTLIER) cc_final: 0.4108 (m170) REVERT: C 976 GLN cc_start: 0.7880 (OUTLIER) cc_final: 0.7530 (mm-40) REVERT: D 112 MET cc_start: 0.7610 (ttm) cc_final: 0.7277 (mtp) REVERT: D 407 MET cc_start: 0.8545 (ttp) cc_final: 0.8178 (tmm) REVERT: D 433 GLN cc_start: 0.9523 (tt0) cc_final: 0.9257 (tm-30) REVERT: D 502 LEU cc_start: 0.3744 (OUTLIER) cc_final: 0.3366 (pp) outliers start: 91 outliers final: 56 residues processed: 235 average time/residue: 0.3138 time to fit residues: 123.5977 Evaluate side-chains 204 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 142 time to evaluate : 2.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 352 ASP Chi-restraints excluded: chain B residue 491 PHE Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 582 SER Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 753 TRP Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 1053 LEU Chi-restraints excluded: chain B residue 1093 TYR Chi-restraints excluded: chain B residue 1109 LEU Chi-restraints excluded: chain B residue 1158 THR Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 419 SER Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 506 ILE Chi-restraints excluded: chain C residue 509 ASP Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain C residue 590 VAL Chi-restraints excluded: chain C residue 612 ILE Chi-restraints excluded: chain C residue 698 SER Chi-restraints excluded: chain C residue 738 ASP Chi-restraints excluded: chain C residue 801 SER Chi-restraints excluded: chain C residue 802 TYR 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 889 VAL Chi-restraints excluded: chain C residue 976 GLN Chi-restraints excluded: chain C residue 1106 VAL Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 169 ILE Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 265 VAL Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 280 SER Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 293 ILE Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 350 ASP Chi-restraints excluded: chain D residue 393 ILE Chi-restraints excluded: chain D residue 493 LEU Chi-restraints excluded: chain D residue 502 LEU Chi-restraints excluded: chain D residue 537 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 43 optimal weight: 6.9990 chunk 46 optimal weight: 8.9990 chunk 191 optimal weight: 9.9990 chunk 108 optimal weight: 7.9990 chunk 230 optimal weight: 0.7980 chunk 149 optimal weight: 6.9990 chunk 283 optimal weight: 20.0000 chunk 76 optimal weight: 10.0000 chunk 210 optimal weight: 8.9990 chunk 259 optimal weight: 50.0000 chunk 84 optimal weight: 2.9990 overall best weight: 5.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 224 GLN ** B 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 539 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.081881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.060132 restraints weight = 99585.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.062073 restraints weight = 53422.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.063306 restraints weight = 36471.379| |-----------------------------------------------------------------------------| r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.4981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 24452 Z= 0.202 Angle : 0.627 12.887 33409 Z= 0.318 Chirality : 0.042 0.169 3673 Planarity : 0.004 0.058 4205 Dihedral : 13.628 89.026 3721 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 3.27 % Allowed : 13.08 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.07 (0.16), residues: 2837 helix: 1.23 (0.14), residues: 1406 sheet: -0.05 (0.30), residues: 285 loop : -1.45 (0.17), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 841 HIS 0.005 0.001 HIS C 233 PHE 0.017 0.002 PHE B 982 TYR 0.016 0.002 TYR B 37 ARG 0.009 0.001 ARG C 23 Details of bonding type rmsd hydrogen bonds : bond 0.04330 ( 1087) hydrogen bonds : angle 4.23883 ( 3152) covalent geometry : bond 0.00463 (24452) covalent geometry : angle 0.62678 (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 232 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 153 time to evaluate : 2.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 354 MET cc_start: 0.6751 (mtm) cc_final: 0.6337 (ptp) REVERT: B 665 MET cc_start: 0.8555 (mtp) cc_final: 0.8126 (tmm) REVERT: B 753 TRP cc_start: 0.7996 (OUTLIER) cc_final: 0.6369 (t60) REVERT: B 1053 LEU cc_start: 0.1963 (OUTLIER) cc_final: 0.1358 (mt) REVERT: B 1061 MET cc_start: 0.8898 (mmm) cc_final: 0.8560 (mmm) REVERT: B 1168 MET cc_start: 0.8922 (mmm) cc_final: 0.8436 (mtp) REVERT: C 96 MET cc_start: 0.8526 (ttt) cc_final: 0.8117 (ttm) REVERT: C 253 ASP cc_start: 0.8806 (p0) cc_final: 0.8276 (p0) REVERT: C 414 ASP cc_start: 0.8114 (t70) cc_final: 0.7791 (p0) REVERT: C 422 ILE cc_start: 0.8551 (tp) cc_final: 0.8293 (tp) REVERT: C 817 HIS cc_start: 0.5585 (OUTLIER) cc_final: 0.4343 (m170) REVERT: D 407 MET cc_start: 0.8513 (ttp) cc_final: 0.8183 (tmm) REVERT: D 433 GLN cc_start: 0.9521 (tt0) cc_final: 0.9235 (tm-30) REVERT: D 502 LEU cc_start: 0.3743 (OUTLIER) cc_final: 0.3386 (pp) outliers start: 79 outliers final: 56 residues processed: 218 average time/residue: 0.3090 time to fit residues: 113.4587 Evaluate side-chains 204 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 144 time to evaluate : 2.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 352 ASP Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 442 THR Chi-restraints excluded: chain B residue 491 PHE Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 582 SER Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 753 TRP Chi-restraints excluded: chain B residue 833 VAL Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 1053 LEU Chi-restraints excluded: chain B residue 1093 TYR Chi-restraints excluded: chain B residue 1109 LEU Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain B residue 1159 ARG Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 362 ASP Chi-restraints excluded: chain C residue 419 SER Chi-restraints excluded: chain C residue 506 ILE Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain C residue 590 VAL Chi-restraints excluded: chain C residue 612 ILE Chi-restraints excluded: chain C residue 698 SER Chi-restraints excluded: chain C residue 738 ASP 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 827 THR Chi-restraints excluded: chain C residue 889 VAL Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 169 ILE Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 265 VAL Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 293 ILE Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 350 ASP Chi-restraints excluded: chain D residue 393 ILE Chi-restraints excluded: chain D residue 502 LEU Chi-restraints excluded: chain D residue 519 ILE Chi-restraints excluded: chain D residue 537 THR Chi-restraints excluded: chain D residue 570 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 134 optimal weight: 3.9990 chunk 162 optimal weight: 3.9990 chunk 110 optimal weight: 0.8980 chunk 208 optimal weight: 7.9990 chunk 26 optimal weight: 10.0000 chunk 277 optimal weight: 5.9990 chunk 203 optimal weight: 6.9990 chunk 89 optimal weight: 30.0000 chunk 194 optimal weight: 0.9980 chunk 182 optimal weight: 0.0070 chunk 144 optimal weight: 6.9990 overall best weight: 1.9802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 261 ASN B 531 GLN B 601 GLN ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 237 HIS C 976 GLN ** D 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 539 HIS ** 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 = 0.3971 r_free = 0.3971 target = 0.083464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.061857 restraints weight = 97688.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.063852 restraints weight = 51926.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.065147 restraints weight = 35256.131| |-----------------------------------------------------------------------------| r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.5017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 24452 Z= 0.115 Angle : 0.562 13.143 33409 Z= 0.281 Chirality : 0.040 0.198 3673 Planarity : 0.004 0.062 4205 Dihedral : 13.509 89.167 3721 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.44 % Allowed : 14.53 % Favored : 83.02 % 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: 0.49 (0.16), residues: 2837 helix: 1.65 (0.14), residues: 1421 sheet: 0.10 (0.31), residues: 276 loop : -1.37 (0.17), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 401 HIS 0.004 0.001 HIS D 65 PHE 0.016 0.001 PHE B 982 TYR 0.013 0.001 TYR D 108 ARG 0.009 0.000 ARG B 974 Details of bonding type rmsd hydrogen bonds : bond 0.03461 ( 1087) hydrogen bonds : angle 3.91194 ( 3152) covalent geometry : bond 0.00259 (24452) covalent geometry : angle 0.56169 (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 212 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 153 time to evaluate : 2.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 264 LYS cc_start: 0.9273 (pttp) cc_final: 0.8922 (pttp) REVERT: B 753 TRP cc_start: 0.8048 (OUTLIER) cc_final: 0.6332 (t60) REVERT: B 1053 LEU cc_start: 0.1968 (OUTLIER) cc_final: 0.1362 (mt) REVERT: B 1061 MET cc_start: 0.8831 (mmm) cc_final: 0.8408 (mmm) REVERT: B 1111 TYR cc_start: 0.8494 (OUTLIER) cc_final: 0.8036 (p90) REVERT: B 1168 MET cc_start: 0.8664 (mmm) cc_final: 0.8146 (mmm) REVERT: B 1171 MET cc_start: 0.9279 (ptt) cc_final: 0.9044 (ptp) REVERT: C 96 MET cc_start: 0.8475 (ttt) cc_final: 0.8027 (ttm) REVERT: C 253 ASP cc_start: 0.8815 (p0) cc_final: 0.8223 (p0) REVERT: C 414 ASP cc_start: 0.7992 (t70) cc_final: 0.7619 (p0) REVERT: C 422 ILE cc_start: 0.8465 (tp) cc_final: 0.8227 (tp) REVERT: C 802 TYR cc_start: 0.6879 (OUTLIER) cc_final: 0.5525 (t80) REVERT: C 976 GLN cc_start: 0.8048 (OUTLIER) cc_final: 0.7730 (mt0) REVERT: D 112 MET cc_start: 0.7434 (OUTLIER) cc_final: 0.7131 (mtp) REVERT: D 407 MET cc_start: 0.8483 (ttp) cc_final: 0.8133 (tmm) REVERT: D 433 GLN cc_start: 0.9510 (tt0) cc_final: 0.9234 (tm-30) REVERT: D 502 LEU cc_start: 0.3859 (OUTLIER) cc_final: 0.3492 (pp) outliers start: 59 outliers final: 40 residues processed: 208 average time/residue: 0.3340 time to fit residues: 115.8410 Evaluate side-chains 191 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 144 time to evaluate : 2.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 198 ASN Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 491 PHE Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 582 SER Chi-restraints excluded: chain B residue 753 TRP Chi-restraints excluded: chain B residue 775 GLU Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 1053 LEU Chi-restraints excluded: chain B residue 1093 TYR Chi-restraints excluded: chain B residue 1111 TYR Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain B residue 1159 ARG Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 419 SER Chi-restraints excluded: chain C residue 506 ILE Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain C residue 612 ILE Chi-restraints excluded: chain C residue 801 SER Chi-restraints excluded: chain C residue 802 TYR Chi-restraints excluded: chain C residue 821 VAL Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 889 VAL Chi-restraints excluded: chain C residue 976 GLN Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 112 MET Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 265 VAL Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 293 ILE Chi-restraints excluded: chain D residue 350 ASP Chi-restraints excluded: chain D residue 393 ILE Chi-restraints excluded: chain D residue 493 LEU Chi-restraints excluded: chain D residue 502 LEU Chi-restraints excluded: chain D residue 537 THR Chi-restraints excluded: chain D residue 570 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 180 optimal weight: 9.9990 chunk 34 optimal weight: 6.9990 chunk 212 optimal weight: 8.9990 chunk 273 optimal weight: 30.0000 chunk 28 optimal weight: 0.0170 chunk 127 optimal weight: 10.0000 chunk 185 optimal weight: 6.9990 chunk 120 optimal weight: 7.9990 chunk 4 optimal weight: 6.9990 chunk 55 optimal weight: 5.9990 chunk 136 optimal weight: 7.9990 overall best weight: 5.4026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 130 HIS ** B 742 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 539 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.081258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.059576 restraints weight = 100060.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.061457 restraints weight = 53712.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.062689 restraints weight = 36845.554| |-----------------------------------------------------------------------------| r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.5429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 24452 Z= 0.214 Angle : 0.645 13.354 33409 Z= 0.326 Chirality : 0.042 0.157 3673 Planarity : 0.004 0.059 4205 Dihedral : 13.533 88.258 3721 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 3.19 % Allowed : 14.45 % Favored : 82.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.31 (0.16), residues: 2837 helix: 1.43 (0.14), residues: 1414 sheet: 0.10 (0.31), residues: 270 loop : -1.34 (0.18), residues: 1153 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 841 HIS 0.005 0.001 HIS B 812 PHE 0.029 0.002 PHE B 289 TYR 0.016 0.002 TYR B 37 ARG 0.010 0.001 ARG B 974 Details of bonding type rmsd hydrogen bonds : bond 0.04421 ( 1087) hydrogen bonds : angle 4.24931 ( 3152) covalent geometry : bond 0.00491 (24452) covalent geometry : angle 0.64508 (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 220 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 143 time to evaluate : 2.771 Fit side-chains revert: symmetry clash REVERT: B 264 LYS cc_start: 0.9295 (pttp) cc_final: 0.8991 (pttp) REVERT: B 306 ARG cc_start: 0.8008 (mmp-170) cc_final: 0.7316 (mmm160) REVERT: B 665 MET cc_start: 0.8521 (mtp) cc_final: 0.8164 (tmm) REVERT: B 753 TRP cc_start: 0.8038 (OUTLIER) cc_final: 0.6476 (t60) REVERT: B 1053 LEU cc_start: 0.2066 (OUTLIER) cc_final: 0.1427 (mt) REVERT: B 1111 TYR cc_start: 0.8456 (OUTLIER) cc_final: 0.8009 (p90) REVERT: B 1141 LEU cc_start: 0.9514 (OUTLIER) cc_final: 0.9264 (mm) REVERT: B 1168 MET cc_start: 0.8871 (mmm) cc_final: 0.8440 (mmm) REVERT: B 1171 MET cc_start: 0.9314 (ptt) cc_final: 0.9056 (ptp) REVERT: C 1 MET cc_start: 0.7733 (tpt) cc_final: 0.7445 (tpt) REVERT: C 96 MET cc_start: 0.8480 (ttt) cc_final: 0.7896 (ttm) REVERT: C 414 ASP cc_start: 0.8055 (t70) cc_final: 0.7691 (p0) REVERT: C 422 ILE cc_start: 0.8576 (tp) cc_final: 0.8327 (tp) REVERT: C 817 HIS cc_start: 0.5614 (OUTLIER) cc_final: 0.4190 (m170) REVERT: C 978 MET cc_start: 0.8502 (tpp) cc_final: 0.8195 (tpp) REVERT: D 407 MET cc_start: 0.8451 (ttp) cc_final: 0.8210 (tmm) REVERT: D 433 GLN cc_start: 0.9519 (tt0) cc_final: 0.9226 (tm-30) REVERT: D 502 LEU cc_start: 0.3766 (OUTLIER) cc_final: 0.3367 (pp) REVERT: D 580 TYR cc_start: 0.6842 (m-80) cc_final: 0.6329 (m-80) outliers start: 77 outliers final: 56 residues processed: 210 average time/residue: 0.3048 time to fit residues: 108.4503 Evaluate side-chains 199 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 137 time to evaluate : 2.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 491 PHE Chi-restraints excluded: chain B residue 501 MET Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 582 SER Chi-restraints excluded: chain B residue 696 GLU Chi-restraints excluded: chain B residue 753 TRP Chi-restraints excluded: chain B residue 775 GLU Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 1019 VAL Chi-restraints excluded: chain B residue 1053 LEU Chi-restraints excluded: chain B residue 1093 TYR Chi-restraints excluded: chain B residue 1102 MET Chi-restraints excluded: chain B residue 1109 LEU Chi-restraints excluded: chain B residue 1111 TYR Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 419 SER Chi-restraints excluded: chain C residue 506 ILE Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain C residue 590 VAL Chi-restraints excluded: chain C residue 612 ILE Chi-restraints excluded: chain C residue 738 ASP Chi-restraints excluded: chain C residue 817 HIS Chi-restraints excluded: chain C residue 821 VAL Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 853 LEU Chi-restraints excluded: chain C residue 889 VAL Chi-restraints excluded: chain C residue 1106 VAL Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 112 MET Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 265 VAL Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 293 ILE Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 350 ASP Chi-restraints excluded: chain D residue 393 ILE Chi-restraints excluded: chain D residue 493 LEU Chi-restraints excluded: chain D residue 502 LEU Chi-restraints excluded: chain D residue 537 THR Chi-restraints excluded: chain D residue 570 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 212 optimal weight: 7.9990 chunk 121 optimal weight: 0.9990 chunk 154 optimal weight: 4.9990 chunk 33 optimal weight: 9.9990 chunk 6 optimal weight: 7.9990 chunk 250 optimal weight: 9.9990 chunk 188 optimal weight: 1.9990 chunk 94 optimal weight: 20.0000 chunk 255 optimal weight: 3.9990 chunk 183 optimal weight: 3.9990 chunk 95 optimal weight: 9.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 976 GLN ** D 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 539 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.082292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.060657 restraints weight = 98809.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.062614 restraints weight = 52728.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.063875 restraints weight = 35943.075| |-----------------------------------------------------------------------------| r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.5505 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= 0.142 Angle : 0.582 13.094 33409 Z= 0.292 Chirality : 0.040 0.168 3673 Planarity : 0.004 0.061 4205 Dihedral : 13.484 89.090 3721 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.44 % Allowed : 15.24 % Favored : 82.32 % 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: 0.57 (0.16), residues: 2837 helix: 1.68 (0.14), residues: 1421 sheet: 0.20 (0.32), residues: 268 loop : -1.28 (0.18), residues: 1148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 841 HIS 0.008 0.001 HIS B 689 PHE 0.013 0.001 PHE B 982 TYR 0.013 0.001 TYR C 437 ARG 0.008 0.000 ARG B 974 Details of bonding type rmsd hydrogen bonds : bond 0.03714 ( 1087) hydrogen bonds : angle 3.98919 ( 3152) covalent geometry : bond 0.00328 (24452) covalent geometry : angle 0.58182 (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 206 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 147 time to evaluate : 2.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 264 LYS cc_start: 0.9291 (pttp) cc_final: 0.9014 (pttp) REVERT: B 306 ARG cc_start: 0.7983 (mmp-170) cc_final: 0.7282 (mmm160) REVERT: B 665 MET cc_start: 0.8584 (mtp) cc_final: 0.8172 (tmm) REVERT: B 753 TRP cc_start: 0.8028 (OUTLIER) cc_final: 0.6450 (t60) REVERT: B 1053 LEU cc_start: 0.2056 (OUTLIER) cc_final: 0.1414 (mt) REVERT: B 1111 TYR cc_start: 0.8431 (OUTLIER) cc_final: 0.7971 (p90) REVERT: B 1141 LEU cc_start: 0.9478 (OUTLIER) cc_final: 0.9221 (mm) REVERT: B 1168 MET cc_start: 0.8907 (mmm) cc_final: 0.8501 (mmm) REVERT: B 1171 MET cc_start: 0.9334 (ptt) cc_final: 0.9080 (ptp) REVERT: C 96 MET cc_start: 0.8489 (ttt) cc_final: 0.7877 (ttm) REVERT: C 414 ASP cc_start: 0.8031 (t70) cc_final: 0.7747 (p0) REVERT: C 422 ILE cc_start: 0.8538 (tp) cc_final: 0.8297 (tp) REVERT: C 817 HIS cc_start: 0.5644 (OUTLIER) cc_final: 0.4254 (m170) REVERT: C 978 MET cc_start: 0.8441 (tpp) cc_final: 0.8175 (tpp) REVERT: D 407 MET cc_start: 0.8399 (ttp) cc_final: 0.8088 (tmm) REVERT: D 433 GLN cc_start: 0.9514 (tt0) cc_final: 0.9234 (tm-30) REVERT: D 502 LEU cc_start: 0.3739 (OUTLIER) cc_final: 0.3347 (pp) REVERT: D 536 MET cc_start: 0.6686 (mmt) cc_final: 0.6380 (mmt) outliers start: 59 outliers final: 48 residues processed: 201 average time/residue: 0.3239 time to fit residues: 108.9308 Evaluate side-chains 193 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 139 time to evaluate : 2.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 198 ASN Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 442 THR Chi-restraints excluded: chain B residue 491 PHE Chi-restraints excluded: chain B residue 501 MET Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 582 SER Chi-restraints excluded: chain B residue 753 TRP Chi-restraints excluded: chain B residue 775 GLU Chi-restraints excluded: chain B residue 833 VAL Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 1019 VAL Chi-restraints excluded: chain B residue 1053 LEU Chi-restraints excluded: chain B residue 1093 TYR Chi-restraints excluded: chain B residue 1102 MET Chi-restraints excluded: chain B residue 1111 TYR Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain B residue 1159 ARG Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 338 ILE Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 419 SER Chi-restraints excluded: chain C residue 506 ILE Chi-restraints excluded: chain C residue 538 GLU Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain C residue 612 ILE Chi-restraints excluded: chain C residue 817 HIS Chi-restraints excluded: chain C residue 821 VAL Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 889 VAL Chi-restraints excluded: chain C residue 959 VAL Chi-restraints excluded: chain C residue 976 GLN Chi-restraints excluded: chain C residue 1106 VAL Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 112 MET Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 350 ASP Chi-restraints excluded: chain D residue 393 ILE Chi-restraints excluded: chain D residue 493 LEU Chi-restraints excluded: chain D residue 502 LEU Chi-restraints excluded: chain D residue 537 THR Chi-restraints excluded: chain D residue 570 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 165 optimal weight: 9.9990 chunk 146 optimal weight: 9.9990 chunk 221 optimal weight: 8.9990 chunk 225 optimal weight: 5.9990 chunk 267 optimal weight: 20.0000 chunk 258 optimal weight: 20.0000 chunk 213 optimal weight: 1.9990 chunk 194 optimal weight: 6.9990 chunk 250 optimal weight: 9.9990 chunk 232 optimal weight: 9.9990 chunk 237 optimal weight: 2.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 134 GLN ** B 742 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 976 GLN ** D 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 539 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.080694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.059083 restraints weight = 99968.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.060926 restraints weight = 54001.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.062125 restraints weight = 37236.251| |-----------------------------------------------------------------------------| r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.5834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 24452 Z= 0.216 Angle : 0.664 13.175 33409 Z= 0.335 Chirality : 0.042 0.182 3673 Planarity : 0.005 0.058 4205 Dihedral : 13.535 83.324 3721 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 3.19 % Allowed : 14.58 % Favored : 82.24 % 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: 0.26 (0.16), residues: 2837 helix: 1.38 (0.14), residues: 1420 sheet: 0.25 (0.32), residues: 249 loop : -1.39 (0.18), residues: 1168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 248 HIS 0.005 0.001 HIS B 812 PHE 0.023 0.002 PHE B 289 TYR 0.017 0.002 TYR B 37 ARG 0.009 0.001 ARG B 974 Details of bonding type rmsd hydrogen bonds : bond 0.04498 ( 1087) hydrogen bonds : angle 4.27558 ( 3152) covalent geometry : bond 0.00497 (24452) covalent geometry : angle 0.66370 (33409) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 140 time to evaluate : 2.631 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 264 LYS cc_start: 0.9308 (pttp) cc_final: 0.8970 (pttp) REVERT: B 306 ARG cc_start: 0.8029 (mmp-170) cc_final: 0.7329 (mmm160) REVERT: B 501 MET cc_start: 0.8855 (OUTLIER) cc_final: 0.8619 (mtm) REVERT: B 665 MET cc_start: 0.8550 (mtp) cc_final: 0.8200 (tmm) REVERT: B 753 TRP cc_start: 0.8149 (OUTLIER) cc_final: 0.6480 (t60) REVERT: B 1053 LEU cc_start: 0.2103 (OUTLIER) cc_final: 0.1419 (mt) REVERT: B 1111 TYR cc_start: 0.8448 (OUTLIER) cc_final: 0.7990 (p90) REVERT: B 1141 LEU cc_start: 0.9517 (OUTLIER) cc_final: 0.9280 (mm) REVERT: C 96 MET cc_start: 0.8595 (ttt) cc_final: 0.7943 (ttm) REVERT: C 414 ASP cc_start: 0.7990 (t70) cc_final: 0.7758 (p0) REVERT: C 422 ILE cc_start: 0.8615 (tp) cc_final: 0.8361 (tp) REVERT: C 817 HIS cc_start: 0.5735 (OUTLIER) cc_final: 0.4287 (m170) REVERT: C 976 GLN cc_start: 0.8043 (OUTLIER) cc_final: 0.7720 (mm-40) REVERT: D 352 LEU cc_start: 0.7720 (mt) cc_final: 0.6949 (pp) REVERT: D 407 MET cc_start: 0.8407 (ttp) cc_final: 0.8159 (tmm) REVERT: D 433 GLN cc_start: 0.9518 (tt0) cc_final: 0.9228 (tm-30) REVERT: D 502 LEU cc_start: 0.3754 (OUTLIER) cc_final: 0.3364 (pp) outliers start: 77 outliers final: 56 residues processed: 210 average time/residue: 0.3419 time to fit residues: 117.9631 Evaluate side-chains 199 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 135 time to evaluate : 2.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 352 ASP Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 442 THR Chi-restraints excluded: chain B residue 491 PHE Chi-restraints excluded: chain B residue 501 MET Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 582 SER Chi-restraints excluded: chain B residue 620 MET Chi-restraints excluded: chain B residue 753 TRP Chi-restraints excluded: chain B residue 775 GLU Chi-restraints excluded: chain B residue 833 VAL Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 1019 VAL Chi-restraints excluded: chain B residue 1053 LEU Chi-restraints excluded: chain B residue 1102 MET Chi-restraints excluded: chain B residue 1109 LEU Chi-restraints excluded: chain B residue 1111 TYR Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain B residue 1159 ARG Chi-restraints excluded: chain B residue 1167 LEU Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 338 ILE Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 419 SER Chi-restraints excluded: chain C residue 506 ILE Chi-restraints excluded: chain C residue 538 GLU Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain C residue 590 VAL Chi-restraints excluded: chain C residue 612 ILE Chi-restraints excluded: chain C residue 738 ASP Chi-restraints excluded: chain C residue 817 HIS Chi-restraints excluded: chain C residue 821 VAL Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 889 VAL Chi-restraints excluded: chain C residue 976 GLN Chi-restraints excluded: chain C residue 1106 VAL Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 112 MET Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 350 ASP Chi-restraints excluded: chain D residue 393 ILE Chi-restraints excluded: chain D residue 493 LEU Chi-restraints excluded: chain D residue 502 LEU Chi-restraints excluded: chain D residue 537 THR Chi-restraints excluded: chain D residue 570 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 95 optimal weight: 7.9990 chunk 175 optimal weight: 0.9980 chunk 202 optimal weight: 7.9990 chunk 30 optimal weight: 5.9990 chunk 201 optimal weight: 6.9990 chunk 57 optimal weight: 4.9990 chunk 245 optimal weight: 20.0000 chunk 154 optimal weight: 7.9990 chunk 80 optimal weight: 0.6980 chunk 138 optimal weight: 6.9990 chunk 125 optimal weight: 6.9990 overall best weight: 3.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 134 GLN ** B 742 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 976 GLN ** D 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 539 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.081238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.059585 restraints weight = 99329.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.062216 restraints weight = 56825.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.063000 restraints weight = 33059.593| |-----------------------------------------------------------------------------| r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.5896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 24452 Z= 0.166 Angle : 0.617 13.214 33409 Z= 0.310 Chirality : 0.041 0.193 3673 Planarity : 0.004 0.059 4205 Dihedral : 13.540 84.399 3721 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.65 % Allowed : 15.07 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.16), residues: 2837 helix: 1.55 (0.14), residues: 1419 sheet: 0.33 (0.32), residues: 247 loop : -1.35 (0.18), residues: 1171 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 841 HIS 0.005 0.001 HIS D 65 PHE 0.013 0.001 PHE C 694 TYR 0.016 0.001 TYR B 430 ARG 0.007 0.000 ARG B 974 Details of bonding type rmsd hydrogen bonds : bond 0.03977 ( 1087) hydrogen bonds : angle 4.12231 ( 3152) covalent geometry : bond 0.00384 (24452) covalent geometry : angle 0.61655 (33409) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 141 time to evaluate : 2.812 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 306 ARG cc_start: 0.8060 (mmp-170) cc_final: 0.7344 (mmm160) REVERT: B 665 MET cc_start: 0.8541 (mtp) cc_final: 0.8188 (tmm) REVERT: B 753 TRP cc_start: 0.8174 (OUTLIER) cc_final: 0.6476 (t60) REVERT: B 1053 LEU cc_start: 0.1753 (OUTLIER) cc_final: 0.1153 (mt) REVERT: B 1111 TYR cc_start: 0.8450 (OUTLIER) cc_final: 0.7983 (p90) REVERT: B 1141 LEU cc_start: 0.9481 (OUTLIER) cc_final: 0.9235 (mm) REVERT: C 96 MET cc_start: 0.8637 (ttt) cc_final: 0.7965 (ttm) REVERT: C 422 ILE cc_start: 0.8603 (tp) cc_final: 0.8344 (tp) REVERT: C 817 HIS cc_start: 0.5673 (OUTLIER) cc_final: 0.4260 (m170) REVERT: C 976 GLN cc_start: 0.8129 (OUTLIER) cc_final: 0.7905 (mp10) REVERT: C 978 MET cc_start: 0.8380 (tpp) cc_final: 0.8056 (tpp) REVERT: D 352 LEU cc_start: 0.7655 (mt) cc_final: 0.6902 (pp) REVERT: D 407 MET cc_start: 0.8405 (ttp) cc_final: 0.8092 (tmm) REVERT: D 433 GLN cc_start: 0.9533 (tt0) cc_final: 0.9239 (tm-30) REVERT: D 502 LEU cc_start: 0.3710 (OUTLIER) cc_final: 0.3324 (pp) REVERT: D 536 MET cc_start: 0.6704 (mmt) cc_final: 0.6405 (mmt) outliers start: 64 outliers final: 53 residues processed: 200 average time/residue: 0.3423 time to fit residues: 114.9088 Evaluate side-chains 195 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 135 time to evaluate : 3.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 442 THR Chi-restraints excluded: chain B residue 491 PHE Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 582 SER Chi-restraints excluded: chain B residue 753 TRP Chi-restraints excluded: chain B residue 775 GLU Chi-restraints excluded: chain B residue 833 VAL Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 1053 LEU Chi-restraints excluded: chain B residue 1093 TYR Chi-restraints excluded: chain B residue 1102 MET Chi-restraints excluded: chain B residue 1111 TYR Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain B residue 1159 ARG Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 338 ILE Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 419 SER Chi-restraints excluded: chain C residue 463 SER Chi-restraints excluded: chain C residue 506 ILE Chi-restraints excluded: chain C residue 538 GLU Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain C residue 590 VAL Chi-restraints excluded: chain C residue 612 ILE Chi-restraints excluded: chain C residue 817 HIS Chi-restraints excluded: chain C residue 821 VAL Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 889 VAL Chi-restraints excluded: chain C residue 959 VAL Chi-restraints excluded: chain C residue 976 GLN Chi-restraints excluded: chain C residue 1106 VAL Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 112 MET Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 350 ASP Chi-restraints excluded: chain D residue 393 ILE Chi-restraints excluded: chain D residue 493 LEU Chi-restraints excluded: chain D residue 502 LEU Chi-restraints excluded: chain D residue 537 THR Chi-restraints excluded: chain D residue 570 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/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-5710/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-5710/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-5710/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-5710/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-5710/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-5710/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-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/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-5710/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-5710/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-5710/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: 50.1613 > 50: distance: 22 - 23: 7.648 distance: 23 - 24: 6.270 distance: 23 - 26: 6.104 distance: 24 - 25: 12.296 distance: 24 - 31: 21.347 distance: 26 - 27: 9.461 distance: 27 - 28: 5.651 distance: 28 - 30: 7.313 distance: 31 - 32: 12.271 distance: 32 - 33: 36.229 distance: 32 - 35: 9.309 distance: 33 - 34: 40.567 distance: 33 - 40: 13.185 distance: 35 - 36: 10.705 distance: 36 - 37: 6.477 distance: 37 - 38: 8.259 distance: 37 - 39: 8.385 distance: 40 - 41: 35.348 distance: 41 - 42: 16.279 distance: 41 - 44: 27.990 distance: 42 - 43: 27.586 distance: 42 - 51: 30.406 distance: 44 - 45: 20.536 distance: 45 - 46: 8.648 distance: 46 - 47: 8.207 distance: 47 - 48: 23.976 distance: 48 - 49: 13.978 distance: 48 - 50: 19.711 distance: 51 - 52: 17.943 distance: 51 - 57: 13.149 distance: 52 - 53: 21.120 distance: 52 - 55: 12.025 distance: 53 - 54: 8.716 distance: 53 - 58: 33.620 distance: 55 - 56: 14.238 distance: 56 - 57: 7.419 distance: 58 - 59: 3.650 distance: 59 - 60: 24.138 distance: 59 - 62: 18.981 distance: 60 - 61: 8.267 distance: 60 - 66: 21.936 distance: 62 - 63: 14.813 distance: 63 - 64: 7.280 distance: 63 - 65: 10.836 distance: 66 - 67: 6.628 distance: 67 - 68: 31.143 distance: 67 - 70: 22.791 distance: 68 - 69: 14.059 distance: 68 - 75: 7.472 distance: 70 - 71: 9.495 distance: 71 - 72: 9.180 distance: 72 - 73: 8.153 distance: 72 - 74: 17.932 distance: 75 - 76: 14.036 distance: 76 - 77: 10.667 distance: 76 - 79: 8.014 distance: 77 - 78: 10.806 distance: 77 - 84: 25.241 distance: 79 - 80: 13.465 distance: 80 - 81: 6.483 distance: 81 - 82: 7.420 distance: 81 - 83: 10.283 distance: 84 - 85: 25.078 distance: 85 - 86: 31.170 distance: 85 - 88: 19.158 distance: 86 - 87: 18.888 distance: 86 - 98: 18.812 distance: 88 - 89: 18.012 distance: 89 - 90: 18.530 distance: 89 - 91: 8.286 distance: 90 - 92: 15.049 distance: 91 - 93: 12.100 distance: 91 - 94: 6.978 distance: 92 - 93: 8.064 distance: 93 - 95: 5.401 distance: 94 - 96: 12.805 distance: 95 - 97: 7.847 distance: 96 - 97: 10.924 distance: 98 - 99: 22.705 distance: 99 - 100: 21.808 distance: 99 - 102: 35.632 distance: 100 - 101: 12.664 distance: 100 - 106: 22.743 distance: 102 - 103: 10.814 distance: 103 - 104: 27.436 distance: 103 - 105: 28.933 distance: 106 - 107: 28.790 distance: 106 - 112: 35.753 distance: 107 - 108: 23.574 distance: 107 - 110: 26.587 distance: 108 - 109: 30.659 distance: 108 - 113: 28.460 distance: 109 - 129: 16.968 distance: 110 - 111: 43.737 distance: 111 - 112: 14.055