Starting phenix.real_space_refine on Sun Sep 13 14:00:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6t2u_10369/09_2026/6t2u_10369.cif Found real_map, /net/cci-nas-00/data/ceres_data/6t2u_10369/09_2026/6t2u_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_10369/09_2026/6t2u_10369.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6t2u_10369/09_2026/6t2u_10369.map" model { file = "/net/cci-nas-00/data/ceres_data/6t2u_10369/09_2026/6t2u_10369.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6t2u_10369/09_2026/6t2u_10369.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 23826 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 9047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1129, 9047 Classifications: {'peptide': 1129} Link IDs: {'PTRANS': 51, 'TRANS': 1077} Chain breaks: 2 Chain: "C" Number of atoms: 9078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1121, 9078 Classifications: {'peptide': 1121} Link IDs: {'PCIS': 1, 'PTRANS': 66, 'TRANS': 1053} Chain: "D" Number of atoms: 4603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4603 Classifications: {'peptide': 597} Link IDs: {'PTRANS': 25, 'TRANS': 571} Chain: "X" Number of atoms: 1098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 1098 Classifications: {'DNA': 54} Link IDs: {'rna3p': 53} Chain breaks: 1 Time building chain proxies: 5.01, per 1000 atoms: 0.21 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: 1.89 Conformation dependent library (CDL) restraints added in 1.0 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: 2.79 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: 5.41 Time building geometry restraints manager: 2.48 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=" C3' DT X 13 " pdb=" C2' DT X 13 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.24e+00 bond pdb=" C3' DG X 59 " pdb=" C2' DG X 59 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.23e+00 bond pdb=" C3' DC X 27 " pdb=" C2' DC X 27 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.44e+00 bond pdb=" C3' DT X 8 " pdb=" C2' DT X 8 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 7.95e+00 bond pdb=" C3' DC X 25 " pdb=" C2' DC X 25 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.23e+00 ... (remaining 24447 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.16: 33081 2.16 - 4.32: 309 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=" N3 DT X 28 " pdb=" C4 DT X 28 " pdb=" O4 DT X 28 " ideal model delta sigma weight residual 119.90 122.45 -2.55 6.00e-01 2.78e+00 1.81e+01 angle pdb=" N3 DT X 60 " pdb=" C4 DT X 60 " pdb=" O4 DT X 60 " ideal model delta sigma weight residual 119.90 122.43 -2.53 6.00e-01 2.78e+00 1.78e+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=" N3 DT X 14 " pdb=" C4 DT X 14 " pdb=" O4 DT X 14 " ideal model delta sigma weight residual 119.90 122.39 -2.49 6.00e-01 2.78e+00 1.73e+01 ... (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: 3445 0.076 - 0.151: 227 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: 0.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 24.410 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7119 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= 0.184 Angle : 0.505 10.801 33409 Z= 0.362 Chirality : 0.037 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 : 4.78 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.59 (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 ARG 0.003 0.000 ARG B 800 TYR 0.006 0.001 TYR D 108 PHE 0.007 0.001 PHE B1023 TRP 0.011 0.001 TRP C 164 HIS 0.002 0.000 HIS C 377 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.18 (24452) covalent geometry : angle 0.50545 / 0.36 (33409) hydrogen bonds : bond 0.14020 / 9.35 ( 1087) hydrogen bonds : angle 6.13571 / 4.37 ( 3152) *********************** 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 : 1.157 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 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: 0.5574 (mmm) REVERT: B 526 ILE cc_start: 0.8364 (mt) cc_final: 0.8034 (mm) REVERT: B 665 MET cc_start: 0.8853 (mtp) cc_final: 0.7921 (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: 0.6044 (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: 0.7783 (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: 0.7433 (t0) REVERT: C 514 LEU cc_start: 0.8805 (mt) cc_final: 0.8453 (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: 0.5832 (t) REVERT: C 665 MET cc_start: 0.7625 (tpp) cc_final: 0.7375 (tpt) REVERT: C 968 ARG cc_start: 0.7864 (mtp180) cc_final: 0.7581 (mtp85) REVERT: D 108 TYR cc_start: 0.5667 (OUTLIER) cc_final: 0.4008 (p90) REVERT: D 112 MET cc_start: 0.7488 (mmt) cc_final: 0.7206 (ttm) 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: 0.1800 time to fit residues: 139.9986 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 : 0.924 ------------------------------------------------------------------------------- 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 197 optimal weight: 10.0000 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 30.0000 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 20.0000 chunk 183 optimal weight: 2.9990 chunk 111 optimal weight: 0.6980 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 120 GLN B 134 GLN B 150 GLN B 181 GLN B 222 HIS B 455 ASN B 458 ASN B 463 GLN B 566 GLN B 594 GLN B 650 GLN B 713 GLN B 765 GLN B 834 HIS B 848 GLN B 943 HIS B1035 GLN B1072 HIS B1084 ASN B1133 HIS B1134 HIS B1150 HIS C 126 GLN ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 HIS C 191 GLN C 390 HIS C 570 GLN C 614 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 C 979 GLN C1091 GLN C1108 GLN D 22 GLN D 89 GLN D 128 HIS D 251 GLN D 469 HIS D 523 GLN Total number of N/Q/H flips: 46 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.091216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.068689 restraints weight = 95283.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.071020 restraints weight = 49020.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.072537 restraints weight = 32340.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.073497 restraints weight = 24825.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.074093 restraints weight = 21056.219| |-----------------------------------------------------------------------------| r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7325 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 24452 Z= 0.154 Angle : 0.611 12.503 33409 Z= 0.312 Chirality : 0.041 0.167 3673 Planarity : 0.005 0.083 4205 Dihedral : 13.604 82.023 3732 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.69 % Allowed : 10.43 % Favored : 86.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.44 (0.14), residues: 2837 helix: -0.22 (0.13), residues: 1412 sheet: -0.70 (0.28), residues: 291 loop : -1.91 (0.16), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 93 TYR 0.018 0.001 TYR C 437 PHE 0.025 0.001 PHE B 982 TRP 0.022 0.001 TRP B 638 HIS 0.009 0.001 HIS B 222 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.15 (24452) covalent geometry : angle 0.61102 / 0.31 (33409) hydrogen bonds : bond 0.03866 / 2.60 ( 1087) hydrogen bonds : angle 4.38257 / 3.11 ( 3152) *********************** 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 272 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 207 time to evaluate : 0.807 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 499 MET cc_start: 0.7401 (tpt) cc_final: 0.7033 (tpt) REVERT: B 518 MET cc_start: 0.6005 (mmm) cc_final: 0.5663 (mmm) REVERT: B 665 MET cc_start: 0.8650 (mtp) cc_final: 0.7834 (tmm) REVERT: B 666 SER cc_start: 0.9044 (t) cc_final: 0.8842 (m) REVERT: B 753 TRP cc_start: 0.7843 (OUTLIER) cc_final: 0.5969 (t60) REVERT: B 966 GLN cc_start: 0.8497 (mt0) cc_final: 0.7923 (pp30) REVERT: B 1053 LEU cc_start: 0.2192 (OUTLIER) cc_final: 0.1911 (mt) REVERT: B 1111 TYR cc_start: 0.8488 (OUTLIER) cc_final: 0.8250 (p90) REVERT: C 96 MET cc_start: 0.8604 (ttt) cc_final: 0.8261 (ttm) REVERT: C 422 ILE cc_start: 0.8464 (tp) cc_final: 0.8198 (tp) REVERT: C 513 GLU cc_start: 0.8378 (tm-30) cc_final: 0.8142 (tm-30) REVERT: C 528 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8633 (tt) REVERT: C 551 ASP cc_start: 0.7999 (t0) cc_final: 0.7457 (p0) REVERT: C 574 TRP cc_start: 0.8237 (m100) cc_final: 0.7948 (m100) REVERT: C 591 CYS cc_start: 0.7083 (OUTLIER) cc_final: 0.6760 (t) REVERT: C 976 GLN cc_start: 0.8005 (OUTLIER) cc_final: 0.7734 (mm-40) REVERT: D 108 TYR cc_start: 0.6056 (OUTLIER) cc_final: 0.4254 (p90) REVERT: D 407 MET cc_start: 0.8583 (ttp) cc_final: 0.8237 (tmm) REVERT: D 433 GLN cc_start: 0.9531 (tt0) cc_final: 0.9286 (tm-30) outliers start: 65 outliers final: 36 residues processed: 260 average time/residue: 0.1607 time to fit residues: 68.0957 Evaluate side-chains 207 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 164 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 101 LEU 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 491 PHE Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 739 VAL 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 1111 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 479 LEU Chi-restraints excluded: chain C residue 528 LEU Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain C residue 591 CYS 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 C residue 976 GLN Chi-restraints excluded: chain C residue 1116 LEU 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 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 393 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 248 optimal weight: 7.9990 chunk 212 optimal weight: 9.9990 chunk 233 optimal weight: 8.9990 chunk 167 optimal weight: 10.0000 chunk 232 optimal weight: 7.9990 chunk 200 optimal weight: 0.9980 chunk 90 optimal weight: 3.9990 chunk 275 optimal weight: 20.0000 chunk 101 optimal weight: 5.9990 chunk 270 optimal weight: 0.9980 chunk 125 optimal weight: 5.9990 overall best weight: 3.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 510 ASN ** C 958 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 50 HIS D 328 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.088387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.065416 restraints weight = 95969.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.068412 restraints weight = 53334.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.069516 restraints weight = 30331.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.069926 restraints weight = 23859.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.070003 restraints weight = 22839.053| |-----------------------------------------------------------------------------| r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.2926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 24452 Z= 0.164 Angle : 0.581 12.018 33409 Z= 0.298 Chirality : 0.040 0.177 3673 Planarity : 0.004 0.060 4205 Dihedral : 13.707 86.913 3731 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.82 % Allowed : 10.23 % Favored : 86.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.15), residues: 2837 helix: 0.78 (0.13), residues: 1418 sheet: -0.41 (0.28), residues: 298 loop : -1.69 (0.17), residues: 1121 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 974 TYR 0.019 0.001 TYR C 437 PHE 0.015 0.002 PHE C 376 TRP 0.013 0.001 TRP B 638 HIS 0.005 0.001 HIS C 233 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.16 (24452) covalent geometry : angle 0.58065 / 0.30 (33409) hydrogen bonds : bond 0.03831 / 2.57 ( 1087) hydrogen bonds : angle 4.09996 / 2.91 ( 3152) *********************** 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 243 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 175 time to evaluate : 0.990 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: 0.8380 (tp30) cc_final: 0.8092 (tm-30) REVERT: B 518 MET cc_start: 0.6021 (mmm) cc_final: 0.5798 (mmm) REVERT: B 596 MET cc_start: 0.8951 (mmm) cc_final: 0.8570 (mtp) REVERT: B 599 LEU cc_start: 0.9266 (OUTLIER) cc_final: 0.9051 (mp) REVERT: B 658 MET cc_start: 0.7881 (tpp) cc_final: 0.7442 (tpt) REVERT: B 665 MET cc_start: 0.8687 (mtp) cc_final: 0.7893 (tmm) REVERT: B 666 SER cc_start: 0.9061 (t) cc_final: 0.8752 (m) REVERT: B 753 TRP cc_start: 0.7993 (OUTLIER) cc_final: 0.6017 (t60) REVERT: B 1053 LEU cc_start: 0.2128 (OUTLIER) cc_final: 0.1892 (mt) REVERT: C 96 MET cc_start: 0.8670 (ttt) cc_final: 0.8293 (ttm) REVERT: C 414 ASP cc_start: 0.7440 (t0) cc_final: 0.6413 (p0) REVERT: C 513 GLU cc_start: 0.8513 (tm-30) cc_final: 0.8228 (tm-30) REVERT: C 528 LEU cc_start: 0.9013 (OUTLIER) cc_final: 0.8666 (tt) REVERT: C 551 ASP cc_start: 0.8030 (t0) cc_final: 0.7558 (p0) REVERT: C 591 CYS cc_start: 0.7503 (OUTLIER) cc_final: 0.7025 (t) REVERT: C 1102 MET cc_start: 0.8511 (OUTLIER) cc_final: 0.7887 (ppp) REVERT: D 112 MET cc_start: 0.7654 (mmt) cc_final: 0.7437 (ttm) REVERT: D 407 MET cc_start: 0.8612 (ttp) cc_final: 0.8245 (tmm) REVERT: D 433 GLN cc_start: 0.9574 (tt0) cc_final: 0.9281 (tm-30) REVERT: D 536 MET cc_start: 0.6623 (mmm) cc_final: 0.6309 (mmt) outliers start: 68 outliers final: 37 residues processed: 232 average time/residue: 0.1502 time to fit residues: 57.2783 Evaluate side-chains 201 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 158 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 LEU 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 549 VAL Chi-restraints excluded: chain B residue 599 LEU 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 1159 ARG Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 230 LEU 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 571 LEU Chi-restraints excluded: chain C residue 590 VAL Chi-restraints excluded: chain C residue 591 CYS Chi-restraints excluded: chain C residue 645 LEU 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 821 VAL Chi-restraints excluded: chain C residue 889 VAL Chi-restraints excluded: chain C residue 1102 MET 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 184 LEU 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 393 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 137 optimal weight: 0.0670 chunk 231 optimal weight: 9.9990 chunk 172 optimal weight: 5.9990 chunk 101 optimal weight: 20.0000 chunk 259 optimal weight: 30.0000 chunk 196 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 chunk 220 optimal weight: 8.9990 chunk 25 optimal weight: 9.9990 chunk 26 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 overall best weight: 3.9924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 109 GLN B 734 HIS ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 725 GLN ** C 958 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 976 GLN ** D 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 542 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.085946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.062973 restraints weight = 95790.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.065097 restraints weight = 50517.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.066517 restraints weight = 34013.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.067409 restraints weight = 26454.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.067981 restraints weight = 22609.564| |-----------------------------------------------------------------------------| r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.3599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 24452 Z= 0.173 Angle : 0.602 11.893 33409 Z= 0.308 Chirality : 0.041 0.198 3673 Planarity : 0.004 0.055 4205 Dihedral : 13.769 88.490 3730 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.94 % Allowed : 10.64 % Favored : 86.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.15), residues: 2837 helix: 1.23 (0.14), residues: 1419 sheet: -0.23 (0.28), residues: 298 loop : -1.52 (0.17), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 254 TYR 0.018 0.002 TYR C 437 PHE 0.033 0.002 PHE B 289 TRP 0.012 0.001 TRP C 574 HIS 0.007 0.001 HIS C 233 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.17 (24452) covalent geometry : angle 0.60162 / 0.31 (33409) hydrogen bonds : bond 0.04027 / 2.66 ( 1087) hydrogen bonds : angle 4.06981 / 2.89 ( 3152) *********************** 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 243 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 172 time to evaluate : 1.403 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 306 ARG cc_start: 0.7973 (mmp-170) cc_final: 0.6922 (mmp-170) REVERT: B 518 MET cc_start: 0.6269 (mmm) cc_final: 0.5975 (mmm) REVERT: B 596 MET cc_start: 0.8923 (mmm) cc_final: 0.8617 (mtp) REVERT: B 658 MET cc_start: 0.7881 (tpp) cc_final: 0.7657 (tpt) REVERT: B 665 MET cc_start: 0.8662 (mtp) cc_final: 0.8048 (tmm) REVERT: B 666 SER cc_start: 0.9087 (t) cc_final: 0.8815 (m) REVERT: B 753 TRP cc_start: 0.8082 (OUTLIER) cc_final: 0.6012 (t60) REVERT: B 1053 LEU cc_start: 0.2289 (OUTLIER) cc_final: 0.1993 (mt) REVERT: C 96 MET cc_start: 0.8647 (ttt) cc_final: 0.8390 (ttm) REVERT: C 414 ASP cc_start: 0.7884 (t0) cc_final: 0.6934 (p0) REVERT: C 513 GLU cc_start: 0.8601 (tm-30) cc_final: 0.8374 (tm-30) REVERT: C 528 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8717 (tt) REVERT: C 551 ASP cc_start: 0.8046 (t0) cc_final: 0.7734 (p0) REVERT: C 591 CYS cc_start: 0.7577 (OUTLIER) cc_final: 0.7283 (t) REVERT: C 976 GLN cc_start: 0.8040 (OUTLIER) cc_final: 0.7690 (mm-40) REVERT: C 978 MET cc_start: 0.8467 (tpp) cc_final: 0.8213 (tpp) REVERT: C 1102 MET cc_start: 0.8497 (ptm) cc_final: 0.8037 (ppp) REVERT: D 239 THR cc_start: 0.7579 (OUTLIER) cc_final: 0.7170 (t) REVERT: D 242 ARG cc_start: 0.8803 (ttt-90) cc_final: 0.8559 (tpp-160) REVERT: D 407 MET cc_start: 0.8577 (ttp) cc_final: 0.8195 (tmm) REVERT: D 433 GLN cc_start: 0.9557 (tt0) cc_final: 0.9286 (tm-30) outliers start: 71 outliers final: 45 residues processed: 231 average time/residue: 0.1582 time to fit residues: 59.0003 Evaluate side-chains 209 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 158 time to evaluate : 0.845 ------------------------------------------------------------------------------- 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 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 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 46 LEU Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 342 ILE 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 568 LEU Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain C residue 590 VAL Chi-restraints excluded: chain C residue 591 CYS Chi-restraints excluded: chain C residue 697 MET 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 821 VAL 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 184 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 393 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 174 optimal weight: 9.9990 chunk 99 optimal weight: 20.0000 chunk 13 optimal weight: 8.9990 chunk 70 optimal weight: 9.9990 chunk 152 optimal weight: 0.0670 chunk 113 optimal weight: 1.9990 chunk 256 optimal weight: 30.0000 chunk 72 optimal weight: 3.9990 chunk 267 optimal weight: 20.0000 chunk 115 optimal weight: 9.9990 chunk 111 optimal weight: 30.0000 overall best weight: 5.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 417 GLN B 463 GLN B 610 ASN ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 237 HIS C 976 GLN ** D 44 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 = 0.3975 r_free = 0.3975 target = 0.084038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.061310 restraints weight = 96735.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.063383 restraints weight = 50993.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.064751 restraints weight = 34369.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.065578 restraints weight = 26858.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.066138 restraints weight = 23091.387| |-----------------------------------------------------------------------------| r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.4079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 24452 Z= 0.201 Angle : 0.617 12.183 33409 Z= 0.315 Chirality : 0.041 0.160 3673 Planarity : 0.004 0.068 4205 Dihedral : 13.817 89.956 3730 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 3.06 % Allowed : 11.47 % Favored : 85.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.16), residues: 2837 helix: 1.33 (0.14), residues: 1417 sheet: -0.22 (0.29), residues: 299 loop : -1.50 (0.17), residues: 1121 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 968 TYR 0.015 0.002 TYR B 37 PHE 0.014 0.002 PHE B 475 TRP 0.013 0.002 TRP C 841 HIS 0.007 0.001 HIS C 233 Details of bonding type rmsd/Z covalent geometry : bond 0.00452 / 0.20 (24452) covalent geometry : angle 0.61685 / 0.32 (33409) hydrogen bonds : bond 0.04217 / 2.79 ( 1087) hydrogen bonds : angle 4.14339 / 2.94 ( 3152) *********************** 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 239 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 165 time to evaluate : 0.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 518 MET cc_start: 0.6237 (mmm) cc_final: 0.5964 (mmm) REVERT: B 596 MET cc_start: 0.8931 (mmm) cc_final: 0.8661 (mtp) REVERT: B 665 MET cc_start: 0.8714 (mtp) cc_final: 0.8090 (tmm) REVERT: B 753 TRP cc_start: 0.8108 (OUTLIER) cc_final: 0.6242 (t60) REVERT: B 1053 LEU cc_start: 0.1970 (OUTLIER) cc_final: 0.1477 (mt) REVERT: B 1111 TYR cc_start: 0.8377 (OUTLIER) cc_final: 0.7902 (p90) REVERT: C 96 MET cc_start: 0.8647 (ttt) cc_final: 0.8323 (ttm) REVERT: C 414 ASP cc_start: 0.7854 (t0) cc_final: 0.7042 (p0) REVERT: C 422 ILE cc_start: 0.8515 (tp) cc_final: 0.8217 (tp) REVERT: C 978 MET cc_start: 0.8462 (OUTLIER) cc_final: 0.8229 (tpp) REVERT: C 1102 MET cc_start: 0.8426 (OUTLIER) cc_final: 0.7921 (ppp) REVERT: D 112 MET cc_start: 0.7935 (mmm) cc_final: 0.7559 (ttm) REVERT: D 169 ILE cc_start: 0.8623 (OUTLIER) cc_final: 0.8343 (mm) REVERT: D 407 MET cc_start: 0.8587 (ttp) cc_final: 0.8212 (tmm) REVERT: D 433 GLN cc_start: 0.9562 (tt0) cc_final: 0.9284 (tm-30) REVERT: D 502 LEU cc_start: 0.3762 (OUTLIER) cc_final: 0.3420 (pp) outliers start: 74 outliers final: 45 residues processed: 227 average time/residue: 0.1512 time to fit residues: 56.4473 Evaluate side-chains 208 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 156 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 339 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 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 1111 TYR Chi-restraints excluded: chain B residue 1159 ARG Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 87 ASN 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 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 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 674 VAL Chi-restraints excluded: chain C residue 738 ASP Chi-restraints excluded: chain C residue 801 SER Chi-restraints excluded: chain C residue 821 VAL Chi-restraints excluded: chain C residue 889 VAL Chi-restraints excluded: chain C residue 959 VAL Chi-restraints excluded: chain C residue 978 MET Chi-restraints excluded: chain C residue 1102 MET 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 169 ILE Chi-restraints excluded: chain D residue 184 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 293 ILE Chi-restraints excluded: chain D residue 322 THR 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 82 optimal weight: 8.9990 chunk 268 optimal weight: 20.0000 chunk 16 optimal weight: 2.9990 chunk 219 optimal weight: 6.9990 chunk 286 optimal weight: 50.0000 chunk 96 optimal weight: 20.0000 chunk 165 optimal weight: 9.9990 chunk 195 optimal weight: 7.9990 chunk 84 optimal weight: 10.0000 chunk 176 optimal weight: 9.9990 chunk 201 optimal weight: 0.6980 overall best weight: 5.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 278 ASN B 531 GLN B 534 GLN B 566 GLN ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 522 HIS ** D 44 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 = 0.3956 r_free = 0.3956 target = 0.082829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.060883 restraints weight = 98912.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.062817 restraints weight = 52972.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.064083 restraints weight = 36200.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.064810 restraints weight = 28601.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.065354 restraints weight = 24886.577| |-----------------------------------------------------------------------------| r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.4547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 24452 Z= 0.217 Angle : 0.644 12.826 33409 Z= 0.329 Chirality : 0.042 0.213 3673 Planarity : 0.005 0.117 4205 Dihedral : 13.818 88.997 3728 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 3.27 % Allowed : 11.93 % Favored : 84.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.16), residues: 2837 helix: 1.29 (0.14), residues: 1409 sheet: -0.15 (0.29), residues: 294 loop : -1.46 (0.17), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG D 576 TYR 0.017 0.002 TYR B 430 PHE 0.017 0.002 PHE B 428 TRP 0.014 0.002 TRP C 841 HIS 0.007 0.001 HIS C 233 Details of bonding type rmsd/Z covalent geometry : bond 0.00492 / 0.22 (24452) covalent geometry : angle 0.64431 / 0.33 (33409) hydrogen bonds : bond 0.04449 / 2.97 ( 1087) hydrogen bonds : angle 4.24306 / 3.01 ( 3152) *********************** 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 238 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 159 time to evaluate : 0.889 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 15 LEU cc_start: 0.8187 (mt) cc_final: 0.7961 (mt) REVERT: B 354 MET cc_start: 0.6779 (mtm) cc_final: 0.6538 (ptt) REVERT: B 518 MET cc_start: 0.6587 (mmm) cc_final: 0.6357 (mmm) REVERT: B 753 TRP cc_start: 0.8103 (OUTLIER) cc_final: 0.6402 (t60) REVERT: B 1053 LEU cc_start: 0.2139 (OUTLIER) cc_final: 0.1616 (mt) REVERT: C 17 MET cc_start: 0.8353 (tmm) cc_final: 0.7963 (ttm) REVERT: C 96 MET cc_start: 0.8471 (ttt) cc_final: 0.8140 (ttm) REVERT: C 414 ASP cc_start: 0.7904 (t0) cc_final: 0.7233 (p0) REVERT: C 422 ILE cc_start: 0.8588 (tp) cc_final: 0.8297 (tp) REVERT: C 817 HIS cc_start: 0.5309 (OUTLIER) cc_final: 0.4146 (m170) REVERT: C 978 MET cc_start: 0.8526 (OUTLIER) cc_final: 0.8159 (tpp) REVERT: C 1102 MET cc_start: 0.8333 (ptm) cc_final: 0.7912 (ppp) REVERT: D 407 MET cc_start: 0.8542 (ttp) cc_final: 0.8170 (tmm) REVERT: D 433 GLN cc_start: 0.9535 (tt0) cc_final: 0.9262 (tm-30) REVERT: D 502 LEU cc_start: 0.3891 (OUTLIER) cc_final: 0.3516 (pp) outliers start: 79 outliers final: 55 residues processed: 227 average time/residue: 0.1434 time to fit residues: 54.4514 Evaluate side-chains 209 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 149 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 66 GLU 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 339 VAL 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 511 VAL 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 1111 TYR Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 230 LEU 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 434 TYR Chi-restraints excluded: chain C residue 435 LEU 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 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 C residue 978 MET 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 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 393 ILE 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 89 optimal weight: 0.0370 chunk 262 optimal weight: 8.9990 chunk 10 optimal weight: 0.4980 chunk 276 optimal weight: 20.0000 chunk 212 optimal weight: 3.9990 chunk 120 optimal weight: 5.9990 chunk 170 optimal weight: 7.9990 chunk 55 optimal weight: 3.9990 chunk 185 optimal weight: 9.9990 chunk 243 optimal weight: 0.7980 chunk 238 optimal weight: 8.9990 overall best weight: 1.8662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 976 GLN ** D 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.084316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.062401 restraints weight = 97692.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.064410 restraints weight = 52012.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.065714 restraints weight = 35398.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.066521 restraints weight = 27782.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.067069 restraints weight = 23939.487| |-----------------------------------------------------------------------------| r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.4596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 24452 Z= 0.120 Angle : 0.577 12.982 33409 Z= 0.292 Chirality : 0.040 0.303 3673 Planarity : 0.004 0.078 4205 Dihedral : 13.741 88.835 3720 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.24 % Allowed : 13.54 % Favored : 84.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.16), residues: 2837 helix: 1.62 (0.14), residues: 1411 sheet: -0.09 (0.29), residues: 295 loop : -1.34 (0.18), residues: 1131 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 974 TYR 0.021 0.001 TYR C1075 PHE 0.024 0.001 PHE B 289 TRP 0.014 0.001 TRP C 841 HIS 0.004 0.001 HIS D 65 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (24452) covalent geometry : angle 0.57665 / 0.29 (33409) hydrogen bonds : bond 0.03675 / 2.46 ( 1087) hydrogen bonds : angle 3.97731 / 2.83 ( 3152) *********************** 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 215 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 161 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 518 MET cc_start: 0.6445 (mmm) cc_final: 0.6189 (mmm) REVERT: B 753 TRP cc_start: 0.8101 (OUTLIER) cc_final: 0.6483 (t60) REVERT: B 1053 LEU cc_start: 0.2065 (OUTLIER) cc_final: 0.1611 (mt) REVERT: B 1102 MET cc_start: 0.7019 (OUTLIER) cc_final: 0.6712 (tpt) REVERT: C 96 MET cc_start: 0.8453 (ttt) cc_final: 0.8118 (ttm) REVERT: C 414 ASP cc_start: 0.7801 (t0) cc_final: 0.7172 (p0) REVERT: C 422 ILE cc_start: 0.8532 (tp) cc_final: 0.8250 (tp) REVERT: C 976 GLN cc_start: 0.7938 (OUTLIER) cc_final: 0.7608 (mm-40) REVERT: C 978 MET cc_start: 0.8445 (tpp) cc_final: 0.8168 (tpp) REVERT: C 1102 MET cc_start: 0.8308 (ptm) cc_final: 0.7743 (ppp) REVERT: D 407 MET cc_start: 0.8479 (ttp) cc_final: 0.8145 (tmm) REVERT: D 433 GLN cc_start: 0.9524 (tt0) cc_final: 0.9253 (tm-30) REVERT: D 502 LEU cc_start: 0.3870 (OUTLIER) cc_final: 0.3540 (pp) outliers start: 54 outliers final: 41 residues processed: 210 average time/residue: 0.1483 time to fit residues: 52.2021 Evaluate side-chains 199 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 153 time to evaluate : 0.961 ------------------------------------------------------------------------------- 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 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 511 VAL 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 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 46 LEU Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 362 ASP Chi-restraints excluded: chain C residue 419 SER Chi-restraints excluded: chain C residue 479 LEU 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 801 SER Chi-restraints excluded: chain C residue 821 VAL 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 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 184 LEU Chi-restraints excluded: chain D residue 216 LEU 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 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 274 optimal weight: 8.9990 chunk 187 optimal weight: 9.9990 chunk 38 optimal weight: 9.9990 chunk 167 optimal weight: 10.0000 chunk 108 optimal weight: 20.0000 chunk 94 optimal weight: 7.9990 chunk 180 optimal weight: 6.9990 chunk 220 optimal weight: 9.9990 chunk 57 optimal weight: 8.9990 chunk 196 optimal weight: 7.9990 chunk 269 optimal weight: 6.9990 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 769 HIS ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 951 GLN ** D 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 124 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.081135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.059240 restraints weight = 99900.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.061096 restraints weight = 54291.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.062327 restraints weight = 37399.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.063082 restraints weight = 29606.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.063499 restraints weight = 25750.701| |-----------------------------------------------------------------------------| r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.5066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.075 24452 Z= 0.298 Angle : 0.741 13.226 33409 Z= 0.377 Chirality : 0.045 0.267 3673 Planarity : 0.005 0.054 4205 Dihedral : 13.858 88.181 3720 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 3.02 % Allowed : 13.08 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.15), residues: 2837 helix: 1.06 (0.14), residues: 1419 sheet: -0.13 (0.30), residues: 276 loop : -1.49 (0.17), residues: 1142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 808 TYR 0.021 0.002 TYR B 37 PHE 0.020 0.002 PHE C 694 TRP 0.018 0.002 TRP B 272 HIS 0.009 0.002 HIS C 233 Details of bonding type rmsd/Z covalent geometry : bond 0.00681 / 0.30 (24452) covalent geometry : angle 0.74136 / 0.38 (33409) hydrogen bonds : bond 0.04950 / 3.27 ( 1087) hydrogen bonds : angle 4.48586 / 3.19 ( 3152) *********************** 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 218 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 145 time to evaluate : 0.906 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 306 ARG cc_start: 0.8054 (mmp-170) cc_final: 0.7362 (mmm160) REVERT: B 596 MET cc_start: 0.8809 (mtp) cc_final: 0.8518 (mtt) REVERT: B 753 TRP cc_start: 0.8126 (OUTLIER) cc_final: 0.6509 (t60) REVERT: B 1053 LEU cc_start: 0.1767 (OUTLIER) cc_final: 0.1268 (mt) REVERT: B 1168 MET cc_start: 0.8597 (mmm) cc_final: 0.8255 (mmm) REVERT: C 96 MET cc_start: 0.8568 (ttt) cc_final: 0.8100 (ttm) REVERT: C 414 ASP cc_start: 0.7950 (t0) cc_final: 0.7337 (p0) REVERT: C 422 ILE cc_start: 0.8581 (tp) cc_final: 0.8295 (tp) REVERT: C 817 HIS cc_start: 0.5620 (OUTLIER) cc_final: 0.4421 (m170) REVERT: C 1102 MET cc_start: 0.8319 (OUTLIER) cc_final: 0.7915 (ppp) REVERT: D 407 MET cc_start: 0.8538 (ttp) cc_final: 0.8182 (tmm) REVERT: D 433 GLN cc_start: 0.9520 (tt0) cc_final: 0.9264 (tm-30) REVERT: D 502 LEU cc_start: 0.3748 (OUTLIER) cc_final: 0.3392 (pp) outliers start: 73 outliers final: 57 residues processed: 206 average time/residue: 0.1478 time to fit residues: 50.9429 Evaluate side-chains 203 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 141 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 66 GLU 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 380 VAL Chi-restraints excluded: chain B residue 442 THR Chi-restraints excluded: chain B residue 491 PHE Chi-restraints excluded: chain B residue 511 VAL 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 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 46 LEU Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 87 ASN 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 571 LEU Chi-restraints excluded: chain C residue 590 VAL Chi-restraints excluded: chain C residue 674 VAL 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 C residue 959 VAL Chi-restraints excluded: chain C residue 1102 MET 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 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 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 57 optimal weight: 0.9990 chunk 241 optimal weight: 10.0000 chunk 278 optimal weight: 4.9990 chunk 238 optimal weight: 30.0000 chunk 53 optimal weight: 6.9990 chunk 29 optimal weight: 9.9990 chunk 205 optimal weight: 9.9990 chunk 133 optimal weight: 0.9980 chunk 167 optimal weight: 7.9990 chunk 150 optimal weight: 2.9990 chunk 83 optimal weight: 6.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 976 GLN ** D 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.082644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.060750 restraints weight = 98934.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.062710 restraints weight = 52981.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.063987 restraints weight = 36074.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.064747 restraints weight = 28445.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.065259 restraints weight = 24667.410| |-----------------------------------------------------------------------------| r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.5092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 24452 Z= 0.155 Angle : 0.617 13.243 33409 Z= 0.313 Chirality : 0.041 0.199 3673 Planarity : 0.004 0.060 4205 Dihedral : 13.825 88.098 3720 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.53 % Allowed : 13.66 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.16), residues: 2837 helix: 1.50 (0.14), residues: 1408 sheet: -0.06 (0.29), residues: 279 loop : -1.36 (0.18), residues: 1150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 360 TYR 0.016 0.001 TYR B 394 PHE 0.011 0.001 PHE C 376 TRP 0.015 0.001 TRP C 841 HIS 0.005 0.001 HIS D 65 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.16 (24452) covalent geometry : angle 0.61670 / 0.31 (33409) hydrogen bonds : bond 0.04012 / 2.68 ( 1087) hydrogen bonds : angle 4.12581 / 2.93 ( 3152) *********************** 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 213 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 152 time to evaluate : 0.961 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 306 ARG cc_start: 0.8049 (mmp-170) cc_final: 0.7345 (mmm160) REVERT: B 596 MET cc_start: 0.8842 (mtp) cc_final: 0.8539 (mtt) REVERT: B 753 TRP cc_start: 0.8084 (OUTLIER) cc_final: 0.6515 (t60) REVERT: B 1053 LEU cc_start: 0.2004 (OUTLIER) cc_final: 0.1519 (mt) REVERT: B 1168 MET cc_start: 0.8585 (mmm) cc_final: 0.7971 (mmm) REVERT: C 96 MET cc_start: 0.8523 (ttt) cc_final: 0.8059 (ttm) REVERT: C 414 ASP cc_start: 0.7873 (t0) cc_final: 0.7318 (p0) REVERT: C 422 ILE cc_start: 0.8499 (tp) cc_final: 0.8238 (tp) REVERT: C 817 HIS cc_start: 0.5651 (OUTLIER) cc_final: 0.4300 (m170) REVERT: C 1102 MET cc_start: 0.8324 (ptm) cc_final: 0.7893 (ppp) REVERT: D 407 MET cc_start: 0.8469 (ttp) cc_final: 0.8143 (tmm) REVERT: D 433 GLN cc_start: 0.9527 (tt0) cc_final: 0.9257 (tm-30) REVERT: D 502 LEU cc_start: 0.3721 (OUTLIER) cc_final: 0.3366 (pp) outliers start: 61 outliers final: 47 residues processed: 205 average time/residue: 0.1461 time to fit residues: 50.2556 Evaluate side-chains 199 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 148 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 GLU 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 380 VAL Chi-restraints excluded: chain B residue 442 THR Chi-restraints excluded: chain B residue 511 VAL 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 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 46 LEU Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 241 THR 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 568 LEU Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain C residue 590 VAL 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 959 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 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 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 184 optimal weight: 10.0000 chunk 26 optimal weight: 0.0870 chunk 227 optimal weight: 3.9990 chunk 192 optimal weight: 20.0000 chunk 220 optimal weight: 9.9990 chunk 37 optimal weight: 5.9990 chunk 258 optimal weight: 9.9990 chunk 93 optimal weight: 8.9990 chunk 223 optimal weight: 0.0270 chunk 70 optimal weight: 0.7980 chunk 244 optimal weight: 7.9990 overall best weight: 2.1820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 65 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.083105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.061241 restraints weight = 98524.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.063217 restraints weight = 53047.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.064519 restraints weight = 36151.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.065322 restraints weight = 28450.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.065730 restraints weight = 24585.328| |-----------------------------------------------------------------------------| r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.5122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 24452 Z= 0.124 Angle : 0.597 13.545 33409 Z= 0.302 Chirality : 0.040 0.204 3673 Planarity : 0.004 0.057 4205 Dihedral : 13.759 88.289 3718 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.99 % Allowed : 14.24 % Favored : 83.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.16), residues: 2837 helix: 1.70 (0.14), residues: 1405 sheet: 0.05 (0.30), residues: 270 loop : -1.26 (0.18), residues: 1162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 974 TYR 0.015 0.001 TYR C 256 PHE 0.027 0.001 PHE B 289 TRP 0.015 0.001 TRP B 401 HIS 0.006 0.001 HIS B 689 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 (24452) covalent geometry : angle 0.59743 / 0.30 (33409) hydrogen bonds : bond 0.03662 / 2.46 ( 1087) hydrogen bonds : angle 3.99451 / 2.84 ( 3152) ********************** 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 201 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 153 time to evaluate : 0.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 596 MET cc_start: 0.8803 (mtp) cc_final: 0.8451 (mtt) REVERT: B 753 TRP cc_start: 0.8061 (OUTLIER) cc_final: 0.6396 (t60) REVERT: B 1053 LEU cc_start: 0.1978 (OUTLIER) cc_final: 0.1496 (mt) REVERT: B 1141 LEU cc_start: 0.9485 (OUTLIER) cc_final: 0.9219 (mm) REVERT: B 1168 MET cc_start: 0.8577 (mmm) cc_final: 0.7941 (mmm) REVERT: C 96 MET cc_start: 0.8534 (ttt) cc_final: 0.8043 (ttm) REVERT: C 414 ASP cc_start: 0.7888 (t0) cc_final: 0.7320 (p0) REVERT: C 422 ILE cc_start: 0.8498 (tp) cc_final: 0.8237 (tp) REVERT: C 817 HIS cc_start: 0.5645 (OUTLIER) cc_final: 0.4328 (m170) REVERT: C 978 MET cc_start: 0.8445 (tpp) cc_final: 0.8217 (tpp) REVERT: C 1102 MET cc_start: 0.8285 (ptm) cc_final: 0.7724 (ppp) REVERT: D 407 MET cc_start: 0.8467 (ttp) cc_final: 0.8130 (tmm) REVERT: D 433 GLN cc_start: 0.9526 (tt0) cc_final: 0.9265 (tm-30) REVERT: D 502 LEU cc_start: 0.3723 (OUTLIER) cc_final: 0.3411 (pp) outliers start: 48 outliers final: 38 residues processed: 197 average time/residue: 0.1393 time to fit residues: 46.9112 Evaluate side-chains 191 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 148 time to evaluate : 0.904 ------------------------------------------------------------------------------- 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 380 VAL Chi-restraints excluded: chain B residue 442 THR Chi-restraints excluded: chain B residue 511 VAL 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 1102 MET Chi-restraints excluded: chain B residue 1111 TYR Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 241 THR 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 568 LEU Chi-restraints excluded: chain C residue 571 LEU 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 959 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 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 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 68 optimal weight: 9.9990 chunk 98 optimal weight: 6.9990 chunk 271 optimal weight: 9.9990 chunk 77 optimal weight: 10.0000 chunk 277 optimal weight: 20.0000 chunk 48 optimal weight: 10.0000 chunk 182 optimal weight: 4.9990 chunk 120 optimal weight: 0.5980 chunk 156 optimal weight: 6.9990 chunk 50 optimal weight: 7.9990 chunk 235 optimal weight: 8.9990 overall best weight: 5.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.081346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.059550 restraints weight = 98698.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.061402 restraints weight = 53946.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.062616 restraints weight = 37162.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.063317 restraints weight = 29568.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.063844 restraints weight = 25802.356| |-----------------------------------------------------------------------------| r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.5412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 24452 Z= 0.212 Angle : 0.662 13.696 33409 Z= 0.335 Chirality : 0.043 0.211 3673 Planarity : 0.004 0.055 4205 Dihedral : 13.818 88.602 3718 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.15 % Allowed : 14.04 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.16), residues: 2837 helix: 1.44 (0.14), residues: 1409 sheet: -0.05 (0.30), residues: 270 loop : -1.31 (0.18), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 808 TYR 0.021 0.002 TYR C 256 PHE 0.017 0.002 PHE C 694 TRP 0.017 0.002 TRP C 248 HIS 0.005 0.001 HIS C 233 Details of bonding type rmsd/Z covalent geometry : bond 0.00490 / 0.21 (24452) covalent geometry : angle 0.66192 / 0.34 (33409) hydrogen bonds : bond 0.04414 / 2.94 ( 1087) hydrogen bonds : angle 4.25999 / 3.03 ( 3152) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4706.75 seconds wall clock time: 81 minutes 43.09 seconds (4903.09 seconds total)